nils-herrmann/clean_scirepeval huggingface dataset:
THE MECHANICS OF SEED EXPULSION IN ACANTHACEAE
Venue: Journal of Theoretical Biology

The bilocular seed capsules of species on the Acanthaceae subfamily Acanthoideae are either hygrochastic or xerochastic, but in both cases the mechanism for seed expulsion is similar; only the “trigger” differs in the two instances. The drying of the capsule results in the storage of elastic energy in the capsule valves. The failure of the seam joining the two values precipitates the conversion of the elastic potential energy stored in the valves and seeds. In the hygrochastic case the failure is due to moisture absorption on wetting of the capsule beak which weakens the pectic “glue”; in the xerochastic case the seam failure is due simply to the high stress in the bonding layer at some degree of desiccation. This paper explains quantitatively how the anatomy of the capsule efficiently imports high initial expulsion velocity to the seeds in order to maximize their range. The specific example considered inRuellia brittonianaLeonard, a cultivated shrub native to Mexico, but the situation is similar for the entire Acanthoideae subfamily.
Thermal windows on Brazilian free-tailed bats facilitate thermoregulation during prolonged flight.
Venue: Integrative and Comparative Biology

The Brazilian free-tailed bat (Tadarida brasiliensis) experiences challenging thermal conditions while roosting in hot caves, flying during warm daylight conditions, and foraging at cool high altitudes. Using thermal infrared cameras, we identified hot spots along the flanks of free-ranging Brazilian free-tailed bats, ventral to the extended wings. These hot spots are absent in syntopic cave myotis (Myotis velifer), a species that forages over relatively short distances, and does not engage in long-distance migration. We hypothesized that the hot spots, or "radiators," on Brazilian free-tailed bats may be adaptations for migration, particularly in this long-distance, high-flying species. We examined the vasculature of radiators on Brazilian free-tailed bats with transillumination to characterize the unique arrangements of arteries and veins that are positioned perpendicular to the body in the proximal region of the wing. We hypothesized that these radiators aid in maintaining heat balance by flushing the uninsulated thermal window with warm blood, thereby dissipating heat while bats are flying under warm conditions, but shunting blood away and conserving heat when they are flying in cooler air at high altitudes. We also examined fluid-preserved specimens representing 122 species from 15 of 18 chiropteran families and radiators appeared present only in species in the family Molossidae, including both sedentary and migratory species and subspecies. Thus, the radiator appears to be a unique trait that may facilitate energy balance and water balance during sustained dispersal, foraging, and long-distance migration.
Nitrogen Mineralization, Ammonia Accumulation, and Emission of Gaseous NH3 by Soil-feeding Termites
Venue: Biogeochemistry

There are numerous reports on the accumulation of ammonia in the mounds of soil-feeding termites. Here, we provided direct evidence for an effective mineralization of nitrogenous soil organic matter in the gut of Cubitermes spp., which gives rise to enormous ammonia concentrations in the intestinal tract. In Cubitermes ugandensis, the ammonia content of the nest material [24.5 μmol (g dry wt.)−1] was about 300-fold higher than that of the parent soil. Large amounts of ammonia were present throughout the intestinal tract, with lowest values in the extremely alkaline gut sections (pH >12) and highest values posterior hindgut [185 μmol (g dry wt.)−1]. Results obtained with other Cubitermes species were similar. Ammonia concentrations in the posterior hindgut of these humivorous species (up to 130 mM) are among the highest values ever reported for soil macroinvertebrates and are matched only by insects feeding on an extremely protein-rich diet (e.g., the sarcophageous larvae of blowflies). Volatilization of ammonia [about 10 nmol (g fresh wt.)−1 h−1], either directly by emission from the termite body or indirectly from their feces, led to NH3 concentrations in the nest atmosphere of C. ugandensis that were three orders of magnitude above the ambient background – a relative accumulation that is considerably higher than that observed with CH4 and CO2. Together with previous results, these observations document that through their feeding activity and due to the physicochemical and biochemical properties of their digestive system, soil-feeding termites effectively catalyze the transformation of refractory soil organic nitrogen to a plant-available form that is protected from leaching by adsorption to the nest soil. Nitrogen mineralization rates of soil-feeding termites may surpass those effected by tropical earthworms and should contribute significantly to nitrogen fluxes in tropical ecosystems.
Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity
Venue: Science

