unlabelled_predictions.csv

label,idx,title,score,rank
distribute_liquids,15,"Aerial roots of epiphytic orchids: the velamen radicum and its role in water and nutrient uptake. The velamen radicum, a spongy, usually multiple epidermis of the roots, which at maturity consists of dead cells, is frequently described as an important adaptation of epiphytic orchids. Yet, quantitative evidence for the alleged functions, e.g., efficient water and nutrient uptake, nutrient retention, reduction of water loss, mechanical protection, or the avoidance of overheating, is rare or missing. We tested the notion originally put forward by Went in 1940 that the velamen allows plants to capture and immobilize the first solutions arriving in a rainfall, which are the most heavily charged with nutrients. In a series of experiments, we examined whether all necessary functional characteristics are given for this scenario to be realistic under ecological conditions. First, we show that the velamen of a large number of orchid species takes up solutions within seconds, while evaporation from the velamen takes several hours. Charged ions are retained in the velamen probably due to positive and negative charges in the cell walls, while uncharged compounds are lost to the external medium. Finally, we demonstrate that nutrient uptake follows biphasic kinetics with a highly efficient, active transport system at low external concentrations. Thus, our results lend strong support to Went’s hypothesis: the velamen fulfills an important function in nutrient uptake in the epiphytic habitat. Most of the other functions outlined above still await similar experimental scrutiny.",0.5498130917549133,1
distribute_liquids,179,Effects of temperature on the cuticular transpiration barrier of two desert plants with water-spender and water-saver strategies. The efficacy of the cuticular transpiration barrier and its resistance to elevated temperatures are significantly higher in a typical water-saver than in a water-spender plant growing in hot desert.,0.48365265130996704,2
distribute_liquids,164,"Self-organization of river vegetation leads to emergent buffering of river flows and water levels. Global climate change is expected to impact hydrodynamic conditions in stream ecosystems. There is limited understanding of how stream ecosystems interact and possibly adapt to novel hydrodynamic conditions. Combining mathematical modelling with field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution triggers spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a spatial separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. This self-organization process decouples both local flow velocities and water levels from the forcing effect of changing stream discharge. Field data from two lowland, baseflow-dominated streams support model predictions and highlight two important stream-level emergent properties: vegetation controls flow conveyance in fast-flowing channels throughout the annual growth cycle, and this buffering of discharge variations maintains water depths and wetted habitat for the stream community. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity.",0.41915127635002136,3
distribute_liquids,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.3223261833190918,4
distribute_liquids,79,"Beaver-induced spatiotemporal patch dynamics affect landscape-level environmental heterogeneity. Beavers (Castor sp.) are ecosystem engineers that cause significant changes to their physical environment and alter the availability of resources to other species. We studied flood dynamics created by American beaver (C. canadensis K.) in a southern boreal landscape in Finland in 1970-2018. We present for the first time, to our knowledge, a temporally continuous long-term study of beaver-induced flood disturbances starting from the appearance of beaver in the area. During the 49 years, the emergence of new sites flooded by beaver and repeated floods (61% of the sites) formed a dynamic mosaic characterized by clustered patterns of beaver sites. As beaver dispersal proceeded, connectivity of beaver sites increased significantly. The mean flood duration was approximately three years, which highlights the importance of datasets with high-temporal resolution in detecting beaver-induced disturbances. An individual site was often part of the active flood mosaic over several decades, although the duration and the number of repeated floods at different sites varied considerably. Variation of flood-inundated and post-flood phases at individual sites resulted in a cumulative number of unique patches that contribute to environmental heterogeneity in space and time. A disturbance mosaic consisting of patches differing by successional age and flood history is likely to support species richness and abundance of different taxa and facilitate whole species communities. Beavers are thus a suitable means to be used in restoration of riparian habitat due to their strong and dynamic influence on abiotic environment and its biotic consequences.",0.23396016657352448,5
distribute_liquids,277,"Encoding memory in tube diameter hierarchy of living flow network. Significance Simple organisms manage to thrive in complex environments. Having memory about the environment is key in taking informed decisions. Physarum polycephalum excels as a giant unicellular eukaryote, being even able to solve optimization problems despite the lack of a nervous system. Here, we follow experimentally the organism’s response to a nutrient source and find that memory about nutrient location is encoded in the morphology of the network-shaped organism. Our theoretical predictions in line with our observations unveil the mechanism behind memory encoding and demonstrate the P. polycephalum’s ability to read out previously stored information. The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment—successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient’s location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes’ capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks’ tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks’ version of associative memory—very likely of relevance for the plethora of living flow networks as well as for bioinspired design.",0.21521058678627014,6
distribute_liquids,309,"Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes. Significance For decades, the propulsion of sperms has been traditionally attributed to the beating or rotating of the soft tails. However, this work disclosed an unusual swimming model of Ray sperms whose propulsion is from not only the helical tail but also the unique spiral head (i.e., the head can contribute ∼31% of the force in propulsion). Such a propulsion mechanism provides Ray sperms with high adaptability to large environmental viscosities along with advantages in linearity, straightness, and efficiency. This study expands our knowledge on the microorganisms’ motion and provides inspirations for engineering design. We disclose a peculiar rotational propulsion mechanism of Ray sperms enabled by its unusual heterogeneous dual helixes with a rigid spiral head and a soft tail, named Heterogeneous Dual Helixes (HDH) model for short. Different from the conventional beating propulsion of sperm, the propulsion of Ray sperms is from both the rotational motion of the soft helical tail and the rigid spiral head. Such heterogeneous dual helical propulsion style provides the Ray sperm with high adaptability in viscous solutions along with advantages in linearity, straightness, and bidirectional motion. This HDH model is further corroborated by a miniature swimming robot actuated via a rigid spiral head and a soft tail, which demonstrates similar superiorities over conventional ones in terms of adaptability and efficiency under the same power input. Such findings expand our knowledge on microorganisms’ motion, motivate further studies on natural fertilization, and inspire engineering designs.",0.19834046065807343,7
distribute_liquids,46,"Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival.. The dynamics of forest ecosystems depend largely on the survival of seedlings in their understories, but seedling survival is known to be limited by preemption of light and soil resources by overstory trees. It has been hypothesized that ""common mycorrhizal networks,"" wherein roots of seedlings are linked to overstory trees by symbiotic mycorrhizal fungi, offset some or all of the negative effects of trees on seedlings. Here we report the results of an unambiguous experimental test of this hypothesis in a monodominant Pinus radiata forest. We also tested the hypothesis that adaptive differentiation among plant populations causes local plant genotypes to respond more positively to mycorrhizal networks than nonlocal plant genotypes. Our results demonstrate large positive effects of overstory mycorrhizal networks on seedling survival, along with simultaneous negative effects of tree roots, regardless of whether plant genotypes were locally derived. Physiological and leaf-chemistry measurements suggest that seedlings connected to common mycorrhizal networks benefited from increased access to soil water. The similar magnitude of the positive and negative overstory effects on seedlings and the ubiquity of mycorrhizal networks in forests suggest that mycorrhizal networks fundamentally influence the demographic and community dynamics of forest trees.",0.1560409665107727,8
distribute_liquids,89,"Microbial diversity drives carbon use efficiency in a model soil. Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes. Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.",0.15092220902442932,9
distribute_liquids,126,Exact Spatiotemporal Dynamics of Confined Lattice Random Walks in Arbitrary Dimensions: A Century after Smoluchowski and Pólya. An exact solution to the discrete diffusion equation allows for accurate predictions of how the probabilities of reaction diffusion processes evolve over time.,0.14785127341747284,10
distribute_liquids,182,"In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs. Abstract The discovery of the ability of microorganisms to exchange electrons with inert electrodes has triggered new areas in fundamental and applied research. However, the field is currently limited to several known electrochemically active microorganisms enriched and isolated in research laboratories. An alternative strategy is to enrich such microorganisms in their native environment by allowing them to exchange electrons with polarized solid electrodes. The use of this approach is currently limited because of a lack of available tools. We developed a low-cost, battery-operated potentiostat that is capable of controlling the potential of a working electrode and can be deployed and operated remotely, allowing the enrichment of microorganisms on electrodes in their native environment. The device was tested in four alkaline hot springs in Heart Lake Geyser Basin in Yellowstone National Park (with a temperature ranging from 45 οC to 91 οC and a relatively constant pH of 8.5–8.7). Microbial community analysis showed a change in microbial community structure after 32 days of polarization. The impact of polarization on microbial community was most substantial on the electrodes that generated the highest cathodic and anodic currents, suggesting a direct impact of polarization on electrode microbial community.",0.1347898691892624,11
distribute_liquids,50,"FEEDING BEHAVIOR OF THE HUMPBACK WHALE, MEGAPTERA NOVAEANGLIAE, IN THE WESTERN NORTH ATLANTIC. Observations on the feeding behavior of the humpback whale, Megapteranovaeangliae, were made from aerial and surface platforms fTom 1977 to 1980 in the continental shelf waters of the north­ eastern United States. The resulting catalog of behaviors includes two principal categories: Swim­ ming/lunging behaviors and bubbling behaviors. A behavior from a given category may be used independently or in association with others, and by individual or groups of humpbacks. The first category includes surface lunging, circular swimming/thrashing, and the ""inside loop"" behavior. In the second category, a wide variety of feeding-associated bubbling behaviors are described, some for the first time. The structures formed by underwater exhalations are of two major types: 1) bubble cloud-a single, relatively large (4-7m diameter), dome-shaped cloud formed of small, uniformly sized bubbles; and 2) bubble column-a smaller (1-1.5 m diameter) structure composed of larger, randomly sized bubbles, used in series or multiples. Both basic structures are employed in a variety of ways. Many of these behaviors are believed to be utilized to maintain naturally occurring concentrations of prey, which have been identified as the American sand lance, Ammodytes americanus, and occasionally as herring, Clupea harengus. This paper reports on the feeding behavior of the humpback whale, Megaptera novaeangliae, in the continental shelf waters of the northeastern United States. We describe several feeding be­ haviors reported for the first time, as well as a number of behaviors known from other areas but not previously reported for these waters. Our col­ lective observations provide the beginning of a more complete catalog than has previously been available.",0.1319761723279953,12
distribute_liquids,82,"B cell zone reticular cell microenvironments shape CXCL13 gradient formation. Through the formation of concentration gradients, morphogens drive graded responses to extracellular signals, thereby fine-tuning cell behaviors in complex tissues. Here we show that the chemokine CXCL13 forms both soluble and immobilized gradients. Specifically, CXCL13+ follicular reticular cells form a small-world network of guidance structures, with computer simulations and optimization analysis predicting that immobilized gradients created by this network promote B cell trafficking. Consistent with this prediction, imaging analysis show that CXCL13 binds to extracellular matrix components in situ, constraining its diffusion. CXCL13 solubilization requires the protease cathepsin B that cleaves CXCL13 into a stable product. Mice lacking cathepsin B display aberrant follicular architecture, a phenotype associated with effective B cell homing to but not within lymph nodes. Our data thus suggest that reticular cells of the B cell zone generate microenvironments that shape both immobilized and soluble CXCL13 gradients. Morphogens such as chemokines form gradients to direct graded responses and modulate cell behaviors. Here the authors show, using imaging and computer simulation, that the chemokine CXCL13 originated from follicular reticular cells in the lymph nodes forms both soluble and immobilized gradients to regulate B cell recruitment and migration.",0.09471923112869263,13
distribute_liquids,271,"Navigation by extrapolation of geomagnetic cues in a migratory songbird. Displacement experiments have demonstrated that experienced migratory birds translocated thousands of kilometers away from their migratory corridor can orient toward and ultimately reach their intended destinations.1 This implies that they are capable of ""true navigation,"" commonly defined2-4 as the ability to return to a known destination after displacement to an unknown location without relying on familiar surroundings, cues that emanate from the destination, or information collected during the outward journey.5-13 In birds, true navigation appears to require previous migratory experience5-7,14,15 (but see Kishkinev et al.16 and Piersma et al.17). It is generally assumed that, to correct for displacements outside the familiar area, birds initially gather information within their year-round distribution range, learn predictable spatial gradients of environmental cues within it, and extrapolate from those to unfamiliar magnitudes-the gradient hypothesis.6,9,18-22 However, the nature of the cues and evidence for actual extrapolation remain elusive. Geomagnetic cues (inclination, declination, and total intensity) provide predictable spatial gradients across large parts of the globe and could serve for navigation. We tested the orientation of long-distance migrants, Eurasian reed warblers, exposing them to geomagnetic cues of unfamiliar magnitude encountered beyond their natural distribution range. The birds demonstrated re-orientation toward their migratory corridor as if they were translocated to the corresponding location but only when all naturally occurring magnetic cues were presented, not when declination was changed alone. This result represents direct evidence for migratory birds' ability to navigate using geomagnetic cues extrapolated beyond their previous experience.",0.09048832207918167,14
distribute_liquids,161,"A specialized avian seed dispersal system in a dry-fruited non-photosynthetic plant, Balanophora yakushimensis.. The family Balanophoraceae are among the most unusual of plants because they have aberrant vegetative bodies, highly reduced flowers, and small and reduced embryos (Hansen 1972, Gonzalez et al. 2019). Because the plants lack chlorophyll and are incapable of photosynthesis, they draw nutrition from other organisms. Indeed, like the well-known parasitic plant, Rafflesia, members of the Balanophoraceae acquire both water and nutrients from host plants. They are, therefore, highly specialized root parasites.",0.08069296181201935,15
distribute_liquids,302,"Map-like use of Earth’s magnetic field in sharks. Migration is common in marine animals,1-5 and use of the map-like information of Earth's magnetic field appears to play an important role.2,6-9 While sharks are iconic migrants10-12 and well known for their sensitivity to electromagnetic fields,13-20 whether this ability is used for navigation is unresolved.14,17,21,22 We conducted magnetic displacement experiments on wild-caught bonnetheads (Sphyrna tiburo) and show that magnetic map cues can elicit homeward orientation. We further show that use of a magnetic map to derive positional information may help explain aspects of the genetic structure of bonnethead populations in the northwest Atlantic.23-26 These results offer a compelling explanation for the puzzle of how migratory routes and population structure are maintained in marine environments, where few physical barriers limit movements of vagile species. VIDEO ABSTRACT.",0.05721396952867508,16
distribute_liquids,184,"Collective ventilation in honeybee nests. European honey bees (Apis mellifera) live in large congested nest cavities with a single opening that limits passive ventilation. When the local air temperature exceeds a threshold, the nests are actively ventilated by bees fanning their wings at the nest entrance. Here, we show that colonies with relatively large nest entrances use an emergent ventilation strategy where fanning bees self-organize to form groups, separating regions of continuous inflow and outflow. The observed spatio-temporal patterns correlate the air velocity and air temperature along the entrances to the distribution of fanning bees. A mathematical model that couples these variables to known fanning behaviour of individuals recapitulates their collective dynamics. Additionally, the model makes predictions about the temporal stability of the fanning group as a function of the temperature difference between the environment and the nest. Consistent with these predictions, we observe that the fanning groups drift, cling to the entrance boundaries, break-up and reform as the ambient temperature varies over a period of days. Overall, our study shows how honeybees use flow-mediated communication to self-organize into a steady state in fluctuating environments.",0.056102607399225235,17
distribute_liquids,298,"Plant-pollinator interactions between generalists persist over time and space.. Generalist species are the linchpins of networks, as they are important for maintaining network structure and function. Previous studies have shown that interactions between generalists tend to occur consistently across years and sites. However, the link between temporal and spatial interaction persistence across scales remains unclear. To address this gap, we collected data on plant-pollinator interactions throughout the flowering period for five years across six plots in a subalpine meadow in the Rocky Mountains. We found that interactions between generalists tended to persist more in time and space such that interactions near the network core were more frequently recorded across years, within seasons, and among plots. We posit that species' tolerance of environmental variation across time and space plays a key role in generalization by regulating spatiotemporal overlap with interaction partners. Our results imply a role of spatiotemporal environmental variation in organizing species interactions, marrying niche concepts that emphasize species environmental constraints and their community role.",0.05204178765416145,18
distribute_liquids,190,"Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.",0.05180273950099945,19
distribute_liquids,258,"Roots hunt nutrients. Plant Science
Soil nutrients such as nitrogen sources are not uniformly distributed. Neither are plant roots. Nonetheless, roots of Arabidopsis seedlings seek out pockets of soil ammonium and nitrate. Otvos et al. clarify how root growth and branching are regulated to optimize nitrogen uptake. The auxin efflux carrier PIN-FORMED 2 (PIN2) is regulated posttranscriptionally by phosphorylation at its serine-439 in response to shifts in ammonium or nitrate availability. Phosphorylation in turn triggers changes in PIN2 subcellular localization, which drives changes in auxin distribution between root cortex and epidermis, causing altered root growth rate or direction.

