nils-herrmann/clean_scirepeval huggingface dataset:
NATURAL FREEZING SURVIVAL IN ANIMALS
Venue: Annual Review of Ecology, Evolution, and Systematics

Natural freeze-tolerance supports the winter survival of many animals including numerous terrestrial insects, many intertidal marine invertebrates, and selected species of terrestrially hibernating amphibians and reptiles. Freeze-tolerant animals typically endure the conversion of 50% or more of total body water into extracellular ice and employ a suite of adaptations that counter the negative consequences of freezing. Specific adaptations control the sites and rate of ice formation to prevent physical damage by ice. Other adaptations regulate cell-volume change: Colligative cryoprotectants minimize cell shrinkage during extracellular ice formation; other protectants stabilize membrane structure; and a high density of membrane transporter proteins ensure rapid cryoprotectant distribution. Cell survival during freezing is also potentiated by anoxia tolerance, mechanisms of metabolic rate depression, and antioxidant defenses. The net result of these protective mechanisms is the ability to reactivate vital functions after days or weeks of continuous freezing. Magnetic resonance imaging has allowed visual examinations of the mode of ice penetration through the body of freeze-tolerant frogs and turtles, and cryomicroscopy has illustrated the effects of freezing on the cellular and microvasculature structure of tissues. Various metabolic adaptations for freezing survival appear to have evolved out of pre-existing physiological capacities of animals, including desiccation-resistance and anoxia-tolerance.
Spawning events in small and large populations of the green sea urchin Strongylocentrotus droebachiensis as recorded using fertilization assays
Venue: Limnology and Oceanography

During the winter and spring of 2002 and 2003, we used time-integrated fertilization assays to monitor sperm availability in three populations of the green sea urchin Strongylocentrotus droebachiensis in Maine: a naturally occurring population of >40,000 urchins and two smaller groups (<1,000) of transplanted urchins isolated from other aggregations. Episodes of sperm release coincided in two populations 10 km apart, suggesting that urchins were responding to a widespread environmental signal. We observed significant lunar periodicity in sperm release events for both of these populations. However, extensive spawning as shown by fertilization rates near 100% and a dramatic drop in gonad mass only occurred in the large natural population around the onset of thermal stratification and the spring phytoplankton bloom. By contrast, in the two small populations we observed low fertilization rates and little or no change in gonad mass. We speculate that a subset of males in these populations responded to a common external spawning signal, but that mass spawning is more likely to occur in large, dense populations where sperm concentrations reach high enough levels to trigger spawning in less responsive urchins.
Partial purification of tomato fruit peroxidase and its effect on the mechanical properties of tomato fruit skin.
Venue: Journal of Experimental Botany

Peroxidase (EC 1.11.1.7)-mediated stiffening of cell walls within the fruit skin of tomato is hypothesized to regulate fruit growth. However, to date, there is no experimental evidence demonstrating that peroxidase affects the mechanical properties of skin tissue. Here, the mechanical properties of skin strips excised from a range of fruits at different ages were determined using an 'Instron' universal material testing instrument. The stiffness of tomato fruit skin strips increases 3-fold with increasing fruit age. Application of partially-purified peroxidase from the cell walls of mature tomato fruit skin significantly increased the stiffness of fruit skin irrespective of the age of fruit. Furthermore, the application of hydrogen peroxide significantly increased the stiffness of skin strips excised from fruit of an age when endogenous peroxidase isozymes associated with the termination of growth are first detected. The results support the hypothesis that the tomato fruit skin plays an integral role in the regulation of tomato fruit growth, and that changes in its mechanical properties may be mediated by peroxidase. As far as is known, this is the first demonstration that peroxidases alter the mechanical properties of the plant cell wall.
Molecular Basis of Infrared Detection by Snakes
Venue: Nature

Snakes possess a unique sensory system for detecting infrared radiation, enabling them to generate a ‘thermal image’ of predators or prey. Infrared signals are initially received by the pit organ, a highly specialized facial structure that is innervated by nerve fibres of the somatosensory system. How this organ detects and transduces infrared signals into nerve impulses is not known. Here we use an unbiased transcriptional profiling approach to identify TRPA1 channels as infrared receptors on sensory nerve fibres that innervate the pit organ. TRPA1 orthologues from pit-bearing snakes (vipers, pythons and boas) are the most heat-sensitive vertebrate ion channels thus far identified, consistent with their role as primary transducers of infrared stimuli. Thus, snakes detect infrared signals through a mechanism involving radiant heating of the pit organ, rather than photochemical transduction. These findings illustrate the broad evolutionary tuning of transient receptor potential (TRP) channels as thermosensors in the vertebrate nervous system.
Spatial vision in the echinoid genus Echinometra
Venue: The Journal of Experimental Biology

