nils-herrmann/clean_scirepeval huggingface dataset:
Both stiff and compliant: morphological and biomechanical adaptations of stick insect antennae for tactile exploration
Venue: Journal of the Royal Society Interface

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.
Traps of carnivorous pitcher plants as a habitat: composition of the fluid, biodiversity and mutualistic activities.
Venue: Annals of Botany

Carnivorous pitcher plants (CPPs) use cone-shaped leaves to trap animals for nutrient supply but are not able to kill all intruders of their traps. Numerous species, ranging from bacteria to vertrebrates, survive and propagate in the otherwise deadly traps. This paper reviews the literature on phytotelmata of CPPs.


PITCHER
Fluid as a Habitat The volumes of pitchers range from 0·2 mL to 1·5 L. In Nepenthes and Cephalotus, the fluid is secreted by the trap; the other genera collect rain water. The fluid is usually acidic, rich in O(2) and contains digestive enzymes. In some taxa, toxins or detergents are found, or the fluid is extremely viscous. In Heliamphora or Sarracenia, the fluid differs little from pure water.


INQUILINE
Diversity Pitcher inquilines comprise bacteria, protozoa, algae, fungi, rotifers, crustaceans, arachnids, insects and amphibia. The dominant groups are protists and Dipteran larvae. The various species of CPPs host different sets of inquilines. Sarracenia purpurea hosts up to 165 species of inquilines, followed by Nepenthes ampullaria with 59 species, compared with only three species from Brocchinia reducta. Reasons for these differences include size, the life span of the pitcher as well as its fluid.  Activities Inquilines closely interact with their host. Some live as parasites, but the vast majority are mutualists. Beneficial activities include secretion of enzymes, feeding on the plant's prey and successive excretion of inorganic nutrients, mechanical break up of the prey, removal of excessive prey and assimilation of atmospheric N(2).



There is strong evidence that CPPs influence their phytotelm. Two strategies can be distinguished: (1) Nepenthes and Cephalotus produce acidic, toxic or digestive fluids and host a limited diversity of inquilines. (2) Genera without efficient enzymes such as Sarracenia or Heliamphora host diverse organisms and depend to a large extent on their symbionts for prey utilization.
Exploring the Role of Habitat on the Wettability of Cicada Wings.
Venue: ACS Applied Materials & Interfaces

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.
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
Venue: Chemical Science

De novo enzymes capable of efficiently catalysis of a non-natural reaction are obtained through minimalist design plus computationally-focused variant library screening.
A Literal Elytral Rainbow: Tunable Structural Colors Using Single Diamond Biophotonic Crystals in Pachyrrhynchus congestus Weevils.
Venue: Small

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.
Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella
Venue: PLOS Pathogens

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.
The Balance between Actomyosin Contractility and Microtubule Polymerization Regulates Hierarchical Protrusions That Govern Efficient Fibroblast-Collagen Interactions.
Venue: ACS Nano

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.
Tillandsia-Inspired Hygroscopic Photothermal Organogels for Efficient Atmospheric Water Harvesting.
Venue: Angewandte Chemie

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.
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.
Physical and behavioral adaptations to prevent overheating of the living wings of butterflies
Venue: arXiv: Biological Physics

The wings of Lepidoptera contain a matrix of living cells whose function requires appropriate temperatures. However, given their small thermal capacity, wings can overheat rapidly in the sun. Here we analyze butterfly wings across a wide range of simulated environmental conditions, and find that regions containing living cells are maintained at cooler temperatures. Diverse scale nanostructures and non-uniform cuticle thicknesses create a heterogeneous distribution of radiative cooling that selectively reduces the temperature of structures such as wing veins and androconial organs. These tissues are supplied by circulatory, neural and tracheal systems throughout the adult lifetime, indicating that the insect wing is a dynamic, living structure. Behavioral assays show that butterflies use wings to sense visible and infrared radiation, responding with specialized behaviors to prevent overheating of their wings. Our work highlights the physiological importance of wing temperature and how it is exquisitely regulated by structural and behavioral adaptations. Butterfly wings have low thermal capacity and thus are vulnerable to damage by overheating. Here, Tsai et al. take an interdisciplinary approach to reveal the organs, nanostructures and behaviors that enable butterflies to sense and regulate their wing temperature.
Self‐Sharpening Mechanism of the Sea Urchin Tooth
Venue: Advanced Functional Materials

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.
Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts
Venue: Science

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.
Species-Specific Evolution of Ebola Virus during Replication in Human and Bat Cells
Venue: Cell Reports

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.
Nest Carbon Dioxide Masks GABA-Dependent Seizure Susceptibility in the Naked Mole-Rat
Venue: Current Biology

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.
Small groups and long memories promote cooperation
Venue: Scientific Reports

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.