nils-herrmann/clean_scirepeval huggingface dataset:
Harnessing disorder: onychophorans use highly unstructured proteins, not silks, for prey capture
Venue: Proceedings of The Royal Society B: Biological Sciences

Onychophora are ancient, carnivorous soft-bodied invertebrates which capture their prey in slime that originates from dedicated glands located on either side of the head. While the biochemical composition of the slime is known, its unusual nature and the mechanism of ensnaring thread formation have remained elusive. We have examined gene expression in the slime gland from an Australian onychophoran, Euperipatoides rowelli, and matched expressed sequence tags to separated proteins from the slime. The analysis revealed three categories of protein present: unique high-molecular-weight proline-rich proteins, and smaller concentrations of lectins and small peptides, the latter two likely to act as protease inhibitors and antimicrobial agents. The predominant proline-rich proteins (200 kDa+) are composed of tandem repeated motifs and distinguished by an unusually high proline and charged residue content. Unlike the highly structured proteins such as silks used for prey capture by spiders and insects, these proteins lack ordered secondary structure over their entire length. We propose that on expulsion of slime from the gland onto prey, evaporative water loss triggers a glass transition change in the protein solution, resulting in adhesive and enmeshing thread formation, assisted by cross-linking of complementary charged and hydrophobic regions of the protein. Euperipatoides rowelli has developed an entirely new method of capturing prey by harnessing disordered proteins rather than structured, silk-like proteins.
Permeability fluctuations in heterogeneous networks with different dimensionality and topology
Venue: Journal of Geophysical Research

The purpose of this work was to relate the spatial fluctuations and scaling properties of the transport properties of porous rocks to their underlying pore geometry. Our approach was to numerically simulate flow through networks of pipes with randomly prescribed radii. The permeability k and inverse formation factor 1/F were calculated in a large number of network realizations of varying size and degree of heterogeneity (i.e., the width of the pipe radius distribution). We generally observed a large decrease of the ensemble arithmetic averages of k and 1/F with increasing network size (i.e., negative scale effect). Conversely, the ensemble geometric averages showed a moderate positive scale effect in three-dimensional simple cubic networks. We also found that in networks smaller than 32 × 32 or 10 × 10 × 10, the ensemble standard deviations of k and 1/F had a power law dependence on network size (defined as the total number of pipes) with an exponent α varying from −0.5 in homogeneous networks to large negative values depending on lattice topology in highly heterogeneous ones (−α increased with increasing lattice connectiveness, i.e., with coordination number). Thus at small scales the network transport properties were characterized by a nonuniversal power law scaling. At larger scales we observed a transition to a presumably “universal” power law scaling with an exponent equal to −0.5 independently on the degree of heterogeneity, dimensionality and lattice topology. Comparing our results to published experimental data, we found a good agreement, except in cases where we suspect that the small-scale measurements suffered a significant bias (indicated by non-nested distributions at increasing scales). We speculate that the strong positive scale effect generally observed in nature is also caused by sampling bias at small scales.
Elastic Energy Stores in Running Vertebrates
Venue: Integrative and Comparative Biology

Large mammals save much of the energy they would otherwise need for running by means of elastic structures in their legs. Kinetic and potential energy, lost at one stage of a stride, is stored temporarily as elastic strain energy and returned later in an elastic recoil. At high speeds, men and kangaroos seem to save in this way more than half the metabolic energy they would otherwise need for locomotion.

It is shown by means of a generalized model that muscles and tendons could both be important as elastic energy stores. Analysis of films and force records of kangaroos hopping shows that strain energy stored while the feet are on the ground must be stored mainly distal to the knee. The principal muscles there have short fibres, and most of the storage must be in tendons. Investigation of camels shows that tendons in the feet, distal to the ankle and wrist, are especially important. The scope for elastic storage while the feet are off the groundis also considered.

