nils-herrmann/clean_scirepeval huggingface dataset:
Mechanism of calcite co-orientation in the sea urchin tooth.
Venue: Journal of the American Chemical Society

Sea urchin teeth are remarkable and complex calcite structures, continuously growing at the forming end and self-sharpening at the mature grinding tip. The calcite (CaCO(3)) crystals of tooth components, plates, fibers, and a high-Mg polycrystalline matrix, have highly co-oriented crystallographic axes. This ability to co-orient calcite in a mineralized structure is shared by all echinoderms. However, the physico-chemical mechanism by which calcite crystals become co-oriented in echinoderms remains enigmatic. Here, we show differences in calcite c-axis orientations in the tooth of the purple sea urchin ( Strongylocentrotus purpuratus ), using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM) and microbeam X-ray diffraction (muXRD). All plates share one crystal orientation, propagated through pillar bridges, while fibers and polycrystalline matrix share another orientation. Furthermore, in the forming end of the tooth, we observe that CaCO(3) is present as amorphous calcium carbonate (ACC). We demonstrate that co-orientation of the nanoparticles in the polycrystalline matrix occurs via solid-state secondary nucleation, propagating out from the previously formed fibers and plates, into the amorphous precursor nanoparticles. Because amorphous precursors were observed in diverse biominerals, solid-state secondary nucleation is likely to be a general mechanism for the co-orientation of biomineral components in organisms from different phyla.
Glueomics: An Expression Survey of the Adhesive Gland of the Sandcastle Worm
Venue: Journal of Adhesion

Random clones were sequenced from a cDNA library constructed from the adhesive gland of Phragmatopoma californica, a marine polycheate that builds protective shells by gluing together sand grains and biogenic mineral fragments. As many as 14 new proteins and two phenoloxidase enzymes were found that may be structural components of or involved in processing the bioadhesive. Glue protein classification was based on the following criteria: (i) the presence of predicted secretion signal peptides, (ii) low complexity sequences, (iii) strongly skewed amino acid compositions enriched with G, Y, K, H, A, or S, (iv) repeating peptide motifs, and (v) homology to known glue proteins, other structural proteins, or enzymes. The new genes provide probes for further characterization of the adhesive gland as well as potential biotechnological resources and insight.
Structure, innervation and response properties of integumentary sensory organs in crocodilians
Venue: The Journal of Experimental Biology

Integumentary sensory organs (ISOs) are densely distributed on the jaws of crocodilians and on body scales of members of the families Crocodilidae and Gavialidae. We examined the distribution, anatomy, innervation and response properties of ISOs on the face and body of crocodilians and documented related behaviors for an alligatorid (Alligator mississippiensis) and a crocodylid (Crocodylus niloticus). Each of the ISOs (roughly 4000 in A. mississippiensis and 9000 in C. niloticus) was innervated by networks of afferents supplying multiple different mechanoreceptors. Electrophysiological recordings from the trigeminal ganglion and peripheral nerves were made to isolate single-unit receptive fields and to test possible osmoreceptive and electroreceptive functions. Multiple small (<0.1 mm2) receptive fields, often from a single ISO, were recorded from the premaxilla, the rostral dentary, the gingivae and the distal digits. These responded to a median threshold of 0.08 mN. The less densely innervated caudal margins of the jaws had larger receptive fields (>100 mm2) and higher thresholds (13.725 mN). Rapidly adapting, slowly adapting type I and slowly adapting type II responses were identified based on neuronal responses. Several rapidly adapting units responded maximally to vibrations at 20–35 Hz, consistent with reports of the ISOs' role in detecting prey-generated water surface ripples. Despite crocodilians' armored bodies, the ISOs imparted a mechanical sensitivity exceeding that of primate fingertips. We conclude that crocodilian ISOs have diverse functions, including detection of water movements, indicating when to bite based on direct contact of pursued prey, and fine tactile discrimination of items held in the jaws.
Bromophycolide A Targets Heme Crystallization in the Human Malaria Parasite Plasmodium falciparum
Venue: ChemMedChem