Although eyes are generally considered necessary for image resolution, a diffuse photoreceptive system with directional sensitivity may also have this ability. Two species of the echinoid genus Echinometra were tested for spatial vision by examining their ability to locate and move towards targets of different sizes. The echinoids were significantly oriented (P<0.0001) towards a target with an angular width of 33° (0.3 sr) but were not oriented to targets with angular widths of 26° and 16°. This ability is probably due to the blocking of off-angle light by the spines, which have approximately the correct spacing for the observed resolution. Spatial vision is advantageous for echinoids of this genus because they leave and return to small dark shelters. This first demonstration of spatial vision in an echinoderm sheds further light on the complex optical structures and photobehaviors found in this phylum.
Nitrogen transformations in a through‐flow wetland revealed using whole‐ecosystem pulsed 15N additions
Venue: Limnology and Oceanography

We used pulsed and continuous additions of 15N together with whole-ecosystem metabolism measurements to elucidate the mechanisms of nitrogen (N) transformations in a small (1170 m2) through-flow wetland situated along a stream. From measurements of the wetland inflow and outflow, we observed a consistent decrease in nitrate (by 10% of inflow concentrations), while ammonium increased by an order of magnitude. Outflow ammonium concentrations oscillated in a diel cycle, inverse to the concentration of dissolved oxygen (i.e., greater ammonium export at night). The pulsed 15N additions showed little uptake of nitrate over time in the wetland and rapid daytime uptake of ammonium from the water column (rate constant, kt 5 0.11 h21). A steady-state 15Nammonium addition demonstrated a similar rate of ammonium uptake (kt 5 0.067 h21), no detectable nitrification, and highlighted the spatial pattern of ammonium and nitrate uptake within the wetland. Porewater concentration profiles suggest high rates of net ammonium diffusion from the sediments. Ecosystem metabolism measurements indicate that release was attenuated during the day by autotrophic uptake, resulting in lower ammonium export during the day. Denitrification rates were modeled from dissolved N2 : Ar ratios, but they were not sufficient to account for the observed loss in nitrate. Nitrate was removed near the pond inflow but not actively cycled throughout the pond, while the balance between sediment release and subsequent uptake of ammonium from the water-column dominated N cycling in this wetland.
The fine structure of Odonata chromatophores.
Venue: Tissue & Cell

The appearance, fine structure and pigment composition of the epidermal chromatophores of mature Austrolestes annulosus (Lestidae) are described and compared with the developing chromatophores of teneral Austrolestes and the mature chromatophores of Diphlebia lestoides (Amphipterygidae) and Ischnura heterosticta (Caenagrionidae). Mature chromatophores contain masses of near spherical light-scattering bodies and larger irregularly shaped pigment vesicles. These effect colour change by migrating in opposite directions, through a system of interconnecting granular endoplasmic reticulum tubules. The pigment, a mixture of xanthommatin and dihydroxanthommatin, has a liquid or gelatinous consistency. Developing chromatophores of teneral insects lack light-scattering bodies and well-defined migratory pigment vesicles, but contain irregular masses of pigment of similar chemical composition.
Structural plasticity and catalysis regulation of a thermosensor histidine kinase
Venue: Proceedings of the National Academy of Sciences of the United States of America

Temperature sensing is essential for the survival of living cells. A major challenge is to understand how a biological thermometer processes thermal information to optimize cellular functions. Using structural and biochemical approaches, we show that the thermosensitive histidine kinase, DesK, from Bacillus subtilis is cold-activated through specific interhelical rearrangements in its central four-helix bundle domain. As revealed by the crystal structures of DesK in different functional states, the plasticity of this helical domain influences the catalytic activities of the protein, either by modifying the mobility of the ATP-binding domains for autokinase activity or by modulating binding of the cognate response regulator to sustain the phosphotransferase and phosphatase activities. The structural and biochemical data suggest a model in which the transmembrane sensor domain of DesK promotes these structural changes through conformational signals transmitted by the membrane-connecting two-helical coiled-coil, ultimately controlling the alternation between output autokinase and phosphatase activities. The structural comparison of the different DesK variants indicates that incoming signals can take the form of helix rotations and asymmetric helical bends similar to those reported for other sensing systems, suggesting that a similar switching mechanism could be operational in a wide range of sensor histidine kinases.
The mineralization and hardness of the radular teeth of the limpet Patella vulgata L.
Venue: Cell and Tissue Research

