nils-herrmann/clean_scirepeval huggingface dataset:
Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal
Venue: Proceedings of the National Academy of Sciences of the United States of America

North American porcupines are well known for their specialized hairs, or quills that feature microscopic backward-facing deployable barbs that are used in self-defense. Herein we show that the natural quill’s geometry enables easy penetration and high tissue adhesion where the barbs specifically contribute to adhesion and unexpectedly, dramatically reduce the force required to penetrate tissue. Reduced penetration force is achieved by topography that appears to create stress concentrations along regions of the quill where the cross sectional diameter grows rapidly, facilitating cutting of the tissue. Barbs located near the first geometrical transition zone exhibit the most substantial impact on minimizing the force required for penetration. Barbs at the tip of the quill independently exhibit the greatest impact on tissue adhesion force and the cooperation between barbs in the 0–2 mm and 2–4 mm regions appears critical to enhance tissue adhesion force. The dual functions of barbs were reproduced with replica molded synthetic polyurethane quills. These findings should serve as the basis for the development of bio-inspired devices such as tissue adhesives or needles, trocars, and vascular tunnelers where minimizing the penetration force is important to prevent collateral damage.
Inhibiting bacterial cooperation is an evolutionarily robust anti-biofilm strategy
Venue: Nature Communications

Bacteria commonly form dense biofilms encased in extracellular polymeric substances (EPS). Biofilms are often extremely tolerant to antimicrobials but their reliance on shared EPS may also be a weakness as social evolution theory predicts that inhibiting shared traits can select against resistance. Here we show that EPS of Salmonella biofilms is a cooperative trait whose benefit is shared among cells, and that EPS inhibition reduces both cell attachment and antimicrobial tolerance. We then compare an EPS inhibitor to conventional antimicrobials in an evolutionary experiment. While resistance against conventional antimicrobials rapidly evolves, we see no evolution of resistance to EPS inhibition. We further show that a resistant strain is outcompeted by a susceptible strain under EPS inhibitor treatment, explaining why resistance does not evolve. Our work suggests that targeting cooperative traits is a viable solution to the problem of antimicrobial resistance. Bacterial biofilms rely on shared extracellular polymeric substances (EPS) and are often highly tolerant to antibiotics. Here, the authors show in in vitro experiments that Salmonella does not evolve resistance to EPS inhibition because such strains are outcompeted by a susceptible strain under inhibitor treatment.
Dead leaves and fire survival in Southern African tree aloes
Venue: Oecologia

SummaryMany aloe species in southern Africa have stems clothed with a layer of persistent dead leaves. The degree of stem coverage is species-specific. The suggestion that persistent dead leaves have an insulatory function and are adaptive in fire-prone habitat was tested on Aloe ferox. Field surveys demonstrated a significant negative relationship between mortality and degree of stem coverage and laboratory studies confirmed the insulating properties of dead leaves. The distribution of southern African tree aloes supprts the prediction that bare-stemmed species would be confined to fire-free habitat whilst fully clothed species would occur in both fire-prone and fire-free habitat. The study suggests that harvesting of Aloe ferox leaves for medicinal purposes could result in significant mortality in fires.
Reflectins: The Unusual Proteins of Squid Reflective Tissues
Venue: Science

A family of unusual proteins is deposited in flat, structural platelets in reflective tissues of the squid Euprymna scolopes. These proteins, which we have named reflectins, are encoded by at least six genes in three subfamilies and have no reported homologs outside of squids. Reflectins possess five repeating domains, which are highly conserved among members of the family. The proteins have a very unusual composition, with four relatively rare residues (tyrosine, methionine, arginine, and tryptophan) comprising ∼57% of a reflectin, and several common residues (alanine, isoleucine, leucine, and lysine) occurring in none of the family members. These protein-based reflectors in squids provide a marked example of nanofabrication in animal systems.
How do ants stick out their tongues?
Venue: Journal of Morphology

