nils-herrmann/clean_scirepeval huggingface dataset:
COMPOSITION OF EXTRACELLULAR POLYMERIC SUBSTANCES FROM PERIPHYTON ASSEMBLAGES IN THE FLORIDA EVERGLADES 1
Venue: Journal of Phycology

In wetland habitats, periphyton is a common component of open‐water areas with species assemblage determined by local water quality. Extracellular polymeric substances (EPS) secreted by algae and bacteria give structure to periphyton, and differences in EPS chemistry affect the functional roles of these polymers. The Florida Everglades provide a unique opportunity to study compositional differences of EPS from distinctive algal assemblages that characterize areas of differing water chemistry. Water conservation area (WCA)‐1 is a soft‐water impoundment; periphyton was loosely associated with Utricularia stems and amorphous in structure, with a diverse desmid and diatom assemblage, and varying cyanobacterial abundance. Extracellular polymers were abundant and were loosely cell‐associated sheaths and slime layers in addition to tightly cell‐associated capsules. The EPS were complex heteropolysaccharides with significant saccharide residues of glucose, xylose, arabinose, and fucose. Carboxylic acids were also prominent, while ester sulfates and proteins were small components. Structured, cohesive cyanobacteria‐dominated periphyton was observed in WCA‐2A, a minerotrophic impoundment, and filaments were heavily encrusted with calcium carbonate and detrital matter. EPS were primarily cell‐associated sheaths, and polymer residues were dominated by glucose, xylose, fucose, and galactose, with uronic acids also a significant component of the polymers. Principal components analysis revealed that periphyton community assemblage determined the monosaccharide composition of EPS, which ultimately determines a range of biogeochemical processes within the periphyton.
Suberin--a biopolyester forming apoplastic plant interfaces.
Venue: Current Opinion in Plant Biology

Suberized cell walls form physiologically important plant-environment interfaces because they act as barriers that limit water and nutrient transport and protect plants from invasion by pathogens. Plants respond to environmental stimuli by modifying the degree of suberization in root cell walls. Salt stress or drought-induced suberization leads to a decrease in radial water transport in roots. Although reinforced, suberized cell walls never act as absolutely impermeable barriers. Deeper insights into the structure and biosynthesis of suberin are required to elucidate what determines the barrier properties. Progress has been obtained from analytical methods that enabled the structural characterization of oligomeric building blocks in suberin, and from the opening of suberin research to molecular genetic approaches by the elucidation of the chemical composition and tissue distribution of suberin in the model species Arabidopsis.
Mimosa pudica: Electrical and mechanical stimulation of plant movements.
Venue: Plant Cell and Environment

Thigmonastic movements in the sensitive plant Mimosa pudica L., associated with fast responses to environmental stimuli, appear to be regulated through electrical and chemical signal transductions. The thigmonastic responses of M. pudica can be considered in three stages: stimulus perception, electrical signal transmission and induction of mechanical, hydrodynamical and biochemical responses. We investigated the mechanical movements of the pinnae and petioles in M. pudica induced by the electrical stimulation of a pulvinus, petiole, secondary pulvinus or pinna by a low electrical voltage and charge. The threshold value was 1.3-1.5 V of applied voltage and 2 to 10 microC of charge for the closing of the pinnules. Both voltage and electrical charge are responsible for the electro-stimulated closing of a leaf. The mechanism behind closing the leaf in M. pudica is discussed. The hydroelastic curvature mechanism closely describes the kinetics of M. pudica leaf movements.
Studies on the morphology and function of the skull in the boidae (Serpentes). Part II. Morphology and function of the jaw apparatus in Python sebae and Python molurus
Venue: Journal of Morphology

Heads of the boid snakes Python sebae and Python molurus were dissected and the arthrology, myology and dentition studied. Living specimens of these species were observed and their feeding behavior analyzed by means of high‐ and regular‐speed motion pictures. Camera speeds of up to 400 frames per second permitted examination of the jaw movements during the striking and seizing of prey. Motion picture studies conducted at regular speeds provided information on cranial movements during the swallowing of prey. The morphology of the head was correlated with observed movements in an attempt to analyze the functional and adaptive implications of the jaw apparatus.
Microbial ecology meets electrochemistry: electricity-driven and driving communities
Venue: The ISME Journal

