nils-herrmann/clean_scirepeval huggingface dataset:
Impact of engineered surface microtopography on biofilm formation of Staphylococcus aureus
Venue: Biointerphases

The surface of an indwelling medical device can be colonized by human pathogens that can form biofilms and cause infections. In most cases, these biofilms are resistant to antimicrobial therapy and eventually necessitate removal or replacement of the device. An engineered surface microtopography based on the skin of sharks, Sharklet AFTM, has been designed on a poly(dimethyl siloxane) elastomer (PDMSe) to disrupt the formation of bacterial biofilms without the use of bactericidal agents. The Sharklet AFTM PDMSe was tested against smooth PDMSe for biofilm formation of Staphylococcus aureus over the course of 21 days. The smooth surface exhibited early-stage biofilm colonies at 7 days and mature biofilms at 14 days, while the topographical surface did not show evidence of early biofilm colonization until day 21. At 14 days, the mean value of percent area coverage of S. aureus on the smooth surface was 54% compared to 7% for the Sharklet AFTM surface (p<0.01). These results suggest that surface modification of indwelling medical devices and exposed sterile surfaces with the Sharklet AFTM engineered topography may be an effective solution in disrupting biofilm formation of S. aureus.
Nutritional toxicology of mammals: regulated intake of plant secondary compounds
Venue: Functional Ecology

Many mammalian herbivores continually face the possibility of being poisoned by the natural toxins in the plants they consume. A recent key discovery in this area is that mammalian herbivores are capable of regulating the dose of plant secondary compounds (PSCs) ingested. 2. The ‘regulation model’ describes the factors driving ingestion of PSCs by mammals and can be dissected into two separate hypotheses related to meal size and inter-meal interval (IMI). Testing these hypotheses independently yields a more thorough understanding of the underlying and potentially interconnected mechanisms. 3. Three mechanisms could influence the size of meals that contain PSCs. These are the plasma concentration of PSCs, conditioned learning, and activation of bitter receptors in the intestine. 4. Two mechanisms are proposed to govern the IMI. The first predicts that IMI is dependent on the concentration of PSC metabolites in the plasma; feeding will not resume until metabolite concentrations are acceptable for further ingestion of PSCs. The second hypothesis proposes that the intestinal bitter receptors modulate IMI through release of satiety compounds.
Rapid increase of vacuolar volume in response to salt stress
Venue: Planta

Suspension-cultured cells of mangrove [Bruguiera sexangula (Lour.) Poir.] showed a rapid increase in vacuolar volume under salt stress, although there was no change in the cell volume. The rapid increase in the vacuolar volume was an active process, which followed the activation of the tonoplast H+-ATPase and the vacuolar acid phosphatase. The same phenomenon was observed in barley (Hordeum vulgare L. cv. Doriru) root meristematic cells under salt stress but not in pea (Pisum sativum L.). Increases in vacuolar volume could potentially protect the cytoplasm by decreasing the cytoplasmic volume during the initial phases of salt stress.
Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth
Venue: Science

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.
Trabecular bone scales allometrically in mammals and birds
Venue: Proceedings of The Royal Society B: Biological Sciences

Many bones are supported internally by a latticework of trabeculae. Scaling of whole bone length and diameter has been extensively investigated, but scaling of the trabecular network is not well characterized. We analysed trabecular geometry in the femora of 90 terrestrial mammalian and avian species with body masses ranging from 3 g to 3400 kg. We found that bone volume fraction does not scale substantially with animal size, while trabeculae in larger animals' femora are thicker, further apart and fewer per unit volume than in smaller animals. Finite element modelling indicates that trabecular scaling does not alter the bulk stiffness of trabecular bone, but does alter strain within trabeculae under equal applied loads. Allometry of bone's trabecular tissue may contribute to the skeleton's ability to withstand load, without incurring the physiological or mechanical costs of increasing bone mass.
Evaluating the social networks of four flocks of captive flamingos over a five-year period: Temporal, environmental, group and health influences on assortment
Venue: Behavioural Processes

