nils-herrmann/clean_scirepeval huggingface dataset:
Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by Vegetation
Venue: Science

Volatiles Versus Vegetation Plants act as both global sources and sinks of highly reactive volatile organic compounds (VOCs). Models typically treat the uptake and degradation of these compounds as if they are mostly unreactive, like other more commonly studied biogenic gases such as ozone. A study by Karl et al. (p. 816, published online 21 October) suggests that VOCs may be more reactive than expected. By monitoring six field sites representing a range of deciduous ecosystems, several oxidized VOCs were found to have high deposition fluxes. Fumigation experiments in the laboratory confirmed that leaves are capable of oxidizing these compounds, and do so through an enzymatic detoxification or stress-response mechanism. Budgets for VOC flux in the atmosphere suggests that, on a global scale, plants may take up significant levels of VOCs in polluted regions, especially in the tropics. Deciduous trees enzymatically remove oxygenated volatile organic compounds from the atmosphere. The biosphere is the major source and sink of nonmethane volatile organic compounds (VOCs) in the atmosphere. Gas-phase chemical reactions initiate the removal of these compounds from the atmosphere, which ultimately proceeds via deposition at the surface or direct oxidation to carbon monoxide or carbon dioxide. We performed ecosystem-scale flux measurements that show that the removal of oxygenated VOC via dry deposition is substantially larger than is currently assumed for deciduous ecosystems. Laboratory experiments indicate efficient enzymatic conversion and potential up-regulation of various stress-related genes, leading to enhanced uptake rates as a response to ozone and methyl vinyl ketone exposure or mechanical wounding. A revised scheme for the uptake of oxygenated VOCs, incorporated into a global chemistry-transport model, predicts appreciable regional changes in annual dry deposition fluxes.
Active-site properties of Phrixotrix railroad worm green and red bioluminescence-eliciting luciferases.
Venue: Journal of Biochemistry

The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green- (PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferin-binding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Mutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the red-emitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.
Scorpion toxins modify phytopathogenic fungus physiology. A possible source of new fungicides.
Venue: Journal of Agricultural and Food Chemistry

Seven toxins (F1-F7) were purified from Tityus discrepans scorpion venom on a C18 HPLC column. The compounds were fungitoxic on Macrophomina phaseolina. The molecular masses of F1-F7 were (Da) 1061.1, 7328.8, 7288.3, 7268.5, 7104.6, 6924.6, and 6823.3, respectively. It is not known if F1 is a small peptide or some other kind of organic molecule. Compounds F2-F7 were peptides. The most potent was F7, with a minimal inhibition concentration of 0.4 μg/μL and a concentration for 50% inhibition of 0.13 μg/μL. Fungal esterase activity was abolished by F2, F3, and F5 and inhibited by 89, 60, 58, and 54% by F4, F6, F7, and F1, respectively. F1, F2, F5, and F7 induced an increase on hyphae chitin wall and septum thickness. Peptides F3-F6 induced efflux of the fluorescent dye Na-CoroNa Red complex from hyphae. Only F5 and F6 were inhibited by the prokaryote sodium channel blockers amiloride and mibefradil. Gas chromatography-mass spectrometry analysis suggested that F1, F5, F6, and F7 altered sterol biosynthesis either by inhibiting ergosterol biosynthesis or by producing ergosterol analogues. The peptides affect M. phaseolina viability by three mechanisms: decreasing esterase activity, altering Na(+) membrane permeability, and altering wall sterol biosynthesis. It seems that interfering with sterol synthesis is an important mechanism behind the effect of the fungicideal toxins. However, the antifungal effects at short times are indicative of a direct esterase inhibition, which, with the increased membrane leakiness to Na(+), makes the fungus inviable.
Characterization of a protein-based adhesive elastomer secreted by the Australian frog Notaden bennetti.
Venue: Biomacromolecules