Though the evidence presented in this paper comes mainly from a few species, the conclusions presumably apply to large mammals in general.
Human defensins: turning defense into offense?
Venue: Infectious disorders drug targets

Defensins are a family of antimicrobial cationic peptides that act as a rapid response force against microbial invasion in a wide range of organisms, including plants, insects, animals and humans. In humans, defensins are produced predominantly by leukocytes and epithelial cells and are an important factor of innate immunity. In addition to their major role as natural antibiotics, defensins are increasingly recognized as signaling molecules in adaptive immunity and aberrant defensin expression has been associated with infectious diseases. In this review, we discuss the role of human defensins in relation to infectious disease and the possibility of novel defensin-based therapeutic approaches.
Interaction of two myosins with microfilaments causes locomotion inLabyrinthula sp.
Venue: Protoplasma

SummaryCytoskeleton elements of aLabyrinthula isolate from the Falkland Islands were studied. The most important characteristic of the genusLabyrinthula is a colourless branched plasmatic network of pseudopodia-like tubes with sliding spindle-shaped uninuclear plasma portions (cell bodies). After fluorescent staining tubulin appears to be uniformly and diffusely distributed throughout the whole network and to form a reticulate structure in the cell bodies. The inhibitor colchicine has no influence on the sliding motility of the cell bodies nor on the movement of the network. Actin is frequently found in the network, partly in the form of microfilament bundles, which are longitudinally arranged. Actin is also present in the cortical region of cell bodies, or of cell body groups. It was difficult to distinguish single cell bodies within groups by fluorescence. The inhibitors cytochalasin B and D stop the movement of cell bodies and network. Myosin is present in the cortical region of each cell body, and the central portions of each individual cell body contain accumulations of this protein. We could not observe any fluorescence in the network after myosin staining with the antibodies we used. An actin-myosin complex is probably responsible for the sliding movement of cell bodies in the Labyrinthula network, because actin is found in the pseudopodia-like tubes, and the cortex of the cell bodies is rich in actin and myosin. This actin-myosin complex seems to differ from another actin-myosin complex that has been postulated to be responsible for the locomotion of pseudopodia-like tubes. We propose that two actin-myosin complexes exist. One of them is responsible for locomotory phenomena of the network, and the second for cell body sliding in the pseudopodia-like tubes. In each case the myosin is probably anchored in the inner matrix membrane of the pseudopodia-like tubes. A model for actin-myosin interaction inLabyrinthula spp. is presented.
Why do pigeon feathers repel water? Hydrophobicity of pennae, Cassie-Baxter wetting hypothesis and Cassie-Wenzel capillarity-induced wetting transition.
Venue: Journal of Colloid and Interface Science

Wetting of pigeon feathers has been studied. It was demonstrated that the Cassie-Baxter wetting regime is inherent for pigeon pennae. The water drop, supported by network formed by barbs and barbules, sits partially on air pockets. Small static apparent angle hysteresis justifies the Cassie-Baxter wetting hypothesis. A twofold structure of a feather favors large contact angles and provides its water repellency. Cassie-Wenzel transition has been observed under drop evaporation, when drop radius becomes small enough for capillarity-induced water penetration into the protrusions, formed by barbules.
Fish schooling as a basis for vertical axis wind turbine farm design.
Venue: arXiv: Fluid Dynamics

Most wind farms consist of horizontal axis wind turbines (HAWTs) due to the high power coefficient (mechanical power output divided by the power of the free-stream air through the turbine cross-sectional area) of an isolated turbine. However when in close proximity to neighboring turbines, HAWTs suffer from a reduced power coefficient. In contrast, previous research on vertical axis wind turbines (VAWTs) suggests that closely spaced VAWTs may experience only small decreases (or even increases) in an individual turbine's power coefficient when placed in close proximity to neighbors, thus yielding much higher power outputs for a given area of land. A potential flow model of inter-VAWT interactions is developed to investigate the effect of changes in VAWT spatial arrangement on the array performance coefficient, which compares the expected average power coefficient of turbines in an array to a spatially isolated turbine. A geometric arrangement based on the configuration of shed vortices in the wake of schooling fish is shown to significantly increase the array performance coefficient based upon an array of 16 x 16 wind turbines. The results suggest increases in power output of over one order of magnitude for a given area of land as compared to HAWTs.
Seal whiskers detect water movements
Venue: Nature