In Living Color Light produced using the chemical process of bioluminescence spans the entire range of the visible spectrum. Bioluminescence has evolved independently several times in the tree of life. However, the majority of bioluminescent organisms reside in the open ocean, where their bioluminescence helps species in over 700 genera evade predators, attract mates, and find food. Widder (p. 704) reviews recent advances in understanding the evolution and distribution of bioluminescence in marine systems. From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships.
Extracellular electron transfer via microbial nanowires
Venue: Nature

Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(iii) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments. Previous investigations on electron transfer to Fe(iii) have focused on the role of outer-membrane c-type cytochromes. However, some Fe(iii) reducers lack c-cytochromes. Geobacter species, which are the predominant Fe(iii) reducers in many environments, must directly contact Fe(iii) oxides to reduce them, and produce monolateral pili that were proposed, on the basis of the role of pili in other organisms, to aid in establishing contact with the Fe(iii) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(iii) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(iii) oxides. Electron transfer through pili indicates possibilities for other unique cell-surface and cell–cell interactions, and for bioengineering of novel conductive materials.
Phenotypic flexibility in cutaneous water loss and lipids of the stratum corneum
Venue: The Journal of Experimental Biology

When vertebrates invaded land during the Carboniferous period, they were exposed not only to new ecological opportunities but also to a desiccating environment. To maintain cellular water homeostasis, natural selection modified the integument of pioneering terrestrial animals, enabling them to reduce water loss through the skin. In desert environments, where ambient temperatures (Ta) can reach 50°C, relative humidities are low and drinking water is scarce, integumentary modifications that reduce cutaneous water loss (CWL) could be fundamental to survival. Previous research has shown that hoopoe larks (Alaemon alaudipes) from the Arabian desert reduced CWL when acclimated to 35°C compared with individuals at 15°C, but skylarks (Alauda arvensis) and woodlarks (Lullula arborea), from The Netherlands, and Dunn's larks (Eremalauda dunni), also from the Arabian desert, did not. Here, we test the idea that hoopoe larks acclimated to 35°C would alter the lipid composition of their stratum corneum (SC), resulting in a decrease in CWL, but that skylarks, woodlarks and Dunn's larks would not. Specifically, we hypothesized that hoopoe larks, acclimated to 35°C, would increase the proportions of polar ceramide content and decrease the proportions of free fatty acids in their SC compared with individuals acclimated to 15°C. Results showed that hoopoe larks at 35°C had lower CWL and higher proportions of total ceramides but lower proportions of free fatty acids and sterols in their SC. We demonstrate that adjustments in ratios of lipid classes in the SC are associated with changes in CWL in hoopoe larks.
Microbial conversion of selected azo dyes and their breakdown products.
Venue: Water Science and Technology

Four selected azo dyes (acid orange 6, acid orange 7, methyl orange and methyl red) were completely decolourised in the presence of anaerobic granular sludge, while only methyl red was degraded in aerobic conditions using a conventional activated sludge. Additional experiments with culture broth devoid of cells showed that anaerobic decolourisation of azo dyes was performed by extracellular reducing agents produced by anaerobic bacteria. This was further confirmed by abiotic experiments with sulphide and NADH. The presence of redox mediators such as riboflavin led to dramatic acceleration of the anaerobic biodecolourisation process. The azo dye reduction products were found to be sulphanilic acid and 4-aminoresorcinol for acid orange 6; sulphanilic acid and 1-amino-2-naphthol for acid orange 7; N,N-dimethyl-1,4-phenylenediamine and sulphanilic acid for methyl orange; and N,N-dimethyl-1,4-phenylenediamine and anthranilic acid for methyl red. Anaerobic toxicity assays showed that the azo dyes were more toxic than their breakdown products (aromatic amines), except 1-amino-2-naphthol. In the presence of activated sludge, only anthranilic acid was completely mineralised while sulphanilic acid was persistent. 4-aminoresorcinol, 1-amino-2-naphthol and N,N-dimethyl-1,4-phenylenediamine underwent autooxidation in aerobic conditions yielding coloured polymeric products. On the contrary, in the presence of granular methanogenic sludge, 4-aminoresorcinol, 1-amino-2-naphthol and anthranilic acid were quantitatively methanised, sulphanilic acid was partially (70%) mineralised while N,N-dimethyl-1,4-phenylenediamine was only demethylated producing 1,4-phenylenediamine as an end product.
Sun and shade leaves of Olea europaea respond differently to plant size, light availability and genetic variation
Venue: Functional Ecology