Plasmodium falciparum, the most deadly human malaria parasite, poses a major threat to human health worldwide, with over 500 million clinical cases and between one and two million deaths annually.[1] Natural products and their synthetic derivatives have provided a significant number of successful antimalarial treatments to date, representing approximately 65 % of current drugs.[2] Quinine, discovered from cinchona tree bark, has been used to treat malaria for centuries and was the primary antimalarial drug until it was replaced by chloroquine, a synthetic derivative, in the 1940s.[3] Chloroquine became the mainstay antimalarial until resistant strains began to appear nearly a decade after its introduction. Artemisinin, isolated from the plant Artemisia annua used in traditional Chinese medicine, ushered in a new wave of antimalarials and became the most potent and rapid-acting drug available.[4] Several synthetic artemisinin derivatives have since been developed, and artemisinin-based combination therapies are currently in use throughout the world to treat this parasitic disease. However, artemisinin-resistant strains have recently been reported,[5] and new antiparasitic drugs are urgently needed to combat these strains.
Pheromone Reception
Venue: The Chemistry of Pheromones and other Semiochemicals II; Journal of Chemical Ecology

Insects are analytical chemists par excellence. They perceive the world through semiochemicals with inordinate sensitivity.A male moth, for example, can detect a “scent of woman,” i.e., a female-produced sex pheromone, even when the signal-to-noise ratio is very low. In a sense the antennae are “signal translators.” The chemicals signals are “translated” into the language of the brain (nerve impulses or spikes) by an array of sensilla mainly located on the antennae. This information is conveyed to the brain for further processing. Chemical ecologists utilize insect antennae as biosensors for the identification of pheromones and other semiochemicals. The insect olfactory system is also highly selective, able to discriminate natural pheromones from molecules with minimal structural changes. In some cases, one stereoisomer functions as an attractant sex pheromone and its antipode is a behavioral antagonist (inhibitory signal). The specificity of the olfactory system seems to be achieved by two layers of filters. The first level of discrimination is determined by odorantbinding proteins (OBPs) that assist the hydrophobic pheromones to cross an aqueous barrier and reach their receptors. Both OBP and odorant receptor (OR) contribute to the specificity of the cell response and lead to the remarkable selectivity of the insect olfactory system. The members of the OBP-gene family, encoding the encapsulins, form a large group with olfactory and non-olfactory proteins. While the functions of many members of the family are yet to be determined, there is solid evidence for the mode of action of OBPs. Pheromones (and other semiochemicals) enter the sensillar lymph through pore tubules in the cuticle (sensillar wall), are solubilized upon being encapsulated by odorant-binding proteins, and transported to the olfactory receptors. Bound pheromone molecules are protected Topics in Current Chemistry (2005) 240: 1– 36 DOI 10.1007/b98314  2005 from odorant-degrading enzymes. Upon interaction with negatively-charged sites at the dendritic membrane, the OBP-ligand complex undergoes a conformational change that leads to the ejection of pheromone. Direct activation of odorant receptors by odorant molecules initiates a cascade of events leading to the generation of spikes. Reverse chemical ecology is a new concept for the screening of attractants based on the binding ability of OBPs to test
Nature's moisture harvesters: a comparative review.
Venue: Bioinspiration & Biomimetics

Nature has adapted different methods for surviving dry, arid, xeric conditions. It is the focus of this comparative review to pull together the relevant information gleaned from the literature that could be utilized to design moisture harvesting devices informed by biomimetics. Most water harvesting devices in current use are not informed by nature and those that do are usually based on a biomimetic principle that has been based on one species only. This review draws on the published literature to establish a list of species (animals (vertebrates/invertebrates) and plants) whose habitat is in mainly dry or arid regions and that are known to harvest airborne moisture. Key findings have been outlined and review comments and discussion set out. Following this, surface feature convergences have been identified, namely hexagonal microstructures, groove-like and cone-like geometries. This has been coupled with direction of water flow that is driven by surface energy. As far as the authors are aware, this convergent evolution has not been brought together in this manner before. In the future this information could be translated into an engineered device for collecting water from airborne sources.
Worms bask in extreme temperatures
Venue: Nature