How do pinnipeds orientate themselves under water? As most pinniped species feed in conditions under which visibility is drastically reduced, for example at night, at great depths or in murky waters, it has been particularly unclear how they succeed in finding food. Here we show that harbour seals (Phoca vitulina) can use their whiskers to detect minute water movements. The high sensitivity of this sensory system should allow a seal to gain hydrodynamic information resulting from movements of other aquatic animals, such as prey, predators or conspecifics.
There are abundant antimicrobial peptides in brains of two kinds of Bombina toads.
Venue: Journal of Proteome Research

It is well-known that there is a large amount of antimicrobial peptides in amphibian skins but few antimicrobial peptides are found in amphibian brains. Twenty-two and four antimicrobial peptides were purified and characterized from the brain homogenate of Bombina maxima and B. microdeladigitora, respectively. One hundred fifty-eight cDNA clones encoding 79 antimicrobial peptides were isolated from brain cDNA libraries of B. maxima and B. microdeladigitora. These antimicrobial peptides belong to two peptide groups (maximin and maximin-H). Twenty of them are identical to previously reported antimicrobial peptides (maximin 1-8, 10, 11, maximin H1, 3-5, 7, 9, 10, 12, 15, 16) from B. maxima skin secretions. Fifty-nine of them are novel antimicrobial peptides. Some of these antimicrobial peptides showed strong antimicrobial activities against tested microorganism strains including Gram-positive and -negative bacteria and fungi. The current diversity in peptide coding cDNA sequences is, to our knowledge, the most extreme yet described for any animal brains. The extreme diversity may give rise to interest to prospect the actual functions of antimicrobial peptides in amphibian brains.
Ionic compensation with no renal response to chronic hypercapnia in chrysemys picta bellii.
Venue: American Journal of Physiology-regulatory Integrative and Comparative Physiology

The ionic compensatory response to CO2 breathing for 3 days was studied on intact and cystectomized turtles at 10 and 20 degrees C. Arterial blood gases, pH, ionized calcium, and the plasma concentrations of Na+, K+, Cl-, total Ca2+, and total Mg2+ were measured periodically. At 20 degrees C, ureteral urine was also collected from bladderless turtles and was analyzed for pH, ions, NH3+, total CO2, osmolality, and titratable acid. When CO2 was breathed there was a compensatory change in the strong-ion difference as manifest by an increase in plasma [HCO3-] that was approximately 10 meq/l both in the 10 and 20 degrees C turtles. The only significant associated strong-ion changes observed consistent with the ionic compensatory response were increases in total and ionized Ca2+ and total Mg2+. These results were unaffected at either temperature by surgical removal of the urinary bladder. Urine collected from cystectomized turtles showed no compensatory increase in acid excretion during hypercapnia; in fact, changes occurred in the opposite direction. Urinary excretion of HCO3- and urine pH increased significantly, whereas titratable acidity decreased significantly. No significant change occurred in ammonia excretion over the three days of hypercapnia. These data argue against compensatory roles for the kidneys and urinary bladder in this species and point to internal ionic exchanges involving bone and shell.
Simple and diversified crop rotations: approach and insight into agroecosystems
Venue: Ecological studies

Farm management and the cultivation of soils for production of fiber and food for men and animais has always raised the question of how far man can interfere with the household of nature without disturbing the basis of vital processes. As hunter and gatherer, man’s influence on nature or natural ecosystems was of little importance. As soon as the world population increased, other methods and forms of producing food developed, namely those of modern agriculture.
Thermal windows on the body surface of African elephants (Loxodonta africana) studied by infrared thermography.
Venue: Journal of Thermal Biology