EMBO J. e106862 (2020).",0.050231773406267166,20
sense_light_in_the_visible_spectrum,101,"Pupil Diameter Tracks Statistical Structure in the Environment to Increase Visual Sensitivity. Pupil diameter determines how much light hits the retina and, thus, how much information is available for visual processing. This is regulated by a brainstem reflex pathway. Here, we investigate whether this pathway is under the control of internal models about the environment. This would allow adjusting pupil dynamics to environmental statistics to augment information transmission. We present image sequences containing internal temporal structure to humans of either sex and male macaque monkeys. We then measure whether the pupil tracks this temporal structure not only at the rate of luminance variations, but also at the rate of statistics not available from luminance information alone. We find entrainment to environmental statistics in both species. This entrainment directly affects visual processing by increasing sensitivity at the environmentally relevant temporal frequency. Thus, pupil dynamics are matched to the temporal structure of the environment to optimize perception, in line with an active sensing account. SIGNIFICANCE STATEMENT When light hits the retina, the pupil reflexively constricts. This determines how much light and thus how much information is available for visual processing. We show that the rate at which the pupil constricts and dilates is matched to the temporal structure of our visual environment, although this information is not directly contained in the light variations that usually trigger reflexive pupil constrictions. Adjusting pupil diameter in accordance with environmental regularities optimizes information transmission at ecologically relevant temporal frequencies. We show that this is the case in humans and macaque monkeys, suggesting that the reflex pathways that regulate pupil diameter are under some degree of cognitive control across primate species.",0.8301466703414917,1
sense_light_in_the_visible_spectrum,145,"Luminance Information Is Required for the Accurate Estimation of Contrast in Rapidly Changing Visual Contexts. Visual perception scales with changes in the visual stimulus, or contrast, irrespective of background illumination. However, visual perception is challenged when adaptation is not fast enough to deal with sudden declines in overall illumination, for example, when gaze follows a moving object from bright sunlight into a shaded area. Here, we show that the visual system of the fly employs a solution by propagating a corrective luminance-sensitive signal. We use in vivo 2-photon imaging and behavioral analyses to demonstrate that distinct OFF-pathway inputs encode contrast and luminance. Predictions of contrast-sensitive neuronal responses show that contrast information alone cannot explain behavioral responses in sudden dim light. The luminance-sensitive pathway via the L3 neuron is required for visual processing in such rapidly changing light conditions, ensuring contrast constancy when pure contrast sensitivity underestimates a stimulus. Thus, retaining a peripheral feature, luminance, in visual processing is required for robust behavioral responses.",0.6401308178901672,2
sense_light_in_the_visible_spectrum,185,"Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes. Dermal phototaxis has been reported in a few aquatic vertebrate lineages spanning fish, amphibians and reptiles. These taxa respond to light on the skin of their elongate hind‐bodies and tails by withdrawing under cover to avoid detection by predators. Here, we investigated tail phototaxis in sea snakes (Hydrophiinae), the only reptiles reported to exhibit this sensory behaviour. We conducted behavioural tests in 17 wild‐caught sea snakes of eight species by illuminating the dorsal surface of the tail and midbody skin using cold white, violet, blue, green and red light. Our results confirmed phototactic tail withdrawal in the previously studied Aipysurus laevis, revealed this trait for the first time in A. duboisii and A. tenuis, and suggested that tail photoreceptors have peak spectral sensitivities between blue and green light (457–514 nm). Based on these results, and an absence of photoresponses in five Aipysurus and Hydrophis species, we tentatively infer that tail phototaxis evolved in the ancestor of a clade of six Aipysurus species (comprising 10% of all sea snakes). Quantifying tail damage, we found that the probability of sustaining tail injuries was not influenced by tail phototactic ability in snakes. Gene profiling showed that transcriptomes of both tail skin and body skin lacked visual opsins but contained melanopsin (opn4x) in addition to key genes of the retinal regeneration and phototransduction cascades. This work suggests that a nonvisual photoreceptor (e.g., Gq rhabdomeric) signalling pathway underlies tail phototaxis, and provides candidate gene targets for future studies of this unusual sensory innovation in reptiles.",0.5658804774284363,3
sense_light_in_the_visible_spectrum,53,"Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods. Transparent zooplankton and nekton are often nearly invisible when viewed under ambient light in the pelagic zone [1-3]. However, in this environment, where the light field is directional (and thus likely to cause reflections), and under the bioluminescent searchlights of potential predators, animals may be revealed by reflections from their body surface [4-7]. We investigated the cuticle surfaces of seven species of hyperiids (Crustacea; Amphipoda) using scanning electron microscopy and found two undocumented features that may reduce reflectance. We found that the legs of Cystisoma spp. (n = 5) are covered with an ordered array of nanoprotuberances 200 ± 20 nm SD in height that function optically as a gradient refractive index material [6, 8, 9]. Additionally, we observed that Cystisoma and six other species of hyperiids are covered with a monolayer of homogenous spheres (diameters ranging from 52 ± 7 nm SD on Cystisoma spp. to 320 ± 15 nm SD on Phronima spp.). Optical modeling using effective medium theory and transfer matrix methods demonstrated that both the nanoprotuberances and the monolayers reduce reflectance by as much as 100-fold, depending on the wavelength and angle of the incident light and the thickness of the gradient layer. Even though we only consider surface reflectance and not internal light scattering, our study demonstrates that these nanoprotuberances and spheres can improve crypsis in a featureless habitat where the smallest reflection can render an animal vulnerable to visual predation.",0.5619884133338928,4
sense_light_in_the_visible_spectrum,120,"Muscle and neuronal guidepost-like cells facilitate planarian visual system regeneration. Guiding regeneration Many adult organisms can regenerate neural circuits after injury. However, it is not clear which guidance mechanisms operate to promote axon path finding in the adult. Scimone et al. addressed this question by investigating regeneration of the planarian visual system (see the Perspective by Roberts-Galbraith). Distinct muscle cell populations were found in close association with photoreceptor axons that, together with a neuron class, facilitated visual system assembly after diverse injuries or eye transplantations. These cells exhibited features similar to embryonic guidepost cells and were specified independently of eyes in precise locations by the action of adult positional information cues. Absence of these guidepost-like cells was associated with defective neuronal wiring in regeneration. Science, this issue p. eaba3203; see also p. 1428 Adult regeneration requires guidepost-like cells for precise rewiring of the eyes in the flatworm Schmidtea mediterranea. INTRODUCTION Multiple strategies exist to promote precise wiring of developing neuronal circuits. One strategy involves guidepost cells, which exist transiently in embryos. Guidepost cells can act as intermediate guidance targets for axons or by providing a scaffold that facilitates axonal targeting. Most guidance mechanisms become dispensable once the circuit is assembled. Loss of guidance mechanisms creates a potential limitation on regeneration of neuronal patterns—yet some animals are capable of functional regeneration of their nervous system. RATIONALE Assuming some adult animals have the ability to regenerate functional neuronal circuits, they must possess mechanism(s) for de novo repair of neuronal patterns. In this study, we aimed to characterize such mechanisms by studying regeneration of the planarian visual system after diverse injuries. RESULTS We identified a rare subset of muscle cells (notum+; frizzled 5/8-4+) concentrated at two precise anatomical locations and in tight association with photoreceptor axons. The first group of these cells was found near the eye, where visual axons project and fasciculate to form a bundle. The second group of these cells was found near choice points, where sorting of contralateral and ipsilateral axons occurs. Both groups of muscle cells were formed during regeneration of the visual system and were always tightly associated with axonal projections, consistent with a possible role in attraction to facilitate visual system assembly. In addition, we found that a notum+ set of neurons, located at the adult anterior brain commissure, regenerated before axonal midline crossing and was associated with optic chiasm regeneration. We reasoned that if the photoreceptor axon–associated notum+; frizzled 5/8-4+ muscle cells have a guidepost-like function, their formation should be independent of eye cells. Eyes transplanted to ectopic anatomical locations did not result in the formation of notum+; frizzled 5/8-4+ muscle cells. Furthermore, animals that were unable to generate eyes [ovo RNA interference (ovo RNAi) animals] were still capable of specifying these muscle cells at the right locations. In addition, we predicted that if these muscle cells were indeed guidepost-like cells, visual axon trajectories should be associated with them after eye transplantation into eyeless heads. In all instances, axons from transplanted eyes projected toward notum+; frizzled 5/8- 4+ muscle cells and often adjusted their trajectories after encountering them. We found that an array of signaling cues, which provide positional information essential for planarian patterning, was required for dictating the precise location of these guidepost-like cells. This provides a visual system–extrinsic mechanism for placing guidepost-like cells in the adult. Finally, with single-cell RNA sequencing and fluorescent in situ hybridization screening, we identified molecules and transcription factors expressed in these cells. RNAi studies reduced or eliminated muscle or neuronal guidepost-like cell subsets and resulted in aberrant patterns of visual axonal trajectories. CONCLUSION Adult molecular and cellular strategies for regenerating neuronal pattern in the absence of embryo-specific contexts must exist to overcome damage or loss after injury. Understanding these mechanisms might provide important insights for regenerative medicine. Here, we found adult guidepost-like cell populations, extrinsic to the visual system and placed by adult positional information, that promote normal visual system regeneration in planarians. Adult guidepost-like cells facilitate visual system regeneration in planarians. Muscle and neuron guidepost-like cells are present at key locations near the planarian visual system and are formed independently of photoreceptor axons. Regenerating and transplanted eyes target projections to guidepost-like cells. Positional information cues provide an eye-extrinsic mechanism to place guidepost-like cells in the adult. Loss of guidepost-like cells is associated with visual system disruption. wnt-5, slit, and ndk are involved in positional control of guidepost-like cell placement. fz5/8-4, frizzled 5/8-4. Neuronal circuits damaged or lost after injury can be regenerated in some adult organisms, but the mechanisms enabling this process are largely unknown. We used the planarian Schmidtea mediterranea to study visual system regeneration after injury. We identify a rare population of muscle cells tightly associated with photoreceptor axons at stereotyped positions in both uninjured and regenerating animals. Together with a neuronal population, these cells promote de novo assembly of the visual system in diverse injury and eye transplantation contexts. These muscle guidepost-like cells are specified independently of eyes, and their position is defined by an extrinsic array of positional information cues. These findings provide a mechanism, involving adult formation of guidepost-like cells typically observed in embryos, for axon pattern restoration in regeneration.",0.4636117219924927,5
sense_light_in_the_visible_spectrum,232,"Scattering of ultraviolet light by avian eggshells.. Eggshells are essential for the reproduction of birds since the optical properties of shells may have an impact on biological functions such as heating and UV protection, recognition by parents or camouflage. Whereas ultraviolet reflection by some bird eggshells has been recently described, its physical origin remains poorly understood. In this study, we identified a porous structure in eggshells. Using Mie scattering modelling, we found it was most likely responsible for reflectance peaks (intensities of ca. 20-50%) observed in the near-UV range. These peaks were observed by spectrophotometric measurements from eggshells of several breeds of hen, one breed of duck and one breed of quail. This optical response was interpreted in terms of the distinct visual perception of hens and humans: eggshells appearing achromatic for humans proved to be chromatic for hens. Fluorescence emission from these eggs was also characterised and attributed to the presence of protoporphyrin IX and biliverdin IXα in the shells. Electron microscopy observations revealed the presence of pores within the so-called calcified shell part (i.e., at depths between ca. 20 μm and ca. 240 μm from the eggshell's outer surface). Mercury intrusion porosimetry allowed us to quantify the pore size distribution. Simulations of the UV response of this porous structure using Mie scattering theory as well as an effective approach accounting for multiple scattering indicate that these pores are responsible for the backscattering peaks observed in the UV range, in the case of beige hen eggshells. Due to the similarities between the pore size distributions observed for beige hen eggshells and other investigated poultry eggshells, we expect Mie backscattering to be the origin of the UV response of the eggshells of many other bird species.",0.29979604482650757,6
sense_light_in_the_visible_spectrum,29,"Optical structure and function of the white filamentary hair covering the edelweiss bracts.. The optical properties of the inflorescence of the high-altitude Leontopodium nivale subsp. alpinum (edelweiss) is investigated, in relation with its submicrometer structure, as determined by scanning electron microscopy. The filaments forming the hair layer have been found to exhibit an internal structure which may be one of the few examples of a photonic structure found in a plant. Measurements of light transmission through a self-supported layer of hair pads taken from the bracts supports the idea that the wooly layer covering the plant absorbs near-ultraviolet radiation before it reaches the cellular tissue. Calculations based on a photonic-crystal model provide insight on the way radiation can be absorbed by the filamentary threads.",0.2516978085041046,7
sense_light_in_the_visible_spectrum,274,"Soft Matter Mechanics and the Mechanisms Underpinning the Infrared Vision of Snakes. Summary Pit-bearing snakes (vipers, pythons, and boas) have the extraordinary ability to “see” and accurately locate their prey and predators in total darkness. These animals use the infrared radiation emanating from objects that are warmer relative to the background environment to form a thermal image. Although enormous progress has been made to identify the key physiological features that enable the infrared vision of these snakes and a few other animals, the precise thermoelectric transduction mechanism that mediates the conversion of infrared heat to processable electrical signals has remained elusive. In this work, we quantitatively outline how cells in the snake's pit membrane organ act as apparent pyroelectric materials and convert infrared radiation into electrical signals. Despite the exceptional simplicity of our proposed mechanism and model, we are able to explain many central experimental results pertaining to the transduction process.",0.20048430562019348,8
sense_light_in_the_visible_spectrum,154,"Broadband omnidirectional light reflection and radiative heat dissipation in white beetles Goliathus goliatus.. Structural whiteness, stemming from biologically evolutionarily refined structures, provides inspiration for designing promising, reflectance-based materials. White beetles Goliathus goliatus, which can survive in high-temperature-equatorial forests, may suggest undiscovered new physical mechanisms for thermoregulation. Their scales' whiteness is created by the exquisite shell/hollow cylinder structure with two thermoregulatory effects, contributing to a lower equilibrium temperature of elytra under direct sunlight. In the visible regime, they enhance the broadband omnidirectional reflection significantly by synergetic structural effects originating from the thin-film interference, Mie resonance and total reflection. In the mid-infrared (MIR) regime, white scales act as antireflective layers to increase the emissivity in the MIR range, enabling the elytra to reradiate heat to the environment and help the beetles reduce their temperature by as much as ∼7.8 °C in air. These biological strategies for thermoregulation could provide new approaches for bioinspired coatings towards passive radiative cooling.",0.11649538576602936,9
sense_light_in_the_visible_spectrum,289,"Reflectin needs its intensity amplifier: Realizing the potential of tunable structural biophotonics. Underwater camouflage and communication in a family of recently evolved squids are controlled, in part, by the reflectin proteins, which regulate dynamic changes in the color and intensity of light reflected from intracellular Bragg reflectors and Mie scatterers. The reflectins act as a signal transducer, precisely tuning the dimensions and refractive index of the membrane-bounded structural reflectors containing them to an extent exactly proportional to neuronal signaling. This calibration between the activating signal and the output color and intensity of reflectance is governed by the physics of the liquid state of reflectin assemblies, which osmotically fine-tune the dimensions and refractive index of the membrane-bounded structural reflectors containing them. While thin-film or genetically engineered assemblies of reflectin deliver changes in the colors of reflection approximating those of the biological system (as do other proteins and polymers), none has delivered the signal-activated increase in the intensity of reflectance characteristic of the native system. The membrane envelopes (Bragg reflector lamellae and Mie-scattering vesicles) containing the reflectins apparently serve as amplifiers, functionally “impedance matched” to the range of tunable sizes of the reflectin assemblies; reflectin films or assemblies lacking such an amplifier fail to deliver signal-activated increases in reflectance intensity.",0.09007575362920761,10
sense_light_in_the_visible_spectrum,231,"Biologically inspired LED lens from cuticular nanostructures of firefly lantern. Cuticular nanostructures found in insects effectively manage light for light polarization, structural color, or optical index matching within an ultrathin natural scale. These nanostructures are mainly dedicated to manage incoming light and recently inspired many imaging and display applications. A bioluminescent organ, such as a firefly lantern, helps to out-couple light from the body in a highly efficient fashion for delivering strong optical signals in sexual communication. However, the cuticular nanostructures, except the light-producing reactions, have not been well investigated for physical principles and engineering biomimetics. Here we report a unique observation of high-transmission nanostructures on a firefly lantern and its biological inspiration for highly efficient LED illumination. Both numerical and experimental results clearly reveal high transmission through the nanostructures inspired from the lantern cuticle. The nanostructures on an LED lens surface were fabricated by using a large-area nanotemplating and reconfigurable nanomolding with heat-induced shear thinning. The biologically inspired LED lens, distinct from a smooth surface lens, substantially increases light transmission over visible ranges, comparable to conventional antireflection coating. This biological inspiration can offer new opportunities for increasing the light extraction efficiency of high-power LED packages.",0.08642970770597458,11
sense_light_in_the_visible_spectrum,111,"Wild hummingbirds discriminate nonspectral colors. Significance Birds have four color cone types in their eyes, compared to three in humans. In theory, this enables birds to discriminate a broad range of colors, including many nonspectral colors. Nonspectral colors are perceived when nonadjacent cone types (sensitive to widely separated parts of the light spectrum) are predominantly stimulated. For humans, purple (stimulation of blue- and red-sensitive cones) is a nonspectral color; birds’ fourth color cone type creates many more possibilities. We trained wild hummingbirds to participate in color vision tests, which revealed that they can discriminate a variety of nonspectral colors, including UV+red, UV+green, purple, and UV+yellow. Additionally, based on an analysis of ∼3,300 plumage and plant colors, we estimate that birds perceive many natural colors as nonspectral. Many animals have the potential to discriminate nonspectral colors. For humans, purple is the clearest example of a nonspectral color. It is perceived when two color cone types in the retina (blue and red) with nonadjacent spectral sensitivity curves are predominantly stimulated. Purple is considered nonspectral because no monochromatic light (such as from a rainbow) can evoke this simultaneous stimulation. Except in primates and bees, few behavioral experiments have directly examined nonspectral color discrimination, and little is known about nonspectral color perception in animals with more than three types of color photoreceptors. Birds have four color cone types (compared to three in humans) and might perceive additional nonspectral colors such as UV+red and UV+green. Can birds discriminate nonspectral colors, and are these colors behaviorally and ecologically relevant? Here, using comprehensive behavioral experiments, we show that wild hummingbirds can discriminate a variety of nonspectral colors. We also show that hummingbirds, relative to humans, likely perceive a greater proportion of natural colors as nonspectral. Our analysis of plumage and plant spectra reveals many colors that would be perceived as nonspectral by birds but not by humans: Birds’ extra cone type allows them not just to see UV light but also to discriminate additional nonspectral colors. Our results support the idea that birds can distinguish colors throughout tetrachromatic color space and indicate that nonspectral color perception is vital for signaling and foraging. Since tetrachromacy appears to have evolved early in vertebrates, this capacity for rich nonspectral color perception is likely widespread.",0.0864136666059494,12
sense_light_in_the_visible_spectrum,240,"Structure, self-assembly, and properties of a truncated reflectin variant. Significance The investigation of protein-based materials has provided a better understanding of living systems and has led to the development of ubiquitous modern technologies. Within this context, unique cephalopod proteins called reflectins have exhibited promise for biophotonics and bioelectronics applications, but the exploration of reflectins as materials has been hindered by an incomplete understanding of their structures and properties. Here, we resolve the molecular-level structure of a model reflectin variant, establish a straightforward approach to controlling the assembly of this protein, and describe a correlation between its structural characteristics and light-manipulating properties. Taken together, our findings advance current understanding of reflectin-based materials, provide insight into the color-changing capabilities of cephalopods, and afford new opportunities in biochemistry, cellular biology, bioengineering, and optics. Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant’s hierarchical assembly, and establish a direct correlation between the protein’s structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells’ color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.",0.08624197542667389,13
sense_light_in_the_visible_spectrum,317,"Bumble bees damage plant leaves and accelerate flower production when pollen is scarce. Bumble bee gardeners Bumble bees rely heavily on pollen resources for essential nutrients as they build their summer colonies. Therefore, we might expect that annual differences in the availability of these resources must simply be tolerated, but Pashalidou et al. made observations suggesting that bees may have strategies to cope with irregular seasonal flowering (see the Perspective by Chittka). When faced with a shortage of pollen, bumble bees actively damaged plant leaves in a characteristic way, and this behavior resulted in earlier flowering by as much as 30 days. Experimenters were not able to fully replicate the results with their own damage, suggesting that there is a distinct method that the bees use to stimulate earlier flowering. Science, this issue p. 881; see also p. 824 Bumble bees manipulate plants to bring about earlier flowering. Maintaining phenological synchrony with flowers is a key ecological challenge for pollinators that may be exacerbated by ongoing environmental change. Here, we show that bumble bee workers facing pollen scarcity damage leaves of flowerless plants and thereby accelerate flower production. Laboratory studies revealed that leaf-damaging behavior is strongly influenced by pollen availability and that bee-damaged plants flower significantly earlier than undamaged or mechanically damaged controls. Subsequent outdoor experiments showed that the intensity of damage inflicted varies with local flower availability; furthermore, workers from wild colonies of two additional bumble bee species were also observed to damage plant leaves. These findings elucidate a feature of bumble bee worker behavior that can influence the local availability of floral resources.",0.08015754073858261,14
sense_light_in_the_visible_spectrum,166,"Improved color constancy in honey bees enabled by parallel visual projections from dorsal ocelli. Significance Color sensing requires a capacity to discount the changing color of natural light. We present a biologically validated mathematical solution to this classic problem based on honey bee color vision. The observed spectral tuning of two simple ocellar photoreceptors in the honey bee allows for an optimal color constancy solution to different light environments, including standard CIE (Commission Internationale de l’Eclairage) illuminations, natural forest light, sunlight, or shade. The model is fully supported by a neural pathway potentially allowing for the transfer of spectral information originating from the ocellar photoreceptors to the centralized information processing regions in the brain and explains previously observed behavioral results. This solution to color constancy can be implemented into color imaging systems to enable accurate color interpretation. How can a pollinator, like the honey bee, perceive the same colors on visited flowers, despite continuous and rapid changes in ambient illumination and background color? A hundred years ago, von Kries proposed an elegant solution to this problem, color constancy, which is currently incorporated in many imaging and technological applications. However, empirical evidence on how this method can operate on animal brains remains tenuous. Our mathematical modeling proposes that the observed spectral tuning of simple ocellar photoreceptors in the honey bee allows for the necessary input for an optimal color constancy solution to most natural light environments. The model is fully supported by our detailed description of a neural pathway allowing for the integration of signals originating from the ocellar photoreceptors to the information processing regions in the bee brain. These findings reveal a neural implementation to the classic color constancy problem that can be easily translated into artificial color imaging systems.",0.07992339134216309,15
sense_light_in_the_visible_spectrum,136,"Ultra-black Camouflage in Deep-Sea Fishes. At oceanic depths >200 m, there is little ambient sunlight, but bioluminescent organisms provide another light source that can reveal animals to visual predators and prey [1-4]. Transparency and mirrored surfaces-common camouflage strategies under the diffuse solar illumination of shallower waters-are conspicuous when illuminated by directed bioluminescent sources due to reflection from the body surface [5, 6]. Pigmentation allows animals to absorb light from bioluminescent sources, rendering them visually undetectable against the dark background of the deep sea [5]. We present evidence suggesting pressure to reduce reflected bioluminescence led to the evolution of ultra-black skin (reflectance <0.5%) in 16 species of deep-sea fishes across seven distantly related orders. Histological data suggest this low reflectance is mediated by a continuous layer of densely packed melanosomes in the exterior-most layer of the dermis [7, 8] and that this layer lacks the unpigmented gaps between pigment cells found in other darkly colored fishes [9-13]. Using finite-difference, time-domain modeling and comparisons with melanosomes found in other ectothermic vertebrates [11, 13-21], we find the melanosomes making up the layer in these ultra-black species are optimized in size and shape to minimize reflectance. Low reflectance results from melanosomes scattering light within the layer, increasing the optical path length and therefore light absorption by the melanin. By reducing reflectance, ultra-black fish can reduce the sighting distance of visual predators more than 6-fold compared to fish with 2% reflectance. This biological example of efficient light absorption via a simple architecture of strongly absorbing and highly scattering particles may inspire new ultra-black materials.",0.06982437521219254,16
sense_light_in_the_visible_spectrum,216,"Nature as model for technical sensors. Summary form only given. Sensors and sensing are essential for all forms of life. Correspondingly there is a fascinating richness and diversity of sensory systems throughout the animal kingdom. Animals use sensory input not only for communication, but also for the detection, discrimination and localization of animate and inanimate objects. In addition sensory systems provide basic cues for spatial orientation and navigation. Both the structure and the physiology of sensory systems reflect the natural environment in which an animal lives and the needs of the animal. Accordingly, the relevant and often complex stimuli and noise conditions, which natural sensors evolved to cope with, have to be found and applied, to fully understand any sensory system. This is a particular challenge in cases where animals show sensory capabilities alien to human perceptions. This presentation focuses on two sensory systems that humans and most animals do not have: the infrared sensory system of pyrophilous beetles and the electrosensory system of weakly electric fish. I will show that these sensory systems not only have remarkable features but can also be used as a model for the development of novel technical sensors.",0.05468529090285301,17
sense_light_in_the_visible_spectrum,253,"How lovebirds maneuver through lateral gusts with minimal visual information. Significance Pilots need complex instruments and training to safely fly through gusts when their vision is deprived. In contrast, birds fly reliably over open water and at night, despite being more susceptible to gusts due to their much lower flight speeds. We found that even inexperienced lovebirds can navigate through strong opposing gusts in the dark, with only a faint point light source as a beacon. Their ability is surprising, because it was previously thought that diurnal animals needed a visual horizon and image features moving over their retina to maneuver. Instead, lovebirds fixate their head on the beacon while reorienting their body into the gust like a weathervane, enabling them to infer gust angle via neck twist and compensate accordingly. Flying birds maneuver effectively through lateral gusts, even when gust speeds are as high as flight speeds. What information birds use to sense gusts and how they compensate is largely unknown. We found that lovebirds can maneuver through 45° lateral gusts similarly well in forest-, lake-, and cave-like visual environments. Despite being diurnal and raised in captivity, the birds fly to their goal perch with only a dim point light source as a beacon, showing that they do not need optic flow or a visual horizon to maneuver. To accomplish this feat, lovebirds primarily yaw their bodies into the gust while fixating their head on the goal using neck angles of up to 30°. Our corroborated model for proportional yaw reorientation and speed control shows how lovebirds can compensate for lateral gusts informed by muscle proprioceptive cues from neck twist. The neck muscles not only stabilize the lovebirds’ visual and inertial head orientations by compensating low-frequency body maneuvers, but also attenuate faster 3D wingbeat-induced perturbations. This head stabilization enables the vestibular system to sense the direction of gravity. Apparently, the visual horizon can be replaced by a gravitational horizon to inform the observed horizontal gust compensation maneuvers in the dark. Our scaling analysis shows how this minimal sensorimotor solution scales favorably for bigger birds, offering local wind angle feedback within a wingbeat. The way lovebirds glean wind orientation may thus inform minimal control algorithms that enable aerial robots to maneuver in similar windy and dark environments.",0.053809452801942825,18
sense_light_in_the_visible_spectrum,128,"A dynamic broadband reflector built from microscopic silica spheres in the ‘disco’ clam Ctenoides ales. The ‘disco’ or ‘electric’ clam Ctenoides ales (Limidae) is the only species of bivalve known to have a behaviourally mediated photic display. This display is so vivid that it has been repeatedly confused for bioluminescence, but it is actually the result of scattered light. The flashing occurs on the mantle lip, where electron microscopy revealed two distinct tissue sides: one highly scattering side that contains dense aggregations of spheres composed of silica, and one highly absorbing side that does not. High-speed video confirmed that the two sides act in concert to alternate between vivid broadband reflectance and strong absorption in the blue region of the spectrum. Optical modelling suggests that the diameter of the spheres is nearly optimal for scattering visible light, especially at shorter wavelengths which predominate in their environment. This simple mechanism produces a striking optical effect that may function as a signal.",0.0525469034910202,19
sense_light_in_the_visible_spectrum,234,"A Pearl Spectrometer.. Information recovery from incomplete measurements, typically performed by a numerical means, is beneficial in a variety of classical and quantum signal processing. Random and sparse sampling with nanophotonic and light scattering approaches has received attention to overcome the hardware limitations of conventional spectrometers and hyperspectral imagers but requires high-precision nanofabrications and bulky media. We report a simple spectral information processing scheme in which light transport through an Anderson-localized medium serves as an entropy source for compressive sampling directly in the frequency domain. As implied by the ""lustrous"" reflection originating from the exquisite multilayered nanostructures, a pearl (or mother-of-pearl) allows us to exploit the spatial and spectral intensity fluctuations originating from strong light localization for extracting salient spectral information with a compact and thin form factor. Pearl-inspired light localization in low-dimensional structures can offer an alternative of spectral information processing by hybridizing digital and physical properties at a material level.",0.051659490913152695,20
optimize_shape/materials,190,"Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.",0.7913474440574646,1
optimize_shape/materials,39,"Mapping the β-Scorpion Toxin Receptor Site on Voltage-Gated Sodium Channels. Voltage-gated sodium channels are molecular targets of β-scorpion toxins, which enhance excitability by shifting the voltage dependence of activation to more negative potentials. These effects result from a voltage sensor trapping mechanism, in which toxins trap the voltage sensor in its activated conformation. Determinants of β-scorpion toxin (CssIV) binding and action on sodium channel (Nav1.2) are located in the S1-S2 and S3-S4 extracellular linkers in the voltage-sensing module in domain II. To completely map these regions, we made substitutions for previously unstudied amino acid residues and examined modulation by CssIVE15A, a highly active toxin derivative. Of 11 positions studied in IIS1-S2, only one significantly altered the toxin effect from wild-type by reducing binding to the resting state and almost abolishing trapping activity. In IIS3-S4, five positions surrounding a previously identified key binding determinant, G845, define a hotspot of high impact residues. Three of these substitutions reduced toxin binding and voltage-sensor trapping. The other two, V843A and E844N, increased voltage-sensor trapping approximately 4-fold and decreased apparent EC50. The rate of voltage sensor trapping upon depolarization was unchanged for V843A and increased approximately 2.5-fold for E844N. The rate at which the toxin releases the voltage sensor upon repolarization was increased 2.2-fold for the V843A but was unchanged for E844N. Thus CssIVE15A interacts with a short segment of IIS1-S2 and a broader region of DIIS3-S4. The bidirectional effects of mutations on toxin efficacy suggest that native residues make both positive and negative interactions with the toxin. Substitutions that increase toxin effects do so by increasing affinity of resting channels for the toxin and further increasing the relative affinity of the activated voltage-sensor for the toxin. These results provide further support for the voltage sensor-trapping model.",0.33287671208381653,2
optimize_shape/materials,282,"How neurons exploit fractal geometry to optimize their network connectivity. We investigate the degree to which neurons are fractal, the origin of this fractality, and its impact on functionality. By analyzing three-dimensional images of rat neurons, we show the way their dendrites fork and weave through space is unexpectedly important for generating fractal-like behavior well-described by an ‘effective’ fractal dimension D. This discovery motivated us to create distorted neuron models by modifying the dendritic patterns, so generating neurons across wide ranges of D extending beyond their natural values. By charting the D-dependent variations in inter-neuron connectivity along with the associated costs, we propose that their D values reflect a network cooperation that optimizes these constraints. We discuss the implications for healthy and pathological neurons, and for connecting neurons to medical implants. Our automated approach also facilitates insights relating form and function, applicable to individual neurons and their networks, providing a crucial tool for addressing massive data collection projects (e.g. connectomes).",0.3203032314777374,3
optimize_shape/materials,127,"Chromatic neuronal jamming in a primitive brain. Jamming models developed in inanimate matter have been widely used to describe cell packing in tissues 1 – 7 , but predominantly neglect cell diversity, despite its prevalence in biology. Most tissues, animal brains in particular, comprise a mix of many cell types, with mounting evidence suggesting that neurons can recognize their respective types as they organize in space 8 – 11 . How cell diversity revises the current jamming paradigm is unknown. Here, in the brain of the flatworm planarian Schmidtea mediterranea , which exhibits remarkable tissue plasticity within a simple, quantifiable nervous system 12 – 16 , we identify a distinct packing state, ‘chromatic’ jamming. Combining experiments with computational modelling, we show that neurons of distinct types form independent percolating networks barring any physical contact. This jammed state emerges as cell packing configurations become constrained by cell type-specific interactions and therefore may extend to describe cell packing in similarly complex tissues composed of multiple cell types. An imaging study of planarian flatworm brains demonstrates that densely packed neural tissues seem to have packing configurations commensurate with a jammed state.",0.267255961894989,4
optimize_shape/materials,87,"Shaping the zebrafish myotome by intertissue friction and active stress. Significance How do tissues self-organize to generate the complex organ shapes observed in vertebrates? Organ formation requires the integration of chemical and mechanical information, yet how this is achieved is poorly understood for most organs. Muscle compartments in zebrafish display a V shape, which is believed to be required for efficient swimming. We investigate how this structure emerges during zebrafish development, combining live imaging and quantitative analysis of cellular movements. We use theoretical modeling to understand how cell differentiation and mechanical interactions between tissues guide the emergence of a specific tissue morphology. Our work reveals how spatially modulating the mechanical environment around and within tissues can lead to complex organ shape formation. Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the future myotome and the surrounding tissues appears to spatially vary, effectively resulting in spatially heterogeneous friction. Using a vertex model combined with experimental validation, we show that the interplay of tissue spreading and friction is sufficient to drive the initial phase of chevron shape formation. However, local anisotropic stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the chevron in wild-type embryos. Finally, tissue plasticity is required for formation and maintenance of the chevron shape, which is mediated by orientated cellular rearrangements. Our work sheds light on how a spatiotemporal sequence of local cellular events can have a nonlocal and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.",0.25851231813430786,5
optimize_shape/materials,104,"Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.",0.25525468587875366,6
optimize_shape/materials,164,"Self-organization of river vegetation leads to emergent buffering of river flows and water levels. Global climate change is expected to impact hydrodynamic conditions in stream ecosystems. There is limited understanding of how stream ecosystems interact and possibly adapt to novel hydrodynamic conditions. Combining mathematical modelling with field data, we demonstrate that bio-physical feedback between plant growth and flow redistribution triggers spatial self-organization of in-channel vegetation that buffers for changed hydrological conditions. The interplay of vegetation growth and hydrodynamics results in a spatial separation of the stream into densely vegetated, low-flow zones divided by unvegetated channels of higher flow velocities. This self-organization process decouples both local flow velocities and water levels from the forcing effect of changing stream discharge. Field data from two lowland, baseflow-dominated streams support model predictions and highlight two important stream-level emergent properties: vegetation controls flow conveyance in fast-flowing channels throughout the annual growth cycle, and this buffering of discharge variations maintains water depths and wetted habitat for the stream community. Our results provide important evidence of how plant-driven self-organization allows stream ecosystems to adapt to changing hydrological conditions, maintaining suitable hydrodynamic conditions to support high biodiversity.",0.23960788547992706,7
optimize_shape/materials,277,"Encoding memory in tube diameter hierarchy of living flow network. Significance Simple organisms manage to thrive in complex environments. Having memory about the environment is key in taking informed decisions. Physarum polycephalum excels as a giant unicellular eukaryote, being even able to solve optimization problems despite the lack of a nervous system. Here, we follow experimentally the organism’s response to a nutrient source and find that memory about nutrient location is encoded in the morphology of the network-shaped organism. Our theoretical predictions in line with our observations unveil the mechanism behind memory encoding and demonstrate the P. polycephalum’s ability to read out previously stored information. The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment—successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient’s location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes’ capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks’ tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks’ version of associative memory—very likely of relevance for the plethora of living flow networks as well as for bioinspired design.",0.23879694938659668,8
optimize_shape/materials,210,"Optimal construction of army ant living bridges.. Integrating the costs and benefits of collective behaviors is a fundamental challenge to understanding the evolution of group living. These costs and benefits can rarely be quantified simultaneously due to the complexity of the interactions within the group, or even compared to each other because of the absence of common metrics between them. The construction of 'living bridges' by New World army ants - which they use to shorten their foraging trails - is a unique example of a collective behavior where costs and benefits have been experimentally measured and related to each other. As a result, it is possible to make quantitative predictions about when and how the behavior will be observed. In this paper, we extend a previous mathematical model of these costs and benefits to much broader domain of applicability. Specifically, we exhibit a procedure for analyzing the optimal formation, and final configuration, of army ant living bridges given a means to express the geometrical configuration of foraging path obstructions. Using this procedure, we provide experimentally testable predictions of the final bridge position, as well as the optimal formation process for certain cases, for a wide range of scenarios, which more closely resemble common terrain obstacles that ants encounter in nature. As such, our framework offers a rare benchmark for determining the evolutionary pressures governing the evolution of a naturally occurring collective animal behavior.",0.2130114734172821,9
optimize_shape/materials,122,"Architecture of a catalytically active homotrimeric plant cellulose synthase complex. Plant cell wall construction crew Plants produce a complex cell wall in which cellulose, a glucose polymer, is a major component. Cellulose fibers are formed from close-packed single chains of cellulose that have been proposed to be formed by multimeric complexes (18 or more subunits) of the enzyme cellulose synthase, which exists in several isoforms. Purushotham et al. determined a cryo–electron microscopy structure of a trimer of a single isoform of cellulose synthase. A large channel forms a path for cellulose chains through the membrane-embedded complex. The structure also reveals oligomeric interfaces and provides a framework for modeling the larger complexes seen in plant membranes. The close arrangement of exit sites for nascent glycan chains is consistent with the enzyme complex playing a role in directing cellulose microfibril formation. Science, this issue p. 1089 The structure of a homotrimeric cellulose synthase complex provides molecular insights into cellulose fibril formation. Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.",0.18693314492702484,10
optimize_shape/materials,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.1790490597486496,11
optimize_shape/materials,194,"Type-I collagen fibrils: From growth morphology to local order. Abstract.The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ($\alpha$α) or coarse ($ \beta$β) have opposite molecular orientations. The $\alpha$α-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for $\alpha$α-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.Graphical abstract",0.1470525562763214,12
optimize_shape/materials,177,"Flight activity in pallid swifts Apus pallidus
 during the non-breeding period. Flight activity recorders have recently confirmed that alpine and common swifts spend the majority of their non-breeding period on the wing, which may last 6–10 months. Here we test the hypothesis that the closely related pallid swift, a species with a breeding distribution around the Mediterranean, lead a similar aerial life-style during its migration and wintering periods. The pallid swift usually lays two clutches in one season and therefore spends more time in the breeding area than the common swift. We successfully tracked four pallid swifts with data loggers that record light for geolocation and acceleration every 5 min to monitor flight activity. The birds wintered south of the Sahel in west Africa from the Ivory Coast to Cameroon. The pallid swifts spent the majority of their non-breeding time in flight, especially the first two months after leaving the breeding area in autumn, while a few landing events occurred during the winter. The total time grounded was < 1%, similar to that of the common and alpine swifts. The mass specific flight metabolic rate of swifts is similar to the average non-breeding metabolic rate of a long distance terrestrial migrant, suggesting swifts are not more likely to procure oxidative damage as a consequence of continuous flight than other migrants. The open airspace used by swifts may provide a relatively safe habitat that explain the high survival rate found in swifts.",0.12527085840702057,13
optimize_shape/materials,155,"Juvenile social dynamics reflect adult reproductive strategies in bottlenose dolphins. The juvenile period is a challenging life-history stage, especially in species with a high degree of fission–fusion dynamics, such as bottlenose dolphins, where maternal protection is virtually absent. Here, we examined how juvenile male and female bottlenose dolphins navigate this vulnerable period. Specifically, we examined their grouping patterns, activity budget, network dynamics, and social associations in the absence of adults. We found that juveniles live in highly dynamic groups, with group composition changing every 10 min on average. Groups were generally segregated by sex, and segregation was driven by same-sex preference rather than opposite-sex avoidance. Juveniles formed strong associations with select individuals, especially kin and same-sex partners, and both sexes formed cliques with their preferred partners. Sex-specific strategies in the juvenile period reflected adult reproductive strategies, in which the exploration of potential social partners may be more important for males (which form long-term alliances in adulthood) than females (which preferentially associate with kin in adulthood). Females spent more time alone and were more focused on foraging than males, but still formed close same-sex associations, especially with kin. Males cast a wider social net than females, with strong same-sex associations and many male associates. Males engaged in more affiliative behavior than females. These results are consistent with the social bonds and skills hypothesis and suggest that delayed sexual maturity in species with relational social complexity may allow individuals to assess potential associates and explore a complex social landscape without the risks associated with sexual maturity (e.g., adult reproductive competition; inbreeding).",0.12284323573112488,14
optimize_shape/materials,126,Exact Spatiotemporal Dynamics of Confined Lattice Random Walks in Arbitrary Dimensions: A Century after Smoluchowski and Pólya. An exact solution to the discrete diffusion equation allows for accurate predictions of how the probabilities of reaction diffusion processes evolve over time.,0.09687723219394684,15
optimize_shape/materials,242,"Dynamics of topological defects and structural synchronization in a forming periodic tissue. Living organisms form a large variety of hierarchically structured extracellular functional tissues. Remarkably, these materials exhibit regularity and structural coherence across multiple length scales, far beyond the size of a single cell. Here, synchrotron-based nanotomographic imaging in combination with machine-learning-based segmentation is used to reveal the structural synchronization process of nacre forming in the shell of the mollusc Unio pictorum . We show that the emergence of this highly regular layered structure is driven by a disorder-to-order transition achieved through the motion and interaction of screw-like structural dislocations with an opposite topological sign. Using an analogy to similar processes observed in liquid-crystalline systems, we demonstrate that these microstructural faults act as dissipative topological defects coupled by an elastic distortion field surrounding their cores. Their mutual annihilation results in structural synchronization that is simulated using the classical Kuramoto model. The developed experimental, theoretical and numerical framework provides a comprehensive physical view of the formation of biogenic materials. Molluscs assemble layers of material in the shells around them with a high level of control. Here the authors observe the structural evolution of layer formation and propose a mechanism reminiscent of topological defect dynamics in liquid crystals.",0.09163541346788406,16
optimize_shape/materials,79,"Beaver-induced spatiotemporal patch dynamics affect landscape-level environmental heterogeneity. Beavers (Castor sp.) are ecosystem engineers that cause significant changes to their physical environment and alter the availability of resources to other species. We studied flood dynamics created by American beaver (C. canadensis K.) in a southern boreal landscape in Finland in 1970-2018. We present for the first time, to our knowledge, a temporally continuous long-term study of beaver-induced flood disturbances starting from the appearance of beaver in the area. During the 49 years, the emergence of new sites flooded by beaver and repeated floods (61% of the sites) formed a dynamic mosaic characterized by clustered patterns of beaver sites. As beaver dispersal proceeded, connectivity of beaver sites increased significantly. The mean flood duration was approximately three years, which highlights the importance of datasets with high-temporal resolution in detecting beaver-induced disturbances. An individual site was often part of the active flood mosaic over several decades, although the duration and the number of repeated floods at different sites varied considerably. Variation of flood-inundated and post-flood phases at individual sites resulted in a cumulative number of unique patches that contribute to environmental heterogeneity in space and time. A disturbance mosaic consisting of patches differing by successional age and flood history is likely to support species richness and abundance of different taxa and facilitate whole species communities. Beavers are thus a suitable means to be used in restoration of riparian habitat due to their strong and dynamic influence on abiotic environment and its biotic consequences.",0.08615416288375854,17
optimize_shape/materials,20,"Epicormic strand structure in Angophora, Eucalyptus and Lophostemon (Myrtaceae): implications for fire resistance and recovery. Summary 
• Epicormic bud producing structures in the eucalypts, a large group of woody plants of considerable ecological, horticultural and silvicultural importance, are described here. 
• The outer portion of epicormic strands excised from the bark of large diameter stems of 18 Eucalyptus species, two Angophora species and Lophostemon confertus was examined anatomically in semithin sections. 
• In the inner bark each eucalypt strand usually possessed 5–12 radially orientated strips of tissue of meristematic appearance. The meristem strips were c. 30–50 µm high, 70–110 µm wide and 2000–10 000 µm long, with a lacuna above the meristem surface. Few buds or bud primordia were associated with the strands and the strands appeared to have a reduced regenerative potential in the outer bark. 
• In most angiosperm trees dormant epicormic buds are present in the outer bark, a position where they could be killed by fire. By contrast, in eucalypts the greatest epicormic bud initiation potential is at the level of the vascular cambium, which is protected by the maximum bark thickness. This might explain the pronounced ability of eucalypts to produce bole and branch epicormic shoots after moderate to intense fire.",0.07086131721735,18
optimize_shape/materials,88,"Collective Computation in Animal Fission-Fusion Dynamics. Recent work suggests that collective computation of social structure can minimize uncertainty about the social and physical environment, facilitating adaptation. We explore these ideas by studying how fission-fusion social structure arises in spider monkey (Ateles geoffroyi) groups, exploring whether monkeys use social knowledge to collectively compute subgroup size distributions adaptive for foraging in variable environments. We assess whether individual decisions to stay in or leave subgroups are conditioned on strategies based on the presence or absence of others. We search for this evidence in a time series of subgroup membership. We find that individuals have multiple strategies, suggesting that the social knowledge of different individuals is important. These stay-leave strategies provide microscopic inputs to a stochastic model of collective computation encoded in a family of circuits. Each circuit represents an hypothesis for how collectives combine strategies to make decisions, and how these produce various subgroup size distributions. By running these circuits forward in simulation we generate new subgroup size distributions and measure how well they match food abundance in the environment using transfer entropies. We find that spider monkeys decide to stay or go using information from multiple individuals and that they can collectively compute a distribution of subgroup size that makes efficient use of ephemeral sources of nutrition. We are able to artificially tune circuits with subgroup size distributions that are a better fit to the environment than the observed. This suggests that a combination of measurement error, constraint, and adaptive lag are diminishing the power of collective computation in this system. These results are relevant for a more general understanding of the emergence of ordered states in multi-scale social systems with adaptive properties–both natural and engineered.",0.0680399164557457,19
optimize_shape/materials,120,"Muscle and neuronal guidepost-like cells facilitate planarian visual system regeneration. Guiding regeneration Many adult organisms can regenerate neural circuits after injury. However, it is not clear which guidance mechanisms operate to promote axon path finding in the adult. Scimone et al. addressed this question by investigating regeneration of the planarian visual system (see the Perspective by Roberts-Galbraith). Distinct muscle cell populations were found in close association with photoreceptor axons that, together with a neuron class, facilitated visual system assembly after diverse injuries or eye transplantations. These cells exhibited features similar to embryonic guidepost cells and were specified independently of eyes in precise locations by the action of adult positional information cues. Absence of these guidepost-like cells was associated with defective neuronal wiring in regeneration. Science, this issue p. eaba3203; see also p. 1428 Adult regeneration requires guidepost-like cells for precise rewiring of the eyes in the flatworm Schmidtea mediterranea. INTRODUCTION Multiple strategies exist to promote precise wiring of developing neuronal circuits. One strategy involves guidepost cells, which exist transiently in embryos. Guidepost cells can act as intermediate guidance targets for axons or by providing a scaffold that facilitates axonal targeting. Most guidance mechanisms become dispensable once the circuit is assembled. Loss of guidance mechanisms creates a potential limitation on regeneration of neuronal patterns—yet some animals are capable of functional regeneration of their nervous system. RATIONALE Assuming some adult animals have the ability to regenerate functional neuronal circuits, they must possess mechanism(s) for de novo repair of neuronal patterns. In this study, we aimed to characterize such mechanisms by studying regeneration of the planarian visual system after diverse injuries. RESULTS We identified a rare subset of muscle cells (notum+; frizzled 5/8-4+) concentrated at two precise anatomical locations and in tight association with photoreceptor axons. The first group of these cells was found near the eye, where visual axons project and fasciculate to form a bundle. The second group of these cells was found near choice points, where sorting of contralateral and ipsilateral axons occurs. Both groups of muscle cells were formed during regeneration of the visual system and were always tightly associated with axonal projections, consistent with a possible role in attraction to facilitate visual system assembly. In addition, we found that a notum+ set of neurons, located at the adult anterior brain commissure, regenerated before axonal midline crossing and was associated with optic chiasm regeneration. We reasoned that if the photoreceptor axon–associated notum+; frizzled 5/8-4+ muscle cells have a guidepost-like function, their formation should be independent of eye cells. Eyes transplanted to ectopic anatomical locations did not result in the formation of notum+; frizzled 5/8-4+ muscle cells. Furthermore, animals that were unable to generate eyes [ovo RNA interference (ovo RNAi) animals] were still capable of specifying these muscle cells at the right locations. In addition, we predicted that if these muscle cells were indeed guidepost-like cells, visual axon trajectories should be associated with them after eye transplantation into eyeless heads. In all instances, axons from transplanted eyes projected toward notum+; frizzled 5/8- 4+ muscle cells and often adjusted their trajectories after encountering them. We found that an array of signaling cues, which provide positional information essential for planarian patterning, was required for dictating the precise location of these guidepost-like cells. This provides a visual system–extrinsic mechanism for placing guidepost-like cells in the adult. Finally, with single-cell RNA sequencing and fluorescent in situ hybridization screening, we identified molecules and transcription factors expressed in these cells. RNAi studies reduced or eliminated muscle or neuronal guidepost-like cell subsets and resulted in aberrant patterns of visual axonal trajectories. CONCLUSION Adult molecular and cellular strategies for regenerating neuronal pattern in the absence of embryo-specific contexts must exist to overcome damage or loss after injury. Understanding these mechanisms might provide important insights for regenerative medicine. Here, we found adult guidepost-like cell populations, extrinsic to the visual system and placed by adult positional information, that promote normal visual system regeneration in planarians. Adult guidepost-like cells facilitate visual system regeneration in planarians. Muscle and neuron guidepost-like cells are present at key locations near the planarian visual system and are formed independently of photoreceptor axons. Regenerating and transplanted eyes target projections to guidepost-like cells. Positional information cues provide an eye-extrinsic mechanism to place guidepost-like cells in the adult. Loss of guidepost-like cells is associated with visual system disruption. wnt-5, slit, and ndk are involved in positional control of guidepost-like cell placement. fz5/8-4, frizzled 5/8-4. Neuronal circuits damaged or lost after injury can be regenerated in some adult organisms, but the mechanisms enabling this process are largely unknown. We used the planarian Schmidtea mediterranea to study visual system regeneration after injury. We identify a rare population of muscle cells tightly associated with photoreceptor axons at stereotyped positions in both uninjured and regenerating animals. Together with a neuronal population, these cells promote de novo assembly of the visual system in diverse injury and eye transplantation contexts. These muscle guidepost-like cells are specified independently of eyes, and their position is defined by an extrinsic array of positional information cues. These findings provide a mechanism, involving adult formation of guidepost-like cells typically observed in embryos, for axon pattern restoration in regeneration.",0.06790980696678162,20
sense_chemicals,147,"Existence and functions of a kisspeptin neuropeptide signaling system in a non-chordate deuterostome species. The kisspeptin system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here, we report the identification and characterization of the kisspeptin system in the sea cucumber Apostichopus japonicus. The gene encoding the kisspeptin precursor generates two mature neuropeptides, AjKiss1a and AjKiss1b. The receptors for these neuropeptides, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate kisspeptins, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide. The A. japonicus kisspeptin system functions in multiple tissues that are closely related to seasonal reproduction and metabolism. Overall, our findings uncover for the first time the existence and function of the kisspeptin system in a non-chordate species and provide new evidence to support the ancient origin of intracellular signaling and physiological functions that are mediated by this molecular system.",0.6148678660392761,1
sense_chemicals,92,"Prey Exploits the Auditory Illusions of Eavesdropping Predators. Mating signals have evolved to attract target receivers, even to the point of exploiting receivers through perceptual manipulation. Signals, however, can also expose signalers to nontarget receivers, including predators and parasites, and thus have also evolved to decrease enemy attraction. Here we show that male tree frogs (Smilisca sila) reduce their attractiveness to eavesdropping enemies (bats and midges) by overlapping their calls at near-perfect synchrony with the calls of neighboring conspecifics. By producing calls that closely follow those of other males, synchronizing S. sila take advantage of an auditory illusion where enemies are more attracted to the leading call. Female S. sila, however, are less susceptible to this illusion. Thus, synchronization among signaling males can result in acoustic crypsis from predators without affecting female attraction. Given the widespread use of conspicuous mating signals and eavesdropping enemies, perceptual exploitation of eavesdroppers is likely a common driver of signal evolution.",0.5552312731742859,2
sense_chemicals,81,"Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance. Plants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including “elicitors”, that are present in herbivores’ oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs’ (HAKs’) actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants. Uemura et al. study the mechanism of herbivore resistance in soybean and Arabidopsis. They show that receptor-like kinases (HAK1/2) respond to a polysaccharide in the oral secretions of Spodoptera litura and then interact with PBL27, resulting in an ethylene-dependent herbivore resistance.",0.46764805912971497,3
sense_chemicals,272,"Social signals mediate oviposition site selection in Drosophila suzukii. The information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila . These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.",0.3582440912723541,4
sense_chemicals,98,"Species richness and redundancy promote persistence of exploited mutualisms in yeast. Species richness maintains mutualisms Mutualistic communities of species that benefit each other are ubiquitous in ecosystems and are important for ecosystem functioning. However, the relationship between the persistence of mutualisms and species richness has remained unclear. Vidal et al. used a synthetic mutualism in brewer's yeast to experimentally test whether species richness buffers mutualistic communities against exploitation by species that do not provide benefits in return. They showed that richer mutualist communities survive exploitation more often than pairwise mutualisms and that higher species richness and functional redundancy allow mutualist communities to persist in the presence of exploiters. These results provide experimental support for the hypothesis that species richness is necessary for the function and maintenance of mutualistic communities. Science, this issue p. 346 Experiments with yeast show that species richness buffers against loss of mutualistic interactions in ecological communities. Mutualisms, or reciprocally beneficial interspecific interactions, constitute the foundation of many ecological communities and agricultural systems. Mutualisms come in different forms, from pairwise interactions to extremely diverse communities, and they are continually challenged with exploitation by nonmutualistic community members (exploiters). Thus, understanding how mutualisms persist remains an essential question in ecology. Theory suggests that high species richness and functional redundancy could promote mutualism persistence in complex mutualistic communities. Using a yeast system (Saccharomyces cerevisiae), we experimentally show that communities with the greatest mutualist richness and functional redundancy are nearly two times more likely to survive exploitation than are simple communities. Persistence increased because diverse communities were better able to mitigate the negative effects of competition with exploiters. Thus, large mutualistic networks may be inherently buffered from exploitation.",0.3238305449485779,5
sense_chemicals,317,"Bumble bees damage plant leaves and accelerate flower production when pollen is scarce. Bumble bee gardeners Bumble bees rely heavily on pollen resources for essential nutrients as they build their summer colonies. Therefore, we might expect that annual differences in the availability of these resources must simply be tolerated, but Pashalidou et al. made observations suggesting that bees may have strategies to cope with irregular seasonal flowering (see the Perspective by Chittka). When faced with a shortage of pollen, bumble bees actively damaged plant leaves in a characteristic way, and this behavior resulted in earlier flowering by as much as 30 days. Experimenters were not able to fully replicate the results with their own damage, suggesting that there is a distinct method that the bees use to stimulate earlier flowering. Science, this issue p. 881; see also p. 824 Bumble bees manipulate plants to bring about earlier flowering. Maintaining phenological synchrony with flowers is a key ecological challenge for pollinators that may be exacerbated by ongoing environmental change. Here, we show that bumble bee workers facing pollen scarcity damage leaves of flowerless plants and thereby accelerate flower production. Laboratory studies revealed that leaf-damaging behavior is strongly influenced by pollen availability and that bee-damaged plants flower significantly earlier than undamaged or mechanically damaged controls. Subsequent outdoor experiments showed that the intensity of damage inflicted varies with local flower availability; furthermore, workers from wild colonies of two additional bumble bee species were also observed to damage plant leaves. These findings elucidate a feature of bumble bee worker behavior that can influence the local availability of floral resources.",0.27041110396385193,6
sense_chemicals,270,"Neural correlates of mating system diversity: oxytocin and vasopressin receptor distributions in monogamous and non-monogamous Eulemur. Contemporary theory that emphasizes the roles of oxytocin and vasopressin in mammalian sociality has been shaped by seminal vole research that revealed interspecific variation in neuroendocrine circuitry by mating system. However, substantial challenges exist in interpreting and translating these rodent findings to other mammalian groups, including humans, making research on nonhuman primates crucial. Both monogamous and non-monogamous species exist within Eulemur, a genus of strepsirrhine primate, offering a rare opportunity to broaden a comparative perspective on oxytocin and vasopressin neurocircuitry with increased evolutionary relevance to humans. We performed oxytocin and arginine vasopressin 1a receptor autoradiography on 12 Eulemur brains from seven closely related species to (1) characterize receptor distributions across the genus, and (2) examine differences between monogamous and non-monogamous species in regions part of putative “pair-bonding circuits”. We find some binding patterns across Eulemur reminiscent of olfactory-guided rodents, but others congruent with more visually oriented anthropoids, consistent with lemurs occupying an ‘intermediary’ evolutionary niche between haplorhine primates and other mammalian groups. We find little evidence of a “pair-bonding circuit” in Eulemur akin to those proposed in previous rodent or primate research. Mapping neuropeptide receptors in these nontraditional species questions existing assumptions and informs proposed evolutionary explanations about the biological bases of monogamy.",0.20768478512763977,7
sense_chemicals,216,"Nature as model for technical sensors. Summary form only given. Sensors and sensing are essential for all forms of life. Correspondingly there is a fascinating richness and diversity of sensory systems throughout the animal kingdom. Animals use sensory input not only for communication, but also for the detection, discrimination and localization of animate and inanimate objects. In addition sensory systems provide basic cues for spatial orientation and navigation. Both the structure and the physiology of sensory systems reflect the natural environment in which an animal lives and the needs of the animal. Accordingly, the relevant and often complex stimuli and noise conditions, which natural sensors evolved to cope with, have to be found and applied, to fully understand any sensory system. This is a particular challenge in cases where animals show sensory capabilities alien to human perceptions. This presentation focuses on two sensory systems that humans and most animals do not have: the infrared sensory system of pyrophilous beetles and the electrosensory system of weakly electric fish. I will show that these sensory systems not only have remarkable features but can also be used as a model for the development of novel technical sensors.",0.1565663069486618,8
sense_chemicals,308,"Phytohormone-dependent plant defense signaling orchestrated by oral bacteria of the herbivore Spodoptera litura.. A vast array of herbivorous arthropods live with symbiotic microorganisms. However, little is known about the nature and functional mechanism of bacterial effects on plant defense responses towards herbivores. We explored the role of microbes present in extracts of oral secretion (OS) isolated from larvae of Spodoptera litura, a generalist herbivore, in phytohormone signaling-dependent defense responses in Arabidopsis thaliana (arabidopsis). In response to mechanical damage (MD) with application of bacteria-free OS (OS- ) prepared by sterilization or filtration of OS, arabidopsis leaves exhibited enhanced de novo synthesis of oxylipins, and induction of transcript levels of the responsible genes, in comparison to those in leaves with MD + non-sterilized OS (OS+ ), indicating that OS bacteria serve as suppressors of these genes. By contrast, de novo synthesis/signaling of salicylic acid and signaling of abscisic acid were enhanced by OS bacteria. These signaling networks were cross-regulated by each other. Meta-analysis of OS bacteria identified 70 bacterial strains. Among them was Staphylococcus epidermidis, an anaerobic staphylococcus that was shown to contribute to the suppression/manipulation of phytohormone-dependent plant defense signaling. The presence of OS bacteria was consequently beneficial for S. litura larvae hosted by Brassicaceae.",0.14175626635551453,9
sense_chemicals,143,"Socially foraging bats discriminate between group members based on search-phase echolocation calls. © The Author(s) 2020. Published by Oxford University Press on behalf of the International Society for Behavioral Ecology. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Original Article",0.1405416876077652,10
sense_chemicals,227,"High-capacity auditory memory for vocal communication in a social songbird. Zebra finches can quickly form long-term auditory memories of up to 50 conspecifics based on their song or distance call. Effective vocal communication often requires the listener to recognize the identity of a vocalizer, and this recognition is dependent on the listener’s ability to form auditory memories. We tested the memory capacity of a social songbird, the zebra finch, for vocalizer identities using conditioning experiments and found that male and female zebra finches can remember a large number of vocalizers (mean, 42) based solely on the individual signatures found in their songs and distance calls. These memories were formed within a few trials, were generalized to previously unheard renditions, and were maintained for up to a month. A fast and high-capacity auditory memory for vocalizer identity has not been demonstrated previously in any nonhuman animals and is an important component of vocal communication in social species.",0.14031533896923065,11
sense_chemicals,271,"Navigation by extrapolation of geomagnetic cues in a migratory songbird. Displacement experiments have demonstrated that experienced migratory birds translocated thousands of kilometers away from their migratory corridor can orient toward and ultimately reach their intended destinations.1 This implies that they are capable of ""true navigation,"" commonly defined2-4 as the ability to return to a known destination after displacement to an unknown location without relying on familiar surroundings, cues that emanate from the destination, or information collected during the outward journey.5-13 In birds, true navigation appears to require previous migratory experience5-7,14,15 (but see Kishkinev et al.16 and Piersma et al.17). It is generally assumed that, to correct for displacements outside the familiar area, birds initially gather information within their year-round distribution range, learn predictable spatial gradients of environmental cues within it, and extrapolate from those to unfamiliar magnitudes-the gradient hypothesis.6,9,18-22 However, the nature of the cues and evidence for actual extrapolation remain elusive. Geomagnetic cues (inclination, declination, and total intensity) provide predictable spatial gradients across large parts of the globe and could serve for navigation. We tested the orientation of long-distance migrants, Eurasian reed warblers, exposing them to geomagnetic cues of unfamiliar magnitude encountered beyond their natural distribution range. The birds demonstrated re-orientation toward their migratory corridor as if they were translocated to the corresponding location but only when all naturally occurring magnetic cues were presented, not when declination was changed alone. This result represents direct evidence for migratory birds' ability to navigate using geomagnetic cues extrapolated beyond their previous experience.",0.12308309227228165,12
sense_chemicals,24,"Predator-released hydrocarbons repel oviposition by a mosquito.. Prey species commonly use predator-released kairomones (PRKs) to detect risk of predation, yet the chemical identity of PRKs remains elusive. Chemical identification of PRKs will facilitate the study of predator-prey interactions and the risk of predation, and when the prey are pests, will potentially provide environmentally friendly means of pest control. In temporary pools of the Mediterranean and Middle East, larvae of the mosquito Culiseta longiareolata Macquart are highly vulnerable to the common predatory backswimmer, Notonecta maculata Fabricius. We demonstrate that N. maculata releases two hydrocarbons, n-heneicosane and n-tricosane, which repel ovipositing females of C. longiareolata. In behavioural tests with environmentally relevant chemical concentrations in outdoor mesocosm experiments, the repellent effects of the two compounds were additive at the tested concentrations.",0.1019534170627594,13
sense_chemicals,298,"Plant-pollinator interactions between generalists persist over time and space.. Generalist species are the linchpins of networks, as they are important for maintaining network structure and function. Previous studies have shown that interactions between generalists tend to occur consistently across years and sites. However, the link between temporal and spatial interaction persistence across scales remains unclear. To address this gap, we collected data on plant-pollinator interactions throughout the flowering period for five years across six plots in a subalpine meadow in the Rocky Mountains. We found that interactions between generalists tended to persist more in time and space such that interactions near the network core were more frequently recorded across years, within seasons, and among plots. We posit that species' tolerance of environmental variation across time and space plays a key role in generalization by regulating spatiotemporal overlap with interaction partners. Our results imply a role of spatiotemporal environmental variation in organizing species interactions, marrying niche concepts that emphasize species environmental constraints and their community role.",0.09543369710445404,14
sense_chemicals,94,"The potential of the solitary parasitoid Microctonus brassicae for the biological control of the adult cabbage stem flea beetle, Psylliodes chrysocephala. The cabbage stem flea beetle (CSFB), Psylliodes chrysocephala L. (Coleoptera: Chrysomelidae), is a major pest of oilseed rape, Brassica napus L. (Brassicaceae), within the UK and continental Europe. Following the withdrawal of many broad‐spectrum pesticides, most importantly neonicotinoids, and with increased incidence of pyrethroid resistance, few chemical control options remain, resulting in the need for alternative pest management strategies. We identified the parasitoid wasp Microctonus brassicae (Haeselbarth) (Hymenoptera: Braconidae) within CSFB collected from three independent sites in Norfolk, UK. Parasitism of adult CSFB was confirmed, and wasp oviposition behaviour was described. Moreover, we show that within captive colonies parasitism rates are sufficient to generate significant biological control of CSFB populations. A sequence of the M. brassicae mitochondrial cytochrome oxidase 1 (MT‐CO1) gene was generated for rapid future identification. Moroccan specimens of Microctonus aethiopoides (Loan), possessing 90% sequence similarity, were the closest identified sequenced species. This study represents the first description published in English of this parasitoid of the adult cabbage stem flea beetle.",0.09082712978124619,15
sense_chemicals,275,"Pseudoflowers produced by Fusarium xyrophilum on yellow-eyed grass (Xyris spp.) in Guyana: a novel floral mimicry system?. Pseudoflower formation is arguably the rarest outcome of a plant-fungus interaction. Here we report on a novel putative floral mimicry system in which the pseudoflowers are composed entirely of fungal tissues in contrast to modified leaves documented in previous mimicry systems. Pseudoflowers on two perennial Xyris species (yellow-eyed grass, X. setigera and X. surinamensis) collected from savannas in Guyana were produced by Fusarium xyrophilum, a novel Fusarium species. These pseudoflowers mimic Xyris flowers in gross morphology and are ultraviolet reflective. Axenic cultures of F. xyrophilum produced two pigments that had fluorescence emission maxima in light ranges that trichromatic insects are sensitive to and volatiles known to attract insect pollinators. One of the volatiles emitted by F. xyrophilum cultures (i.e., 2-ethylhexanol) was also detected in the head space of X. laxifolia var. iridifolia flowers, a perennial species native to the New World. Results of microscopic and PCR analyses, combined with examination of gross morphology of the pseudoflowers, provide evidence that the fungus had established a systemic infection in both Xyris species, sterilized them and formed fungal pseudoflowers containing both mating type idiomorphs. Fusarium xyrophilum cultures also produced the auxin indole-3-acetic acid (IAA) and the cytokinin isopentenyl adenosine (iPR). Field observations revealed that pseudoflowers and Xyris flowers were both visited by bees. Together, the results suggest that F. xyrophilum pseudoflowers are a novel floral mimicry system that attracts insect pollinators, via visual and olfactory cues, into vectoring its conidia, which might facilitate outcrossing of this putatively heterothallic fungus and infection of previously uninfected plants.",0.08762291073799133,16
sense_chemicals,257,"Burying Beetle Parents Adaptively Manipulate Information Broadcast from a Microbial Community. Microbial volatiles provide essential information for animals, which compete to detect, respond to, and perhaps control this information. Burying beetle parents have the opportunity to influence microbially derived semiochemicals, because they monopolize a small carcass for their family, repairing feeding holes and applying exudates that alter the microbial community. To study adaptive manipulation of microbial cues, we integrated mechanistic and functional approaches. We contrasted gas chromatography–mass spectrometry (GC-MS) volatile profiles from carcasses that were or were not prepared by a resident pair of Nicrophorus orbicollis. Methyl thiocyanate (MeSCN), the primary attractant for burying beetles seeking a fresh carcass, was reduced 20-fold by carcass preparation, while dimethyl trisulfide (DMTS), which deters breeding beetles, was increased 20-fold. These results suggest that parental care serves to make previously public information more private (crypsis, MeSCN) and to disinform rivals with a deterrent (DMTS). Functional tests in the field demonstrated that carcass preparation reduced discovery and use by congeners (threefold) as well as by dipteran rivals. Because microbes and their chemicals influence nearly every aspect of animal ecology, animal manipulation of microbial cues may be as widespread as manipulation of their own signals.",0.0703372210264206,17
sense_chemicals,108,"Dynamic, Non-binary Specification of Sexual State in the C. elegans Nervous System. Biological sex in animals is often considered a fixed, individual-level characteristic. However, not all sex-specific features are static: for example, C. elegans males (XO) can sometimes exhibit hermaphrodite (XX)-like feeding behavior [1, 2]. (C. elegans hermaphrodites are somatic females that transiently produce self-sperm.) Essentially all somatic sex differences in C. elegans are governed by the master regulator tra-1, whose activity is controlled by chromosomal sex and is necessary and sufficient to specify the hermaphrodite state [3]. One aspect of this state is high expression of the chemoreceptor odr-10. In hermaphrodites, high odr-10 expression promotes feeding, but in males, low odr-10 expression facilitates exploration [4]. However, males suppress this sex difference in two contexts: juvenile males exhibit high odr-10 expression and food deprivation activates odr-10 in adult males [4-6]. Remarkably, we find that both of these phenomena require tra-1. In juvenile (L3) males, tra-1 is expressed in numerous neurons; this expression diminishes as individuals mature into adulthood, a process that requires conserved regulators of sexual maturation. tra-1 remains expressed in a small number of neurons in adult males, where it likely has a permissive role in odr-10 activation. Thus, the neuronal functions of tra-1 are not limited to hermaphrodites; rather, tra-1 also acts in the male nervous system to transiently suppress a sexual dimorphism, developmentally and in response to nutritional stress. Our results show that the molecular and functional representation of sexual state in C. elegans is neither static nor homogeneous, challenging traditional notions about the nature of biological sex.",0.06397158652544022,18
sense_chemicals,284,"Cuttlefish exert self-control in a delay of gratification task. The ability to exert self-control varies within and across taxa. Some species can exert self-control for several seconds whereas others, such as large-brained vertebrates, can tolerate delays of up to several minutes. Advanced self-control has been linked to better performance in cognitive tasks and has been hypothesized to evolve in response to specific socio-ecological pressures. These pressures are difficult to uncouple because previously studied species face similar socio-ecological challenges. Here, we investigate self-control and learning performance in cuttlefish, an invertebrate that is thought to have evolved under partially different pressures to previously studied vertebrates. To test self-control, cuttlefish were presented with a delay maintenance task, which measures an individual's ability to forgo immediate gratification and sustain a delay for a better but delayed reward. Cuttlefish maintained delay durations for up to 50–130 s. To test learning performance, we used a reversal-learning task, whereby cuttlefish were required to learn to associate the reward with one of two stimuli and then subsequently learn to associate the reward with the alternative stimulus. Cuttlefish that delayed gratification for longer had better learning performance. Our results demonstrate that cuttlefish can tolerate delays to obtain food of higher quality comparable to that of some large-brained vertebrates.",0.05945770442485809,19
sense_chemicals,291,"Hard to catch: experimental evidence supports evasive mimicry. Most research on aposematism has focused on chemically defended prey, but the signalling difficulty of capture remains poorly explored. Similar to classical Batesian and Müllerian mimicry related to distastefulness, such ‘evasive aposematism' may also lead to convergence in warning colours, known as evasive mimicry. A prime candidate group for evasive mimicry are Adelpha butterflies, which are agile insects and show remarkable colour pattern convergence. We tested the ability of naive blue tits to learn to avoid and generalize Adelpha wing patterns associated with the difficulty of capture and compared their response to that of birds that learned to associate the same wing patterns with distastefulness. Birds learned to avoid all wing patterns tested and generalized their aversion to other prey to some extent, but learning was faster with evasive prey compared to distasteful prey. Our results on generalization agree with longstanding observations of striking convergence in wing colour patterns among Adelpha species, since, in our experiments, perfect mimics of evasive and distasteful models were always protected during generalization and suffered the lowest attack rate. Moreover, generalization on evasive prey was broader compared to that on distasteful prey. Our results suggest that being hard to catch may deter predators at least as effectively as distastefulness. This study provides empirical evidence for evasive mimicry, a potentially widespread but poorly understood form of morphological convergence driven by predator selection.",0.05080118402838707,20
manage_stress/strain,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.9777427911758423,1
manage_stress/strain,223,"Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets. Nacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design. The hierarchical structure of nacre is known to contribute to its high strength and toughness, providing inspiration for many biomimetic materials. Here, co-oriented 20 µm stacks of aragonite platelets are shown to contribute to the toughness of nacre, defining a new characteristic length scale.",0.9372186064720154,2
manage_stress/strain,300,"Extreme strength observed in limpet teeth. The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.",0.9237610101699829,3
manage_stress/strain,78,"Bioinspired Materials with Self-Adaptable Mechanical Properties.. Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.",0.8965993523597717,4
manage_stress/strain,292,"A Graphic Way For Notch Shape Optimization. Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.",0.826263427734375,5
manage_stress/strain,305,"The structure and mechanics of Moso bamboo material. Although bamboo has been used structurally for millennia, there is currently increasing interest in the development of renewable and sustainable structural bamboo products (SBPs). These SBPs are analogous to wood products such as plywood, oriented strand board and glue-laminated wood. In this study, the properties of natural Moso bamboo (Phyllostachys pubescens) are investigated to further enable the processing and design of SBPs. The radial and longitudinal density gradients in bamboo give rise to variations in the mechanical properties. Here, we measure the flexural properties of Moso bamboo in the axial direction, along with the compressive strengths in the axial and transverse directions. Based on the microstructural variations (observed with scanning electron microscopy) and extrapolated solid cell wall properties of bamboo, we develop models, which describe the experimental results well. Compared to common North American construction woods loaded along the axial direction, Moso bamboo is approximately as stiff and substantially stronger, in both flexure and compression but denser. This work contributes to critical knowledge surrounding the microstructure and mechanical properties of bamboo, which are vital to the engineering and design of sustainable SBPs.",0.7541300058364868,6
manage_stress/strain,250,"Biomechanical insights into the dentition of megatooth sharks (Lamniformes: Otodontidae). The evolution of gigantism in extinct otodontid sharks was paralleled by a series of drastic modifications in their dentition including widening of the crowns, loss of lateral cusplets, and acquisition of serrated cutting edges. These traits have generally been interpreted as key functional features that enabled the transition from piscivory to more energetic diets based on marine mammals, ultimately leading to the evolution of titanic body sizes in the most recent forms (including the emblematic Otodus megalodon ). To investigate this hypothesis, we evaluate the biomechanics of the anterior, lateral, and posterior teeth of five otodontid species under different loading conditions by using two-dimensional finite element analysis. Stress distribution patterns are remarkably similar among all models under puncture and draw (i.e., when subjected to vertical and lateral forces, respectively). Contrary to expectation, higher average stress values are detected under both loading scenarios in more recent species. Altogether, this suggests little correlation between tooth morphology and key aspects of biomechanical behaviour in otodontids, making it difficult to frame the morphological trend of their dentitions within an adaptive scenario. We propose that this pattern most likely emerged as a non-functional by-product of heterochronic processes driven by selection towards larger body sizes.",0.7449040412902832,7
manage_stress/strain,76,"Bone-inspired microarchitectures achieve enhanced fatigue life. Significance Microarchitectured materials, such as foams and lattice structures, can achieve high stiffness and strength while remaining extremely lightweight. Applying high-porosity microarchitectured materials to durable devices, such as vehicles, however, will require the materials to also resist failure during cyclic loading. Here, we identify an aspect of microstructure in cancellous bone that greatly influences failure under cyclic loading and show that the effect is generalizable to synthetic microarchitectured materials. Our findings demonstrate that a common design strategy to improve stiffness and strength of microarchitectured materials comes at the cost of impaired service life. Our findings are useful for the design and application of microarchitectured materials and additionally provide insight into human health in situations of osteoporosis. Microarchitectured materials achieve superior mechanical properties through geometry rather than composition. Although ultralightweight microarchitectured materials can have high stiffness and strength, application to durable devices will require sufficient service life under cyclic loading. Naturally occurring materials provide useful models for high-performance materials. Here, we show that in cancellous bone, a naturally occurring lightweight microarchitectured material, resistance to fatigue failure is sensitive to a microarchitectural trait that has negligible effects on stiffness and strength—the proportion of material oriented transverse to applied loads. Using models generated with additive manufacturing, we show that small increases in the thickness of elements oriented transverse to loading can increase fatigue life by 10 to 100 times, far exceeding what is expected from the associated change in density. Transversely oriented struts enhance resistance to fatigue by acting as sacrificial elements. We show that this mechanism is also present in synthetic microlattice structures, where fatigue life can be altered by 5 to 9 times with only negligible changes in density and stiffness. The effects of microstructure on fatigue life in cancellous bone and lattice structures are described empirically by normalizing stress in traditional stress vs. life (S-N) curves by √ψ, where ψ is the proportion of material oriented transverse to load. The mechanical performance of cancellous bone and microarchitectured materials is enhanced by aligning structural elements with expected loading; our findings demonstrate that this strategy comes at the cost of reduced fatigue life, with consequences to the use of microarchitectured materials in durable devices and to human health in the context of osteoporosis.",0.624177098274231,8
manage_stress/strain,167,"The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts. The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.",0.5977813005447388,9
manage_stress/strain,220,"Structure and Mechanical Adaptability of a Modern Elasmoid Fish Scale from the Common Carp. Summary The carp (Cyprinus carpio) has typical elasmoid scales commonly found on teleosts. They provide protection while retaining flexibility and maneuverability of the fish. The exterior surface of the scale consists of an ultrathin discontinuous mineral layer on top of mineralized woven collagen fibrils. The underlying foundation is composed of two collagenous components. The major one consists of a single-twisted “Bouligand” structure with a twisting angle of 36°. A secondary “sheet-like” structure, formed by thinner collagen fibrils oriented along the thickness direction, acts to increase the integrity of the scale. Here, we identify the deformation and failure mechanisms of the carp scale, revealing slight tensile anisotropy. Using in situ small-angle X-ray scattering during tensile testing, the toughening mechanisms of the scale, including the adaptive structural reorientation of lamellae as well as fibrillar sliding and elastic deformation, are quantified and compared with those of other fish scales.",0.5482552647590637,10
manage_stress/strain,22,"Pummelos as Concept Generators for Biomimetically Inspired Low Weight Structures with Excellent Damping Properties. Natural materials often exhibit excellent mechanical properties. An example of outstanding impact resistance is the pummelo fruit (Citrus maxima) which can drop from heights of 10 m and more without showing significant outer damage. Our data suggest that this impact resistance is due to the hierarchical organization of the fruit peel, called pericarp. The project presented in the current paper aims at transferring structural features from the pummelo pericarp to engineering materials, in our case metal foams, produced by the investment casting process. The transfer necessitates a detailed structural and mechanical analysis of the biological model on the one hand, and the identification and development of adequate materials and processes on the other hand. Based on this analysis, engineering composite foam structures are developed and processed which show enhanced damping and impact properties. The modified investment casting process and the model alloy Bi57Sn43 proved to be excellent candidates to make these bio-inspired structures. Mechanical testing of both the natural and the engineering structures has to consider the necessity to evaluate the impact of the different hierarchical features. Therefore, specimens of largely varying sizes have to be tested and size effects cannot be ignored, especially as the engineering structures might be upscaled in comparison with the natural role model. All in all, the present results are very promising: the basis for a transfer of bio-inspired structural hierarchical levels has been set.",0.45466622710227966,11
manage_stress/strain,297,"Nature's forms are frilly, flexible, and functional.. A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.",0.44955378770828247,12
manage_stress/strain,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.4291934669017792,13
manage_stress/strain,206,"Deciphering an extreme morphology: bone microarchitecture of the hero shrew backbone (Soricidae: Scutisorex). Biological structures with extreme morphologies are puzzling because they often lack obvious functions and stymie comparisons to homologous or analogous features with more typical shapes. An example of such an extreme morphotype is the uniquely modified vertebral column of the hero shrew Scutisorex, which features numerous accessory intervertebral articulations and massively expanded transverse processes. The function of these vertebral structures is unknown, and it is difficult to meaningfully compare them to vertebrae from animals with known behavioural patterns and spinal adaptations. Here, we use trabecular bone architecture of vertebral centra and quantitative external vertebral morphology to elucidate the forces that may act on the spine of Scutisorex and that of another large shrew with unmodified vertebrae (Crocidura goliath). X-ray micro-computed tomography (µCT) scans of thoracolumbar columns show that Scutisorex thori is structurally intermediate between C. goliath and S. somereni internally and externally, and both Scutisorex species exhibit trabecular bone characteristics indicative of higher in vivo axial compressive loads than C. goliath. Under compressive load, Scutisorex vertebral morphology is adapted to largely restrict bending to the sagittal plane (flexion). Although these findings do not solve the mystery of how Scutisorex uses its byzantine spine in vivo, our work suggests potentially fruitful new avenues of investigation for learning more about the function of this perplexing structure.",0.4229671359062195,14
manage_stress/strain,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.3824531137943268,15
manage_stress/strain,91,"Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts. Significance Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.",0.3351491689682007,16
manage_stress/strain,198,"Universal elastic mechanism for stinger design. Living organisms use stingers that vary in length L over eight orders of magnitude, from a few tens of nanometres to several metres, across a wide array of biological taxa. Despite the extreme variation in size, their structures are strikingly similar. However, the mechanism responsible for this remarkable morphological convergence remains unknown. Using basic physical arguments and biomimetic experiments, we reveal an optimal design strategy that links their length, base diameter d 0 , Young’s modulus E and friction force per unit area μ p 0 . This principle can be framed simply as $${d}_{0} \approx {(\mu {p}_{0}/E)}^{1/3}L$$ d 0 ≈ ( μ p 0 / E ) 1 / 3 L . Existing data from measurements on viruses, algae, marine invertebrates, terrestrial invertebrates, plants, terrestrial vertebrates, marine vertebrates—as well as man-made objects such as nails, needles and weapons—are consistent with our predictions. Our results highlight the evolutionary adaptation of mechanical traits to the constraints imposed by friction, elastic stability and cost. The structures of stingers of living organisms are surprisingly similar despite their vastly different lengths. Now, stingers are found to obey a unifying mechanistic principle that characterizes the stingers resistance to buckling.",0.18627521395683289,17
manage_stress/strain,191,"Geometry and self-righting of turtles. Terrestrial animals with rigid shells face imminent danger when turned upside down. A rich variety of righting strategies of beetle and turtle species have been described, but the exact role of the shell's geometry in righting is so far unknown. These strategies are often based on active mechanisms, e.g. most beetles self-right via motion of their legs or wings; flat, aquatic turtles use their muscular neck to flip back. On the other hand, highly domed, terrestrial turtles with short limbs and necks have virtually no active control: here shape itself may serve as a fundamental tool. Based on field data gathered on a broad spectrum of aquatic and terrestrial turtle species we develop a geometric model of the shell. Inspired by recent mathematical results, we demonstrate that a simple mechanical classification of the model is closely linked to the animals' righting strategy. Specifically, we show that the exact geometry of highly domed terrestrial species is close to optimal for self-righting, and the shell's shape is the predominant factor of their ability to flip back. Our study illustrates how evolution solved a far-from-trivial geometrical problem and equipped some turtles with monostatic shells: beautiful forms, which rarely appear in nature otherwise.",0.17853416502475739,18
manage_stress/strain,192,"Spider dragline silk as torsional actuator driven by humidity. Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.",0.15533840656280518,19
manage_stress/strain,71,"Self‐Sharpening Mechanism of the Sea Urchin Tooth. The sea urchin tooth is a mosaic of calcite crystals shaped precisely into plates and fibers, cemented together by a robust calcitic polycrystalline matrix. The tooth is formed continuously at one end, while it grinds and wears at the opposite end, the sharp tip. Remarkably, these teeth enable the sea urchin to scrape and bore holes into rock, yet the teeth remain sharp rather than dull with use. Here we describe the detailed structure of the tooth of the California purple sea urchin Strongylocentrotus purpuratus, and focus on the self-sharpening mechanism. Using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM), scanning electron microscopy (SEM), EDX analysis, nanoindentation, and X-ray micro-tomography, we deduce that the sea urchin tooth self-sharpens by fracturing at discontinuities in the material. These are organic layers surrounding plates and fibers that behave as the “fault lines” in the tooth structure, as shown by nanoindentation. Shedding of tooth components at these discontinuities exposes the robust central part of the tooth, aptly termed “the stone”, which becomes the grinding tip. The precise design and position of the plates and fibers determines the profile of the tooth tip, so as the tooth wears it maintains a tip that is continually renewed and remains sharp. This strategy may be used for the top-down or bottom-up fabrication of lamellar materials, to be used for mechanical functions at the nano- and micrometer scale.",0.13845837116241455,20
actively_move_through/on_liquids,180,"Wake-induced ‘slaloming’ response explains exquisite sensitivity of seal whisker-like sensors. Blindfolded harbour seals are able to use their uniquely shaped whiskers to track vortex wakes left by moving animals and identify objects that passed by 30 s earlier, an impressive feat, as the flow features have velocities as low as $1~\text{mm}~\text{s}^{-1}$ . The seals sense while swimming, hence their whiskers are sensitive enough to detect small-scale changes in the flow, while rejecting self-generated flow noise. Here we identify and illustrate a novel flow mechanism, causing a large-amplitude ‘slaloming’ whisker response, which allows artificial whiskers with the identical unique undulatory geometry as those of the harbour seal to detect the features of minute flow fluctuations when placed within wakes. Whereas in open water the whisker responds with very low-amplitude vibration, once within a wake, it oscillates with large amplitude and, importantly, its response frequency coincides with the Strouhal frequency of the upstream cylinder, making the detection of an upstream wake and an estimation of the size and shape of the wake-generating body possible. This mechanism has some similarities with the flow mechanisms observed in actively controlled propulsive foils within upstream wakes and trout swimming behind bluff cylinders in a stream, but there are also differences caused by the unique whisker morphology, which enables it to respond passively and within a much wider parametric range.",0.9163500070571899,1
actively_move_through/on_liquids,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.8230805397033691,2
actively_move_through/on_liquids,36,"Hydrodynamic Trail-Following in Harbor Seals (Phoca vitulina). Marine mammals often forage in dark or turbid waters. Whereas dolphins use echolocation under such conditions, pinnipeds apparently lack this sensory ability. For seals hunting in the dark, one source of sensory information may consist of fish-generated water movements, which seals can detect with their highly sensitive whiskers. Water movements in the wake of fishes persist for several minutes. Here we show that blindfolded seals can use their whiskers to detect and accurately follow hydrodynamic trails generated by a miniature submarine. This shows that hydrodynamic information can be used for long-distance prey location.",0.8202652335166931,3
actively_move_through/on_liquids,279,"Control of Helical Navigation by Three-Dimensional Flagellar Beating.. Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellate Chlamydomonas reinhardtii rotates at a constant 1-2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, nonplanar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully 3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer toward or away from light by modulating the sign of biflagellar dominance.",0.7858851552009583,4
actively_move_through/on_liquids,116,"Curvature-induced stiffening of a fish fin. How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel (Scomber japonicus) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish.",0.7185359597206116,5
actively_move_through/on_liquids,213,"Remoras pick where they stick on blue whales. ABSTRACT Animal-borne video recordings from blue whales in the open ocean show that remoras preferentially adhere to specific regions on the surface of the whale. Using empirical and computational fluid dynamics analyses, we show that remora attachment was specific to regions of separating flow and wakes caused by surface features on the whale. Adhesion at these locations offers remoras drag reduction of up to 71–84% compared with the freestream. Remoras were observed to move freely along the surface of the whale using skimming and sliding behaviors. Skimming provided drag reduction as high as 50–72% at some locations for some remora sizes, but little to none was available in regions where few to no remoras were observed. Experimental work suggests that the Venturi effect may help remoras stay near the whale while skimming. Understanding the flow environment around a swimming blue whale will inform the placement of biosensor tags to increase attachment time for extended ecological monitoring. Highlighted Article: Analysis of previously undocumented skimming and sliding behaviors used by remoras reveals they preferentially adhere to areas with reduced drag on blue whales.",0.5338581204414368,6
actively_move_through/on_liquids,64,"Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella. Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.",0.2958938479423523,7
actively_move_through/on_liquids,160,"Group structure and kinship in beluga whale societies. Evolutionary explanations for mammalian sociality typically center on inclusive-fitness benefits of associating and cooperating with close kin, or close maternal kin as in some whale societies, including killer and sperm whales. Their matrilineal structure has strongly influenced the thinking about social structure in less well-studied cetaceans, including beluga whales. In a cross-sectional study of group structure and kinship we found that belugas formed a limited number of distinct group types, consistently observed across populations and habitats. Certain behaviours were associated with group type, but group membership was often dynamic. MtDNA-microsatellite profiling combined with relatedness and network analysis revealed, contrary to predictions, that most social groupings were not predominantly organized around close maternal relatives. They comprised both kin and non-kin, many group members were paternal rather than maternal relatives, and unrelated adult males often traveled together. The evolutionary mechanisms that shape beluga societies are likely complex; fitness benefits may be achieved through reciprocity, mutualism and kin selection. At the largest scales these societies are communities comprising all ages and both sexes where multiple social learning pathways involving kin and non-kin can foster the emergence of cultures. We explore the implications of these findings for species management and the evolution of menopause.",0.28806811571121216,8
actively_move_through/on_liquids,248,"The most efficient metazoan swimmer creates a ‘virtual wall’ to enhance performance. It has been well documented that animals (and machines) swimming or flying near a solid boundary get a boost in performance. This ground effect is often modelled as an interaction between a mirrored pair of vortices represented by a true vortex and an opposite sign ‘virtual vortex’ on the other side of the wall. However, most animals do not swim near solid surfaces and thus near body vortex–vortex interactions in open-water swimmers have been poorly investigated. In this study, we examine the most energetically efficient metazoan swimmer known to date, the jellyfish Aurelia aurita, to elucidate the role that vortex interactions can play in animals that swim away from solid boundaries. We used high-speed video tracking, laser-based digital particle image velocimetry (dPIV) and an algorithm for extracting pressure fields from flow velocity vectors to quantify swimming performance and the effect of near body vortex–vortex interactions. Here, we show that a vortex ring (stopping vortex), created underneath the animal during the previous swim cycle, is critical for increasing propulsive performance. This well-positioned stopping vortex acts in the same way as a virtual vortex during wall-effect performance enhancement, by helping converge fluid at the underside of the propulsive surface and generating significantly higher pressures which result in greater thrust. These findings advocate that jellyfish can generate a wall-effect boost in open water by creating what amounts to a ‘virtual wall’ between two real, opposite sign vortex rings. This explains the significant propulsive advantage jellyfish possess over other metazoans and represents important implications for bio-engineered propulsion systems.",0.28568124771118164,9
actively_move_through/on_liquids,95,"Automatic control: the vertebral column of dogfish sharks behaves as a continuously variable transmission with smoothly shifting functions. ABSTRACT During swimming in dogfish sharks, Squalus acanthias, both the intervertebral joints and the vertebral centra undergo significant strain. To investigate this system, unique among vertebrates, we cyclically bent isolated segments of 10 vertebrae and nine joints. For the first time in the biomechanics of fish vertebral columns, we simultaneously characterized non-linear elasticity and viscosity throughout the bending oscillation, extending recently proposed techniques for large-amplitude oscillatory shear (LAOS) characterization to large-amplitude oscillatory bending (LAOB). The vertebral column segments behave as non-linear viscoelastic springs. Elastic properties dominate for all frequencies and curvatures tested, increasing as either variable increases. Non-linearities within a bending cycle are most in evidence at the highest frequency, 2.0 Hz, and curvature, 5 m−1. Viscous bending properties are greatest at low frequencies and high curvatures, with non-linear effects occurring at all frequencies and curvatures. The range of mechanical behaviors includes that of springs and brakes, with smooth transitions between them that allow for continuously variable power transmission by the vertebral column to assist in the mechanics of undulatory propulsion. Highlighted Article: Characterization of non-linear elasticity and viscosity throughout the bending oscillation reveals that the shark vertebral column behaves as both a spring and a brake, with smooth transitions between them for continuously variable power transmission.",0.2732951045036316,10
actively_move_through/on_liquids,146,"Universal metabolic constraints shape the evolutionary ecology of diving in animals. Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.",0.2657902240753174,11
actively_move_through/on_liquids,112,"Three-dimensional scaling laws of cetacean propulsion characterize the hydrodynamic interplay of flukes' shape and kinematics. Cetaceans convert dorsoventral body oscillations into forward velocity with a complex interplay between their morphological and kinematic features and the fluid environment. However, it is unknown to what extent morpho-kinematic features of cetaceans are intertwined to maximize their efficiency. By interchanging the shape and kinematic variables of five cetacean species, the interplay of their flukes morpho-kinematic features is examined by characterizing their thrust, power and propulsive efficiency. It is determined that the shape and kinematics of the flukes have considerable influence on force production and power consumption. Three-dimensional heaving and pitching scaling laws are developed by considering both added mass and circulatory-based forces, which are shown to closely model the numerical data. Using the scaling relations as a guide, it is determined that the added mass forces are important in predicting the trend between the efficiency and aspect ratio, however, the thrust and power are driven predominately by the circulatory forces. The scaling laws also reveal that there is an optimal dimensionless heave-to-pitch ratio h* that maximizes the efficiency. Moreover, the optimal h* varies with the aspect ratio, the amplitude-to-chord ratio and the Lighthill number. This indicates that the shape and kinematics of propulsors are intertwined, that is, there are specific kinematics that are tailored to the shape of a propulsor in order to maximize its propulsive efficiency.",0.2370988130569458,12
actively_move_through/on_liquids,10,"Aerodynamic force generation, performance and control of body orientation during gliding in sugar gliders (Petaurus breviceps). SUMMARY Gliding has often been discussed in the literature as a possible precursor to powered flight in vertebrates, but few studies exist on the mechanics of gliding in living animals. In this study I analyzed the 3D kinematics of sugar gliders (Petaurus breviceps) during short glides in an enclosed space. Short segments of the glide were captured on video, and the positions of marked anatomical landmarks were used to compute linear distances and angles, as well as whole body velocities and accelerations. From the whole body accelerations I estimated the aerodynamic forces generated by the animals. I computed the correlations between movements of the limbs and body rotations to examine the control of orientation during flight. Finally, I compared these results to those of my earlier study on the similarly sized and distantly related southern flying squirrel (Glaucomys volans). The sugar gliders in this study accelerated downward slightly (1.0±0.5 m s–2), and also accelerated forward (2.1±0.6 m s–2) in all but one trial, indicating that the body weight was not fully supported by aerodynamic forces and that some of the lift produced forward acceleration rather than just balancing body weight. The gliders used high angles of attack (44.15±3.12°), far higher than the angles at which airplane wings would stall, yet generated higher lift coefficients (1.48±0.18) than would be expected for a stalled wing. Movements of the limbs were strongly correlated with body rotations, suggesting that sugar gliders make extensive use of limb movements to control their orientation during gliding flight. In addition, among individuals, different limb movements were associated with a given body rotation, suggesting that individual variation exists in the control of body rotations. Under similar conditions, flying squirrels generated higher lift coefficients and lower drag coefficients than sugar gliders, yet had only marginally shallower glides. Flying squirrels have a number of morphological specializations not shared by sugar gliders that may help to explain their greater lift generating performance.",0.18386244773864746,13
actively_move_through/on_liquids,58,"Both stiff and compliant: morphological and biomechanical adaptations of stick insect antennae for tactile exploration. Active tactile exploration behaviour is constrained to a large extent by the morphological and biomechanical properties of the animal's somatosensory system. In the model organism Carausius morosus, the main tactile sensory organs are long, thin, seemingly delicate, but very robust antennae. Previous studies have shown that these antennae are compliant under contact, yet stiff enough to maintain a straight shape during active exploration. Overcritical damping of the flagellum, on the other hand, allows for a rapid return to the straight shape after release of contact. Which roles do the morphological and biomechanical adaptations of the flagellum play in determining these special mechanical properties? To investigate this question, we used a combination of biomechanical experiments and numerical modelling. A set of four finite-element (FE) model variants was derived to investigate the effect of the distinct geometrical and material properties of the flagellum on its static (bending) and dynamic (damping) characteristics. The results of our numerical simulations show that the tapered shape of the flagellum had the strongest influence on its static biomechanical behaviour. The annulated structure and thickness gradient affected the deformability of the flagellum to a lesser degree. The inner endocuticle layer of the flagellum was confirmed to be essential for explaining the strongly damped return behaviour of the antenna. By highlighting the significance of two out of the four main structural features of the insect flagellum, our study provides a basis for mechanical design of biomimetic touch sensors tuned to become maximally flexible while quickly resuming a straight shape after contact.",0.1084844172000885,14
actively_move_through/on_liquids,303,"Repeated evolution of underwater rebreathing in diving Anolis lizards. Air-based respiration limits the use of aquatic environments by ancestrally terrestrial animals. To overcome this challenge, diving arthropods have evolved to respire without resurfacing using air held between their cuticle and surrounding water.1-4 Inspired by natural history observations in Haiti (unpublished data) and Costa Rica,5,6 we conducted experiments documenting routine air-based underwater respiration in several distantly related semi-aquatic Anolis lizard species. Semi-aquatic anoles live along neotropical streams and frequently dive for refuge or food,7-12 remaining underwater for up to 18 min. While submerged, these lizards iteratively expire and re-inspire narial air bubbles-underwater ""rebreathing."" Rebreathed air is used in respiration, as the partial pressure of oxygen in the bubbles decreases with experimental submersion time in living anoles, but not in mechanical controls. Non-aquatic anoles occasionally rebreathe when submerged but exhibit more rudimentary rebreathing behaviors. Anole rebreathing is facilitated by a thin air layer (i.e., a ""plastron,"" sensu Brocher13) supported by the animal's rugose skin upon submergence. We suggest that hydrophobic skin, which we observed in all sampled anoles,14,15 may have been exaptative, facilitating the repeated evolution of specialized rebreathing in species that regularly dive. Phylogenetic analyses strongly suggest that specialized rebreathing is adaptive for semi-aquatic habitat specialists. Air-based rebreathing may enhance dive performance by incorporating dead space air from the buccal cavity or plastron into the lungs, facilitating clearance of carbon dioxide, or allowing uptake of oxygen from surrounding water (i.e., a ""physical gill"" mechanism4,16).",0.10686516761779785,15
actively_move_through/on_liquids,87,"Shaping the zebrafish myotome by intertissue friction and active stress. Significance How do tissues self-organize to generate the complex organ shapes observed in vertebrates? Organ formation requires the integration of chemical and mechanical information, yet how this is achieved is poorly understood for most organs. Muscle compartments in zebrafish display a V shape, which is believed to be required for efficient swimming. We investigate how this structure emerges during zebrafish development, combining live imaging and quantitative analysis of cellular movements. We use theoretical modeling to understand how cell differentiation and mechanical interactions between tissues guide the emergence of a specific tissue morphology. Our work reveals how spatially modulating the mechanical environment around and within tissues can lead to complex organ shape formation. Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the future myotome and the surrounding tissues appears to spatially vary, effectively resulting in spatially heterogeneous friction. Using a vertex model combined with experimental validation, we show that the interplay of tissue spreading and friction is sufficient to drive the initial phase of chevron shape formation. However, local anisotropic stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the chevron in wild-type embryos. Finally, tissue plasticity is required for formation and maintenance of the chevron shape, which is mediated by orientated cellular rearrangements. Our work sheds light on how a spatiotemporal sequence of local cellular events can have a nonlocal and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.",0.09629509598016739,16
actively_move_through/on_liquids,183,"Gyroscopic stabilization minimizes drag on Ruellia ciliatiflora seeds. Fruits of Ruellia ciliatiflora (Acanthaceae) explosively launch small (2.5 mm diameter × 0.46 mm thick), disc-shaped seeds at velocities over 15 m s−1, reaching distances of up to 7 m. Through high-speed video analysis, we observe that seeds fly with extraordinary backspin of up to 1660 Hz. By modelling the seeds as spinning discs, we show that flying with backspin is stable against gyroscopic precession. This stable backspin orientation minimizes the frontal area during flight, decreasing drag force on the seeds and thus increasing dispersal distance. From high-speed video of the seeds' flight, we experimentally determine drag forces that are 40% less than those calculated for a sphere of the same volume and density. This reduces the energy costs for seed dispersal by up to a factor of five.",0.0905018076300621,17
actively_move_through/on_liquids,209,"Locomotion of Mexican jumping beans.. The Mexican jumping bean, Laspeyresia saltitans, consists of a hollow seed housing a moth larva. Heating by the sun induces movements by the larva which appear as rolls, jumps and flips by the bean. In this combined experimental, numerical and robotic study, we investigate this unique means of rolling locomotion. Time-lapse videography is used to record bean trajectories across a series of terrain types, including one-dimensional channels and planar surfaces of varying inclination. We find that the shell encumbers the larva's locomotion, decreasing its speed on flat surfaces by threefold. We also observe that the two-dimensional search algorithm of the bean resembles the run-and-tumble search of bacteria. We test this search algorithm using both an agent-based simulation and a wheeled Scribbler robot. The algorithm succeeds in propelling the robot away from regions of high temperature and may have application in biomimetic micro-scale navigation systems.",0.0865454226732254,18
actively_move_through/on_liquids,52,"The jump of the click beetle (Coleoptera: Elateridae)—energetics and mechanics. Some aspects of the energetics and mechanics of two jumps made by a single specimen of Athous haemorrhoidalis (Fab.) are considered. In the first jump, the 40 mg beetle had a take-off velocity of 2–4 m/s and the jumping action occurred in about 064 ms; in the second jump, the take/off velocity was 2–26 m/s and the jumping action took about 0–53 ms. Energy budgets have been constructed in two different ways for each jump, and the total energy involved in each case was estimated to lie between 1–6 × 10−4 J and 3–8 × 10−4 J. Power output during the jumping action (a “catapult”) lay between 80 × 103 W/kg muscle and 180 × 103 W/kg muscle, whilst power output during the energy storing pre-jump period (of about 0–4 s) was at least 130 W/kg muscle (at over 25°C). Forces and tensile stresses in the jumping muscles and their apodemes have also been calculated. The method of jumping appears to be fairly inefficient in that only about 50–60% of the energy expended in the jumping action is energy of translation, which actually raises the beetle.",0.08540942519903183,19
actively_move_through/on_liquids,301,"Wave-slope soaring of the brown pelican. Background From the laboratory at Scripps Institution of Oceanography, it is common to see the brown pelican ( Pelecanus occidentalis ) traveling along the crests of ocean waves just offshore of the surf-zone. When flying in this manner, the birds can travel long distances without flapping, centimeters above the ocean’s surface. Here we derive a theoretical framework for assessing the energetic savings related to this behavior, ‘wave-slope soaring,’ in which an organism in flight takes advantage of localized updrafts caused by traveling ocean surface gravity waves. Methods The energy cost of steady, constant altitude flight in and out of ground effect are analyzed as controls. Potential flow theory is used to quantify the ocean wave-induced wind associated with near-shoaling, weakly nonlinear, shallow water ocean surface gravity waves moving through an atmosphere initially at rest. Using perturbation theory and the Green’s function for Laplace’s equation in 2D with Dirichlet boundary conditions, we obtain integrals for the horizontal and vertical components of the wave-induced wind in a frame of reference moving with the wave. Wave-slope soaring flight is then analyzed using an energetics-based approach for waves under a range of ocean conditions and the body plan of P. occidentalis. Results For ground effect flight, we calculate a ∼15 - 25% reduction in cost of transport as compared with steady, level flight out of ground effect. When wave-slope soaring is employed at flight heights ∼2m in typical ocean conditions (2m wave height, 15s period), we calculate 60-70% reduction in cost of transport as compared with flight in ground effect. A relatively small increase in swell amplitude or decrease in flight height allows up to 100% of the cost of transport to be offset by wave-slope soaring behavior. Conclusions The theoretical development presented here suggests there are energy savings associated with wave-slope soaring. Individual brown pelicans may significantly decrease their cost of transport utilizing this mode of flight under typical ocean conditions. Thus wave-slope soaring may provide fitness benefit to these highly mobile organisms that depend on patchy prey distribution over large home ranges.",0.0748453214764595,20
manage_shear,292,"A Graphic Way For Notch Shape Optimization. Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.",0.7944312691688538,1
manage_shear,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.11840623617172241,2
manage_shear,91,"Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts. Significance Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.",0.09574975818395615,3
manage_shear,78,"Bioinspired Materials with Self-Adaptable Mechanical Properties.. Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.",0.07559876888990402,4
manage_shear,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.06691449135541916,5
manage_shear,198,"Universal elastic mechanism for stinger design. Living organisms use stingers that vary in length L over eight orders of magnitude, from a few tens of nanometres to several metres, across a wide array of biological taxa. Despite the extreme variation in size, their structures are strikingly similar. However, the mechanism responsible for this remarkable morphological convergence remains unknown. Using basic physical arguments and biomimetic experiments, we reveal an optimal design strategy that links their length, base diameter d 0 , Young’s modulus E and friction force per unit area μ p 0 . This principle can be framed simply as $${d}_{0} \approx {(\mu {p}_{0}/E)}^{1/3}L$$ d 0 ≈ ( μ p 0 / E ) 1 / 3 L . Existing data from measurements on viruses, algae, marine invertebrates, terrestrial invertebrates, plants, terrestrial vertebrates, marine vertebrates—as well as man-made objects such as nails, needles and weapons—are consistent with our predictions. Our results highlight the evolutionary adaptation of mechanical traits to the constraints imposed by friction, elastic stability and cost. The structures of stingers of living organisms are surprisingly similar despite their vastly different lengths. Now, stingers are found to obey a unifying mechanistic principle that characterizes the stingers resistance to buckling.",0.06415463984012604,6
manage_shear,223,"Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets. Nacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design. The hierarchical structure of nacre is known to contribute to its high strength and toughness, providing inspiration for many biomimetic materials. Here, co-oriented 20 µm stacks of aragonite platelets are shown to contribute to the toughness of nacre, defining a new characteristic length scale.",0.042341023683547974,7
manage_shear,250,"Biomechanical insights into the dentition of megatooth sharks (Lamniformes: Otodontidae). The evolution of gigantism in extinct otodontid sharks was paralleled by a series of drastic modifications in their dentition including widening of the crowns, loss of lateral cusplets, and acquisition of serrated cutting edges. These traits have generally been interpreted as key functional features that enabled the transition from piscivory to more energetic diets based on marine mammals, ultimately leading to the evolution of titanic body sizes in the most recent forms (including the emblematic Otodus megalodon ). To investigate this hypothesis, we evaluate the biomechanics of the anterior, lateral, and posterior teeth of five otodontid species under different loading conditions by using two-dimensional finite element analysis. Stress distribution patterns are remarkably similar among all models under puncture and draw (i.e., when subjected to vertical and lateral forces, respectively). Contrary to expectation, higher average stress values are detected under both loading scenarios in more recent species. Altogether, this suggests little correlation between tooth morphology and key aspects of biomechanical behaviour in otodontids, making it difficult to frame the morphological trend of their dentitions within an adaptive scenario. We propose that this pattern most likely emerged as a non-functional by-product of heterochronic processes driven by selection towards larger body sizes.",0.04232310131192207,8
manage_shear,297,"Nature's forms are frilly, flexible, and functional.. A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.",0.03840859606862068,9
manage_shear,300,"Extreme strength observed in limpet teeth. The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.",0.036964669823646545,10
manage_shear,76,"Bone-inspired microarchitectures achieve enhanced fatigue life. Significance Microarchitectured materials, such as foams and lattice structures, can achieve high stiffness and strength while remaining extremely lightweight. Applying high-porosity microarchitectured materials to durable devices, such as vehicles, however, will require the materials to also resist failure during cyclic loading. Here, we identify an aspect of microstructure in cancellous bone that greatly influences failure under cyclic loading and show that the effect is generalizable to synthetic microarchitectured materials. Our findings demonstrate that a common design strategy to improve stiffness and strength of microarchitectured materials comes at the cost of impaired service life. Our findings are useful for the design and application of microarchitectured materials and additionally provide insight into human health in situations of osteoporosis. Microarchitectured materials achieve superior mechanical properties through geometry rather than composition. Although ultralightweight microarchitectured materials can have high stiffness and strength, application to durable devices will require sufficient service life under cyclic loading. Naturally occurring materials provide useful models for high-performance materials. Here, we show that in cancellous bone, a naturally occurring lightweight microarchitectured material, resistance to fatigue failure is sensitive to a microarchitectural trait that has negligible effects on stiffness and strength—the proportion of material oriented transverse to applied loads. Using models generated with additive manufacturing, we show that small increases in the thickness of elements oriented transverse to loading can increase fatigue life by 10 to 100 times, far exceeding what is expected from the associated change in density. Transversely oriented struts enhance resistance to fatigue by acting as sacrificial elements. We show that this mechanism is also present in synthetic microlattice structures, where fatigue life can be altered by 5 to 9 times with only negligible changes in density and stiffness. The effects of microstructure on fatigue life in cancellous bone and lattice structures are described empirically by normalizing stress in traditional stress vs. life (S-N) curves by √ψ, where ψ is the proportion of material oriented transverse to load. The mechanical performance of cancellous bone and microarchitectured materials is enhanced by aligning structural elements with expected loading; our findings demonstrate that this strategy comes at the cost of reduced fatigue life, with consequences to the use of microarchitectured materials in durable devices and to human health in the context of osteoporosis.",0.035284679383039474,11
manage_shear,167,"The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts. The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.",0.025194985792040825,12
manage_shear,206,"Deciphering an extreme morphology: bone microarchitecture of the hero shrew backbone (Soricidae: Scutisorex). Biological structures with extreme morphologies are puzzling because they often lack obvious functions and stymie comparisons to homologous or analogous features with more typical shapes. An example of such an extreme morphotype is the uniquely modified vertebral column of the hero shrew Scutisorex, which features numerous accessory intervertebral articulations and massively expanded transverse processes. The function of these vertebral structures is unknown, and it is difficult to meaningfully compare them to vertebrae from animals with known behavioural patterns and spinal adaptations. Here, we use trabecular bone architecture of vertebral centra and quantitative external vertebral morphology to elucidate the forces that may act on the spine of Scutisorex and that of another large shrew with unmodified vertebrae (Crocidura goliath). X-ray micro-computed tomography (µCT) scans of thoracolumbar columns show that Scutisorex thori is structurally intermediate between C. goliath and S. somereni internally and externally, and both Scutisorex species exhibit trabecular bone characteristics indicative of higher in vivo axial compressive loads than C. goliath. Under compressive load, Scutisorex vertebral morphology is adapted to largely restrict bending to the sagittal plane (flexion). Although these findings do not solve the mystery of how Scutisorex uses its byzantine spine in vivo, our work suggests potentially fruitful new avenues of investigation for learning more about the function of this perplexing structure.",0.02504945732653141,13
manage_shear,264,"The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo. The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.",0.02464507520198822,14
manage_shear,22,"Pummelos as Concept Generators for Biomimetically Inspired Low Weight Structures with Excellent Damping Properties. Natural materials often exhibit excellent mechanical properties. An example of outstanding impact resistance is the pummelo fruit (Citrus maxima) which can drop from heights of 10 m and more without showing significant outer damage. Our data suggest that this impact resistance is due to the hierarchical organization of the fruit peel, called pericarp. The project presented in the current paper aims at transferring structural features from the pummelo pericarp to engineering materials, in our case metal foams, produced by the investment casting process. The transfer necessitates a detailed structural and mechanical analysis of the biological model on the one hand, and the identification and development of adequate materials and processes on the other hand. Based on this analysis, engineering composite foam structures are developed and processed which show enhanced damping and impact properties. The modified investment casting process and the model alloy Bi57Sn43 proved to be excellent candidates to make these bio-inspired structures. Mechanical testing of both the natural and the engineering structures has to consider the necessity to evaluate the impact of the different hierarchical features. Therefore, specimens of largely varying sizes have to be tested and size effects cannot be ignored, especially as the engineering structures might be upscaled in comparison with the natural role model. All in all, the present results are very promising: the basis for a transfer of bio-inspired structural hierarchical levels has been set.",0.023986659944057465,15
manage_shear,303,"Repeated evolution of underwater rebreathing in diving Anolis lizards. Air-based respiration limits the use of aquatic environments by ancestrally terrestrial animals. To overcome this challenge, diving arthropods have evolved to respire without resurfacing using air held between their cuticle and surrounding water.1-4 Inspired by natural history observations in Haiti (unpublished data) and Costa Rica,5,6 we conducted experiments documenting routine air-based underwater respiration in several distantly related semi-aquatic Anolis lizard species. Semi-aquatic anoles live along neotropical streams and frequently dive for refuge or food,7-12 remaining underwater for up to 18 min. While submerged, these lizards iteratively expire and re-inspire narial air bubbles-underwater ""rebreathing."" Rebreathed air is used in respiration, as the partial pressure of oxygen in the bubbles decreases with experimental submersion time in living anoles, but not in mechanical controls. Non-aquatic anoles occasionally rebreathe when submerged but exhibit more rudimentary rebreathing behaviors. Anole rebreathing is facilitated by a thin air layer (i.e., a ""plastron,"" sensu Brocher13) supported by the animal's rugose skin upon submergence. We suggest that hydrophobic skin, which we observed in all sampled anoles,14,15 may have been exaptative, facilitating the repeated evolution of specialized rebreathing in species that regularly dive. Phylogenetic analyses strongly suggest that specialized rebreathing is adaptive for semi-aquatic habitat specialists. Air-based rebreathing may enhance dive performance by incorporating dead space air from the buccal cavity or plastron into the lungs, facilitating clearance of carbon dioxide, or allowing uptake of oxygen from surrounding water (i.e., a ""physical gill"" mechanism4,16).",0.022934334352612495,16
manage_shear,146,"Universal metabolic constraints shape the evolutionary ecology of diving in animals. Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.",0.022600321099162102,17
manage_shear,192,"Spider dragline silk as torsional actuator driven by humidity. Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.",0.02250935696065426,18
manage_shear,71,"Self‐Sharpening Mechanism of the Sea Urchin Tooth. The sea urchin tooth is a mosaic of calcite crystals shaped precisely into plates and fibers, cemented together by a robust calcitic polycrystalline matrix. The tooth is formed continuously at one end, while it grinds and wears at the opposite end, the sharp tip. Remarkably, these teeth enable the sea urchin to scrape and bore holes into rock, yet the teeth remain sharp rather than dull with use. Here we describe the detailed structure of the tooth of the California purple sea urchin Strongylocentrotus purpuratus, and focus on the self-sharpening mechanism. Using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM), scanning electron microscopy (SEM), EDX analysis, nanoindentation, and X-ray micro-tomography, we deduce that the sea urchin tooth self-sharpens by fracturing at discontinuities in the material. These are organic layers surrounding plates and fibers that behave as the “fault lines” in the tooth structure, as shown by nanoindentation. Shedding of tooth components at these discontinuities exposes the robust central part of the tooth, aptly termed “the stone”, which becomes the grinding tip. The precise design and position of the plates and fibers determines the profile of the tooth tip, so as the tooth wears it maintains a tip that is continually renewed and remains sharp. This strategy may be used for the top-down or bottom-up fabrication of lamellar materials, to be used for mechanical functions at the nano- and micrometer scale.",0.02232753299176693,19
manage_shear,314,"Dragonfly wing nodus: A one-way hinge contributing to the asymmetric wing deformation.. Dragonfly wings are highly specialized locomotor systems, which are formed by a combination of several structural components. The wing components, also known as structural elements, are responsible for the various aspects of the wing functionality. Considering the complex interactions between the wing components, modelling of the wings as a whole is only possible with inevitable huge oversimplifications. In order to overcome this difficulty, we have recently proposed a new approach to model individual components of complex wings comparatively. Here, we use this approach to study nodus, a structural element of dragonfly wings which has been less studied to date. Using a combination of several imaging techniques including scanning electron microscopy (SEM), wide-field fluorescence microscopy (WFM), confocal laser scanning microscopy (CLSM) and micro-computed tomography (micro-CT) scanning, we aim to characterize the spatial morphology and material composition of fore- and hindwing nodi of the dragonfly Brachythemis contaminata. The microscopy results show the presence of resilin in the nodi, which is expected to help the deformability of the wings. The computational results based on three-dimensional (3D) structural data suggest that the specific geometry of the nodus restrains its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is expected to contribute to the dorso-ventral asymmetry of wing deformation and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings.