Temperature is one of the most important environmental factors that governs a species' distribution. Some highly specialized prokaryotes can grow at temperatures above 113 °C (ref. 1), but eukaryotes appear less versatile and do not normally occur above 55 °C. Here we show that a colony-dwelling polychaete worm, inhabiting deep-sea hydrothermal vent chimneys, regularly experiences temperatures above 80 °C and a thermal gradient of 60 °C or more over its body length.
Nests, Petal Usage, Floral Preferences, and Immatures of Osmia (Ozbekosmia) avosetta (Megachilidae: Megachilinae: Osmiini), Including Biological Comparisons with Other Osmiine Bees
Venue: American Museum Novitates

Herein we describe the nests (including construction, closure, orientation, and depth of cells) of the bee Osmia (Ozbekosmia) avosetta Warncke found nesting near Antalya, Turkey, and Sepidan, Iran. Cells are unusual in that they are lined by two layers of colorful flower petals that sandwich a thin middle layer of mud. Analyses of pollen taken from scopal hairs of specimens from the Turkish site were identified as solely from Onobrychis viciifolia Scop. (Fabaceae) whereas those from the Iranian site were from a related plant, Hedysarum elymaiticum Boiss. and Hausskn. These facts coupled with analyses of scopal pollen from 11 other sites in Turkey, Jordan, and Syria strongly suggest that this bee is oligolectic with respect to the plant tribe Hedysareae. The egg and last larval instar of Osmia avosetta are described. The presence of an egg taken from a cell and provisionally identified as belonging to Sapyga pulcherrima Morawitz suggests that this cleptoparasite may have this bee as one of its hosts. In addition, we report new information on and review published accounts concerning the use of whole petals or large petal pieces in the construction of cell walls of osmiine bees. Only Osmia (Ozbekosmia) avosetta and species of Osmia (Tergosmia) have three-layered cell walls with the middle layer made of mud. Recorded also are the similarities and differences exhibited in pollen and petal preferences and nest characteristics of species in these two related subgenera.
Occurrence of ultraviolet radiation-absorbing mycosporine-like amino acids in coral mucus and whole corals of French Polynesia
Venue: Marine and Freshwater Research

Specimens of six scleractinian species were gathered during the austral spring (October–November) 1994 on the external slope of the barrier reef of Arue, Tahiti, and in the lagoon of Arutua, a Tuamotu island. Mucus of each specimen was collected and the optical density and volume excreted were measured. After treatment, mucus was analysed for mycosporine-like amino acids (MAAs) by high-performance liquid chromatography (HPLC). Nine UV-absorbing compounds were present in coral mucus at concentrations between 1 and 500 ng g-1 mucus. Palythine and mycosporine–gly were found in all mucus studied. Mycosporine–2glycine was recovered in 71% of specimens and shinorine in 28%. Porphyra-334 and palythinol were identified as minor MAAs. Three recently identified MAAs, palythine–serine, mycosporine–methylamine:serine and mycosporine–methylamine:threonine, were also found in mucus from Pocillopora. Within a genus, there was a qualitative similarity in MAAs determined by HPLC, irrespective of locality. Values for optical density of the mucus showed the ability of MAAs to protect the animal host and endosymbiotic algae from UV-solar flux and, as inferred from the recent literature, from oxidative forms of oxygen (HO2 . , O 2 - , HO.) derived from photosynthesis.
Solutes determine the temperature windows for microbial survival and growth
Venue: Proceedings of the National Academy of Sciences of the United States of America