In this study, we examined infrared thermograms in the course of time of six African zoo elephants and observed two phenomena. First, we noticed independent thermal windows, highly vascularised skin areas, on the whole elephants’ body and second we observed distinct and sharply delimited hot sections on the elephants’ pinnae. The frequency of thermal windows increased with increasing ambient temperature and body weight. We assume that the restriction of an enhanced cutaneous blood flow to thermal windows might enable the animal to react more flexibly to its needs with regard to heat loss. With this understanding, the use of thermal windows in heat loss might be seen as a fine-tuning mechanism under thermoneutral conditions.
Discovery of skin alkaloids in a miniaturized eleutherodactylid frog from Cuba
Venue: Biology Letters

Four phylogenetically independent lineages of frogs are currently known to sequester lipid-soluble skin alkaloids for which a dietary source has been demonstrated. We report here a remarkable fifth such instance, in Eleutherodactylus iberia and Eleutherodactylus orientalis, two species of miniaturized frogs of the family Eleutherodactylidae from Cuba. Six pumiliotoxins and two indolizidines were found in E. iberia, one of the smallest frogs in the world and characterized by a contrasting colour pattern for which we hypothesize an aposematic function. Analyses of stomach content indicated a numerical prevalence of mites with an important proportion of oribatids—a group of arthropods known to contain one of the pumiliotoxins detected in E. iberia. This suggests that miniaturization and specialization to small prey may have favoured the acquisition of dietary skin alkaloids in these amphibians.
Hurricane Hugo wind damage to southeastern U.S. coastal forest tree species
Venue: Biotropica

One percent of Hobcaw Forest, a 3077 ha tract in South Carolina's lower coastal plain, was inventoried with fixed area plots within four months after the eye of Hurricane Hugo passed 97 km south of the forest. Results of this sampling confirmed our hypotheses that the amount and nature of hurricane wind damage differed among the tree species sampled. Approximately 73 percent of the 16,870 trees inventoried were either not damaged or had light crown damage. Longleaf pine (Pinus palustris) was less damaged than loblolly pine (Pinus taeda) or pond pine (Pinus serotina). Bald cypress (Taxodium distichum) suffered light crown damage. Upland oaks were more heavily damaged than the pine species. Live oak (Quercus virginiana) was less damaged than laurel oak (Quercus laurifolia) and water oak (Quercus nigra). Those tree species commonly found in the lower coastal plain (longleaf pine, bald cypress, and live oak) suffered less damage than species with larger natural ranges.
Di-myo-inositol phosphate and novel UDP-sugars accumulate in the extreme hyperthermophile Pyrolobus fumarii
Venue: Extremophiles

The archaeon Pyrolobus fumarii, one of the most extreme members of hyperthermophiles known thus far, is able to grow at temperatures up to 113°C. Over a decade after the description of this organism our knowledge about the structures and strategies underlying its remarkable thermal resistance remains incipient. The accumulation of a restricted number of charged organic solutes is a common response to heat stress in hyperthermophilic organisms and accordingly their role in thermoprotection has been often postulated. In this work, the organic solute pool of P. fumarii was characterized using 1H, 13C, and 31P NMR. Di-myo-inositol phosphate was the major solute (0.21 μmol/mg protein), reinforcing the correlation between the occurrence of this solute and hyperthermophily; in addition, UDP-sugars (total concentration 0.11 μmol/mg protein) were present. The structures of the two major UDP-sugars were identified as UDP-α-GlcNAc3NAc and UDP-α-GlcNAc3NAc-(4 ← 1)-β-GlcpNAc3NAc. Interestingly, the latter compound appears to be derived from the first one by addition of a 2,3-N-acetylglucoronic acid unit, suggesting that these UDP-sugars are intermediates of an N-linked glycosylation pathway. To our knowledge the UDP-disaccharide has not been reported elsewhere. The physiological roles of these organic solutes are discussed.
Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants
Venue: Science