Bio-electrochemical systems (BESs) have recently emerged as an exciting technology. In a BES, bacteria interact with electrodes using electrons, which are either removed or supplied through an electrical circuit. The most-described type of BES is microbial fuel cells (MFCs), in which useful power is generated from electron donors as, for example, present in wastewater. This form of charge transport, known as extracellular electron transfer, was previously extensively described with respect to metals such as iron and manganese. The importance of these interactions in global biogeochemical cycles is essentially undisputed. A wide variety of bacteria can participate in extracellular electron transfer, and this phenomenon is far more widespread than previously thought. The use of BESs in diverse research projects is helping elucidate the mechanism by which bacteria shuttle electrons externally. New forms of interactions between bacteria have been discovered demonstrating how multiple populations within microbial communities can co-operate to achieve energy generation. New environmental processes that were difficult to observe or study previously can now be simulated and improved via BESs. Whereas pure culture studies make up the majority of the studies performed thus far, even greater contributions of BESs are expected to occur in natural environments and with mixed microbial communities. Owing to their versatility, unmatched level of control and capacity to sustain novel processes, BESs might well serve as the foundation of a new environmental biotechnology. While highlighting some of the major breakthroughs and addressing only recently obtained data, this review points out that despite rapid progress, many questions remain unanswered.
The magnetic compass of domestic chickens, Gallus gallus
Venue: The Journal of Experimental Biology

By directional training, young domestic chickens have been shown to use a magnetic compass; the same method has now been used to analyse the functional characteristics and the physical principles underlying the chickens' magnetic compass. Tests in magnetic fields with different intensities revealed a functional window around the intensity of the local geomagnetic field, with this window extending further towards lower than higher intensities. Testing chickens under monochromatic 465 nm blue and 645 nm red light suggested a wavelength dependence, with orientation possible under blue but not under red light. Exposing chickens to an oscillating field of 1.566 MHz led to disorientation, identifying an underlying radical pair mechanism. Local anesthesia of the upper beak, where iron-rich structures have been described as potential magnetoreceptors, did not affect the performance, suggesting that these receptors are not involved in compass orientation. These findings show obvious parallels to the magnetic compass described for European robins, indicating that chickens and small passerines use the same type of magnetic compass mechanism. This suggests that the avian magnetic compass may have evolved in the common ancestor of all present-day birds to facilitate orientation within the home range.
Adaptations of frogs to survive freezing
Venue: Climate Research

Five species of frogs from North A n ~ e n c a survive extensive freezing of their body fluids to temperatures as low as 8 ° C for periods lasting at least 2 wk. These frogs hibernate in leaf litter where subzero temperatures commonly occur during the winter. The onset of freezing triggers Liver glycogenolysis and the production of high concentrations of glucose or glycerol (to 100 X normal) that functions as a cryoprotectant against freezing Injury. Concomitantly the release of the latent heat of crystallization as body water freezes promotes the continued function of the cardiovascular system for many hours and serves to distribute glucose throughout the body. The water content of major organs is reduced by 50 U/:> or more during the first 24 h of freezing, wlth the water being relocated and frozen in other body spaces. Organ dehydration functions to concentrate cryoprotectant and to reduce mechanical damage by ice during freezing. As freezing progresses, breathing, heart beat , and most other v ~ t a l functions cease, but reanimation occurs ~ v ~ t h l n a few hours after thawing. The evolution of freeze tolerance in these animals illustrates the h~gh ly flexible capacities of frogs to adapt to stressful environments
Superhydrophobic Metallic Surfaces and Their Wetting Properties
Venue: Journal of Adhesion Science and Technology

Two-scaled polymer patterns possessing high roughness are produced using the hot-embossing technique and coating with chromium. After covering the rough polymer surface with this metal, the resulting surface demonstrates pronounced hydrophobic properties, with water drops having apparent contact angles as high as 150°. As revealed by SEM, the surface is patterned on two scales which is known to be an important condition for superhydrophobicity of inherently wettable surfaces. The modified Cassie–Baxter approach has been used for the present relief. The calculated values of the apparent contact angles agree with the observed ones. It is important to note that the apparent contact angles almost do not depend on the local contact angles.
Influence of physiological effort of growth and chemical composition on antler bone mechanical properties.
Venue: Bone