Flamingos are well known for their gregarious habits and aggregations in large flocks, but evaluation of the mechanisms behind social grouping remain poorly understood. Captive birds provide a useful model for investigating aspects of social choice in highly gregarious, long-lived species. Animals invest in social relationships that convey fitness benefits and bonds can be long-lasting. For some species, field-based measurement of social networks can be difficult. Captive populations therefore provide a useful alternative for measuring social choices. Data were collected on flamingos at WWT Slimbridge Wetland Centre from 2013 to 2016 and compared to data from 2012. For three flocks, associations were analysed along with individual foot health scores to identify any relationship between health and social behaviour. Long-term partnerships were present in all flocks; preferred associates noted in 2012 were present in 2016. Matrix correlations across years were positive; arrangements of dyads, trios and quartets with higher ties strengths were visible at the beginning and end of the study. Both male-male and female-female bonds were stable over time. All flamingos were more frequently seen socialising than solitary; those in the largest flock showed the highest occurrence of social behaviour (irrespective of enclosure size differences). The number of connections realised from all available within a network was significantly influenced by season. Foot health did not predict associations in these three flamingo networks. Our results indicate that flamingo societies are complex (i.e. formed of long-standing preferential partnerships and not loose, random connections) and the impact of flock size and environment on sociality should be investigated further. These results are helpful for those working with captive flamingos to consider the number of birds housed so that an array of opportunities for choice of associate and/or breeding partner are available in zoo-housed flocks.
Chemically mediated antifouling in the red alga Delisea pulchra
Venue: Marine Ecology Progress Series

Using laboratory assays, we tested whether the secondary metabolites (furanones) on the surface of the red alga Delisea pulchra deter the settlement and growth of a range of ecologically relevant fouling organisms. D. pulchra and 4 other co-occurring seaweeds were almost exclusively fouled by other algae. Consequently, we carried out laboratory assays using propagules from 4 fouling algae (Ulva sp., Ceramium sp., Polysiphonia sp. and Ectocarpus siliculosis) representing the natural fouling community. The crude surface extract of D. pulchra at the same concentration as on the surface of the plant, the furanone fraction of this extract, and pure furnaones, deterred the settlement of fouling organisms in ecologically relevant assays. These data, coupled with knowledge of the surface concentration of furanones on D. pulchra and a mechanism by which furanones are sequestered onto the surface of the plant, provide a rigorous demonstration of chemically mediated antifouling.
Barotolerance of fungi isolated from deep-sea sediments of the Indian Ocean
Venue: Aquatic Microbial Ecology

Two species of filamentous fungi, AspergiUus ustus (Bain.) Thom & Church and Graphium sp., were isolated from calcareous animal shells at depths of 860 m in the Arabian Sea and 965 m in the Bay of Bengal. Laboratory experiments showed germination of conidia, growth of hyphae and microconidiation in both the fungi at 100 bar pressure at 10 and 30°C suggesting barotolerance The fungi also secreted barotolerant protease under these conditions. Protease synthesised and secreted in cultures grown at 1 bar was also active under 100 bar pressure at 10 and 30°C. At 1O0C, the fungi showed better conidial germination, growth and protease secretion when subjected to 100 bar than when grown at 1 atmosphere. The results indicate barotolerance of terrestrial species of fungl and suggest that they might be active under deep-sea conditions.
Adhesion of single bacterial cells in the micronewton range.
Venue: Proceedings of the National Academy of Sciences of the United States of America

The adhesion of bacteria to surfaces plays critical roles in the environment, disease, and industry. In aquatic environments, Caulobacter crescentus is one of the first colonizers of submerged surfaces. Using a micromanipulation technique, we measured the adhesion force of single C. crescentus cells attached to borosilicate substrates through their adhesive holdfast. The detachment forces measured for 14 cells ranged over 0.11 to 2.26 microN, averaging 0.59 +/- 0.62 microN. Based on the calculation of stress distribution with the finite element analysis method (dividing an object into small grids and calculating relevant parameters for all of the elements), the adhesion strength between the holdfast and the substrate is >68 N/mm(2) in the central region of contact. To our knowledge, this strength of adhesion is the strongest ever measured for biological adhesives.
Shape of tropoelastin, the highly extensible protein that controls human tissue elasticity
Venue: Proceedings of the National Academy of Sciences of the United States of America

Elastin enables the reversible deformation of elastic tissues and can withstand decades of repetitive forces. Tropoelastin is the soluble precursor to elastin, the main elastic protein found in mammals. Little is known of the shape and mechanism of assembly of tropoelastin as its unique composition and propensity to self-associate has hampered structural studies. In this study, we solve the nanostructure of full-length and corresponding overlapping fragments of tropoelastin using small angle X-ray and neutron scattering, allowing us to identify discrete regions of the molecule. Tropoelastin is an asymmetric coil, with a protruding foot that encompasses the C-terminal cell interaction motif. We show that individual tropoelastin molecules are highly extensible yet elastic without hysteresis to perform as highly efficient molecular nanosprings. Our findings shed light on how biology uses this single protein to build durable elastic structures that allow for cell attachment to an appended foot. We present a unique model for head-to-tail assembly which allows for the propagation of the molecule’s asymmetric coil through a stacked spring design.
The protective role of aquaporins in the freeze-tolerant insect Eurosta solidaginis: functional characterization and tissue abundance of EsAQP1
Venue: The Journal of Experimental Biology