STATEMENT OF SIGNIFICANCE
In this study, we investigate the wing nodus, a specialized wing component in dragonflies. Using a combination of modern imaging techniques, we demonstrate the presence of resilin in the nodus, which is expected to facilitate the wing deformability in flight. The specific geometry of the nodus, however, seems to restrain its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is suggested to contribute to dorso-ventral asymmetry of wing deformations and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings and might help to design more efficient wings for biomimetic micro-air vehicles.",0.02085767686367035,20
chemically_assemble_organic_compounds,225,"Natural hybrid silica/protein superstructure at atomic resolution. Significance Using hybrid silica/protein templates, nature has mastered the fabrication of extremely complex macroscopic glass assemblies. Highly symmetric skeletal elements in demosponges are formed following a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by highly ordered proteinaceous filaments. Here we provide a comprehensive three-dimensional atomistic view of this hybrid assembly. The structure, occurring in the crystalline form in vivo, was measured in situ using the serial crystallography method. Together with a high-resolution transmission electron microscopy and energy-dispersive X-ray spectroscopy study, we provide structural, chemical, and functional information on a naturally forming hybrid mineral/organic crystal. Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.",0.8380410075187683,1
chemically_assemble_organic_compounds,122,"Architecture of a catalytically active homotrimeric plant cellulose synthase complex. Plant cell wall construction crew Plants produce a complex cell wall in which cellulose, a glucose polymer, is a major component. Cellulose fibers are formed from close-packed single chains of cellulose that have been proposed to be formed by multimeric complexes (18 or more subunits) of the enzyme cellulose synthase, which exists in several isoforms. Purushotham et al. determined a cryo–electron microscopy structure of a trimer of a single isoform of cellulose synthase. A large channel forms a path for cellulose chains through the membrane-embedded complex. The structure also reveals oligomeric interfaces and provides a framework for modeling the larger complexes seen in plant membranes. The close arrangement of exit sites for nascent glycan chains is consistent with the enzyme complex playing a role in directing cellulose microfibril formation. Science, this issue p. 1089 The structure of a homotrimeric cellulose synthase complex provides molecular insights into cellulose fibril formation. Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.",0.5689634084701538,2
chemically_assemble_organic_compounds,41,"Calcium Carbonate in Termite Mounds. THE presence of appreciable quantities of calcium carbonate in termite mounds on non-calcareous soil has intrigued pedologists for many years. Milne6, for example, found a termite mound with 7% calcium carbonate and estimated that it contained about 2 t of calcium carbonate excluding the hard limestone (53% CaCO3) base of the mound. The soil below the base of a termite mound may also be calcareous. The soil underneath one termite mound in an area of non-calcareous soil was found to have a mean of 1.7% calcium carbonate to a depth of 6 m, or about 20 t of calcium carbonate9.",0.5172165632247925,3
chemically_assemble_organic_compounds,80,"Synthesis and characterization of molybdenum disulfide nanoparticles in Shewanella oneidensis MR-1 biofilms.. Shewanella oneidensis MR-1 is a dissimilatory metal-reducing bacterium capable of reducing various metal and sulfur compounds and precipitating them in nanoparticulate form. Here, we report the synthesis of molybdenum disulfide nanomaterials at the site of S. oneidensis biofilms grown in the presence of molybdenum trioxide and sodium thiosulfate. Samples from the growth medium were imaged using scanning electron microscopy and characterized using transmission electron microscopy, energy-dispersive x-ray spectroscopy, absorbance spectroscopy, and x-ray diffraction. These methods revealed the presence of molybdenum disulfide nanoparticle aggregates 50-300 nm in diameter with both hexagonal and rhombohedral polytypes. As a biosynthesis method for molybdenum sulfide, the use of S. oneidensis offers the advantage of significantly reduced heat and chemical solvent input compared to conventional methods of synthesizing molybdenum disulfide nanoparticles.",0.4701847732067108,4
chemically_assemble_organic_compounds,246,"Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.",0.45823201537132263,5
chemically_assemble_organic_compounds,72,"Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Hybrid approach catches light Plant chloroplasts enclose two major photosynthetic processes: light reactions, which generate the energy carriers adenosine triphosphate and reduced nicotinamide dinucleotide phosphate (NADPH), and dark reactions, which use these molecules to fix carbon dioxide and build biomass. Miller et al. appropriated natural components, thylakoid membranes from spinach, for the light reactions and showed that these could be coupled to a synthetic enzymatic cycle that fixes carbon dioxide within water-in-oil droplets. The composition of the droplets could be tuned and optimized and the metabolic activity monitored in real time by NADPH fluorescence (see the Perspective by Gaut and Adamala). These chloroplast-mimicking droplets bring together natural and synthetic components in a small space and are amenable to further functionalization to perform complex biosynthetic tasks. Science, this issue p. 649; see also p. 587 Natural photosynthetic components power a synthetic CO2 fixation pathway in picoliter droplets. Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl–coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.",0.4129025638103485,6
chemically_assemble_organic_compounds,159,"The Scaly-foot Snail genome and implications for the origins of biomineralised armour. The Scaly-foot Snail, Chrysomallon squamiferum , presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome. The Scaly-foot Snail, Chrysomallon squamiferum , is a model for understanding the evolution of biomineralised armour. Here, the authors present a chromosome-level reference genome assembly and tissue-specific transcriptomic data for this enigmatic organism.",0.281149297952652,7
chemically_assemble_organic_compounds,109,"Life cycle of a cyanobacterial carboxysome. Single cell and organelle measurements reveal activity dynamics and degradation of the carbon-fixing cyanobacterial carboxysome. Carboxysomes, prototypical bacterial microcompartments (BMCs) found in cyanobacteria, are large (~1 GDa) and essential protein complexes that enhance CO2 fixation. While carboxysome biogenesis has been elucidated, the activity dynamics, lifetime, and degradation of these structures have not been investigated, owing to the inability of tracking individual BMCs over time in vivo. We have developed a fluorescence-imaging platform to simultaneously measure carboxysome number, position, and activity over time in a growing cyanobacterial population, allowing individual carboxysomes to be clustered on the basis of activity and spatial dynamics. We have demonstrated both BMC degradation, characterized by abrupt activity loss followed by polar recruitment of the deactivated complex, and a subclass of ultraproductive carboxysomes. Together, our results reveal the BMC life cycle after biogenesis and describe the first method for measuring activity of single BMCs in vivo.",0.22628794610500336,8
chemically_assemble_organic_compounds,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.19329991936683655,9
chemically_assemble_organic_compounds,186,"Bacterial chemolithoautotrophy via manganese oxidation. Manganese is one of the most abundant elements on Earth. The oxidation of manganese has long been theorized1—yet has not been demonstrated2–4—to fuel the growth of chemolithoautotrophic microorganisms. Here we refine an enrichment culture that exhibits exponential growth dependent on Mn(II) oxidation to a co-culture of two microbial species. Oxidation required viable bacteria at permissive temperatures, which resulted in the generation of small nodules of manganese oxide with which the cells associated. The majority member of the culture—which we designate ‘Candidatus Manganitrophus noduliformans’—is affiliated to the phylum Nitrospirae (also known as Nitrospirota), but is distantly related to known species of Nitrospira and Leptospirillum. We isolated the minority member, a betaproteobacterium that does not oxidize Mn(II) alone, and designate it Ramlibacter lithotrophicus. Stable-isotope probing revealed 13CO2 fixation into cellular biomass that was dependent upon Mn(II) oxidation. Transcriptomic analysis revealed candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and autotrophic CO2 fixation. These findings expand the known diversity of inorganic metabolisms that support life, and complete a biogeochemical energy cycle for manganese5,6 that may interface with other major global elemental cycles. A co-culture of two newly identified microorganisms—‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus—exhibits exponential growth that is dependent on manganese(II) oxidation, demonstrating the viability of this metabolism for supporting life.",0.12833170592784882,10
chemically_assemble_organic_compounds,173,"Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication. Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.",0.11712046712636948,11
chemically_assemble_organic_compounds,188,"The central role of Clark's nutcracker in the dispersal and establishment of whitebark pine. SummaryWhitebark pine (Pinus albicaulis) is known to have its seeds harvested and cached in the soil by Clark's Nutcracker (Nucifraga columbiana), and unretrieved seeds are known to be capable of germinating and establishing new pines. Many other vertebrates also harvest and feed on these seeds, however, and the roles of these animals as dispersers and establishers of whitebark pine has been uncertain. This work demonstrates that birds other than the nutcracker, rodents, and other mammals do not have the requisite behaviors to systematically disperse or establish whitebark pine, and that the pine is therefore dependent on the nutcracker for its regeneration. These findings support previous suggestions that Clark's Nutcracker is a specialized frugivore that has profoundly influenced the ecology and the evolution of whitebark pine.",0.10526808351278305,12
chemically_assemble_organic_compounds,196,"Copper-bottomed: electrochemically active bacteria exploit conductive sulphide networks for enhanced electrogeneity. In this study, we demonstrate that anodic electroactive bacteria like Geobacter sulfurreducens generate copper(I) and copper(II) sulphides when grown on copper electrodes. The insoluble copper sulphides form a conductive network within the biofilms, strongly enhancing the biofilm electrogeneity – i.e., the ability of the biofilm to produce electric currents. Compared to biofilms grown on graphite, the average relative current density of copper-based biofilms was 237%, with a maximum geometric current density of 1.59 ± 0.23 mA cm−2. An additional electrochemical CuS deposition prior to biofilm cultivation further increased the bioelectrocatalytic current generation to 2 mA cm−2. The chemical deposition of CuS onto graphite allowed cultivating biofilms with current densities 134% higher than at unmodified graphite. This approach – the chemical CuS deposition onto inexpensive electrode materials – thus represents a promising pathway for the development of scalable, high-performance electrode materials for microbial electrochemical technologies.",0.10428602248430252,13
chemically_assemble_organic_compounds,107,"Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Type II polyketide synthases (PKSs) are multi-enzyme complexes that produce secondary metabolites of medical relevance. Chemical backbones of such polyketides are produced by minimal PKS systems that consist of a malonyl transacylase, an acyl carrier protein and an α/β heterodimeric ketosynthase. Here, we present X-ray structures of all ternary complexes that constitute the minimal PKS system for anthraquinone biosynthesis in Photorhabdus luminescens . In addition, we characterize this invariable core using molecular simulations, mutagenesis experiments and functional assays. We show that malonylation of the acyl carrier protein is accompanied by major structural rearrangements in the transacylase. Principles of an ongoing chain elongation are derived from the ternary complex with a hexaketide covalently linking the heterodimeric ketosynthase with the acyl carrier protein. Our results for the minimal PKS system provide mechanistic understanding of PKSs and a fundamental basis for engineering PKS pathways for future applications. The invariable core of a type II polyketide synthase has been characterized using X-ray crystallography, simulations, mutagenesis experiments and functional assays. The characterization of the ternary acyl carrier protein complexes provides a mechanistic understanding of the reactivity and could inform future engineering of this complex biosynthetic machinery.",0.09053915739059448,14
chemically_assemble_organic_compounds,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.07961796224117279,15
chemically_assemble_organic_compounds,104,"Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.",0.06889044493436813,16
chemically_assemble_organic_compounds,130,"Fires prime terrestrial organic carbon for riverine export to the global oceans. Black carbon (BC) is a recalcitrant form of organic carbon (OC) produced by landscape fires. BC is an important component of the global carbon cycle because, compared to unburned biogenic OC, it is selectively conserved in terrestrial and oceanic pools. Here we show that the dissolved BC (DBC) content of dissolved OC (DOC) is twice greater in major (sub)tropical and high-latitude rivers than in major temperate rivers, with further significant differences between biomes. We estimate that rivers export 18 ± 4 Tg DBC year −1 globally and that, including particulate BC fluxes, total riverine export amounts to 43 ± 15 Tg BC year −1 (12 ± 5% of the OC flux). While rivers export ~1% of the OC sequestered by terrestrial vegetation, our estimates suggest that 34 ± 26% of the BC produced by landscape fires has an oceanic fate. Biogeochemical models require modification to account for the unique dynamics of BC and to predict the response of recalcitrant OC export to changing environmental conditions. Black carbon is a recalcitrant and unique form of organic carbon formed from incomplete combustion. Here the authors use global sampling to reduce uncertainty in the flux of terrestrial black carbon to the oceans, predicting that 34% of black carbon produced by fires has an oceanic fate.",0.05727219954133034,17
chemically_assemble_organic_compounds,190,"Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.",0.053672291338443756,18
chemically_assemble_organic_compounds,242,"Dynamics of topological defects and structural synchronization in a forming periodic tissue. Living organisms form a large variety of hierarchically structured extracellular functional tissues. Remarkably, these materials exhibit regularity and structural coherence across multiple length scales, far beyond the size of a single cell. Here, synchrotron-based nanotomographic imaging in combination with machine-learning-based segmentation is used to reveal the structural synchronization process of nacre forming in the shell of the mollusc Unio pictorum . We show that the emergence of this highly regular layered structure is driven by a disorder-to-order transition achieved through the motion and interaction of screw-like structural dislocations with an opposite topological sign. Using an analogy to similar processes observed in liquid-crystalline systems, we demonstrate that these microstructural faults act as dissipative topological defects coupled by an elastic distortion field surrounding their cores. Their mutual annihilation results in structural synchronization that is simulated using the classical Kuramoto model. The developed experimental, theoretical and numerical framework provides a comprehensive physical view of the formation of biogenic materials. Molluscs assemble layers of material in the shells around them with a high level of control. Here the authors observe the structural evolution of layer formation and propose a mechanism reminiscent of topological defect dynamics in liquid crystals.",0.05055635794997215,19
chemically_assemble_organic_compounds,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.04579076170921326,20
change_size/shape,288,"Extreme autotomy and whole-body regeneration in photosynthetic sea slugs. Autotomy, the voluntary shedding of a body part, is common to distantly-related animals such as arthropods, gastropods, asteroids, amphibians, and lizards1,2. Autotomy is generally followed by regeneration of shed terminal body parts, such as appendages or tails. Here, we identify a new type of extreme autotomy in two species of sacoglossan sea slug (Mollusca: Gastropoda). Surprisingly, they shed the main body, including the whole heart, and regenerated a new body. In contrast, the shed body did not regenerate the head. These sacoglossans can incorporate chloroplasts from algal food into their cells to utilise for photosynthesis (kleptoplasty3), and we propose that this unique characteristic may facilitate survival after autotomy and subsequent regeneration.",0.6282201409339905,1
change_size/shape,194,"Type-I collagen fibrils: From growth morphology to local order. Abstract.The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ($\alpha$α) or coarse ($ \beta$β) have opposite molecular orientations. The $\alpha$α-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for $\alpha$α-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.Graphical abstract",0.4656272232532501,2
change_size/shape,247,"Evolution of fold switching in a metamorphic protein. One sequence encoding two structures Most proteins have stable, folded structures, but there are rare examples of metamorphic proteins that can switch between two different folds that may each have a different function. Dishman et al. investigated the evolution of XCL1, which is a member of the chemokine family that interconverts between the chemokine fold and a second, noncanonical fold that forms dimers. The authors used nuclear magnetic resonance spectroscopy to investigate the structures of inferred evolutionary ancestral sequences. Their results suggest that XCL1 evolved from an ancestor with the chemokine fold and then transitioned to prefer the noncanonical fold before reaching the modern-day metamorphic protein. Science, this issue p. 86 The human protein XCL1 evolved to switch between two completely different folds with different functions. Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering.",0.40327581763267517,3
change_size/shape,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.3974473774433136,4
change_size/shape,121,"Stochastic Mechanisms of Cell-Size Regulation in Bacteria.. How bacteria are able to maintain their sizes remains an open question. It is believed that cells have narrow distributions of sizes as a consequence of a homeostasis that allows bacteria to function at the optimal conditions. Several phenomenological approaches to explain these observations have been presented, but the microscopic origins of the cell-size regulation are still not understood. Here, we propose a new stochastic approach to investigate the molecular mechanisms of maintaining the cell sizes in bacteria. It is argued that the cell-size regulation is a result of coupling of two stochastic processes, cell growth and division, which eliminates the need for introducing the thresholds. Dynamic properties of the system are explicitly evaluated, and it is shown that the model is consistent with the experimentally supported adder principle of the cell-size regulation. In addition, theoretical predictions agree with experimental observations on E. coli bacteria. Theoretical analysis clarifies some important features of bacterial cell growth.",0.379510760307312,5
change_size/shape,117,"The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings. The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogenesis–but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here we develop and characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-Like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 minutes, and increased transcript levels of mechano-inducible genes within 60 minutes. We also show that cell swelling induces programmed cell death within 3 hours, also in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N-terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.",0.3778075575828552,6
change_size/shape,87,"Shaping the zebrafish myotome by intertissue friction and active stress. Significance How do tissues self-organize to generate the complex organ shapes observed in vertebrates? Organ formation requires the integration of chemical and mechanical information, yet how this is achieved is poorly understood for most organs. Muscle compartments in zebrafish display a V shape, which is believed to be required for efficient swimming. We investigate how this structure emerges during zebrafish development, combining live imaging and quantitative analysis of cellular movements. We use theoretical modeling to understand how cell differentiation and mechanical interactions between tissues guide the emergence of a specific tissue morphology. Our work reveals how spatially modulating the mechanical environment around and within tissues can lead to complex organ shape formation. Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the future myotome and the surrounding tissues appears to spatially vary, effectively resulting in spatially heterogeneous friction. Using a vertex model combined with experimental validation, we show that the interplay of tissue spreading and friction is sufficient to drive the initial phase of chevron shape formation. However, local anisotropic stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the chevron in wild-type embryos. Finally, tissue plasticity is required for formation and maintenance of the chevron shape, which is mediated by orientated cellular rearrangements. Our work sheds light on how a spatiotemporal sequence of local cellular events can have a nonlocal and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.",0.3325500786304474,7
change_size/shape,146,"Universal metabolic constraints shape the evolutionary ecology of diving in animals. Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.",0.32562902569770813,8
change_size/shape,138,Cellulose synthase interactive1- and microtubule-dependent cell wall architecture is required for acid growth in Arabidopsis hypocotyls. We observed a correlation between acid growth and crossed-polylamellate cell walls which was dependent on CSI1 and microtubules. This is significant for re-evaluating current models of cell morphogenesis.,0.3077259659767151,9
change_size/shape,200,"A seismic monitoring approach to detect and quantify river sediment mobilization by steelhead redd‐building activity. The role of spawning salmonids in altering river bed morphology and sediment transport is significant, yet poorly understood. This is due, in large part, to limitations in monitoring the redd‐build ...",0.27162572741508484,10
change_size/shape,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.2534645199775696,11
change_size/shape,116,"Curvature-induced stiffening of a fish fin. How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel (Scomber japonicus) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish.",0.21114835143089294,12
change_size/shape,280,"Sea stars generate downforce to stay attached to surfaces. Intertidal sea stars often function in environments with extreme hydrodynamic loads that can compromise their ability to remain attached to surfaces. While behavioral responses such as burrowing into sand or sheltering in rock crevices can help minimize hydrodynamic loads, previous work shows that sea stars also alter body shape in response to flow conditions. This morphological plasticity suggests that sea star body shape may play an important hydrodynamic role. In this study, we measured the fluid forces acting on surface-mounted sea star and spherical dome models in water channel tests. All sea star models created downforce, i.e., the fluid pushed the body towards the surface. In contrast, the spherical dome generated lift. We also used Particle Image Velocimetry (PIV) to measure the midplane flow field around the models. Control volume analyses based on the PIV data show that downforce arises because the sea star bodies serve as ramps that divert fluid away from the surface. These observations are further rationalized using force predictions and flow visualizations from numerical simulations. The discovery of downforce generation could explain why sea stars are shaped as they are: the pentaradial geometry aids attachment to surfaces in the presence of high hydrodynamic loads.",0.19796253740787506,13
change_size/shape,303,"Repeated evolution of underwater rebreathing in diving Anolis lizards. Air-based respiration limits the use of aquatic environments by ancestrally terrestrial animals. To overcome this challenge, diving arthropods have evolved to respire without resurfacing using air held between their cuticle and surrounding water.1-4 Inspired by natural history observations in Haiti (unpublished data) and Costa Rica,5,6 we conducted experiments documenting routine air-based underwater respiration in several distantly related semi-aquatic Anolis lizard species. Semi-aquatic anoles live along neotropical streams and frequently dive for refuge or food,7-12 remaining underwater for up to 18 min. While submerged, these lizards iteratively expire and re-inspire narial air bubbles-underwater ""rebreathing."" Rebreathed air is used in respiration, as the partial pressure of oxygen in the bubbles decreases with experimental submersion time in living anoles, but not in mechanical controls. Non-aquatic anoles occasionally rebreathe when submerged but exhibit more rudimentary rebreathing behaviors. Anole rebreathing is facilitated by a thin air layer (i.e., a ""plastron,"" sensu Brocher13) supported by the animal's rugose skin upon submergence. We suggest that hydrophobic skin, which we observed in all sampled anoles,14,15 may have been exaptative, facilitating the repeated evolution of specialized rebreathing in species that regularly dive. Phylogenetic analyses strongly suggest that specialized rebreathing is adaptive for semi-aquatic habitat specialists. Air-based rebreathing may enhance dive performance by incorporating dead space air from the buccal cavity or plastron into the lungs, facilitating clearance of carbon dioxide, or allowing uptake of oxygen from surrounding water (i.e., a ""physical gill"" mechanism4,16).",0.18140988051891327,14
change_size/shape,190,"Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.",0.1752973049879074,15
change_size/shape,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.1484546810388565,16
change_size/shape,282,"How neurons exploit fractal geometry to optimize their network connectivity. We investigate the degree to which neurons are fractal, the origin of this fractality, and its impact on functionality. By analyzing three-dimensional images of rat neurons, we show the way their dendrites fork and weave through space is unexpectedly important for generating fractal-like behavior well-described by an ‘effective’ fractal dimension D. This discovery motivated us to create distorted neuron models by modifying the dendritic patterns, so generating neurons across wide ranges of D extending beyond their natural values. By charting the D-dependent variations in inter-neuron connectivity along with the associated costs, we propose that their D values reflect a network cooperation that optimizes these constraints. We discuss the implications for healthy and pathological neurons, and for connecting neurons to medical implants. Our automated approach also facilitates insights relating form and function, applicable to individual neurons and their networks, providing a crucial tool for addressing massive data collection projects (e.g. connectomes).",0.1315954476594925,17
change_size/shape,162,"Sexual and natural selection on pollen morphology in Taraxacum.. PREMISE
Spiny pollen has evolved independently in multiple entomophilous lineages. Sexual selection may act on exine traits that facilitate male mating success by influencing the transfer of pollen from the anther to the body of the pollinator, while natural selection acts to increase pollen survival. We postulated that relative to sexual congeners, apomictic dandelions undergo relaxed selection on traits associated with male mating success.


METHODS
We explored sexual selection on exine traits by measuring the propensity for Taraxacum spp. pollen to attach to hairs of flower-visiting bumblebees (Bombus spp.) or flies (Diptera: Syrphidae and Muscoidea) and assessed natural selection by testing whether pollen traits defend against consumption.


RESULTS
Pollen picked up by bumblebees exhibited a narrower subset of spine-spacing phenotypes, consistent with stabilizing selection. Flies picked up larger pollen from flowers than expected at random. Surveys of corbiculae (pollen basket) contents from foraging bumblebees and feces of flies showed that pollen grains consumed by both kinds of visitors are similar in spine characteristics and size to those produced by the donor. When bees visit inflorescences of apomictic T. officinale, they pick up pollen with spine-spacing phenotypes above the mean and shifted toward those of sexual T. ceratophorum.


CONCLUSIONS
We demonstrate that traits under sexual selection during pollen pickup vary among pollinators, while natural selection for pollen defense is nil in T. ceratophorum. In hybrid zones between apomictic and sexual dandelions, pollen traits place apomictic donors at a dispersal disadvantage, potentially reinforcing reproductive isolation.",0.11955691874027252,18
change_size/shape,279,"Control of Helical Navigation by Three-Dimensional Flagellar Beating.. Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellate Chlamydomonas reinhardtii rotates at a constant 1-2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, nonplanar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully 3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer toward or away from light by modulating the sign of biflagellar dominance.",0.10731282085180283,19
change_size/shape,203,"Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography. Significance Hindwings in ladybird beetles successfully achieve compatibility between the deformability (instability) required for wing folding and strength property (stability) required for flying. This study demonstrates how ladybird beetles address these two conflicting requirements by an unprecedented technique using artificial wings. Our results, which clarify the detailed wing-folding process and reveal the supporting structures, provide indispensable initial knowledge for revealing this naturally evolved optimization system. Investigating the characteristics in the venations and crease patterns revealed in this study could provide an innovative designing method, enabling the integration of structural stability and deformability, and thus could have a considerable impact on engineering science. Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: (i) the wing rigidity with relatively thick veins and (ii) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure.",0.09863054752349854,20
attach_temporarily,315,"Hierarchical architecture of spider attachment setae reconstructed from scanning nanofocus X-ray diffraction data. When sitting and walking, the feet of wandering spiders reversibly attach to many surfaces without the use of gluey secretions. Responsible for the spiders' dry adhesion are the hairy attachment pads that are built of specially shaped cuticular hairs (setae) equipped with approximately 1 µm wide and 20 nm thick plate-like contact elements (spatulae) facing the substrate. Using synchrotron-based scanning nanofocus X-ray diffraction methods, combining wide-angle X-ray diffraction/scattering and small-angle X-ray scattering, allowed substantial quantitative information to be gained about the structure and materials of these fibrous adhesive structures with 200 nm resolution. The fibre diffraction patterns showed the crystalline chitin chains oriented along the long axis of the attachment setae and increased intensity of the chitin signal dorsally within the seta shaft. The small-angle scattering signals clearly indicated an angular shift by approximately 80° of the microtrich structures that branch off the bulk hair shaft and end as the adhesive contact elements in the tip region of the seta. The results reveal the specific structural arrangement and distribution of the chitin fibres within the attachment hair's cuticle preventing material failure by tensile reinforcement and proper distribution of stresses that arise upon attachment and detachment.",0.9224851131439209,1
attach_temporarily,77,"Attachment to challenging substrates – fouling, roughness and limits of adhesion in the northern clingfish (Gobiesox maeandricus). Northern clingfish use a ventral suction disc to stick to rough substrates in the intertidal zone. Bacteria, algae and invertebrates grow on these surfaces (fouling) and change the surface properties of the primary substrate, and therefore the attachment conditions for benthic organisms. In this study, we investigate the influence of fouling and surface roughness on the adhesive strength of northern clingfish, Gobiesox maeandricus. We measured clingfish tenacity on unfouled and fouled substrates over four surface roughnesses. We exposed surfaces for 6 weeks in the Pacific Ocean, until they were covered with periphyton. Clingfish tenacity is equivalent on both fouled and unfouled smooth substrates; however, tenacity on fouled rough surfaces is less compared with tenacity on unfouled ones. We hypothesize that parts of biofilm may act as a lubricant and decrease friction of the disc margin, thereby making disc margins slip inwards and fail at lower tenacities. Nevertheless, even on fouled surfaces the adhesive forces are approximately 150 times the body weight of the fish. To identify the upper threshold of surface roughness the fish can cling to, we tested seven unfouled substrates of increasing surface roughness. The threshold roughness at which northern clingfish failed increased with specimen size. We hypothesize that because of the elastic properties of the disc margin, a larger disc can adapt to larger surface irregularities. The largest specimens (length 10–12 cm) were able to cling to surfaces with 2–4 mm grain size. The fish can attach to surfaces with roughness between 2 and 9% of the suction disc width.",0.9141575694084167,2
attach_temporarily,322,"Attachment-based mechanisms underlying capture and release of pollen grains. Successful insect pollination can be achieved by a sequence of numerous attachment and detachment events at various biological surfaces. However, the quantitative measurements of pollen adhesion on biological surfaces have been poorly studied so far. We performed atomic force microscopy adhesion measurements of pollen on two most important floral parts for Asteraceae in a course of pollination: the stigma and style of Hypochaeris radicata plant. The results indicated distinct adhesive properties of them—the pollen adhesion on stigmatic surfaces drastically increased over prolonged contact time, while the pollen adhesion increase on stylar surfaces was rather restrained. Based on the observation with cryo-scanning electron microscopy, we explained the experimental results by the presence of morphological features in form of flexible stigmatic papillae that may play a crucial role in enhancing both capillary attraction and van der Waals forces. The distinct adhesive properties seemingly originate from the unique adhesive tasks that each of the floral parts requires to achieve successful pollination. The insights into the adhesive interaction between pollen and the floral parts, obtained in the present study, may lead to better understanding of pollination mechanisms, which are strongly related to our food production. Additionally, the novel pollen adhesive mechanisms learned from the stigma of the studied Asteraceae plant can inspire biomimetic designs of spontaneous gripping systems.",0.9050537943840027,3
attach_temporarily,294,"Multimodal and multifunctional signaling? – Web reduction courtship behavior in a North American population of the false black widow spider. Males of widow spiders courting on the web of females engage in web-reduction behavior which entails excising a section of the web, bundling it up, and wrapping it with their silk. Males of the false black widow spider, Steatoda grossa, in European populations also produce stridulatory courtship sound which has not yet been studied in their invaded North American range. Working with a North American population of S. grossa, we tested the hypotheses that (1) web reduction by males renders webs less attractive to rival males; (2) deposition of silk by courting males has an inter-sexual (male-female) signal function that enhances their likelihood of copulation; and (3) stridulatory sound is a courtship signal of males. Testing anemotactic attraction of males in Y-tube olfactometer experiments revealed that reduced webs (indicative of a mated female) and intact webs (indicative of a virgin female) were equally attractive to males. Recording courtship behavior of males with either functional (silk-releasing) spinnerets or spinnerets experimentally occluded on the web of virgin females showed that males with functional spinnerets were more likely to copulate with the female they courted. Although males possess the stridulatory apparatus to produce courtship sound, they did not stridulate when courting or copulating on the web of females. Our data support the conclusion that web-reduction behavior of S. grossa males in their invaded North American range has no long-range effect on mate seeking males. Instead, web-reduction behavior has an inter-sexual signaling function that seems to be linked to functional spinnerets of the courting male. The signal produced by a male likely entails a volatile silk-borne pheromone, but may also embody a gauge of his endurance (the amount of time he engages in web reduction causing web vibrations).",0.8798996806144714,4
attach_temporarily,321,"Versatility of Turing patterns potentiates rapid evolution in tarsal attachment microstructures of stick and leaf insects (Phasmatodea). In its evolution, the diverse group of stick and leaf insects (Phasmatodea) has undergone a rapid radiation. These insects evolved specialized structures to adhere to different surfaces typical for their specific ecological environments. The cuticle of their tarsal attachment pads (euplantulae) is known to possess a high diversity of attachment microstructures (AMS) which are suggested to reflect ecological specializations of different groups within phasmids. However, the origin of these microstructures and their developmental background remain largely unknown. Here, based on the detailed scanning electron microscopy study of pad surfaces, we present a theoretical approach to mathematically model an outstanding diversity of phasmid AMS using the reaction–diffusion model by Alan Turing. In general, this model explains pattern formation in nature. For the first time, we were able to identify eight principal patterns and simulate the transitions among these. In addition, intermediate transitional patterns were predicted by the model. The ease of transformation suggests a high adaptability of the microstructures that might explain the rapid evolution of pad characters. We additionally discuss the functional morphology of the different microstructures and their assumed advantages in the context of the ecological background of species.",0.784866213798523,5
attach_temporarily,64,"Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella. Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.",0.7788873910903931,6
attach_temporarily,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.6769497394561768,7
attach_temporarily,33,"Oysters produce an organic-inorganic adhesive for intertidal reef construction.. Coastal ecosystems rely upon oyster reefs to filter water, provide protection from storms, and build habitat for other species. From a chemistry perspective, few details are available to illustrate how these shellfish construct such extensive reef systems. Experiments presented here show that oysters generate a biomineralized adhesive material for aggregating into large communities. This cement is an organic-inorganic hybrid and differs from the surrounding shells by displaying an alternate CaCO(3) crystal form, a cross-linked organic matrix, and an elevated protein content. Emerging themes and unique aspects are both revealed when comparing oyster cement to the adhesives of other marine organisms. The presence of cross-linked proteins provides an analogy to mussel and barnacle adhesives whereas the high inorganic content is exclusive to oysters. With a description of oyster cement in hand we gain strategies for developing synthetic composite materials as well as a better understanding of the components needed for healthy coastal environments.",0.6722302436828613,8
attach_temporarily,309,"Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes. Significance For decades, the propulsion of sperms has been traditionally attributed to the beating or rotating of the soft tails. However, this work disclosed an unusual swimming model of Ray sperms whose propulsion is from not only the helical tail but also the unique spiral head (i.e., the head can contribute ∼31% of the force in propulsion). Such a propulsion mechanism provides Ray sperms with high adaptability to large environmental viscosities along with advantages in linearity, straightness, and efficiency. This study expands our knowledge on the microorganisms’ motion and provides inspirations for engineering design. We disclose a peculiar rotational propulsion mechanism of Ray sperms enabled by its unusual heterogeneous dual helixes with a rigid spiral head and a soft tail, named Heterogeneous Dual Helixes (HDH) model for short. Different from the conventional beating propulsion of sperm, the propulsion of Ray sperms is from both the rotational motion of the soft helical tail and the rigid spiral head. Such heterogeneous dual helical propulsion style provides the Ray sperm with high adaptability in viscous solutions along with advantages in linearity, straightness, and bidirectional motion. This HDH model is further corroborated by a miniature swimming robot actuated via a rigid spiral head and a soft tail, which demonstrates similar superiorities over conventional ones in terms of adaptability and efficiency under the same power input. Such findings expand our knowledge on microorganisms’ motion, motivate further studies on natural fertilization, and inspire engineering designs.",0.40283113718032837,9
attach_temporarily,28,"Novel barnacle underwater adhesive protein is a charged amino acid-rich protein constituted by a Cys-rich repetitive sequence.. Barnacle cement is an underwater adhesive that is used for permanent settlement, and is an insoluble protein complex. A method for rendering soluble the cement of Megabalanus rosa has been developed, and three major proteins have been identified in a previous study. To survey the M. rosa cement proteins in a lower molecular mass range, the cement proteins were separated by reversed-phase HPLC and a previously unidentified protein named 20 kDa M. rosa cement protein (Mrcp-20k) was found. Mrcp-20k cDNA was cloned to reveal its primary structure. This cDNA was 902 bp long and encoded a 202 amino acid-long open reading frame, including 19 amino acids of the signal sequence. The molecular mass in the disulphide form was calculated to be 20357 Da and the isoelectric point of the mature polypeptide was 4.72. Mrcp-20k was characterized by an abundance of Cys residues and charged amino acids. The most common amino acid was Cys (17.5%), with Asp (11.5%), Glu (10.4%) and His (10.4%) following in order of magnitude. The alignment of the Cys residues indicated the primary structure of this protein to consist of six degenerated repeats, each about 30 residues long. Mrcp-20k has no intermolecular disulphide bonds and no free thiol groups of Cys in the insoluble cement complex. Abundant Cys is thought to play a role in maintaining the topology of charged amino acids on the molecular surface by intramolecular disulphide-bond formation. The possible function of abundant charged amino acids, including the interaction with a variety of surface metals on the substratum, is discussed.",0.39156296849250793,10
attach_temporarily,58,"Both stiff and compliant: morphological and biomechanical adaptations of stick insect antennae for tactile exploration. Active tactile exploration behaviour is constrained to a large extent by the morphological and biomechanical properties of the animal's somatosensory system. In the model organism Carausius morosus, the main tactile sensory organs are long, thin, seemingly delicate, but very robust antennae. Previous studies have shown that these antennae are compliant under contact, yet stiff enough to maintain a straight shape during active exploration. Overcritical damping of the flagellum, on the other hand, allows for a rapid return to the straight shape after release of contact. Which roles do the morphological and biomechanical adaptations of the flagellum play in determining these special mechanical properties? To investigate this question, we used a combination of biomechanical experiments and numerical modelling. A set of four finite-element (FE) model variants was derived to investigate the effect of the distinct geometrical and material properties of the flagellum on its static (bending) and dynamic (damping) characteristics. The results of our numerical simulations show that the tapered shape of the flagellum had the strongest influence on its static biomechanical behaviour. The annulated structure and thickness gradient affected the deformability of the flagellum to a lesser degree. The inner endocuticle layer of the flagellum was confirmed to be essential for explaining the strongly damped return behaviour of the antenna. By highlighting the significance of two out of the four main structural features of the insect flagellum, our study provides a basis for mechanical design of biomimetic touch sensors tuned to become maximally flexible while quickly resuming a straight shape after contact.",0.3841441571712494,11
attach_temporarily,295,"Role of multiple, adjustable toes in distributed control shown by sideways wall-running in geckos. Remarkable progress has been made characterizing one of nature's most integrated, hierarchical structures––the fibrillar adhesive system of geckos. Nonetheless, we lack an understanding of how multiple toes coordinate to facilitate geckos' acrobatic locomotion. Here, we tested the control function of gecko toes by running them on vertical substrates varying in orientation, friction and roughness. Sideways wall-running geckos realigned the toes of their top feet upward to resist gravity. Toe contact area was not compromised, but redistributed. Geckos aligned all toes upward to resist slipping when encountering low-friction patches during sideways wall-running. Negotiation of intermittent slippery strips showed an increased contribution of particular toes to compensate for toes that lost adhesion. Increasing substrate roughness using discrete rods perpendicular to sideways locomotion resulted in geckos bending and/or rotating toes to conform to and even grasp the rods, with potential forces more than five times body weight. Geckos increase their effectiveness of manoeuvrability in demanding environments by taking advantage of the distributed control afforded by multiple toes. Our findings provide insight on biological attachment and offer inspiration to advance gecko-inspired robotics and other biomimetic applications.",0.27788448333740234,12
attach_temporarily,276,"Conus venom fractions inhibit the adhesion of Plasmodium falciparum erythrocyte membrane protein 1 domains to the host vascular receptors.. Using high-throughput BioPlex assays, we determined that six fractions from the venom of Conus nux inhibit the adhesion of various recombinant PfEMP-1 protein domains (PF08_0106 CIDR1α3.1, PF11_0521 DBL2β3, and PFL0030c DBL3X and DBL5e) to their corresponding receptors (CD36, ICAM-1, and CSA, respectively). The protein domain-receptor interactions permit P. falciparum-infected erythrocytes (IE) to evade elimination in the spleen by adhering to the microvasculature in various organs including the placenta. The sequences for the main components of the fractions, determined by tandem mass spectrometry, yielded four T-superfamily conotoxins, one (CC-Loop-CC) with I-IV, II-III connectivity and three (CC-Loop-CXaaC) with a I-III, II-IV connectivity. The 3D structure for one of the latter, NuxVA = GCCPAPLTCHCVIY, revealed a novel scaffold defined by double turns forming a hairpin-like structure stabilized by the two disulfide bonds. Two other main fraction components were a miniM conotoxin, and a O2-superfamily conotoxin with cysteine framework VI/VII. This study is the first one of its kind suggesting the use of conotoxins for developing pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as inhibitors of protein-protein interactions as treatment. BIOLOGICAL SIGNIFICANCE: Among the 850+ species of cone snail species there are hundreds of thousands of diverse venom exopeptides that have been selected throughout several million years of evolution to capture prey and deter predators. They do so by targeting several surface proteins present in target excitable cells. This immense biomolecular library of conopeptides can be explored for potential use as therapeutic leads against persistent and emerging diseases affecting non-excitable systems. We aim to expand the pharmacological reach of conotoxins/conopeptides by revealing their in vitro capacity to disrupt protein-protein and protein-polysaccharide interactions that directly contribute to pathology of Plasmodium falciparum malaria. This is significant for severe forms of malaria, which might be deadly even after treated with current parasite-killing drugs because of persistent cytoadhesion of P. falciparum infected erythrocytes even when parasites within red blood cells are dead. Anti-adhesion adjunct drugs would de-sequester or prevent additional sequestration of infected erythrocytes and may significantly improve survival of malaria patients. These results provide a lead for further investigations into conotoxins and other venom peptides as potential candidates for anti-adhesion or blockade-therapies. This study is the first of its kind and it suggests that conotoxins can be developed as pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as potential inhibitors of protein-protein interactions as treatment.",0.18433165550231934,13
attach_temporarily,279,"Control of Helical Navigation by Three-Dimensional Flagellar Beating.. Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellate Chlamydomonas reinhardtii rotates at a constant 1-2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, nonplanar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully 3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer toward or away from light by modulating the sign of biflagellar dominance.",0.17978405952453613,14
attach_temporarily,25,"PREHENSILE USE OF PERIORAL BRISTLES DURING FEEDING AND ASSOCIATED BEHAVIORS OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS). The use of perioral bristles (modified vibrissae) by 17 captive Florida manatees and approximately 20 wild manatees was analyzed. Captive manatees were fed six species of aquatic vegetation normally eaten in the wild (four freshwater species and two seagrasses). Inanimate objects were placed in the holding tanks with manatees at Lowry Park Zoological Gardens (Tampa, FL) to determine the degree to which perioral bristles were used in exploration and to define the range of manipulative behavior. In addition, behavioral observations were made on the use of perioral bristles during social interactions with conspecifics. Observations were recorded using a Hi8-format video camera. Florida manatees possess an unusually large degree of fine motor control of the snout and perioral bristles. The large and robust perioral bristle fields of the upper lip were used in a prehensile manner during feeding. Bristle use by manatees feeding on submerged vegetation differed from that seen during feeding on floating vegetation. Other behavioral use of the perioral bristles shows variation depending upon the situation encountered. The degree of plasticity of perioral bristle use supports our hypothesis that the vibrissal-muscular complex of the Florida manatee has evolved to increase the efficiency of grazing and browsing on aquatic vegetation and to fully maximize the potential of the manatee as a generalist feeder. The manipulative and sensitive nature of the manatee snout is likely a manifestation of a complex sensory and motor system which has evolved for marine mammal aquatic herbivores living in shallow turbid habitats.",0.15536420047283173,15
attach_temporarily,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.12458178400993347,16
attach_temporarily,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.09832997620105743,17
attach_temporarily,40,"Bacterial Adhesion and Entry into Host Cells. Successful establishment of infection by bacterial pathogens requires adhesion to host cells, colonization of tissues, and in certain cases, cellular invasion-followed by intracellular multiplication, dissemination to other tissues, or persistence. Bacteria use monomeric adhesins/invasins or highly sophisticated macromolecular machines such as type III secretion systems and retractile type IV pili to establish a complex host/pathogen molecular crosstalk that leads to subversion of cellular functions and establishment of disease.",0.09694686532020569,18
attach_temporarily,280,"Sea stars generate downforce to stay attached to surfaces. Intertidal sea stars often function in environments with extreme hydrodynamic loads that can compromise their ability to remain attached to surfaces. While behavioral responses such as burrowing into sand or sheltering in rock crevices can help minimize hydrodynamic loads, previous work shows that sea stars also alter body shape in response to flow conditions. This morphological plasticity suggests that sea star body shape may play an important hydrodynamic role. In this study, we measured the fluid forces acting on surface-mounted sea star and spherical dome models in water channel tests. All sea star models created downforce, i.e., the fluid pushed the body towards the surface. In contrast, the spherical dome generated lift. We also used Particle Image Velocimetry (PIV) to measure the midplane flow field around the models. Control volume analyses based on the PIV data show that downforce arises because the sea star bodies serve as ramps that divert fluid away from the surface. These observations are further rationalized using force predictions and flow visualizations from numerical simulations. The discovery of downforce generation could explain why sea stars are shaped as they are: the pentaradial geometry aids attachment to surfaces in the presence of high hydrodynamic loads.",0.09292896091938019,19
attach_temporarily,161,"A specialized avian seed dispersal system in a dry-fruited non-photosynthetic plant, Balanophora yakushimensis.. The family Balanophoraceae are among the most unusual of plants because they have aberrant vegetative bodies, highly reduced flowers, and small and reduced embryos (Hansen 1972, Gonzalez et al. 2019). Because the plants lack chlorophyll and are incapable of photosynthesis, they draw nutrition from other organisms. Indeed, like the well-known parasitic plant, Rafflesia, members of the Balanophoraceae acquire both water and nutrients from host plants. They are, therefore, highly specialized root parasites.",0.08144118636846542,20
protect_from_chemicals,47,"Anemonefish symbiosis: vulnerability and resistance of fish to the toxin of the sea anemone.. Protein toxins (20 kD molecular mass) causing lysis of human erythrocytes were isolated from sea anemones (Heteractis magnifica, Madang, Papua New Guinea, and Entacmaea quadricolor, Red Sea), which host anemonefish (Amphiprion sp.). These toxins are also ichthyotoxic. Freshwater and marine fish exposed to toxin concentrations of 0.5 micrograms/ml water were killed within 2 hr and exhibited extensive pathological alterations of the gill filaments. Amphiprion species, e.g. clarkii and percula, which live in the sea anemones Heteractis crispa and Stichodactyla mertensii, were highly vulnerable to the Heteractis magnifica toxin, whereas A. percula from the sea anemone H. magnifica proved to be toxin resistant. However, another species, A. perideraion also living in H. magnifica, was highly sensitive to the toxin. The two toxins exhibited cross-reactivity: Amphiprion, resistant to H. magnifica toxin, was also resistant to Entacmaea quadricolor toxin; but all fish were killed by other membrane-active substances such as gramicidin, saponin and latrunculin. The results of the study indicate that resistance to toxins secreted by the sea anemone has evolved in some Amphiprion species, but it is not an essential or a major factor in the anemonefish symbiosis. The skin's mucus layer seems to provide protection from nematocyst discharge.",0.7534711360931396,1
protect_from_chemicals,176,"The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals.",0.6513763070106506,2
protect_from_chemicals,1,"Molecular Mechanisms of Selenium Tolerance and Hyperaccumulation in Stanleya pinnata1[W][OA]. The molecular mechanisms responsible for selenium (Se) tolerance and hyperaccumulation were studied in the Se hyperaccumulator Stanleya pinnata (Brassicaceae) by comparing it with the related secondary Se accumulator Stanleya albescens using a combination of physiological, structural, genomic, and biochemical approaches. S. pinnata accumulated 3.6-fold more Se and was tolerant to 20 μm selenate, while S. albescens suffered reduced growth, chlorosis and necrosis, impaired photosynthesis, and high levels of reactive oxygen species. Levels of ascorbic acid, glutathione, total sulfur, and nonprotein thiols were higher in S. pinnata, suggesting that Se tolerance may in part be due to increased antioxidants and up-regulated sulfur assimilation. S. pinnata had higher selenocysteine methyltransferase protein levels and, judged from liquid chromatography-mass spectrometry, mainly accumulated the free amino acid methylselenocysteine, while S. albescens accumulated mainly the free amino acid selenocystathionine. S. albescens leaf x-ray absorption near-edge structure scans mainly detected a carbon-Se-carbon compound (presumably selenocystathionine) in addition to some selenocysteine and selenate. Thus, S. albescens may accumulate more toxic forms of Se in its leaves than S. pinnata. The species also showed different leaf Se sequestration patterns: while S. albescens showed a diffuse pattern, S. pinnata sequestered Se in localized epidermal cell clusters along leaf margins and tips, concentrated inside of epidermal cells. Transcript analyses of S. pinnata showed a constitutively higher expression of genes involved in sulfur assimilation, antioxidant activities, defense, and response to (methyl)jasmonic acid, salicylic acid, or ethylene. The levels of some of these hormones were constitutively elevated in S. pinnata compared with S. albescens, and leaf Se accumulation was slightly enhanced in both species when these hormones were supplied. Thus, defense-related phytohormones may play an important signaling role in the Se hyperaccumulation of S. pinnata, perhaps by constitutively up-regulating sulfur/Se assimilation followed by methylation of selenocysteine and the targeted sequestration of methylselenocysteine.",0.5996023416519165,3
protect_from_chemicals,37,"Bacterial nitric oxide synthases.. Nitric oxide synthases (NOSs) are multidomain metalloproteins first identified in mammals as being responsible for the synthesis of the wide-spread signaling and protective agent nitric oxide (NO). Over the past 10 years, prokaryotic proteins that are homologous to animal NOSs have been identified and characterized, both in terms of enzymology and biological function. Despite some interesting differences in cofactor utilization and redox partners, the bacterial enzymes are in many ways similar to their mammalian NOS (mNOS) counterparts and, as such, have provided insight into the structural and catalytic properties of the NOS family. In particular, spectroscopic studies of thermostable bacterial NOSs have revealed key oxyheme intermediates involved in the oxidation of substrate L-arginine (Arg) to product NO. The biological functions of some bacterial NOSs have only more recently come to light. These studies disclose new roles for NO in biology, such as taking part in toxin biosynthesis, protection against oxidative stress, and regulation of recovery from radiation damage.",0.35083407163619995,4
protect_from_chemicals,197,"Nickel hyperaccumulation mechanisms: a review on the current state of knowledge. BackgroundHyperaccumulator plants are unusual plants that accumulate particular metals or metalloids, such as nickel, zinc, cadmium and arsenic, in their living tissues to concentrations that are hundreds to thousands of times greater than what is normal for most plants. The hyperaccumulation phenomenon is rare (exhibited by less than 0.2% of all angiosperms), with most of the ~500 hyperaccumulator species known globally for nickel.ScopeThis review highlights the contemporary understanding of nickel hyperaccumulation processes, which include root uptake and sequestration, xylem loading and transport, leaf compartmentation and phloem translocation processes.ConclusionsHyperaccumulator plants have evolved highly efficient physiological mechanisms for taking up nickel in their roots followed by rapid translocation and sequestration into the aerial shoots. The uptake of nickel is mainly involved with low affinity transport systems, presumably from the ZIP family. The presence of high concentrations of histidine prevents nickel sequestration in roots. Nickel is efficiently loaded into the xylem, where it mainly presents as Ni2+. The leaf is the main storage organ, which sequestrates nickel in non-active sites, e.g. vacuoles and apoplast. Recent studies show that phloem translocates high levels of nickel, which has a strong impact on nickel accumulation in young growing tissues.",0.219687819480896,5
protect_from_chemicals,104,"Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.",0.12492774426937103,6
protect_from_chemicals,90,"Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries. Significance Dental caries remains an unresolved public health problem. The etiology is poorly understood, as the oral cavity harbors diverse communities of microorganisms. Using multiple imaging modalities on human teeth from patients with caries, we discovered a microbial community precisely arranged in a corona-like architecture. Moreover, this organization is mediated by the pathogen Streptococcus mutans through production of an extracellular scaffold that directs positioning of other oral microbes. We developed a methodology to quantify the spatial structure of microbial communities at the micron scale and found a precise spatial patterning of bacteria associated with localized caries onset. These findings are relevant as we approach the post-microbiome era, whereby quantifying the community structural organization may be essential for understanding microbiome function. Tooth decay (dental caries) is a widespread human disease caused by microbial biofilms. Streptococcus mutans, a biofilm-former, has been consistently associated with severe childhood caries; however, how this bacterium is spatially organized with other microorganisms in the oral cavity to promote disease remains unknown. Using intact biofilms formed on teeth of toddlers affected by caries, we discovered a unique 3D rotund-shaped architecture composed of multiple species precisely arranged in a corona-like structure with an inner core of S. mutans encompassed by outer layers of other bacteria. This architecture creates localized regions of acidic pH and acute enamel demineralization (caries) in a mixed-species biofilm model on human teeth, suggesting this highly ordered community as the causative agent. Notably, the construction of this architecture was found to be an active process initiated by production of an extracellular scaffold by S. mutans that assembles the corona cell arrangement, encapsulating the pathogen core. In addition, this spatial patterning creates a protective barrier against antimicrobials while increasing bacterial acid fitness associated with the disease-causing state. Our data reveal a precise biogeography in a polymicrobial community associated with human caries that can modulate the pathogen positioning and virulence potential in situ, indicating that micron-scale spatial structure of the microbiome may mediate the function and outcome of host–pathogen interactions.",0.10036713629961014,7
protect_from_chemicals,323,"Pygidial glands of Harpalus pensylvanicus (Coleoptera: Carabidae) contain resilin-rich structures.. The pygidial gland system is a key innovation in adephagan beetles, producing, storing, and spraying defensive chemical compounds. As the source of defensive chemical production and storage, the pygidial gland system experiences severe chemical stress which challenges the integrity of the entire gland system. Here, we utilize autofluorescence-based confocal laser scanning microscopy to examine the morphology of pygidial gland secretory lobes and collecting ductules in a common Pennsylvanian harpaline species, Harpalus pensylvanicus. The glandular units are composed of type-III exocrine cells which empty into resilin-rich ductules, which themselves lead into a larger resilin-rich collecting duct, and ultimately the pygidial reservoir pump. We also utilize histological staining with toluidine blue and brightfield imaging to provide additional support for the presence of resilin in the collecting duct, as toluidine blue has been shown to stain resilin without metachromasia. We hypothesize that the high resilin content of the collecting ducts might be a widespread key evolutionary adaptation to prevent damage caused by physical and chemical stress generated in pump-containing insect exocrine gland systems.",0.07878263294696808,8
protect_from_chemicals,156,"Character Displacement Promotes Cooperation in Bacterial Biofilms. Resource competition within a group of cooperators is expected to decrease selection for cooperative behavior but can also result in diversifying selection for the use of different resources, which in turn could retard the breakdown of cooperation. Diverse groups are likely to be less susceptible to invasion by noncooperating social cheats: First, competition repression resulting from character displacement may provide less of a selective advantage to cheating; second, cheats may trade off the ability to exploit cooperators that specialize in one type of resource against cooperators that specialize in another ; third, diverse communities of any kind may have higher invasion resistance because there are fewer resources available for an invader to use . Furthermore, diverse groups are likely to be more productive than clonal groups if a wider range of total resources are being used . We addressed these issues by using the cooperative trait of biofilm formation in Pseudomonas fluorescens. Character displacement through resource competition evolved within biofilms; productivity increased with increasing character displacement, and diverse biofilms were less susceptible to invasion by cheats. These results demonstrate that diversification into different ecological niches can minimize selection against cooperation in the face of local resource competition.",0.07789449393749237,9
protect_from_chemicals,137,"Hepatitis C virus exploits cyclophilin A to evade PKR. Counteracting innate immunity is essential for successful viral replication. Host cyclophilins (Cyps) have been implicated in viral evasion of host antiviral responses, although the mechanisms are still unclear. Here, we show that hepatitis C virus (HCV) co-opts the host protein CypA to aid evasion of antiviral responses dependent on the effector protein kinase R (PKR). Pharmacological inhibition of CypA rescues PKR from antagonism by HCV NS5A, leading to activation of an interferon regulatory factor-1 (IRF1)-driven cell intrinsic antiviral program that inhibits viral replication. These findings further the understanding of the complexity of Cyp-virus interactions, provide mechanistic insight into the remarkably broad antiviral spectrum of Cyp inhibitors, and uncover novel aspects of PKR activity and regulation. Collectively, our study identifies a novel antiviral mechanism that harnesses cellular antiviral immunity to suppress viral replication.",0.07536542415618896,10
protect_from_chemicals,66,"Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. PS is widely produced in the modern world, but it is robust against biodegradation. A few studies reported the biodegradation of PS, but most of them merely observed its weight loss; fewer were able to find its chemical modifications, which are rather direct evidence of biodegradation, by using limited organisms. Therefore, it is required to find an effective way to decompose PS using various kinds of organisms. Herein, we discovered a new PS-degrading insect species and bacterial strain, and we found that the genus that includes the PS-degrading bacterial strain occurs in significant amounts in the larval gut flora, and the proportion of this genus increased as the larvae were fed Styrofoam. Our research offers a wider selection of PS-degrading insects and the possibility of using a certain mixture of bacteria that resemble the gut flora of a PS-degrading insect to biodegrade PS, and thus could contribute to solving the global plastic crisis. ABSTRACT Polystyrene (PS), which accounts for a significant fraction of plastic wastes, is difficult to biodegrade due to its unique molecular structure. Therefore, biodegradation and chemical modification of PS are limited. In this study, we report PS biodegradation by the larvae of the darkling beetle Plesiophthalmus davidis (Coleoptera: Tenebrionidae). In 14 days, P. davidis ingested 34.27 ± 4.04 mg of Styrofoam (PS foam) per larva and survived by feeding only on Styrofoam. Fourier transform infrared spectroscopy confirmed that the ingested Styrofoam was oxidized. Gel permeation chromatography analysis indicated the decrease in average molecular weight of the residual PS in the frass compared with the feed Styrofoam. When the extracted gut flora was cultured for 20 days with PS films, biofilm and cavities were observed by scanning electron microscopy and atomic force microscopy. X-ray photoelectron spectroscopy (XPS) studies revealed that C-O bonding was introduced into the biodegraded PS film. Serratia sp. strain WSW (KCTC 82146), which was isolated from the gut flora, also formed a biofilm and cavities on the PS film in 20 days, but its degradation was less prominent than the gut flora. XPS confirmed that C-O and C=O bonds were introduced into the biodegraded PS film by Serratia sp. WSW. Microbial community analysis revealed that Serratia was in the gut flora in significant amounts and increased sixfold when the larvae were fed Styrofoam for 2 weeks. This suggests that P. davidis larvae and its gut bacteria could be used to chemically modify and rapidly degrade PS. IMPORTANCE PS is widely produced in the modern world, but it is robust against biodegradation. A few studies reported the biodegradation of PS, but most of them merely observed its weight loss; fewer were able to find its chemical modifications, which are rather direct evidence of biodegradation, by using limited organisms. Therefore, it is required to find an effective way to decompose PS using various kinds of organisms. Herein, we discovered a new PS-degrading insect species and bacterial strain, and we found that the genus that includes the PS-degrading bacterial strain occurs in significant amounts in the larval gut flora, and the proportion of this genus increased as the larvae were fed Styrofoam. Our research offers a wider selection of PS-degrading insects and the possibility of using a certain mixture of bacteria that resemble the gut flora of a PS-degrading insect to biodegrade PS, and thus could contribute to solving the global plastic crisis.",0.06244387477636337,11
protect_from_chemicals,261,"Gut bacteria are essential for normal cuticle development in herbivorous turtle ants. Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.",0.055832814425230026,12
protect_from_chemicals,14,"Biodegradation of new quaternary ammonium compounds in treated wood by mould fungi. The degradation of seven potential wood preservatives based on imidazolium compounds (ICs) and quaternary ammonium compounds (QACs) with a modified anion structure by mould fungi was determined using soil-block method. Experiments were carried out on Scots pine (Pinus sylvestris L.) wood. Two-phase titration and high-performance liquid chromatography (HPLC) method were used to detect and quantify the degradation products. The performed soil-block tests showed that the ICs and QACs with alkoxymethyl substituents were leached from the experimental wood when in contact with moist soil and revealed their fungal detoxification by mould fungi, especially by Gliocladium roseum. The degree of biological decomposition of new compounds was higher than didecyldimethylammonium chloride and didecylmethylpoli(oxyethyl)ammonium propionate. The observations of the colonization by mould fungi were made using the scanning electron microscope (SEM). Decay of treated wood by mould fungi showed its tolerance to QACs.",0.04758026450872421,13
protect_from_chemicals,157,"Communication versus waterproofing: the physics of insect cuticular hydrocarbons. ABSTRACT Understanding the evolution of complex traits is among the major challenges in biology. One such trait is the cuticular hydrocarbon (CHC) layer in insects. It protects against desiccation and provides communication signals, especially in social insects. CHC composition is highly diverse within and across species. To understand the adaptive value of this chemical diversity, we must understand how it affects biological functionality. So far, CHCs have received ample research attention, but their physical properties were little studied. We argue that these properties determine their biological functionality, and are vital to understanding how CHC composition affects their adaptive value. We investigated melting behaviour and viscosity of CHCs from 11 ant species using differential scanning calorimetry and a novel microrheological technique. CHCs began melting below −45°C, and often were entirely liquid only above 30°C. Thus, they formed a solid–liquid mixture under ambient conditions, which contrasts to previous assumptions of entirely solid layers in many species. This may be adaptive as only biphasic CHC layers ensure uniform coating of the insect body, which is necessary for waterproofing. CHC viscosity was mostly between 0.1 and 0.2 Pa s−1, thus similar to motor oils. Surprisingly, chemically different CHC profiles had similar viscosities, suggesting that a certain viscosity level is adaptive and ensures that communication signals can be perceived. With this study, we draw attention to the importance of studying the physics of CHC layers. Only by understanding how chemical and physical mechanisms enable CHC functionality can we understand the causes and consequences of CHC diversification. Summary: Cuticular hydrocarbons protect insects from desiccation and allow chemical communication, and contain both liquid and solid parts. This complex phase behaviour appears vital to ensure biological functioning.",0.04733884334564209,14
protect_from_chemicals,45,"Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi. Extracellular vesicles (EVs) are produced by all domains of life. In Gram-negative bacteria, EVs are produced by the pinching off of the outer membrane; however, how EVs escape the thick cell walls of Gram-positive bacteria, mycobacteria and fungi is still unknown. Nonetheless, EVs have been described in a variety of cell-walled organisms, including Staphylococcus aureus, Mycobacterium tuberculosis and Cryptococcus neoformans. These EVs contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes, and have important roles in microbial physiology and pathogenesis. In this Review, we describe the current status of vesiculogenesis research in thick-walled microorganisms and discuss the cargo and functions associated with EVs in these species.",0.04292741045355797,15
protect_from_chemicals,254,"Electrostatic resistance to alpha-neurotoxins conferred by charge reversal mutations in nicotinic acetylcholine receptors. The evolution of venom resistance through coevolutionary chemical arms races has arisen multiple times throughout animalia. Prior documentation of resistance to snake venom α-neurotoxins consists of the N-glycosylation motif or the hypothesized introduction of arginine at positions 187 at the α-1 nicotinic acetylcholine receptor orthosteric site. However, no further studies have investigated the possibility of other potential forms of resistance. Using a biolayer interferometry assay, we first confirm that the previously hypothesized resistance conferred by arginine at position 187 in the honey badger does reduce binding to α-neurotoxins, which has never been functionally tested. We further discovered a novel form of α-neurotoxin resistance conferred by charge reversal mutations, whereby a negatively charged amino acid is replaced by the positively charged amino acid lysine. As venom α-neurotoxins have evolved strong positive charges on their surface to facilitate binding to the negatively charged α-1 orthosteric site, these mutations result in a positive charge/positive charge interaction electrostatically repelling the α-neurotoxins. Such a novel mechanism for resistance has gone completely undiscovered, yet this form of resistance has convergently evolved at least 10 times within snakes. These coevolutionary innovations seem to have arisen through convergent phenotypes to ultimately evolve a similar biophysical mechanism of resistance across snakes.",0.04288094490766525,16
protect_from_chemicals,49,"Evolutionary aspects of intestinal bicarbonate secretion in fish.. Experiments compared intestinal HCO3- secretion in the intestine of marine teleost Gulf toadfish, Opsanus beta, to representatives of early chondrostean and chondrichthyan fishes, the Siberian sturgeon, Acipenser baerii, and white-spotted bamboo shark, Chiloscyllium plagiosum, respectively. As seen in marine teleosts, luminal HCO3- concentrations were 10-fold plasma levels in all species when exposed to hyperosmotic conditions. While intestinal water absorption left Mg2+ and SO4(2-) concentrated in intestinal fluids up to four-fold ambient seawater concentrations, HCO3- was concentrated up to 50 times ambient levels as a result of intestinal HCO3- secretion. Reduced luminal Cl- concentrations in the intestine of all species suggest that HCO3- secretion also occurs via Cl-/HCO3- exchange in chondrostean and chondrichthyan fishes. Sturgeon began precipitating carbonates from the gut after only 3 days at 14 per thousand, a mechanism utilized by marine teleosts to reduce intestinal fluid osmolality and maintain calcium homeostasis. Analysis of published intestinal fluid composition in the cyclostome Lampetra fluviatilis reveals that this species likely also utilize intestinal HCO3- secretion for osmoregulation. Analysis of existing cyclostome data and our results indicate that intestinal Cl-/HCO3- exchange plays an integral role in maintaining hydromineral balance not only in teleosts, but in all fish (and perhaps other animals) with a need to drink seawater.",0.04163452982902527,17
protect_from_chemicals,153,"Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. The gut microbiome is structured by social groups in a variety of host taxa. Whether this pattern is driven by relatedness, similar diets or shared social environments is under debate because few studies have had access to the data necessary to disentangle these factors in wild populations. We investigated whether diet, relatedness or the 1 m proximity network best explains differences in the gut microbiome among 45 female colobus monkeys in eight social groups residing at Boabeng-Fiema, Ghana. We combined demographic and behavioural data collected during May – August 2007 and October 2008 – April 2009 with 16S rRNA sequencing of faecal samples collected during the latter part of each observation period. Depending on the beta diversity index, social group identity explained 19–28% of the variation in gut microbiome beta diversity. When comparing the predictive power of dietary dissimilarity, relatedness and connectedness in the 1 m proximity network, the models with social connectedness received the strongest support, even in our analyses that excluded within-group dyads. This novel finding indicates that microbes may be transmitted during intergroup encounters, which could occur either indirectly via shared environments or directly via social contact. Lastly, some of the gut microbial taxa that appear to be transmitted via 1 m proximity are associated with digestion of plant material. Further research is needed to investigate whether this type of gut microbe transmission yields health benefits, which could provide an incentive for the formation and maintenance of social bonds within and between social groups.",0.03809848427772522,18
protect_from_chemicals,142,"Antiviral and virucidal effects of curcumin on transmissible gastroenteritis virus in vitro.. Emerging coronaviruses represent serious threats to human and animal health worldwide, and no approved therapeutics are currently available. Here, we used Transmissible gastroenteritis virus (TGEV) as the alpha-coronavirus model, and investigated the antiviral properties of curcumin against TGEV. Our results demonstrated that curcumin strongly inhibited TGEV proliferation and viral protein expression in a dose-dependent manner. We also observed that curcumin exhibited direct virucidal abilities in a dose-, temperature- and time-dependent manner. Furthermore, time-of-addition assays showed that curcumin mainly acted in the early phase of TGEV replication. Notably, in an adsorption assay, curcumin at 40 µM resulted in a reduction in viral titres of 3.55 log TCID50 ml-1, indicating that curcumin possesses excellent inhibitory effects on the adsorption of TGEV. Collectively, we demonstrate for the first time that curcumin has virucidal activity and virtual inhibition against TGEV, suggesting that curcumin might be a candidate drug for effective control of TGEV infection.",0.03803372010588646,19
protect_from_chemicals,251,"Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity. Diterpenoids inhibit lipid biosynthesis Plants make a variety of molecules that serve to protect them against hungry insects. Li et al. analyzed the balance between plants defending themselves and plants poisoning themselves. In wild tobacco (Nicotiana attenuata), two cytochrome P450 enzymes work within the biosynthetic pathway of 17-hydroxygeranyllinalool diterpene glycosides to help prevent the accumulation of toxic diterpene derivatives. Those same diterpene derivatives are formed in an insect herbivore after ingestion and cause toxicity by inhibiting sphingolipid biosynthesis in both plant and insect. Science, this issue p. 255 In tobacco plants, diterpenoid hydroxylations inhibit sphingolipid biosynthesis, explaining their autotoxicity and role in defense from insect herbivores. Many plant specialized metabolites function in herbivore defense, and abrogating particular steps in their biosynthetic pathways frequently causes autotoxicity. However, the molecular mechanisms underlying their defense and autotoxicity remain unclear. Here, we show that silencing two cytochrome P450s involved in diterpene biosynthesis in the wild tobacco Nicotiana attenuata causes severe autotoxicity symptoms that result from the inhibition of sphingolipid biosynthesis by noncontrolled hydroxylated diterpene derivatives. Moreover, the diterpenes’ defensive function is achieved by inhibiting herbivore sphingolipid biosynthesis through postingestive backbone hydroxylation products. Thus, by regulating metabolic modifications, tobacco plants avoid autotoxicity and gain herbivore defense. The postdigestive duet that occurs between plants and their insect herbivores can reflect the plant’s solutions to the “toxic waste dump” problem of using potent chemical defenses.",0.03784758970141411,20
regulate_reproduction_or_growth,162,"Sexual and natural selection on pollen morphology in Taraxacum.. PREMISE
Spiny pollen has evolved independently in multiple entomophilous lineages. Sexual selection may act on exine traits that facilitate male mating success by influencing the transfer of pollen from the anther to the body of the pollinator, while natural selection acts to increase pollen survival. We postulated that relative to sexual congeners, apomictic dandelions undergo relaxed selection on traits associated with male mating success.


METHODS
We explored sexual selection on exine traits by measuring the propensity for Taraxacum spp. pollen to attach to hairs of flower-visiting bumblebees (Bombus spp.) or flies (Diptera: Syrphidae and Muscoidea) and assessed natural selection by testing whether pollen traits defend against consumption.


RESULTS
Pollen picked up by bumblebees exhibited a narrower subset of spine-spacing phenotypes, consistent with stabilizing selection. Flies picked up larger pollen from flowers than expected at random. Surveys of corbiculae (pollen basket) contents from foraging bumblebees and feces of flies showed that pollen grains consumed by both kinds of visitors are similar in spine characteristics and size to those produced by the donor. When bees visit inflorescences of apomictic T. officinale, they pick up pollen with spine-spacing phenotypes above the mean and shifted toward those of sexual T. ceratophorum.