1. Canopy plasticity, the expression of different leaf phenotypes within the crown of an individual tree has complex functional and evolutionary implications that remain to be thoroughly assessed. We hypothesized that it can lead to disparity in how leaves in different positions of the canopy change with allometric growth and population genetic structure. 
2. Leaf phenotypes of the inner and outer canopy were estimated using eight morphological and physiological characters. All traits were measured under field conditions in six populations of Olea europaea and again in a common garden for a subset of the genotypes. The same populations were characterized genetically with amplified fragment length polymorphisms (AFLP) genomic scans. With these data, we investigated the extent to which leaf phenotypes change with plant size, genetic processes and in response to environmental conditions inside and outside the canopy. 
3. The size of trees measured in the field was clearly associated with the phenotype of sun but not to that of shade leaves. The phenotype of sun leaves depended on both direct and diffuse light, while that of shade leaves was found to correlate only with diffuse radiation. Additionally, light availability inside the canopy was conditioned by the shape of external leaves, and increasing elongation of sun leaves led to higher radiation in the inner canopy. 
4. The field phenotypes of both inner and outer canopy leaves were correlated with genetic variation among populations. Conversely, in the common garden, the different genotypes expressed a homogeneous sun phenotype, while phenotypic differences among populations remained apparent in shade leaves. 
5. We conclude that, in agreement with our working hypothesis, canopy plasticity is both cause and consequence of the environment experienced by the plant and might lead to the differential expression of genetic polymorphisms among leaves. Furthermore, we propose that it can contribute to buffer abiotic stress and to the partition of light use within the tree crown.
Knickkopf protein protects and organizes chitin in the newly synthesized insect exoskeleton
Venue: Proceedings of the National Academy of Sciences of the United States of America

During each molting cycle of insect development, synthesis of new cuticle occurs concurrently with the partial degradation of the overlying old exoskeleton. Protection of the newly synthesized cuticle from molting fluid enzymes has long been attributed to the presence of an impermeable envelope layer that was thought to serve as a physical barrier, preventing molting fluid enzymes from accessing the new cuticle and thereby ensuring selective degradation of only the old one. In this study, using the red flour beetle, Tribolium castaneum, as a model insect species, we show that an entirely different and unexpected mechanism accounts for the selective action of chitinases and possibly other molting enzymes. The molting fluid enzyme chitinase, which degrades the matrix polysaccharide chitin, is not excluded from the newly synthesized cuticle as previously assumed. Instead, the new cuticle is protected from chitinase action by the T. castaneum Knickkopf (TcKnk) protein. TcKnk colocalizes with chitin in the new cuticle and organizes it into laminae. Down-regulation of TcKnk results in chitinase-dependent loss of chitin, severe molting defects, and lethality at all developmental stages. The conservation of Knickkopf across insect, crustacean, and nematode taxa suggests that its critical roles in the laminar ordering and protection of exoskeletal chitin may be common to all chitinous invertebrates.
Circumferential spicule growth by pericellular silica deposition in the hexactinellid sponge Monorhaphis chuni
Venue: The Journal of Experimental Biology

The giant basal spicule of the hexactinellid sponge Monorhaphis chuni represents the longest natural siliceous structure on Earth. This spicule is composed of concentrically arranged lamellae that are approximately 10 μm thick. In the present study, we investigated the formation of outer lamellae on a cellular level using microscopic and spectroscopic techniques. It is shown that the formation of an outermost lamella begins with the association of cell clusters with the surface of the thickening and/or growing spicule. The cells release silica for controlled formation of a lamella. The pericellular (silica) material fuses to a delimited and textured layer of silica with depressions approximately 20–30 μm in diameter. The newly formed layer initially displays 40 μm wide, well-structured banded ribbons and only attains its plain surface in a final step. The chemical composition in the depressions was studied using energy dispersive X-ray spectroscopy and by staining with Texas Red. The data suggest that those depressions are the nests for the silica-forming cells and that silica formation starts with a direct association of silica-forming cells with the outer surface of the spicule, where they remain and initiate the development of the next lamellae.
Regulation of CONSTANS and FLOWERING LOCUS T Expression in Response to Changing Light Quality1[C][OA]
Venue: Plant Physiology