The movement of water and small solutes is integral to the survival of freezing and desiccation in insects, yet the underlying mechanisms of these processes are not fully known. Recent evidence suggests that aquaporin (AQP) water channels play critical roles in protecting cells from osmotic damage during freezing and desiccation. Our study sequenced, functionally characterized and measured the tissue abundance of an AQP from freeze-tolerant larvae of the gall fly, Eurosta solidaginis (Diptera: Tephritidae). The newly characterized EsAQP1 contains two NPA motifs and six transmembrane regions, and is phylogenetically related to an AQP from the anhydrobiotic chironomid Polypedilum vanderplanki. Using a Xenopus laevis oocyte swelling assay, we demonstrated that EsAQP1 increases water permeability to nine times that of simple diffusion through the membrane. In contrast to its high water permeability, EsAQP1 was impermeable to both glycerol and urea. The abundance of EsAQP1 increased from October to December in all tissues tested and was most abundant in the brain of winter larvae. Because the nervous system is thought to be the primary site of freezing injury, EsAQP1 may cryoprotect the brain from damage associated with water imbalance. The sequence, phylogenetic relationship, osmotic permeability, tissue distribution and seasonal abundance of EsAQP1 further support the role of AQPs in promoting freezing tolerance.
Supercontraction forces in spider dragline silk depend on hydration rate.
Venue: Zoology

Spider dragline silk is a model biological polymer for biomimetic research due to its many desirable and unusual properties. 'Supercontraction' describes the dramatic shrinking of dragline silk fibers when wetted. In restrained silk fibers, supercontraction generates substantial stresses of 40-50 MPa above a critical humidity of approximately 70% relative humidity (RH). This stress may maintain tension in webs under the weight of rain or dew and could be used in industry for robotics, sensor technology, and other applications. Our own findings indicate that supercontraction can generate stress over a much broader range than previously reported, from 10 to 140 MPa. Here we show that this variation in supercontraction stress depends upon the rate at which the environment reaches the critical level of humidity causing supercontraction. Slow humidity increase, over several minutes, leads to relatively low supercontraction stress, while fast humidity increase, over a few seconds, typically results in higher supercontraction stress. Slowly supercontracted fibers take up less water and differ in thermostability from rapidly supercontracted fibers, as shown by thermogravimetric analysis. This suggests that spider silk achieves different molecular configurations depending upon the speed at which supercontraction occurs. Ultimately, rate-dependent supercontraction may provide a mechanism to tailor the properties of silk or biomimetic fibers for various applications.
Walrus ethology. I. The social role of tusks and applications of multidimensional scaling
Venue: Canadian Journal of Zoology

Social behavior of male Pacific walruses. Odobenus rosmarus (L.), summering (i.e. outside the breeding season) on an Alaskan hauling ground is described. Social interaction on land is mostly agonistic. Visual presentation of tusks and striking with tusks feature prominently in most agonistic interactions: vocal communication occurs in a minority of them. Agonistic interactions are analyzed in R- and Q-approaches with MIN1SSA, a fully non-metric multidimensional scaling procedure programmed in the Guttman-Lingoes series. Large body size and long tusks characterize dominant walruses. Dominants are most frequently aggressive and threatening, and least frequently exhibit submissive, defensive, protective, and avoidance behavior. Subordinate walruses show the opposite trend. Walruses are bullies; individuals strongly disadvantaged in body size or tusk length, or both, receive numerous strikes and visual threats. Walruses tend to initiate agonistic interactions with smaller individuals. Walrus tusks are importa...
Remarkable resilience of teeth
Venue: Proceedings of the National Academy of Sciences of the United States of America

Tooth enamel is inherently weak, with fracture toughness comparable with glass, yet it is remarkably resilient, surviving millions of functional contacts over a lifetime. We propose a microstructural mechanism of damage resistance, based on observations from ex situ loading of human and sea otter molars (teeth with strikingly similar structural features). Section views of the enamel implicate tufts, hypomineralized crack-like defects at the enamel–dentin junction, as primary fracture sources. We report a stabilization in the evolution of these defects, by “stress shielding” from neighbors, by inhibition of ensuing crack extension from prism interweaving (decussation), and by self-healing. These factors, coupled with the capacity of the tooth configuration to limit the generation of tensile stresses in largely compressive biting, explain how teeth may absorb considerable damage over time without catastrophic failure, an outcome with strong implications concerning the adaptation of animal species to diet.
Mosquito proboscis: an elegant biomicroelectromechanical system.
Venue: Physical Review E