CONCLUSIONS
We demonstrate that traits under sexual selection during pollen pickup vary among pollinators, while natural selection for pollen defense is nil in T. ceratophorum. In hybrid zones between apomictic and sexual dandelions, pollen traits place apomictic donors at a dispersal disadvantage, potentially reinforcing reproductive isolation.",0.8487107753753662,1
regulate_reproduction_or_growth,204,"Pollen adaptation to ant pollination: a case study from the Proteaceae. Abstract Background and Aims Ant–plant associations are widely diverse and distributed throughout the world, leading to antagonistic and/or mutualistic interactions. Ant pollination is a rare mutualistic association and reports of ants as effective pollinators are limited to a few studies. Conospermum (Proteaceae) is an insect-pollinated genus well represented in the south-western Australia biodiversity hotspot, and here we aimed to evaluate the role of ants as pollinators of C. undulatum. Methods Pollen germination after contact with several species of ants and bees was tested for C. undulatum and five co-flowering species for comparison. We then sampled the pollen load of floral visitors of C. undulatum to assess whether ants carried a pollen load sufficient to enable pollination. Lastly, we performed exclusion treatments to assess the relative effect of flying- and non-flying-invertebrate floral visitors on the reproduction of C. undulatum. For this, we measured the seed set under different conditions: ants exclusion, flying-insects exclusion and control. Key Results Pollen of C. undulatum, along with the other Conospermum species, had a germination rate after contact with ants of ~80 % which did not differ from the effect of bees; in contrast, the other plant species tested showed a drop in the germination rate to ~10 % following ant treatments. Although ants were generalist visitors, they carried a pollen load with 68–86 % of suitable grains. Moreover, ants significantly contributed to the seed set of C. undulatum. Conclusions Our study highlights the complexity of ant–flower interactions and suggests that generalizations neglecting the importance of ants as pollinators cannot be made. Conospermum undulatum has evolved pollen with resistance to the negative effect of ant secretions on pollen grains, with ants providing effective pollination services to this threatened species.",0.7908492684364319,2
regulate_reproduction_or_growth,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.6129902005195618,3
regulate_reproduction_or_growth,188,"The central role of Clark's nutcracker in the dispersal and establishment of whitebark pine. SummaryWhitebark pine (Pinus albicaulis) is known to have its seeds harvested and cached in the soil by Clark's Nutcracker (Nucifraga columbiana), and unretrieved seeds are known to be capable of germinating and establishing new pines. Many other vertebrates also harvest and feed on these seeds, however, and the roles of these animals as dispersers and establishers of whitebark pine has been uncertain. This work demonstrates that birds other than the nutcracker, rodents, and other mammals do not have the requisite behaviors to systematically disperse or establish whitebark pine, and that the pine is therefore dependent on the nutcracker for its regeneration. These findings support previous suggestions that Clark's Nutcracker is a specialized frugivore that has profoundly influenced the ecology and the evolution of whitebark pine.",0.5370305776596069,4
regulate_reproduction_or_growth,121,"Stochastic Mechanisms of Cell-Size Regulation in Bacteria.. How bacteria are able to maintain their sizes remains an open question. It is believed that cells have narrow distributions of sizes as a consequence of a homeostasis that allows bacteria to function at the optimal conditions. Several phenomenological approaches to explain these observations have been presented, but the microscopic origins of the cell-size regulation are still not understood. Here, we propose a new stochastic approach to investigate the molecular mechanisms of maintaining the cell sizes in bacteria. It is argued that the cell-size regulation is a result of coupling of two stochastic processes, cell growth and division, which eliminates the need for introducing the thresholds. Dynamic properties of the system are explicitly evaluated, and it is shown that the model is consistent with the experimentally supported adder principle of the cell-size regulation. In addition, theoretical predictions agree with experimental observations on E. coli bacteria. Theoretical analysis clarifies some important features of bacterial cell growth.",0.5036419630050659,5
regulate_reproduction_or_growth,99,"Longer-lived tropical songbirds reduce breeding activity as they buffer impacts of drought. Droughts are expected to increase in frequency and severity with climate change. Population impacts of such harsh environmental events are theorized to vary with life history strategies among species. However, existing demographic models generally do not consider behavioural plasticity that may modify the impact of harsh events. Here we show that tropical songbirds in the New and Old Worlds reduced reproduction during drought, with greater reductions in species with higher average long-term survival. Large reductions in reproduction by longer-lived species were associated with higher survival during drought than predrought years in Malaysia, whereas shorter-lived species maintained reproduction and survival decreased. Behavioural strategies of longer-lived, but not shorter-lived, species mitigated the effect of increasing drought frequency on long-term population growth. Behavioural plasticity can buffer the impact of climate change on populations of some species and differences in plasticity among species related to their life histories are critical for predicting population trajectories. Climate change impacts on population dynamics will depend on species’ life history strategies. In contrast to short-lived species, longer-lived tropical songbirds reduced reproduction during drought, leading to higher survival and mitigating the effect on long-term population growth.",0.48644039034843445,6
regulate_reproduction_or_growth,245,"Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.",0.2816103398799896,7
regulate_reproduction_or_growth,117,"The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings. The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogenesis–but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here we develop and characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-Like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 minutes, and increased transcript levels of mechano-inducible genes within 60 minutes. We also show that cell swelling induces programmed cell death within 3 hours, also in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N-terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.",0.2117106169462204,8
regulate_reproduction_or_growth,152,"The Ccr4-Not complex monitors the translating ribosome for codon optimality. Coupling translation and mRNA decay Gene expression requires messenger RNAs (mRNAs)—DNA-derived blueprints of genes—to be translated by protein-producing ribosomes. The levels of mRNAs are tightly regulated, in part by controlling their half-lives. In eukaryotic cells, mRNA half-life is largely linked to translational efficiency, but the mechanism underlying this link has remained elusive. Buschauer et al. used cryo–electron microscopy and RNA sequencing to show how a key regulator of mRNA degradation, the Ccr4-Not complex, monitors the ribosome during mRNA translation. They found that the Not5 subunit directly binds to a ribosomal site exposed specifically during inefficient decoding, thereby triggering mRNA degradation. Analysis of mutants revealed the importance of this sensing mechanism for mRNA homeostasis. Science, this issue p. eaay6912 A protein complex binds to ribosomes that lack bound tRNAs, thus connecting translation elongation problems and mRNA decay. INTRODUCTION The tightly controlled process of gene expression requires messenger RNAs (mRNAs), which represent DNA-derived blueprints for polypeptides, to be translated by the protein-producing machinery of the cell, the ribosomes. Therefore, protein levels depend largely on cellular mRNA levels, and the control of mRNA decay is one of the most critical processes for setting the overall level of gene expression. Half-lives of mRNAs vary greatly between different transcripts, and regulation of the mRNA decay rate is intimately connected to the elongation phase of mRNA translation. To that end, codon optimality has been established as a key parameter for determining mRNA half-life in multiple eukaryotic organisms. It has also been established that the timely decay of short-lived mRNAs enriched with nonoptimal codons requires the Ccr4-Not complex. Ccr4-Not is an essential protein complex, with its best understood role in mRNA degradation, where it serves as the major cytoplasmic 3′-poly(A)-tail deadenylase that initiates decay of most mRNAs. By deadenylation and subsequent activation of the mRNA decapping machinery, the Ccr4-Not complex renders mRNAs accessible to the major degrading exonucleases, such as Xrn1 on the 5′ end and the exosome on the 3′ end. The molecular mechanism underlying codon optimality monitoring and coordination with mRNA decay by the Ccr4-Not complex has remained elusive. RATIONALE Because nonoptimal codons affect decoding kinetics of the ribosome and mRNA degradation occurs largely cotranslationally, it is highly plausible that codon optimality is directly monitored on the ribosome. In addition, a direct physical link between the participating Ccr4-Not complex and the ribosome has been suggested previously, and the Not4 subunit of the complex, an E3 ligase, ubiquitinates the eS7 protein of the 40S ribosomal subunit in yeast. Therefore, we set out to gain insights into the connection between the Ccr4-Not complex and the translation machinery in the context of mRNA homeostasis by combining cryo–electron microscopy (cryo-EM), ribosome profiling, and biochemical analysis. RESULTS We used affinity-purified native Ccr4-Not–ribosome complexes from Saccharomyces cerevisiae for analysis by cryo-EM and found that recruitment of Ccr4-Not to the ribosome occurs via the Not5 subunit. The N terminus of Not5—in particular, a three α-helix bundle—interacted specifically with the ribosomal E-site, and deletion of the Not5 N-terminus resulted in the loss of stable ribosome association of the Ccr4-Not complex. However, ubiquitination of the small ribosomal subunit protein eS7 through the Not4 subunit still occurred. The Not5 interaction involved the ribosomal protein eS25 of the small subunit, in addition to transfer RNA (tRNA) and ribosomal RNAs (rRNAs). We found that Ccr4-Not interacts with both initiating and elongating ribosomes. In either case, Not5 engaged the E-site only when the ribosome adopted a distinct conformation lacking accommodated tRNA in the A-site, indicative of impaired decoding kinetics. Ribosome profiling revealed that low-optimality codons were enriched in the A-site in the Ccr4-Not–bound elongating ribosomes. This observation explained the low A-site tRNA occupancy observed with cryo-EM and suggested a link to codon optimality monitoring. Consistently, using mRNA stability assays, we found that loss of Not5 resulted in the inability of the mRNA degradation machinery to sense codon optimality. The observed dysregulation of mRNA half-life was detected upon Not5 deletion, Not5 N-terminal deletion, eS25 deletion, and loss of eS7 ubiquitination by Not4, which apparently serves as an upstream prerequisite for further Ccr4-Not activity on the ribosome. In addition, mRNA decapping was found to be impaired in these mutants, which confirmed that, in this pathway, Ccr4-Not triggers decapping downstream of optimality monitoring. CONCLUSION Our analysis elucidates a direct physical link between the mRNA decay–mediating Ccr4-Not complex and the ribosome. Dependent on preceding ubiquitination of eS7 by the Not4 subunit, the Ccr4-Not complex binds (via the Not5 subunit) specifically to the ribosomal E-site when the A-site lacks tRNA because of slow decoding kinetics. This state of the ribosome occurs in the presence of nonoptimal codons in the A-site, which explains the shorter half-lives of transcripts enriched in nonoptimal codons. Thus, our findings provide mechanistic insights into the coordination of translation efficiency with mRNA stability through the Ccr4-Not complex. Ccr4-Not couples translation efficiency to mRNA degradation. When ribosomes encounter nonoptimal codons, low decoding efficiency leads to an increased likelihood of dissociation of the E-site tRNA before the cognate tRNA is accommodated in the A-site. As a result, the ribosomal E-site adopts a specific conformation, which is recognized by the Ccr4-Not complex through the N-terminus of its Not5 subunit, eventually triggering mRNA degradation by Xrn1. Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo–electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae. This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.",0.20121784508228302,9
regulate_reproduction_or_growth,317,"Bumble bees damage plant leaves and accelerate flower production when pollen is scarce. Bumble bee gardeners Bumble bees rely heavily on pollen resources for essential nutrients as they build their summer colonies. Therefore, we might expect that annual differences in the availability of these resources must simply be tolerated, but Pashalidou et al. made observations suggesting that bees may have strategies to cope with irregular seasonal flowering (see the Perspective by Chittka). When faced with a shortage of pollen, bumble bees actively damaged plant leaves in a characteristic way, and this behavior resulted in earlier flowering by as much as 30 days. Experimenters were not able to fully replicate the results with their own damage, suggesting that there is a distinct method that the bees use to stimulate earlier flowering. Science, this issue p. 881; see also p. 824 Bumble bees manipulate plants to bring about earlier flowering. Maintaining phenological synchrony with flowers is a key ecological challenge for pollinators that may be exacerbated by ongoing environmental change. Here, we show that bumble bee workers facing pollen scarcity damage leaves of flowerless plants and thereby accelerate flower production. Laboratory studies revealed that leaf-damaging behavior is strongly influenced by pollen availability and that bee-damaged plants flower significantly earlier than undamaged or mechanically damaged controls. Subsequent outdoor experiments showed that the intensity of damage inflicted varies with local flower availability; furthermore, workers from wild colonies of two additional bumble bee species were also observed to damage plant leaves. These findings elucidate a feature of bumble bee worker behavior that can influence the local availability of floral resources.",0.17781434953212738,10
regulate_reproduction_or_growth,0,"Increased Food and Ecosystem Security via Perennial Grains. Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.",0.16395767033100128,11
regulate_reproduction_or_growth,258,"Roots hunt nutrients. Plant Science
Soil nutrients such as nitrogen sources are not uniformly distributed. Neither are plant roots. Nonetheless, roots of Arabidopsis seedlings seek out pockets of soil ammonium and nitrate. Otvos et al. clarify how root growth and branching are regulated to optimize nitrogen uptake. The auxin efflux carrier PIN-FORMED 2 (PIN2) is regulated posttranscriptionally by phosphorylation at its serine-439 in response to shifts in ammonium or nitrate availability. Phosphorylation in turn triggers changes in PIN2 subcellular localization, which drives changes in auxin distribution between root cortex and epidermis, causing altered root growth rate or direction.

EMBO J. e106862 (2020).",0.1548939347267151,12
regulate_reproduction_or_growth,200,"A seismic monitoring approach to detect and quantify river sediment mobilization by steelhead redd‐building activity. The role of spawning salmonids in altering river bed morphology and sediment transport is significant, yet poorly understood. This is due, in large part, to limitations in monitoring the redd‐build ...",0.1526644229888916,13
regulate_reproduction_or_growth,138,Cellulose synthase interactive1- and microtubule-dependent cell wall architecture is required for acid growth in Arabidopsis hypocotyls. We observed a correlation between acid growth and crossed-polylamellate cell walls which was dependent on CSI1 and microtubules. This is significant for re-evaluating current models of cell morphogenesis.,0.14953772723674774,14
regulate_reproduction_or_growth,272,"Social signals mediate oviposition site selection in Drosophila suzukii. The information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila . These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.",0.13387809693813324,15
regulate_reproduction_or_growth,168,"IGF1R is an entry receptor for respiratory syncytial virus. Pneumonia resulting from infection is one of the leading causes of death worldwide. Pulmonary infection by the respiratory syncytial virus (RSV) is a large burden on human health, for which there are few therapeutic options 1 . RSV targets ciliated epithelial cells in the airways, but how viruses such as RSV interact with receptors on these cells is not understood. Nucleolin is an entry coreceptor for RSV 2 and also mediates the cellular entry of influenza, the parainfluenza virus, some enteroviruses and the bacterium that causes tularaemia 3 , 4 . Here we show a mechanism of RSV entry into cells in which outside-in signalling, involving binding of the prefusion RSV-F glycoprotein with the insulin-like growth factor-1 receptor, triggers the activation of protein kinase C zeta (PKCζ). This cellular signalling cascade recruits nucleolin from the nuclei of cells to the plasma membrane, where it also binds to RSV-F on virions. We find that inhibiting PKCζ activation prevents the trafficking of nucleolin to RSV particles on airway organoid cultures, and reduces viral replication and pathology in RSV-infected mice. These findings reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface, and could form the basis of new therapeutics to treat RSV infection. Respiratory syncytial virus enters cells by binding to cell-surface IGFR1, which activates PKCζ and induces trafficking of the NCL coreceptor to the RSV particles at the cell surface.",0.10761085897684097,16
regulate_reproduction_or_growth,161,"A specialized avian seed dispersal system in a dry-fruited non-photosynthetic plant, Balanophora yakushimensis.. The family Balanophoraceae are among the most unusual of plants because they have aberrant vegetative bodies, highly reduced flowers, and small and reduced embryos (Hansen 1972, Gonzalez et al. 2019). Because the plants lack chlorophyll and are incapable of photosynthesis, they draw nutrition from other organisms. Indeed, like the well-known parasitic plant, Rafflesia, members of the Balanophoraceae acquire both water and nutrients from host plants. They are, therefore, highly specialized root parasites.",0.10365951061248779,17
regulate_reproduction_or_growth,73,"Species-Specific Evolution of Ebola Virus during Replication in Human and Bat Cells. 
 Summary
 
 Ebola virus (EBOV) causes a severe, often fatal disease in humans and nonhuman primates. Within the past decade, EBOV has caused two large and difficult-to-control outbreaks, one of which recently ended in the Democratic Republic of the Congo. Bats are the likely reservoir of EBOV, but little is known of their relationship with the virus. We perform serial passages of EBOV in human and bat cells and use circular sequencing to compare the short-term evolution of the virus. Virus populations passaged in bat cells have sequence markers indicative of host RNA editing enzyme activity, including evidence for ADAR editing of the EBOV glycoprotein. Multiple regions in the EBOV genome appear to have undergone adaptive evolution when passaged in bat and human cells. Individual mutated viruses are rescued and characterized. Our results provide insight into the host species-specific evolution of EBOV and highlight the adaptive flexibility of the virus.
 
",0.0756344124674797,18
regulate_reproduction_or_growth,137,"Hepatitis C virus exploits cyclophilin A to evade PKR. Counteracting innate immunity is essential for successful viral replication. Host cyclophilins (Cyps) have been implicated in viral evasion of host antiviral responses, although the mechanisms are still unclear. Here, we show that hepatitis C virus (HCV) co-opts the host protein CypA to aid evasion of antiviral responses dependent on the effector protein kinase R (PKR). Pharmacological inhibition of CypA rescues PKR from antagonism by HCV NS5A, leading to activation of an interferon regulatory factor-1 (IRF1)-driven cell intrinsic antiviral program that inhibits viral replication. These findings further the understanding of the complexity of Cyp-virus interactions, provide mechanistic insight into the remarkably broad antiviral spectrum of Cyp inhibitors, and uncover novel aspects of PKR activity and regulation. Collectively, our study identifies a novel antiviral mechanism that harnesses cellular antiviral immunity to suppress viral replication.",0.0747869685292244,19
regulate_reproduction_or_growth,147,"Existence and functions of a kisspeptin neuropeptide signaling system in a non-chordate deuterostome species. The kisspeptin system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here, we report the identification and characterization of the kisspeptin system in the sea cucumber Apostichopus japonicus. The gene encoding the kisspeptin precursor generates two mature neuropeptides, AjKiss1a and AjKiss1b. The receptors for these neuropeptides, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate kisspeptins, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide. The A. japonicus kisspeptin system functions in multiple tissues that are closely related to seasonal reproduction and metabolism. Overall, our findings uncover for the first time the existence and function of the kisspeptin system in a non-chordate species and provide new evidence to support the ancient origin of intracellular signaling and physiological functions that are mediated by this molecular system.",0.06555823236703873,20
chemically_break_down_organic_compounds,14,"Biodegradation of new quaternary ammonium compounds in treated wood by mould fungi. The degradation of seven potential wood preservatives based on imidazolium compounds (ICs) and quaternary ammonium compounds (QACs) with a modified anion structure by mould fungi was determined using soil-block method. Experiments were carried out on Scots pine (Pinus sylvestris L.) wood. Two-phase titration and high-performance liquid chromatography (HPLC) method were used to detect and quantify the degradation products. The performed soil-block tests showed that the ICs and QACs with alkoxymethyl substituents were leached from the experimental wood when in contact with moist soil and revealed their fungal detoxification by mould fungi, especially by Gliocladium roseum. The degree of biological decomposition of new compounds was higher than didecyldimethylammonium chloride and didecylmethylpoli(oxyethyl)ammonium propionate. The observations of the colonization by mould fungi were made using the scanning electron microscope (SEM). Decay of treated wood by mould fungi showed its tolerance to QACs.",0.904405415058136,1
chemically_break_down_organic_compounds,31,"Eisenia fetida (Oligochaeta, Lumbricidae) Activates Fungal Growth, Triggering Cellulose Decomposition During Vermicomposting. Cellulose is the most abundant polymer in nature and constitutes a large pool of carbon for microorganisms, the main agents responsible for soil organic matter decomposition. Cellulolysis occurs as the result of the combined action of fungi and bacteria with different requirements. Earthworms influence decomposition indirectly by affecting microbial population structure and dynamics and also directly because the guts of some species possess cellulolytic activity. Here we assess whether the earthworm Eisenia fetida (Savigny 1826) digests cellulose directly (i.e., with its associated gut microbiota) and also whether the effects of E. fetida on microbial biomass and activity lead to a change in the equilibrium between fungi and bacteria. By enhancing fungal communities, E. fetida would presumably trigger more efficient cellulose decomposition. To evaluate the role of E. fetida in cellulose decomposition, we carried out an experiment in which pig slurry, a microbial-rich substrate, was treated in small-scale vermireactors with and without earthworms. The presence of earthworms in vermireactors significantly increased the rate of cellulose decomposition (0.43 and 0.26% cellulose loss day−1, with and without earthworms, respectively). However, the direct contribution of E. fetida to degradation of cellulose was not significant, although its presence increased microbial biomass (Cmic) and enzyme activity (cellulase and β-glucosidase). Surprisingly, as fungi may be part of the diet of earthworms, the activity of E. fetida triggered fungal growth during vermicomposting. We suggest that this activation is a key step leading to more intense and efficient cellulolysis during vermicomposting of organic wastes.",0.7864648103713989,2
chemically_break_down_organic_compounds,124,"Evolutionary diverse Chlamydomonas reinhardtii Old Yellow Enzymes reveal distinctive catalytic properties and potential for whole-cell biotransformations. Abstract Old Yellow Enzymes (OYEs) selectively reduce carbon‑carbon double bonds of a broad range of substrates with excellent stereoselectivity. Current challenges of their application in bio-based industrial processes are the cost-efficient regeneration of the nicotinamide co-substrate and expanding the range of industrially relevant substrates. Microalgae represent a rich and mostly untapped source for OYEs with novel catalytic properties and are promising whole-cell factories that regenerate nicotinamide by photosynthesis. By comparative phylogenetics, we identified 20 putative OYEs in eleven algal species. Three recombinant OYEs from the unicellular green alga Chlamydomonas reinhardtii (CrOYEs) reveal diverse biocatalytic properties and potential for enzyme optimization. High substrate conversion activities of living algal wild type and mutant cells linked the biocatalytic profiles to in vivo functionality and demonstrate the potential of microalgae as sources for distinctive OYE activities and for light-driven biotransformations.",0.7717560529708862,3
chemically_break_down_organic_compounds,66,"Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. PS is widely produced in the modern world, but it is robust against biodegradation. A few studies reported the biodegradation of PS, but most of them merely observed its weight loss; fewer were able to find its chemical modifications, which are rather direct evidence of biodegradation, by using limited organisms. Therefore, it is required to find an effective way to decompose PS using various kinds of organisms. Herein, we discovered a new PS-degrading insect species and bacterial strain, and we found that the genus that includes the PS-degrading bacterial strain occurs in significant amounts in the larval gut flora, and the proportion of this genus increased as the larvae were fed Styrofoam. Our research offers a wider selection of PS-degrading insects and the possibility of using a certain mixture of bacteria that resemble the gut flora of a PS-degrading insect to biodegrade PS, and thus could contribute to solving the global plastic crisis. ABSTRACT Polystyrene (PS), which accounts for a significant fraction of plastic wastes, is difficult to biodegrade due to its unique molecular structure. Therefore, biodegradation and chemical modification of PS are limited. In this study, we report PS biodegradation by the larvae of the darkling beetle Plesiophthalmus davidis (Coleoptera: Tenebrionidae). In 14 days, P. davidis ingested 34.27 ± 4.04 mg of Styrofoam (PS foam) per larva and survived by feeding only on Styrofoam. Fourier transform infrared spectroscopy confirmed that the ingested Styrofoam was oxidized. Gel permeation chromatography analysis indicated the decrease in average molecular weight of the residual PS in the frass compared with the feed Styrofoam. When the extracted gut flora was cultured for 20 days with PS films, biofilm and cavities were observed by scanning electron microscopy and atomic force microscopy. X-ray photoelectron spectroscopy (XPS) studies revealed that C-O bonding was introduced into the biodegraded PS film. Serratia sp. strain WSW (KCTC 82146), which was isolated from the gut flora, also formed a biofilm and cavities on the PS film in 20 days, but its degradation was less prominent than the gut flora. XPS confirmed that C-O and C=O bonds were introduced into the biodegraded PS film by Serratia sp. WSW. Microbial community analysis revealed that Serratia was in the gut flora in significant amounts and increased sixfold when the larvae were fed Styrofoam for 2 weeks. This suggests that P. davidis larvae and its gut bacteria could be used to chemically modify and rapidly degrade PS. IMPORTANCE PS is widely produced in the modern world, but it is robust against biodegradation. A few studies reported the biodegradation of PS, but most of them merely observed its weight loss; fewer were able to find its chemical modifications, which are rather direct evidence of biodegradation, by using limited organisms. Therefore, it is required to find an effective way to decompose PS using various kinds of organisms. Herein, we discovered a new PS-degrading insect species and bacterial strain, and we found that the genus that includes the PS-degrading bacterial strain occurs in significant amounts in the larval gut flora, and the proportion of this genus increased as the larvae were fed Styrofoam. Our research offers a wider selection of PS-degrading insects and the possibility of using a certain mixture of bacteria that resemble the gut flora of a PS-degrading insect to biodegrade PS, and thus could contribute to solving the global plastic crisis.",0.756497859954834,4
chemically_break_down_organic_compounds,110,"Biosynthetic origin of benzoquinones in the explosive discharge of the bombardier beetle Brachinus elongatulus. Bombardier beetles are well-known for their remarkable defensive mechanism. Their defensive apparatus consists of two compartments known as the reservoir and the reaction chamber. When challenged, muscles surrounding the reservoir contract sending chemical precursors into the reaction chamber where they mix with enzymes resulting in an explosive discharge of a hot noxious chemical spray containing two major quinones: 1,4-benzoquinone and 2-methyl-1,4-benzoquinone (toluquinone). Previously, it has been speculated that the biosynthesis of all benzoquinones originates from one core precursor, 1,4-hydroquinone. Careful ligation of the base of the reservoir chamber enabled us to prevent the explosive reaction and sample untransformed reservoir fluid, which showed that it accumulates significant quantities of 1,4-hydroquinone and 2-methyl-1,4-hydroquinone. We investigated the biosynthetic mechanisms leading to quinone formation by injecting or feeding Brachinus elongatulus beetles with stable-isotope-labeled precursors. Chemical analysis of defensive secretion samples obtained from 1,4-hydroquinone-d6-administered beetles demonstrated that it underwent conversion specifically to 1,4-benzoquinone. Analogously, results from m-cresol-d8 injected or fed beetles confirmed that m-cresol is metabolized to 2-methyl-1,4-hydroquinone, which is then oxidized to 2-methyl-1,4-benzoquinone in the hot spray. Our results refute the previous claim that 1,4-hydroquinone is the precursor of all substituted benzoquinones in bombardier beetles and reveal that they are biosynthetic products of two independent pathways. Most likely, the aforementioned biosynthetic channel of hydroxylation of appropriate phenolic precursors and subsequent oxidation is not restricted to bombardier beetles; it could well be a general pathway that leads to the formation of all congeners of benzoquinones, one of the most widely distributed groups of defensive compounds in arthropods. Graphical abstract Graphical abstract",0.6994494795799255,5
chemically_break_down_organic_compounds,237,"Eco-Mimicry Opens New Doors for Bioprocess Engineers. The natural world blends microenvironments to create a continuum of spatial niches wherein microbial consortia participate in metabolic exchanges. The capability with which nature selects a consortium to complement a given niche is often taken for granted. Not by Shahab et al. (2020), however, who created a synthetic microbial consortium to mediate a multi-step bioprocess in a single bioreactor system. The concept affords a fair degree of modularity in the choice of biocatalyst and a reasonable level of process control, thus making it an engineering tool.",0.6142684817314148,6
chemically_break_down_organic_compounds,61,Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening† †Electronic supplementary information (ESI) available: Additional simulation details and table of the full list of variants predicted by FuncLib. See DOI: 10.1039/d0sc01935f. De novo enzymes capable of efficiently catalysis of a non-natural reaction are obtained through minimalist design plus computationally-focused variant library screening.,0.4170422852039337,7
chemically_break_down_organic_compounds,251,"Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity. Diterpenoids inhibit lipid biosynthesis Plants make a variety of molecules that serve to protect them against hungry insects. Li et al. analyzed the balance between plants defending themselves and plants poisoning themselves. In wild tobacco (Nicotiana attenuata), two cytochrome P450 enzymes work within the biosynthetic pathway of 17-hydroxygeranyllinalool diterpene glycosides to help prevent the accumulation of toxic diterpene derivatives. Those same diterpene derivatives are formed in an insect herbivore after ingestion and cause toxicity by inhibiting sphingolipid biosynthesis in both plant and insect. Science, this issue p. 255 In tobacco plants, diterpenoid hydroxylations inhibit sphingolipid biosynthesis, explaining their autotoxicity and role in defense from insect herbivores. Many plant specialized metabolites function in herbivore defense, and abrogating particular steps in their biosynthetic pathways frequently causes autotoxicity. However, the molecular mechanisms underlying their defense and autotoxicity remain unclear. Here, we show that silencing two cytochrome P450s involved in diterpene biosynthesis in the wild tobacco Nicotiana attenuata causes severe autotoxicity symptoms that result from the inhibition of sphingolipid biosynthesis by noncontrolled hydroxylated diterpene derivatives. Moreover, the diterpenes’ defensive function is achieved by inhibiting herbivore sphingolipid biosynthesis through postingestive backbone hydroxylation products. Thus, by regulating metabolic modifications, tobacco plants avoid autotoxicity and gain herbivore defense. The postdigestive duet that occurs between plants and their insect herbivores can reflect the plant’s solutions to the “toxic waste dump” problem of using potent chemical defenses.",0.36523959040641785,8
chemically_break_down_organic_compounds,107,"Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Type II polyketide synthases (PKSs) are multi-enzyme complexes that produce secondary metabolites of medical relevance. Chemical backbones of such polyketides are produced by minimal PKS systems that consist of a malonyl transacylase, an acyl carrier protein and an α/β heterodimeric ketosynthase. Here, we present X-ray structures of all ternary complexes that constitute the minimal PKS system for anthraquinone biosynthesis in Photorhabdus luminescens . In addition, we characterize this invariable core using molecular simulations, mutagenesis experiments and functional assays. We show that malonylation of the acyl carrier protein is accompanied by major structural rearrangements in the transacylase. Principles of an ongoing chain elongation are derived from the ternary complex with a hexaketide covalently linking the heterodimeric ketosynthase with the acyl carrier protein. Our results for the minimal PKS system provide mechanistic understanding of PKSs and a fundamental basis for engineering PKS pathways for future applications. The invariable core of a type II polyketide synthase has been characterized using X-ray crystallography, simulations, mutagenesis experiments and functional assays. The characterization of the ternary acyl carrier protein complexes provides a mechanistic understanding of the reactivity and could inform future engineering of this complex biosynthetic machinery.",0.2860749065876007,9
chemically_break_down_organic_compounds,130,"Fires prime terrestrial organic carbon for riverine export to the global oceans. Black carbon (BC) is a recalcitrant form of organic carbon (OC) produced by landscape fires. BC is an important component of the global carbon cycle because, compared to unburned biogenic OC, it is selectively conserved in terrestrial and oceanic pools. Here we show that the dissolved BC (DBC) content of dissolved OC (DOC) is twice greater in major (sub)tropical and high-latitude rivers than in major temperate rivers, with further significant differences between biomes. We estimate that rivers export 18 ± 4 Tg DBC year −1 globally and that, including particulate BC fluxes, total riverine export amounts to 43 ± 15 Tg BC year −1 (12 ± 5% of the OC flux). While rivers export ~1% of the OC sequestered by terrestrial vegetation, our estimates suggest that 34 ± 26% of the BC produced by landscape fires has an oceanic fate. Biogeochemical models require modification to account for the unique dynamics of BC and to predict the response of recalcitrant OC export to changing environmental conditions. Black carbon is a recalcitrant and unique form of organic carbon formed from incomplete combustion. Here the authors use global sampling to reduce uncertainty in the flux of terrestrial black carbon to the oceans, predicting that 34% of black carbon produced by fires has an oceanic fate.",0.2666763961315155,10
chemically_break_down_organic_compounds,37,"Bacterial nitric oxide synthases.. Nitric oxide synthases (NOSs) are multidomain metalloproteins first identified in mammals as being responsible for the synthesis of the wide-spread signaling and protective agent nitric oxide (NO). Over the past 10 years, prokaryotic proteins that are homologous to animal NOSs have been identified and characterized, both in terms of enzymology and biological function. Despite some interesting differences in cofactor utilization and redox partners, the bacterial enzymes are in many ways similar to their mammalian NOS (mNOS) counterparts and, as such, have provided insight into the structural and catalytic properties of the NOS family. In particular, spectroscopic studies of thermostable bacterial NOSs have revealed key oxyheme intermediates involved in the oxidation of substrate L-arginine (Arg) to product NO. The biological functions of some bacterial NOSs have only more recently come to light. These studies disclose new roles for NO in biology, such as taking part in toxin biosynthesis, protection against oxidative stress, and regulation of recovery from radiation damage.",0.2576889395713806,11
chemically_break_down_organic_compounds,246,"Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.",0.23717059195041656,12
chemically_break_down_organic_compounds,243,"Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15 N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N 2 O) production among five iconic species of reef-building corals ( Acropora palmata , Diploria labyrinthiformis , Orbicella faveolata , Porites astreoides , and Porites porites ) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N 2 O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis , at rates of ~1 nmol cm −2  d −1 . In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N 2 O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.",0.22536322474479675,13
chemically_break_down_organic_compounds,16,"Average nanorough skin surface of the pilot whale (Globicephalamelas, Delphinidae): considerations on the self-cleaning abilities based on nanoroughness. Abstract. In aquatic environments, the biofouling process is assumed to initiate from the conditioning layer of absorbed organic carbon residues on wetted surfaces. Microfouling organisms attach to this conditioning layer, building up a biofilm on which further biofouling proceeds. In dolphins, biofouling reduces hydrodynamic efficiency and may negatively affect health if not managed. In the present study we examined the skin surface of the pilot whale (Globicephalamelas). Employing cryo-scanning electron microscopic techniques combined with various sample preparations, the skin displayed an average nanorough surface characterized by a pattern of nanoridge-enclosed pores; the average pore size (approximately 0.20 µm2) was below the size of most marine biofouling organisms. Further, the implications of this type of surface to the self-cleaning abilities of the skin of pilot whales are discussed, based on reduced available space for biofouler attachment, the lack of any particular microniches as shelters for biofoulers, and the challenges of turbulent water flow and liquid–air interfaces during surfacing and jumping of the dolphin.",0.20560240745544434,14
chemically_break_down_organic_compounds,118,"The phytopathogenic fungus Sclerotinia sclerotiorum detoxifies plant glucosinolate hydrolysis products via an isothiocyanate hydrolase. Brassicales plants produce glucosinolates and myrosinases that generate toxic isothiocyanates conferring broad resistance against pathogens and herbivorous insects. Nevertheless, some cosmopolitan fungal pathogens, such as the necrotrophic white mold Sclerotinia sclerotiorum, are able to infect many plant hosts including glucosinolate producers. Here, we show that S. sclerotiorum infection activates the glucosinolate-myrosinase system, and isothiocyanates contribute to resistance against this fungus. S. sclerotiorum metabolizes isothiocyanates via two independent pathways: conjugation to glutathione and, more effectively, hydrolysis to amines. The latter pathway features an isothiocyanate hydrolase that is homologous to a previously characterized bacterial enzyme, and converts isothiocyanate into products that are not toxic to the fungus. The isothiocyanate hydrolase promotes fungal growth in the presence of the toxins, and contributes to the virulence of S. sclerotiorum on glucosinolate-producing plants. Some plants produce toxic isothiocyanates that protect them against pathogens. Here, Chen et al. show that the plant pathogenic fungus Sclerotinia sclerotiorum converts isothiocyanates into non-toxic compounds via glutathione conjugation and, more effectively, via hydrolysis to amines using an isothiocyanate hydrolase.",0.18748536705970764,15
chemically_break_down_organic_compounds,3,"Cutin and Cutan Biopolymers: Their Role as Natural Sorbents. The aliphatic biopolymers cutin and cutan are important precursors of soil organic matter. In this study, we examined the effects of these biopolymers' decomposition and transformation in the soil on their sorptive properties. The levels of cutin and cutan decreased by 35 and 30%, respectively, after 20 mo of incubation. Carbon-13 nuclear magnetic resonance and differential scanning calorimeter analyses suggested that the rigid (crystalline) polymethylene moieties of cutan decompose with time. This observation is in contrast to previous reports, which suggested that this alkyl-C moiety is resistant to biodegradation. Cutin, however, exhibited mainly decomposition of the mobile (amorphous) polymethylene moieties. Moreover, some of its degraded materials were transformed into humic materials. The phenanthrene sorption coefficient decreased by 80 and 37% with incubation time of the cutin and cutan samples, respectively. For 1-naphthol, the sorption capacity decreased by 90% due to cutin decomposition. With cutan, this parameter did not show any changes correlated with incubation time. Phenanthrene exhibited linear and reversible sorption isotherms. In contrast, pronounced desorption hysteresis was obtained for 1-naphthol with the 20-mo-incubated cutin sample and with all cutan samples. With all cutan samples, desorption hysteresis increased with decomposition. Our data suggest that the sorptive nature of both biopolymers was affected by soil decomposition. With degradation, the role of cutin as a natural sorbent decreases while cutan acts as a natural highly efficient sorbent for organic compounds in the soil.",0.18118953704833984,16
chemically_break_down_organic_compounds,72,"Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Hybrid approach catches light Plant chloroplasts enclose two major photosynthetic processes: light reactions, which generate the energy carriers adenosine triphosphate and reduced nicotinamide dinucleotide phosphate (NADPH), and dark reactions, which use these molecules to fix carbon dioxide and build biomass. Miller et al. appropriated natural components, thylakoid membranes from spinach, for the light reactions and showed that these could be coupled to a synthetic enzymatic cycle that fixes carbon dioxide within water-in-oil droplets. The composition of the droplets could be tuned and optimized and the metabolic activity monitored in real time by NADPH fluorescence (see the Perspective by Gaut and Adamala). These chloroplast-mimicking droplets bring together natural and synthetic components in a small space and are amenable to further functionalization to perform complex biosynthetic tasks. Science, this issue p. 649; see also p. 587 Natural photosynthetic components power a synthetic CO2 fixation pathway in picoliter droplets. Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl–coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.",0.1630007028579712,17
chemically_break_down_organic_compounds,186,"Bacterial chemolithoautotrophy via manganese oxidation. Manganese is one of the most abundant elements on Earth. The oxidation of manganese has long been theorized1—yet has not been demonstrated2–4—to fuel the growth of chemolithoautotrophic microorganisms. Here we refine an enrichment culture that exhibits exponential growth dependent on Mn(II) oxidation to a co-culture of two microbial species. Oxidation required viable bacteria at permissive temperatures, which resulted in the generation of small nodules of manganese oxide with which the cells associated. The majority member of the culture—which we designate ‘Candidatus Manganitrophus noduliformans’—is affiliated to the phylum Nitrospirae (also known as Nitrospirota), but is distantly related to known species of Nitrospira and Leptospirillum. We isolated the minority member, a betaproteobacterium that does not oxidize Mn(II) alone, and designate it Ramlibacter lithotrophicus. Stable-isotope probing revealed 13CO2 fixation into cellular biomass that was dependent upon Mn(II) oxidation. Transcriptomic analysis revealed candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and autotrophic CO2 fixation. These findings expand the known diversity of inorganic metabolisms that support life, and complete a biogeochemical energy cycle for manganese5,6 that may interface with other major global elemental cycles. A co-culture of two newly identified microorganisms—‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus—exhibits exponential growth that is dependent on manganese(II) oxidation, demonstrating the viability of this metabolism for supporting life.",0.13905061781406403,18
chemically_break_down_organic_compounds,109,"Life cycle of a cyanobacterial carboxysome. Single cell and organelle measurements reveal activity dynamics and degradation of the carbon-fixing cyanobacterial carboxysome. Carboxysomes, prototypical bacterial microcompartments (BMCs) found in cyanobacteria, are large (~1 GDa) and essential protein complexes that enhance CO2 fixation. While carboxysome biogenesis has been elucidated, the activity dynamics, lifetime, and degradation of these structures have not been investigated, owing to the inability of tracking individual BMCs over time in vivo. We have developed a fluorescence-imaging platform to simultaneously measure carboxysome number, position, and activity over time in a growing cyanobacterial population, allowing individual carboxysomes to be clustered on the basis of activity and spatial dynamics. We have demonstrated both BMC degradation, characterized by abrupt activity loss followed by polar recruitment of the deactivated complex, and a subclass of ultraproductive carboxysomes. Together, our results reveal the BMC life cycle after biogenesis and describe the first method for measuring activity of single BMCs in vivo.",0.06381818652153015,19
chemically_break_down_organic_compounds,196,"Copper-bottomed: electrochemically active bacteria exploit conductive sulphide networks for enhanced electrogeneity. In this study, we demonstrate that anodic electroactive bacteria like Geobacter sulfurreducens generate copper(I) and copper(II) sulphides when grown on copper electrodes. The insoluble copper sulphides form a conductive network within the biofilms, strongly enhancing the biofilm electrogeneity – i.e., the ability of the biofilm to produce electric currents. Compared to biofilms grown on graphite, the average relative current density of copper-based biofilms was 237%, with a maximum geometric current density of 1.59 ± 0.23 mA cm−2. An additional electrochemical CuS deposition prior to biofilm cultivation further increased the bioelectrocatalytic current generation to 2 mA cm−2. The chemical deposition of CuS onto graphite allowed cultivating biofilms with current densities 134% higher than at unmodified graphite. This approach – the chemical CuS deposition onto inexpensive electrode materials – thus represents a promising pathway for the development of scalable, high-performance electrode materials for microbial electrochemical technologies.",0.057089366018772125,20
send_chemical_signals,24,"Predator-released hydrocarbons repel oviposition by a mosquito.. Prey species commonly use predator-released kairomones (PRKs) to detect risk of predation, yet the chemical identity of PRKs remains elusive. Chemical identification of PRKs will facilitate the study of predator-prey interactions and the risk of predation, and when the prey are pests, will potentially provide environmentally friendly means of pest control. In temporary pools of the Mediterranean and Middle East, larvae of the mosquito Culiseta longiareolata Macquart are highly vulnerable to the common predatory backswimmer, Notonecta maculata Fabricius. We demonstrate that N. maculata releases two hydrocarbons, n-heneicosane and n-tricosane, which repel ovipositing females of C. longiareolata. In behavioural tests with environmentally relevant chemical concentrations in outdoor mesocosm experiments, the repellent effects of the two compounds were additive at the tested concentrations.",0.8371778130531311,1
send_chemical_signals,81,"Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance. Plants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including “elicitors”, that are present in herbivores’ oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs’ (HAKs’) actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants. Uemura et al. study the mechanism of herbivore resistance in soybean and Arabidopsis. They show that receptor-like kinases (HAK1/2) respond to a polysaccharide in the oral secretions of Spodoptera litura and then interact with PBL27, resulting in an ethylene-dependent herbivore resistance.",0.7657113075256348,2
send_chemical_signals,317,"Bumble bees damage plant leaves and accelerate flower production when pollen is scarce. Bumble bee gardeners Bumble bees rely heavily on pollen resources for essential nutrients as they build their summer colonies. Therefore, we might expect that annual differences in the availability of these resources must simply be tolerated, but Pashalidou et al. made observations suggesting that bees may have strategies to cope with irregular seasonal flowering (see the Perspective by Chittka). When faced with a shortage of pollen, bumble bees actively damaged plant leaves in a characteristic way, and this behavior resulted in earlier flowering by as much as 30 days. Experimenters were not able to fully replicate the results with their own damage, suggesting that there is a distinct method that the bees use to stimulate earlier flowering. Science, this issue p. 881; see also p. 824 Bumble bees manipulate plants to bring about earlier flowering. Maintaining phenological synchrony with flowers is a key ecological challenge for pollinators that may be exacerbated by ongoing environmental change. Here, we show that bumble bee workers facing pollen scarcity damage leaves of flowerless plants and thereby accelerate flower production. Laboratory studies revealed that leaf-damaging behavior is strongly influenced by pollen availability and that bee-damaged plants flower significantly earlier than undamaged or mechanically damaged controls. Subsequent outdoor experiments showed that the intensity of damage inflicted varies with local flower availability; furthermore, workers from wild colonies of two additional bumble bee species were also observed to damage plant leaves. These findings elucidate a feature of bumble bee worker behavior that can influence the local availability of floral resources.",0.7350975275039673,3
send_chemical_signals,298,"Plant-pollinator interactions between generalists persist over time and space.. Generalist species are the linchpins of networks, as they are important for maintaining network structure and function. Previous studies have shown that interactions between generalists tend to occur consistently across years and sites. However, the link between temporal and spatial interaction persistence across scales remains unclear. To address this gap, we collected data on plant-pollinator interactions throughout the flowering period for five years across six plots in a subalpine meadow in the Rocky Mountains. We found that interactions between generalists tended to persist more in time and space such that interactions near the network core were more frequently recorded across years, within seasons, and among plots. We posit that species' tolerance of environmental variation across time and space plays a key role in generalization by regulating spatiotemporal overlap with interaction partners. Our results imply a role of spatiotemporal environmental variation in organizing species interactions, marrying niche concepts that emphasize species environmental constraints and their community role.",0.6685000658035278,4
send_chemical_signals,94,"The potential of the solitary parasitoid Microctonus brassicae for the biological control of the adult cabbage stem flea beetle, Psylliodes chrysocephala. The cabbage stem flea beetle (CSFB), Psylliodes chrysocephala L. (Coleoptera: Chrysomelidae), is a major pest of oilseed rape, Brassica napus L. (Brassicaceae), within the UK and continental Europe. Following the withdrawal of many broad‐spectrum pesticides, most importantly neonicotinoids, and with increased incidence of pyrethroid resistance, few chemical control options remain, resulting in the need for alternative pest management strategies. We identified the parasitoid wasp Microctonus brassicae (Haeselbarth) (Hymenoptera: Braconidae) within CSFB collected from three independent sites in Norfolk, UK. Parasitism of adult CSFB was confirmed, and wasp oviposition behaviour was described. Moreover, we show that within captive colonies parasitism rates are sufficient to generate significant biological control of CSFB populations. A sequence of the M. brassicae mitochondrial cytochrome oxidase 1 (MT‐CO1) gene was generated for rapid future identification. Moroccan specimens of Microctonus aethiopoides (Loan), possessing 90% sequence similarity, were the closest identified sequenced species. This study represents the first description published in English of this parasitoid of the adult cabbage stem flea beetle.",0.5700424313545227,5
send_chemical_signals,308,"Phytohormone-dependent plant defense signaling orchestrated by oral bacteria of the herbivore Spodoptera litura.. A vast array of herbivorous arthropods live with symbiotic microorganisms. However, little is known about the nature and functional mechanism of bacterial effects on plant defense responses towards herbivores. We explored the role of microbes present in extracts of oral secretion (OS) isolated from larvae of Spodoptera litura, a generalist herbivore, in phytohormone signaling-dependent defense responses in Arabidopsis thaliana (arabidopsis). In response to mechanical damage (MD) with application of bacteria-free OS (OS- ) prepared by sterilization or filtration of OS, arabidopsis leaves exhibited enhanced de novo synthesis of oxylipins, and induction of transcript levels of the responsible genes, in comparison to those in leaves with MD + non-sterilized OS (OS+ ), indicating that OS bacteria serve as suppressors of these genes. By contrast, de novo synthesis/signaling of salicylic acid and signaling of abscisic acid were enhanced by OS bacteria. These signaling networks were cross-regulated by each other. Meta-analysis of OS bacteria identified 70 bacterial strains. Among them was Staphylococcus epidermidis, an anaerobic staphylococcus that was shown to contribute to the suppression/manipulation of phytohormone-dependent plant defense signaling. The presence of OS bacteria was consequently beneficial for S. litura larvae hosted by Brassicaceae.",0.5230281949043274,6
send_chemical_signals,275,"Pseudoflowers produced by Fusarium xyrophilum on yellow-eyed grass (Xyris spp.) in Guyana: a novel floral mimicry system?. Pseudoflower formation is arguably the rarest outcome of a plant-fungus interaction. Here we report on a novel putative floral mimicry system in which the pseudoflowers are composed entirely of fungal tissues in contrast to modified leaves documented in previous mimicry systems. Pseudoflowers on two perennial Xyris species (yellow-eyed grass, X. setigera and X. surinamensis) collected from savannas in Guyana were produced by Fusarium xyrophilum, a novel Fusarium species. These pseudoflowers mimic Xyris flowers in gross morphology and are ultraviolet reflective. Axenic cultures of F. xyrophilum produced two pigments that had fluorescence emission maxima in light ranges that trichromatic insects are sensitive to and volatiles known to attract insect pollinators. One of the volatiles emitted by F. xyrophilum cultures (i.e., 2-ethylhexanol) was also detected in the head space of X. laxifolia var. iridifolia flowers, a perennial species native to the New World. Results of microscopic and PCR analyses, combined with examination of gross morphology of the pseudoflowers, provide evidence that the fungus had established a systemic infection in both Xyris species, sterilized them and formed fungal pseudoflowers containing both mating type idiomorphs. Fusarium xyrophilum cultures also produced the auxin indole-3-acetic acid (IAA) and the cytokinin isopentenyl adenosine (iPR). Field observations revealed that pseudoflowers and Xyris flowers were both visited by bees. Together, the results suggest that F. xyrophilum pseudoflowers are a novel floral mimicry system that attracts insect pollinators, via visual and olfactory cues, into vectoring its conidia, which might facilitate outcrossing of this putatively heterothallic fungus and infection of previously uninfected plants.",0.4113866686820984,7
send_chemical_signals,239,"Honey bees (Apis cerana) use animal feces as a tool to defend colonies against group attack by giant hornets (Vespa soror). Honey bees (genus Apis) are well known for the impressive suite of nest defenses they have evolved to protect their abundant stockpiles of food and the large colonies they sustain. In Asia, honey bees have evolved under tremendous predatory pressure from social wasps in the genus Vespa, the most formidable of which are the giant hornets that attack colonies in groups, kill adult defenders, and prey on brood. We document for the first time an extraordinary collective defense used by Apis cerana against the giant hornet Vespa soror. In response to attack by V. soror, A. cerana workers foraged for and applied spots of animal feces around their nest entrances. Fecal spotting increased after colonies were exposed either to naturally occurring attacks or to chemicals that scout hornets use to target colonies for mass attack. Spotting continued for days after attacks ceased and occurred in response to V. soror, which frequently landed at and chewed on entrances to breach nests, but not Vespa velutina, a smaller hornet that rarely landed at entrances. Moderate to heavy fecal spotting suppressed attempts by V. soror to penetrate nests by lowering the incidence of multiple-hornet attacks and substantially reducing the likelihood of them approaching and chewing on entrances. We argue that A. cerana forages for animal feces because it has properties that repel this deadly predator from nest entrances, providing the first report of tool use by honey bees and the first evidence that they forage for solids that are not derived from plants. Our study describes a remarkable weapon in the already sophisticated portfolio of defenses that honey bees have evolved in response to the predatory threats they face. It also highlights the strong selective pressure honey bees will encounter if giant hornets, recently detected in western North America, become established.",0.3053496181964874,8
send_chemical_signals,147,"Existence and functions of a kisspeptin neuropeptide signaling system in a non-chordate deuterostome species. The kisspeptin system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here, we report the identification and characterization of the kisspeptin system in the sea cucumber Apostichopus japonicus. The gene encoding the kisspeptin precursor generates two mature neuropeptides, AjKiss1a and AjKiss1b. The receptors for these neuropeptides, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate kisspeptins, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide. The A. japonicus kisspeptin system functions in multiple tissues that are closely related to seasonal reproduction and metabolism. Overall, our findings uncover for the first time the existence and function of the kisspeptin system in a non-chordate species and provide new evidence to support the ancient origin of intracellular signaling and physiological functions that are mediated by this molecular system.",0.215438112616539,9
send_chemical_signals,103,"Friend or Foe? Orb-Weaver Spiders Inhabiting Ant–Acacias Capture Both Herbivorous Insects and Acacia Ant Alates. Abstract The orb-weaver spiders Eustala oblonga (Chickering) and Eustala illicita (O. Picard-Cambridge) (Araneae: Araneidae) inhabit the ant-defended acacias Vachellia melanocerus (Beurling) and Vachellia collinsii (Safford) (Fabales: Fabaceae), respectively, in Panama. These spiders do not capture patrolling Pseudomyrmex ants but exploit their plant-protection services to escape predation. What effect the spiders have on the ant-acacia mutualisms is unknown. They may provide an additional layer of plant defense by capturing flying herbivorous insects in their webs. Alternatively, the spiders may disrupt the ant–acacia mutualisms by capturing alate acacia ants during nuptial flights. We evaluated these two hypotheses by sampling insects flying through acacia foliage and by identifying prey remains in webs. The proportions of insects captured on sticky card traps and in webs varied with taxonomic order and ecological role. Herbivorous insects greatly outnumbered other groups captured on sticky cards and were captured in spiders’ webs in both acacia species but made up a minority of prey remains in webs. Instead, insect predators and parasitoids made up the majority of prey remains and were comprised primarily by alate ant mutualists of the host acacias. These results provide indirect support for both hypotheses and suggest that the spiders potentially both benefit and harm their host ant-acacia mutualisms. The net effect of spider exploitation, however, is unclear and is likely based on both the effectiveness of plant protection from herbivory provided by the spiders relative to that provided by acacia ants, as well as the overall proportion of the ant reproductive caste the spiders actually capture.",0.18503372371196747,10
send_chemical_signals,98,"Species richness and redundancy promote persistence of exploited mutualisms in yeast. Species richness maintains mutualisms Mutualistic communities of species that benefit each other are ubiquitous in ecosystems and are important for ecosystem functioning. However, the relationship between the persistence of mutualisms and species richness has remained unclear. Vidal et al. used a synthetic mutualism in brewer's yeast to experimentally test whether species richness buffers mutualistic communities against exploitation by species that do not provide benefits in return. They showed that richer mutualist communities survive exploitation more often than pairwise mutualisms and that higher species richness and functional redundancy allow mutualist communities to persist in the presence of exploiters. These results provide experimental support for the hypothesis that species richness is necessary for the function and maintenance of mutualistic communities. Science, this issue p. 346 Experiments with yeast show that species richness buffers against loss of mutualistic interactions in ecological communities. Mutualisms, or reciprocally beneficial interspecific interactions, constitute the foundation of many ecological communities and agricultural systems. Mutualisms come in different forms, from pairwise interactions to extremely diverse communities, and they are continually challenged with exploitation by nonmutualistic community members (exploiters). Thus, understanding how mutualisms persist remains an essential question in ecology. Theory suggests that high species richness and functional redundancy could promote mutualism persistence in complex mutualistic communities. Using a yeast system (Saccharomyces cerevisiae), we experimentally show that communities with the greatest mutualist richness and functional redundancy are nearly two times more likely to survive exploitation than are simple communities. Persistence increased because diverse communities were better able to mitigate the negative effects of competition with exploiters. Thus, large mutualistic networks may be inherently buffered from exploitation.",0.16848501563072205,11
send_chemical_signals,92,"Prey Exploits the Auditory Illusions of Eavesdropping Predators. Mating signals have evolved to attract target receivers, even to the point of exploiting receivers through perceptual manipulation. Signals, however, can also expose signalers to nontarget receivers, including predators and parasites, and thus have also evolved to decrease enemy attraction. Here we show that male tree frogs (Smilisca sila) reduce their attractiveness to eavesdropping enemies (bats and midges) by overlapping their calls at near-perfect synchrony with the calls of neighboring conspecifics. By producing calls that closely follow those of other males, synchronizing S. sila take advantage of an auditory illusion where enemies are more attracted to the leading call. Female S. sila, however, are less susceptible to this illusion. Thus, synchronization among signaling males can result in acoustic crypsis from predators without affecting female attraction. Given the widespread use of conspicuous mating signals and eavesdropping enemies, perceptual exploitation of eavesdroppers is likely a common driver of signal evolution.",0.15091651678085327,12
send_chemical_signals,46,"Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival.. The dynamics of forest ecosystems depend largely on the survival of seedlings in their understories, but seedling survival is known to be limited by preemption of light and soil resources by overstory trees. It has been hypothesized that ""common mycorrhizal networks,"" wherein roots of seedlings are linked to overstory trees by symbiotic mycorrhizal fungi, offset some or all of the negative effects of trees on seedlings. Here we report the results of an unambiguous experimental test of this hypothesis in a monodominant Pinus radiata forest. We also tested the hypothesis that adaptive differentiation among plant populations causes local plant genotypes to respond more positively to mycorrhizal networks than nonlocal plant genotypes. Our results demonstrate large positive effects of overstory mycorrhizal networks on seedling survival, along with simultaneous negative effects of tree roots, regardless of whether plant genotypes were locally derived. Physiological and leaf-chemistry measurements suggest that seedlings connected to common mycorrhizal networks benefited from increased access to soil water. The similar magnitude of the positive and negative overstory effects on seedlings and the ubiquity of mycorrhizal networks in forests suggest that mycorrhizal networks fundamentally influence the demographic and community dynamics of forest trees.",0.14619004726409912,13
send_chemical_signals,204,"Pollen adaptation to ant pollination: a case study from the Proteaceae. Abstract Background and Aims Ant–plant associations are widely diverse and distributed throughout the world, leading to antagonistic and/or mutualistic interactions. Ant pollination is a rare mutualistic association and reports of ants as effective pollinators are limited to a few studies. Conospermum (Proteaceae) is an insect-pollinated genus well represented in the south-western Australia biodiversity hotspot, and here we aimed to evaluate the role of ants as pollinators of C. undulatum. Methods Pollen germination after contact with several species of ants and bees was tested for C. undulatum and five co-flowering species for comparison. We then sampled the pollen load of floral visitors of C. undulatum to assess whether ants carried a pollen load sufficient to enable pollination. Lastly, we performed exclusion treatments to assess the relative effect of flying- and non-flying-invertebrate floral visitors on the reproduction of C. undulatum. For this, we measured the seed set under different conditions: ants exclusion, flying-insects exclusion and control. Key Results Pollen of C. undulatum, along with the other Conospermum species, had a germination rate after contact with ants of ~80 % which did not differ from the effect of bees; in contrast, the other plant species tested showed a drop in the germination rate to ~10 % following ant treatments. Although ants were generalist visitors, they carried a pollen load with 68–86 % of suitable grains. Moreover, ants significantly contributed to the seed set of C. undulatum. Conclusions Our study highlights the complexity of ant–flower interactions and suggests that generalizations neglecting the importance of ants as pollinators cannot be made. Conospermum undulatum has evolved pollen with resistance to the negative effect of ant secretions on pollen grains, with ants providing effective pollination services to this threatened species.",0.13899973034858704,14
send_chemical_signals,272,"Social signals mediate oviposition site selection in Drosophila suzukii. The information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila . These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.",0.10134994238615036,15
send_chemical_signals,188,"The central role of Clark's nutcracker in the dispersal and establishment of whitebark pine. SummaryWhitebark pine (Pinus albicaulis) is known to have its seeds harvested and cached in the soil by Clark's Nutcracker (Nucifraga columbiana), and unretrieved seeds are known to be capable of germinating and establishing new pines. Many other vertebrates also harvest and feed on these seeds, however, and the roles of these animals as dispersers and establishers of whitebark pine has been uncertain. This work demonstrates that birds other than the nutcracker, rodents, and other mammals do not have the requisite behaviors to systematically disperse or establish whitebark pine, and that the pine is therefore dependent on the nutcracker for its regeneration. These findings support previous suggestions that Clark's Nutcracker is a specialized frugivore that has profoundly influenced the ecology and the evolution of whitebark pine.",0.0927417129278183,16
send_chemical_signals,316,"Soft and ion-conducting hydrogel artificial tongue for astringency perception. Artificial tongue for astringency perception is demonstrated with a saliva-like chemiresistive ionic hydrogel. Artificial tongues have been receiving increasing attention for the perception of five basic tastes. However, it is still challenging to fully mimic human tongue–like performance for tastes such as astringency. Mimicking the mechanism of astringency perception on the human tongue, we use a saliva-like chemiresistive ionic hydrogel anchored to a flexible substrate as a soft artificial tongue. When exposed to astringent compounds, hydrophobic aggregates form inside the microporous network and transform it into a micro/nanoporous structure with enhanced ionic conductivity. This unique human tongue–like performance enables tannic acid to be detected over a wide range (0.0005 to 1 wt %) with high sensitivity (0.292 wt %−1) and fast response time (~10 s). As a proof of concept, our sensor can detect the degree of astringency in beverages and fruits using a simple wipe-and-detection method, making a powerful platform for future applications involving humanoid robots and taste monitoring devices.",0.06919078528881073,17
send_chemical_signals,118,"The phytopathogenic fungus Sclerotinia sclerotiorum detoxifies plant glucosinolate hydrolysis products via an isothiocyanate hydrolase. Brassicales plants produce glucosinolates and myrosinases that generate toxic isothiocyanates conferring broad resistance against pathogens and herbivorous insects. Nevertheless, some cosmopolitan fungal pathogens, such as the necrotrophic white mold Sclerotinia sclerotiorum, are able to infect many plant hosts including glucosinolate producers. Here, we show that S. sclerotiorum infection activates the glucosinolate-myrosinase system, and isothiocyanates contribute to resistance against this fungus. S. sclerotiorum metabolizes isothiocyanates via two independent pathways: conjugation to glutathione and, more effectively, hydrolysis to amines. The latter pathway features an isothiocyanate hydrolase that is homologous to a previously characterized bacterial enzyme, and converts isothiocyanate into products that are not toxic to the fungus. The isothiocyanate hydrolase promotes fungal growth in the presence of the toxins, and contributes to the virulence of S. sclerotiorum on glucosinolate-producing plants. Some plants produce toxic isothiocyanates that protect them against pathogens. Here, Chen et al. show that the plant pathogenic fungus Sclerotinia sclerotiorum converts isothiocyanates into non-toxic compounds via glutathione conjugation and, more effectively, via hydrolysis to amines using an isothiocyanate hydrolase.",0.05821497365832329,18
send_chemical_signals,238,"Mammals repel mosquitoes with their tails. ABSTRACT The swinging of a mammal's tail has long been thought to deter biting insects, which, in cows, can drain up to 0.3 liters of blood per day. How effective is a mammal's tail at repelling insects? In this combined experimental and theoretical study, we filmed horses, zebras, elephants, giraffes and dogs swinging their tails. The tail swings at triple the frequency of a gravity-driven pendulum, and requires 27 times more power input. Tails can also be used like a whip to directly strike at insects. This whip-like effect requires substantial torques from the base of the tail on the order of 101–102 N m, comparable to the torque of a sedan, but still within the physical limits of the mammal. Based on our findings, we designed and built a mammal tail simulator to simulate the swinging of the tail. The simulator generates mild breezes of 1 m s–1, comparable to a mosquito's flight speed, and sufficient to deter up to 50% of mosquitoes from landing. This study may help us determine new mosquito-repelling strategies that do not depend on chemicals. Highlighted Article: Mammals swing their tails three times faster than a gravity-driven pendulum. Our experiments with artificial tails show that tail motion generates winds sufficient to repel mosquitoes.",0.053439393639564514,19
send_chemical_signals,255,"Nocturnal visual displays and call description of the cascade specialist glassfrog Sachatamia orejuela. Although most male frogs call to attract females, vocalizations alone can be ineffective long-range signals in certain environments. To increase conspicuousness and counter the background noise generated by rushing water, a few frog species around the world have evolved visual communication modalities in addition to advertisement calls. These species belong to different families on different continents: a clear example of behavioural convergent evolution. Until now, long-distance visual signalling has not been recorded for any species in the glassfrog family (Centrolenidae). Sachatamia orejuela, an exceptionally camouflaged glassfrog species found within the spray zone of waterfalls, has remained poorly studied. Here, we document its advertisement call for the first time — the frequency of which is higher than perhaps any other glassfrog species, likely an evolutionary response to its disruptive acoustic space — as well as a sequence of non-antagonistic visual signals (foot-flagging, hand-waving, and head-bobbing) that we observed at night.",0.04973357915878296,20
attach_permanently,28,"Novel barnacle underwater adhesive protein is a charged amino acid-rich protein constituted by a Cys-rich repetitive sequence.. Barnacle cement is an underwater adhesive that is used for permanent settlement, and is an insoluble protein complex. A method for rendering soluble the cement of Megabalanus rosa has been developed, and three major proteins have been identified in a previous study. To survey the M. rosa cement proteins in a lower molecular mass range, the cement proteins were separated by reversed-phase HPLC and a previously unidentified protein named 20 kDa M. rosa cement protein (Mrcp-20k) was found. Mrcp-20k cDNA was cloned to reveal its primary structure. This cDNA was 902 bp long and encoded a 202 amino acid-long open reading frame, including 19 amino acids of the signal sequence. The molecular mass in the disulphide form was calculated to be 20357 Da and the isoelectric point of the mature polypeptide was 4.72. Mrcp-20k was characterized by an abundance of Cys residues and charged amino acids. The most common amino acid was Cys (17.5%), with Asp (11.5%), Glu (10.4%) and His (10.4%) following in order of magnitude. The alignment of the Cys residues indicated the primary structure of this protein to consist of six degenerated repeats, each about 30 residues long. Mrcp-20k has no intermolecular disulphide bonds and no free thiol groups of Cys in the insoluble cement complex. Abundant Cys is thought to play a role in maintaining the topology of charged amino acids on the molecular surface by intramolecular disulphide-bond formation. The possible function of abundant charged amino acids, including the interaction with a variety of surface metals on the substratum, is discussed.",0.6787576675415039,1
attach_permanently,33,"Oysters produce an organic-inorganic adhesive for intertidal reef construction.. Coastal ecosystems rely upon oyster reefs to filter water, provide protection from storms, and build habitat for other species. From a chemistry perspective, few details are available to illustrate how these shellfish construct such extensive reef systems. Experiments presented here show that oysters generate a biomineralized adhesive material for aggregating into large communities. This cement is an organic-inorganic hybrid and differs from the surrounding shells by displaying an alternate CaCO(3) crystal form, a cross-linked organic matrix, and an elevated protein content. Emerging themes and unique aspects are both revealed when comparing oyster cement to the adhesives of other marine organisms. The presence of cross-linked proteins provides an analogy to mussel and barnacle adhesives whereas the high inorganic content is exclusive to oysters. With a description of oyster cement in hand we gain strategies for developing synthetic composite materials as well as a better understanding of the components needed for healthy coastal environments.",0.4844301640987396,2
attach_permanently,321,"Versatility of Turing patterns potentiates rapid evolution in tarsal attachment microstructures of stick and leaf insects (Phasmatodea). In its evolution, the diverse group of stick and leaf insects (Phasmatodea) has undergone a rapid radiation. These insects evolved specialized structures to adhere to different surfaces typical for their specific ecological environments. The cuticle of their tarsal attachment pads (euplantulae) is known to possess a high diversity of attachment microstructures (AMS) which are suggested to reflect ecological specializations of different groups within phasmids. However, the origin of these microstructures and their developmental background remain largely unknown. Here, based on the detailed scanning electron microscopy study of pad surfaces, we present a theoretical approach to mathematically model an outstanding diversity of phasmid AMS using the reaction–diffusion model by Alan Turing. In general, this model explains pattern formation in nature. For the first time, we were able to identify eight principal patterns and simulate the transitions among these. In addition, intermediate transitional patterns were predicted by the model. The ease of transformation suggests a high adaptability of the microstructures that might explain the rapid evolution of pad characters. We additionally discuss the functional morphology of the different microstructures and their assumed advantages in the context of the ecological background of species.",0.29809439182281494,3
attach_permanently,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.2573603689670563,4
attach_permanently,315,"Hierarchical architecture of spider attachment setae reconstructed from scanning nanofocus X-ray diffraction data. When sitting and walking, the feet of wandering spiders reversibly attach to many surfaces without the use of gluey secretions. Responsible for the spiders' dry adhesion are the hairy attachment pads that are built of specially shaped cuticular hairs (setae) equipped with approximately 1 µm wide and 20 nm thick plate-like contact elements (spatulae) facing the substrate. Using synchrotron-based scanning nanofocus X-ray diffraction methods, combining wide-angle X-ray diffraction/scattering and small-angle X-ray scattering, allowed substantial quantitative information to be gained about the structure and materials of these fibrous adhesive structures with 200 nm resolution. The fibre diffraction patterns showed the crystalline chitin chains oriented along the long axis of the attachment setae and increased intensity of the chitin signal dorsally within the seta shaft. The small-angle scattering signals clearly indicated an angular shift by approximately 80° of the microtrich structures that branch off the bulk hair shaft and end as the adhesive contact elements in the tip region of the seta. The results reveal the specific structural arrangement and distribution of the chitin fibres within the attachment hair's cuticle preventing material failure by tensile reinforcement and proper distribution of stresses that arise upon attachment and detachment.",0.1786569058895111,5
attach_permanently,173,"Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication. Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.",0.1407471001148224,6
attach_permanently,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.11405180394649506,7
attach_permanently,40,"Bacterial Adhesion and Entry into Host Cells. Successful establishment of infection by bacterial pathogens requires adhesion to host cells, colonization of tissues, and in certain cases, cellular invasion-followed by intracellular multiplication, dissemination to other tissues, or persistence. Bacteria use monomeric adhesins/invasins or highly sophisticated macromolecular machines such as type III secretion systems and retractile type IV pili to establish a complex host/pathogen molecular crosstalk that leads to subversion of cellular functions and establishment of disease.",0.10943987220525742,8
attach_permanently,122,"Architecture of a catalytically active homotrimeric plant cellulose synthase complex. Plant cell wall construction crew Plants produce a complex cell wall in which cellulose, a glucose polymer, is a major component. Cellulose fibers are formed from close-packed single chains of cellulose that have been proposed to be formed by multimeric complexes (18 or more subunits) of the enzyme cellulose synthase, which exists in several isoforms. Purushotham et al. determined a cryo–electron microscopy structure of a trimer of a single isoform of cellulose synthase. A large channel forms a path for cellulose chains through the membrane-embedded complex. The structure also reveals oligomeric interfaces and provides a framework for modeling the larger complexes seen in plant membranes. The close arrangement of exit sites for nascent glycan chains is consistent with the enzyme complex playing a role in directing cellulose microfibril formation. Science, this issue p. 1089 The structure of a homotrimeric cellulose synthase complex provides molecular insights into cellulose fibril formation. Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.",0.09938380122184753,9
attach_permanently,245,"Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.",0.09853342920541763,10
attach_permanently,214,"Quadratic resource value assessment during mantis shrimp (Stomatopoda) contests. Resource value assessment, in which competitors adjust behaviours according to the perceived value of a contested resource, is well described in animal contests. Such assessment is usually assumed to be categorical or linear; for example, males fight more aggressively when females are present than absent, or as female fecundity increases. Here, to our knowledge for the first time, we show quadratic resource value assessment, in which resource value is highest at a certain level and decreases in either direction. The mantis shrimp Neogonodactylus bredini occupies coral rubble burrows in a size-assortative manner: individuals of a certain body size inhabit burrows of a certain size. Using mock burrows of various sizes, we tested whether mantis shrimp (1) chose burrows predicted to be the best fit for their body size and (2) were more aggressive during, endured higher costs during and were more likely to win contests over burrows predicted to be best fit. Individuals chose burrows larger than their predicted best fit burrows. In contests, intruders without burrows were more likely to evict burrow residents when the burrow was slightly smaller than the intruder's predicted best fit size. Intruder success decreased as relative burrow size increased or decreased from this value. Intruders won by delivering more strikes and by being aggressive first. In contrast to intruders, burrow residents showed little evidence of resource value assessment. A literature review revealed that quadratic resource value assessment may play a role in contests over resources from territories to parasite hosts. Therefore, our results impact theoretical models of contest behaviour and may lend insight to how contests affect resource distributions.",0.07845944166183472,11
attach_permanently,244,"DNA Origami Design: A How-To Tutorial. While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.",0.07483673840761185,12
attach_permanently,242,"Dynamics of topological defects and structural synchronization in a forming periodic tissue. Living organisms form a large variety of hierarchically structured extracellular functional tissues. Remarkably, these materials exhibit regularity and structural coherence across multiple length scales, far beyond the size of a single cell. Here, synchrotron-based nanotomographic imaging in combination with machine-learning-based segmentation is used to reveal the structural synchronization process of nacre forming in the shell of the mollusc Unio pictorum . We show that the emergence of this highly regular layered structure is driven by a disorder-to-order transition achieved through the motion and interaction of screw-like structural dislocations with an opposite topological sign. Using an analogy to similar processes observed in liquid-crystalline systems, we demonstrate that these microstructural faults act as dissipative topological defects coupled by an elastic distortion field surrounding their cores. Their mutual annihilation results in structural synchronization that is simulated using the classical Kuramoto model. The developed experimental, theoretical and numerical framework provides a comprehensive physical view of the formation of biogenic materials. Molluscs assemble layers of material in the shells around them with a high level of control. Here the authors observe the structural evolution of layer formation and propose a mechanism reminiscent of topological defect dynamics in liquid crystals.",0.0629023015499115,13
attach_permanently,264,"The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo. The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.",0.061724547296762466,14
attach_permanently,235,"Multiple Degrees of Freedom in the Fish Skull and Their Relation to Hydraulic Transport of Prey in Channel Catfish. Synopsis Fish perform many complex manipulation behaviors without hands or flexible muscular tongues, instead relying on more than 20 movable skeletal elements in their highly kinetic skulls. How fish use their skulls to accomplish these behaviors, however, remains unclear. Most previous mechanical models have represented the fish skull using one or more planar four-bar linkages, which have just a single degree of freedom (DoF). In contrast, truncated-cone hydrodynamic models have assumed up to five DoFs. In this study, we introduce and validate a 3D mechanical linkage model of a fish skull that incorporates the pectoral girdle and mandibular and hyoid arches. We validate this model using an in vivo motion dataset of suction feeding in channel catfish and then use this model to quantify the DoFs in the fish skull, to categorize the motion patterns of the cranial linkage during feeding, and to evaluate the association between these patterns and food motion. We find that the channel catfish skull functions as a 17-link, five-loop parallel mechanism. Despite having 19 potential DoFs, we find that seven DoFs are sufficient to describe most of the motion of the cranial linkage, consistent with the fish skull functioning as a multi-DoF, manipulation system. Channel catfish use this linkage to generate three different motion patterns (rostrocaudal wave, caudorostral wave, and compressive wave), each with its own associated food velocity profile. These results suggest that biomechanical manipulation systems must have a minimum number of DoFs to effectively control objects, whether in water or air.",0.05941157788038254,15
attach_permanently,133,"Comparative Analysis of Tear Composition in Humans, Domestic Mammals, Reptiles, and Birds. Tears are an important component of the ocular surface protection mechanism and are in close contact with the corneal epithelium and the environment. Their composition is well-known in humans; however, there are few investigations on the composition and function of tears in reptiles, birds and others mammals, which would elucidate the mechanisms governing the maintenance of ocular homeostasis. In this work, electrophoretic profiles and an evaluation of total protein, albumin, urea, glucose, and cholesterol concentrations in tears of semi-aquatic, terrestrial, and marine reptiles (Caiman latirostris, Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Lepidochelys olivacea, and Chelonoidis carbonaria), birds (Tyto furcata, Rupornis magnirostris and Ara ararauna), and mammals (Equus caballus and Canis lupus familiaris) were apresented. Human tear components and respective blood serum samples were used as references. The electrophoretic analysis revealed similarities whithin same Classes. The results of the tear–blood serum relationship and the comparison to human tear components showed particularities that are potentially derived from a homeostatic response to the environment. When the tear compositions of animals belonging to different ecological clusters were compared, marked differences were observed in total protein and urea concentrations. Thus, reptile, bird, and mammalian tears are complex fluids with differing concentrations of biochemical components that are potentially a result of the animals' adaptation to different environments.",0.05819178745150566,16
attach_permanently,276,"Conus venom fractions inhibit the adhesion of Plasmodium falciparum erythrocyte membrane protein 1 domains to the host vascular receptors.. Using high-throughput BioPlex assays, we determined that six fractions from the venom of Conus nux inhibit the adhesion of various recombinant PfEMP-1 protein domains (PF08_0106 CIDR1α3.1, PF11_0521 DBL2β3, and PFL0030c DBL3X and DBL5e) to their corresponding receptors (CD36, ICAM-1, and CSA, respectively). The protein domain-receptor interactions permit P. falciparum-infected erythrocytes (IE) to evade elimination in the spleen by adhering to the microvasculature in various organs including the placenta. The sequences for the main components of the fractions, determined by tandem mass spectrometry, yielded four T-superfamily conotoxins, one (CC-Loop-CC) with I-IV, II-III connectivity and three (CC-Loop-CXaaC) with a I-III, II-IV connectivity. The 3D structure for one of the latter, NuxVA = GCCPAPLTCHCVIY, revealed a novel scaffold defined by double turns forming a hairpin-like structure stabilized by the two disulfide bonds. Two other main fraction components were a miniM conotoxin, and a O2-superfamily conotoxin with cysteine framework VI/VII. This study is the first one of its kind suggesting the use of conotoxins for developing pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as inhibitors of protein-protein interactions as treatment. BIOLOGICAL SIGNIFICANCE: Among the 850+ species of cone snail species there are hundreds of thousands of diverse venom exopeptides that have been selected throughout several million years of evolution to capture prey and deter predators. They do so by targeting several surface proteins present in target excitable cells. This immense biomolecular library of conopeptides can be explored for potential use as therapeutic leads against persistent and emerging diseases affecting non-excitable systems. We aim to expand the pharmacological reach of conotoxins/conopeptides by revealing their in vitro capacity to disrupt protein-protein and protein-polysaccharide interactions that directly contribute to pathology of Plasmodium falciparum malaria. This is significant for severe forms of malaria, which might be deadly even after treated with current parasite-killing drugs because of persistent cytoadhesion of P. falciparum infected erythrocytes even when parasites within red blood cells are dead. Anti-adhesion adjunct drugs would de-sequester or prevent additional sequestration of infected erythrocytes and may significantly improve survival of malaria patients. These results provide a lead for further investigations into conotoxins and other venom peptides as potential candidates for anti-adhesion or blockade-therapies. This study is the first of its kind and it suggests that conotoxins can be developed as pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as potential inhibitors of protein-protein interactions as treatment.",0.05817653238773346,17
attach_permanently,77,"Attachment to challenging substrates – fouling, roughness and limits of adhesion in the northern clingfish (Gobiesox maeandricus). Northern clingfish use a ventral suction disc to stick to rough substrates in the intertidal zone. Bacteria, algae and invertebrates grow on these surfaces (fouling) and change the surface properties of the primary substrate, and therefore the attachment conditions for benthic organisms. In this study, we investigate the influence of fouling and surface roughness on the adhesive strength of northern clingfish, Gobiesox maeandricus. We measured clingfish tenacity on unfouled and fouled substrates over four surface roughnesses. We exposed surfaces for 6 weeks in the Pacific Ocean, until they were covered with periphyton. Clingfish tenacity is equivalent on both fouled and unfouled smooth substrates; however, tenacity on fouled rough surfaces is less compared with tenacity on unfouled ones. We hypothesize that parts of biofilm may act as a lubricant and decrease friction of the disc margin, thereby making disc margins slip inwards and fail at lower tenacities. Nevertheless, even on fouled surfaces the adhesive forces are approximately 150 times the body weight of the fish. To identify the upper threshold of surface roughness the fish can cling to, we tested seven unfouled substrates of increasing surface roughness. The threshold roughness at which northern clingfish failed increased with specimen size. We hypothesize that because of the elastic properties of the disc margin, a larger disc can adapt to larger surface irregularities. The largest specimens (length 10–12 cm) were able to cling to surfaces with 2–4 mm grain size. The fish can attach to surfaces with roughness between 2 and 9% of the suction disc width.",0.04361290857195854,18
attach_permanently,198,"Universal elastic mechanism for stinger design. Living organisms use stingers that vary in length L over eight orders of magnitude, from a few tens of nanometres to several metres, across a wide array of biological taxa. Despite the extreme variation in size, their structures are strikingly similar. However, the mechanism responsible for this remarkable morphological convergence remains unknown. Using basic physical arguments and biomimetic experiments, we reveal an optimal design strategy that links their length, base diameter d 0 , Young’s modulus E and friction force per unit area μ p 0 . This principle can be framed simply as $${d}_{0} \approx {(\mu {p}_{0}/E)}^{1/3}L$$ d 0 ≈ ( μ p 0 / E ) 1 / 3 L . Existing data from measurements on viruses, algae, marine invertebrates, terrestrial invertebrates, plants, terrestrial vertebrates, marine vertebrates—as well as man-made objects such as nails, needles and weapons—are consistent with our predictions. Our results highlight the evolutionary adaptation of mechanical traits to the constraints imposed by friction, elastic stability and cost. The structures of stingers of living organisms are surprisingly similar despite their vastly different lengths. Now, stingers are found to obey a unifying mechanistic principle that characterizes the stingers resistance to buckling.",0.0434754341840744,19
attach_permanently,83,"The immunogenetics of sexual parasitism. Reconfiguring an immune response The deep sea is a vast and generally empty environment. Finding a mate can thus be difficult. In response to this situation, one group of deep-sea denizens, the anglerfishes, have evolved a system in which males attach to females, in some cases permanently, through fusion of tissues and connection of circulatory systems. Such attachment greatly challenges the immune systems of the fish. Swann et al. found that these challenges have been met by the evolution of increasingly reduced immune responses among anglerfish species, including the loss of what have been considered essential vertebrate responses. These shifts suggest that vertebrate immune systems may be more flexible over evolutionary time than was previously thought. Science, this issue p. 1608 Anglerfish display altered immune responses to accommodate an unusual male attachment reproductive strategy. Sexual parasitism has evolved as a distinctive mode of reproduction among deep-sea anglerfishes. The permanent attachment of males to host females observed in these species represents a form of anatomical joining, which is otherwise unknown in nature. Pronounced modifications to immune facilities are associated with this reproductive trait. The genomes of species with temporarily attaching males lack functional aicda genes that underpin affinity maturation of antibodies. Permanent attachment is associated with additional alterations, culminating in the loss of functional rag genes in some species, abolishing somatic diversification of antigen receptor genes, the hallmark of canonical adaptive immunity. In anglerfishes, coevolution of innate and adaptive immunity has been disentangled, implying that an alternative form of immunity supported the emergence of this evolutionarily successful group of vertebrates.",0.0425180085003376,20
protect_from_loss_of_liquids,2,"Hypoxia and Anoxia Tolerance in the Annual Killifish Austrofundulus limnaeus.. Embryos of the annual killifish Austrofundulus limnaeus are routinely exposed to oxygen limitation during development and are extremely tolerant of anoxia. Importantly, tolerance of anoxia is not strictly associated with entrance into metabolic dormancy associated with diapause II, but rather any embryo will respond to anoxia by entering into a state of anoxia-induced quiescence. Hypoxia causes a reduction in the rate of development, reduced heart rates, and reduced capacities for metabolic enzyme activity in both aerobic and anaerobic pathways. Embryos of A. limnaeus begin life as oxyconformers, and transition into oxyregulators near the completion of embryonic development. As this transition occurs, extreme anoxia tolerance is lost. The rate of early development is independent of oxygen partial pressure, despite the fact that the embryos are oxyconformers. This suggests a contribution from anaerobic pathways to support early development. However, the specific pathways supporting this metabolism are unknown. The response of A. limnaeus embryos to hypoxia and anoxia is unique compared to other fishes and most other vertebrates, and thus future studies on this species may lend insight into novel mechanisms that support survival during prolonged oxygen limitation.",0.8329682350158691,1
protect_from_loss_of_liquids,157,"Communication versus waterproofing: the physics of insect cuticular hydrocarbons. ABSTRACT Understanding the evolution of complex traits is among the major challenges in biology. One such trait is the cuticular hydrocarbon (CHC) layer in insects. It protects against desiccation and provides communication signals, especially in social insects. CHC composition is highly diverse within and across species. To understand the adaptive value of this chemical diversity, we must understand how it affects biological functionality. So far, CHCs have received ample research attention, but their physical properties were little studied. We argue that these properties determine their biological functionality, and are vital to understanding how CHC composition affects their adaptive value. We investigated melting behaviour and viscosity of CHCs from 11 ant species using differential scanning calorimetry and a novel microrheological technique. CHCs began melting below −45°C, and often were entirely liquid only above 30°C. Thus, they formed a solid–liquid mixture under ambient conditions, which contrasts to previous assumptions of entirely solid layers in many species. This may be adaptive as only biphasic CHC layers ensure uniform coating of the insect body, which is necessary for waterproofing. CHC viscosity was mostly between 0.1 and 0.2 Pa s−1, thus similar to motor oils. Surprisingly, chemically different CHC profiles had similar viscosities, suggesting that a certain viscosity level is adaptive and ensures that communication signals can be perceived. With this study, we draw attention to the importance of studying the physics of CHC layers. Only by understanding how chemical and physical mechanisms enable CHC functionality can we understand the causes and consequences of CHC diversification. Summary: Cuticular hydrocarbons protect insects from desiccation and allow chemical communication, and contain both liquid and solid parts. This complex phase behaviour appears vital to ensure biological functioning.",0.8236908912658691,2
protect_from_loss_of_liquids,261,"Gut bacteria are essential for normal cuticle development in herbivorous turtle ants. Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.",0.6967676281929016,3
protect_from_loss_of_liquids,138,Cellulose synthase interactive1- and microtubule-dependent cell wall architecture is required for acid growth in Arabidopsis hypocotyls. We observed a correlation between acid growth and crossed-polylamellate cell walls which was dependent on CSI1 and microtubules. This is significant for re-evaluating current models of cell morphogenesis.,0.3641276955604553,4
protect_from_loss_of_liquids,125,"Life under quartz: Hypolithic mosses in the Mojave Desert. Several species of dryland cyanobacteria are known to occur as hypoliths under semi-translucent rocks. In the Mojave Desert, these organisms find refuge from intense solar radiation under milky quartz where moisture persists for a longer period of time than in adjacent soil surface habitat. Desert mosses, which are extremely desiccation-tolerant, can also occur in these hypolithic spaces, though little is known about this unique moss microhabitat and how species composition compares to that of adjacent soil surface communities. To address this question, we deployed microclimate dataloggers and collected moss samples from under and adjacent to 18 milky quartz rocks (quartz mean center thickness 26 ± 15 mm) in a western high elevation Mojave Desert site. Light transmission through Mojave quartz rocks may be as low as 1.2%, and data from microclimate loggers deployed for five months support the hypothesis that quartz provides thermal buffering and higher relative humidity compared to the soil surface. Of the 53 samples collected from hypolith and surface microhabitats, 68% were Syntrichia caninervis, the dominant bryophyte of the Mojave Desert biological soil crust. Tortula inermis accounted for 28% of the samples and 4% were Bryum argenteum. In a comparison of moss community composition, we found that S. caninervis was more likely to be on the soil surface, though it was abundant in both microhabitats, while T. inermis was more restricted to hypoliths, perhaps due to protection from temperature extremes. In our study site, the differences between hypolithic and surface microhabitats enable niche partitioning between T. inermis and S. caninervis, enhancing alpha diversity. This work points to the need to thoroughly consider microhabitats when assessing bryophyte species diversity and modelling species distributions. This focus is particularly important in extreme environments, where mosses may find refuge from the prevailing macroclimatic conditions in microhabitats such as hypoliths.",0.1901416927576065,5
protect_from_loss_of_liquids,117,"The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings. The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogenesis–but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here we develop and characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-Like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 minutes, and increased transcript levels of mechano-inducible genes within 60 minutes. We also show that cell swelling induces programmed cell death within 3 hours, also in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N-terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.",0.18494489789009094,6
protect_from_loss_of_liquids,27,"Mycosporine‐glutaminol‐glucoside, a UV‐absorbing compound of two Rhodotorula yeast species. High‐performance liquid chromatography (HPLC), alone or in combination with mass spectrometry (MS), was used to screen the basidiomycetous yeasts Rhodotorula minuta and R. slooffiae isolated from lakes for the presence of UV‐absorbing compounds. Mycosporine‐glutaminol‐glucoside (maximum absorption, 310 nm), a UV‐photoprotective mycosporine known in terrestrial fungi, was the major UV‐absorbing compound found in these species. This is the first identification of a mycosporine in yeasts. The presence of this compound seems to be a promising chemotaxonomical marker for yeast systematics. Copyright © 2004 John Wiley & Sons, Ltd.",0.17618130147457123,7
protect_from_loss_of_liquids,179,Effects of temperature on the cuticular transpiration barrier of two desert plants with water-spender and water-saver strategies. The efficacy of the cuticular transpiration barrier and its resistance to elevated temperatures are significantly higher in a typical water-saver than in a water-spender plant growing in hot desert.,0.15461449325084686,8
protect_from_loss_of_liquids,189,"Superhydrophobic diving flies (Ephydra hians) and the hypersaline waters of Mono Lake. Significance Superhydrophobic surfaces have been of key academic and commercial interest since the discovery of the so-called lotus effect in 1977. The effect of different ions on complex superhydrophobic biological systems, however, has received little attention. By bringing together ecology, biomechanics, physics, and chemistry our study provides insight into the ion-specific effects of wetting in the presence of sodium carbonate and its large-scale consequences. By comparing the surface structure and chemistry of the alkali fly—an important food source for migrating birds—to other species we show that their uniquely hydrophobic properties arise from very small physical and chemical changes, thereby connecting picoscale physics with globally important ecological impacts. The remarkable alkali fly, Ephydra hians, deliberately crawls into the alkaline waters of Mono Lake to feed and lay eggs. These diving flies are protected by an air bubble that forms around their superhydrophobic cuticle upon entering the lake. To study the physical mechanisms underlying this process we measured the work required for flies to enter and leave various aqueous solutions. Our measurements show that it is more difficult for the flies to escape from Mono Lake water than from fresh water, due to the high concentration of Na2CO3 which causes water to penetrate and thus wet their setose cuticle. Other less kosmotropic salts do not have this effect, suggesting that the phenomenon is governed by Hofmeister effects as well as specific interactions between ion pairs. These effects likely create a small negative charge at the air–water interface, generating an electric double layer that facilitates wetting. Compared with six other species of flies, alkali flies are better able to resist wetting in a 0.5 M Na2CO3 solution. This trait arises from a combination of factors including a denser layer of setae on their cuticle and the prevalence of smaller cuticular hydrocarbons compared with other species. Although superbly adapted to resisting wetting, alkali flies are vulnerable to getting stuck in natural and artificial oils, including dimethicone, a common ingredient in sunscreen and other cosmetics. Mono Lake’s alkali flies are a compelling example of how the evolution of picoscale physical and chemical changes can allow an animal to occupy an entirely new ecological niche.",0.09351319819688797,9
protect_from_loss_of_liquids,45,"Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi. Extracellular vesicles (EVs) are produced by all domains of life. In Gram-negative bacteria, EVs are produced by the pinching off of the outer membrane; however, how EVs escape the thick cell walls of Gram-positive bacteria, mycobacteria and fungi is still unknown. Nonetheless, EVs have been described in a variety of cell-walled organisms, including Staphylococcus aureus, Mycobacterium tuberculosis and Cryptococcus neoformans. These EVs contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes, and have important roles in microbial physiology and pathogenesis. In this Review, we describe the current status of vesiculogenesis research in thick-walled microorganisms and discuss the cargo and functions associated with EVs in these species.",0.08104582875967026,10
protect_from_loss_of_liquids,68,"Tillandsia-Inspired Hygroscopic Photothermal Organogels for Efficient Atmospheric Water Harvesting.. Tillandsia species with degenerated roots have evolved into hygroscopic leaves that absorb moisture from air. This interesting biological adaptability has inspired us to develop an integrated hygroscopic photothermal organogel (POG) to achieve a solar-powered atmospheric water harvesting (AWH). The well-designed hydrophilic co-polymeric skeleton is fabricated to accommodate hygroscopic glycerin medium, which enables the POG self-contained property, mechanically flexibility and synergistic enhancement of moisture sorption. The integration of interpenetrated photothermal component of poly-pyrrole-dopamine (P-Py-DA) can endow the POG an efficient solar-to-thermal property for controllable solar-driven interfacial water releasing. The integrated POG has an equilibrium moisture sorption of 16.01 kg m-2 at the RH of 90 %, and daily water production as high as 2.43 kg m-2 day-1 is achieved in actual outdoor experiments.",0.06433272361755371,11
protect_from_loss_of_liquids,21,"Ultrastructural architecture of the microtrichia of the insect cuticle. The ultrastructure of the microtrichia (MT) of the insect cuticle was studied using scanning electron microscopy (SEM). After dissolving the protein matrix of chitin‐protein microfibrils with NaOH, the orientation of the axial chitin fibers was three‐dimensionally demonstrated. Microfibrils of the outermost exocuticular lamella lie parallel to the slope of the cone surface of the MT and rotate slightly on the top of the MT. Microfibrils of the external lamella of the transitional area between planar cuticle and conical cuticle of the MT corresponded to the shape of the surface within one lamella and preferred directions of MT's microfibrils in the successive lamella rotated. In the deeper layers of the cuticle, the rotation of both the microfibrils and successive lamella results in the twisted straw architecture of the microfibrils' composition within the MT. The deepest microfibrils that are located close to the axis of the MT form compact clusters of fibrils (1.0–1.5 μm length). The twisted‐straw architecture of microfibrils in the MT is derived from principles of development of extracellular fibrous composites. It is suggested, however, that this architecture has an additional functional significance as a strategic design with particular mechanical properties. J. Morphol. 234:1–10, 1997. © 1997 Wiley‐Liss, Inc.",0.05765087902545929,12
protect_from_loss_of_liquids,9,"Hypoxic survival strategies in two fishes: extreme anoxia tolerance in the North European crucian carp and natural hypoxic preconditioning in a coral-reef shark. SUMMARY Especially in aquatic habitats, hypoxia can be an important evolutionary driving force resulting in both convergent and divergent physiological strategies for hypoxic survival. Examining adaptations to anoxic/hypoxic survival in hypoxia-tolerant animals may offer fresh ideas for the treatment of hypoxia-related diseases. Here, we summarise our present knowledge of two fishes that have evolved to survive hypoxia under very different circumstances. The crucian carp (Carassius carassius) is of particular interest because of its extreme anoxia tolerance. During the long North European winter, it survives for months in completely oxygen-deprived freshwater habitats. The crucian carp also tolerates a few days of anoxia at room temperature and, unlike anoxia-tolerant freshwater turtles, it is still physically active in anoxia. Moreover, the crucian carp does not appear to reduce neuronal ion permeability during anoxia and may primarily rely on more subtle neuromodulatory mechanisms for anoxic metabolic depression. The epaulette shark (Hemiscyllium ocellatum) is a tropical marine vertebrate. It lives on shallow reef platforms that repeatedly become cut off from the ocean during periods of low tides. During nocturnal low tides, the water [O2] can fall by 80% due to respiration of the coral and associated organisms. Since the tides become lower and lower over a period of a few days, the hypoxic exposure during subsequent low tides will become progressively longer and more severe. Thus, this shark is under a natural hypoxic preconditioning regimen. Interestingly, hypoxic preconditioning lowers its metabolic rate and its critical PO2. Moreover, repeated anoxia appears to stimulate metabolic depression in an adenosine-dependent way.",0.054849568754434586,13
protect_from_loss_of_liquids,133,"Comparative Analysis of Tear Composition in Humans, Domestic Mammals, Reptiles, and Birds. Tears are an important component of the ocular surface protection mechanism and are in close contact with the corneal epithelium and the environment. Their composition is well-known in humans; however, there are few investigations on the composition and function of tears in reptiles, birds and others mammals, which would elucidate the mechanisms governing the maintenance of ocular homeostasis. In this work, electrophoretic profiles and an evaluation of total protein, albumin, urea, glucose, and cholesterol concentrations in tears of semi-aquatic, terrestrial, and marine reptiles (Caiman latirostris, Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Lepidochelys olivacea, and Chelonoidis carbonaria), birds (Tyto furcata, Rupornis magnirostris and Ara ararauna), and mammals (Equus caballus and Canis lupus familiaris) were apresented. Human tear components and respective blood serum samples were used as references. The electrophoretic analysis revealed similarities whithin same Classes. The results of the tear–blood serum relationship and the comparison to human tear components showed particularities that are potentially derived from a homeostatic response to the environment. When the tear compositions of animals belonging to different ecological clusters were compared, marked differences were observed in total protein and urea concentrations. Thus, reptile, bird, and mammalian tears are complex fluids with differing concentrations of biochemical components that are potentially a result of the animals' adaptation to different environments.",0.04932519048452377,14
protect_from_loss_of_liquids,55,"Metabolic rate in common shrews is unaffected by temperature, leading to lower energetic costs through seasonal size reduction. Small endothermic mammals have high metabolisms, particularly at cold temperatures. In the light of this, some species have evolved a seemingly illogical strategy: they reduce the size of the brain and several organs to become even smaller in winter. To test how this morphological strategy affects energy consumption across seasonally shifting ambient temperatures, we measured oxygen consumption and behaviour in the three seasonal phenotypes of the common shrew (Sorex araneus), which differ in size by about 20%. Body mass was the main driver of oxygen consumption, not the reduction of metabolically expensive brain mass. Against our expectations, we found no change in relative oxygen consumption with low ambient temperature. Thus, smaller body size in winter resulted in significant absolute energy savings. This finding could only partly be explained by an increase of lower cost behaviours in the activity budgets. Our findings highlight that these shrews manage to avoid one of the most fundamental and intuitive rules of ecology, allowing them to subsist with lower resource availability and successfully survive the harsh conditions of winter.",0.042632028460502625,15
protect_from_loss_of_liquids,19,"Bionic photovoltaic panels bio-inspired by green leaves. In strong solar light, silicon solar panels can heat up by 70°C and, thereby, loose approximately one third of their efficiency for electricity generation. Leaf structures of plants on the other hand, have developed a series of technological adaptations, which allow them to limit their temperature to 40–45°C in full sunlight, even if water evaporation is suppressed. This is accomplished by several strategies such as limitation of leaf size, optimization of aerodynamics in wind, limitation of absorbed solar energy only to the useful fraction of radiation and by efficient thermal emission. Optical and infrared thermographic measurements under a solar simulator and in a streaming channel were used to investigate the corresponding properties of leaves and to identify suitable bionic model systems. Experiments started with the serrated structure of ordinary green leaves distributed over typical twig structures and finally identified the Australian palm tree Licuala ramsayi as a more useful bionic model. It combines a large area for solar energy harvesting with optimized aerodynamic properties for cooling and is able to restructure itself as a protection against strong winds. The bionic models, which were constructed and built, are analyzed and discussed.",0.04183107241988182,16
protect_from_loss_of_liquids,74,"Nest Carbon Dioxide Masks GABA-Dependent Seizure Susceptibility in the Naked Mole-Rat. African naked mole-rats were likely the first mammals to evolve eusociality, and thus required adaptations to conserve energy and tolerate the low oxygen (O2) and high carbon dioxide (CO2) of a densely populated fossorial nest. As hypercapnia is known to suppress neuronal activity, we studied whether naked mole-rats might demonstrate energy savings in GABAergic inhibition. Using whole-colony behavioral monitoring of captive naked mole-rats, we found a durable nest, characterized by high CO2 levels, where all colony members spent the majority of their time. Analysis of the naked mole-rat genome revealed, uniquely among mammals, a histidine point variation in the neuronal potassium-chloride cotransporter 2 (KCC2). A histidine missense substitution mutation at this locus in the human ortholog of KCC2, found previously in patients with febrile seizures and epilepsy, has been demonstrated to diminish neuronal Cl- extrusion capacity, and thus impairs GABAergic inhibition. Seizures were observed, without pharmacological intervention, in adult naked mole-rats exposed to a simulated hyperthermic surface environment, causing systemic hypocapnic alkalosis. Consistent with the diminished function of KCC2, adult naked mole-rats demonstrate a reduced efficacy of inhibition that manifests as triggering of seizures at room temperature by the GABAA receptor (GABAAR) positive allosteric modulator diazepam. These seizures are blocked in the presence of nest-like levels of CO2 and likely to be mediated through GABAAR activity, based on in vitro recordings. Thus, altered GABAergic inhibition adds to a growing list of adaptations in the naked mole-rat and provides a plausible proximate mechanism for nesting behavior, where a return to the colony nest restores GABA-mediated inhibition.",0.04076381027698517,17
protect_from_loss_of_liquids,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.03610238805413246,18
protect_from_loss_of_liquids,34,"Antifreeze glycoprotein activity correlates with long-range protein-water dynamics.. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) enable the survival of organisms living in subfreezing habitats and serve as preservatives. Although their function is known, the underlying molecular mechanism was not understood. Mutagenesis experiments questioned the previous assumption of hydrogen bonding as the dominant mechanism. We use terahertz spectroscopy to show that antifreeze activity is directly correlated with long-range collective hydration dynamics. Our results provide evidence for a new model of how AFGPs prevent water from freezing. We suggest that antifreeze activity may be induced because the AFGP perturbs the aqueous solvent over long distances. Retarded water dynamics in the large hydration shell does not favor freezing. The complexation of the carbohydrate cis-hydroxyl groups by borate suppresses the long-range hydration shell detected by terahertz absorption. The hydration dynamics shift toward bulk water behavior strongly reduces the AFGP antifreeze activity, further supporting our model.",0.03487386554479599,19
protect_from_loss_of_liquids,60,"Exploring the Role of Habitat on the Wettability of Cicada Wings.. Evolutionary pressure has pushed many extant species to develop micro/nanostructures that can significantly affect wettability and enable functionalities such as droplet jumping, self-cleaning, antifogging, antimicrobial, and antireflectivity. In particular, significant effort is underway to understand the insect wing surface structure to establish rational design tools for the development of novel engineered materials. Most studies, however, have focused on superhydrophobic wings obtained from a single insect species, in particular, the Psaltoda claripennis cicada. Here, we investigate the relationship between the spatially dependent wing wettability, topology, and droplet jumping behavior of multiple cicada species and their habitat, lifecycle, and interspecies relatedness. We focus on cicada wings of four different species: Neotibicen pruinosus, N. tibicen, Megatibicen dorsatus, and Magicicada septendecim and take a comparative approach. Using spatially resolved microgoniometry, scanning electron microscopy, atomic force microscopy, and high speed optical microscopy, we show that within cicada species, the wettability of wings is spatially homogeneous across wing cells. All four species were shown to have truncated conical pillars with widely varying length scales ranging from 50 to 400 nm in height. Comparison of the wettability revealed three cicada species with wings that are superhydrophobic (>150°) with low contact angle hysteresis (<5°), resulting in stable droplet jumping behavior. The fourth, more distantly related species (Ma. septendecim) showed only moderate hydrophobic behavior, eliminating some of the beneficial surface functional aspects for this cicada. Correlation between cicada habitat and wing wettability yielded little connection as wetter, swampy environments do not necessarily equate to higher measured wing hydrophobicity. The results, however, do point to species relatedness and reproductive strategy as a closer proxy for predicting wettability and surface structure and resultant enhanced wing surface functionality. This work not only elucidates the differences between inter- and intraspecies cicada wing topology, wettability, and water shedding behavior but also enables the development of rational design tools for the manufacture of artificial surfaces for energy and water applications.",0.03447815403342247,20
actively_move_through_gases,256,"Butterflies fly using efficient propulsive clap mechanism owing to flexible wings. Butterflies look like no other flying animal, with unusually short, broad and large wings relative to their body size. Previous studies have suggested butterflies use several unsteady aerodynamic mechanisms to boost force production with upstroke wing clap being a prominent feature. When the wings clap together at the end of upstroke the air between the wings is pressed out, creating a jet, pushing the animal in the opposite direction. Although viewed, for the last 50 years, as a crucial mechanism in insect flight, quantitative aerodynamic measurements of the clap in freely flying animals are lacking. Using quantitative flow measurements behind freely flying butterflies during take-off and a mechanical clapper, we provide aerodynamic performance estimates for the wing clap. We show that flexible butterfly wings, forming a cupped shape during the upstroke and clap, thrust the butterfly forwards, while the downstroke is used for weight support. We further show that flexible wings dramatically increase the useful impulse (+22%) and efficiency (+28%) of the clap compared to rigid wings. Combined, our results suggest butterflies evolved a highly effective clap, which provides a mechanistic hypothesis for their unique wing morphology. Furthermore, our findings could aid the design of man-made flapping drones, boosting propulsive performance.",0.9013339877128601,1
actively_move_through_gases,314,"Dragonfly wing nodus: A one-way hinge contributing to the asymmetric wing deformation.. Dragonfly wings are highly specialized locomotor systems, which are formed by a combination of several structural components. The wing components, also known as structural elements, are responsible for the various aspects of the wing functionality. Considering the complex interactions between the wing components, modelling of the wings as a whole is only possible with inevitable huge oversimplifications. In order to overcome this difficulty, we have recently proposed a new approach to model individual components of complex wings comparatively. Here, we use this approach to study nodus, a structural element of dragonfly wings which has been less studied to date. Using a combination of several imaging techniques including scanning electron microscopy (SEM), wide-field fluorescence microscopy (WFM), confocal laser scanning microscopy (CLSM) and micro-computed tomography (micro-CT) scanning, we aim to characterize the spatial morphology and material composition of fore- and hindwing nodi of the dragonfly Brachythemis contaminata. The microscopy results show the presence of resilin in the nodi, which is expected to help the deformability of the wings. The computational results based on three-dimensional (3D) structural data suggest that the specific geometry of the nodus restrains its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is expected to contribute to the dorso-ventral asymmetry of wing deformation and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings.