In addition to pathways that regulate flowering in response to environmental signals such as photoperiod or cold temperatures (vernalization), flowering time is also regulated by light quality. In many species, far-red (FR) light is known to accelerate flowering. This is environmentally significant because leaves absorb more red light than FR light; thus, plants growing under a canopy experience light that is enriched in FR light. In this article, we have explored the promotion of flowering by FR-enriched light (FREL) in Arabidopsis (Arabidopsis thaliana). Previous work has shown that the floral promoter CONSTANS (CO) plays a critical role in day-length perception and exhibits complex regulation; CO mRNA is regulated by the circadian clock and CO protein is stabilized by light and degraded in darkness. We find that plants grown under FREL contain higher levels of CO mRNA in the early part of the day than plants under white light. Furthermore, transgenic plants expressing CO under the control of a constitutive promoter accumulate higher levels of CO protein under FREL, indicating that FREL can increase CO protein levels independently of transcription. Consistent with the model that FREL promotes flowering through CO, mutants for co or gigantea, which are required for CO transcript accumulation, are relatively insensitive to FREL. Because the red:FR ratios used in these experiments are in the range of what plants would experience under a canopy, these results indicate that the regulation of CO by light quality likely plays a key role in the regulation of flowering time in natural environments.
How Archer Fish Achieve a Powerful Impact: Hydrodynamic Instability of a Pulsed Jet in Toxotes jaculatrix
Venue: PLOS ONE

Archer fish knock down insects anchored to vegetation by hitting them with a precisely aimed jet of water. The striking force of the jet at the impact is such to overcome the strong anchoring forces of insects. The origin of the effectiveness of such hunting mechanism has been long searched for inside of the fish, in the unsuccessful attempt to identify internal structures dedicated to the amplification of muscular power. Here we perform a kinematic analysis of the jet emitted by two specimens of Toxotes jaculatrix. We estimate that at the impact the jet conveys a typical specific power of about 3000 W/kg, which is well above the maximum specific power of the order of 500 W/kg deliverable by a vertebrate muscle. Unexpectedly, we find that the amplification of muscular power occurs outside of the fish, and is due to a hydrodynamic instability of the jet akin to those occurring in Drop-on-Demand inkjet printing. The investigated fish are found to modulate the velocity of the jet at the orifice to favor the formation of a single, large, water drop that hits the prey abruptly with a large momentum. The observed mechanism represents a remarkable example of use of an external hydrodynamic lever that does possibly not entail the high evolutionary cost needed for the development of highly specialized internal structures dedicated to the storing of mechanical energy.
Diverse Strategies of Protein Sclerotization in Marine Invertebrates: Structure–Property Relationships in Natural Biomaterials
Venue: Advances in Insect Physiology

The conventional wisdom regarding sclerotization in arthropod exoskeletons is that tissue stiffness and polyphenolic content are tightly coupled. Recent progress on the biochemistry and mechanics of sclerotized structures from non-arthropod invertebrates such as mussels, polychaetes and squid suggests that this premise is too simple and needs to be more closely scrutinized. Emerging mechanistic insights about structure–property relationships in sclerotized extracellular composites include the following: (1) tissue stiffness can be significantly adjusted by the relative organization and density of rigid versus flexible domains in the protein components (mussel byssal thread); (2) structures can be rich in polyphenols without being sclerotized (mussel adhesive plaque); (3) stiffness and hardness can be adjusted by the relative abundance of interactions between protein-based imidazole and catecholate ligands and transition metals (polychaete jaws and mussel cuticle); (4) polyphenol-derived covalent cross-link density in a protein–chitin composite offers some stiffening, but gains from incrementally controlled dehydration are far greater (squid beak); and finally, (5) protein domains, ligand and metal densities, covalent cross-linking and dehydration are elaborately manipulated to create stiffness gradients between mechanically mismatched tissues.
“Magnetic” termite mound surfaces are oriented to suit wind and shade conditions
Venue: Oecologia

SummaryThe termites Amitermes meridionalis and A. laurensis construct remarkable meridional or “magnetic” mounds in northern Australia. These mounds vary geographically in mean orientation in a manner that suggests such variation is an adaptive response to local environmental conditions. Theoretical modelling of solar irradiance and mound rotation experiments show that maintenance of an eastern face temperature plateau during the dry season is the most likely physical basis for the mound orientation response. Subsequent heat transfer analysis shows that habitat wind speed and shading conditions also affect face temperature gradients such as the rate of eastern face temperature change. It is then demonstrated that the geographic variation in mean mound orientation follows the geographic variation in long-term wind speed and shading conditions across northern Australia such that an eastern face temperature plateau is maintained in all locations.
Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning
Venue: Science

Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coliaquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a “proton wire,” while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.