The mouthparts are very important tools for almost any task performed by ants. In particular, the labiomaxillary complex is essential for food intake. In the present study we investigated the anatomical design of the labiomaxillary complex in various ant species, focusing on movement mechanisms. Six labial and six maxillary muscles with different functions control the several joints and ensure the proper performance of the labiomaxillary complex. According to our measurements of sarcomere lengths, muscle fiber lengths and diameters, and the relative muscle volumes, the labial and maxillary muscles feature rather slow than fast muscle characteristics and do not seem to be specialized for specific tasks. Since glossa protractor muscles are absent, the protraction of the glossa, the distal end of the labium, is a nonmuscular movement. By histological measurements of hemolymph volumes we could exclude a pressure‐driven mechanism. Additional experiments showed that, upon relaxation of the glossa retractor muscles, the glossa protracts elastically. This elastic mechanism possibly sets an upper limit to licking frequency, thus influencing food intake rates and ultimately foraging behavior. In contrast to many other elastic mechanisms among arthropods, glossa protraction in ants is based on a mechanism where elasticity works as an actual antagonist to muscles. We compared the design of the labiomaxillary complex of ants with that of the honeybee and suggest an elastic mechanism for glossa protraction in honeybees as well.  2002.
Correlation between the Circadian Rhythm of Resistance to Extreme Temperatures and Changes in Fatty Acid Composition in Cotton Seedlings
Venue: Plant Physiology

Fluctuations in fatty acid composition were examined in cotton (Gossypium hirsutum L. cv Deltapine 50) leaves during light-dark cycles of 12:12 h and under continuous light and were correlated to the rhythmic changes in chilling (5[deg]C) resistance (CR) and heat (53[deg]C) resistance (HR). The chilling-resistant and chilling-sensitive phases developed in the dark or the light period, respectively, and this rhythm persisted under continuous light for three cycles. The heat-resistant phase developed in the light period and an additional peak of HR occurred in the middle of the dark period. Under continuous light, only one peak of HR developed, lasting from the middle of the subjective night to the middle of the subjective day. The amounts of palmitic and oleic acids were constant during the light-dark cycle and under continuous light, but those of linoleic and linolenic acids fluctuated, attaining a high level in the middle of the dark period or the subjective night, and a low level in the middle of the light period or the subjective day. A low temperature of 20[deg]C induced CR and affected changes in fatty acid composition similar to those that occurred during the daily CR phase. A high temperature of 40[deg]C induced HR but did not affect changes in fatty acid composition. The results in their entirety show that the CR that develops rhythmically as well as the low-temperature-induced CR coincide with increased levels of polyunsaturated fatty acids. No correlation is found between changes in fatty acid composition and the HR that develops rhythmically or the high-temperature-induced HR.
A Unique Resource Mutualism between the Giant Bornean Pitcher Plant, Nepenthes rajah, and Members of a Small Mammal Community
Venue: PLOS ONE

The carnivorous pitcher plant genus Nepenthes grows in nutrient-deficient substrates and produce jug-shaped leaf organs (pitchers) that trap arthropods as a source of N and P. A number of Bornean Nepenthes demonstrate novel nutrient acquisition strategies. Notably, three giant montane species are engaged in a mutualistic association with the mountain treeshrew, Tupaia montana, in which the treeshrew defecates into the pitchers while visiting them to feed on nectar secretions on the pitchers' lids. Although the basis of this resource mutualism has been elucidated, many aspects are yet to be investigated. We sought to provide insights into the value of the mutualism to each participant. During initial observations we discovered that the summit rat, R. baluensis, also feeds on sugary exudates of N. rajah pitchers and defecates into them, and that this behavior appears to be habitual. The scope of the study was therefore expanded to assess to what degree N. rajah interacts with the small mammal community. We found that both T. montana and R. baluensis are engaged in a mutualistic interaction with N. rajah. T .montana visit pitchers more frequently than R. baluensis, but daily scat deposition rates within pitchers do not differ, suggesting that the mutualistic relationships are of a similar strength. This study is the first to demonstrate that a mutualism exists between a carnivorous plant species and multiple members of a small mammal community. Further, the newly discovered mutualism between R. baluensis and N. rajah represents only the second ever example of a multidirectional resource-based mutualism between a mammal and a carnivorous plant.
Stationary underwater prey missed by reef herons,Egretta gularis: head position and light refraction at the moment of strike
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