STATEMENT OF SIGNIFICANCE
In this study, we investigate the wing nodus, a specialized wing component in dragonflies. Using a combination of modern imaging techniques, we demonstrate the presence of resilin in the nodus, which is expected to facilitate the wing deformability in flight. The specific geometry of the nodus, however, seems to restrain its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is suggested to contribute to dorso-ventral asymmetry of wing deformations and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings and might help to design more efficient wings for biomimetic micro-air vehicles.",0.8735840916633606,2
actively_move_through_gases,212,"Bird wings act as a suspension system that rejects gusts. Musculoskeletal systems cope with many environmental perturbations without neurological control. These passive preflex responses aid animals to move swiftly through complex terrain. Whether preflexes play a substantial role in animal flight is uncertain. We investigated how birds cope with gusty environments and found that their wings can act as a suspension system, reducing the effects of vertical gusts by elevating rapidly about the shoulder. This preflex mechanism rejected the gust impulse through inertial effects, diminishing the predicted impulse to the torso and head by 32% over the first 80 ms, before aerodynamic mechanisms took effect. For each wing, the centre of aerodynamic loading aligns with the centre of percussion, consistent with enhancing passive inertial gust rejection. The reduced motion of the torso in demanding conditions simplifies crucial tasks, such as landing, prey capture and visual tracking. Implementing a similar preflex mechanism in future small-scale aircraft will help to mitigate the effects of gusts and turbulence without added computational burden.",0.8650226593017578,3
actively_move_through_gases,211,"Aerodynamic performance of flexible flapping wings deformed by slack angle.. Wing flexibility is unavoidable for flapping wing flyers to ensure a lightweight body and for higher payload allowances on board. It also effectively minimizes the inertia force from high-frequency wingbeat motion. However, related studies that attempt to clarify the essence of wing flexibility remain insufficient. Here, a parametric study of a flexible wing was conducted as part of the effort to build an aerodynamic model and analyze its aerodynamic performance. The Quasi-steady (QS) modelling was adopted with experimentally determined translational forces. These forces were determined from 84 flexible wing cases while varying the angle of attack at the wing root and the flexibility parameter, slack angle , with 19 additional rigid wing cases. This study found for optimum lift generation to exceed 45° irrespective of . The coefficient curves were well-fitted with a cubed-sine function. The model was rigorously validated with various wing kinematics, giving a good estimation of the experimental results. The estimated error was less than 5%, 6%, and 8% for the lift, drag, and moment, respectively, considering fast to moderate wing kinematics. The study was extended to analyze the pure aerodynamic performance of the flexible wing. The most suitable wing for a flapping-wing micro-aerial vehicle (FWMAV) wing design with a simple vein structure was found to be the 5° slack-angled wing. The inference from this study further shows that a small amount of deformation is needed to increase the lift, as observed in natural flyers. Thus, wing deformation could allow living flyers to undertake less pitching motion in order to reduce the mechanical power and increase the efficiency of their wings.",0.8570712208747864,4
actively_move_through_gases,170,"Physical limits of flight performance in the heaviest soaring bird. Significance Flapping flight is extremely costly for large birds, yet little is known about the conditions that force them to flap. We attached custom-made “flight recorders” to Andean condors, the world’s heaviest soaring birds, documenting every single wingbeat and when and how individuals gained altitude. Remarkably, condors flapped for only 1% of their flight time, specifically during takeoff and when close to the ground. This is particularly striking as the birds were immature. Thus, our results demonstrate that even inexperienced birds can cover vast distances over land without flapping. Overall, this can help explain how extinct birds with twice the wingspan of condors could have flown. Flight costs are predicted to vary with environmental conditions, and this should ultimately determine the movement capacity and distributions of large soaring birds. Despite this, little is known about how flight effort varies with environmental parameters. We deployed bio-logging devices on the world’s heaviest soaring bird, the Andean condor (Vultur gryphus), to assess the extent to which these birds can operate without resorting to powered flight. Our records of individual wingbeats in >216 h of flight show that condors can sustain soaring across a wide range of wind and thermal conditions, flapping for only 1% of their flight time. This is among the very lowest estimated movement costs in vertebrates. One bird even flew for >5 h without flapping, covering ∼172 km. Overall, > 75% of flapping flight was associated with takeoffs. Movement between weak thermal updrafts at the start of the day also imposed a metabolic cost, with birds flapping toward the end of glides to reach ephemeral thermal updrafts. Nonetheless, the investment required was still remarkably low, and even in winter conditions with weak thermals, condors are only predicted to flap for ∼2 s per kilometer. Therefore, the overall flight effort in the largest soaring birds appears to be constrained by the requirements for takeoff.",0.8086175322532654,5
actively_move_through_gases,67,"Alcids ‘fly’ at efficient Strouhal numbers in both air and water but vary stroke velocity and angle. Birds that use their wings for ‘flight’ in both air and water are expected to fly poorly in each fluid relative to single-fluid specialists; that is, these jacks-of-all-trades should be the masters of none. Alcids exhibit exceptional dive performance while retaining aerial flight. We hypothesized that alcids maintain efficient Strouhal numbers and stroke velocities across air and water, allowing them to mitigate the costs of their ‘fluid generalism’. We show that alcids cruise at Strouhal numbers between 0.10 and 0.40 – on par with single-fluid specialists – in both air and water but flap their wings ~ 50% slower in water. Thus, these species either contract their muscles at inefficient velocities or maintain a two-geared muscle system, highlighting a clear cost to using the same morphology for locomotion in two fluids. Additionally, alcids varied stroke-plane angle between air and water and chord angle during aquatic flight, expanding their performance envelope.",0.7271378040313721,6
actively_move_through_gases,10,"Aerodynamic force generation, performance and control of body orientation during gliding in sugar gliders (Petaurus breviceps). SUMMARY Gliding has often been discussed in the literature as a possible precursor to powered flight in vertebrates, but few studies exist on the mechanics of gliding in living animals. In this study I analyzed the 3D kinematics of sugar gliders (Petaurus breviceps) during short glides in an enclosed space. Short segments of the glide were captured on video, and the positions of marked anatomical landmarks were used to compute linear distances and angles, as well as whole body velocities and accelerations. From the whole body accelerations I estimated the aerodynamic forces generated by the animals. I computed the correlations between movements of the limbs and body rotations to examine the control of orientation during flight. Finally, I compared these results to those of my earlier study on the similarly sized and distantly related southern flying squirrel (Glaucomys volans). The sugar gliders in this study accelerated downward slightly (1.0±0.5 m s–2), and also accelerated forward (2.1±0.6 m s–2) in all but one trial, indicating that the body weight was not fully supported by aerodynamic forces and that some of the lift produced forward acceleration rather than just balancing body weight. The gliders used high angles of attack (44.15±3.12°), far higher than the angles at which airplane wings would stall, yet generated higher lift coefficients (1.48±0.18) than would be expected for a stalled wing. Movements of the limbs were strongly correlated with body rotations, suggesting that sugar gliders make extensive use of limb movements to control their orientation during gliding flight. In addition, among individuals, different limb movements were associated with a given body rotation, suggesting that individual variation exists in the control of body rotations. Under similar conditions, flying squirrels generated higher lift coefficients and lower drag coefficients than sugar gliders, yet had only marginally shallower glides. Flying squirrels have a number of morphological specializations not shared by sugar gliders that may help to explain their greater lift generating performance.",0.696100652217865,7
actively_move_through_gases,56,"The jumping mechanism of flea beetles (Coleoptera, Chrysomelidae, Alticini), its application to bionics and preliminary design for a robotic jumping leg.. Flea beetles (Coleoptera, Chrysomelidae, Galerucinae, Alticini) are a hyperdiverse group of organisms with approximately 9900 species worldwide. In addition to walking as most insects do, nearly all the species of flea beetles have an ability to jump and this ability is commonly understood as one of the key adaptations responsible for its diversity. Our investigation of flea beetle jumping is based on high-speed filming, micro-CT scans and 3D reconstructions, and provides a mechanical description of the jump. We reveal that the flea beetle jumping mechanism is a catapult in nature and is enabled by a small structure in the hind femur called an 'elastic plate' which powers the explosive jump and protects other structures from potential injury. The explosive catapult jump of flea beetles involves a unique 'high-efficiency mechanism' and 'positive feedback mechanism'. As this catapult mechanism could inspire the design of bionic jumping limbs, we provide a preliminary design for a robotic jumping leg, which could be a resource for the bionics industry.",0.6806385517120361,8
actively_move_through_gases,201,"Undulation enables gliding in flying snakes. When flying snakes glide, they use aerial undulation. To determine if aerial undulation is a flight control strategy or a non-functional behavioural vestige of lateral undulation, we measured snake glides using high-speed motion capture and developed a new dynamical model of gliding. Reconstructions of the snake’s wing-body reveal that aerial undulation is composed of horizontal and vertical waves, whose phases differ by 90° and whose frequencies differ by a factor of two. Using these results, we developed a three-dimensional mathematical model of snake flight that incorporates aerodynamic and inertial effects. Although simulated glides without undulation attained some horizontal distance, they are biologically unrealistic because they failed due to roll and pitch instabilities. In contrast, the inclusion of undulation stabilized the rotational motion and markedly increased glide performance. This work demonstrates that aerial undulation in snakes serves a different function than known uses of undulation in other animals, and suggests a new template of control for dynamic flying robots. Observations of flying snakes inform the development of a dynamical model of gliding taking undulation into account. This work suggests that aerial undulation has a different function in snakes than in other animals.",0.6367154121398926,9
actively_move_through_gases,141,"How do hoverflies use their righting reflex?. ABSTRACT When taking off from a sloping surface, flies have to reorient themselves dorsoventrally and stabilize their body by actively controlling their flapping wings. We have observed that righting is achieved solely by performing a rolling manoeuvre. How flies manage to do this has not yet been elucidated. It was observed here for the first time that hoverfly reorientation is entirely achieved within 6 wingbeats (48.8 ms) at angular roll velocities of up to 10×103 deg s−1 and that the onset of their head rotation consistently follows that of their body rotation after a time lag of 16 ms. The insects' body roll was found to be triggered by the asymmetric wing stroke amplitude, as expected. The righting process starts immediately with the first wingbeat and seems unlikely to depend on visual feedback. A dynamic model for the fly's righting reflex is presented, which accounts for the head/body movements and the time lag recorded in these experiments. This model consists of a closed-loop control of the body roll, combined with a feedforward control of the head/body angle. During the righting manoeuvre, a strong coupling seems to exist between the activation of the halteres (which measure the body's angular speed) and the gaze stabilization reflex. These findings again confirm the fundamental role played by the halteres in both body and head stabilization processes. Summary: Hoverfly righting is achieved by performing a rolling manoeuvre; reorientation is achieved within 6 wingbeats and hoverfly head rotation follows that of their body after a time lag of 16 ms.",0.5922451615333557,10
actively_move_through_gases,203,"Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography. Significance Hindwings in ladybird beetles successfully achieve compatibility between the deformability (instability) required for wing folding and strength property (stability) required for flying. This study demonstrates how ladybird beetles address these two conflicting requirements by an unprecedented technique using artificial wings. Our results, which clarify the detailed wing-folding process and reveal the supporting structures, provide indispensable initial knowledge for revealing this naturally evolved optimization system. Investigating the characteristics in the venations and crease patterns revealed in this study could provide an innovative designing method, enabling the integration of structural stability and deformability, and thus could have a considerable impact on engineering science. Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: (i) the wing rigidity with relatively thick veins and (ii) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure.",0.4019811749458313,11
actively_move_through_gases,253,"How lovebirds maneuver through lateral gusts with minimal visual information. Significance Pilots need complex instruments and training to safely fly through gusts when their vision is deprived. In contrast, birds fly reliably over open water and at night, despite being more susceptible to gusts due to their much lower flight speeds. We found that even inexperienced lovebirds can navigate through strong opposing gusts in the dark, with only a faint point light source as a beacon. Their ability is surprising, because it was previously thought that diurnal animals needed a visual horizon and image features moving over their retina to maneuver. Instead, lovebirds fixate their head on the beacon while reorienting their body into the gust like a weathervane, enabling them to infer gust angle via neck twist and compensate accordingly. Flying birds maneuver effectively through lateral gusts, even when gust speeds are as high as flight speeds. What information birds use to sense gusts and how they compensate is largely unknown. We found that lovebirds can maneuver through 45° lateral gusts similarly well in forest-, lake-, and cave-like visual environments. Despite being diurnal and raised in captivity, the birds fly to their goal perch with only a dim point light source as a beacon, showing that they do not need optic flow or a visual horizon to maneuver. To accomplish this feat, lovebirds primarily yaw their bodies into the gust while fixating their head on the goal using neck angles of up to 30°. Our corroborated model for proportional yaw reorientation and speed control shows how lovebirds can compensate for lateral gusts informed by muscle proprioceptive cues from neck twist. The neck muscles not only stabilize the lovebirds’ visual and inertial head orientations by compensating low-frequency body maneuvers, but also attenuate faster 3D wingbeat-induced perturbations. This head stabilization enables the vestibular system to sense the direction of gravity. Apparently, the visual horizon can be replaced by a gravitational horizon to inform the observed horizontal gust compensation maneuvers in the dark. Our scaling analysis shows how this minimal sensorimotor solution scales favorably for bigger birds, offering local wind angle feedback within a wingbeat. The way lovebirds glean wind orientation may thus inform minimal control algorithms that enable aerial robots to maneuver in similar windy and dark environments.",0.2511313557624817,12
actively_move_through_gases,180,"Wake-induced ‘slaloming’ response explains exquisite sensitivity of seal whisker-like sensors. Blindfolded harbour seals are able to use their uniquely shaped whiskers to track vortex wakes left by moving animals and identify objects that passed by 30 s earlier, an impressive feat, as the flow features have velocities as low as $1~\text{mm}~\text{s}^{-1}$ . The seals sense while swimming, hence their whiskers are sensitive enough to detect small-scale changes in the flow, while rejecting self-generated flow noise. Here we identify and illustrate a novel flow mechanism, causing a large-amplitude ‘slaloming’ whisker response, which allows artificial whiskers with the identical unique undulatory geometry as those of the harbour seal to detect the features of minute flow fluctuations when placed within wakes. Whereas in open water the whisker responds with very low-amplitude vibration, once within a wake, it oscillates with large amplitude and, importantly, its response frequency coincides with the Strouhal frequency of the upstream cylinder, making the detection of an upstream wake and an estimation of the size and shape of the wake-generating body possible. This mechanism has some similarities with the flow mechanisms observed in actively controlled propulsive foils within upstream wakes and trout swimming behind bluff cylinders in a stream, but there are also differences caused by the unique whisker morphology, which enables it to respond passively and within a much wider parametric range.",0.22967387735843658,13
actively_move_through_gases,52,"The jump of the click beetle (Coleoptera: Elateridae)—energetics and mechanics. Some aspects of the energetics and mechanics of two jumps made by a single specimen of Athous haemorrhoidalis (Fab.) are considered. In the first jump, the 40 mg beetle had a take-off velocity of 2–4 m/s and the jumping action occurred in about 064 ms; in the second jump, the take/off velocity was 2–26 m/s and the jumping action took about 0–53 ms. Energy budgets have been constructed in two different ways for each jump, and the total energy involved in each case was estimated to lie between 1–6 × 10−4 J and 3–8 × 10−4 J. Power output during the jumping action (a “catapult”) lay between 80 × 103 W/kg muscle and 180 × 103 W/kg muscle, whilst power output during the energy storing pre-jump period (of about 0–4 s) was at least 130 W/kg muscle (at over 25°C). Forces and tensile stresses in the jumping muscles and their apodemes have also been calculated. The method of jumping appears to be fairly inefficient in that only about 50–60% of the energy expended in the jumping action is energy of translation, which actually raises the beetle.",0.19575096666812897,14
actively_move_through_gases,306,"Neurophysiological coordination of duet singing. Significance Cooperation, turn taking, and other social behaviors often depend on temporal coordination between individuals. How brains use sensory cues from participants to synchronize performances is not known. We examined the interactions between sensory cues and motor activity in the brains of female and male plain-tailed wrens that rapidly take turns to produce a duet that sounds as if a single bird is singing. We made simultaneous neurophysiological recordings from the brains of pairs of awake, duetting wrens. We discovered that inhibition driven by auditory feedback from the partner alternated with the premotor activity used by each individual to produce its own vocalizations. These data show how sensory feedback links the brains of cooperating animals through the modulation of motor circuits. Coordination of behavior for cooperative performances often relies on linkages mediated by sensory cues exchanged between participants. How neurophysiological responses to sensory information affect motor programs to coordinate behavior between individuals is not known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use acoustic feedback to coordinate extraordinary duet performances in which females and males rapidly take turns singing. We made simultaneous neurophysiological recordings in a song control area “HVC” in pairs of singing wrens at a field site in Ecuador. HVC is a premotor area that integrates auditory feedback and is necessary for song production. We found that spiking activity of HVC neurons in each sex increased for production of its own syllables. In contrast, hearing sensory feedback produced by the bird’s partner decreased HVC activity during duet singing, potentially coordinating HVC premotor activity in each bird through inhibition. When birds sang alone, HVC neurons in females but not males were inhibited by hearing the partner bird. When birds were anesthetized with urethane, which antagonizes GABAergic (γ-aminobutyric acid) transmission, HVC neurons were excited rather than inhibited, suggesting a role for GABA in the coordination of duet singing. These data suggest that HVC integrates information across partners during duets and that rapid turn taking may be mediated, in part, by inhibition.",0.11275491118431091,15
actively_move_through_gases,267,"Dragondrop: a novel passive mechanism for aerial righting in the dragonfly. Dragonflies perform dramatic aerial manoeuvres when chasing targets but glide for periods during cruising flights. This makes dragonflies a great system to explore the role of passive stabilizing mechanisms that do not compromise manoeuvrability. We challenged dragonflies by dropping them from selected inverted attitudes and collected 6-degrees-of-freedom aerial recovery kinematics via custom motion capture techniques. From these kinematic data, we performed rigid-body inverse dynamics to reconstruct the forces and torques involved in righting behaviour. We found that inverted dragonflies typically recover themselves with the shortest rotation from the initial body inclination. Additionally, they exhibited a strong tendency to pitch-up with their head leading out of the manoeuvre, despite the lower moment of inertia in the roll axis. Surprisingly, anaesthetized dragonflies could also complete aerial righting reliably. Such passive righting disappeared in recently dead dragonflies but could be partially recovered by waxing their wings to the anaesthetised posture. Our kinematics data, inverse dynamics model and wind-tunnel experiments suggest that the dragonfly's long abdomen and wing posture generate a rotational tendency and passive attitude recovery mechanism during falling. This work demonstrates an aerodynamically stable body configuration in a flying insect and raises new questions in sensorimotor control for small flying systems.",0.10275889188051224,16
actively_move_through_gases,293,"A controllable dual-catapult system inspired by the biomechanics of the dragonfly larvae’s predatory strike. The independently loaded synchronized dual-catapult system of dragonfly larvae can serve as a model for bioinspired robotics. The biomechanics underlying the predatory strike of dragonfly larvae is not yet understood. Dragonfly larvae are aquatic ambush predators, capturing their prey with a strongly modified extensible mouthpart. The current theory of hydraulic pressure being the driving force of the predatory strike can be refuted by our manipulation experiments and reinterpretation of former studies. Here, we report evidence for an independently loaded synchronized dual-catapult system. To power the ballistic movement of a single specialized mouthpart, two independently loaded springs simultaneously release and actuate two separate joints in a kinematic chain. Energy for the movement is stored by straining an elastic structure at each joint and, possibly, the surrounding cuticle, which is preloaded by muscle contraction. As a proof of concept, we developed a bioinspired robotic model resembling the morphology and functional principle of the extensible mouthpart. Understanding the biomechanics of the independently loaded synchronized dual-catapult system found in dragonfly larvae can be used to control the extension direction and, thereby, thrust vector of a power-modulated robotic system.",0.09914344549179077,17
actively_move_through_gases,36,"Hydrodynamic Trail-Following in Harbor Seals (Phoca vitulina). Marine mammals often forage in dark or turbid waters. Whereas dolphins use echolocation under such conditions, pinnipeds apparently lack this sensory ability. For seals hunting in the dark, one source of sensory information may consist of fish-generated water movements, which seals can detect with their highly sensitive whiskers. Water movements in the wake of fishes persist for several minutes. Here we show that blindfolded seals can use their whiskers to detect and accurately follow hydrodynamic trails generated by a miniature submarine. This shows that hydrodynamic information can be used for long-distance prey location.",0.09364772588014603,18
actively_move_through_gases,114,"Snapping mechanics of the Venus flytrap (Dionaea muscipula). Significance The rapid closure of the carnivorous Venus flytrap (Dionaea muscipula) snap-trap incorporates snap-buckling instability as a speed boost. The trap actuation principles required to overcome the involved energy barrier, as determined by the double-lobe curvature, have remained speculative until now. Here we used 3D digital image correlation for the analysis of trap deformation during closure for both the outer and the inner trap surfaces. Accompanying biomechanical and physiological experiments revealed that successful snapping relies on full trap hydration. In combination with FEM simulations elucidating the mechanical contribution of the various trap tissues to the motion, we show that the trapping mechanics incorporate an elaborate interplay between swelling/shrinking processes of the various tissue layers and the release of trap-internal prestress. The mechanical principles for fast snapping in the iconic Venus flytrap are not yet fully understood. In this study, we obtained time-resolved strain distributions via three-dimensional digital image correlation (DIC) for the outer and inner trap-lobe surfaces throughout the closing motion. In combination with finite element models, the various possible contributions of the trap tissue layers were investigated with respect to the trap’s movement behavior and the amount of strain required for snapping. Supported by in vivo experiments, we show that full trap turgescence is a mechanical–physiological prerequisite for successful (fast and geometrically correct) snapping, driven by differential tissue changes (swelling, shrinking, or no contribution). These are probably the result of the previous accumulation of internal hydrostatic pressure (prestress), which is released after trap triggering. Our research leads to an in-depth mechanical understanding of a complex plant movement incorporating various actuation principles.",0.0864756852388382,19
actively_move_through_gases,222,"Evolution of the acoustic startle response of Mexican cavefish.. The ability to detect threatening stimuli and initiate an escape response is essential for survival and under stringent evolutionary pressure. In diverse fish species, acoustic stimuli activate Mauthner neurons, which initiate a C-start escape response. This reflexive behavior is highly conserved across aquatic species and provides a model for investigating the neural mechanism underlying the evolution of escape behavior. Here, we characterize evolved differences in the C-start response between populations of the Mexican cavefish, Astyanax mexicanus. Cave populations of A. mexicanus inhabit an environment devoid of light and macroscopic predators, resulting in evolved differences in various morphological and behavioral traits. We find that the C-start is present in river-dwelling surface fish and multiple populations of cavefish, but that response kinematics and probability differ between populations. The Pachón population of cavefish exhibits an increased response probability, a slower response latency and speed, and reduction of the maximum bend angle, revealing evolved differences between surface and cave populations. Analysis of the responses of two other independently evolved populations of cavefish, revealed the repeated evolution of reduced angular speed. Investigation of surface-cave hybrids reveals a correlation between angular speed and peak angle, suggesting these two kinematic characteristics are related at the genetic or functional levels. Together, these findings provide support for the use of A. mexicanus as a model to investigate the evolution of escape behavior.",0.06871986389160156,20
send_light_signals_in_the_visible_spectrum,97,"Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Chromatophore organs in cephalopod skin are known to produce ultra-fast changes in appearance for camouflage and communication. Light-scattering pigment granules within chromatocytes have been presumed to be the sole source of coloration in these complex organs. We report the discovery of structural coloration emanating in precise register with expanded pigmented chromatocytes. Concurrently, using an annotated squid chromatophore proteome together with microscopy, we identify a likely biochemical component of this reflective coloration as reflectin proteins distributed in sheath cells that envelop each chromatocyte. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules. These findings offer fresh perspectives on the intricate biophotonic interplay between pigmentary and structural coloration elements tightly co-located within the same dynamic flexible organ - a feature that may help inspire the development of new classes of engineered materials that change color and pattern.Chromatophores in cephalopod skin are known for fast changes in coloration due to light-scattering pigment granules. Here, authors demonstrate structural coloration facilitated by reflectin in sheath cells and offer insights into the interplay between structural and pigmentary coloration elements.",0.8908349871635437,1
send_light_signals_in_the_visible_spectrum,228,"Photonics in nature and bioinspired designs: sustainable approaches for a colourful world. Biological systems possess nanoarchitectures that have evolved for specific purposes and whose ability to modulate the flow of light creates an extraordinary diversity of natural photonic structures. In particular, the striking beauty of the structural colouration observed in nature has inspired technological innovation in many fields. Intense research has been devoted to mimicking the unique vivid colours with newly designed photonic structures presenting stimuli-responsive properties, with remarkable applications in health care, safety and security. This review highlights bioinspired photonic approaches in this context, starting by presenting many appealing examples of structural colours in nature, followed by describing the versatility of fabrication methods and designed coloured structures. A particular focus is given to optical sensing for medical diagnosis, food control and environmental monitoring, which has experienced a significant growth, especially considering the advances in obtaining inexpensive miniaturized systems, more reliability, fast responses, and the use of label-free layouts. Additionally, naturally derived biomaterials and synthetic polymers are versatile and fit many different structural designs that are underlined. Progress in bioinspired photonic polymers and their integration in novel devices is discussed since recent developments have emerged to lift the expectations of smart, flexible, wearable and portable sensors. The discussion is expanded to give emphasis on additional functionalities offered to related biomedical applications and the use of structural colours in new sustainable strategies that could meet the needs of technological development.",0.8648891448974609,2
send_light_signals_in_the_visible_spectrum,150,"Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity. Natural selection on structural color in tarantulas resulted in convergence on color through diverse structural mechanisms. Slight shifts in arrangement within biological photonic nanostructures can produce large color differences, and sexual selection often leads to high color diversity in clades with structural colors. We use phylogenetic reconstruction, electron microscopy, spectrophotometry, and optical modeling to show an opposing pattern of nanostructural diversification accompanied by unusual conservation of blue color in tarantulas (Araneae: Theraphosidae). In contrast to other clades, blue coloration in phylogenetically distant tarantulas peaks within a narrow 20-nm region around 450 nm. Both quasi-ordered and multilayer nanostructures found in different tarantulas produce this blue color. Thus, even within monophyletic lineages, tarantulas have evolved strikingly similar blue coloration through divergent mechanisms. The poor color perception and lack of conspicuous display during courtship of tarantulas argue that these colors are not sexually selected. Therefore, our data contrast with sexual selection that typically produces a diverse array of colors with a single structural mechanism by showing that natural selection on structural color in tarantulas resulted in convergence on similar color through diverse structural mechanisms.",0.8628913760185242,3
send_light_signals_in_the_visible_spectrum,144,"Structural color in Junonia butterflies evolves by tuning scale lamina thickness. In diverse organisms, nanostructures that coherently scatter light create structural color, but how such structures are built remains mysterious. We investigate the evolution and genetic regulation of butterfly scale laminae, which are simple photonic nanostructures. In a lineage of buckeye butterflies artificially selected for blue wing color, we found that thickened laminae caused a color shift from brown to blue. Deletion of the optix patterning gene also altered color via lamina thickening, revealing shared regulation of pigments and lamina thickness. Finally, we show how lamina thickness variation contributes to the color diversity that distinguishes sexes and species throughout the genus Junonia. Thus, quantitatively tuning one dimension of scale architecture facilitates both the microevolution and macroevolution of a broad spectrum of hues. Because the lamina is an intrinsic component of typical butterfly scales, our findings suggest that tuning lamina thickness is an available mechanism to create structural color across the Lepidoptera.",0.8450422883033752,4
send_light_signals_in_the_visible_spectrum,151,"Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin. Significance Green coloration of vertebrates is normally attributed to pigments and structural components inside skin chromatophores cells. However, these components do not account for the vivid blue-green colors of hundreds of species of frogs with sparse chromatophores. Our study shows that green coloration originates in proteins of the serpin superfamily that bind the pigment biliverdin, modulating its absorbance properties. Using a South American treefrog, we demonstrated that these serpins have a clear ecological role in modulating the reflectance properties and rendering animals cryptic in the foliage even in the near-infrared portion of the spectrum. These findings open up exciting research perspectives both in biochemistry and evolution of serpins, as well as in the study of extracellular protein-mediated coloration in vertebrates. Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations—a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism—the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.",0.8421156406402588,5
send_light_signals_in_the_visible_spectrum,62,"A Literal Elytral Rainbow: Tunable Structural Colors Using Single Diamond Biophotonic Crystals in Pachyrrhynchus congestus Weevils.. The brilliant colors of many insects arise from the interference of incident light with complex nanostructured biomaterials that are present in their cuticle. Here, the rainbow-colored spots on the elytra of a snout weevil, Pachyrrhynchus congestus pavonius (Coleoptera: Curculionidae), are investigated using synchrotron small-angle X-ray scattering, scanning electron microscopy, microspectrophotometry, and photonic bandgap modeling. It is shown that the iridescent scales present in the rainbow-hued spots are due to a 3D photonic crystal network of chitin in air with a single diamond (Fd-3m) symmetry. In many insects, different orientations of photonic crystal domains are used to create various hues. In this weevil, however, both the chitin volume fractions as well as the lattice parameters of the biologically self-assembled single diamond nanostructure are varied to achieve the remarkable tuning of the structural colors across the visible light spectrum on a scale-by-scale basis. Uncovering the precise mechanism of color tuning employed by this weevil has important implications for further structural and developmental research on biophotonic nanostructures and may provide fresh impetus for bioinspired and biomimetic multifunctional applications, as synthesis of photonic crystals at visible length scales is currently challenging.",0.8312837481498718,6
send_light_signals_in_the_visible_spectrum,140,"Diverse nanostructures underlie thin ultra-black scales in butterflies. Recently, it has been shown that animals such as jumping spiders, birds, and butterflies have evolved ultra-black coloration comparable to the blackest synthetic materials. Of these, certain papilionid butterflies have reflectances approaching 0.2%, resulting from a polydisperse honeycomb structure. It is unknown if other ultra-black butterflies use this mechanism. Here, we examine a phylogenetically diverse set of butterflies and demonstrate that other butterflies employ simpler nanostructures that achieve ultra-black coloration in scales thinner than synthetic alternatives. Using scanning electron microscopy, we find considerable interspecific variation in the geometry of the holes in the structures, and verify with finite-difference time-domain modeling that expanded trabeculae and ridges, found across ultra-black butterflies, reduce reflectance up to 16-fold. Our results demonstrate that butterflies produce ultra-black by creating a sparse material with high surface area to increase absorption and minimize surface reflection. We hypothesize that butterflies use ultra-black to increase the contrast of color signals. Nature has developed the ability to produce a wide range of optical effects most notably in the butterfly wing. Here, the authors report on the analysis of the structures responsible for ultra-black coloration across different butterflies and combine this with modelling to identify the key characteristics",0.8144243955612183,7
send_light_signals_in_the_visible_spectrum,132,"
 Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color. Viburnum tinus is an evergreen shrub that is native to the Mediterranean region but cultivated widely in Europe and around the world. It produces ripe metallic blue fruits throughout winter [1]. Despite its limited fleshy pulp [2], its high lipid content [3] makes it a valuable resource to the small birds [4] that act as its seed-dispersers [5]. Here, we find that the metallic blue appearance of the fruits is produced by globular lipid inclusions arranged in a disordered multilayer structure. This structure is embedded in the cell walls of the epicarp and underlaid with a dark layer of anthocyanin pigments. The presence of such large, organized lipid aggregates in plant cell walls represents a new mechanism for structural coloration and may serve as an honest signal of nutritional content.",0.7954422235488892,8
send_light_signals_in_the_visible_spectrum,149,"Brilliant angle-independent structural colours preserved in weevil scales from the Swiss Pleistocene. Extant weevils exhibit a remarkable colour palette that ranges from muted monochromatic tones to rainbow-like iridescence, with the most vibrant colours produced by three-dimensional photonic nanostructures housed within cuticular scales. Although the optical properties of these nanostructures are well understood, their evolutionary history is not fully resolved, in part due to a poor knowledge of their fossil record. Here, we report three-dimensional photonic nanostructures preserved in brightly coloured scales of two weevils, belonging to the genus Phyllobius or Polydrusus, from the Pleistocene (16–10 ka) of Switzerland. The scales display vibrant blue, green and yellow hues that resemble those of extant Phyllobius/Polydrusus. Scanning electron microscopy and small-angle X-ray scattering analyses reveal that the subfossil scales possess a single-diamond photonic crystal nanostructure. In extant Phyllobius/Polydrusus, the near-angle-independent blue and green hues function primarily in crypsis. The preservation of far-field, angle-independent structural colours in the Swiss subfossil weevils and their likely function in substrate matching confirm the importance of investigating fossil and subfossil photonic nanostructures to understand the evolutionary origins and diversification of colours and associated behaviours (e.g. crypsis) in insects.",0.7921497821807861,9
send_light_signals_in_the_visible_spectrum,128,"A dynamic broadband reflector built from microscopic silica spheres in the ‘disco’ clam Ctenoides ales. The ‘disco’ or ‘electric’ clam Ctenoides ales (Limidae) is the only species of bivalve known to have a behaviourally mediated photic display. This display is so vivid that it has been repeatedly confused for bioluminescence, but it is actually the result of scattered light. The flashing occurs on the mantle lip, where electron microscopy revealed two distinct tissue sides: one highly scattering side that contains dense aggregations of spheres composed of silica, and one highly absorbing side that does not. High-speed video confirmed that the two sides act in concert to alternate between vivid broadband reflectance and strong absorption in the blue region of the spectrum. Optical modelling suggests that the diameter of the spheres is nearly optimal for scattering visible light, especially at shorter wavelengths which predominate in their environment. This simple mechanism produces a striking optical effect that may function as a signal.",0.7056771516799927,10
send_light_signals_in_the_visible_spectrum,287,"Protective coloration of European vipers throughout the predation sequence. Antipredator adaptations in the form of animal coloration are common and often multifunctional. European vipers (genus Vipera) have a characteristic dorsal zigzag pattern, which has been shown to serve as a warning signal to potential predators. At the same time, it has been suggested to decrease detection risk, and to cause a motion dazzle or flicker–fusion effect during movement. We tested these hypotheses by asking whether (1) the zigzag pattern decreases detection risk and (2) the detection is dependent on the base coloration (grey or brown) or the snake's posture (coiled, basking form or S-shaped, active form). Additionally, (3) we measured the fleeing speed of adders, Vipera berus, and calculated the flicker rate of the zigzag pattern, to see whether it is fast enough to cause a flicker–fusion effect against predators. Our results show that the zigzag pattern reduced detectability regardless of base coloration or posture of the snake. The brown zigzag morph was detected less often than the grey zigzag morph. The fleeing speed of adders appeared to be fast enough to induce a flicker–fusion effect for mammalian predators. However, it is unlikely to be fast enough to induce the flicker–fusion effect for raptors. Our findings highlight that the colour pattern of animals can be multifunctional. The same colour pattern that can decrease detection by predators can also serve as a warning function once detected, and potentially hinder capture during an attack.",0.695356547832489,11
send_light_signals_in_the_visible_spectrum,136,"Ultra-black Camouflage in Deep-Sea Fishes. At oceanic depths >200 m, there is little ambient sunlight, but bioluminescent organisms provide another light source that can reveal animals to visual predators and prey [1-4]. Transparency and mirrored surfaces-common camouflage strategies under the diffuse solar illumination of shallower waters-are conspicuous when illuminated by directed bioluminescent sources due to reflection from the body surface [5, 6]. Pigmentation allows animals to absorb light from bioluminescent sources, rendering them visually undetectable against the dark background of the deep sea [5]. We present evidence suggesting pressure to reduce reflected bioluminescence led to the evolution of ultra-black skin (reflectance <0.5%) in 16 species of deep-sea fishes across seven distantly related orders. Histological data suggest this low reflectance is mediated by a continuous layer of densely packed melanosomes in the exterior-most layer of the dermis [7, 8] and that this layer lacks the unpigmented gaps between pigment cells found in other darkly colored fishes [9-13]. Using finite-difference, time-domain modeling and comparisons with melanosomes found in other ectothermic vertebrates [11, 13-21], we find the melanosomes making up the layer in these ultra-black species are optimized in size and shape to minimize reflectance. Low reflectance results from melanosomes scattering light within the layer, increasing the optical path length and therefore light absorption by the melanin. By reducing reflectance, ultra-black fish can reduce the sighting distance of visual predators more than 6-fold compared to fish with 2% reflectance. This biological example of efficient light absorption via a simple architecture of strongly absorbing and highly scattering particles may inspire new ultra-black materials.",0.6323641538619995,12
send_light_signals_in_the_visible_spectrum,166,"Improved color constancy in honey bees enabled by parallel visual projections from dorsal ocelli. Significance Color sensing requires a capacity to discount the changing color of natural light. We present a biologically validated mathematical solution to this classic problem based on honey bee color vision. The observed spectral tuning of two simple ocellar photoreceptors in the honey bee allows for an optimal color constancy solution to different light environments, including standard CIE (Commission Internationale de l’Eclairage) illuminations, natural forest light, sunlight, or shade. The model is fully supported by a neural pathway potentially allowing for the transfer of spectral information originating from the ocellar photoreceptors to the centralized information processing regions in the brain and explains previously observed behavioral results. This solution to color constancy can be implemented into color imaging systems to enable accurate color interpretation. How can a pollinator, like the honey bee, perceive the same colors on visited flowers, despite continuous and rapid changes in ambient illumination and background color? A hundred years ago, von Kries proposed an elegant solution to this problem, color constancy, which is currently incorporated in many imaging and technological applications. However, empirical evidence on how this method can operate on animal brains remains tenuous. Our mathematical modeling proposes that the observed spectral tuning of simple ocellar photoreceptors in the honey bee allows for the necessary input for an optimal color constancy solution to most natural light environments. The model is fully supported by our detailed description of a neural pathway allowing for the integration of signals originating from the ocellar photoreceptors to the information processing regions in the bee brain. These findings reveal a neural implementation to the classic color constancy problem that can be easily translated into artificial color imaging systems.",0.5729502439498901,13
send_light_signals_in_the_visible_spectrum,289,"Reflectin needs its intensity amplifier: Realizing the potential of tunable structural biophotonics. Underwater camouflage and communication in a family of recently evolved squids are controlled, in part, by the reflectin proteins, which regulate dynamic changes in the color and intensity of light reflected from intracellular Bragg reflectors and Mie scatterers. The reflectins act as a signal transducer, precisely tuning the dimensions and refractive index of the membrane-bounded structural reflectors containing them to an extent exactly proportional to neuronal signaling. This calibration between the activating signal and the output color and intensity of reflectance is governed by the physics of the liquid state of reflectin assemblies, which osmotically fine-tune the dimensions and refractive index of the membrane-bounded structural reflectors containing them. While thin-film or genetically engineered assemblies of reflectin deliver changes in the colors of reflection approximating those of the biological system (as do other proteins and polymers), none has delivered the signal-activated increase in the intensity of reflectance characteristic of the native system. The membrane envelopes (Bragg reflector lamellae and Mie-scattering vesicles) containing the reflectins apparently serve as amplifiers, functionally “impedance matched” to the range of tunable sizes of the reflectin assemblies; reflectin films or assemblies lacking such an amplifier fail to deliver signal-activated increases in reflectance intensity.",0.5513038635253906,14
send_light_signals_in_the_visible_spectrum,255,"Nocturnal visual displays and call description of the cascade specialist glassfrog Sachatamia orejuela. Although most male frogs call to attract females, vocalizations alone can be ineffective long-range signals in certain environments. To increase conspicuousness and counter the background noise generated by rushing water, a few frog species around the world have evolved visual communication modalities in addition to advertisement calls. These species belong to different families on different continents: a clear example of behavioural convergent evolution. Until now, long-distance visual signalling has not been recorded for any species in the glassfrog family (Centrolenidae). Sachatamia orejuela, an exceptionally camouflaged glassfrog species found within the spray zone of waterfalls, has remained poorly studied. Here, we document its advertisement call for the first time — the frequency of which is higher than perhaps any other glassfrog species, likely an evolutionary response to its disruptive acoustic space — as well as a sequence of non-antagonistic visual signals (foot-flagging, hand-waving, and head-bobbing) that we observed at night.",0.529416561126709,15
send_light_signals_in_the_visible_spectrum,290,"A Small Molecule Coordinates Symbiotic Behaviors in a Host Organ. The complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. ABSTRACT The lifelong relationship between the Hawaiian bobtail squid Euprymna scolopes and its microbial symbiont Vibrio fischeri represents a simplified model system for studying microbiome establishment and maintenance. The bacteria colonize a dedicated symbiotic light organ in the squid, from which bacterial luminescence camouflages the host in a process termed counterillumination. The squid host hatches without its symbionts, which must be acquired from the ocean amidst a diversity of nonbeneficial bacteria, such that precise molecular communication is required for initiation of the specific relationship. Therefore it is likely there are specialized metabolites used in the light organ microenvironment to modulate these processes. To identify small molecules that may influence the establishment of this symbiosis, we used imaging mass spectrometry to analyze metabolite production in V. fischeri with altered biofilm production, which correlates directly to colonization capability in its host. “Biofilm-up” and “biofilm-down” mutants were compared to a wild-type strain, and ions that were more abundantly produced by the biofilm-up mutant were detected. Using a combination of structural elucidation and synthetic chemistry, one such signal was determined to be a diketopiperazine, cyclo(d-histidyl-l-proline). This diketopiperazine modulated luminescence in V. fischeri and, using imaging mass spectrometry, was directly detected in the light organ of the colonized host. This work highlights the continued need for untargeted discovery efforts in host-microbe interactions and showcases the benefits of the squid-Vibrio system for identification and characterization of small molecules that modulate microbiome behaviors. IMPORTANCE The complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. We have detected and characterized a diketopiperazine produced by strong biofilm-forming V. fischeri strains that was detectable in the host symbiotic organ, and which influences bacterial luminescence. Biofilm formation and luminescence are critical for initiation and maintenance of the association, respectively, suggesting that the compound may link early and later development stages, providing further evidence that multiple small molecules are important in establishing these beneficial relationships.",0.43114930391311646,16
send_light_signals_in_the_visible_spectrum,111,"Wild hummingbirds discriminate nonspectral colors. Significance Birds have four color cone types in their eyes, compared to three in humans. In theory, this enables birds to discriminate a broad range of colors, including many nonspectral colors. Nonspectral colors are perceived when nonadjacent cone types (sensitive to widely separated parts of the light spectrum) are predominantly stimulated. For humans, purple (stimulation of blue- and red-sensitive cones) is a nonspectral color; birds’ fourth color cone type creates many more possibilities. We trained wild hummingbirds to participate in color vision tests, which revealed that they can discriminate a variety of nonspectral colors, including UV+red, UV+green, purple, and UV+yellow. Additionally, based on an analysis of ∼3,300 plumage and plant colors, we estimate that birds perceive many natural colors as nonspectral. Many animals have the potential to discriminate nonspectral colors. For humans, purple is the clearest example of a nonspectral color. It is perceived when two color cone types in the retina (blue and red) with nonadjacent spectral sensitivity curves are predominantly stimulated. Purple is considered nonspectral because no monochromatic light (such as from a rainbow) can evoke this simultaneous stimulation. Except in primates and bees, few behavioral experiments have directly examined nonspectral color discrimination, and little is known about nonspectral color perception in animals with more than three types of color photoreceptors. Birds have four color cone types (compared to three in humans) and might perceive additional nonspectral colors such as UV+red and UV+green. Can birds discriminate nonspectral colors, and are these colors behaviorally and ecologically relevant? Here, using comprehensive behavioral experiments, we show that wild hummingbirds can discriminate a variety of nonspectral colors. We also show that hummingbirds, relative to humans, likely perceive a greater proportion of natural colors as nonspectral. Our analysis of plumage and plant spectra reveals many colors that would be perceived as nonspectral by birds but not by humans: Birds’ extra cone type allows them not just to see UV light but also to discriminate additional nonspectral colors. Our results support the idea that birds can distinguish colors throughout tetrachromatic color space and indicate that nonspectral color perception is vital for signaling and foraging. Since tetrachromacy appears to have evolved early in vertebrates, this capacity for rich nonspectral color perception is likely widespread.",0.42974206805229187,17
send_light_signals_in_the_visible_spectrum,231,"Biologically inspired LED lens from cuticular nanostructures of firefly lantern. Cuticular nanostructures found in insects effectively manage light for light polarization, structural color, or optical index matching within an ultrathin natural scale. These nanostructures are mainly dedicated to manage incoming light and recently inspired many imaging and display applications. A bioluminescent organ, such as a firefly lantern, helps to out-couple light from the body in a highly efficient fashion for delivering strong optical signals in sexual communication. However, the cuticular nanostructures, except the light-producing reactions, have not been well investigated for physical principles and engineering biomimetics. Here we report a unique observation of high-transmission nanostructures on a firefly lantern and its biological inspiration for highly efficient LED illumination. Both numerical and experimental results clearly reveal high transmission through the nanostructures inspired from the lantern cuticle. The nanostructures on an LED lens surface were fabricated by using a large-area nanotemplating and reconfigurable nanomolding with heat-induced shear thinning. The biologically inspired LED lens, distinct from a smooth surface lens, substantially increases light transmission over visible ranges, comparable to conventional antireflection coating. This biological inspiration can offer new opportunities for increasing the light extraction efficiency of high-power LED packages.",0.38292479515075684,18
send_light_signals_in_the_visible_spectrum,240,"Structure, self-assembly, and properties of a truncated reflectin variant. Significance The investigation of protein-based materials has provided a better understanding of living systems and has led to the development of ubiquitous modern technologies. Within this context, unique cephalopod proteins called reflectins have exhibited promise for biophotonics and bioelectronics applications, but the exploration of reflectins as materials has been hindered by an incomplete understanding of their structures and properties. Here, we resolve the molecular-level structure of a model reflectin variant, establish a straightforward approach to controlling the assembly of this protein, and describe a correlation between its structural characteristics and light-manipulating properties. Taken together, our findings advance current understanding of reflectin-based materials, provide insight into the color-changing capabilities of cephalopods, and afford new opportunities in biochemistry, cellular biology, bioengineering, and optics. Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant’s hierarchical assembly, and establish a direct correlation between the protein’s structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells’ color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.",0.3133437931537628,19
send_light_signals_in_the_visible_spectrum,291,"Hard to catch: experimental evidence supports evasive mimicry. Most research on aposematism has focused on chemically defended prey, but the signalling difficulty of capture remains poorly explored. Similar to classical Batesian and Müllerian mimicry related to distastefulness, such ‘evasive aposematism' may also lead to convergence in warning colours, known as evasive mimicry. A prime candidate group for evasive mimicry are Adelpha butterflies, which are agile insects and show remarkable colour pattern convergence. We tested the ability of naive blue tits to learn to avoid and generalize Adelpha wing patterns associated with the difficulty of capture and compared their response to that of birds that learned to associate the same wing patterns with distastefulness. Birds learned to avoid all wing patterns tested and generalized their aversion to other prey to some extent, but learning was faster with evasive prey compared to distasteful prey. Our results on generalization agree with longstanding observations of striking convergence in wing colour patterns among Adelpha species, since, in our experiments, perfect mimics of evasive and distasteful models were always protected during generalization and suffered the lowest attack rate. Moreover, generalization on evasive prey was broader compared to that on distasteful prey. Our results suggest that being hard to catch may deter predators at least as effectively as distastefulness. This study provides empirical evidence for evasive mimicry, a potentially widespread but poorly understood form of morphological convergence driven by predator selection.",0.3026035726070404,20
distribute_solids,161,"A specialized avian seed dispersal system in a dry-fruited non-photosynthetic plant, Balanophora yakushimensis.. The family Balanophoraceae are among the most unusual of plants because they have aberrant vegetative bodies, highly reduced flowers, and small and reduced embryos (Hansen 1972, Gonzalez et al. 2019). Because the plants lack chlorophyll and are incapable of photosynthesis, they draw nutrition from other organisms. Indeed, like the well-known parasitic plant, Rafflesia, members of the Balanophoraceae acquire both water and nutrients from host plants. They are, therefore, highly specialized root parasites.",0.7724990844726562,1
distribute_solids,188,"The central role of Clark's nutcracker in the dispersal and establishment of whitebark pine. SummaryWhitebark pine (Pinus albicaulis) is known to have its seeds harvested and cached in the soil by Clark's Nutcracker (Nucifraga columbiana), and unretrieved seeds are known to be capable of germinating and establishing new pines. Many other vertebrates also harvest and feed on these seeds, however, and the roles of these animals as dispersers and establishers of whitebark pine has been uncertain. This work demonstrates that birds other than the nutcracker, rodents, and other mammals do not have the requisite behaviors to systematically disperse or establish whitebark pine, and that the pine is therefore dependent on the nutcracker for its regeneration. These findings support previous suggestions that Clark's Nutcracker is a specialized frugivore that has profoundly influenced the ecology and the evolution of whitebark pine.",0.403911828994751,2
distribute_solids,46,"Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival.. The dynamics of forest ecosystems depend largely on the survival of seedlings in their understories, but seedling survival is known to be limited by preemption of light and soil resources by overstory trees. It has been hypothesized that ""common mycorrhizal networks,"" wherein roots of seedlings are linked to overstory trees by symbiotic mycorrhizal fungi, offset some or all of the negative effects of trees on seedlings. Here we report the results of an unambiguous experimental test of this hypothesis in a monodominant Pinus radiata forest. We also tested the hypothesis that adaptive differentiation among plant populations causes local plant genotypes to respond more positively to mycorrhizal networks than nonlocal plant genotypes. Our results demonstrate large positive effects of overstory mycorrhizal networks on seedling survival, along with simultaneous negative effects of tree roots, regardless of whether plant genotypes were locally derived. Physiological and leaf-chemistry measurements suggest that seedlings connected to common mycorrhizal networks benefited from increased access to soil water. The similar magnitude of the positive and negative overstory effects on seedlings and the ubiquity of mycorrhizal networks in forests suggest that mycorrhizal networks fundamentally influence the demographic and community dynamics of forest trees.",0.30012422800064087,3
distribute_solids,204,"Pollen adaptation to ant pollination: a case study from the Proteaceae. Abstract Background and Aims Ant–plant associations are widely diverse and distributed throughout the world, leading to antagonistic and/or mutualistic interactions. Ant pollination is a rare mutualistic association and reports of ants as effective pollinators are limited to a few studies. Conospermum (Proteaceae) is an insect-pollinated genus well represented in the south-western Australia biodiversity hotspot, and here we aimed to evaluate the role of ants as pollinators of C. undulatum. Methods Pollen germination after contact with several species of ants and bees was tested for C. undulatum and five co-flowering species for comparison. We then sampled the pollen load of floral visitors of C. undulatum to assess whether ants carried a pollen load sufficient to enable pollination. Lastly, we performed exclusion treatments to assess the relative effect of flying- and non-flying-invertebrate floral visitors on the reproduction of C. undulatum. For this, we measured the seed set under different conditions: ants exclusion, flying-insects exclusion and control. Key Results Pollen of C. undulatum, along with the other Conospermum species, had a germination rate after contact with ants of ~80 % which did not differ from the effect of bees; in contrast, the other plant species tested showed a drop in the germination rate to ~10 % following ant treatments. Although ants were generalist visitors, they carried a pollen load with 68–86 % of suitable grains. Moreover, ants significantly contributed to the seed set of C. undulatum. Conclusions Our study highlights the complexity of ant–flower interactions and suggests that generalizations neglecting the importance of ants as pollinators cannot be made. Conospermum undulatum has evolved pollen with resistance to the negative effect of ant secretions on pollen grains, with ants providing effective pollination services to this threatened species.",0.27924463152885437,4
distribute_solids,298,"Plant-pollinator interactions between generalists persist over time and space.. Generalist species are the linchpins of networks, as they are important for maintaining network structure and function. Previous studies have shown that interactions between generalists tend to occur consistently across years and sites. However, the link between temporal and spatial interaction persistence across scales remains unclear. To address this gap, we collected data on plant-pollinator interactions throughout the flowering period for five years across six plots in a subalpine meadow in the Rocky Mountains. We found that interactions between generalists tended to persist more in time and space such that interactions near the network core were more frequently recorded across years, within seasons, and among plots. We posit that species' tolerance of environmental variation across time and space plays a key role in generalization by regulating spatiotemporal overlap with interaction partners. Our results imply a role of spatiotemporal environmental variation in organizing species interactions, marrying niche concepts that emphasize species environmental constraints and their community role.",0.18560399115085602,5
distribute_solids,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.1732219010591507,6
distribute_solids,309,"Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes. Significance For decades, the propulsion of sperms has been traditionally attributed to the beating or rotating of the soft tails. However, this work disclosed an unusual swimming model of Ray sperms whose propulsion is from not only the helical tail but also the unique spiral head (i.e., the head can contribute ∼31% of the force in propulsion). Such a propulsion mechanism provides Ray sperms with high adaptability to large environmental viscosities along with advantages in linearity, straightness, and efficiency. This study expands our knowledge on the microorganisms’ motion and provides inspirations for engineering design. We disclose a peculiar rotational propulsion mechanism of Ray sperms enabled by its unusual heterogeneous dual helixes with a rigid spiral head and a soft tail, named Heterogeneous Dual Helixes (HDH) model for short. Different from the conventional beating propulsion of sperm, the propulsion of Ray sperms is from both the rotational motion of the soft helical tail and the rigid spiral head. Such heterogeneous dual helical propulsion style provides the Ray sperm with high adaptability in viscous solutions along with advantages in linearity, straightness, and bidirectional motion. This HDH model is further corroborated by a miniature swimming robot actuated via a rigid spiral head and a soft tail, which demonstrates similar superiorities over conventional ones in terms of adaptability and efficiency under the same power input. Such findings expand our knowledge on microorganisms’ motion, motivate further studies on natural fertilization, and inspire engineering designs.",0.12416395545005798,7
distribute_solids,162,"Sexual and natural selection on pollen morphology in Taraxacum.. PREMISE
Spiny pollen has evolved independently in multiple entomophilous lineages. Sexual selection may act on exine traits that facilitate male mating success by influencing the transfer of pollen from the anther to the body of the pollinator, while natural selection acts to increase pollen survival. We postulated that relative to sexual congeners, apomictic dandelions undergo relaxed selection on traits associated with male mating success.