Microbial cells, and ultimately the Earth's biosphere, function within a narrow range of physicochemical conditions. For the majority of ecosystems, productivity is cold-limited, and it is microbes that represent the failure point. This study was carried out to determine if naturally occurring solutes can extend the temperature windows for activity of microorganisms. We found that substances known to disorder cellular macromolecules (chaotropes) did expand microbial growth windows, fungi preferentially accumulated chaotropic metabolites at low temperature, and chemical activities of solutes determined microbial survival at extremes of temperature as well as pressure. This information can enhance the precision of models used to predict if extraterrestrial and other hostile environments are able to support life; furthermore, chaotropes may be used to extend the growth windows for key microbes, such as saprotrophs, in cold ecosystems and manmade biomes.
A novel stiffening factor inducing the stiffest state of holothurian catch connective tissue
Venue: The Journal of Experimental Biology

The dermis of sea cucumbers is a catch connective tissue or mutable collagenous tissue that shows large changes in stiffness. Extensive studies on the dermis revealed that it can adopt three different states having different mechanical properties that can be reversibly converted. These are the stiff, standard and soft states. The standard state is readily produced when a dermal piece is immersed in the sea water containing Ca2+, whereas the soft state can be produced by removal of Ca2+. A stiffening protein, tensilin, has been isolated from some sea cucumbers (Cucumaria frondosa and Holothuria leucospilota). Although tensilin converts the state of the dermis from soft to standard, it cannot convert from standard to stiff. In this study, we isolated and partially purified a novel stiffening factor from the dermis of Holothuria leucospilota. The factor stiffened the dermis in normal artificial sea water (ASW) but did not stiffen the soft dermis in Ca2+-free ASW. It also stiffened the dermis that had been converted to the standard state in Ca2+-free ASW by the action of tensilin. These results suggest that the factor produces the stiff dermis from the standard state but cannot work as a stiffener on the soft dermis. Its addition to longitudinal muscles of the sea cucumber produced no effects, suggesting that its effect is specific to the catch connective tissue. Its stiffening activity was susceptible to trypsin, meaning that it is a polypeptide, and its molecular mass estimated from gel filtration chromatography was 2.4 kDa.
Causes and Consequences of Fluctuating Coelomic Pressure in Sea Urchins.
Venue: The Biological Bulletin

We measured coelomic pressure in sea urchins to determine whether it was high enough to support a pneu hypothesis of growth. In Strongylocentrotus purpuratus the pressure was found to fluctuate rhythmically about a mean of -8 Pa, and was negative for 70% of the time. This is at variance with the theoretically required positive pressures of the pneu hypothesis. Furthermore, there were no sustained significant differences between the pressure patterns of fed and starved urchins, presumed to be growing and not growing, respectively. The rhythmical fluctuations in pressure were caused by movements of the lantern which changed the curvature and tension of the peristomial membrane. We developed a mathematical and morphological model relating lantern movements, membrane tension, and pressure, that correctly predicts the magnitude of the fluctuations. Pressures predicted by the model depend also on coelomic volume changes. In Lytechinus variegatus simultaneous retraction of the podia, which causes expansion of the ampullae, resulted in an 8.8 Pa increase in coelomic pressure, relative to the pressure during simultaneous podial protraction.
Magnetosome formation in prokaryotes
Venue: Nature Reviews Microbiology

Magnetotactic bacteria were discovered almost 30 years ago, and for many years and many different reasons, the number of researchers working in this field was few and progress was slow. Recently, however, thanks to the isolation of new strains and the development of new techniques for manipulating these strains, researchers from several laboratories have made significant progress in elucidating the molecular, biochemical, chemical and genetic bases of magnetosome formation and understanding how these unique intracellular organelles function. We focus here on this progress.
Emergency networking: famine relief in ant colonies
Venue: Animal Behaviour