When provoked, Notaden bennetti frogs secrete an exudate which rapidly forms a tacky elastic solid ("frog glue"). This protein-based material acts as a promiscuous pressure-sensitive adhesive that functions even in wet conditions. We conducted macroscopic tests in air to assess the tensile strength of moist glue (up to 78 +/- 8 kPa) and the shear strength of dry glue (1.7 +/- 0.3 MPa). We also performed nanomechanical measurements in water to determine the adhesion (1.9-7.2 nN or greater), resilience (43-56%), and elastic modulus (170-1035 kPa) of solid glue collected in different ways. Dry glue contains little carbohydrate and consists mainly of protein. The protein complement is rich in Gly (15.8 mol %), Pro (8.8 mol %), and Glu/Gln (14.1 mol %); it also contains some 4-hydroxyproline (4.6 mol %) but no 5-hydroxylysine or 3,4-dihydroxyphenylalanine (L-Dopa). Denaturing gel electrophoresis of the glue reveals a characteristic pattern of proteins spanning 13-400 kDa. The largest protein (Nb-1R, apparent molecular mass 350-500 kDa) is also the most abundant, and this protein appears to be the key structural component. The solid glue can be dissolved in dilute acids; raising the ionic strength causes the glue components to self-assemble spontaneously into a solid which resembles the starting material. We describe scattering studies on dissolved and solid glue and provide microscopy images of glue surfaces and sections, revealing a porous interior that is consistent with the high water content (85-90 wt %) of moist glue. In addition to compositional similarities with other biological adhesives and well-known elastomeric proteins, the circular dichroism spectrum of dissolved glue is almost identical to that for soluble elastin and electron and scanning probe microscopy images invite comparison with silk fibroins. Covalent cross-linking does not seem to be necessary for the glue to set.
Heat storage in running antelopes: independence of brain and body temperatures.
Venue: American Journal of Physiology

TAYLOR, C. RICHARD, AND C. P. LYMAN. Heat storage in running antelopes: independence of brain and body temperatures.  1972.-Tremendous amounts of heat are produced when antelopes run at high speed. This study tried I) to determine how much of this heat was stored, and 2) to find out if antelopes possess unusual physiological mechanisms for coping with high body temperatures. Large increases in rectal temperature of Thomson’s gazelles (Gasella thomsonii, wt 15 kg) were measured during running : + 3.9 C after 5 min at 40 km hr-1; +4.6 C after 11 min at 25 km hr-l; and +4.3 C after 20 min at 15 km hr? Heat storage accounted for 80-989;‘, of the calculated heat production during running. Brain temperature rose more slowly than rectal or carotid artery temperature. After a 5 min run at 40 km hr-r the brain was 2.7 C cooler than blood in the carotid artery. Blood supplying the brain appears to be cooled via a countercurrent heat exchange with cool blood draining the nasal mucosa (in the carotid rete). Elands (Taurotragus oryx, wt 200 kg) sweated profusely and their rectal temperature equilibrated after a few minutes of running at a slightly higher level: +0.8 C at 25 km hr-l; +0.8 C at 20 km hr-l; +0.7 C at 15 km hr-l; and 3-0.5 C at 10 km hr?
Screening Microalgal Cultures in Search of Microbial Exopolysaccharides with Potential as Adhesives
Venue: Journal of Adhesion

Nearly 800 cultures from the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Collection of Living Microalgae (CCLM) were screened for exopolysaccharide (EPS) production by examining the viscosity of conditioned media supernatants. We first established dose-response relationships for the viscosity of reference polysaccharides dissolved in microalgal growth media. Then, using the 40 most viscous CCLM cultures, we confirmed that the viscosity of culture supernatants correlated well with their total sugar (and thus EPS) content. The conditioned medium with the highest viscosity (6.55 cP, equivalent to 1.16 g/L xanthan gum) was produced by a non-axenic isolate of the cyanobacterium Microcystis aeruginosa f. flos-aquae. Two types of bacteria, designated CSIRO501 (Gram-positive) and CSIRO505 (Gram-negative), were subcultured from it. At 20 dry wt% sugar, an exopolymer preparation from CSIRO505 contained substantially more EPS than its counterparts from CSIRO501 or from axenic Microcystis cultures, and it resembled a well-known bacterial EPS (xanthan gum) in being much more effective at bonding wood than PVC. It bonded wooden lap joints with a dry shear strength of 1.5 MPa, four times the value obtained in equivalent tests of a commercial polyvinyl acetate (PVA) glue.
A buckling region in locust hindlegs contains resilin and absorbs energy when jumping or kicking goes wrong
Venue: The Journal of Experimental Biology