SummaryA study of the Patella vulgata radula has been made using: the scanning electron microscope in its normal and compositional contrast modes of operation, the electron microprobe analyser, ion etching with argon ions and microhardness testing.Only iron, silicon and small amounts of sulphur were detected in the radula. The teeth can be subdivided into a cusp, a junctional area where the cusp is joined to the base, and the base which is embedded in the radular membrane. From a study of longitudinal vertical and transverse sections of the mature teeth it was found that the cusp could be subdivided into a posterior iron-rich area (44–51% Fe, 1–6% Si) and an anterior silicon-rich area (22–30% Fe, 27–32% Si). The junctional zone consisted of a poorly mineralised layer at its border with the cusp and an iron-rich layer where it joined the base. The upper part of the base (5% Fe, 16% Si) could be clearly differentiated from the silicon-rich anterior and lower parts of the base (3–4% Fe, 28–35% Si). No minerals were detected in the membrane. The changes in the mineral content of the teeth cusps along the length of the radula were studied. Iron appeared in the cusps at the 25th row and the concentration increased to 28% at the 50th row. The iron was here evenly distributed throughout the cusp. Silicon appeared in the anterior part of the cusp at the 50th row and as it increased in concentration so the iron was displaced, and at the same time the concentration of iron increased in the posterior part of the cusp. Mineralization appeared to be complete by the 150th row.The teeth cusps appear to consist of 800 Å fibres grouped into 1μ thick bundles and the tooth appears to be covered by a thin enamel-like layer. It is suggested that the fibres contain the silicon-rich phase and the matrix the iron-rich phase.The significance of the arrangement of the fibres and the distribution of the minerals are discussed with relation to the function of the teeth.
High Abrasion Resistance with Sparse Mineralization: Copper Biomineral in Worm Jaws
Venue: Science

Biominerals are widely exploited to harden or stiffen tissues in living organisms, with calcium-, silicon-, and iron-based minerals being most common. In notable contrast, the jaws of the marine bloodworm Glycera dibranchiata contain the copper-based biomineral atacamite [Cu2(OH)3Cl]. Polycrystalline fibers are oriented with the outer contour of the jaw. Using nanoindentation, we show that the mineral has a structural role and enhances hardness and stiffness. Despite the low degree of mineralization, bloodworm jaws exhibit an extraordinary resistance to abrasion, significantly exceeding that of vertebrate dentin and approaching that of tooth enamel.
Stimulation of DNA repair as an evolutionary drive for bacterial luminescence.
Venue: Luminescence

It was demonstrated recently that luminescence of a free-living marine bacterium, Vibrio harveyi, stimulates DNA repair, most probably by activation of the photoreactivation process. Here, we ask whether the stimulation of DNA repair could be an evolutionary drive that ensured maintenance and development of early bacterial luminescent systems. To test this hypothesis, we cultivated V. harveyi lux(+) bacteria and luxA mutants in mixed cultures. Initial cultures were mixed to obtain a culture consisting of roughly 50% lux(+) cells and 50% luxA mutants. Then bacteria were cultivated for several days and ratio of luminescent to dark bacteria was measured. Under these conditions, luxA mutants became highly predominant within a few days of cultivation. This indicates that, without a selective pressure, the luminescence is a disadvantage for bacteria, perhaps due to consumption of significant portion of cell energy. However, when the same experiments were repeated but cultures were irradiated with low UV doses, luminescent bacteria started to predominate shortly after the irradiation. Therefore, we conclude that stimulation of photoreactivation may be an evolutionary drive for bacterial bioluminescence.
The influence of the nasal mucosa and the carotid rete upon hypothalamic temperature in sheep
Venue: The Journal of Physiology

1. In chronically‐prepared sheep, intracranial temperatures were measured in the cavernous sinus among the vessels of the carotid rete and at the circle of Willis extravascularly, and in the preoptic area and in other brain stem regions. Extracranial temperatures were measured intravascularly in the carotid or internal maxillary arteries and on the nasal mucosa and the skin of the ear.
The dehesa system of southern Spain and Portugal as a natural ecosystem mimic
Venue: Agroforestry Systems

The dehesas of the southwestern Iberian Peninsula are 'man-made' ecosystems characterised by a savannah-like physiognomy. The trees are viewed as an integrated part of the system, and as a result are planted, managed, and regularly pruned. Palynological and historical evidence of the manipulation of initial ecosystems by man to obtain a savannah-like ecosystem is presented. The ecological functions of the tree are detailed using results obtained at two complementary scales. At the local scale, strong soil structural differences and functional differences in water budget and patterns of water use are observed under and outside the tree canopy. Using the concept of ecosystem mimicry, the two coexistent components of dehesas can be compared to two distant stages of a secondary succession characterised by very different behaviours. At the regional scale, evidence of relationships between tree density and mean annual precipitation over more than 5000 km2 suggests that the structure of these man-made agroecosystems have adjusted over the long-term and correspond to an optimal functional equilibrium based on the hydrological equilibrium hypothesis. Finally, the future of dehesas in the face of contemporary exogenous threats of economic and global environmental origin is discussed.
Energy saving in flight formation
Venue: Nature