METHODS
We explored sexual selection on exine traits by measuring the propensity for Taraxacum spp. pollen to attach to hairs of flower-visiting bumblebees (Bombus spp.) or flies (Diptera: Syrphidae and Muscoidea) and assessed natural selection by testing whether pollen traits defend against consumption.


RESULTS
Pollen picked up by bumblebees exhibited a narrower subset of spine-spacing phenotypes, consistent with stabilizing selection. Flies picked up larger pollen from flowers than expected at random. Surveys of corbiculae (pollen basket) contents from foraging bumblebees and feces of flies showed that pollen grains consumed by both kinds of visitors are similar in spine characteristics and size to those produced by the donor. When bees visit inflorescences of apomictic T. officinale, they pick up pollen with spine-spacing phenotypes above the mean and shifted toward those of sexual T. ceratophorum.


CONCLUSIONS
We demonstrate that traits under sexual selection during pollen pickup vary among pollinators, while natural selection for pollen defense is nil in T. ceratophorum. In hybrid zones between apomictic and sexual dandelions, pollen traits place apomictic donors at a dispersal disadvantage, potentially reinforcing reproductive isolation.",0.11883922666311264,8
distribute_solids,258,"Roots hunt nutrients. Plant Science
Soil nutrients such as nitrogen sources are not uniformly distributed. Neither are plant roots. Nonetheless, roots of Arabidopsis seedlings seek out pockets of soil ammonium and nitrate. Otvos et al. clarify how root growth and branching are regulated to optimize nitrogen uptake. The auxin efflux carrier PIN-FORMED 2 (PIN2) is regulated posttranscriptionally by phosphorylation at its serine-439 in response to shifts in ammonium or nitrate availability. Phosphorylation in turn triggers changes in PIN2 subcellular localization, which drives changes in auxin distribution between root cortex and epidermis, causing altered root growth rate or direction.

EMBO J. e106862 (2020).",0.09436928480863571,9
distribute_solids,89,"Microbial diversity drives carbon use efficiency in a model soil. Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes. Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.",0.08737456798553467,10
distribute_solids,200,"A seismic monitoring approach to detect and quantify river sediment mobilization by steelhead redd‐building activity. The role of spawning salmonids in altering river bed morphology and sediment transport is significant, yet poorly understood. This is due, in large part, to limitations in monitoring the redd‐build ...",0.06737767904996872,11
distribute_solids,126,Exact Spatiotemporal Dynamics of Confined Lattice Random Walks in Arbitrary Dimensions: A Century after Smoluchowski and Pólya. An exact solution to the discrete diffusion equation allows for accurate predictions of how the probabilities of reaction diffusion processes evolve over time.,0.06060077250003815,12
distribute_solids,317,"Bumble bees damage plant leaves and accelerate flower production when pollen is scarce. Bumble bee gardeners Bumble bees rely heavily on pollen resources for essential nutrients as they build their summer colonies. Therefore, we might expect that annual differences in the availability of these resources must simply be tolerated, but Pashalidou et al. made observations suggesting that bees may have strategies to cope with irregular seasonal flowering (see the Perspective by Chittka). When faced with a shortage of pollen, bumble bees actively damaged plant leaves in a characteristic way, and this behavior resulted in earlier flowering by as much as 30 days. Experimenters were not able to fully replicate the results with their own damage, suggesting that there is a distinct method that the bees use to stimulate earlier flowering. Science, this issue p. 881; see also p. 824 Bumble bees manipulate plants to bring about earlier flowering. Maintaining phenological synchrony with flowers is a key ecological challenge for pollinators that may be exacerbated by ongoing environmental change. Here, we show that bumble bee workers facing pollen scarcity damage leaves of flowerless plants and thereby accelerate flower production. Laboratory studies revealed that leaf-damaging behavior is strongly influenced by pollen availability and that bee-damaged plants flower significantly earlier than undamaged or mechanically damaged controls. Subsequent outdoor experiments showed that the intensity of damage inflicted varies with local flower availability; furthermore, workers from wild colonies of two additional bumble bee species were also observed to damage plant leaves. These findings elucidate a feature of bumble bee worker behavior that can influence the local availability of floral resources.",0.058871716260910034,13
distribute_solids,218,"Biomimicry as a design tool for nanocontainers: The “shape of things to come” in drug delivery. Abstract Nanocontainers embody a “compartmentalized” structural archetype with the potential to operate on a dimensional scale that can either assimilate or be integrated within bio-driven processes. With expected improvements in sensitive diagnostic assays for early disease detection (e.g., CTCs or circulating tumor cells), this has important implications for developing drug delivery technologies to areas of small confinement in the body. Functionalized nanocontainers with tunable surface properties can help stabilize and release therapeutic chemical and biological drugs within nano- and sub-nano spaced cavities. Here, we discuss recent developments in the field of “nanocontainers” that show promise for addressing some of the more challenging aspects of drug therapeutics.",0.05848255008459091,14
distribute_solids,323,"Pygidial glands of Harpalus pensylvanicus (Coleoptera: Carabidae) contain resilin-rich structures.. The pygidial gland system is a key innovation in adephagan beetles, producing, storing, and spraying defensive chemical compounds. As the source of defensive chemical production and storage, the pygidial gland system experiences severe chemical stress which challenges the integrity of the entire gland system. Here, we utilize autofluorescence-based confocal laser scanning microscopy to examine the morphology of pygidial gland secretory lobes and collecting ductules in a common Pennsylvanian harpaline species, Harpalus pensylvanicus. The glandular units are composed of type-III exocrine cells which empty into resilin-rich ductules, which themselves lead into a larger resilin-rich collecting duct, and ultimately the pygidial reservoir pump. We also utilize histological staining with toluidine blue and brightfield imaging to provide additional support for the presence of resilin in the collecting duct, as toluidine blue has been shown to stain resilin without metachromasia. We hypothesize that the high resilin content of the collecting ducts might be a widespread key evolutionary adaptation to prevent damage caused by physical and chemical stress generated in pump-containing insect exocrine gland systems.",0.05775400251150131,15
distribute_solids,5,"Phase transitions of wax esters adjust buoyancy in diapausing Calanoides acutus. We study the composition and biophysical properties of wax esters extracted from the Antarctic copepod, Calanoides acutus, to explore if these factors adjust buoyancy in diapausing copepods. Levels of wax ester in the copepods were correlated with depth, with deeper animals containing higher amounts. An unsaturation index was used to determine the proportions of polyunsaturated wax esters in the oil sac of the copepods. The proportion of polyunsaturated wax ester in copepods that had descended to depth was always close to 50% and attributable to high amounts of the diatom biomarker fatty acid 20:5(n-3) contained in these storage lipids. High-pressure differential scanning calorimetry indicated that wax esters with such high levels of unsaturation exhibited unusual properties, changing from a liquid to a solid phase at pressures and temperatures below 500 m in the ocean. The dense, solid wax esters reduce the overall buoyancy of the lipid-rich copepods at depth and help facilitate neutral buoyancy. The composition of wax esters is a key factor in buoyancy control in these organisms during diapause. Many calanoid copepods inhabiting high-latitude environments overwinter at great depths in the oceans in a state of diapause, a condition where metabolic processes are either arrested or greatly reduced (Dahms 1995). A fundamental requirement of successful overwintering is the acquisition of substantial lipid reserves during summer when microplankton and particularly diatom production is",0.05129881948232651,16
distribute_solids,277,"Encoding memory in tube diameter hierarchy of living flow network. Significance Simple organisms manage to thrive in complex environments. Having memory about the environment is key in taking informed decisions. Physarum polycephalum excels as a giant unicellular eukaryote, being even able to solve optimization problems despite the lack of a nervous system. Here, we follow experimentally the organism’s response to a nutrient source and find that memory about nutrient location is encoded in the morphology of the network-shaped organism. Our theoretical predictions in line with our observations unveil the mechanism behind memory encoding and demonstrate the P. polycephalum’s ability to read out previously stored information. The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment—successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient’s location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes’ capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks’ tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks’ version of associative memory—very likely of relevance for the plethora of living flow networks as well as for bioinspired design.",0.05040430277585983,17
distribute_solids,322,"Attachment-based mechanisms underlying capture and release of pollen grains. Successful insect pollination can be achieved by a sequence of numerous attachment and detachment events at various biological surfaces. However, the quantitative measurements of pollen adhesion on biological surfaces have been poorly studied so far. We performed atomic force microscopy adhesion measurements of pollen on two most important floral parts for Asteraceae in a course of pollination: the stigma and style of Hypochaeris radicata plant. The results indicated distinct adhesive properties of them—the pollen adhesion on stigmatic surfaces drastically increased over prolonged contact time, while the pollen adhesion increase on stylar surfaces was rather restrained. Based on the observation with cryo-scanning electron microscopy, we explained the experimental results by the presence of morphological features in form of flexible stigmatic papillae that may play a crucial role in enhancing both capillary attraction and van der Waals forces. The distinct adhesive properties seemingly originate from the unique adhesive tasks that each of the floral parts requires to achieve successful pollination. The insights into the adhesive interaction between pollen and the floral parts, obtained in the present study, may lead to better understanding of pollination mechanisms, which are strongly related to our food production. Additionally, the novel pollen adhesive mechanisms learned from the stigma of the studied Asteraceae plant can inspire biomimetic designs of spontaneous gripping systems.",0.04800143465399742,18
distribute_solids,15,"Aerial roots of epiphytic orchids: the velamen radicum and its role in water and nutrient uptake. The velamen radicum, a spongy, usually multiple epidermis of the roots, which at maturity consists of dead cells, is frequently described as an important adaptation of epiphytic orchids. Yet, quantitative evidence for the alleged functions, e.g., efficient water and nutrient uptake, nutrient retention, reduction of water loss, mechanical protection, or the avoidance of overheating, is rare or missing. We tested the notion originally put forward by Went in 1940 that the velamen allows plants to capture and immobilize the first solutions arriving in a rainfall, which are the most heavily charged with nutrients. In a series of experiments, we examined whether all necessary functional characteristics are given for this scenario to be realistic under ecological conditions. First, we show that the velamen of a large number of orchid species takes up solutions within seconds, while evaporation from the velamen takes several hours. Charged ions are retained in the velamen probably due to positive and negative charges in the cell walls, while uncharged compounds are lost to the external medium. Finally, we demonstrate that nutrient uptake follows biphasic kinetics with a highly efficient, active transport system at low external concentrations. Thus, our results lend strong support to Went’s hypothesis: the velamen fulfills an important function in nutrient uptake in the epiphytic habitat. Most of the other functions outlined above still await similar experimental scrutiny.",0.047511037439107895,19
distribute_solids,0,"Increased Food and Ecosystem Security via Perennial Grains. Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.",0.046967990696430206,20
passively_move_through/on_liquids,248,"The most efficient metazoan swimmer creates a ‘virtual wall’ to enhance performance. It has been well documented that animals (and machines) swimming or flying near a solid boundary get a boost in performance. This ground effect is often modelled as an interaction between a mirrored pair of vortices represented by a true vortex and an opposite sign ‘virtual vortex’ on the other side of the wall. However, most animals do not swim near solid surfaces and thus near body vortex–vortex interactions in open-water swimmers have been poorly investigated. In this study, we examine the most energetically efficient metazoan swimmer known to date, the jellyfish Aurelia aurita, to elucidate the role that vortex interactions can play in animals that swim away from solid boundaries. We used high-speed video tracking, laser-based digital particle image velocimetry (dPIV) and an algorithm for extracting pressure fields from flow velocity vectors to quantify swimming performance and the effect of near body vortex–vortex interactions. Here, we show that a vortex ring (stopping vortex), created underneath the animal during the previous swim cycle, is critical for increasing propulsive performance. This well-positioned stopping vortex acts in the same way as a virtual vortex during wall-effect performance enhancement, by helping converge fluid at the underside of the propulsive surface and generating significantly higher pressures which result in greater thrust. These findings advocate that jellyfish can generate a wall-effect boost in open water by creating what amounts to a ‘virtual wall’ between two real, opposite sign vortex rings. This explains the significant propulsive advantage jellyfish possess over other metazoans and represents important implications for bio-engineered propulsion systems.",0.7757673859596252,1
passively_move_through/on_liquids,180,"Wake-induced ‘slaloming’ response explains exquisite sensitivity of seal whisker-like sensors. Blindfolded harbour seals are able to use their uniquely shaped whiskers to track vortex wakes left by moving animals and identify objects that passed by 30 s earlier, an impressive feat, as the flow features have velocities as low as $1~\text{mm}~\text{s}^{-1}$ . The seals sense while swimming, hence their whiskers are sensitive enough to detect small-scale changes in the flow, while rejecting self-generated flow noise. Here we identify and illustrate a novel flow mechanism, causing a large-amplitude ‘slaloming’ whisker response, which allows artificial whiskers with the identical unique undulatory geometry as those of the harbour seal to detect the features of minute flow fluctuations when placed within wakes. Whereas in open water the whisker responds with very low-amplitude vibration, once within a wake, it oscillates with large amplitude and, importantly, its response frequency coincides with the Strouhal frequency of the upstream cylinder, making the detection of an upstream wake and an estimation of the size and shape of the wake-generating body possible. This mechanism has some similarities with the flow mechanisms observed in actively controlled propulsive foils within upstream wakes and trout swimming behind bluff cylinders in a stream, but there are also differences caused by the unique whisker morphology, which enables it to respond passively and within a much wider parametric range.",0.5571905374526978,2
passively_move_through/on_liquids,213,"Remoras pick where they stick on blue whales. ABSTRACT Animal-borne video recordings from blue whales in the open ocean show that remoras preferentially adhere to specific regions on the surface of the whale. Using empirical and computational fluid dynamics analyses, we show that remora attachment was specific to regions of separating flow and wakes caused by surface features on the whale. Adhesion at these locations offers remoras drag reduction of up to 71–84% compared with the freestream. Remoras were observed to move freely along the surface of the whale using skimming and sliding behaviors. Skimming provided drag reduction as high as 50–72% at some locations for some remora sizes, but little to none was available in regions where few to no remoras were observed. Experimental work suggests that the Venturi effect may help remoras stay near the whale while skimming. Understanding the flow environment around a swimming blue whale will inform the placement of biosensor tags to increase attachment time for extended ecological monitoring. Highlighted Article: Analysis of previously undocumented skimming and sliding behaviors used by remoras reveals they preferentially adhere to areas with reduced drag on blue whales.",0.39858511090278625,3
passively_move_through/on_liquids,112,"Three-dimensional scaling laws of cetacean propulsion characterize the hydrodynamic interplay of flukes' shape and kinematics. Cetaceans convert dorsoventral body oscillations into forward velocity with a complex interplay between their morphological and kinematic features and the fluid environment. However, it is unknown to what extent morpho-kinematic features of cetaceans are intertwined to maximize their efficiency. By interchanging the shape and kinematic variables of five cetacean species, the interplay of their flukes morpho-kinematic features is examined by characterizing their thrust, power and propulsive efficiency. It is determined that the shape and kinematics of the flukes have considerable influence on force production and power consumption. Three-dimensional heaving and pitching scaling laws are developed by considering both added mass and circulatory-based forces, which are shown to closely model the numerical data. Using the scaling relations as a guide, it is determined that the added mass forces are important in predicting the trend between the efficiency and aspect ratio, however, the thrust and power are driven predominately by the circulatory forces. The scaling laws also reveal that there is an optimal dimensionless heave-to-pitch ratio h* that maximizes the efficiency. Moreover, the optimal h* varies with the aspect ratio, the amplitude-to-chord ratio and the Lighthill number. This indicates that the shape and kinematics of propulsors are intertwined, that is, there are specific kinematics that are tailored to the shape of a propulsor in order to maximize its propulsive efficiency.",0.23843075335025787,4
passively_move_through/on_liquids,183,"Gyroscopic stabilization minimizes drag on Ruellia ciliatiflora seeds. Fruits of Ruellia ciliatiflora (Acanthaceae) explosively launch small (2.5 mm diameter × 0.46 mm thick), disc-shaped seeds at velocities over 15 m s−1, reaching distances of up to 7 m. Through high-speed video analysis, we observe that seeds fly with extraordinary backspin of up to 1660 Hz. By modelling the seeds as spinning discs, we show that flying with backspin is stable against gyroscopic precession. This stable backspin orientation minimizes the frontal area during flight, decreasing drag force on the seeds and thus increasing dispersal distance. From high-speed video of the seeds' flight, we experimentally determine drag forces that are 40% less than those calculated for a sphere of the same volume and density. This reduces the energy costs for seed dispersal by up to a factor of five.",0.19115985929965973,5
passively_move_through/on_liquids,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.17026367783546448,6
passively_move_through/on_liquids,36,"Hydrodynamic Trail-Following in Harbor Seals (Phoca vitulina). Marine mammals often forage in dark or turbid waters. Whereas dolphins use echolocation under such conditions, pinnipeds apparently lack this sensory ability. For seals hunting in the dark, one source of sensory information may consist of fish-generated water movements, which seals can detect with their highly sensitive whiskers. Water movements in the wake of fishes persist for several minutes. Here we show that blindfolded seals can use their whiskers to detect and accurately follow hydrodynamic trails generated by a miniature submarine. This shows that hydrodynamic information can be used for long-distance prey location.",0.1599041372537613,7
passively_move_through/on_liquids,279,"Control of Helical Navigation by Three-Dimensional Flagellar Beating.. Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellate Chlamydomonas reinhardtii rotates at a constant 1-2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, nonplanar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully 3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer toward or away from light by modulating the sign of biflagellar dominance.",0.10046651214361191,8
passively_move_through/on_liquids,116,"Curvature-induced stiffening of a fish fin. How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel (Scomber japonicus) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish.",0.09957268834114075,9
passively_move_through/on_liquids,280,"Sea stars generate downforce to stay attached to surfaces. Intertidal sea stars often function in environments with extreme hydrodynamic loads that can compromise their ability to remain attached to surfaces. While behavioral responses such as burrowing into sand or sheltering in rock crevices can help minimize hydrodynamic loads, previous work shows that sea stars also alter body shape in response to flow conditions. This morphological plasticity suggests that sea star body shape may play an important hydrodynamic role. In this study, we measured the fluid forces acting on surface-mounted sea star and spherical dome models in water channel tests. All sea star models created downforce, i.e., the fluid pushed the body towards the surface. In contrast, the spherical dome generated lift. We also used Particle Image Velocimetry (PIV) to measure the midplane flow field around the models. Control volume analyses based on the PIV data show that downforce arises because the sea star bodies serve as ramps that divert fluid away from the surface. These observations are further rationalized using force predictions and flow visualizations from numerical simulations. The discovery of downforce generation could explain why sea stars are shaped as they are: the pentaradial geometry aids attachment to surfaces in the presence of high hydrodynamic loads.",0.08176247030496597,10
passively_move_through/on_liquids,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.07387060672044754,11
passively_move_through/on_liquids,10,"Aerodynamic force generation, performance and control of body orientation during gliding in sugar gliders (Petaurus breviceps). SUMMARY Gliding has often been discussed in the literature as a possible precursor to powered flight in vertebrates, but few studies exist on the mechanics of gliding in living animals. In this study I analyzed the 3D kinematics of sugar gliders (Petaurus breviceps) during short glides in an enclosed space. Short segments of the glide were captured on video, and the positions of marked anatomical landmarks were used to compute linear distances and angles, as well as whole body velocities and accelerations. From the whole body accelerations I estimated the aerodynamic forces generated by the animals. I computed the correlations between movements of the limbs and body rotations to examine the control of orientation during flight. Finally, I compared these results to those of my earlier study on the similarly sized and distantly related southern flying squirrel (Glaucomys volans). The sugar gliders in this study accelerated downward slightly (1.0±0.5 m s–2), and also accelerated forward (2.1±0.6 m s–2) in all but one trial, indicating that the body weight was not fully supported by aerodynamic forces and that some of the lift produced forward acceleration rather than just balancing body weight. The gliders used high angles of attack (44.15±3.12°), far higher than the angles at which airplane wings would stall, yet generated higher lift coefficients (1.48±0.18) than would be expected for a stalled wing. Movements of the limbs were strongly correlated with body rotations, suggesting that sugar gliders make extensive use of limb movements to control their orientation during gliding flight. In addition, among individuals, different limb movements were associated with a given body rotation, suggesting that individual variation exists in the control of body rotations. Under similar conditions, flying squirrels generated higher lift coefficients and lower drag coefficients than sugar gliders, yet had only marginally shallower glides. Flying squirrels have a number of morphological specializations not shared by sugar gliders that may help to explain their greater lift generating performance.",0.06731804460287094,12
passively_move_through/on_liquids,309,"Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes. Significance For decades, the propulsion of sperms has been traditionally attributed to the beating or rotating of the soft tails. However, this work disclosed an unusual swimming model of Ray sperms whose propulsion is from not only the helical tail but also the unique spiral head (i.e., the head can contribute ∼31% of the force in propulsion). Such a propulsion mechanism provides Ray sperms with high adaptability to large environmental viscosities along with advantages in linearity, straightness, and efficiency. This study expands our knowledge on the microorganisms’ motion and provides inspirations for engineering design. We disclose a peculiar rotational propulsion mechanism of Ray sperms enabled by its unusual heterogeneous dual helixes with a rigid spiral head and a soft tail, named Heterogeneous Dual Helixes (HDH) model for short. Different from the conventional beating propulsion of sperm, the propulsion of Ray sperms is from both the rotational motion of the soft helical tail and the rigid spiral head. Such heterogeneous dual helical propulsion style provides the Ray sperm with high adaptability in viscous solutions along with advantages in linearity, straightness, and bidirectional motion. This HDH model is further corroborated by a miniature swimming robot actuated via a rigid spiral head and a soft tail, which demonstrates similar superiorities over conventional ones in terms of adaptability and efficiency under the same power input. Such findings expand our knowledge on microorganisms’ motion, motivate further studies on natural fertilization, and inspire engineering designs.",0.061186496168375015,13
passively_move_through/on_liquids,50,"FEEDING BEHAVIOR OF THE HUMPBACK WHALE, MEGAPTERA NOVAEANGLIAE, IN THE WESTERN NORTH ATLANTIC. Observations on the feeding behavior of the humpback whale, Megapteranovaeangliae, were made from aerial and surface platforms fTom 1977 to 1980 in the continental shelf waters of the north­ eastern United States. The resulting catalog of behaviors includes two principal categories: Swim­ ming/lunging behaviors and bubbling behaviors. A behavior from a given category may be used independently or in association with others, and by individual or groups of humpbacks. The first category includes surface lunging, circular swimming/thrashing, and the ""inside loop"" behavior. In the second category, a wide variety of feeding-associated bubbling behaviors are described, some for the first time. The structures formed by underwater exhalations are of two major types: 1) bubble cloud-a single, relatively large (4-7m diameter), dome-shaped cloud formed of small, uniformly sized bubbles; and 2) bubble column-a smaller (1-1.5 m diameter) structure composed of larger, randomly sized bubbles, used in series or multiples. Both basic structures are employed in a variety of ways. Many of these behaviors are believed to be utilized to maintain naturally occurring concentrations of prey, which have been identified as the American sand lance, Ammodytes americanus, and occasionally as herring, Clupea harengus. This paper reports on the feeding behavior of the humpback whale, Megaptera novaeangliae, in the continental shelf waters of the northeastern United States. We describe several feeding be­ haviors reported for the first time, as well as a number of behaviors known from other areas but not previously reported for these waters. Our col­ lective observations provide the beginning of a more complete catalog than has previously been available.",0.06112151965498924,14
passively_move_through/on_liquids,236,"Eyelashes divert airflow to protect the eye. Eyelashes are ubiquitous, although their function has long remained a mystery. In this study, we elucidate the aerodynamic benefits of eyelashes. Through anatomical measurements, we find that 22 species of mammals possess eyelashes of a length one-third the eye width. Wind tunnel experiments confirm that this optimal eyelash length reduces both deposition of airborne particles and evaporation of the tear film by a factor of two. Using scaling theory, we find this optimum arises because of the incoming flow's interactions with both the eye and eyelashes. Short eyelashes create a stagnation zone above the ocular surface that thickens the boundary layer, causing shear stress to decrease with increasing eyelash length. Long eyelashes channel flow towards the ocular surface, causing shear stress to increase with increasing eyelash length. These competing effects result in a minimum shear stress for intermediate eyelash lengths. This design may be employed in creating eyelash-inspired protection for optical sensors.",0.046544164419174194,15
passively_move_through/on_liquids,301,"Wave-slope soaring of the brown pelican. Background From the laboratory at Scripps Institution of Oceanography, it is common to see the brown pelican ( Pelecanus occidentalis ) traveling along the crests of ocean waves just offshore of the surf-zone. When flying in this manner, the birds can travel long distances without flapping, centimeters above the ocean’s surface. Here we derive a theoretical framework for assessing the energetic savings related to this behavior, ‘wave-slope soaring,’ in which an organism in flight takes advantage of localized updrafts caused by traveling ocean surface gravity waves. Methods The energy cost of steady, constant altitude flight in and out of ground effect are analyzed as controls. Potential flow theory is used to quantify the ocean wave-induced wind associated with near-shoaling, weakly nonlinear, shallow water ocean surface gravity waves moving through an atmosphere initially at rest. Using perturbation theory and the Green’s function for Laplace’s equation in 2D with Dirichlet boundary conditions, we obtain integrals for the horizontal and vertical components of the wave-induced wind in a frame of reference moving with the wave. Wave-slope soaring flight is then analyzed using an energetics-based approach for waves under a range of ocean conditions and the body plan of P. occidentalis. Results For ground effect flight, we calculate a ∼15 - 25% reduction in cost of transport as compared with steady, level flight out of ground effect. When wave-slope soaring is employed at flight heights ∼2m in typical ocean conditions (2m wave height, 15s period), we calculate 60-70% reduction in cost of transport as compared with flight in ground effect. A relatively small increase in swell amplitude or decrease in flight height allows up to 100% of the cost of transport to be offset by wave-slope soaring behavior. Conclusions The theoretical development presented here suggests there are energy savings associated with wave-slope soaring. Individual brown pelicans may significantly decrease their cost of transport utilizing this mode of flight under typical ocean conditions. Thus wave-slope soaring may provide fitness benefit to these highly mobile organisms that depend on patchy prey distribution over large home ranges.",0.04175268113613129,16
passively_move_through/on_liquids,64,"Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella. Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.",0.04004755988717079,17
passively_move_through/on_liquids,217,"An energy landscape approach to locomotor transitions in complex 3D terrain. Significance Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Using laboratory experiments on a model system, we demonstrate that an energy landscape approach helps understand how multipathway transitions across locomotor modes in complex 3D terrain statistically emerge from physical interaction. Animals’ and robots’ locomotor modes are attracted to basins of a potential energy landscape. They can use kinetic energy fluctuation from oscillatory self-propulsion to cross potential energy barriers, escaping from one basin and reaching another to make locomotor transitions. Our first-principle energy landscape approach is the beginning of a statistical physics theory of locomotor transitions in complex terrain. It will help understand and predict how animals, and how robots should, move through the real world. Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around near–steady-state movement in a single mode. We still know little about how locomotor transitions emerge from physical interaction with complex terrain. Consequently, robots largely rely on geometric maps to avoid obstacles, not traverse them. Recent studies revealed that locomotor transitions in complex three-dimensional (3D) terrain occur probabilistically via multiple pathways. Here, we show that an energy landscape approach elucidates the underlying physical principles. We discovered that locomotor transitions of animals and robots self-propelled through complex 3D terrain correspond to barrier-crossing transitions on a potential energy landscape. Locomotor modes are attracted to landscape basins separated by potential energy barriers. Kinetic energy fluctuation from oscillatory self-propulsion helps the system stochastically escape from one basin and reach another to make transitions. Escape is more likely toward lower barrier direction. These principles are surprisingly similar to those of near-equilibrium, microscopic systems. Analogous to free-energy landscapes for multipathway protein folding transitions, our energy landscape approach from first principles is the beginning of a statistical physics theory of multipathway locomotor transitions in complex terrain. This will not only help understand how the organization of animal behavior emerges from multiscale interactions between their neural and mechanical systems and the physical environment, but also guide robot design, control, and planning over the large, intractable locomotor-terrain parameter space to generate robust locomotor transitions through the real world.",0.03919646143913269,18
passively_move_through/on_liquids,201,"Undulation enables gliding in flying snakes. When flying snakes glide, they use aerial undulation. To determine if aerial undulation is a flight control strategy or a non-functional behavioural vestige of lateral undulation, we measured snake glides using high-speed motion capture and developed a new dynamical model of gliding. Reconstructions of the snake’s wing-body reveal that aerial undulation is composed of horizontal and vertical waves, whose phases differ by 90° and whose frequencies differ by a factor of two. Using these results, we developed a three-dimensional mathematical model of snake flight that incorporates aerodynamic and inertial effects. Although simulated glides without undulation attained some horizontal distance, they are biologically unrealistic because they failed due to roll and pitch instabilities. In contrast, the inclusion of undulation stabilized the rotational motion and markedly increased glide performance. This work demonstrates that aerial undulation in snakes serves a different function than known uses of undulation in other animals, and suggests a new template of control for dynamic flying robots. Observations of flying snakes inform the development of a dynamical model of gliding taking undulation into account. This work suggests that aerial undulation has a different function in snakes than in other animals.",0.037968117743730545,19
passively_move_through/on_liquids,146,"Universal metabolic constraints shape the evolutionary ecology of diving in animals. Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.",0.03078550659120083,20
manage_wear,71,"Self‐Sharpening Mechanism of the Sea Urchin Tooth. The sea urchin tooth is a mosaic of calcite crystals shaped precisely into plates and fibers, cemented together by a robust calcitic polycrystalline matrix. The tooth is formed continuously at one end, while it grinds and wears at the opposite end, the sharp tip. Remarkably, these teeth enable the sea urchin to scrape and bore holes into rock, yet the teeth remain sharp rather than dull with use. Here we describe the detailed structure of the tooth of the California purple sea urchin Strongylocentrotus purpuratus, and focus on the self-sharpening mechanism. Using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM), scanning electron microscopy (SEM), EDX analysis, nanoindentation, and X-ray micro-tomography, we deduce that the sea urchin tooth self-sharpens by fracturing at discontinuities in the material. These are organic layers surrounding plates and fibers that behave as the “fault lines” in the tooth structure, as shown by nanoindentation. Shedding of tooth components at these discontinuities exposes the robust central part of the tooth, aptly termed “the stone”, which becomes the grinding tip. The precise design and position of the plates and fibers determines the profile of the tooth tip, so as the tooth wears it maintains a tip that is continually renewed and remains sharp. This strategy may be used for the top-down or bottom-up fabrication of lamellar materials, to be used for mechanical functions at the nano- and micrometer scale.",0.15411660075187683,1
manage_wear,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.09503976255655289,2
manage_wear,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.0678335502743721,3
manage_wear,292,"A Graphic Way For Notch Shape Optimization. Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.",0.06765952706336975,4
manage_wear,114,"Snapping mechanics of the Venus flytrap (Dionaea muscipula). Significance The rapid closure of the carnivorous Venus flytrap (Dionaea muscipula) snap-trap incorporates snap-buckling instability as a speed boost. The trap actuation principles required to overcome the involved energy barrier, as determined by the double-lobe curvature, have remained speculative until now. Here we used 3D digital image correlation for the analysis of trap deformation during closure for both the outer and the inner trap surfaces. Accompanying biomechanical and physiological experiments revealed that successful snapping relies on full trap hydration. In combination with FEM simulations elucidating the mechanical contribution of the various trap tissues to the motion, we show that the trapping mechanics incorporate an elaborate interplay between swelling/shrinking processes of the various tissue layers and the release of trap-internal prestress. The mechanical principles for fast snapping in the iconic Venus flytrap are not yet fully understood. In this study, we obtained time-resolved strain distributions via three-dimensional digital image correlation (DIC) for the outer and inner trap-lobe surfaces throughout the closing motion. In combination with finite element models, the various possible contributions of the trap tissue layers were investigated with respect to the trap’s movement behavior and the amount of strain required for snapping. Supported by in vivo experiments, we show that full trap turgescence is a mechanical–physiological prerequisite for successful (fast and geometrically correct) snapping, driven by differential tissue changes (swelling, shrinking, or no contribution). These are probably the result of the previous accumulation of internal hydrostatic pressure (prestress), which is released after trap triggering. Our research leads to an in-depth mechanical understanding of a complex plant movement incorporating various actuation principles.",0.04924038052558899,5
manage_wear,250,"Biomechanical insights into the dentition of megatooth sharks (Lamniformes: Otodontidae). The evolution of gigantism in extinct otodontid sharks was paralleled by a series of drastic modifications in their dentition including widening of the crowns, loss of lateral cusplets, and acquisition of serrated cutting edges. These traits have generally been interpreted as key functional features that enabled the transition from piscivory to more energetic diets based on marine mammals, ultimately leading to the evolution of titanic body sizes in the most recent forms (including the emblematic Otodus megalodon ). To investigate this hypothesis, we evaluate the biomechanics of the anterior, lateral, and posterior teeth of five otodontid species under different loading conditions by using two-dimensional finite element analysis. Stress distribution patterns are remarkably similar among all models under puncture and draw (i.e., when subjected to vertical and lateral forces, respectively). Contrary to expectation, higher average stress values are detected under both loading scenarios in more recent species. Altogether, this suggests little correlation between tooth morphology and key aspects of biomechanical behaviour in otodontids, making it difficult to frame the morphological trend of their dentitions within an adaptive scenario. We propose that this pattern most likely emerged as a non-functional by-product of heterochronic processes driven by selection towards larger body sizes.",0.04613874480128288,6
manage_wear,78,"Bioinspired Materials with Self-Adaptable Mechanical Properties.. Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.",0.04499456286430359,7
manage_wear,173,"Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication. Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.",0.044800251722335815,8
manage_wear,264,"The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo. The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.",0.04267388954758644,9
manage_wear,313,"Temporomandibular joint and Giant Panda’s (Ailuropoda melanoleuca) adaptation to bamboo diet. Here, we present new evidence that evolutionary adaptation of the Ailuripodinae lineage to bamboo diet has taken place by morphological adaptations in the masticatory system. The giant panda in the wild and in captivity removes without an exception the outer skin of all bamboo shoots, rich in abrasive and toxic compounds, by the highly adapted premolars P3 and P4. The temporomandibular joint (TMJ) allows sidewise movement of the jaw and the premolars can, in a cusp-to-cusp position, remove the poorly digestible outer skin of the bamboo before crushing the bamboo with molars. Based on the evidence presented here, we suggest that adaptation of TMJ to lateral movement for enabling cusp-to-cusp contact of premolars is the crucial evolutionary factor as which we consider the key to understand the Ailuropodinae lineage adaptive pathway to utilize the bamboo resource.",0.039440713822841644,10
manage_wear,176,"The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals.",0.039080798625946045,11
manage_wear,297,"Nature's forms are frilly, flexible, and functional.. A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.",0.03801072761416435,12
manage_wear,220,"Structure and Mechanical Adaptability of a Modern Elasmoid Fish Scale from the Common Carp. Summary The carp (Cyprinus carpio) has typical elasmoid scales commonly found on teleosts. They provide protection while retaining flexibility and maneuverability of the fish. The exterior surface of the scale consists of an ultrathin discontinuous mineral layer on top of mineralized woven collagen fibrils. The underlying foundation is composed of two collagenous components. The major one consists of a single-twisted “Bouligand” structure with a twisting angle of 36°. A secondary “sheet-like” structure, formed by thinner collagen fibrils oriented along the thickness direction, acts to increase the integrity of the scale. Here, we identify the deformation and failure mechanisms of the carp scale, revealing slight tensile anisotropy. Using in situ small-angle X-ray scattering during tensile testing, the toughening mechanisms of the scale, including the adaptive structural reorientation of lamellae as well as fibrillar sliding and elastic deformation, are quantified and compared with those of other fish scales.",0.035486772656440735,13
manage_wear,223,"Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets. Nacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design. The hierarchical structure of nacre is known to contribute to its high strength and toughness, providing inspiration for many biomimetic materials. Here, co-oriented 20 µm stacks of aragonite platelets are shown to contribute to the toughness of nacre, defining a new characteristic length scale.",0.031084317713975906,14
manage_wear,203,"Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography. Significance Hindwings in ladybird beetles successfully achieve compatibility between the deformability (instability) required for wing folding and strength property (stability) required for flying. This study demonstrates how ladybird beetles address these two conflicting requirements by an unprecedented technique using artificial wings. Our results, which clarify the detailed wing-folding process and reveal the supporting structures, provide indispensable initial knowledge for revealing this naturally evolved optimization system. Investigating the characteristics in the venations and crease patterns revealed in this study could provide an innovative designing method, enabling the integration of structural stability and deformability, and thus could have a considerable impact on engineering science. Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: (i) the wing rigidity with relatively thick veins and (ii) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure.",0.030600177124142647,15
manage_wear,167,"The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts. The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.",0.0305324736982584,16
manage_wear,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.029735546559095383,17
manage_wear,91,"Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts. Significance Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.",0.02866571769118309,18
manage_wear,314,"Dragonfly wing nodus: A one-way hinge contributing to the asymmetric wing deformation.. Dragonfly wings are highly specialized locomotor systems, which are formed by a combination of several structural components. The wing components, also known as structural elements, are responsible for the various aspects of the wing functionality. Considering the complex interactions between the wing components, modelling of the wings as a whole is only possible with inevitable huge oversimplifications. In order to overcome this difficulty, we have recently proposed a new approach to model individual components of complex wings comparatively. Here, we use this approach to study nodus, a structural element of dragonfly wings which has been less studied to date. Using a combination of several imaging techniques including scanning electron microscopy (SEM), wide-field fluorescence microscopy (WFM), confocal laser scanning microscopy (CLSM) and micro-computed tomography (micro-CT) scanning, we aim to characterize the spatial morphology and material composition of fore- and hindwing nodi of the dragonfly Brachythemis contaminata. The microscopy results show the presence of resilin in the nodi, which is expected to help the deformability of the wings. The computational results based on three-dimensional (3D) structural data suggest that the specific geometry of the nodus restrains its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is expected to contribute to the dorso-ventral asymmetry of wing deformation and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings.