Gardening for Ants and Termites Among the social insects, ants and termites are the most diverse and ecologically dominant. Termites are known to engage in a mutualism with nitrogen-fixing bacteria, and Pinto-Tomás et al. (p. 1120) have identified similar relationships occurring among leaf-cutter ants, which maintain specialized nitrogen-fixing bacteria in their fungus gardens. Together, these mutualisms are a major source of nitrogen in terrestrial ecosystems. How is the evolutionary stability of such mutualistic cooperation maintained? Aanen et al. (p. 1103) show that the Termitomyces fungus cultured by termites remains highly related because mycelia of the same clone fuse together and grow more efficiently to out-compete rare clones. Leaf-cutting ants engage in a mutualism with nitrogen-fixing bacteria that help fertilize their fungus gardens. Bacteria-mediated acquisition of atmospheric N2 serves as a critical source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene reduction and stable isotope experiments, we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant−microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.
Adaptations to environmental extremes by multicellular organisms
Venue: International Journal of Astrobiology

Microbes, particularly Archaea, are well-known for their superb adaptation to extreme environments. However, amazing adaptations to extreme stresses do not only occur in microbes, but also in many multicellular organisms. Examples include tardigrades and their capability to survive freezing to near absolute zero, the Pompeii worm withstanding temperatures of up to 105°C, the Crucian carp remaining active in anoxic conditions for several months, and resurrection plants, which can survive near-complete desiccation. Here, we review some of the cryptobiotic strategies and adaptations exhibited in multicellular organisms, and point out their relevance to astrobiology.
Mechanosensory hairs in bumblebees (Bombus terrestris) detect weak electric fields
Venue: Proceedings of the National Academy of Sciences of the United States of America

Electroreception in terrestrial animals is poorly understood. In bumblebees, the mechanical response of filiform hairs in the presence of electric fields provides key evidence for electrosensitivity to ecologically relevant electric fields. Mechanosensory hairs in arthropods have been shown to function as fluid flow or sound particle velocity receivers. The present work provides direct evidence for additional, nonexclusive functionality involving electrical Coulomb-force coupling between distant charged objects and mechanosensory hairs. Thus, the sensory mechanism is proposed to rely on electromechanical coupling, whereby many light thin hairs serve the detection of the electrical field surrounding a bumblebee approaching a flower. This finding prompts the possibility that other terrestrial animals use such sensory hairs to detect and respond to electric fields. Bumblebees (Bombus terrestris) use information from surrounding electric fields to make foraging decisions. Electroreception in air, a nonconductive medium, is a recently discovered sensory capacity of insects, yet the sensory mechanisms remain elusive. Here, we investigate two putative electric field sensors: antennae and mechanosensory hairs. Examining their mechanical and neural response, we show that electric fields cause deflections in both antennae and hairs. Hairs respond with a greater median velocity, displacement, and angular displacement than antennae. Extracellular recordings from the antennae do not show any electrophysiological correlates to these mechanical deflections. In contrast, hair deflections in response to an electric field elicited neural activity. Mechanical deflections of both hairs and antennae increase with the electric charge carried by the bumblebee. From this evidence, we conclude that sensory hairs are a site of electroreception in the bumblebee.
Modelling of the frictional behaviour of the snake skin covered by anisotropic surface nanostructures
Venue: Scientific Reports

Previous experimental data clearly revealed anisotropic friction on the ventral scale surface of snakes. However, it is known that frictional properties of the ventral surface of the snake skin range in a very broad range and the degree of anisotropy ranges as well to a quite strong extent. This might be due to the variety of species studied, diversity of approaches used for the friction characterization, and/or due to the variety of substrates used as a counterpart in the experiments. In order to understand the interactions between the nanostructure arrays of the ventral surface of the snake skin, this study was undertaken, which is aimed at numerical modeling of frictional properties of the structurally anisotropic surfaces in contact with various size of asperities. The model shows that frictional anisotropy appears on the snake skin only on the substrates with a characteristic range of roughness, which is less or comparable with dimensions of the skin microstructure. In other words, scale of the skin relief should reflect an adaptation to the particular range of surfaces asperities of the substrate.