Antler is a good model to study bone biology both because it is accessible and because it grows and is shed every year. Previous studies have shown that chemical composition changes as the antler is grown, implying constraints in mineral availability and the physiological effort made to grow it. This study aimed at examining antler mechanical properties to assess whether they reflect physiological effort and whether they are associated with precise mineral bone composition rather than just ash content, which is usually the main factor affecting mechanical properties. We examined Young's modulus of elasticity (E), strength, and work to maximum load, as well as bone mineral composition, along the antler shaft. Then we compared trends between antlers from two populations: captive, well-fed, health-managed deer (n=15), and free-ranging deer with lower food quality and no health treatment (n=10). Greater E, strength and work were found for better fed and health managed deer. In addition, antler chemical composition of both populations differed in Na, Mg, K, Fe and Si, and marginally in Zn, but not in ash or Ca content. Significant and clear divergent trends in mechanical properties supporting greater physiological exhaustion in free-ranging deer were found for all mechanical variables. Detailed models showed that, in addition to ash content, independent factors extracted from principal component analyses on composition affected E and strength, but not work to maximum load. The results suggest that there is an association between bone chemical composition and mechanical properties independently of ash content.
Biomechanics: Turning the key on Drosophila audition
Venue: Nature

The genetic dissection of Drosophila audition is advancing considerably, but complementary studies are needed to unravel the chain of mechanosensory events that bring about hearing in the fly. Here we investigate the delicate biomechanics of the fly's minute antennal hearing organs and show that they look and work like a lock and key. Rotating in response to sound, the antenna's distal segment mechanically activates the auditory receptors — thereby 'unlocking' the mechanism of Drosophila audition.
The pupils and optical systems of gecko eyes.
Venue: Journal of Vision

The nocturnal helmet gecko, Tarentola chazaliae, discriminates colors in dim moonlight when humans are color blind. The sensitivity of the helmet gecko eye has been calculated to be 350 times higher than human cone vision at the color vision threshold. The optics and the large cones of the gecko are important reasons why they can use color vision at low light intensities. Using photorefractometry and an adapted laboratory Hartmann-Shack wavefront sensor of high resolution, we also show that the optical system of the helmet gecko has distinct concentric zones of different refractive powers, a so-called multifocal optical system. The intraspecific variation is large but in most of the individuals studied the zones differed by 15 diopters. This is of the same magnitude as needed to focus light of the wavelength range to which gecko photoreceptors are most sensitive. We compare the optical system of the helmet gecko to that of the diurnal day gecko, Phelsuma madagascariensis grandis. The optical system of the day gecko shows no signs of distinct concentric zones and is thereby monofocal.
Obligate oil-degrading marine bacteria.
Venue: Current Opinion in Biotechnology

Over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (OHCB) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)--which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temperature, salinity, redox and other prevailing physical-chemical factors. These blooms result in the rapid degradation of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic analysis of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecological success. These and other studies have revealed the potential of OHCB for multiple biotechnological applications that include not only oil pollution mitigation, but also biopolymer production and biocatalysis.
Subnanometer atomic force microscopy of peptide-mineral interactions links clustering and competition to acceleration and catastrophe.
Venue: Proceedings of the National Academy of Sciences of the United States of America

In vitro observations have revealed major effects on the structure, growth, and composition of biomineral phases, including stabilization of amorphous precursors, acceleration and inhibition of kinetics, and alteration of impurity signatures. However, deciphering the mechanistic sources of these effects has been problematic due to a lack of tools to resolve molecular structures on mineral surfaces during growth. Here we report atomic force microscopy investigations using a system designed to maximize resolution while minimizing contact force. By imaging the growth of calcium-oxalate monohydrate under the influence of aspartic-rich peptides at single-molecule resolution, we reveal how the unique interactions of polypeptides with mineral surfaces lead to acceleration, inhibition, and switching of growth between two distinct states. Interaction with the positively charged face of calcium-oxalate monohydrate leads to formation of a peptide film, but the slow adsorption kinetics and gradual relaxation to a well-bound state result in time-dependent effects. These include a positive feedback between peptide adsorption and step inhibition described by a mathematical catastrophe that results in growth hysteresis, characterized by rapid switching from fast to near-zero growth rates for very small reductions in supersaturation. Interactions with the negatively charged face result in formation of peptide clusters that impede step advancement. The result is a competition between accelerated solute attachment and inhibition due to blocking of the steps by the clusters. The findings have implications for control of pathological mineralization and suggest artificial strategies for directing crystallization.
Butterfly wing colors: glass scales of Graphium sarpedon cause polarized iridescence and enhance blue/green pigment coloration of the wing membrane
Venue: The Journal of Experimental Biology