Resource distribution is fundamental to social organization, but it poses a dilemma. How to facilitate the spread of useful resources but restrict harmful substances? This dilemma reaches a zenith in famine relief. Survival depends on distributing food fast but that could increase vulnerability to poisons. We tested how Temnothorax albipennis ants solve this dilemma in the distribution of honey solution after 48 h of starvation in four colonies with individually marked workers. We constructed the complete network of liquid food transmission (trophallaxis) between individuals. Within the first 30 min of famine relief, 95% of the workers received food and the distribution rate was an order of magnitude faster compared to the controls. We tested the assumptions of a simple analytical model that best fitted our data. Good mixing during famine relief was facilitated by the movement of internal workers away from the brood pile and the movement of foragers with food away from the nest entrance. This is intriguing because T. albipennis workers have spatial fidelity zones and in the controls internal and external workers were segregated. We discovered that colony vulnerability to poisons during famine relief might be mitigated by: (1) the dilution of food from the same source through mixing, (2) the concentration of food in workers positioned midway between the colony centre and its periphery and (3) the existence of living 'silos'. The latter are expendable foragers, who stay inside the nest and store food during famine relief, thus acting as potential disposable testers for food toxicity.
How the Cucumber Tendril Coils and Overwinds
Venue: Science

Curls Beget More Curls Cucumber tendrils reach up to find an attachment, and then coil to shorten and drag the plant up toward the sunlight. Gerbode et al. (p. 1087) analyzed the biomechanics of cucumber tendril coiling. The process depends on a thin layer of cells within the tendril that becomes lignified during the coiling process. A construct of pre-strained silicon sheets, fabric ribbon, and copper wire reproduced the coiling functions in abiotic materials. Physical and mathematical models explained the peculiar response by which the cucumber tendril initially overwinds when pulled further. Plants climb via lifelines that are a mix of strength and flexibility. The helical coiling of plant tendrils has fascinated scientists for centuries, yet the underlying mechanism remains elusive. Moreover, despite Darwin’s widely accepted interpretation of coiled tendrils as soft springs, their mechanical behavior remains unknown. Our experiments on cucumber tendrils demonstrate that tendril coiling occurs via asymmetric contraction of an internal fiber ribbon of specialized cells. Under tension, both extracted fiber ribbons and old tendrils exhibit twistless overwinding rather than unwinding, with an initially soft response followed by strong strain-stiffening at large extensions. We explain this behavior using physical models of prestrained rubber strips, geometric arguments, and mathematical models of elastic filaments. Collectively, our study illuminates the origin of tendril coiling, quantifies Darwin’s original proposal, and suggests designs for biomimetic twistless springs with tunable mechanical responses.
Energetic Cost of Locomotion in Kangaroos
Venue: Nature

THE hopping of kangaroos is reminiscent of a bouncing ball or the action of a pogo stick. This suggests a significant storage and recovery of energy in elastic elements. One might surmise that the kangaroo's first hop would require a large amount of energy whereas subsequent hops could rely extensively on elastic rebound. If this were the case, then the kangaroo's unusual saltatory mode of locomotion should be an energetically inexpensive way to move.
Signatures of functional constraint at aye-aye opsin genes: the potential of adaptive color vision in a nocturnal primate.
Venue: Molecular Biology and Evolution

While color vision perception is thought to be adaptively correlated with foraging efficiency for diurnal mammals, those that forage exclusively at night may not need color vision nor have the capacity for it. Indeed, although the basic condition for mammals is dichromacy, diverse nocturnal mammals have only monochromatic vision, resulting from functional loss of the short-wavelength sensitive opsin gene. However, many nocturnal primates maintain intact two opsin genes and thus have dichromatic capacity. The evolutionary significance of this surprising observation has not yet been elucidated. We used a molecular population genetics approach to test evolutionary hypotheses for the two intact opsin genes of the fully nocturnal aye-aye (Daubentonia madagascariensis), a highly unusual and endangered Madagascar primate. No evidence of gene degradation in either opsin gene was observed for any of 8 aye-aye individuals examined. Furthermore, levels of nucleotide diversity for opsin gene functional sites were lower than those for 15 neutrally evolving intergenic regions (>25 kb in total), which is consistent with a history of purifying selection on aye-aye opsin genes. The most likely explanation for these findings is that dichromacy is advantageous for aye-ayes despite their nocturnal activity pattern. We speculate that dichromatic nocturnal primates may be able to perceive color while foraging under moonlight conditions, and suggest that behavioral and ecological comparisons among dichromatic and monochromatic nocturnal primates will help to elucidate the specific activities for which color vision perception is advantageous.