STATEMENT OF SIGNIFICANCE
In this study, we investigate the wing nodus, a specialized wing component in dragonflies. Using a combination of modern imaging techniques, we demonstrate the presence of resilin in the nodus, which is expected to facilitate the wing deformability in flight. The specific geometry of the nodus, however, seems to restrain its displacements when subjected to pressure on the ventral side. This effect, resulting from an interlocking mechanism, is suggested to contribute to dorso-ventral asymmetry of wing deformations and to provide a higher resistance to aerodynamic forces during the downstroke. Our results provide an important step towards better understanding of the structure-property-function relationship in dragonfly wings and might help to design more efficient wings for biomimetic micro-air vehicles.",0.02767474576830864,19
manage_wear,300,"Extreme strength observed in limpet teeth. The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.",0.027409836649894714,20
respond_to_signals,216,"Nature as model for technical sensors. Summary form only given. Sensors and sensing are essential for all forms of life. Correspondingly there is a fascinating richness and diversity of sensory systems throughout the animal kingdom. Animals use sensory input not only for communication, but also for the detection, discrimination and localization of animate and inanimate objects. In addition sensory systems provide basic cues for spatial orientation and navigation. Both the structure and the physiology of sensory systems reflect the natural environment in which an animal lives and the needs of the animal. Accordingly, the relevant and often complex stimuli and noise conditions, which natural sensors evolved to cope with, have to be found and applied, to fully understand any sensory system. This is a particular challenge in cases where animals show sensory capabilities alien to human perceptions. This presentation focuses on two sensory systems that humans and most animals do not have: the infrared sensory system of pyrophilous beetles and the electrosensory system of weakly electric fish. I will show that these sensory systems not only have remarkable features but can also be used as a model for the development of novel technical sensors.",0.9089034199714661,1
respond_to_signals,266,"Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. How do cells make efficient collective decisions during tissue morphogenesis? Humans and other organisms use feedback between movement and sensing known as ‘sensorimotor coordination’ or ‘active perception’ to inform behaviour, but active perception has not before been investigated at a cellular level within organs. Here we provide the first proof of concept in silico/in vivo study demonstrating that filopodia (actin-rich, dynamic, finger-like cell membrane protrusions) play an unexpected role in speeding up collective endothelial decisions during the time-constrained process of ‘tip cell’ selection during blood vessel formation (angiogenesis). We first validate simulation predictions in vivo with live imaging of zebrafish intersegmental vessel growth. Further simulation studies then indicate the effect is due to the coupled positive feedback between movement and sensing on filopodia conferring a bistable switch-like property to Notch lateral inhibition, ensuring tip selection is a rapid and robust process. We then employ measures from computational neuroscience to assess whether filopodia function as a primitive (basal) form of active perception and find evidence in support. By viewing cell behaviour through the ‘basal cognitive lens' we acquire a fresh perspective on the tip cell selection process, revealing a hidden, yet vital time-keeping role for filopodia. Finally, we discuss a myriad of new and exciting research directions stemming from our conceptual approach to interpreting cell behaviour. This article is part of the theme issue ‘Basal cognition: multicellularity, neurons and the cognitive lens’.",0.8006902933120728,2
respond_to_signals,227,"High-capacity auditory memory for vocal communication in a social songbird. Zebra finches can quickly form long-term auditory memories of up to 50 conspecifics based on their song or distance call. Effective vocal communication often requires the listener to recognize the identity of a vocalizer, and this recognition is dependent on the listener’s ability to form auditory memories. We tested the memory capacity of a social songbird, the zebra finch, for vocalizer identities using conditioning experiments and found that male and female zebra finches can remember a large number of vocalizers (mean, 42) based solely on the individual signatures found in their songs and distance calls. These memories were formed within a few trials, were generalized to previously unheard renditions, and were maintained for up to a month. A fast and high-capacity auditory memory for vocalizer identity has not been demonstrated previously in any nonhuman animals and is an important component of vocal communication in social species.",0.7340673804283142,3
respond_to_signals,75,"Small groups and long memories promote cooperation. Complex social behaviors lie at the heart of many of the challenges facing evolutionary biology, sociology, economics, and beyond. For evolutionary biologists the question is often how group behaviors such as collective action, or decision making that accounts for memories of past experience, can emerge and persist in an evolving system. Evolutionary game theory provides a framework for formalizing these questions and admitting them to rigorous study. Here we develop such a framework to study the evolution of sustained collective action in multi-player public-goods games, in which players have arbitrarily long memories of prior rounds of play and can react to their experience in an arbitrary way. We construct a coordinate system for memory-m strategies in iterated n-player games that permits us to characterize all cooperative strategies that resist invasion by any mutant strategy, and stabilize cooperative behavior. We show that, especially when groups are small, longer-memory strategies make cooperation easier to evolve, by increasing the number of ways to stabilize cooperation. We also explore the co-evolution of behavior and memory. We find that even when memory has a cost, longer-memory strategies often evolve, which in turn drives the evolution of cooperation, even when the benefits for cooperation are low.",0.7320273518562317,4
respond_to_signals,165,"Ant collective cognition allows for efficient navigation through disordered environments. The cognitive abilities of biological organisms only make sense in the context of their environment. Here, we study longhorn crazy ant collective navigation skills within the context of a semi-natural, randomized environment. Mapping this biological setting into the ‘Ant-in-a-Labyrinth’ framework which studies physical transport through disordered media allows us to formulate precise links between the statistics of environmental challenges and the ants’ collective navigation abilities. We show that, in this environment, the ants use their numbers to collectively extend their sensing range. Although this extension is moderate, it nevertheless allows for extremely fast traversal times that overshadow known physical solutions to the ‘Ant-in-a-Labyrinth’ problem. To explain this large payoff, we use percolation theory and prove that whenever the labyrinth is solvable, a logarithmically small sensing range suffices for extreme speedup. Overall, our work demonstrates the potential advantages of group living and collective cognition in increasing a species’ habitable range.",0.725695788860321,5
respond_to_signals,174,"School formation characteristics and stimuli based modeling of Tetra fish.. Self-organizing motion is an important yet inadequately understood phenomena in the field of collective behavior. For birds flocks, insect swarms, and fish schools, group behavior can provide a mechanism for defense against predators, better foraging and mating capabilities and increased hydro/aerodynamic efficiency in long-distance migration events. Although collective motion has received much scientific attention, more work is required to model and understand the mechanisms responsible for school initiation and formation, and information transfer within these groups. Here we investigate schooling of Black Tetra (Gymnocorymbus ternetzi) fish triggered by startle stimuli in the form of approaching objects. High-speed video and tagging techniques were used to track the school and individual members. We then measured several variables including reaction times, group formation shapes, fish velocity, group density, and leadership within the group. These data reveal three things: 1) information propagates through the group as a wave, indicating that each fish is not reacting individually to the stimulus, 2) the time taken for information to transfer across the group is independent of group density, and 3) information propagates across large groups faster than would be expected if the fish were simply responding to the motion of their nearest neighbor. A model was then built wherein simulated fish have a simple `stimuli/escape' vector based on a hypothetical field of vision. The model was used to simulate a group of individual fish with initial conditions, size, and stimuli similar to the biological experiments. The model revealed similar behavior to the biological experiments and provide insights into the observed patterns, response times, and wave speeds.",0.6943221688270569,6
respond_to_signals,143,"Socially foraging bats discriminate between group members based on search-phase echolocation calls. © The Author(s) 2020. Published by Oxford University Press on behalf of the International Society for Behavioral Ecology. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Original Article",0.6506716012954712,7
respond_to_signals,271,"Navigation by extrapolation of geomagnetic cues in a migratory songbird. Displacement experiments have demonstrated that experienced migratory birds translocated thousands of kilometers away from their migratory corridor can orient toward and ultimately reach their intended destinations.1 This implies that they are capable of ""true navigation,"" commonly defined2-4 as the ability to return to a known destination after displacement to an unknown location without relying on familiar surroundings, cues that emanate from the destination, or information collected during the outward journey.5-13 In birds, true navigation appears to require previous migratory experience5-7,14,15 (but see Kishkinev et al.16 and Piersma et al.17). It is generally assumed that, to correct for displacements outside the familiar area, birds initially gather information within their year-round distribution range, learn predictable spatial gradients of environmental cues within it, and extrapolate from those to unfamiliar magnitudes-the gradient hypothesis.6,9,18-22 However, the nature of the cues and evidence for actual extrapolation remain elusive. Geomagnetic cues (inclination, declination, and total intensity) provide predictable spatial gradients across large parts of the globe and could serve for navigation. We tested the orientation of long-distance migrants, Eurasian reed warblers, exposing them to geomagnetic cues of unfamiliar magnitude encountered beyond their natural distribution range. The birds demonstrated re-orientation toward their migratory corridor as if they were translocated to the corresponding location but only when all naturally occurring magnetic cues were presented, not when declination was changed alone. This result represents direct evidence for migratory birds' ability to navigate using geomagnetic cues extrapolated beyond their previous experience.",0.6261146664619446,8
respond_to_signals,175,"Transitive inference in Polistes paper wasps. Transitive inference (TI) is a form of logical reasoning that involves using known relationships to infer unknown relationships (A > B; B > C; then A > C). TI has been found in a wide range of vertebrates but not in insects. Here, we test whether Polistes dominula and Polistes metricus paper wasps can solve a TI problem. Wasps were trained to discriminate between five elements in series (A0B−, B0C−, C0D−, D0E−), then tested on novel, untrained pairs (B versus D). Consistent with TI, wasps chose B more frequently than D. Wasps organized the trained stimuli into an implicit hierarchy and used TI to choose between untrained pairs. Species that form social hierarchies like Polistes may be predisposed to spontaneously organize information along a common underlying dimension. This work contributes to a growing body of evidence that the miniature nervous system of insects does not limit sophisticated behaviours.",0.6176857948303223,9
respond_to_signals,113,"Temporal Signatures of Criticality in Human Cortical Excitability as Probed by Early Somatosensory Responses. Brain responses vary considerably from moment to moment, even to identical sensory stimuli. This has been attributed to changes in instantaneous neuronal states determining the system's excitability. Yet the spatiotemporal organization of these dynamics remains poorly understood. Here we test whether variability in stimulus-evoked activity can be interpreted within the framework of criticality, which postulates dynamics of neural systems to be tuned toward the phase transition between stability and instability as is reflected in scale-free fluctuations in spontaneous neural activity. Using a novel noninvasive approach in 33 male human participants, we tracked instantaneous cortical excitability by inferring the magnitude of excitatory postsynaptic currents from the N20 component of the somatosensory evoked potential. Fluctuations of cortical excitability demonstrated long-range temporal dependencies decaying according to a power law across trials, a hallmark of systems at critical states. As these dynamics covaried with changes in prestimulus oscillatory activity in the alpha band (8-13 Hz), we establish a mechanistic link between ongoing and evoked activity through cortical excitability and argue that the co-emergence of common temporal power laws may indeed originate from neural networks poised close to a critical state. In contrast, no signatures of criticality were found in subcortical or peripheral nerve activity. Thus, criticality may represent a parsimonious organizing principle of variability in stimulus-related brain processes on a cortical level, possibly reflecting a delicate equilibrium between robustness and flexibility of neural responses to external stimuli. SIGNIFICANCE STATEMENT Variability of neural responses in primary sensory areas is puzzling, as it is detrimental to the exact mapping between stimulus features and neural activity. However, such variability can be beneficial for information processing in neural networks if it is of a specific nature, namely, if dynamics are poised at a so-called critical state characterized by a scale-free spatiotemporal structure. Here, we demonstrate the existence of a link between signatures of criticality in ongoing and evoked activity through cortical excitability, which fills the long-standing gap between two major directions of research on neural variability: the impact of instantaneous brain states on stimulus processing on the one hand and the scale-free organization of spatiotemporal network dynamics of spontaneous activity on the other.",0.5780360698699951,10
respond_to_signals,35,"Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups. Members of social groups need to coordinate their behaviour when choosing between alternative activities. Consensus decisions enable group members to maintain group cohesion and one way to reach consensus is to rely on quorums. A quorum response is where the probability of an activity change sharply increases with the number of individuals supporting the new activity. Here, we investigated how meerkats (Suricata suricatta) use vocalizations in the context of movement decisions. Moving calls emitted by meerkats increased the speed of the group, with a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three. These calls had no apparent effect on the group's movement direction. When dominant individuals were involved in the chorus, the group's reaction was not stronger than when only subordinates called. Groups only increased speed in response to playbacks of moving calls from one individual when other group members emitted moving calls as well. The voting mechanism linked to a quorum probably allows meerkat groups to change foraging patches cohesively with increased speed. Such vocal coordination may reflect an aggregation rule linking individual assessment of foraging patch quality to group travel route.",0.5583488345146179,11
respond_to_signals,284,"Cuttlefish exert self-control in a delay of gratification task. The ability to exert self-control varies within and across taxa. Some species can exert self-control for several seconds whereas others, such as large-brained vertebrates, can tolerate delays of up to several minutes. Advanced self-control has been linked to better performance in cognitive tasks and has been hypothesized to evolve in response to specific socio-ecological pressures. These pressures are difficult to uncouple because previously studied species face similar socio-ecological challenges. Here, we investigate self-control and learning performance in cuttlefish, an invertebrate that is thought to have evolved under partially different pressures to previously studied vertebrates. To test self-control, cuttlefish were presented with a delay maintenance task, which measures an individual's ability to forgo immediate gratification and sustain a delay for a better but delayed reward. Cuttlefish maintained delay durations for up to 50–130 s. To test learning performance, we used a reversal-learning task, whereby cuttlefish were required to learn to associate the reward with one of two stimuli and then subsequently learn to associate the reward with the alternative stimulus. Cuttlefish that delayed gratification for longer had better learning performance. Our results demonstrate that cuttlefish can tolerate delays to obtain food of higher quality comparable to that of some large-brained vertebrates.",0.5531796216964722,12
respond_to_signals,319,"Encoding Membrane-Potential-Based Memory within a Microbial Community.. Cellular membrane potential plays a key role in the formation and retrieval of memories in the metazoan brain, but it remains unclear whether such memory can also be encoded in simpler organisms like bacteria. Here, we show that single-cell-level memory patterns can be imprinted in bacterial biofilms by light-induced changes in the membrane potential. We demonstrate that transient optical perturbations generate a persistent and robust potassium-channel-mediated change in the membrane potential of bacteria within the biofilm. The light-exposed cells respond in an anti-phase manner, relative to unexposed cells, to both natural and induced oscillations in extracellular ion concentrations. This anti-phase response, which persists for hours following the transient optical stimulus, enables a direct single-cell resolution visualization of spatial memory patterns within the biofilm. The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria.",0.5430501699447632,13
respond_to_signals,226,"Time cells in the human hippocampus and entorhinal cortex support episodic memory. Significance Time cells are neurons in the hippocampus and entorhinal cortex that fire at specific moments within a cognitive task or experience. While many prominent theories of memory encoding offer time cells as the source of the temporal component to memory, they have never been observed in human recordings. We identify time cell populations in the medial temporal lobe of humans during memory encoding and retrieval. Further, we demonstrate that the stability of the time signal provided by time cells during encoding influences the ability to temporally order memories at time of retrieval. The organization of temporal information is critical for the encoding and retrieval of episodic memories. In the rodent hippocampus and entorhinal cortex, evidence accumulated over the last decade suggests that populations of “time cells” in the hippocampus encode temporal information. We identify time cells in humans using intracranial microelectrode recordings obtained from 27 human epilepsy patients who performed an episodic memory task. We show that time cell activity predicts the temporal organization of retrieved memory items. We also uncover evidence of ramping cell activity in humans, which represents a complementary type of temporal information. These findings establish a cellular mechanism for the representation of temporal information in the human brain needed to form episodic memories.",0.5221381783485413,14
respond_to_signals,39,"Mapping the β-Scorpion Toxin Receptor Site on Voltage-Gated Sodium Channels. Voltage-gated sodium channels are molecular targets of β-scorpion toxins, which enhance excitability by shifting the voltage dependence of activation to more negative potentials. These effects result from a voltage sensor trapping mechanism, in which toxins trap the voltage sensor in its activated conformation. Determinants of β-scorpion toxin (CssIV) binding and action on sodium channel (Nav1.2) are located in the S1-S2 and S3-S4 extracellular linkers in the voltage-sensing module in domain II. To completely map these regions, we made substitutions for previously unstudied amino acid residues and examined modulation by CssIVE15A, a highly active toxin derivative. Of 11 positions studied in IIS1-S2, only one significantly altered the toxin effect from wild-type by reducing binding to the resting state and almost abolishing trapping activity. In IIS3-S4, five positions surrounding a previously identified key binding determinant, G845, define a hotspot of high impact residues. Three of these substitutions reduced toxin binding and voltage-sensor trapping. The other two, V843A and E844N, increased voltage-sensor trapping approximately 4-fold and decreased apparent EC50. The rate of voltage sensor trapping upon depolarization was unchanged for V843A and increased approximately 2.5-fold for E844N. The rate at which the toxin releases the voltage sensor upon repolarization was increased 2.2-fold for the V843A but was unchanged for E844N. Thus CssIVE15A interacts with a short segment of IIS1-S2 and a broader region of DIIS3-S4. The bidirectional effects of mutations on toxin efficacy suggest that native residues make both positive and negative interactions with the toxin. Substitutions that increase toxin effects do so by increasing affinity of resting channels for the toxin and further increasing the relative affinity of the activated voltage-sensor for the toxin. These results provide further support for the voltage sensor-trapping model.",0.5218976140022278,15
respond_to_signals,92,"Prey Exploits the Auditory Illusions of Eavesdropping Predators. Mating signals have evolved to attract target receivers, even to the point of exploiting receivers through perceptual manipulation. Signals, however, can also expose signalers to nontarget receivers, including predators and parasites, and thus have also evolved to decrease enemy attraction. Here we show that male tree frogs (Smilisca sila) reduce their attractiveness to eavesdropping enemies (bats and midges) by overlapping their calls at near-perfect synchrony with the calls of neighboring conspecifics. By producing calls that closely follow those of other males, synchronizing S. sila take advantage of an auditory illusion where enemies are more attracted to the leading call. Female S. sila, however, are less susceptible to this illusion. Thus, synchronization among signaling males can result in acoustic crypsis from predators without affecting female attraction. Given the widespread use of conspicuous mating signals and eavesdropping enemies, perceptual exploitation of eavesdroppers is likely a common driver of signal evolution.",0.5128579139709473,16
respond_to_signals,306,"Neurophysiological coordination of duet singing. Significance Cooperation, turn taking, and other social behaviors often depend on temporal coordination between individuals. How brains use sensory cues from participants to synchronize performances is not known. We examined the interactions between sensory cues and motor activity in the brains of female and male plain-tailed wrens that rapidly take turns to produce a duet that sounds as if a single bird is singing. We made simultaneous neurophysiological recordings from the brains of pairs of awake, duetting wrens. We discovered that inhibition driven by auditory feedback from the partner alternated with the premotor activity used by each individual to produce its own vocalizations. These data show how sensory feedback links the brains of cooperating animals through the modulation of motor circuits. Coordination of behavior for cooperative performances often relies on linkages mediated by sensory cues exchanged between participants. How neurophysiological responses to sensory information affect motor programs to coordinate behavior between individuals is not known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use acoustic feedback to coordinate extraordinary duet performances in which females and males rapidly take turns singing. We made simultaneous neurophysiological recordings in a song control area “HVC” in pairs of singing wrens at a field site in Ecuador. HVC is a premotor area that integrates auditory feedback and is necessary for song production. We found that spiking activity of HVC neurons in each sex increased for production of its own syllables. In contrast, hearing sensory feedback produced by the bird’s partner decreased HVC activity during duet singing, potentially coordinating HVC premotor activity in each bird through inhibition. When birds sang alone, HVC neurons in females but not males were inhibited by hearing the partner bird. When birds were anesthetized with urethane, which antagonizes GABAergic (γ-aminobutyric acid) transmission, HVC neurons were excited rather than inhibited, suggesting a role for GABA in the coordination of duet singing. These data suggest that HVC integrates information across partners during duets and that rapid turn taking may be mediated, in part, by inhibition.",0.4928005635738373,17
respond_to_signals,222,"Evolution of the acoustic startle response of Mexican cavefish.. The ability to detect threatening stimuli and initiate an escape response is essential for survival and under stringent evolutionary pressure. In diverse fish species, acoustic stimuli activate Mauthner neurons, which initiate a C-start escape response. This reflexive behavior is highly conserved across aquatic species and provides a model for investigating the neural mechanism underlying the evolution of escape behavior. Here, we characterize evolved differences in the C-start response between populations of the Mexican cavefish, Astyanax mexicanus. Cave populations of A. mexicanus inhabit an environment devoid of light and macroscopic predators, resulting in evolved differences in various morphological and behavioral traits. We find that the C-start is present in river-dwelling surface fish and multiple populations of cavefish, but that response kinematics and probability differ between populations. The Pachón population of cavefish exhibits an increased response probability, a slower response latency and speed, and reduction of the maximum bend angle, revealing evolved differences between surface and cave populations. Analysis of the responses of two other independently evolved populations of cavefish, revealed the repeated evolution of reduced angular speed. Investigation of surface-cave hybrids reveals a correlation between angular speed and peak angle, suggesting these two kinematic characteristics are related at the genetic or functional levels. Together, these findings provide support for the use of A. mexicanus as a model to investigate the evolution of escape behavior.",0.47431275248527527,18
respond_to_signals,286,"Lung mediated auditory contrast enhancement improves the Signal-to-noise ratio for communication in frogs. Environmental noise is a major source of selection on animal sensory and communication systems. The acoustic signals of other animals represent particularly potent sources of noise for chorusing insects, frogs, and birds, which contend with a multi-species analog of the human ""cocktail party problem"" (i.e., our difficulty following speech in crowds). However, current knowledge of the diverse adaptations that function to solve noise problems in nonhuman animals remains limited. Here, we show that a lung-to-ear sound transmission pathway in frogs serves a heretofore unknown noise-control function in vertebrate hearing and sound communication. Inflated lungs improve the signal-to-noise ratio for communication by enhancing the spectral contrast in received vocalizations in ways analogous to signal processing algorithms used in hearing aids and cochlear implants. Laser vibrometry revealed that the resonance of inflated lungs selectively reduces the tympanum's sensitivity to frequencies between the two spectral peaks present in conspecific mating calls. Social network analysis of continent-scale citizen science data on frog calling behavior revealed that the calls of other frog species in multi-species choruses can be a prominent source of environmental noise attenuated by the lungs. Physiological modeling of peripheral frequency tuning indicated that inflated lungs could reduce both auditory masking and suppression of neural responses to mating calls by environmental noise. Together, these data suggest an ancient adaptation for detecting sound via the lungs has been evolutionarily co-opted to create auditory contrast enhancement that contributes to solving a multi-species cocktail party problem.",0.36408236622810364,19
respond_to_signals,88,"Collective Computation in Animal Fission-Fusion Dynamics. Recent work suggests that collective computation of social structure can minimize uncertainty about the social and physical environment, facilitating adaptation. We explore these ideas by studying how fission-fusion social structure arises in spider monkey (Ateles geoffroyi) groups, exploring whether monkeys use social knowledge to collectively compute subgroup size distributions adaptive for foraging in variable environments. We assess whether individual decisions to stay in or leave subgroups are conditioned on strategies based on the presence or absence of others. We search for this evidence in a time series of subgroup membership. We find that individuals have multiple strategies, suggesting that the social knowledge of different individuals is important. These stay-leave strategies provide microscopic inputs to a stochastic model of collective computation encoded in a family of circuits. Each circuit represents an hypothesis for how collectives combine strategies to make decisions, and how these produce various subgroup size distributions. By running these circuits forward in simulation we generate new subgroup size distributions and measure how well they match food abundance in the environment using transfer entropies. We find that spider monkeys decide to stay or go using information from multiple individuals and that they can collectively compute a distribution of subgroup size that makes efficient use of ephemeral sources of nutrition. We are able to artificially tune circuits with subgroup size distributions that are a better fit to the environment than the observed. This suggests that a combination of measurement error, constraint, and adaptive lag are diminishing the power of collective computation in this system. These results are relevant for a more general understanding of the emergence of ordered states in multi-scale social systems with adaptive properties–both natural and engineered.",0.34430035948753357,20
protect_from_temperature,32,"The avian “hibernation” enigma: thermoregulatory patterns and roost choice of the common poorwill. Compared to mammals, there are relatively few studies examining heterothermy in birds. In 13 bird families known to contain heterothermic species, the common poorwill (Phalaenoptilus nuttallii) is the only species that ostensibly hibernates. We used temperature-sensitive radio-transmitters to collect roost and skin temperature (Tskin) data, and winter roost preferences for free-ranging poorwills in southern Arizona. Further, to determine the effect of passive rewarming on torpor bout duration and active rewarming (i.e., the use of metabolic heat to increase Tskin), we experimentally shaded seven birds during winter to prevent them from passively rewarming via solar radiation. Poorwills selected winter roosts that were open to the south or southwest, facilitating passive solar warming in the late afternoon. Shaded birds actively rewarmed following at least 3 days of continuous torpor. Average torpor bout duration by shaded birds was 122 h and ranged from 91 to 164 h. Active rewarming by shaded birds occurred on significantly warmer days than those when poorwills remained torpid. One shaded bird remained inactive for 45 days, during which it spontaneously rewarmed actively on eight occasions. Our findings show that during winter poorwills exhibit physiological patterns and active rewarming similar to hibernating mammals.",0.9702757000923157,1
protect_from_temperature,215,"Molecular Physiology of Freeze Tolerance in Vertebrates.. Freeze tolerance is an amazing winter survival strategy used by various amphibians and reptiles living in seasonally cold environments. These animals may spend weeks or months with up to ∼65% of their total body water frozen as extracellular ice and no physiological vital signs, and yet after thawing they return to normal life within a few hours. Two main principles of animal freeze tolerance have received much attention: the production of high concentrations of organic osmolytes (glucose, glycerol, urea among amphibians) that protect the intracellular environment, and the control of ice within the body (the first putative ice-binding protein in a frog was recently identified), but many other strategies of biochemical adaptation also contribute to freezing survival. Discussed herein are recent advances in our understanding of amphibian and reptile freeze tolerance with a focus on cell preservation strategies (chaperones, antioxidants, damage defense mechanisms), membrane transporters for water and cryoprotectants, energy metabolism, gene/protein adaptations, and the regulatory control of freeze-responsive hypometabolism at multiple levels (epigenetic regulation of DNA, microRNA action, cell signaling and transcription factor regulation, cell cycle control, and anti-apoptosis). All are providing a much more complete picture of life in the frozen state.",0.9575110673904419,2
protect_from_temperature,312,"Skeletal muscle thermogenesis enables aquatic life in the smallest marine mammal. Keeping warm when small Several mammal species live in cold-water environments, enabled by adaptations such as blubber and large size. A notable exception to this rule is the sea otter, a species that is orders of magnitude smaller and skinnier than the others. It is known that the sea otter's unusually thick fur helps, but Wright et al. show that they are also internally warmed by thermogenic leak from skeletal muscle, a process that elevates their metabolic rate three times above that expected for their size. This mechanism is present even in infants with immature muscles, providing these animals with internal warmth from birth. Science, abf4557, this issue p. 223 Thermogenesis is a primary regulator of sea otter muscle metabolism, allowing them to inhabit cold water. Basal metabolic rate generally scales with body mass in mammals, and variation from predicted levels indicates adaptive metabolic remodeling. As a thermogenic adaptation for living in cool water, sea otters have a basal metabolic rate approximately three times that of the predicted rate; however, the tissue-level source of this hypermetabolism is unknown. Because skeletal muscle is a major determinant of whole-body metabolism, we characterized respiratory capacity and thermogenic leak in sea otter muscle. Compared with that of previously sampled mammals, thermogenic muscle leak capacity was elevated and could account for sea otter hypermetabolism. Muscle respiratory capacity was modestly elevated and reached adult levels in neonates. Premature metabolic development and high leak rate indicate that sea otter muscle metabolism is regulated by thermogenic demand and is the source of basal hypermetabolism.",0.9560046195983887,3
protect_from_temperature,269,"Thermoregulation in reindeer. Thermoregulation was studied in Finnish reindeer (Rangifer tarandus L) on captive and herded individuals during 1977-85. Newborn calves maintained a high rectal temperature (Tre) (+39 to +41°C) even at —23°C by increasing heat production 5- to 6-fold through non-shivering thermogenesis, stimulated by cold-induced noradrenaline (NA). Plasma NA and thyroxine (T4) were high (18 ng/ml and 459 nmol/1) in neonatal reindeer. Sensitivity to exogenous NA was lost during the first 3-4 weeks of life. At +20°C and above, calves increased Tre (ca 1°C), oxygen consumption and heart rate, thereby showing poor heat tolerance. Thermal conductance was low in a cold environment, but rose sharply as ambient temperature (Ta) increased above + 10°C. The Tre of adults (+ 38 to +39°C) was independent of Ta (—28 to +15°C). Coarse (hollow) hair density and length in adults averaged 2000/cm2 and 12 mm on the legs, 1000/cm3 and 30 mm on the abdomen and 1700/cm2 and 30 mm on the back (calves 3200/cm2, 10 mm), respectively. The dependence of skin temperature on the Ta was linear in excised fur samples, but complex in living animals being strongest in the legs. Serum adrenaline correlated with the weight, age and total lipids. Serum NA and dopamine-fi-hydroxylase were highest in spring and decreased by autumn. Serum T4 was highest in summer and lowest in spring.",0.9465798735618591,4
protect_from_temperature,6,"Preparing for hibernation in ground squirrels: adrenal androgen production in summer linked to environmental severity in winter. Summary 
1. At high latitudes, evolutionary adaptations focus on those that maximize survival, with hibernation being a major one used by many smaller mammals. Typically, mammalian hibernators overwinter in sites that are ≈0°C. However, in arctic regions, such sites do not exist, necessitating hibernation at sites well below 0°C. Lipid, the normal fuel of most hibernators, may not provide sufficient glucose needed by certain tissues to permit survival, with muscle breakdown being required. Critical to enhancing muscle stores are high concentrations of anabolic androgens prior to hibernation when the gonads are inactive. 
 
2. We compare and contrast androgen levels in arctic ground squirrels (AGS) (Urocitellus parryii Richardson) from the Yukon and Columbian ground squirrel (CGS) (U. columbianus Ord) from southern Alberta. 
 
3. In males, changes in testes mass over the active season were similar between AGS and CGS. In contrast, during the breeding and the nonbreeding, pre-hibernation periods, androgen levels in AGS were 6–10 and 20–25 times, respectively, those of CGS. From the breeding to the pre-hibernation periods, androgen levels declined 41% in AGS, but 86% in CGS. In females, androgen levels in AGS were high throughout the active season and, prior to hibernation, were 24 times those in CGS. 
 
4. In pre-hibernating AGS, we determined the source of these high androgen levels from two studies. First, using a hormonal challenge protocol to probe the hypothalamic-pituitary-adrenal axis, we found that androgen levels in both females and males decreased ≥10% in response to suppression by dexamethasone (an artificial glucocorticoid that inhibits ACTH release) and increased ≥18% in response to direct adrenal stimulation by adrenocorticorticotropic homone (ACTH). Second, by sequential hormonal injections in males of gonadotropin-releasing hormone (GnRH) and of ACTH coupled with gonadectomy (GDX), followed by adrenalectomy (ADX), we found that GnRH had no effect, whereas ACTH stimulated androgen levels by >40%, both before and after GDX. After ADX, levels fell by 80%. Thus, the adrenals, not the gonads, are the source of these androgens. 
 