If a hindleg of a locust slips during jumping, or misses its target during kicking, energy generated by the two extensor tibiae muscles is no longer expended in raising the body or striking a target. How, then, is the energy in a jump (4100–4800 μJ) or kick (1700 μJ) dissipated? A specialised buckling region found in the proximal hind-tibia where the bending moment is high, but not present in the other legs, buckled and allowed the distal part of the tibia to extend. In jumps when a hindleg slipped, it bent by a mean of 23±14 deg at a velocity of 13.4±9.5 deg ms–1; in kicks that failed to contact a target it bent by 32±16 deg at a velocity of 32.9±9.5 deg ms–1. It also buckled 8.5±4.0 deg at a rate of 0.063±0.005 deg ms–1 when the tibia was prevented from flexing fully about the femur in preparation for both these movements. By experimentally buckling this region through 40 deg at velocities of 0.001–0.65 deg ms–1, we showed that one hindleg could store about 870 μJ on bending, of which 210 μJ was dissipated back to the leg on release. A band of blue fluorescence was revealed at the buckling region under UV illumination that had the two key signatures of the elastic protein resilin. A group of campaniform sensilla 300 μm proximal to the buckling region responded to imposed buckling movements. The features of the buckling region show that it can act as a shock absorber as proposed previously when jumping and kicking movements go wrong.
Natural strategies for the molecular engineer
Venue: Nanotechnology

The idea of nature as engineer is an old one, but the realization that this metaphor can be extended (should we say retracted?) to the molecular scale has become common currency only over the past two decades or so. Two reasons for this are perhaps paramount. First, the picture of the cell has been transformed from that of a 'wet chemical' melange—'a vessel, filled with a homogeneous solution, in which all chemical processes take place', as Franz Hofmeister put it in 1901—into an image of a sort of fluid factory, a production plant in which molecular machinery works in near-fantastic orchestration to generate complex products from raw materials. This mechanism is self-assembling, self-repairing and self-replicating. The concept of proteins and nucleic acids as 'molecular machines' is now a mainstream one in cell biology. Second, technological advances have made us accustomed to the idea that engineering can be conducted at scales too small to see with the naked eye, yet employing principles—mechanical, electrical, hydraulic, optical, tribological—familiar from the macroscopic world. Molecular electronics and computing, microelectromechanical devices and nanotechnology, are now mainstream concepts, and are validated by at least some degree of physical realization. In this article I shall briefly review some of nature's principles and practices at the molecular, supramolecular and submicrometre scales, and attempt to illustrate how these can be adapted for developing synthetic chemical and materials systems sharing the kind of superior properties and special functions that natural systems exhibit.
Spider web glue: two proteins expressed from opposite strands of the same DNA sequence.
Venue: Biomacromolecules

The various silks that make up the web of the orb web spiders have been studied extensively. However, success in prey capture depends as much on the web glue as on the fibers. Spider silk glue, which is considered one of the strongest and most effective biological glues, is an aqueous solution secreted from the orb weaving spider's aggregate glands and coats the spiral prey capturing threads of their webs. Studies identified the major component of the glue as microscopic nodules made of a glycoprotein. This study describes two newly discovered proteins that form the glue-glycoprotein of the golden orb weaving spider Nephila clavipes . Our results demonstrate that both proteins contain unique 110 amino acid repetitive domains that are encoded by opposite strands of the same DNA sequence. Thus, the genome of the spider encodes two distinct yet functionally related genes by using both strands of an identical DNA sequence. Moreover, the closest match for the nonrepetitive region of one of the proteins is chitin binding proteins. The web glue appears to have evolved a substantial level of sophistication matching that of the spider silk fibers.
Elastic response of the resurrection fern Polypodium polypodioides during rehydration
Venue: Applied Physics Letters