Many species of large bird fly together in formation, perhaps because flight power demands and energy expenditure can be reduced when the birds fly at an optimal spacing, or because orientation is improved by communication within groups. We have measured heart rates as an estimate of energy expenditure in imprinted great white pelicans (Pelecanus onocrotalus) trained to fly in 'V' formation, and show that these birds save a significant amount of energy by flying in formation. This advantage is probably a principal reason for the evolution of flight formation in large birds that migrate in groups.
Circadian Regulation of Bioluminescence in the Prey-Luring Glowworm, Arachnocampa flava
Venue: Journal of Biological Rhythms

The glowworms of New Zealand and Australia are bioluminescent fly larvae that generate light to attract prey into their webs. Some species inhabit the constant darkness of caves as well as the dim, natural photophase of rain-forests. Given the diversity of light regimens experienced by glowworms in their natural environment, true circadian rhythmicity of light output could be present. Consequently the light emission characteristics of the Australian subtropical species Arachnocampa flava, both in their natural rainforest habitat and in artificial conditions in the laboratory, were established. Larvae were taken from rainforest and kept alive in individual containers. When placed in constant darkness (DD) in the laboratory they maintained free-running, cyclical light output for at least 28 days, indicating that light output is regulated by an endogenous rhythm. The characteristics of the light emission changed in DD: individuals showed an increase in the time spent glowing per day and a reduction in the maximum light output. Most individuals show a free-running period greater than 24 h. Manipulation of the photophase and exposure to skeleton photoperiods showed that light acts as both a masking and an entraining agent and suggests that the underlying circadian rhythm is sinusoidal in the absence of light-based masking. Manipulation of thermoperiod in DD showed that temperature cycles are an alternative entraining agent. Exposure to a period of daily feeding in DD failed to entrain the rhythm in the laboratory. The endogenous regulation of luminescence poses questions about periodicity and synchronization of bioluminescence in cave glowworms.
Discovering the flight autostabilizer of fruit flies by inducing aerial stumbles
Venue: Proceedings of the National Academy of Sciences of the United States of America

Just as the Wright brothers implemented controls to achieve stable airplane flight, flying insects have evolved behavioral strategies that ensure recovery from flight disturbances. Pioneering studies performed on tethered and dissected insects demonstrate that the sensory, neurological, and musculoskeletal systems play important roles in flight control. Such studies, however, cannot produce an integrative model of insect flight stability because they do not incorporate the interaction of these systems with free-flight aerodynamics. We directly investigate control and stability through the application of torque impulses to freely flying fruit flies (Drosophila melanogaster) and measurement of their behavioral response. High-speed video and a new motion tracking method capture the aerial “stumble,” and we discover that flies respond to gentle disturbances by accurately returning to their original orientation. These insects take advantage of a stabilizing aerodynamic influence and active torque generation to recover their heading to within 2° in < 60 ms. To explain this recovery behavior, we form a feedback control model that includes the fly’s ability to sense body rotations, process this information, and actuate the wing motions that generate corrective aerodynamic torque. Thus, like early man-made aircraft and modern fighter jets, the fruit fly employs an automatic stabilization scheme that reacts to short time-scale disturbances.
Characterization of mechanisms for Ca2+ and HCO3–/CO32– acquisition for shell formation in embryos of the freshwater common pond snail Lymnaea stagnalis
Venue: The Journal of Experimental Biology

The freshwater common pond snail Lymnaea stagnalis produces embryos that complete direct development, hatching as shell-bearing individuals within 10 days despite relatively low ambient calcium and carbonate availability. This development is impaired by removal of ambient total calcium but not by removal of bicarbonate and/or carbonate. In this study we utilized pharmacological agents to target possible acquisition pathways for both Ca2+ and accumulation of carbonate in post-metamorphic, shell-laying embryos. Using whole egg mass flux measurements and ion-specific microelectrode analytical techniques, we have demonstrated that carbonic anhydrase-catalyzed hydration of CO2 is central in the acquisition of both shell-forming ions because it provides the hydrogen ions for an electrogenic vacuolar-type H+-ATPase that fuels the uptake of Ca2+ via voltage-dependent Ca2+ channels and possibly an electrogenic Ca2+/1H+ exchanger. Additionally, CO2 hydration provides an endogenous source of HCO –3. Thus, hydration of endogenous CO2 forms HCO –3 for calcification while hydrogen ions are excreted, contributing to continued Ca2+ uptake, as well as creating favorable alkaline internal conditions for calcification. The connections between Ca2+ and HCO –3 acquisition mechanisms that we describe here provide new insight into this efficient, embryonic calcification in freshwater.