SummaryThis paper attempts to verify the importance of spatial positioning of the eyes of reef heronsEgretta gularis schistacea, when coping with light refraction at the air-water interface. The herons' striking of prey, while their approach angle was restricted, was observed. (a) The herons' capture success in the restricted situation was markedly lower than in the unrestricted situation. (b) The points of strike (STR) in unsuccessful strikes differed from those of successful strikes, and from those of the unrestricted situation. (c) The larger the difference between the observed and the predicted ratio of prey depth to apparent prey depth, the higher the probability of missing a prey. These results support predictions of a model presented elsewhere (Katzir and Intrator 1987) that a heron will attempt to reach spatial positions at which prey's real depth and apparent depth are linearly correlated.
Honey Bee Nest Thermoregulation: Diversity Promotes Stability
Venue: Science

A honey bee colony is characterized by high genetic diversity among its workers, generated by high levels of multiple mating by its queen. Few clear benefits of this genetic diversity are known. Here we show that brood nest temperatures in genetically diverse colonies (i.e., those sired by several males) tend to be more stable than in genetically uniform ones (i.e., those sired by one male). One reason this increased stability arises is because genetically determined diversity in workers' temperature response thresholds modulates the hive-ventilating behavior of individual workers, preventing excessive colony-level responses to temperature fluctuations.
Decay of cacti and carbon cycling
Venue: Naturwissenschaften

Cacti contain large quantities of Ca-oxalate biominerals, with C derived from atmospheric CO2. Their death releases these biominerals into the environment, which subsequently transform to calcite via a monohydrocalcite intermediate. Here, the fate of Ca-oxalates released by plants in arid environments is investigated. This novel and widespread form of biomineralization has unexpected consequences on C cycling and calcite accumulation in areas with large numbers of cacti. The magnitude of this mineralization is revealed by studying the large columnar cactus Carnegiea gigantea (Engelm.) Britton and Rose in southwestern Arizona (locally called the saguaro). A large C. gigantea contains on the order of 1×105 g of the Ca-oxalate weddellite—CaC2O4·2H2O. In areas with high C. gigantea density, there is an estimated 40 g Catm m−2 sequestered in Ca-oxalates. Following the death of the plant, the weddellite transforms to calcite on the order to 10–20 years. In areas with high saguaro density, there is an estimated release of up to 2.4 g calcite m−2 year−1 onto the desert soil. Similar transformation mechanisms occur with the Ca-oxalates that are abundant in the majority of cacti. Thus, the total atmospheric C returned to the soil of areas with a high number density of cacti is large, suggesting that there may be a significant long-term accumulation of atmospheric C in these soils derived from Ca-oxalate biominerals. These findings demonstrate that plant decay in arid environments may have locally significant impacts on the Ca and inorganic C cycles.
Self-assembly of amorphous biophotonic nanostructures by phase separation
Venue: Soft Matter