The resurrection fern (Polypodium polypodioides) has a remarkable elastic reponse, where the fast water uptake of the fern upon rehydration is accompanied by a significant reduction in its Young’s modulus. In this letter, we discuss the fern’s elastic response and suggest that by mimicking its structure, one should be able to design materials exhibiting interesting elastic behavior.
Spider silk as a novel high performance biomimetic muscle driven by humidity
Venue: The Journal of Experimental Biology

The abrupt halt of a bumble bee's flight when it impacts the almost invisible threads of an orb web provides an elegant example of the amazing strength and toughness of spider silk. Spiders depend upon these properties for survival, yet the impressive performance of silk is not limited solely to tensile mechanics. Here, we show that silk also exhibits powerful cyclic contractions, allowing it to act as a high performance mimic of biological muscles. These contractions are actuated by changes in humidity alone and repeatedly generate work 50 times greater than the equivalent mass of human muscle. Although we demonstrate that this response is general and occurs weakly in diverse hydrophilic materials, the high modulus of spider silk is such that it generates exceptional force. Furthermore, because this effect already operates at the level of single silk fibers, only 5 μm in diameter, it can easily be scaled across the entire size range at which biological muscles operate. By contrast, the most successful synthetic muscles developed so far are driven by electric voltage, such that they cannot scale easily across large ranges in cross-sectional areas. The potential applicability of silk muscles is further enhanced by our finding that silkworm fibers also exhibit cyclic contraction because they are already available in commercial quantities. The simplicity of using wet or dry air to drive the biomimetic silk muscle fibers and the incredible power generated by silk offer unique possibilities in designing lightweight and compact actuators for robots and micro-machines, new sensors, and green energy production.
Function of the Dufour’s gland in solitary and social Hymenoptera
Venue: Journal of Hymenoptera Research

The poison gland and Dufour's gland are the two glands associated with the sting apparatus in female Apocrita (Hymenoptera). While the poison gland usually functions as an integral part of the venom delivery system, the Dufour's gland has been found to differ in its function in various hymenopteran groups. Like all exocrine glands, the function of the Dufour's gland is to secrete chemicals, but the nature and function of the secretions varies in different taxa. Functions of the Dufour's gland secretions range from serving as a component of material used in nest building, larval food, and pheromones involved in communicative functions that are important for both solitary and social species. This review summarizes the different functions reported for the Dufour's gland in hymenopterans, illustrating how the Dufour's gland secretions can be adapted to give rise to various functions in response to different challenges posed by the ways of life followed by different taxa. Aspects of development, structure, chemistry and the evolution of different functions are also touched upon briefly.
Bioluminescent signals spatially amplified by wavelength-specific diffusion through the shell of a marine snail
Venue: Proceedings of The Royal Society B: Biological Sciences

Some living organisms produce visible light (bioluminescence) for intra- or interspecific visual communication. Here, we describe a remarkable bioluminescent adaptation in the marine snail Hinea brasiliana. This species produces a luminous display in response to mechanical stimulation caused by encounters with other motile organisms. The light is produced from discrete areas on the snail's body beneath the snail's shell, and must thus overcome this structural barrier to be viewed by an external receiver. The diffusion and transmission efficiency of the shell is greater than a commercial diffuser reference material. Most strikingly, the shell, although opaque and pigmented, selectively diffuses the blue-green wavelength of the species bioluminescence. This diffusion generates a luminous display that is enlarged relative to the original light source. This unusual shell thus allows spatially amplified outward transmission of light communication signals from the snail, while allowing the animal to remain safely inside its hard protective shell.
Archerfish Actively Control the Hydrodynamics of Their Jets
Venue: Current Biology