The mouthparts of female mosquitoes have evolved to form a special proboscis, a natural biomicroelectromechanical system (BMEMS), which is used for painlessly penetrating human skin and sucking blood. Scanning electron microscope observations show that the mosquito proboscis consists of a small bundle of long, tapering, and feeding stylets that are collectively called the fascicle, and a large scaly outer lower lip called the labium. During blood feeding, only the fascicle penetrates into the skin while the labium buckles back to remain on the surface of the skin. Here, we measured the dynamic force of penetration of the fascicle into human skin to reveal the mechanical principle underlying the painless process of penetration. High-speed video observations of movements associated with insertion of the fascicle indicate that the "smart" mosquito does not directly pierce its victim's skin with the fascicle. Instead, it uses the two maxillas as variable frequency microsaws with nanosharp teeth to advance into the skin tissue. This elegant BMEMS enables the mosquito to insert its feeding fascicle into human skin using an exceedingly small force (average of 16.5 μN).
Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits
Venue: Cell

Gene regulatory circuits with different architectures (patterns of regulatory interactions) can generate similar dynamics. This raises the question of why a particular circuit architecture is selected to implement a given cellular process. To investigate this problem, we compared the Bacillus subtilis circuit that regulates differentiation into the competence state to an engineered circuit with an alternative architecture (SynEx) in silico and in vivo. Time-lapse microscopy measurements showed that SynEx cells generated competence dynamics similar to native cells and reconstituted the physiology of differentiation. However, architectural differences between the circuits altered the dynamic distribution of stochastic fluctuations (noise) during circuit operation. This distinction in noise causes functional differences between the circuits by selectively controlling the timing of competence episodes and response of the system to various DNA concentrations. These results reveal a tradeoff between temporal precision and physiological response range that is controlled by distinct noise characteristics of alternative circuit architectures.
Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates
Venue: Proceedings of the National Academy of Sciences of the United States of America

Shape transformations during an organism’s development often arise from mechanical instabilities driven by nonuniform growth. A remarkable example is the formation of 3D wrinkles in bacterial biofilms growing on soft substrates, which may enhance the availability of nutrients and signaling molecules. To investigate the formation of biofilm wrinkle patterns, we developed a chemomechanical model that incorporates nutrient-limited inhomogeneous growth, surface friction, and the ensuing mechanical stresses and deformations. We predict the spatiotemporal stress field in a growing biofilm and how it dictates the formation of 3D biofilm morphology. Our model provides insight into the observed stages of expansion of Vibrio cholerae biofilms and suggests that universal mechanical principles may underlie the formation of 3D morphologies in biofilms across species. During development, organisms acquire three-dimensional (3D) shapes with important physiological consequences. While basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developing Vibrio cholerae biofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat but later undergo a mechanical instability and become wrinkled. To gain mechanistic insights into this dynamic pattern-formation process, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the substrate, and the friction between them. Our model shows quantitative agreement with experimental measurements of biofilm expansion dynamics, and it accurately predicts two distinct spatiotemporal patterns observed in the experiments—the wrinkles initially appear either in the peripheral region and propagate inward (soft substrate/low friction) or in the central region and propagate outward (stiff substrate/high friction). Our results, which establish that nonuniform growth and friction are fundamental determinants of stress anisotropy and hence biofilm morphology, are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns. We discuss the implications of forming undulated biofilm morphologies, which may enhance the availability of nutrients and signaling molecules and serve as a “bet hedging” strategy.
Spider signals: are web decorations visible to birds and bees?
Venue: Biology Letters

We are becoming increasingly aware of animal communication outside the range of human sensitivity. Web decorations are silk structures used by orb-web spiders to deceive prey and predators. However, despite the level of interest in these structures, their visibility to prey and predators has never, to our knowledge, been objectively assessed. Here, we use spectrophotometric analyses to show that the decorations of all five tested spider species are visible to honey bees and birds over short and long distances. Furthermore, the discoid decorations of one species may provide some protection against arthropod predators. However, these decorations are inefficient at camouflaging the spider against birds, despite the overlap between the spider's body and web decoration.