The wings of the swordtail butterfly Graphium sarpedon nipponum contain the bile pigment sarpedobilin, which causes blue/green colored wing patches. Locally the bile pigment is combined with the strongly blue-absorbing carotenoid lutein, resulting in green wing patches and thus improving camouflage. In the dorsal forewings, the colored patches lack the usual wing scales, but instead have bristles. We have found that on the ventral side most of these patches have very transparent scales that enhance, by reflection, the wing coloration when illuminated from the dorsal side. These glass scales furthermore create a strongly polarized iridescence when illuminated by obliquely incident light from the ventral side, presumably for intraspecific signaling. A few ventral forewing patches have diffusely scattering, white scales that also enhance the blue/green wing coloration when observed from the dorsal side.
Optimal Localization by Pointing Off Axis
Venue: Science

Detection Versus Localization Active-sensing systems allow an animal some control over the information acquired from the environment. For example, echolocating bats are known to control many aspects of their sonar signal design. However, their sensory data-acquisition strategies are still not fully understood. Yovel et al. (p. 701) found that Egyptian fruit bats (Rousettus aegyptiacus) did not aim their sonar beams directly on target in a standard localization task. Instead, the bats pointed the main lobe of their sonar beam off-axis. Bats approaching the target emitted sounds to the left and right of its localization, in an alternating manner, so that the maximum slope of the change in intensity of the sonar beam was often positioned close to the target. This echolocation strategy is ideal for target localization but occurs at the cost of target detection. Echolocating Egyptian fruit bats do not center their sonar clicks on a target, thereby maximizing localization of the target. Is centering a stimulus in the field of view an optimal strategy to localize and track it? We demonstrated, through experimental and computational studies, that the answer is no. We trained echolocating Egyptian fruit bats to localize a target in complete darkness, and we measured the directional aim of their sonar clicks. The bats did not center the sonar beam on the target, but instead pointed it off axis, accurately directing the maximum slope (“edge”) of the beam onto the target. Information-theoretic calculations showed that using the maximum slope is optimal for localizing the target, at the cost of detection. We propose that the tradeoff between detection (optimized at stimulus peak) and localization (optimized at maximum slope) is fundamental to spatial localization and tracking accomplished through hearing, olfaction, and vision.
Influence of neighboring plants on the dynamics of an ant-acacia protection mutualism.
Venue: Ecology

Ant-plant protection symbioses, in which plants provide food and/or shelter for ants in exchange for protection from herbivory, are model systems for understanding the ecology of mutualism. While interactions between ants, host plants, and herbivores have been intensively studied, we know little about how plant-plant interactions influence the dynamics of these mutualisms, despite strong evidence that plants compete for resources, that hosting ants can be costly, and that host-plant provisioning to ants can therefore be constrained by resource availability. We used field experiments in a semiarid Kenyan savanna to examine interactions between the ant-plant Acacia drepanolobium, neighboring grasses, and two species of symbiotic acacia-ants with divergent behaviors: Crematogaster mimosae, an aggressive symbiont that imposes high costs to host trees via consumption of extrafloral nectar, and Tetraponera penzigi, a less-protective symbiont that imposes lower costs because it does not consume nectar. We hypothesized that by competing with acacias for resources, neighboring grasses (1) reduce hosts' ability to support costly C. mimosae, while having little or no effect on the ability of hosts to support low-cost T. penzigi, and (2) reduce sapling growth rates irrespective of ant occupant. We factorially manipulated the presence/absence of grasses and the identity of ant occupants on saplings and evaluated effects on colony survivorship and sapling growth rates over 40 weeks. Contrary to prediction, the high-cost/high-reward nectar-dependent mutualist C. mimosae had higher colony-survival rates on saplings with grass neighbors present. Grasses appear to have indirectly facilitated the survival of C. mimosae by reducing water stress on host plants; soils under saplings shaded by grasses had higher moisture content, and these saplings produced more active nectaries than grass-removal saplings. Consistent with prediction, survival of low-cost/low-reward T. penzigi did not differ significantly between grass-removal treatments. Saplings occupied by low-cost/low-reward T. penzigi grew 100% more on average than saplings occupied by high-cost/high-reward C. mimosae, demonstrating that mutualist-partner identity strongly and differentially influences demographic rates of young plants. In contrast, contrary to prediction, grass neighbors had no significant net impact on sapling growth rates. Our results suggest that neighboring plants can exert strong and counterintuitive effects on ant-plant protection symbioses, highlighting the need to integrate plant-plant interactions into our understanding of these mutualisms.