Among tool-using animals [1-4], none are known to adaptively change the hydrodynamic properties of a free jet of water--a task considered difficult in human technology [5-7]. Hunting archerfish can strike their targets with precisely aimed water jets (e.g., [8, 9]), but they are also presently thought to be unable to actively control the hydrodynamics of their jets [8-13]. By using specifically trained fish, we were able to monitor several aspects of jet production and propagation as the fish fired at targets over a much wider range of distances than previously explored [10, 13]. We show that jets that have to travel farther also live longer. Furthermore, the time needed until water assembles at the jet tip is not fixed. Rather, it is adjusted so that maximum focusing occurs just before impact. Surprisingly, the fish achieve this by modulating the dynamics of changes in the cross-section of their mouth opening, a mechanism that seems to not have been applied yet in human-built nozzles. The timing adjustments archerfish make in order to powerfully hit targets over an extended range strikingly parallel the situation in the "uniquely human" ability of powerful throwing [14-18]. Based on the key role throwing played in human encephalization and cognitive evolution [14-20], skillfully "throwing" water should similarly have led to the correlated rapid evolution of cognitive skills in this animal.
Ecology and Biology of the Pacific Walrus, Odobenus Rosmarus Divergens Illiger
Venue: North American Fauna

AbstractThe distribution, physical development, pelage, dentition, feeding behavior, reproduction, causes of mortality, and population structure of the Pacific walrus (Odobenus rosmarus divergens) were studied intermittently from 1952 to 1979. In winter, these animals tend to concentrate in north-central and southeastern Bering Sea, where sea ice conditions are most favorable for them. In summer, they concentrate mainly in northwestern and northeastern Chukchi Sea, along the edge of the ice. Most of the northward migrants are females and young; a large proportion of the adult males remains in the Bering Sea throughout the summer. Pacific walruses show strong sexual dimorphism; adult males are about 18% longer and 45% heavier and tend to have larger, more divergent tusks, as well as thicker, lighter-colored, and less hairy skin than adult females. As in other sexually dimorphic otarioid pinnipeds, males undergo secondary growth, beginning about the time of puberty and ending in full physical maturity about...
Quadrupedal locomotor performance in two species of arboreal squirrels: predicting energy savings of gliding
Venue: Journal of Comparative Physiology B-biochemical Systemic and Environmental Physiology

Gliding allows mammals to exploit canopy habitats of old-growth forests possibly as a means to save energy. To assess costs of quadrupedal locomotion for a gliding arboreal mammal, we used open-flow respirometry and a variable-speed treadmill to measure oxygen consumption and to calculate cost of transport, excess exercise oxygen consumption, and excess post-exercise oxygen consumption for nine northern flying squirrels (Glaucomys sabrinus) and four fox squirrels (Sciurus niger). Our results indicate that oxygen consumption during exercise by flying squirrels was 1.26–1.65 times higher than predicted based on body mass, and exponentially increased with velocity (from 0.84 ± 0.03 ml O2 kg−1 s−1 at 0.40 m s−1 to 1.55 ± 0.03 ml O2 kg−1 s−1 at 0.67 m s−1). Also, cost of transport in flying squirrels increased with velocity, although excess exercise oxygen consumption and excess post-exercise oxygen consumption did not. In contrast, oxygen consumption during exercise for fox squirrels was similar to predicted, varying from 0.51 (±0.02) ml O2 kg−1 s−1 at 0.63 m s−1 to 0.54 (±0.03) ml O2 kg−1 s−1 at 1.25 m s−1. In addition, the cost of transport for fox squirrels decreased with velocity, while excess exercise oxygen consumption and excess post-exercise oxygen consumption did not. Collectively, these observations suggest that unlike fox squirrels, flying squirrels are poorly adapted to prolonged bouts of quadrupedal locomotion. The evolution of skeletal adaptations to climbing, leaping, and landing and the development of a gliding membrane likely has increased the cost of quadrupedal locomotion by >50% while resulting in energy savings during gliding and reduction in travel time between foraging patches.