Some of the most vivid colors in the animal kingdom are created not by pigments, but by wavelength-selective scattering of light from nanostructures. Here we investigate quasi-ordered nanostructures of avian feather barbs which produce vivid non-iridescent colors. These β-keratin and air nanostructures are found in two basic morphologies: tortuous channels and amorphous packings of spheres. Each class of nanostructure is isotropic and has a pronounced characteristic length scale of variation in composition. These local structural correlations lead to strong backscattering over a narrow range of optical frequencies and little variation with angle of incidence. Such optical properties play important roles in social and sexual communication. To be effective, birds need to precisely control the development of these nanoscale structures, yet little is known about how they grow. We hypothesize that multiple lineages of birds have convergently evolved to exploit phase separation and kinetic arrest to self-assemble spongy color-producing nanostructures in feather barbs. Observed avian nanostructures are strikingly similar to those self-assembled during the phase separation of fluid mixtures; the channel and sphere morphologies are characteristic of phase separation by spinodal decomposition and nucleation and growth, respectively. These unstable structures are locked-in by the kinetic arrest of the β-keratin matrix, likely through the entanglement or cross-linking of supermolecular β-keratin fibers. Using the power of self-assembly, birds can robustly realize a diverse range of nanoscopic morphologies with relatively small physical and chemical changes during feather development.
A Dynamical System for Plant Pattern Formation: A Rigorous Analysis

Venue: Journal of Nonlinear Science

SummaryWe present a rigorous mathematical analysis of a discrete dynamical system modeling plant pattern formation. In this model, based on the work of physicists Douady and Couder, fixed points are the spiral or helical lattices often occurring in plants. The frequent occurrence of the Fibonacci sequence in the number of visible spirals is explained by the stability of the fixed points in this system, as well as by the structure of their bifurcation diagram. We provide a detailed study of this diagram.
Mussel-Inspired Surface Chemistry for Multifunctional Coatings
Venue: Science

We report a method to form multifunctional polymer coatings through simple dip-coating of objects in an aqueous solution of dopamine. Inspired by the composition of adhesive proteins in mussels, we used dopamine self-polymerization to form thin, surface-adherent polydopamine films onto a wide range of inorganic and organic materials, including noble metals, oxides, polymers, semiconductors, and ceramics. Secondary reactions can be used to create a variety of ad-layers, including self-assembled monolayers through deposition of long-chain molecular building blocks, metal films by electroless metallization, and bioinert and bioactive surfaces via grafting of macromolecules.
Photoprotection of green plants: a mechanism of ultra-fast thermal energy dissipation in desiccated lichens
Venue: Planta

In order to survive sunlight in the absence of water, desiccation-tolerant green plants need to be protected against photooxidation. During drying of the chlorolichen Cladonia rangiformis and the cyanolichen Peltigera neckeri, chlorophyll fluorescence decreased and stable light-dependent charge separation in reaction centers of the photosynthetic apparatus was lost. The presence of light during desiccation increased loss of fluorescence in the chlorolichen more than that in the cyanolichen. Heating of desiccated Cladonia thalli, but not of Peltigera thalli, increased fluorescence emission more after the lichen had been dried in the light than after drying in darkness. Activation of zeaxanthin-dependent energy dissipation by protonation of the PsbS protein of thylakoid membranes was not responsible for the increased loss of chlorophyll fluorescence by the chlorolichen during drying in the light. Glutaraldehyde inhibited loss of chlorophyll fluorescence during drying. Desiccation-induced loss of chlorophyll fluorescence and of light-dependent charge separation are interpreted to indicate activation of a highly effective mechanism of photoprotection in the lichens. Activation is based on desiccation-induced conformational changes of a pigment–protein complex. Absorbed light energy is converted into heat within a picosecond or femtosecond time domain. When present during desiccation, light interacts with the structural changes of the protein providing increased photoprotection. Energy dissipation is inactivated and structural changes are reversed when water becomes available again. Reversibility of ultra-fast thermal dissipation of light energy avoids photo-damage in the absence of water and facilitates the use of light for photosynthesis almost as soon as water becomes available.
A new perspective on radiation resistance based on Deinococcus radiodurans
Venue: Nature Reviews Microbiology