5. We hypothesize that pre-hibernating AGS have evolved a solution seen in no other known mammal: exploiting the benefits of high adrenal androgen levels prior to hibernation to build muscle that is then catabolized overwinter. The unknown is how AGS have mitigated the costs of these high androgen levels.",0.9457284212112427,5
protect_from_temperature,154,"Broadband omnidirectional light reflection and radiative heat dissipation in white beetles Goliathus goliatus.. Structural whiteness, stemming from biologically evolutionarily refined structures, provides inspiration for designing promising, reflectance-based materials. White beetles Goliathus goliatus, which can survive in high-temperature-equatorial forests, may suggest undiscovered new physical mechanisms for thermoregulation. Their scales' whiteness is created by the exquisite shell/hollow cylinder structure with two thermoregulatory effects, contributing to a lower equilibrium temperature of elytra under direct sunlight. In the visible regime, they enhance the broadband omnidirectional reflection significantly by synergetic structural effects originating from the thin-film interference, Mie resonance and total reflection. In the mid-infrared (MIR) regime, white scales act as antireflective layers to increase the emissivity in the MIR range, enabling the elytra to reradiate heat to the environment and help the beetles reduce their temperature by as much as ∼7.8 °C in air. These biological strategies for thermoregulation could provide new approaches for bioinspired coatings towards passive radiative cooling.",0.9429756999015808,6
protect_from_temperature,11,"Thermoperception in the common vampire bat (Desmodus rotundus). Summary1.The common vampire bat,Desmodus rotundus, is known to be capable of detecting temperature differences. In the experiments described here two animals were trained to give preference to the radiation emitted by a warm signal unit (the negative unit was left at room temperature). The distance between the decision line and the signal units was 8, 12 or 16 cm. Both animals responded to radiation as low as 0.5 × 10−4 W cm−2 (Fig. 3).2.Based on calculations of the radiation emitted by the human skin, vampires should be capable of detecting warm-blooded animals at a distance up to 16 cm (Fig. 4). This sense for thermal radiation may aid these bats in localizing or selecting a suitable biting site.3.Histological studies of the bats' facial structures indicate that thermal stimuli are most probably perceived in the three pits surrounding the central nose leaf: the thin, hairless and glandless skin is underlaid with dense connective tissue. Thermography reveals that the surface temperature of the nasal region is up to 9 °C lower than that of the neighboring parts of the face (Fig. 2).",0.9347600936889648,7
protect_from_temperature,13,"The evolution of sweat glands. Mammals have two kinds of sweat glands, apocrine and eccrine, which provide for thermal cooling. In this paper we describe the distribution and characteristics of these glands in selected mammals, especially primates, and reject the suggested development of the eccrine gland from the apocrine gland during the Tertiary geological period. The evidence strongly suggests that the two glands, depending on the presence or absence of fur, have equal and similar functions among mammals; apocrine glands are not primitive. However, there is a unique and remarkable thermal eccrine system in humans; we suggest that this system evolved in concert with bipedalism and a smooth hairless skin.",0.9346636533737183,8
protect_from_temperature,260,"Antifreeze proteins in Alaskan insects and spiders.. Prior to this study, antifreeze proteins (AFPs) had not been identified in terrestrial arthropods from the Arctic or anywhere in Alaska. The hemolymph of 75 species of insects and six spiders from interior and arctic Alaska were screened for thermal hysteresis (a difference between the freezing and melting points), characteristic of the presence of AFPs. Eighteen species of insects and three spiders were shown to have AFPs. Ten of the insects with AFPs were beetles including the first species from the families Chrysomelidae, Pythidae, Silphidae and Carabidae. In addition, the first Neuropteran to have AFPs was identified, the lacewing Hemerobius simulans together with the second and third Diptera (the first Tipulids) and the second and third Hemiptera, the stinkbug Elasmostethus interstinctus (the first Pentatomid), and the water strider Limnoporus dissortis (the first Gerrid). Prior to this study, 33 species of insects and three spiders had been reported to have AFPs. Most AFP-producing terrestrial arthropods are freeze avoiding, and the AFPs function to prevent freezing. However, some of the AFP- producing insects identified in this study are known to be freeze tolerant (able to survive freezing) to very low temperatures (-40 to -70 degrees C).",0.9301576614379883,9
protect_from_temperature,229,"Bio-inspired cooling technologies and the applications in buildings. Abstract In response to the growing demand for indoor environmental quality (IEQ) and energy efficiency, abundant innovative bio-inspired cooling technologies have been proposed and their applications in buildings have been greatly demonstrated in the previous decades to enhance the benefits of building occupants. IEQ is associated with human health and productivity but maintaining good IEQ requires continuous air-conditioning resulting in a high energy consumption, especially space cooling. Bio-inspired cooling technologies focus on the fundamental mechanisms of heat transfer used by animals or plants which are considered as the keys to create a harmony between buildings and the nature, whereby IEQ can be enhanced while achieving energy efficiency. This review provides a comprehensive summary on the current bio-inspired cooling technologies, including the concepts in the research stage and the well-developed products applied in buildings, and discusses some promising designs that have the most potential for future applications. This paper is structured according to building elements, in which technologies regarding HVAC system, building materials, opaque building envelope and transparent building envelope are reviewed. The heat transfer mechanisms behind each technology including conduction, convection, evaporation or phase change and radiation are discussed. Yet successful green buildings involve a smart thermal management system for which a section is dedicated to discussing various approaches in design optimization. In the last section, a case study simulation of implementation of bio-inspired cooling technologies in a house and its energy efficient performance are analyzed. The authors attempt to motivate the future research and development in energy efficient buildings.",0.9112051129341125,10
protect_from_temperature,268,"An Investigation on Surface Characteristics of Hair Fibres of Cold-Resistant Animals. Cold weather and the subsequent demand for lightweight apparel have prompted research work in the field of thermal insulation clothing. In addition to natural fibres, such as wool and cashmere, hollow chemical fibres, such as polyester or polypropylene fibre, have been studied and used to make thermal-insulation clothing. Primarily, modifications are made to increase the hollow ratio; however, this results in the fibre becoming brittle and prone to collapse. Yet many animals survive in harsh and cold conditions, and their hair plays a key role in keeping the body warm. In the research under discussion, 4 types of cold-resistant animals are selected for observation of their hair fibres based on optical and scanning electronic microscopies. The characteristics of the hair fibres of cold-resistant animals are examined, including colour, scale density, scale thickness, medullary distribution and morphology of cross sections. The conclusions show that there are some common characteristics among cold-resistant ...",0.9013465642929077,11
protect_from_temperature,19,"Bionic photovoltaic panels bio-inspired by green leaves. In strong solar light, silicon solar panels can heat up by 70°C and, thereby, loose approximately one third of their efficiency for electricity generation. Leaf structures of plants on the other hand, have developed a series of technological adaptations, which allow them to limit their temperature to 40–45°C in full sunlight, even if water evaporation is suppressed. This is accomplished by several strategies such as limitation of leaf size, optimization of aerodynamics in wind, limitation of absorbed solar energy only to the useful fraction of radiation and by efficient thermal emission. Optical and infrared thermographic measurements under a solar simulator and in a streaming channel were used to investigate the corresponding properties of leaves and to identify suitable bionic model systems. Experiments started with the serrated structure of ordinary green leaves distributed over typical twig structures and finally identified the Australian palm tree Licuala ramsayi as a more useful bionic model. It combines a large area for solar energy harvesting with optimized aerodynamic properties for cooling and is able to restructure itself as a protection against strong winds. The bionic models, which were constructed and built, are analyzed and discussed.",0.8817110061645508,12
protect_from_temperature,195,"Delay of ice formation on penguin feathers. Cold-weather penguins continually dive in and out of the water and get splashed by waves during the frigid Antarctic winter. Yet, even under these extreme sub-zero conditions, macroscopic ice crystals are typically not observed on their feathers. In this work, we hypothesize that the origin of the anti-icing properties of a cold-weather penguin’s feathers comes from a unique combination of the feather’s macroscopic structure, the nanoscale topography of its barbules, and the hydrophobicity of its preen oil. We show that, the combination of all three, make cold-weather penguin feathers both highly water repellant and icephobic. In this paper, we present the results from a series of droplet freezing experiments performed on feathers from a number of species of both cold-weather and warm-weather penguins. Compared to a smooth glass substrate, freezing was delayed by a factor of 30-times for drops deposited on warm-weather penguin feathers and 60-times for cold-weather penguins. The difference in freezing time between warm- and cold-weather penguins was statistically significant and can be attributed to the increase in the contact angle measured between the drop and the feather of the cold-weather penguin. This increased contact angle is the result of an increase in the hydrophobicity of the preen oil and the inclusion of nanoscale, air-trapping dimples on the surface of the barbules. The physics of this delay are explained through the development of a simple heat transfer model which demonstrates that increasing contact angle is a primary cause of increased freezing time and icephobicity. The results of this study can be used to motivate the designs of biomimetic surfaces to minimize ice formation in extreme conditions for a number of important engineering applications.",0.877612292766571,13
protect_from_temperature,55,"Metabolic rate in common shrews is unaffected by temperature, leading to lower energetic costs through seasonal size reduction. Small endothermic mammals have high metabolisms, particularly at cold temperatures. In the light of this, some species have evolved a seemingly illogical strategy: they reduce the size of the brain and several organs to become even smaller in winter. To test how this morphological strategy affects energy consumption across seasonally shifting ambient temperatures, we measured oxygen consumption and behaviour in the three seasonal phenotypes of the common shrew (Sorex araneus), which differ in size by about 20%. Body mass was the main driver of oxygen consumption, not the reduction of metabolically expensive brain mass. Against our expectations, we found no change in relative oxygen consumption with low ambient temperature. Thus, smaller body size in winter resulted in significant absolute energy savings. This finding could only partly be explained by an increase of lower cost behaviours in the activity budgets. Our findings highlight that these shrews manage to avoid one of the most fundamental and intuitive rules of ecology, allowing them to subsist with lower resource availability and successfully survive the harsh conditions of winter.",0.8705354332923889,14
protect_from_temperature,34,"Antifreeze glycoprotein activity correlates with long-range protein-water dynamics.. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) enable the survival of organisms living in subfreezing habitats and serve as preservatives. Although their function is known, the underlying molecular mechanism was not understood. Mutagenesis experiments questioned the previous assumption of hydrogen bonding as the dominant mechanism. We use terahertz spectroscopy to show that antifreeze activity is directly correlated with long-range collective hydration dynamics. Our results provide evidence for a new model of how AFGPs prevent water from freezing. We suggest that antifreeze activity may be induced because the AFGP perturbs the aqueous solvent over long distances. Retarded water dynamics in the large hydration shell does not favor freezing. The complexation of the carbohydrate cis-hydroxyl groups by borate suppresses the long-range hydration shell detected by terahertz absorption. The hydration dynamics shift toward bulk water behavior strongly reduces the AFGP antifreeze activity, further supporting our model.",0.868142306804657,15
protect_from_temperature,125,"Life under quartz: Hypolithic mosses in the Mojave Desert. Several species of dryland cyanobacteria are known to occur as hypoliths under semi-translucent rocks. In the Mojave Desert, these organisms find refuge from intense solar radiation under milky quartz where moisture persists for a longer period of time than in adjacent soil surface habitat. Desert mosses, which are extremely desiccation-tolerant, can also occur in these hypolithic spaces, though little is known about this unique moss microhabitat and how species composition compares to that of adjacent soil surface communities. To address this question, we deployed microclimate dataloggers and collected moss samples from under and adjacent to 18 milky quartz rocks (quartz mean center thickness 26 ± 15 mm) in a western high elevation Mojave Desert site. Light transmission through Mojave quartz rocks may be as low as 1.2%, and data from microclimate loggers deployed for five months support the hypothesis that quartz provides thermal buffering and higher relative humidity compared to the soil surface. Of the 53 samples collected from hypolith and surface microhabitats, 68% were Syntrichia caninervis, the dominant bryophyte of the Mojave Desert biological soil crust. Tortula inermis accounted for 28% of the samples and 4% were Bryum argenteum. In a comparison of moss community composition, we found that S. caninervis was more likely to be on the soil surface, though it was abundant in both microhabitats, while T. inermis was more restricted to hypoliths, perhaps due to protection from temperature extremes. In our study site, the differences between hypolithic and surface microhabitats enable niche partitioning between T. inermis and S. caninervis, enhancing alpha diversity. This work points to the need to thoroughly consider microhabitats when assessing bryophyte species diversity and modelling species distributions. This focus is particularly important in extreme environments, where mosses may find refuge from the prevailing macroclimatic conditions in microhabitats such as hypoliths.",0.8565272688865662,16
protect_from_temperature,51,"Theoretical and experimental studies of energy exchange from jackrabbit ears and cylindrically shaped appendages.. Convection properties of jackrabbit ears were examined in a wind tunnel and in the field in an attempt to study the possible thermal role of the large ears. This work was part of a study on energy exchange of appendages. Cylindrical copper models of various shapes, aluminum castings of domestic and jackrabbit ears, and an amputated jackrabbit ear were studied in a wind tunnel (a) to define the range for convective heat loss for appendages of various shapes, and (b) to study the effect on convection of model shape and orientation to the wind. Shape, i.e. length and closure, proved important. Orientation to the wind produced no consistent or significant variation in the convection coefficient. The convection coefficients from the ear castings fell within the range generated from the cylindrical models. The convection coefficients for the amputated rabbit ear fell partially within the range. Net thermal radiation loss at midday from the jackrabbit ears was found to be small. Convection from the ears, however, could account for the loss of over 100% of the animal's metabolic heat at an air temperature of 30 degrees C. If air temperature exceeds body temperature, the animal must either store heat or resort to the evaporation of water.",0.8336219191551208,17
protect_from_temperature,274,"Soft Matter Mechanics and the Mechanisms Underpinning the Infrared Vision of Snakes. Summary Pit-bearing snakes (vipers, pythons, and boas) have the extraordinary ability to “see” and accurately locate their prey and predators in total darkness. These animals use the infrared radiation emanating from objects that are warmer relative to the background environment to form a thermal image. Although enormous progress has been made to identify the key physiological features that enable the infrared vision of these snakes and a few other animals, the precise thermoelectric transduction mechanism that mediates the conversion of infrared heat to processable electrical signals has remained elusive. In this work, we quantitatively outline how cells in the snake's pit membrane organ act as apparent pyroelectric materials and convert infrared radiation into electrical signals. Despite the exceptional simplicity of our proposed mechanism and model, we are able to explain many central experimental results pertaining to the transduction process.",0.7342402935028076,18
protect_from_temperature,181,"Contrasting Behavior of Antifreeze Proteins: Ice Growth Inhibitors and Ice Nucleation Promoters.. Several types of natural molecules interact specifically with ice crystals. Small antifreeze proteins (AFPs) adsorb to particular facets of ice crystals, thus inhibiting their growth, whereas larger ice-nucleating proteins (INPs) can trigger the formation of new ice crystals at temperatures much higher than the homogeneous ice nucleation temperature of pure water. It has been proposed that both types of proteins interact similarly with ice and that, in principle, they may be able to exhibit both functions. Here we investigated two naturally occurring antifreeze proteins, one from fish, type-III AFP, and one from beetles, TmAFP. We show that in addition to ice growth inhibition, both can also trigger ice nucleation above the homogeneous freezing temperature, providing unambiguous experimental proof for their contrasting behavior. Our analysis suggests that the predominant difference between AFPs and INPs is their molecular size, which is a very good predictor of their ice nucleation temperature.",0.7243232727050781,19
protect_from_temperature,30,"Ice Nucleation Activity in Lichens. A newly discovered form of biological ice nucleus associated with lichens is described. Ice nucleation spectra of a variety of lichens from the southwestern United States were measured by the drop-freezing method. Several epilithic lichen samples of the genera Rhizoplaca, Xanthoparmelia, and Xanthoria had nuclei active at temperatures as warm as −2.3°C and had densities of 2.3 × 106 to more than 1 × 108 nuclei g−1 at −5°C (2 to 4 orders of magnitude higher than any plants infected with ice nucleation-active bacteria). Most lichens tested had nucleation activity above −8°C. Lichen substrates (rocks, plants, and soil) showed negligible activity above −8°C. Ice nucleation-active bacteria were not isolated from the lichens, and activity was not destroyed by heat (70°C) or sonication, indicating that lichen-associated ice nuclei are nonbacterial in origin and differ chemically from previously described biological ice nuclei. An axenic culture of the lichen fungus Rhizoplaca chrysoleuca showed detectable ice nucleation activity at −1.9°C and an ice nucleation density of 4.5 × 106 nuclei g−1 at −5°C. It is hypothesized that these lichens, which are both frost tolerant and dependent on atmospheric moisture, derive benefit in the form of increased moisture deposition as a result of ice nucleation.",0.7189710736274719,20
physically_assemble_structure,104,"Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.",0.8810368180274963,1
physically_assemble_structure,242,"Dynamics of topological defects and structural synchronization in a forming periodic tissue. Living organisms form a large variety of hierarchically structured extracellular functional tissues. Remarkably, these materials exhibit regularity and structural coherence across multiple length scales, far beyond the size of a single cell. Here, synchrotron-based nanotomographic imaging in combination with machine-learning-based segmentation is used to reveal the structural synchronization process of nacre forming in the shell of the mollusc Unio pictorum . We show that the emergence of this highly regular layered structure is driven by a disorder-to-order transition achieved through the motion and interaction of screw-like structural dislocations with an opposite topological sign. Using an analogy to similar processes observed in liquid-crystalline systems, we demonstrate that these microstructural faults act as dissipative topological defects coupled by an elastic distortion field surrounding their cores. Their mutual annihilation results in structural synchronization that is simulated using the classical Kuramoto model. The developed experimental, theoretical and numerical framework provides a comprehensive physical view of the formation of biogenic materials. Molluscs assemble layers of material in the shells around them with a high level of control. Here the authors observe the structural evolution of layer formation and propose a mechanism reminiscent of topological defect dynamics in liquid crystals.",0.851263701915741,2
physically_assemble_structure,245,"Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.",0.6237163543701172,3
physically_assemble_structure,190,"Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Significance Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.",0.6071041822433472,4
physically_assemble_structure,138,Cellulose synthase interactive1- and microtubule-dependent cell wall architecture is required for acid growth in Arabidopsis hypocotyls. We observed a correlation between acid growth and crossed-polylamellate cell walls which was dependent on CSI1 and microtubules. This is significant for re-evaluating current models of cell morphogenesis.,0.5028939247131348,5
physically_assemble_structure,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.5013623833656311,6
physically_assemble_structure,159,"The Scaly-foot Snail genome and implications for the origins of biomineralised armour. The Scaly-foot Snail, Chrysomallon squamiferum , presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome. The Scaly-foot Snail, Chrysomallon squamiferum , is a model for understanding the evolution of biomineralised armour. Here, the authors present a chromosome-level reference genome assembly and tissue-specific transcriptomic data for this enigmatic organism.",0.3279581367969513,7
physically_assemble_structure,214,"Quadratic resource value assessment during mantis shrimp (Stomatopoda) contests. Resource value assessment, in which competitors adjust behaviours according to the perceived value of a contested resource, is well described in animal contests. Such assessment is usually assumed to be categorical or linear; for example, males fight more aggressively when females are present than absent, or as female fecundity increases. Here, to our knowledge for the first time, we show quadratic resource value assessment, in which resource value is highest at a certain level and decreases in either direction. The mantis shrimp Neogonodactylus bredini occupies coral rubble burrows in a size-assortative manner: individuals of a certain body size inhabit burrows of a certain size. Using mock burrows of various sizes, we tested whether mantis shrimp (1) chose burrows predicted to be the best fit for their body size and (2) were more aggressive during, endured higher costs during and were more likely to win contests over burrows predicted to be best fit. Individuals chose burrows larger than their predicted best fit burrows. In contests, intruders without burrows were more likely to evict burrow residents when the burrow was slightly smaller than the intruder's predicted best fit size. Intruder success decreased as relative burrow size increased or decreased from this value. Intruders won by delivering more strikes and by being aggressive first. In contrast to intruders, burrow residents showed little evidence of resource value assessment. A literature review revealed that quadratic resource value assessment may play a role in contests over resources from territories to parasite hosts. Therefore, our results impact theoretical models of contest behaviour and may lend insight to how contests affect resource distributions.",0.3111514747142792,8
physically_assemble_structure,41,"Calcium Carbonate in Termite Mounds. THE presence of appreciable quantities of calcium carbonate in termite mounds on non-calcareous soil has intrigued pedologists for many years. Milne6, for example, found a termite mound with 7% calcium carbonate and estimated that it contained about 2 t of calcium carbonate excluding the hard limestone (53% CaCO3) base of the mound. The soil below the base of a termite mound may also be calcareous. The soil underneath one termite mound in an area of non-calcareous soil was found to have a mean of 1.7% calcium carbonate to a depth of 6 m, or about 20 t of calcium carbonate9.",0.3081223666667938,9
physically_assemble_structure,210,"Optimal construction of army ant living bridges.. Integrating the costs and benefits of collective behaviors is a fundamental challenge to understanding the evolution of group living. These costs and benefits can rarely be quantified simultaneously due to the complexity of the interactions within the group, or even compared to each other because of the absence of common metrics between them. The construction of 'living bridges' by New World army ants - which they use to shorten their foraging trails - is a unique example of a collective behavior where costs and benefits have been experimentally measured and related to each other. As a result, it is possible to make quantitative predictions about when and how the behavior will be observed. In this paper, we extend a previous mathematical model of these costs and benefits to much broader domain of applicability. Specifically, we exhibit a procedure for analyzing the optimal formation, and final configuration, of army ant living bridges given a means to express the geometrical configuration of foraging path obstructions. Using this procedure, we provide experimentally testable predictions of the final bridge position, as well as the optimal formation process for certain cases, for a wide range of scenarios, which more closely resemble common terrain obstacles that ants encounter in nature. As such, our framework offers a rare benchmark for determining the evolutionary pressures governing the evolution of a naturally occurring collective animal behavior.",0.27701306343078613,10
physically_assemble_structure,244,"DNA Origami Design: A How-To Tutorial. While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.",0.2519739866256714,11
physically_assemble_structure,297,"Nature's forms are frilly, flexible, and functional.. A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.",0.2033100128173828,12
physically_assemble_structure,122,"Architecture of a catalytically active homotrimeric plant cellulose synthase complex. Plant cell wall construction crew Plants produce a complex cell wall in which cellulose, a glucose polymer, is a major component. Cellulose fibers are formed from close-packed single chains of cellulose that have been proposed to be formed by multimeric complexes (18 or more subunits) of the enzyme cellulose synthase, which exists in several isoforms. Purushotham et al. determined a cryo–electron microscopy structure of a trimer of a single isoform of cellulose synthase. A large channel forms a path for cellulose chains through the membrane-embedded complex. The structure also reveals oligomeric interfaces and provides a framework for modeling the larger complexes seen in plant membranes. The close arrangement of exit sites for nascent glycan chains is consistent with the enzyme complex playing a role in directing cellulose microfibril formation. Science, this issue p. 1089 The structure of a homotrimeric cellulose synthase complex provides molecular insights into cellulose fibril formation. Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.",0.19251473248004913,13
physically_assemble_structure,173,"Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication. Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.",0.1920330822467804,14
physically_assemble_structure,90,"Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries. Significance Dental caries remains an unresolved public health problem. The etiology is poorly understood, as the oral cavity harbors diverse communities of microorganisms. Using multiple imaging modalities on human teeth from patients with caries, we discovered a microbial community precisely arranged in a corona-like architecture. Moreover, this organization is mediated by the pathogen Streptococcus mutans through production of an extracellular scaffold that directs positioning of other oral microbes. We developed a methodology to quantify the spatial structure of microbial communities at the micron scale and found a precise spatial patterning of bacteria associated with localized caries onset. These findings are relevant as we approach the post-microbiome era, whereby quantifying the community structural organization may be essential for understanding microbiome function. Tooth decay (dental caries) is a widespread human disease caused by microbial biofilms. Streptococcus mutans, a biofilm-former, has been consistently associated with severe childhood caries; however, how this bacterium is spatially organized with other microorganisms in the oral cavity to promote disease remains unknown. Using intact biofilms formed on teeth of toddlers affected by caries, we discovered a unique 3D rotund-shaped architecture composed of multiple species precisely arranged in a corona-like structure with an inner core of S. mutans encompassed by outer layers of other bacteria. This architecture creates localized regions of acidic pH and acute enamel demineralization (caries) in a mixed-species biofilm model on human teeth, suggesting this highly ordered community as the causative agent. Notably, the construction of this architecture was found to be an active process initiated by production of an extracellular scaffold by S. mutans that assembles the corona cell arrangement, encapsulating the pathogen core. In addition, this spatial patterning creates a protective barrier against antimicrobials while increasing bacterial acid fitness associated with the disease-causing state. Our data reveal a precise biogeography in a polymicrobial community associated with human caries that can modulate the pathogen positioning and virulence potential in situ, indicating that micron-scale spatial structure of the microbiome may mediate the function and outcome of host–pathogen interactions.",0.1758967489004135,15
physically_assemble_structure,156,"Character Displacement Promotes Cooperation in Bacterial Biofilms. Resource competition within a group of cooperators is expected to decrease selection for cooperative behavior but can also result in diversifying selection for the use of different resources, which in turn could retard the breakdown of cooperation. Diverse groups are likely to be less susceptible to invasion by noncooperating social cheats: First, competition repression resulting from character displacement may provide less of a selective advantage to cheating; second, cheats may trade off the ability to exploit cooperators that specialize in one type of resource against cooperators that specialize in another ; third, diverse communities of any kind may have higher invasion resistance because there are fewer resources available for an invader to use . Furthermore, diverse groups are likely to be more productive than clonal groups if a wider range of total resources are being used . We addressed these issues by using the cooperative trait of biofilm formation in Pseudomonas fluorescens. Character displacement through resource competition evolved within biofilms; productivity increased with increasing character displacement, and diverse biofilms were less susceptible to invasion by cheats. These results demonstrate that diversification into different ecological niches can minimize selection against cooperation in the face of local resource competition.",0.16079120337963104,16
physically_assemble_structure,194,"Type-I collagen fibrils: From growth morphology to local order. Abstract.The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ($\alpha$α) or coarse ($ \beta$β) have opposite molecular orientations. The $\alpha$α-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for $\alpha$α-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.Graphical abstract",0.1569596230983734,17
physically_assemble_structure,96,"Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life. Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38 ×  10−6 per bp per generation) that is two orders of magnitude higher than reported for any non-viral organism, with 93–98% of mutations being RIP-associated. RIP mutations are, however, relatively rare in coding sequence, in part because RIP preferentially attacks GC-poor long duplicates that interact in three dimensional space, while coding sequence duplicates are rare, GC-rich, short, and tend not to interact. Despite this, with over 5 coding sequence mutations per genome per generation, the mutational burden is an order of magnitude higher than the previously highest observed. Unexpectedly, the majority of these coding sequence mutations appear not to be the direct product of RIP being mostly in non-duplicate sequence and predominantly not C→T mutations. Nonetheless, RIP-deficient strains have over an order of magnitude fewer coding sequence mutations outside of duplicated domains than RIP-proficient strains. Neurospora crassa has the highest mutation rate and mutational burden of any non-viral life. While the high rate is largely due to the action of RIP, the mutational burden appears to be RIP-associated but not directly caused by RIP.",0.12962733209133148,18
physically_assemble_structure,127,"Chromatic neuronal jamming in a primitive brain. Jamming models developed in inanimate matter have been widely used to describe cell packing in tissues 1 – 7 , but predominantly neglect cell diversity, despite its prevalence in biology. Most tissues, animal brains in particular, comprise a mix of many cell types, with mounting evidence suggesting that neurons can recognize their respective types as they organize in space 8 – 11 . How cell diversity revises the current jamming paradigm is unknown. Here, in the brain of the flatworm planarian Schmidtea mediterranea , which exhibits remarkable tissue plasticity within a simple, quantifiable nervous system 12 – 16 , we identify a distinct packing state, ‘chromatic’ jamming. Combining experiments with computational modelling, we show that neurons of distinct types form independent percolating networks barring any physical contact. This jammed state emerges as cell packing configurations become constrained by cell type-specific interactions and therefore may extend to describe cell packing in similarly complex tissues composed of multiple cell types. An imaging study of planarian flatworm brains demonstrates that densely packed neural tissues seem to have packing configurations commensurate with a jammed state.",0.12779061496257782,19
physically_assemble_structure,255,"Nocturnal visual displays and call description of the cascade specialist glassfrog Sachatamia orejuela. Although most male frogs call to attract females, vocalizations alone can be ineffective long-range signals in certain environments. To increase conspicuousness and counter the background noise generated by rushing water, a few frog species around the world have evolved visual communication modalities in addition to advertisement calls. These species belong to different families on different continents: a clear example of behavioural convergent evolution. Until now, long-distance visual signalling has not been recorded for any species in the glassfrog family (Centrolenidae). Sachatamia orejuela, an exceptionally camouflaged glassfrog species found within the spray zone of waterfalls, has remained poorly studied. Here, we document its advertisement call for the first time — the frequency of which is higher than perhaps any other glassfrog species, likely an evolutionary response to its disruptive acoustic space — as well as a sequence of non-antagonistic visual signals (foot-flagging, hand-waving, and head-bobbing) that we observed at night.",0.11781453341245651,20
prevent_fracture/rupture,76,"Bone-inspired microarchitectures achieve enhanced fatigue life. Significance Microarchitectured materials, such as foams and lattice structures, can achieve high stiffness and strength while remaining extremely lightweight. Applying high-porosity microarchitectured materials to durable devices, such as vehicles, however, will require the materials to also resist failure during cyclic loading. Here, we identify an aspect of microstructure in cancellous bone that greatly influences failure under cyclic loading and show that the effect is generalizable to synthetic microarchitectured materials. Our findings demonstrate that a common design strategy to improve stiffness and strength of microarchitectured materials comes at the cost of impaired service life. Our findings are useful for the design and application of microarchitectured materials and additionally provide insight into human health in situations of osteoporosis. Microarchitectured materials achieve superior mechanical properties through geometry rather than composition. Although ultralightweight microarchitectured materials can have high stiffness and strength, application to durable devices will require sufficient service life under cyclic loading. Naturally occurring materials provide useful models for high-performance materials. Here, we show that in cancellous bone, a naturally occurring lightweight microarchitectured material, resistance to fatigue failure is sensitive to a microarchitectural trait that has negligible effects on stiffness and strength—the proportion of material oriented transverse to applied loads. Using models generated with additive manufacturing, we show that small increases in the thickness of elements oriented transverse to loading can increase fatigue life by 10 to 100 times, far exceeding what is expected from the associated change in density. Transversely oriented struts enhance resistance to fatigue by acting as sacrificial elements. We show that this mechanism is also present in synthetic microlattice structures, where fatigue life can be altered by 5 to 9 times with only negligible changes in density and stiffness. The effects of microstructure on fatigue life in cancellous bone and lattice structures are described empirically by normalizing stress in traditional stress vs. life (S-N) curves by √ψ, where ψ is the proportion of material oriented transverse to load. The mechanical performance of cancellous bone and microarchitectured materials is enhanced by aligning structural elements with expected loading; our findings demonstrate that this strategy comes at the cost of reduced fatigue life, with consequences to the use of microarchitectured materials in durable devices and to human health in the context of osteoporosis.",0.8735204339027405,1
prevent_fracture/rupture,223,"Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets. Nacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design. The hierarchical structure of nacre is known to contribute to its high strength and toughness, providing inspiration for many biomimetic materials. Here, co-oriented 20 µm stacks of aragonite platelets are shown to contribute to the toughness of nacre, defining a new characteristic length scale.",0.7978224754333496,2
prevent_fracture/rupture,78,"Bioinspired Materials with Self-Adaptable Mechanical Properties.. Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.",0.7703883647918701,3
prevent_fracture/rupture,300,"Extreme strength observed in limpet teeth. The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.",0.6024464964866638,4
prevent_fracture/rupture,206,"Deciphering an extreme morphology: bone microarchitecture of the hero shrew backbone (Soricidae: Scutisorex). Biological structures with extreme morphologies are puzzling because they often lack obvious functions and stymie comparisons to homologous or analogous features with more typical shapes. An example of such an extreme morphotype is the uniquely modified vertebral column of the hero shrew Scutisorex, which features numerous accessory intervertebral articulations and massively expanded transverse processes. The function of these vertebral structures is unknown, and it is difficult to meaningfully compare them to vertebrae from animals with known behavioural patterns and spinal adaptations. Here, we use trabecular bone architecture of vertebral centra and quantitative external vertebral morphology to elucidate the forces that may act on the spine of Scutisorex and that of another large shrew with unmodified vertebrae (Crocidura goliath). X-ray micro-computed tomography (µCT) scans of thoracolumbar columns show that Scutisorex thori is structurally intermediate between C. goliath and S. somereni internally and externally, and both Scutisorex species exhibit trabecular bone characteristics indicative of higher in vivo axial compressive loads than C. goliath. Under compressive load, Scutisorex vertebral morphology is adapted to largely restrict bending to the sagittal plane (flexion). Although these findings do not solve the mystery of how Scutisorex uses its byzantine spine in vivo, our work suggests potentially fruitful new avenues of investigation for learning more about the function of this perplexing structure.",0.519931435585022,5
prevent_fracture/rupture,22,"Pummelos as Concept Generators for Biomimetically Inspired Low Weight Structures with Excellent Damping Properties. Natural materials often exhibit excellent mechanical properties. An example of outstanding impact resistance is the pummelo fruit (Citrus maxima) which can drop from heights of 10 m and more without showing significant outer damage. Our data suggest that this impact resistance is due to the hierarchical organization of the fruit peel, called pericarp. The project presented in the current paper aims at transferring structural features from the pummelo pericarp to engineering materials, in our case metal foams, produced by the investment casting process. The transfer necessitates a detailed structural and mechanical analysis of the biological model on the one hand, and the identification and development of adequate materials and processes on the other hand. Based on this analysis, engineering composite foam structures are developed and processed which show enhanced damping and impact properties. The modified investment casting process and the model alloy Bi57Sn43 proved to be excellent candidates to make these bio-inspired structures. Mechanical testing of both the natural and the engineering structures has to consider the necessity to evaluate the impact of the different hierarchical features. Therefore, specimens of largely varying sizes have to be tested and size effects cannot be ignored, especially as the engineering structures might be upscaled in comparison with the natural role model. All in all, the present results are very promising: the basis for a transfer of bio-inspired structural hierarchical levels has been set.",0.3520166873931885,6
prevent_fracture/rupture,192,"Spider dragline silk as torsional actuator driven by humidity. Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.",0.3078788220882416,7
prevent_fracture/rupture,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.2023412585258484,8
prevent_fracture/rupture,16,"Average nanorough skin surface of the pilot whale (Globicephalamelas, Delphinidae): considerations on the self-cleaning abilities based on nanoroughness. Abstract. In aquatic environments, the biofouling process is assumed to initiate from the conditioning layer of absorbed organic carbon residues on wetted surfaces. Microfouling organisms attach to this conditioning layer, building up a biofilm on which further biofouling proceeds. In dolphins, biofouling reduces hydrodynamic efficiency and may negatively affect health if not managed. In the present study we examined the skin surface of the pilot whale (Globicephalamelas). Employing cryo-scanning electron microscopic techniques combined with various sample preparations, the skin displayed an average nanorough surface characterized by a pattern of nanoridge-enclosed pores; the average pore size (approximately 0.20 µm2) was below the size of most marine biofouling organisms. Further, the implications of this type of surface to the self-cleaning abilities of the skin of pilot whales are discussed, based on reduced available space for biofouler attachment, the lack of any particular microniches as shelters for biofoulers, and the challenges of turbulent water flow and liquid–air interfaces during surfacing and jumping of the dolphin.",0.14926469326019287,9
prevent_fracture/rupture,310,"Antlers - Evolution, development, structure, composition, and biomechanics of an outstanding type of bone.. Antlers are bony appendages of deer that undergo periodic regeneration from the top of permanent outgrowths (the pedicles) of the frontal bones. Of the ""less familiar"" bone types whose study was advocated by John Currey to gain a better understanding of structure-function relationships of mineralized tissues and organs, antlers were of special interest to him. The present review summarizes our current knowledge about the evolution, development, structure, mineralization, and biomechanics of antlers and how their formation is affected by environmental factors like nutrition. Furthermore, the potential role of antlers as a model in bone biology and several fields of biomedicine as well as their use as a monitoring tool in environmental studies are discussed.",0.10202355682849884,10
prevent_fracture/rupture,292,"A Graphic Way For Notch Shape Optimization. Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.",0.09109900146722794,11
prevent_fracture/rupture,91,"Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts. Significance Phenotypic plasticity has emerged as an important concept in evolutionary biology. It is thought to contribute to an organism’s ability to adapt to environmental change within a single generation, which may facilitate survival and increase fitness. Furthermore, plasticity has the potential to bias the direction and/or speed of evolution by changing patterns of phenotypic variation and exposing new genetic variation to selection (i.e., flexible stem evolution). Our understanding of this important phenomenon is incomplete owing to limited knowledge of the molecular underpinnings of reaction norm evolution. Using the teleost feeding apparatus as a model, we explore this open question and show that the Hh signaling pathway underlies the ability of this structure to respond plastically to alternate feeding regimes. Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations.",0.054634544998407364,12
prevent_fracture/rupture,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.05037470534443855,13
prevent_fracture/rupture,220,"Structure and Mechanical Adaptability of a Modern Elasmoid Fish Scale from the Common Carp. Summary The carp (Cyprinus carpio) has typical elasmoid scales commonly found on teleosts. They provide protection while retaining flexibility and maneuverability of the fish. The exterior surface of the scale consists of an ultrathin discontinuous mineral layer on top of mineralized woven collagen fibrils. The underlying foundation is composed of two collagenous components. The major one consists of a single-twisted “Bouligand” structure with a twisting angle of 36°. A secondary “sheet-like” structure, formed by thinner collagen fibrils oriented along the thickness direction, acts to increase the integrity of the scale. Here, we identify the deformation and failure mechanisms of the carp scale, revealing slight tensile anisotropy. Using in situ small-angle X-ray scattering during tensile testing, the toughening mechanisms of the scale, including the adaptive structural reorientation of lamellae as well as fibrillar sliding and elastic deformation, are quantified and compared with those of other fish scales.",0.048415202647447586,14
prevent_fracture/rupture,167,"The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts. The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.",0.04280725494027138,15
prevent_fracture/rupture,41,"Calcium Carbonate in Termite Mounds. THE presence of appreciable quantities of calcium carbonate in termite mounds on non-calcareous soil has intrigued pedologists for many years. Milne6, for example, found a termite mound with 7% calcium carbonate and estimated that it contained about 2 t of calcium carbonate excluding the hard limestone (53% CaCO3) base of the mound. The soil below the base of a termite mound may also be calcareous. The soil underneath one termite mound in an area of non-calcareous soil was found to have a mean of 1.7% calcium carbonate to a depth of 6 m, or about 20 t of calcium carbonate9.",0.040090691298246384,16
prevent_fracture/rupture,250,"Biomechanical insights into the dentition of megatooth sharks (Lamniformes: Otodontidae). The evolution of gigantism in extinct otodontid sharks was paralleled by a series of drastic modifications in their dentition including widening of the crowns, loss of lateral cusplets, and acquisition of serrated cutting edges. These traits have generally been interpreted as key functional features that enabled the transition from piscivory to more energetic diets based on marine mammals, ultimately leading to the evolution of titanic body sizes in the most recent forms (including the emblematic Otodus megalodon ). To investigate this hypothesis, we evaluate the biomechanics of the anterior, lateral, and posterior teeth of five otodontid species under different loading conditions by using two-dimensional finite element analysis. Stress distribution patterns are remarkably similar among all models under puncture and draw (i.e., when subjected to vertical and lateral forces, respectively). Contrary to expectation, higher average stress values are detected under both loading scenarios in more recent species. Altogether, this suggests little correlation between tooth morphology and key aspects of biomechanical behaviour in otodontids, making it difficult to frame the morphological trend of their dentitions within an adaptive scenario. We propose that this pattern most likely emerged as a non-functional by-product of heterochronic processes driven by selection towards larger body sizes.",0.03527826815843582,17
prevent_fracture/rupture,305,"The structure and mechanics of Moso bamboo material. Although bamboo has been used structurally for millennia, there is currently increasing interest in the development of renewable and sustainable structural bamboo products (SBPs). These SBPs are analogous to wood products such as plywood, oriented strand board and glue-laminated wood. In this study, the properties of natural Moso bamboo (Phyllostachys pubescens) are investigated to further enable the processing and design of SBPs. The radial and longitudinal density gradients in bamboo give rise to variations in the mechanical properties. Here, we measure the flexural properties of Moso bamboo in the axial direction, along with the compressive strengths in the axial and transverse directions. Based on the microstructural variations (observed with scanning electron microscopy) and extrapolated solid cell wall properties of bamboo, we develop models, which describe the experimental results well. Compared to common North American construction woods loaded along the axial direction, Moso bamboo is approximately as stiff and substantially stronger, in both flexure and compression but denser. This work contributes to critical knowledge surrounding the microstructure and mechanical properties of bamboo, which are vital to the engineering and design of sustainable SBPs.",0.03247426822781563,18
prevent_fracture/rupture,264,"The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo. The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.",0.028336910530924797,19
prevent_fracture/rupture,81,"Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance. Plants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including “elicitors”, that are present in herbivores’ oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs’ (HAKs’) actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants. Uemura et al. study the mechanism of herbivore resistance in soybean and Arabidopsis. They show that receptor-like kinases (HAK1/2) respond to a polysaccharide in the oral secretions of Spodoptera litura and then interact with PBL27, resulting in an ethylene-dependent herbivore resistance.",0.021157361567020416,20
protect_from_microbes,44,"Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics.. Lipopeptides constitute a structurally diverse group of metabolites produced by various bacterial and fungal genera. In the past decades, research on lipopeptides has been fueled by their antimicrobial, antitumour, immunosuppressant and surfactant activities. However, the natural functions of lipopeptides in the lifestyles of the producing microorganisms have received considerably less attention. The substantial structural diversity of lipopeptides suggests that these metabolites have different natural roles, some of which may be unique to the biology of the producing organism. This review gives a detailed overview of the versatile functions of lipopeptides in the biology of Pseudomonas and Bacillus species, and highlights their role in competitive interactions with coexisting organisms, including bacteria, fungi, oomycetes, protozoa, nematodes and plants. Their functions in cell motility, leading to colonization of novel habitats, and in the formation and development of highly structured biofilms are discussed in detail. Finally, this review provides an update on lipopeptide detection and discovery as well as on novel regulatory mechanisms and genes involved in lipopeptide biosynthesis in these two bacterial genera.",0.9710875749588013,1
protect_from_microbes,54,"Bioactive Molecular Networking for Mapping the Antimicrobial Constituents of the Baltic Brown Alga Fucus vesiculosus. The brown alga Fucus vesiculosus is common to the intertidal zones of the Baltic Sea, where it is exposed to high fouling pressures by microorganisms. Our previous studies showed, repeatedly, the consistent antimicrobial activity of F. vesiculosus crude extracts against human pathogens, while untargeted metabolomics analyses have revealed a variety of metabolites. In this study, we applied the UPLC-QToF-MS/MS-based “bioactive molecular networking” (BMN) concept on the most bioactive n-hexane and n-butanol subextracts of Baltic F. vesiculosus coupled with in silico dereplication tools to identify the compounds responsible for antimicrobial activity. The first antimicrobial cluster identified by BMN was galactolipids. Our targeted isolation efforts for this class led to the isolation of six monogalactosyldiacylglycerol (MGDG) derivatives (1–6) and one digalactosyldiacylglycerol (DGDG, 7). The MGDGs 5 and 6 and the DGDG 7 exhibited activity against Staphylococcus aureus. The second compound class with high bioactivity was phlorotannins. In particular, phlorethol-type phlorotannins showed high correlations with antimicrobial activity based on the BMN approach, and two phlorotannins (8–9) were isolated. This study shows that antimicrobial components of F. vesiculosus reside in the algal cell walls and membranes and that BMN provides a complementary tool for the targeted isolation of bioactive metabolites.",0.9452769756317139,2
protect_from_microbes,187,"Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules. Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.Autotransporter proteins are localised to the bacterial surface and promote colonisation of host epithelial surfaces. Here, the authors present the crystal structure of autotransporter UpaB and show evidence for distinct binding sites for glycosaminoglycans and host fibronectin.",0.9399811625480652,3
protect_from_microbes,38,"Cell-cell communication in gram-positive bacteria.. In gram-positive bacteria, many important processes are controlled by cell-to-cell communication, which is mediated by extracellular signal molecules produced by the bacteria. Most of these signaling molecules are peptides or modified peptides. Signal processing, in most cases, involves either transduction across the cytoplasmic membrane or import of the signal and subsequent interaction with intracellular effectors. Concentrations of signal in the nanomolar range or below are frequently sufficient for biological activity. The microbial processes controlled by extracellular signaling include the expression of virulence factors, the expression of gene transfer functions, and the production of antibiotics.",0.938174843788147,4
protect_from_microbes,129,"A Clerodane Diterpene from Callicarpa americana Resensitizes Methicillin-Resistant Staphylococcus aureus to ß-Lactam Antibiotics.. The rise of antibiotic resistance presents a significant healthcare challenge and precludes the use of many otherwise valuable antibiotics. One potential solution to this problem is the use of antibiotics in combination with resistance-modifying agents, compounds that act synergistically with existing antibiotics to resensitize previously resistant bacteria. In this study, 12(S),16ξ-dihydroxycleroda-3,13-dien-15,16-olide, a clerodane diterpene isolated from the medicinal plant Callicarpa americana, was found to synergize with oxacillin against methicillin-resistant Staphylococcus aureus. This synergy was confirmed by checkerboard (FICI = 0.125) and time-kill assays, with a sub-inhibitory dose of 12(S),16ξ-dihydroxycleroda-3,13-dien-15,16-olide causing the effective concentration of oxacillin to fall below the susceptibility breakpoint for S. aureus, a > 32-fold decrease in both cases.",0.9377897381782532,5
protect_from_microbes,23,"Antibacterial properties of larval secretions of the blowfly, Lucilia sericata. Abstract.  The antibacterial properties of secretions aseptically collected from larvae of the greenbottle fly Lucilia sericata (Meigen) (Diptera: Calliphoridae) were examined. These investigations revealed the presence of small (<1 kDa) antibacterial factor(s) within the larval secretions, active against a range of bacteria. These include the Gram‐positive Staphylococcus aureus, both methicillin‐resistant Staphylococcus aureus (MRSA) and methicillin‐sensitive Staphylococcus aureus (MSSA), Streptococcus pyogenes and to a lesser extent the Gram‐negative Pseudomonas aeruginosa. These secretions were shown to be highly stable as a freeze‐dried preparation and, considering the activity against organisms typically associated with clinical infection, may be a source of novel antibiotic‐like compounds that may be used for infection control and in the fight against MRSA.",0.9244620203971863,6
protect_from_microbes,85,"The Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus: an Untargeted Metabolomics Study. Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin. ABSTRACT Antibiotics have served humankind through their use in modern medicine as effective treatments for otherwise fatal bacterial infections. Teixobactin is a first member of newly discovered natural antibiotics that was recently identified from a hitherto-unculturable soil bacterium, Eleftheria terrae, and recognized as a potent antibacterial agent against various Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. The most distinctive characteristic of teixobactin as an effective antibiotic is that teixobactin resistance could not be evolved in a laboratory setting. It is purported that teixobactin’s “resistance-resistant” mechanism of action includes binding to the essential bacterial cell wall synthesis building blocks lipid II and lipid III. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of the synthetic teixobactin analogue Leu10-teixobactin against a MRSA strain, S. aureus ATCC 700699. The metabolomes of S. aureus ATCC 700699 cells 1, 3, and 6 h following treatment with Leu10-teixobactin (0.5 μg/ml, i.e., 0.5× MIC) were compared to those of the untreated controls. Leu10-teixobactin significantly perturbed bacterial membrane lipids (glycerophospholipids and fatty acids), peptidoglycan (lipid I and II) metabolism, and cell wall teichoic acid (lipid III) biosynthesis as early as after 1 h of treatment, reflecting an initial activity on the cell envelope. Concordant with its time-dependent antibacterial killing action, Leu10-teixobactin caused more perturbations in the levels of key intermediates in pathways of amino-sugar and nucleotide-sugar metabolism and their downstream peptidoglycan and teichoic acid biosynthesis at 3 and 6 h. Significant perturbations in arginine metabolism and the interrelated tricarboxylic acid cycle, histidine metabolism, pantothenate, and coenzyme A biosynthesis were also observed at 3 and 6 h. To conclude, this is the first study to provide novel metabolomics mechanistic information, which lends support to the development of teixobactin as an antibacterial drug for the treatment of multidrug-resistant Gram-positive infections. IMPORTANCE Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin.",0.9194202423095703,7
protect_from_microbes,100,"Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection. Significance Several nodule-specific cysteine-rich (NCR) peptides expressed in a model legume Medicago truncatula exhibit potent antimicrobial activity. However, their structure–activity relationships and mechanisms of action against fungal pathogens of plants are still largely unknown. A small highly cationic peptide NCR044 with potent antifungal activity has been identified. This peptide has a unique highly dynamic structure and exhibits multifaceted mechanisms of action against a fungal pathogen Botrytis cinerea. Exogenous application of this peptide confers resistance to a gray mold disease caused by B. cinerea in tobacco and tomato plants as well as postharvest products. Our work paves the way for future development of NCR peptides as spray-on antifungal agents. In the indeterminate nodules of a model legume Medicago truncatula, ∼700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.",0.9143021702766418,8
protect_from_microbes,45,"Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi. Extracellular vesicles (EVs) are produced by all domains of life. In Gram-negative bacteria, EVs are produced by the pinching off of the outer membrane; however, how EVs escape the thick cell walls of Gram-positive bacteria, mycobacteria and fungi is still unknown. Nonetheless, EVs have been described in a variety of cell-walled organisms, including Staphylococcus aureus, Mycobacterium tuberculosis and Cryptococcus neoformans. These EVs contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes, and have important roles in microbial physiology and pathogenesis. In this Review, we describe the current status of vesiculogenesis research in thick-walled microorganisms and discuss the cargo and functions associated with EVs in these species.",0.9093685150146484,9
protect_from_microbes,43,"Macrophages employ quorum licensing to regulate collective activation. Macrophage-initiated inflammation is tightly regulated to eliminate threats such as infections while suppressing harmful immune activation. However, individual cells’ signaling responses to pro-inflammatory cues are heterogeneous, with subpopulations emerging with high or low activation states. Here, we use single-cell tracking and dynamical modeling to develop and validate a revised model for lipopolysaccharide (LPS)-induced macrophage activation that invokes a mechanism we term quorum licensing. The results show that bimodal phenotypic partitioning of macrophages is primed during the resting state, dependent on cumulative history of cell density, predicted by extrinsic noise in transcription factor expression, and independent of canonical LPS-induced intercellular feedback in the tumor necrosis factor (TNF) response. Our analysis shows how this density-dependent coupling produces a nonlinear effect on collective TNF production. We speculate that by linking macrophage density to activation, this mechanism could amplify local responses to threats and prevent false alarms. Macrophage activation is tightly regulated to maintain immune homeostasis, yet activation is also heterogeneous. Here, the authors show that macrophages coordinate activation by partitioning into two phenotypes that can nonlinearly amplify collective inflammatory cytokine production as a function of cell density.",0.9041010737419128,10
protect_from_microbes,40,"Bacterial Adhesion and Entry into Host Cells. Successful establishment of infection by bacterial pathogens requires adhesion to host cells, colonization of tissues, and in certain cases, cellular invasion-followed by intracellular multiplication, dissemination to other tissues, or persistence. Bacteria use monomeric adhesins/invasins or highly sophisticated macromolecular machines such as type III secretion systems and retractile type IV pili to establish a complex host/pathogen molecular crosstalk that leads to subversion of cellular functions and establishment of disease.",0.9031946063041687,11
protect_from_microbes,249,"Exploring the Anti-Infective Value of Inuloxin A Isolated from Inula viscosa against the Brain-Eating Amoeba (Naegleria fowleri) by Activation of Programmed Cell Death.. Primary amoebic meningoencephalitis (PAM), caused by the pathogenic free-living amoeba Naegleria fowleri, is a rare but fatal disease. Nowadays, no fully effective therapy is available to erradicate or prevent this disease. Natural products could constitute a promising source of useful bioactive compounds in drug discovery. The present study is a characterization of main active compounds from the ethanolic extract of Inula viscosa (Asteraceae) leaves against N. fowleri trophozoites. Four compounds (1-4) were successfully identified by spectroscopic techniques, but only inuloxin A displayed a potential antiamoebic activity with an IC50 of 21.27 μM. The specificity of this compound toward the studied strain leads us to analyze the insight into its mechanism of action by performing in vitro assays of programmed cell death markers and to discuss the structure-activity relationship (SAR). The obtained results demonstrated that inuloxin A interferes with various processes leading to membrane damage, mitochondria alteration, chromatin condensation, and ROS accumulation, which highlight features specific to apoptosis. The current findings could be a promising step for developing new effective drugs against PAM.",0.8883315324783325,12
protect_from_microbes,202,"Social immunity in insects. When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege).",0.8836498260498047,13
protect_from_microbes,69,"Mode of action of teixobactins in cellular membranes. The natural antibiotic teixobactin kills pathogenic bacteria without detectable resistance. The difficult synthesis and unfavourable solubility of teixobactin require modifications, yet insufficient knowledge on its binding mode impedes the hunt for superior analogues. Thus far, teixobactins are assumed to kill bacteria by binding to cognate cell wall precursors (Lipid II and III). Here we present the binding mode of teixobactins in cellular membranes using solid-state NMR, microscopy, and affinity assays. We solve the structure of the complex formed by an improved teixobactin-analogue and Lipid II and reveal how teixobactins recognize a broad spectrum of targets. Unexpectedly, we find that teixobactins only weakly bind to Lipid II in cellular membranes, implying the direct interaction with cell wall precursors is not the sole killing mechanism. Our data suggest an additional mechanism affords the excellent activity of teixobactins, which can block the cell wall biosynthesis by capturing precursors in massive clusters on membranes. The natural antibiotic teixobactin kills bacteria by direct binding to their cognate cell wall precursors (Lipid II and III). Here authors use solid-state NMR to reveal the native binding mode of teixobactins and show that teixobactins only weakly bind to Lipid II in anionic cellular membranes.",0.8801828026771545,14
protect_from_microbes,63,"Multimeric single-domain antibody complexes protect against bunyavirus infections. The World Health Organization has included three bunyaviruses posing an increasing threat to human health on the Blueprint list of viruses likely to cause major epidemics and for which no, or insufficient countermeasures exist. Here, we describe a broadly applicable strategy, based on llama-derived single-domain antibodies (VHHs), for the development of bunyavirus biotherapeutics. The method was validated using the zoonotic Rift Valley fever virus (RVFV) and Schmallenberg virus (SBV), an emerging pathogen of ruminants, as model pathogens. VHH building blocks were assembled into highly potent neutralizing complexes using bacterial superglue technology. The multimeric complexes were shown to reduce and prevent virus-induced morbidity and mortality in mice upon prophylactic administration. Bispecific molecules engineered to present two different VHHs fused to an Fc domain were further shown to be effective upon therapeutic administration. The presented VHH-based technology holds great promise for the development of bunyavirus antiviral therapies.",0.8438434600830078,15
protect_from_microbes,135,"A symbiotic bacterium of shipworms produces a compound with broad spectrum anti-apicomplexan activity. Apicomplexan parasites cause severe disease in both humans and their domesticated animals. Since these parasites readily develop drug resistance, development of new, effective drugs to treat infection caused by these parasites is an ongoing challenge for the medical and veterinary communities. We hypothesized that invertebrate-bacterial symbioses might be a rich source of anti-apicomplexan compounds because invertebrates are susceptible to infections with gregarines, parasites that are ancestral to all apicomplexans. We chose to explore the therapeutic potential of shipworm symbiotic bacteria as they are bona fide symbionts, are easily grown in axenic culture and have genomes rich in secondary metabolite loci [1,2]. Two strains of the shipworm symbiotic bacterium, Teredinibacter turnerae, were screened for activity against Toxoplasma gondii and one strain, T7901, exhibited activity against intracellular stages of the parasite. Bioassay-guided fractionation identified tartrolon E (trtE) as the source of the activity. TrtE has an EC50 of 3 nM against T. gondii, acts directly on the parasite itself and kills the parasites after two hours of treatment. TrtE exhibits nanomolar to picomolar level activity against Cryptosporidium, Plasmodium, Babesia, Theileria, and Sarcocystis; parasites representing all branches of the apicomplexan phylogenetic tree. The compound also proved effective against Cryptosporidium parvum infection in neonatal mice, indicating that trtE may be a potential lead compound for preclinical development. Identification of a promising new compound after such limited screening strongly encourages further mining of invertebrate symbionts for new anti-parasitic therapeutics.",0.8429762125015259,16
protect_from_microbes,42,"Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors. One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for non-transitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children's game rock–paper–scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.",0.8429747819900513,17
protect_from_microbes,4,"The Bacterially Produced Metabolite Violacein Is Associated with Survival of Amphibians Infected with a Lethal Fungus. ABSTRACT The disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis, is associated with recent declines in amphibian populations. Susceptibility to this disease varies among amphibian populations and species, and resistance appears to be attributable in part to the presence of antifungal microbial species associated with the skin of amphibians. The betaproteobacterium Janthinobacterium lividum has been isolated from the skins of several amphibian species and produces the antifungal metabolite violacein, which inhibits B. dendrobatidis. In this study, we added J. lividum to red-backed salamanders (Plethodon cinereus) to obtain an increased range of violacein concentrations on the skin. Adding J. lividum to the skin of the salamander increased the concentration of violacein on the skin, which was strongly associated with survival after experimental exposure to B. dendrobatidis. As expected from previous work, some individuals that did not receive J. lividum and were exposed to B. dendrobatidis survived. These individuals had concentrations of bacterially produced violacein on their skins that were predicted to kill B. dendrobatidis. Our study suggests that a threshold violacein concentration of about 18 μM on a salamander's skin prevents mortality and morbidity caused by B. dendrobatidis. In addition, we show that over one-half of individuals in nature support antifungal bacteria that produce violacein, which suggests that there is a mutualism between violacein-producing bacteria and P. cinereus and that adding J. lividum is effective for protecting individuals that lack violacein-producing skin bacteria.",0.842398464679718,18
protect_from_microbes,16,"Average nanorough skin surface of the pilot whale (Globicephalamelas, Delphinidae): considerations on the self-cleaning abilities based on nanoroughness. Abstract. In aquatic environments, the biofouling process is assumed to initiate from the conditioning layer of absorbed organic carbon residues on wetted surfaces. Microfouling organisms attach to this conditioning layer, building up a biofilm on which further biofouling proceeds. In dolphins, biofouling reduces hydrodynamic efficiency and may negatively affect health if not managed. In the present study we examined the skin surface of the pilot whale (Globicephalamelas). Employing cryo-scanning electron microscopic techniques combined with various sample preparations, the skin displayed an average nanorough surface characterized by a pattern of nanoridge-enclosed pores; the average pore size (approximately 0.20 µm2) was below the size of most marine biofouling organisms. Further, the implications of this type of surface to the self-cleaning abilities of the skin of pilot whales are discussed, based on reduced available space for biofouler attachment, the lack of any particular microniches as shelters for biofoulers, and the challenges of turbulent water flow and liquid–air interfaces during surfacing and jumping of the dolphin.",0.8284382224082947,19
protect_from_microbes,265,"Agricultural land use disrupts biodiversity mediation of virus infections in wild plant populations. Summary Human alteration of natural habitats may change the processes governing species interactions in wild communities. Wild populations are increasingly impacted by agricultural intensification, yet it is unknown whether this alters biodiversity mediation of disease dynamics. We investigated the association between plant diversity (species richness, diversity) and infection risk (virus richness, prevalence) in populations of Plantago lanceolata in natural landscapes as well as those occurring at the edges of cultivated fields. Altogether, 27 P. lanceolata populations were surveyed for population characteristics and sampled for PCR detection of five recently characterized viruses. We find that plant species richness and diversity correlated negatively with virus infection prevalence. Virus species richness declined with increasing plant diversity and richness in natural populations while in agricultural edge populations species richness was moderately higher, and not associated with plant richness. This difference was not explained by changes in host richness between these two habitats, suggesting potential pathogen spill‐over and increased transmission of viruses across the agro‐ecological interface. Host population connectivity significantly decreased virus infection prevalence. We conclude that human use of landscapes may change the ecological laws by which natural communities are formed with far reaching implications for ecosystem functioning and disease.",0.7983987331390381,20
manage_impact,192,"Spider dragline silk as torsional actuator driven by humidity. Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.",0.5793513655662537,1
manage_impact,220,"Structure and Mechanical Adaptability of a Modern Elasmoid Fish Scale from the Common Carp. Summary The carp (Cyprinus carpio) has typical elasmoid scales commonly found on teleosts. They provide protection while retaining flexibility and maneuverability of the fish. The exterior surface of the scale consists of an ultrathin discontinuous mineral layer on top of mineralized woven collagen fibrils. The underlying foundation is composed of two collagenous components. The major one consists of a single-twisted “Bouligand” structure with a twisting angle of 36°. A secondary “sheet-like” structure, formed by thinner collagen fibrils oriented along the thickness direction, acts to increase the integrity of the scale. Here, we identify the deformation and failure mechanisms of the carp scale, revealing slight tensile anisotropy. Using in situ small-angle X-ray scattering during tensile testing, the toughening mechanisms of the scale, including the adaptive structural reorientation of lamellae as well as fibrillar sliding and elastic deformation, are quantified and compared with those of other fish scales.",0.43765899538993835,2
manage_impact,250,"Biomechanical insights into the dentition of megatooth sharks (Lamniformes: Otodontidae). The evolution of gigantism in extinct otodontid sharks was paralleled by a series of drastic modifications in their dentition including widening of the crowns, loss of lateral cusplets, and acquisition of serrated cutting edges. These traits have generally been interpreted as key functional features that enabled the transition from piscivory to more energetic diets based on marine mammals, ultimately leading to the evolution of titanic body sizes in the most recent forms (including the emblematic Otodus megalodon ). To investigate this hypothesis, we evaluate the biomechanics of the anterior, lateral, and posterior teeth of five otodontid species under different loading conditions by using two-dimensional finite element analysis. Stress distribution patterns are remarkably similar among all models under puncture and draw (i.e., when subjected to vertical and lateral forces, respectively). Contrary to expectation, higher average stress values are detected under both loading scenarios in more recent species. Altogether, this suggests little correlation between tooth morphology and key aspects of biomechanical behaviour in otodontids, making it difficult to frame the morphological trend of their dentitions within an adaptive scenario. We propose that this pattern most likely emerged as a non-functional by-product of heterochronic processes driven by selection towards larger body sizes.",0.29913267493247986,3
manage_impact,193,"Detecting a Prey in a Spider Orb Web. We consider the inverse problem of localizing a prey hitting a spider orb-web from dynamic measurements taken near the center of the web, where the spider is supposed to stay. The actual discrete orb-web, formed by a finite number of radial and circumferential threads, is modelled as a continuous membrane. The membrane has a specific fibrous structure, which is inherited from the original discrete web, and it is subject to tensile pre-stress in the referential configuration. The transverse load describing the prey's impact is assumed of the form $g(t)f(x)$, where $g(t)$ is a known function of time and $f(x)$ is the unknown term depending on the position variable $x$. For axially-symmetric orb-webs supported at the boundary and undergoing infinitesimal transverse deformations, we prove a uniqueness result for $f(x)$ in terms of measurements of the transverse dynamic displacement taken on an arbitrarily small and thin ring centered at the origin of the web, for a sufficiently large interval of time.",0.2841549217700958,4
manage_impact,167,"The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts. The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.",0.25717151165008545,5
manage_impact,297,"Nature's forms are frilly, flexible, and functional.. A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.",0.22388501465320587,6
manage_impact,206,"Deciphering an extreme morphology: bone microarchitecture of the hero shrew backbone (Soricidae: Scutisorex). Biological structures with extreme morphologies are puzzling because they often lack obvious functions and stymie comparisons to homologous or analogous features with more typical shapes. An example of such an extreme morphotype is the uniquely modified vertebral column of the hero shrew Scutisorex, which features numerous accessory intervertebral articulations and massively expanded transverse processes. The function of these vertebral structures is unknown, and it is difficult to meaningfully compare them to vertebrae from animals with known behavioural patterns and spinal adaptations. Here, we use trabecular bone architecture of vertebral centra and quantitative external vertebral morphology to elucidate the forces that may act on the spine of Scutisorex and that of another large shrew with unmodified vertebrae (Crocidura goliath). X-ray micro-computed tomography (µCT) scans of thoracolumbar columns show that Scutisorex thori is structurally intermediate between C. goliath and S. somereni internally and externally, and both Scutisorex species exhibit trabecular bone characteristics indicative of higher in vivo axial compressive loads than C. goliath. Under compressive load, Scutisorex vertebral morphology is adapted to largely restrict bending to the sagittal plane (flexion). Although these findings do not solve the mystery of how Scutisorex uses its byzantine spine in vivo, our work suggests potentially fruitful new avenues of investigation for learning more about the function of this perplexing structure.",0.19645683467388153,7
manage_impact,22,"Pummelos as Concept Generators for Biomimetically Inspired Low Weight Structures with Excellent Damping Properties. Natural materials often exhibit excellent mechanical properties. An example of outstanding impact resistance is the pummelo fruit (Citrus maxima) which can drop from heights of 10 m and more without showing significant outer damage. Our data suggest that this impact resistance is due to the hierarchical organization of the fruit peel, called pericarp. The project presented in the current paper aims at transferring structural features from the pummelo pericarp to engineering materials, in our case metal foams, produced by the investment casting process. The transfer necessitates a detailed structural and mechanical analysis of the biological model on the one hand, and the identification and development of adequate materials and processes on the other hand. Based on this analysis, engineering composite foam structures are developed and processed which show enhanced damping and impact properties. The modified investment casting process and the model alloy Bi57Sn43 proved to be excellent candidates to make these bio-inspired structures. Mechanical testing of both the natural and the engineering structures has to consider the necessity to evaluate the impact of the different hierarchical features. Therefore, specimens of largely varying sizes have to be tested and size effects cannot be ignored, especially as the engineering structures might be upscaled in comparison with the natural role model. All in all, the present results are very promising: the basis for a transfer of bio-inspired structural hierarchical levels has been set.",0.19440791010856628,8
manage_impact,191,"Geometry and self-righting of turtles. Terrestrial animals with rigid shells face imminent danger when turned upside down. A rich variety of righting strategies of beetle and turtle species have been described, but the exact role of the shell's geometry in righting is so far unknown. These strategies are often based on active mechanisms, e.g. most beetles self-right via motion of their legs or wings; flat, aquatic turtles use their muscular neck to flip back. On the other hand, highly domed, terrestrial turtles with short limbs and necks have virtually no active control: here shape itself may serve as a fundamental tool. Based on field data gathered on a broad spectrum of aquatic and terrestrial turtle species we develop a geometric model of the shell. Inspired by recent mathematical results, we demonstrate that a simple mechanical classification of the model is closely linked to the animals' righting strategy. Specifically, we show that the exact geometry of highly domed terrestrial species is close to optimal for self-righting, and the shell's shape is the predominant factor of their ability to flip back. Our study illustrates how evolution solved a far-from-trivial geometrical problem and equipped some turtles with monostatic shells: beautiful forms, which rarely appear in nature otherwise.",0.1665777564048767,9
manage_impact,158,"Free-standing spider silk webs of the thomisid Saccodomus formivorus are made of composites comprising micro- and submicron fibers. Our understanding of the extraordinary mechanical and physico-chemical properties of spider silk is largely confined to the fibers produced by orb-weaving spiders, despite the diversity of foraging webs that occur across numerous spider families. Crab spiders (Thomisidae) are described as ambush predators that do not build webs, but nevertheless use silk for draglines, egg cases and assembling leaf-nests. A little-known exception is the Australian thomisid Saccodomus formivorus, which constructs a basket-like silk web of extraordinary dimensional stability and structural integrity that facilitates the capture of its ant prey. We examined the physical and chemical properties of this unusual web and revealed that the web threads comprise microfibers that are embedded within a biopolymeric matrix containing additionally longitudinally-oriented submicron fibers. We showed that the micro- and submicron fibers differ in their chemical composition and that the web threads show a remarkable lateral resilience compared with that of the major ampullate silk of a well-investigated orb weaver. Our novel analyses of these unusual web and silk characteristics highlight how investigations of non-model species can broaden our understanding of silks and the evolution of foraging webs.",0.14170227944850922,10
manage_impact,305,"The structure and mechanics of Moso bamboo material. Although bamboo has been used structurally for millennia, there is currently increasing interest in the development of renewable and sustainable structural bamboo products (SBPs). These SBPs are analogous to wood products such as plywood, oriented strand board and glue-laminated wood. In this study, the properties of natural Moso bamboo (Phyllostachys pubescens) are investigated to further enable the processing and design of SBPs. The radial and longitudinal density gradients in bamboo give rise to variations in the mechanical properties. Here, we measure the flexural properties of Moso bamboo in the axial direction, along with the compressive strengths in the axial and transverse directions. Based on the microstructural variations (observed with scanning electron microscopy) and extrapolated solid cell wall properties of bamboo, we develop models, which describe the experimental results well. Compared to common North American construction woods loaded along the axial direction, Moso bamboo is approximately as stiff and substantially stronger, in both flexure and compression but denser. This work contributes to critical knowledge surrounding the microstructure and mechanical properties of bamboo, which are vital to the engineering and design of sustainable SBPs.",0.13719090819358826,11
manage_impact,300,"Extreme strength observed in limpet teeth. The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.",0.13313570618629456,12
manage_impact,264,"The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo. The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.",0.12166465818881989,13
manage_impact,259,"Bioinspired Polymer Systems with Stimuli-Responsive Mechanical Properties.. Materials with switchable mechanical properties are widespread in living organisms and endow many species with traits that are essential for their survival. Many of the mechanically morphing materials systems found in nature are based on hierarchical structures, which are the basis for mechanical robustness and often also the key to responsive behavior. Many ""operating principles"" involve cascades of events that translate cues from the environment into changes of the overall structure and/or the connectivity of the constituting building blocks at various levels. These concepts permit dramatic property variations without significant compositional changes. Inspired by the function and the growing understanding of the operating principles at play in biological materials with the capability to change their mechanical properties, significant efforts have been made toward mimicking such architectures and functions in artificial materials. Research in this domain has rapidly grown in the last two decades and afforded many examples of bioinspired materials that are able to reversibly alter their stiffness, shape, porosity, density, or hardness upon remote stimulation. This review summarizes the state of research in this field.",0.11331216245889664,14
manage_impact,198,"Universal elastic mechanism for stinger design. Living organisms use stingers that vary in length L over eight orders of magnitude, from a few tens of nanometres to several metres, across a wide array of biological taxa. Despite the extreme variation in size, their structures are strikingly similar. However, the mechanism responsible for this remarkable morphological convergence remains unknown. Using basic physical arguments and biomimetic experiments, we reveal an optimal design strategy that links their length, base diameter d 0 , Young’s modulus E and friction force per unit area μ p 0 . This principle can be framed simply as $${d}_{0} \approx {(\mu {p}_{0}/E)}^{1/3}L$$ d 0 ≈ ( μ p 0 / E ) 1 / 3 L . Existing data from measurements on viruses, algae, marine invertebrates, terrestrial invertebrates, plants, terrestrial vertebrates, marine vertebrates—as well as man-made objects such as nails, needles and weapons—are consistent with our predictions. Our results highlight the evolutionary adaptation of mechanical traits to the constraints imposed by friction, elastic stability and cost. The structures of stingers of living organisms are surprisingly similar despite their vastly different lengths. Now, stingers are found to obey a unifying mechanistic principle that characterizes the stingers resistance to buckling.",0.11037468910217285,15
manage_impact,223,"Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets. Nacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design. The hierarchical structure of nacre is known to contribute to its high strength and toughness, providing inspiration for many biomimetic materials. Here, co-oriented 20 µm stacks of aragonite platelets are shown to contribute to the toughness of nacre, defining a new characteristic length scale.",0.10878172516822815,16
manage_impact,78,"Bioinspired Materials with Self-Adaptable Mechanical Properties.. Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.",0.1052369549870491,17
manage_impact,267,"Dragondrop: a novel passive mechanism for aerial righting in the dragonfly. Dragonflies perform dramatic aerial manoeuvres when chasing targets but glide for periods during cruising flights. This makes dragonflies a great system to explore the role of passive stabilizing mechanisms that do not compromise manoeuvrability. We challenged dragonflies by dropping them from selected inverted attitudes and collected 6-degrees-of-freedom aerial recovery kinematics via custom motion capture techniques. From these kinematic data, we performed rigid-body inverse dynamics to reconstruct the forces and torques involved in righting behaviour. We found that inverted dragonflies typically recover themselves with the shortest rotation from the initial body inclination. Additionally, they exhibited a strong tendency to pitch-up with their head leading out of the manoeuvre, despite the lower moment of inertia in the roll axis. Surprisingly, anaesthetized dragonflies could also complete aerial righting reliably. Such passive righting disappeared in recently dead dragonflies but could be partially recovered by waxing their wings to the anaesthetised posture. Our kinematics data, inverse dynamics model and wind-tunnel experiments suggest that the dragonfly's long abdomen and wing posture generate a rotational tendency and passive attitude recovery mechanism during falling. This work demonstrates an aerodynamically stable body configuration in a flying insect and raises new questions in sensorimotor control for small flying systems.",0.07017332315444946,18
manage_impact,292,"A Graphic Way For Notch Shape Optimization. Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.",0.059804774820804596,19
manage_impact,76,"Bone-inspired microarchitectures achieve enhanced fatigue life. Significance Microarchitectured materials, such as foams and lattice structures, can achieve high stiffness and strength while remaining extremely lightweight. Applying high-porosity microarchitectured materials to durable devices, such as vehicles, however, will require the materials to also resist failure during cyclic loading. Here, we identify an aspect of microstructure in cancellous bone that greatly influences failure under cyclic loading and show that the effect is generalizable to synthetic microarchitectured materials. Our findings demonstrate that a common design strategy to improve stiffness and strength of microarchitectured materials comes at the cost of impaired service life. Our findings are useful for the design and application of microarchitectured materials and additionally provide insight into human health in situations of osteoporosis. Microarchitectured materials achieve superior mechanical properties through geometry rather than composition. Although ultralightweight microarchitectured materials can have high stiffness and strength, application to durable devices will require sufficient service life under cyclic loading. Naturally occurring materials provide useful models for high-performance materials. Here, we show that in cancellous bone, a naturally occurring lightweight microarchitectured material, resistance to fatigue failure is sensitive to a microarchitectural trait that has negligible effects on stiffness and strength—the proportion of material oriented transverse to applied loads. Using models generated with additive manufacturing, we show that small increases in the thickness of elements oriented transverse to loading can increase fatigue life by 10 to 100 times, far exceeding what is expected from the associated change in density. Transversely oriented struts enhance resistance to fatigue by acting as sacrificial elements. We show that this mechanism is also present in synthetic microlattice structures, where fatigue life can be altered by 5 to 9 times with only negligible changes in density and stiffness. The effects of microstructure on fatigue life in cancellous bone and lattice structures are described empirically by normalizing stress in traditional stress vs. life (S-N) curves by √ψ, where ψ is the proportion of material oriented transverse to load. The mechanical performance of cancellous bone and microarchitectured materials is enhanced by aligning structural elements with expected loading; our findings demonstrate that this strategy comes at the cost of reduced fatigue life, with consequences to the use of microarchitectured materials in durable devices and to human health in the context of osteoporosis.",0.05702868849039078,20
protect_from_excess_liquids,189,"Superhydrophobic diving flies (Ephydra hians) and the hypersaline waters of Mono Lake. Significance Superhydrophobic surfaces have been of key academic and commercial interest since the discovery of the so-called lotus effect in 1977. The effect of different ions on complex superhydrophobic biological systems, however, has received little attention. By bringing together ecology, biomechanics, physics, and chemistry our study provides insight into the ion-specific effects of wetting in the presence of sodium carbonate and its large-scale consequences. By comparing the surface structure and chemistry of the alkali fly—an important food source for migrating birds—to other species we show that their uniquely hydrophobic properties arise from very small physical and chemical changes, thereby connecting picoscale physics with globally important ecological impacts. The remarkable alkali fly, Ephydra hians, deliberately crawls into the alkaline waters of Mono Lake to feed and lay eggs. These diving flies are protected by an air bubble that forms around their superhydrophobic cuticle upon entering the lake. To study the physical mechanisms underlying this process we measured the work required for flies to enter and leave various aqueous solutions. Our measurements show that it is more difficult for the flies to escape from Mono Lake water than from fresh water, due to the high concentration of Na2CO3 which causes water to penetrate and thus wet their setose cuticle. Other less kosmotropic salts do not have this effect, suggesting that the phenomenon is governed by Hofmeister effects as well as specific interactions between ion pairs. These effects likely create a small negative charge at the air–water interface, generating an electric double layer that facilitates wetting. Compared with six other species of flies, alkali flies are better able to resist wetting in a 0.5 M Na2CO3 solution. This trait arises from a combination of factors including a denser layer of setae on their cuticle and the prevalence of smaller cuticular hydrocarbons compared with other species. Although superbly adapted to resisting wetting, alkali flies are vulnerable to getting stuck in natural and artificial oils, including dimethicone, a common ingredient in sunscreen and other cosmetics. Mono Lake’s alkali flies are a compelling example of how the evolution of picoscale physical and chemical changes can allow an animal to occupy an entirely new ecological niche.",0.8120670318603516,1
protect_from_excess_liquids,60,"Exploring the Role of Habitat on the Wettability of Cicada Wings.. Evolutionary pressure has pushed many extant species to develop micro/nanostructures that can significantly affect wettability and enable functionalities such as droplet jumping, self-cleaning, antifogging, antimicrobial, and antireflectivity. In particular, significant effort is underway to understand the insect wing surface structure to establish rational design tools for the development of novel engineered materials. Most studies, however, have focused on superhydrophobic wings obtained from a single insect species, in particular, the Psaltoda claripennis cicada. Here, we investigate the relationship between the spatially dependent wing wettability, topology, and droplet jumping behavior of multiple cicada species and their habitat, lifecycle, and interspecies relatedness. We focus on cicada wings of four different species: Neotibicen pruinosus, N. tibicen, Megatibicen dorsatus, and Magicicada septendecim and take a comparative approach. Using spatially resolved microgoniometry, scanning electron microscopy, atomic force microscopy, and high speed optical microscopy, we show that within cicada species, the wettability of wings is spatially homogeneous across wing cells. All four species were shown to have truncated conical pillars with widely varying length scales ranging from 50 to 400 nm in height. Comparison of the wettability revealed three cicada species with wings that are superhydrophobic (>150°) with low contact angle hysteresis (<5°), resulting in stable droplet jumping behavior. The fourth, more distantly related species (Ma. septendecim) showed only moderate hydrophobic behavior, eliminating some of the beneficial surface functional aspects for this cicada. Correlation between cicada habitat and wing wettability yielded little connection as wetter, swampy environments do not necessarily equate to higher measured wing hydrophobicity. The results, however, do point to species relatedness and reproductive strategy as a closer proxy for predicting wettability and surface structure and resultant enhanced wing surface functionality. This work not only elucidates the differences between inter- and intraspecies cicada wing topology, wettability, and water shedding behavior but also enables the development of rational design tools for the manufacture of artificial surfaces for energy and water applications.",0.5272858142852783,2
protect_from_excess_liquids,178,"Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade‐off in sperm evolution. Sperm morphology varies enormously across the animal kingdom. Whilst knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterized by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light and scanning electron microscopy, we examined among‐species correlations between the occurrence of sperm head abnormalities and sperm morphology, as well as the correlation between sperm head abnormalities and two indicators of sperm competition. We found that species with more helically shaped sperm heads (i.e., a wider helical membrane and more pronounced cell waveform) had a higher percentage of abnormal sperm heads than species with less helical sperm (i.e., relatively straight sperm) and that sperm head traits were better predictors of head abnormalities than total sperm length. In contrast, there was no correlation between sperm abnormalities and the level of sperm competition. Given that songbird species with more pronounced helical sperm have higher average sperm swimming speed, our results suggest an evolutionary trade‐off between sperm performance and the structural integrity of the sperm head. As such, susceptibility to morphological abnormalities may constrain the evolution of helical sperm morphology in songbirds.",0.335097998380661,3
protect_from_excess_liquids,261,"Gut bacteria are essential for normal cuticle development in herbivorous turtle ants. Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.",0.316057950258255,4
protect_from_excess_liquids,192,"Spider dragline silk as torsional actuator driven by humidity. Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.",0.286336749792099,5
protect_from_excess_liquids,199,"Compact nanoscale textures reduce contact time of bouncing droplets. Compact nanoscale textures reduce contact time of bouncing droplets with implications in insect survival and miniature drones. Many natural surfaces are capable of rapidly shedding water droplets—a phenomenon that has been attributed to the presence of low solid fraction textures (Φs ~ 0.01). However, recent observations revealed the presence of unusually high solid fraction nanoscale textures (Φs ~ 0.25 to 0.64) on water-repellent insect surfaces, which cannot be explained by existing wetting theories. Here, we show that the contact time of bouncing droplets on high solid fraction surfaces can be reduced by reducing the texture size to ~100 nm. We demonstrated that the texture size–dependent contact time reduction could be attributed to the dominance of line tension on nanotextures and that compact arrangement of nanotextures is essential to withstand the impact pressure of raindrops. Our findings illustrate a potential survival strategy of insects to rapidly shed impacting raindrops, and suggest a previously unidentified design principle to engineering robust water-repellent materials for applications including miniaturized drones.",0.2358376681804657,6
protect_from_excess_liquids,218,"Biomimicry as a design tool for nanocontainers: The “shape of things to come” in drug delivery. Abstract Nanocontainers embody a “compartmentalized” structural archetype with the potential to operate on a dimensional scale that can either assimilate or be integrated within bio-driven processes. With expected improvements in sensitive diagnostic assays for early disease detection (e.g., CTCs or circulating tumor cells), this has important implications for developing drug delivery technologies to areas of small confinement in the body. Functionalized nanocontainers with tunable surface properties can help stabilize and release therapeutic chemical and biological drugs within nano- and sub-nano spaced cavities. Here, we discuss recent developments in the field of “nanocontainers” that show promise for addressing some of the more challenging aspects of drug therapeutics.",0.1850617527961731,7
protect_from_excess_liquids,304,"Eggshell membrane biomaterial as a platform for applications in materials science.. Eggshell membrane (ESM) is a unique biomaterial, which is generally considered as waste. However, it has extraordinary properties which can be utilized in various fields and its potential applications are therefore now being widely studied. The first part of this review focuses on the chemical composition and morphology of ESM. The main areas of ESM application are discussed in the second part. These applications include its utilization as a biotemplate for the synthesis of nanoparticles; as a sorbent of heavy metals, organics, dyes, sulfonates and fluorides; as the main component of biosensors; in medicine; and various other applications. For each area of interest, a detailed literature survey is given.",0.0866859033703804,8
protect_from_excess_liquids,157,"Communication versus waterproofing: the physics of insect cuticular hydrocarbons. ABSTRACT Understanding the evolution of complex traits is among the major challenges in biology. One such trait is the cuticular hydrocarbon (CHC) layer in insects. It protects against desiccation and provides communication signals, especially in social insects. CHC composition is highly diverse within and across species. To understand the adaptive value of this chemical diversity, we must understand how it affects biological functionality. So far, CHCs have received ample research attention, but their physical properties were little studied. We argue that these properties determine their biological functionality, and are vital to understanding how CHC composition affects their adaptive value. We investigated melting behaviour and viscosity of CHCs from 11 ant species using differential scanning calorimetry and a novel microrheological technique. CHCs began melting below −45°C, and often were entirely liquid only above 30°C. Thus, they formed a solid–liquid mixture under ambient conditions, which contrasts to previous assumptions of entirely solid layers in many species. This may be adaptive as only biphasic CHC layers ensure uniform coating of the insect body, which is necessary for waterproofing. CHC viscosity was mostly between 0.1 and 0.2 Pa s−1, thus similar to motor oils. Surprisingly, chemically different CHC profiles had similar viscosities, suggesting that a certain viscosity level is adaptive and ensures that communication signals can be perceived. With this study, we draw attention to the importance of studying the physics of CHC layers. Only by understanding how chemical and physical mechanisms enable CHC functionality can we understand the causes and consequences of CHC diversification. Summary: Cuticular hydrocarbons protect insects from desiccation and allow chemical communication, and contain both liquid and solid parts. This complex phase behaviour appears vital to ensure biological functioning.",0.08564196527004242,9
protect_from_excess_liquids,68,"Tillandsia-Inspired Hygroscopic Photothermal Organogels for Efficient Atmospheric Water Harvesting.. Tillandsia species with degenerated roots have evolved into hygroscopic leaves that absorb moisture from air. This interesting biological adaptability has inspired us to develop an integrated hygroscopic photothermal organogel (POG) to achieve a solar-powered atmospheric water harvesting (AWH). The well-designed hydrophilic co-polymeric skeleton is fabricated to accommodate hygroscopic glycerin medium, which enables the POG self-contained property, mechanically flexibility and synergistic enhancement of moisture sorption. The integration of interpenetrated photothermal component of poly-pyrrole-dopamine (P-Py-DA) can endow the POG an efficient solar-to-thermal property for controllable solar-driven interfacial water releasing. The integrated POG has an equilibrium moisture sorption of 16.01 kg m-2 at the RH of 90 %, and daily water production as high as 2.43 kg m-2 day-1 is achieved in actual outdoor experiments.",0.07845408469438553,10
protect_from_excess_liquids,316,"Soft and ion-conducting hydrogel artificial tongue for astringency perception. Artificial tongue for astringency perception is demonstrated with a saliva-like chemiresistive ionic hydrogel. Artificial tongues have been receiving increasing attention for the perception of five basic tastes. However, it is still challenging to fully mimic human tongue–like performance for tastes such as astringency. Mimicking the mechanism of astringency perception on the human tongue, we use a saliva-like chemiresistive ionic hydrogel anchored to a flexible substrate as a soft artificial tongue. When exposed to astringent compounds, hydrophobic aggregates form inside the microporous network and transform it into a micro/nanoporous structure with enhanced ionic conductivity. This unique human tongue–like performance enables tannic acid to be detected over a wide range (0.0005 to 1 wt %) with high sensitivity (0.292 wt %−1) and fast response time (~10 s). As a proof of concept, our sensor can detect the degree of astringency in beverages and fruits using a simple wipe-and-detection method, making a powerful platform for future applications involving humanoid robots and taste monitoring devices.",0.06316451728343964,11
protect_from_excess_liquids,21,"Ultrastructural architecture of the microtrichia of the insect cuticle. The ultrastructure of the microtrichia (MT) of the insect cuticle was studied using scanning electron microscopy (SEM). After dissolving the protein matrix of chitin‐protein microfibrils with NaOH, the orientation of the axial chitin fibers was three‐dimensionally demonstrated. Microfibrils of the outermost exocuticular lamella lie parallel to the slope of the cone surface of the MT and rotate slightly on the top of the MT. Microfibrils of the external lamella of the transitional area between planar cuticle and conical cuticle of the MT corresponded to the shape of the surface within one lamella and preferred directions of MT's microfibrils in the successive lamella rotated. In the deeper layers of the cuticle, the rotation of both the microfibrils and successive lamella results in the twisted straw architecture of the microfibrils' composition within the MT. The deepest microfibrils that are located close to the axis of the MT form compact clusters of fibrils (1.0–1.5 μm length). The twisted‐straw architecture of microfibrils in the MT is derived from principles of development of extracellular fibrous composites. It is suggested, however, that this architecture has an additional functional significance as a strategic design with particular mechanical properties. J. Morphol. 234:1–10, 1997. © 1997 Wiley‐Liss, Inc.",0.05574612319469452,12
protect_from_excess_liquids,0,"Increased Food and Ecosystem Security via Perennial Grains. Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.",0.053328439593315125,13
protect_from_excess_liquids,272,"Social signals mediate oviposition site selection in Drosophila suzukii. The information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila . These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.",0.053254127502441406,14
protect_from_excess_liquids,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.05219480022788048,15
protect_from_excess_liquids,16,"Average nanorough skin surface of the pilot whale (Globicephalamelas, Delphinidae): considerations on the self-cleaning abilities based on nanoroughness. Abstract. In aquatic environments, the biofouling process is assumed to initiate from the conditioning layer of absorbed organic carbon residues on wetted surfaces. Microfouling organisms attach to this conditioning layer, building up a biofilm on which further biofouling proceeds. In dolphins, biofouling reduces hydrodynamic efficiency and may negatively affect health if not managed. In the present study we examined the skin surface of the pilot whale (Globicephalamelas). Employing cryo-scanning electron microscopic techniques combined with various sample preparations, the skin displayed an average nanorough surface characterized by a pattern of nanoridge-enclosed pores; the average pore size (approximately 0.20 µm2) was below the size of most marine biofouling organisms. Further, the implications of this type of surface to the self-cleaning abilities of the skin of pilot whales are discussed, based on reduced available space for biofouler attachment, the lack of any particular microniches as shelters for biofoulers, and the challenges of turbulent water flow and liquid–air interfaces during surfacing and jumping of the dolphin.",0.04819369688630104,16
protect_from_excess_liquids,191,"Geometry and self-righting of turtles. Terrestrial animals with rigid shells face imminent danger when turned upside down. A rich variety of righting strategies of beetle and turtle species have been described, but the exact role of the shell's geometry in righting is so far unknown. These strategies are often based on active mechanisms, e.g. most beetles self-right via motion of their legs or wings; flat, aquatic turtles use their muscular neck to flip back. On the other hand, highly domed, terrestrial turtles with short limbs and necks have virtually no active control: here shape itself may serve as a fundamental tool. Based on field data gathered on a broad spectrum of aquatic and terrestrial turtle species we develop a geometric model of the shell. Inspired by recent mathematical results, we demonstrate that a simple mechanical classification of the model is closely linked to the animals' righting strategy. Specifically, we show that the exact geometry of highly domed terrestrial species is close to optimal for self-righting, and the shell's shape is the predominant factor of their ability to flip back. Our study illustrates how evolution solved a far-from-trivial geometrical problem and equipped some turtles with monostatic shells: beautiful forms, which rarely appear in nature otherwise.",0.04423326998949051,17
protect_from_excess_liquids,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.04320305213332176,18
protect_from_excess_liquids,244,"DNA Origami Design: A How-To Tutorial. While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.",0.040860485285520554,19
protect_from_excess_liquids,2,"Hypoxia and Anoxia Tolerance in the Annual Killifish Austrofundulus limnaeus.. Embryos of the annual killifish Austrofundulus limnaeus are routinely exposed to oxygen limitation during development and are extremely tolerant of anoxia. Importantly, tolerance of anoxia is not strictly associated with entrance into metabolic dormancy associated with diapause II, but rather any embryo will respond to anoxia by entering into a state of anoxia-induced quiescence. Hypoxia causes a reduction in the rate of development, reduced heart rates, and reduced capacities for metabolic enzyme activity in both aerobic and anaerobic pathways. Embryos of A. limnaeus begin life as oxyconformers, and transition into oxyregulators near the completion of embryonic development. As this transition occurs, extreme anoxia tolerance is lost. The rate of early development is independent of oxygen partial pressure, despite the fact that the embryos are oxyconformers. This suggests a contribution from anaerobic pathways to support early development. However, the specific pathways supporting this metabolism are unknown. The response of A. limnaeus embryos to hypoxia and anoxia is unique compared to other fishes and most other vertebrates, and thus future studies on this species may lend insight into novel mechanisms that support survival during prolonged oxygen limitation.",0.03750283643603325,20
actively_move_through/on_solids,241,"Limb work and joint work minimization reveal an energetic benefit to the elbows-back, knees-forward limb design in parasagittal quadrupeds. Quadrupedal animal locomotion is energetically costly. We explore two forms of mechanical work that may be relevant in imposing these physiological demands. Limb work, due to the forces and velocities between the stance foot and the centre of mass, could theoretically be zero given vertical limb forces and horizontal centre of mass path. To prevent pitching, skewed vertical force profiles would then be required, with forelimb forces high in late stance and hindlimb forces high in early stance. By contrast, joint work—the positive mechanical work performed by the limb joints—would be reduced with forces directed through the hip or shoulder joints. Measured quadruped kinetics show features consistent with compromised reduction of both forms of work, suggesting some degree of, but not perfect, inter-joint energy transfer. The elbows-back, knees-forward design reduces the joint work demand of a low limb-work, skewed, vertical force profile. This geometry allows periods of high force to be supported when the distal segment is near vertical, imposing low moments about the elbow or knee, while the shoulder or hip avoids high joint power despite high moments because the proximal segment barely rotates—translation over this period is due to rotation of the distal segment.",0.9172001481056213,1
actively_move_through/on_solids,293,"A controllable dual-catapult system inspired by the biomechanics of the dragonfly larvae’s predatory strike. The independently loaded synchronized dual-catapult system of dragonfly larvae can serve as a model for bioinspired robotics. The biomechanics underlying the predatory strike of dragonfly larvae is not yet understood. Dragonfly larvae are aquatic ambush predators, capturing their prey with a strongly modified extensible mouthpart. The current theory of hydraulic pressure being the driving force of the predatory strike can be refuted by our manipulation experiments and reinterpretation of former studies. Here, we report evidence for an independently loaded synchronized dual-catapult system. To power the ballistic movement of a single specialized mouthpart, two independently loaded springs simultaneously release and actuate two separate joints in a kinematic chain. Energy for the movement is stored by straining an elastic structure at each joint and, possibly, the surrounding cuticle, which is preloaded by muscle contraction. As a proof of concept, we developed a bioinspired robotic model resembling the morphology and functional principle of the extensible mouthpart. Understanding the biomechanics of the independently loaded synchronized dual-catapult system found in dragonfly larvae can be used to control the extension direction and, thereby, thrust vector of a power-modulated robotic system.",0.8923439979553223,2
actively_move_through/on_solids,296,"Dynamics and stability of running on rough terrains. Stability of running on rough terrain depends on the propagation of perturbations due to the ground. We consider stability within the sagittal plane and model the dynamics of running as a two-dimensional body with alternating aerial and stance phases. Stance is modelled as a passive, impulsive collision followed by an active, impulsive push-off that compensates for collisional losses. Such a runner has infinitely many strategies to maintain periodic gaits on flat ground. However, these strategies differ in how perturbations due to terrain unevenness are propagated. Instabilities manifest as tumbling (orientational instability) or failing to maintain a steady speed (translational instability). We find that open-loop strategies that avoid sensory feedback are sufficient to maintain stability on step-like terrains with piecewise flat surfaces that randomly vary in height. However, these open-loop runners lose orientational stability on rough terrains whose slope also varies randomly. The orientational instability is significantly mitigated by minimizing the tangential collision, which typically requires sensory information and anticipatory strategies such as leg retraction. By analysing the propagation of perturbations, we derive a single dimensionless parameter that governs stability. This parameter provides guidelines for the design and control of both biological and robotic runners.",0.8887378573417664,3
actively_move_through/on_solids,295,"Role of multiple, adjustable toes in distributed control shown by sideways wall-running in geckos. Remarkable progress has been made characterizing one of nature's most integrated, hierarchical structures––the fibrillar adhesive system of geckos. Nonetheless, we lack an understanding of how multiple toes coordinate to facilitate geckos' acrobatic locomotion. Here, we tested the control function of gecko toes by running them on vertical substrates varying in orientation, friction and roughness. Sideways wall-running geckos realigned the toes of their top feet upward to resist gravity. Toe contact area was not compromised, but redistributed. Geckos aligned all toes upward to resist slipping when encountering low-friction patches during sideways wall-running. Negotiation of intermittent slippery strips showed an increased contribution of particular toes to compensate for toes that lost adhesion. Increasing substrate roughness using discrete rods perpendicular to sideways locomotion resulted in geckos bending and/or rotating toes to conform to and even grasp the rods, with potential forces more than five times body weight. Geckos increase their effectiveness of manoeuvrability in demanding environments by taking advantage of the distributed control afforded by multiple toes. Our findings provide insight on biological attachment and offer inspiration to advance gecko-inspired robotics and other biomimetic applications.",0.8795662522315979,4
actively_move_through/on_solids,217,"An energy landscape approach to locomotor transitions in complex 3D terrain. Significance Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Using laboratory experiments on a model system, we demonstrate that an energy landscape approach helps understand how multipathway transitions across locomotor modes in complex 3D terrain statistically emerge from physical interaction. Animals’ and robots’ locomotor modes are attracted to basins of a potential energy landscape. They can use kinetic energy fluctuation from oscillatory self-propulsion to cross potential energy barriers, escaping from one basin and reaching another to make locomotor transitions. Our first-principle energy landscape approach is the beginning of a statistical physics theory of locomotor transitions in complex terrain. It will help understand and predict how animals, and how robots should, move through the real world. Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around near–steady-state movement in a single mode. We still know little about how locomotor transitions emerge from physical interaction with complex terrain. Consequently, robots largely rely on geometric maps to avoid obstacles, not traverse them. Recent studies revealed that locomotor transitions in complex three-dimensional (3D) terrain occur probabilistically via multiple pathways. Here, we show that an energy landscape approach elucidates the underlying physical principles. We discovered that locomotor transitions of animals and robots self-propelled through complex 3D terrain correspond to barrier-crossing transitions on a potential energy landscape. Locomotor modes are attracted to landscape basins separated by potential energy barriers. Kinetic energy fluctuation from oscillatory self-propulsion helps the system stochastically escape from one basin and reach another to make transitions. Escape is more likely toward lower barrier direction. These principles are surprisingly similar to those of near-equilibrium, microscopic systems. Analogous to free-energy landscapes for multipathway protein folding transitions, our energy landscape approach from first principles is the beginning of a statistical physics theory of multipathway locomotor transitions in complex terrain. This will not only help understand how the organization of animal behavior emerges from multiscale interactions between their neural and mechanical systems and the physical environment, but also guide robot design, control, and planning over the large, intractable locomotor-terrain parameter space to generate robust locomotor transitions through the real world.",0.7394461035728455,5
actively_move_through/on_solids,56,"The jumping mechanism of flea beetles (Coleoptera, Chrysomelidae, Alticini), its application to bionics and preliminary design for a robotic jumping leg.. Flea beetles (Coleoptera, Chrysomelidae, Galerucinae, Alticini) are a hyperdiverse group of organisms with approximately 9900 species worldwide. In addition to walking as most insects do, nearly all the species of flea beetles have an ability to jump and this ability is commonly understood as one of the key adaptations responsible for its diversity. Our investigation of flea beetle jumping is based on high-speed filming, micro-CT scans and 3D reconstructions, and provides a mechanical description of the jump. We reveal that the flea beetle jumping mechanism is a catapult in nature and is enabled by a small structure in the hind femur called an 'elastic plate' which powers the explosive jump and protects other structures from potential injury. The explosive catapult jump of flea beetles involves a unique 'high-efficiency mechanism' and 'positive feedback mechanism'. As this catapult mechanism could inspire the design of bionic jumping limbs, we provide a preliminary design for a robotic jumping leg, which could be a resource for the bionics industry.",0.7194089889526367,6
actively_move_through/on_solids,26,"THE MUSCULAR HYDROSTAT OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS): A FUNCTIONAL MORPHOLOGICAL MODEL OF PERIORAL BRISTLE USE. Facial musculature was examined in the Florida manatee, Tricbecbus manatus latirostris, in order to develop a functional model of perioral bristle use. Muscles identified include the M. levator nasolabialis, M. buccinatorius, M. maxillonasolabialis, M. centralis nasi, M. lateralis nasi, M. spbincter colli profundus pars oris, M. orbicularis oris, M. mandibularis, and M. mentalis. A new muscle, M. centralis nasi, has been named and is an integral part of perioral bristle movement. The snout of the Florida manatee is capable of performing complex movements. The prehensile ability of Florida manatees can be explained in the context of a muscular hydrostat as defined by Kier and Smith (1985). Eversion of certain bristles in the upper lip occurs by shortening longitudinal, transverse, and semicircular muscles in combination with volume displacement due to compensatory changes in the shape of the snout. Midline sweeping of these bristles is accomplished by the contraction of M. centralis nasi. Eversion of bristles on the lower jaw is a result of shortening of M. mentalis. Contraction of M. orbicularis oris pushes vegetation into the oral cavity. All observed movement patterns and uses of perioral bristles can be explained by variation of these sequences within the context of muscular hydrostat function.",0.7126145958900452,7
actively_move_through/on_solids,52,"The jump of the click beetle (Coleoptera: Elateridae)—energetics and mechanics. Some aspects of the energetics and mechanics of two jumps made by a single specimen of Athous haemorrhoidalis (Fab.) are considered. In the first jump, the 40 mg beetle had a take-off velocity of 2–4 m/s and the jumping action occurred in about 064 ms; in the second jump, the take/off velocity was 2–26 m/s and the jumping action took about 0–53 ms. Energy budgets have been constructed in two different ways for each jump, and the total energy involved in each case was estimated to lie between 1–6 × 10−4 J and 3–8 × 10−4 J. Power output during the jumping action (a “catapult”) lay between 80 × 103 W/kg muscle and 180 × 103 W/kg muscle, whilst power output during the energy storing pre-jump period (of about 0–4 s) was at least 130 W/kg muscle (at over 25°C). Forces and tensile stresses in the jumping muscles and their apodemes have also been calculated. The method of jumping appears to be fairly inefficient in that only about 50–60% of the energy expended in the jumping action is energy of translation, which actually raises the beetle.",0.49486854672431946,8
actively_move_through/on_solids,263,"Lasso locomotion expands the climbing repertoire of snakes. The diverse ways and environments in which animals move are correlated with morphology1, but morphology is not sufficient to predict how animals move because behavioral innovations can create new capacities. We document a new mode of snake locomotion - 'lasso locomotion' - that allows the brown treesnake (Boiga irregularis) to ascend much larger smooth cylinders than any previously known behavior. This lasso locomotion may facilitate exploiting resources that might otherwise be unobtainable and contribute to the success and impact of this highly invasive species. VIDEO ABSTRACT.",0.31951016187667847,9
actively_move_through/on_solids,235,"Multiple Degrees of Freedom in the Fish Skull and Their Relation to Hydraulic Transport of Prey in Channel Catfish. Synopsis Fish perform many complex manipulation behaviors without hands or flexible muscular tongues, instead relying on more than 20 movable skeletal elements in their highly kinetic skulls. How fish use their skulls to accomplish these behaviors, however, remains unclear. Most previous mechanical models have represented the fish skull using one or more planar four-bar linkages, which have just a single degree of freedom (DoF). In contrast, truncated-cone hydrodynamic models have assumed up to five DoFs. In this study, we introduce and validate a 3D mechanical linkage model of a fish skull that incorporates the pectoral girdle and mandibular and hyoid arches. We validate this model using an in vivo motion dataset of suction feeding in channel catfish and then use this model to quantify the DoFs in the fish skull, to categorize the motion patterns of the cranial linkage during feeding, and to evaluate the association between these patterns and food motion. We find that the channel catfish skull functions as a 17-link, five-loop parallel mechanism. Despite having 19 potential DoFs, we find that seven DoFs are sufficient to describe most of the motion of the cranial linkage, consistent with the fish skull functioning as a multi-DoF, manipulation system. Channel catfish use this linkage to generate three different motion patterns (rostrocaudal wave, caudorostral wave, and compressive wave), each with its own associated food velocity profile. These results suggest that biomechanical manipulation systems must have a minimum number of DoFs to effectively control objects, whether in water or air.",0.256411612033844,10
actively_move_through/on_solids,65,"The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.. Fibroblasts undergo a critical transformation from an initially inactive state to a morphologically different and contractile state after several hours of being embedded within a physiologically relevant three-dimensional (3D) fibrous collagen-based extracellular matrix (ECM). However, little is known about the critical mechanisms by which fibroblasts adapt themselves and their microenvironment in the earliest stage of cell-matrix interaction. Here, we identified the mechanisms by which fibroblasts interact with their 3D collagen fibrous matrices in the early stages of cell-matrix interaction and showed that fibroblasts use energetically efficient hierarchical micro/nano scaled protrusions in these stages as the primary means for the transformation and adaptation. We found that actomyosin contractility in these protrusions in the early stages of cell-matrix interaction restricts the growth of microtubules by applying compressive forces on them. Our results show that actomyosin contractility and microtubules work in concert in the early stages of cell-matrix interaction to adapt fibroblasts and their microenvironment to one another. These early-stage interactions result in responses to disruption of the microtubule network and/or actomyosin contractility that are opposite to well-known responses to late-stage disruption, and reveal insight into the ways that cells adapt themselves and their ECM recursively.",0.21804669499397278,11
actively_move_through/on_solids,209,"Locomotion of Mexican jumping beans.. The Mexican jumping bean, Laspeyresia saltitans, consists of a hollow seed housing a moth larva. Heating by the sun induces movements by the larva which appear as rolls, jumps and flips by the bean. In this combined experimental, numerical and robotic study, we investigate this unique means of rolling locomotion. Time-lapse videography is used to record bean trajectories across a series of terrain types, including one-dimensional channels and planar surfaces of varying inclination. We find that the shell encumbers the larva's locomotion, decreasing its speed on flat surfaces by threefold. We also observe that the two-dimensional search algorithm of the bean resembles the run-and-tumble search of bacteria. We test this search algorithm using both an agent-based simulation and a wheeled Scribbler robot. The algorithm succeeds in propelling the robot away from regions of high temperature and may have application in biomimetic micro-scale navigation systems.",0.18012595176696777,12
actively_move_through/on_solids,25,"PREHENSILE USE OF PERIORAL BRISTLES DURING FEEDING AND ASSOCIATED BEHAVIORS OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS). The use of perioral bristles (modified vibrissae) by 17 captive Florida manatees and approximately 20 wild manatees was analyzed. Captive manatees were fed six species of aquatic vegetation normally eaten in the wild (four freshwater species and two seagrasses). Inanimate objects were placed in the holding tanks with manatees at Lowry Park Zoological Gardens (Tampa, FL) to determine the degree to which perioral bristles were used in exploration and to define the range of manipulative behavior. In addition, behavioral observations were made on the use of perioral bristles during social interactions with conspecifics. Observations were recorded using a Hi8-format video camera. Florida manatees possess an unusually large degree of fine motor control of the snout and perioral bristles. The large and robust perioral bristle fields of the upper lip were used in a prehensile manner during feeding. Bristle use by manatees feeding on submerged vegetation differed from that seen during feeding on floating vegetation. Other behavioral use of the perioral bristles shows variation depending upon the situation encountered. The degree of plasticity of perioral bristle use supports our hypothesis that the vibrissal-muscular complex of the Florida manatee has evolved to increase the efficiency of grazing and browsing on aquatic vegetation and to fully maximize the potential of the manatee as a generalist feeder. The manipulative and sensitive nature of the manatee snout is likely a manifestation of a complex sensory and motor system which has evolved for marine mammal aquatic herbivores living in shallow turbid habitats.",0.1299801617860794,13
actively_move_through/on_solids,205,"Drones become even more insect-like. Mosquitoes' exceptional sensitivity to sound and airflow inspires new collision avoidance technology Evolutionary pressures in the animal kingdom have, over the course of several hundred million years, produced a diverse array of creatures highly adapted to survival within their own niche environments. Such adaptations coincide with optimized and efficient materials, body structure, and behavior. Humans have long drawn inspiration from nature in the creation of new technologies—for example, the earliest attempts at flight based on emulation of birds—and many benefits stem from the study of processes, materials, methods, and organizational structures of living organisms. On page 634 of this issue, Nakata et al. (1) exemplify the bioinspired design methodology through their investigation of the sound- and airflow-sensing capabilities of the southern house mosquito Culex quinquefasciatus and subsequent creation of a small quad-copter drone with an autonomous collision avoidance system based on the same sensing principles. The sensor displays compelling advantages in weight, power, and deployability over existing technology.",0.06373220682144165,14
actively_move_through/on_solids,313,"Temporomandibular joint and Giant Panda’s (Ailuropoda melanoleuca) adaptation to bamboo diet. Here, we present new evidence that evolutionary adaptation of the Ailuripodinae lineage to bamboo diet has taken place by morphological adaptations in the masticatory system. The giant panda in the wild and in captivity removes without an exception the outer skin of all bamboo shoots, rich in abrasive and toxic compounds, by the highly adapted premolars P3 and P4. The temporomandibular joint (TMJ) allows sidewise movement of the jaw and the premolars can, in a cusp-to-cusp position, remove the poorly digestible outer skin of the bamboo before crushing the bamboo with molars. Based on the evidence presented here, we suggest that adaptation of TMJ to lateral movement for enabling cusp-to-cusp contact of premolars is the crucial evolutionary factor as which we consider the key to understand the Ailuropodinae lineage adaptive pathway to utilize the bamboo resource.",0.05648243799805641,15
actively_move_through/on_solids,134,"Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.. Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.",0.049637969583272934,16
actively_move_through/on_solids,201,"Undulation enables gliding in flying snakes. When flying snakes glide, they use aerial undulation. To determine if aerial undulation is a flight control strategy or a non-functional behavioural vestige of lateral undulation, we measured snake glides using high-speed motion capture and developed a new dynamical model of gliding. Reconstructions of the snake’s wing-body reveal that aerial undulation is composed of horizontal and vertical waves, whose phases differ by 90° and whose frequencies differ by a factor of two. Using these results, we developed a three-dimensional mathematical model of snake flight that incorporates aerodynamic and inertial effects. Although simulated glides without undulation attained some horizontal distance, they are biologically unrealistic because they failed due to roll and pitch instabilities. In contrast, the inclusion of undulation stabilized the rotational motion and markedly increased glide performance. This work demonstrates that aerial undulation in snakes serves a different function than known uses of undulation in other animals, and suggests a new template of control for dynamic flying robots. Observations of flying snakes inform the development of a dynamical model of gliding taking undulation into account. This work suggests that aerial undulation has a different function in snakes than in other animals.",0.049471933394670486,17
actively_move_through/on_solids,64,"Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella. Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.",0.04471959173679352,18
actively_move_through/on_solids,93,"The high speed radular prey strike of a fish-hunting cone snail. Cone snails are venomous marine gastropods that hydraulically propel a hollow, chitinous radular harpoon into prey [1,2]. This radular harpoon serves both as projectile and conduit for venom delivery. In the fish-hunting cone snail Conus catus, the radular harpoon is also utilized to tether the snail to its prey, rapidly paralyzed by neuroexcitatory peptides [2,3]. Effective prey capture in C. catus requires both fast-acting neurotoxins and a delivery system quick enough to exceed the prey fish's rapid escape responses [4]. We report here that the cone snail's prey strike is one of the fastest in the animal kingdom. A unique cellular latch mechanism prevents harpoon release until sufficient pressure builds and overcomes the forces of the latch, resulting in rapid acceleration into prey [2]. The radular harpoon then rapidly decelerates as its bulbous base reaches the end of the proboscis, a distensible hydrostatic skeleton extended toward the prey [2], with little slowing during prey impalement. The velocities achieved are the fastest movements of any mollusk and exceed previous estimates by over an order of magnitude [1].",0.04037240147590637,19
actively_move_through/on_solids,95,"Automatic control: the vertebral column of dogfish sharks behaves as a continuously variable transmission with smoothly shifting functions. ABSTRACT During swimming in dogfish sharks, Squalus acanthias, both the intervertebral joints and the vertebral centra undergo significant strain. To investigate this system, unique among vertebrates, we cyclically bent isolated segments of 10 vertebrae and nine joints. For the first time in the biomechanics of fish vertebral columns, we simultaneously characterized non-linear elasticity and viscosity throughout the bending oscillation, extending recently proposed techniques for large-amplitude oscillatory shear (LAOS) characterization to large-amplitude oscillatory bending (LAOB). The vertebral column segments behave as non-linear viscoelastic springs. Elastic properties dominate for all frequencies and curvatures tested, increasing as either variable increases. Non-linearities within a bending cycle are most in evidence at the highest frequency, 2.0 Hz, and curvature, 5 m−1. Viscous bending properties are greatest at low frequencies and high curvatures, with non-linear effects occurring at all frequencies and curvatures. The range of mechanical behaviors includes that of springs and brakes, with smooth transitions between them that allow for continuously variable power transmission by the vertebral column to assist in the mechanics of undulatory propulsion. Highlighted Article: Characterization of non-linear elasticity and viscosity throughout the bending oscillation reveals that the shark vertebral column behaves as both a spring and a brake, with smooth transitions between them for continuously variable power transmission.",0.03786684572696686,20