In classical models of radiation toxicity, DNA is the molecule that is most affected by ionizing radiation (IR). However, recent data show that the amount of protein damage caused during irradiation of bacteria is better related to survival than to DNA damage. In this Opinion article, a new model is presented in which proteins are the most important target in the hierarchy of macromolecules affected by IR. A first line of defence against IR in extremely radiation-resistant bacteria might be the accumulation of manganese complexes, which can prevent the production of iron-dependent reactive oxygen species. This would allow an irradiated cell to protect sufficient enzymatic activity needed to repair DNA and survive.
Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases
Venue: Applied Microbiology and Biotechnology

The conversion of the heterocycle dibenzothiophene (DBT) by the agaric basidiomycetes Agrocybe aegerita and Coprinellus radians was studied in vivo and in vitro with whole cells and with purified extracellular peroxygenases, respectively. A. aegerita oxidized DBT (110 μM) by 100% within 16 days into eight different metabolites. Among the latter were mainly S-oxidation products (DBT sulfoxide, DBT sulfone) and in lower amounts, ring-hydroxylation compounds (e.g., 2-hydroxy-DBT). C. radians converted about 60% of DBT into DBT sulfoxide and DBT sulfone as the sole metabolites. In vitro tests with purified peroxygenases were performed to compare the product pattern with the metabolites formed in vivo. Using ascorbic acid as radical scavenger, a total of 19 and seven oxygenation products were detected after DBT conversion by the peroxygenases of A. aegerita (AaP) and C. radians (CrP), respectively. Whereas ring hydroxylation was favored over S-oxidation by AaP (again 2-hydroxy-DBT was identified), CrP formed DBT sulfoxide as major product. This finding suggests that fungal peroxygenases can considerably differ in their catalytic properties. Using H218O2, the origin of oxygen was proved to be the peroxide. Based on these results, we propose that extracellular peroxygenases may be involved in the oxidation of heterocycles by fungi also under natural conditions.
A reliable method of manufacturing metallic hierarchical superhydrophobic surfaces
Venue: Applied Physics Letters

A method of manufacturing hierarchical metallic surfaces demonstrating superhydrophobic properties is presented. The surfaces showed apparent contact angles as high as 153° and sliding angles of 10° for 50–100 μl droplets. The Cassie-like model [A. B. D. Cassie and S. Baxter,  (1944)], considering the hierarchical topography of the relief, predicts apparent contact angles in a satisfactory agreement with the measured values.
Ant search strategies after interrupted tandem runs
Venue: The Journal of Experimental Biology

Tandem runs are a form of recruitment in ants. During a tandem run, a single leader teaches one follower the route to important resources such as sources of food or better nest sites. In the present study, we investigate what tandem leaders and followers do, in the context of nest emigration, if their partner goes missing. Our experiments involved removing either leaders or followers at set points during tandem runs. Former leaders first stand still and wait for their missing follower but then most often proceed alone to the new nest site. By contrast, former followers often first engage in a Brownian search, for almost exactly the time that their former leader should have waited for them, and then former followers switch to a superdiffusive search. In this way, former followers first search their immediate neighbourhood for their lost leader before becoming ever more wide ranging so that in the absence of their former leader they can often find the new nest, re-encounter the old one or meet a new leader. We also show that followers gain useful information even from incomplete tandem runs. These observations point to the important principle that sophisticated communication behaviours may have evolved as anytime algorithms, i.e. procedures that are beneficial even if they do not run to completion.
A lichen protected by a super-hydrophobic and breathable structure.
Venue: Journal of Plant Physiology

A species of lichen, Lecanora conizaeoides, is shown to be super-hydrophobic. It uses a combination of hydrophobic compounds and multi-layered roughness to shed water effectively. This is combined with gas channels to produce a biological analogue of a waterproof, breathable garment. The particular lichen grows mostly during wet seasons and is unusually resistant to acid rain [Hauck, M., 2003. The Bryologist 106(2), 257-269; Honegger, R., 1998. Lichenologist 30(3),193-212]. The waterproof, breathable surface allows this lichen to photosynthesise when other species are covered with a layer of water. In addition, rainwater runs off the surface of the organism, reducing its intake of water from above and probably contributing to its resistance to acid rain.