nils-herrmann/clean_scirepeval huggingface dataset:
Modeling Pseudomonas syringae Ice-Nucleation Protein as aβ-Helical Protein
Venue: Biophysical Journal

Antifreeze proteins (AFPs) inhibit the growth of ice, whereas ice-nucleation proteins (INPs) promote its formation. Although the structures of several AFPs are known, the structure of INP has been modeled thus far because of the difficulty in determining membrane protein structures. Here, we present a novel model of an INP structure from Pseudomonas syringae based on comparison with two newly determined insect AFP structures. The results suggest that both this class of AFPs and INPs may have a similar beta-helical fold and that they could interact with water through the repetitive TXT motif. By theoretical arguments, we show that the distinguishing feature between an ice inhibitor and an ice nucleator lies in the size of the ice-interacting surface. For INPs, the larger surface area acts as a template that is larger than the critical ice embryo surface area required for growth. In contrast, AFPs are small enough so that they bind to ice and inhibit further growth without acting as a nucleator.
Divergent investment strategies of Acacia myrmecophytes and the coexistence of mutualists and exploiters
Venue: Proceedings of the National Academy of Sciences of the United States of America

Ant-plant interactions represent a diversity of strategies, from exploitative to mutualistic, and how these strategies evolve is poorly understood. Here, we link physiological, ecological, and phylogenetic approaches to study the evolution and coexistence of strategies in the Acacia–Pseudomyrmex system. Host plant species represented 2 different strategies. High-reward hosts produced significantly more extrafloral nectar (EFN), food bodies, and nesting space than low-reward hosts, even when being inhabited by the same species of ant mutualist. High-reward hosts were more effectively defended against herbivores and exploited to a lower extent by nondefending ants than low-reward hosts. At the phenotypic level, secretion of EFN and ant activity were positively correlated and a mutualistic ant species induced nectar secretion, whereas a nondefending exploiter did not. All of these mechanisms contribute to the stable association of high-reward hosts with defending ant species. However, exploiter ants are less dependent on the host-derived rewards and can colonize considerable proportions of the low-reward hosts. Mapping these strategies onto phylogenetic trees demonstrated that the low-reward hosts represent the derived clade within a monophyletic group of obligate ant plants and that the observed exploiter ant species evolved their strategy without having a mutualistic ancestor. We conclude that both types of host strategies coexist because of variable net outcomes of different investment–payoff regimes and that the effects of exploiters on the outcome of mutualisms can, thus, increase the diversity within the taxa involved.
Comparative morphology of the tapetum lucidum (among selected species).
Venue: Veterinary Ophthalmology

The phenomenon of 'eye-shine' is seen in a variety of animal species, and is generally thought to be related to the presence of an intraocular reflecting structure, the tapetum lucidum. The tapetum lucidum is a biologic reflector system that is a common feature in the eyes of vertebrates. It normally functions to provide the light-sensitive retinal cells with a second opportunity for photon-photoreceptor stimulation, thereby enhancing visual sensitivity at low light levels. The tapetum lucidum is presented here according to a classification based on the location, as well as the composition, of this reflective layer. Finally, the physical and chemical properties, as well as the origins of the different tapeta lucida, are discussed and compared.



The anatomic and biochemical aspects of the tapetum lucidum in various vertebrates are examined. Morphologic observations were made from paraffin and plastic embedded specimens. Specimens were treated with traditional stains and observed by light and transmission electron microscopy.



Some species (primates, squirrels, birds, red kangaroo and pig) do not have this structure and they usually are diurnal animals. In vertebrates, the tapetum lucidum exhibits diverse structure, organization and composition. Therefore, the retinal tapetum (teleosts, crocodilians, marsupials, fruit bat), the choroidal guanine tapetum (elasmobranchs), the choroidal tapetum cellulosum (carnivores, rodents, cetacea), and the choroidal tapetum fibrosum (cow, sheep, goat, horse) are described.



The tapetum lucidum represents a remarkable example of neural cell and tissue specialization as an adaptation to a dim light environment and, despite these differences, all tapetal variants act to increase retinal sensitivity by reflecting light back through the photoreceptor layer. These variations regarding both its location and structure, as well as the choice of reflective material, may represent selective visual adaptations associated with their feeding behavior, in response to the use of specific wavelengths and amount of reflectance required.
The Implications of Niche Construction and Ecosystem Engineering for Conservation Biology
Venue: BioScience

Although strategies to conserve biodiversity (e.g., the establishment of reserves and the management of flagship, umbrella, indicator, and keystone species) are valuable, they entail practical and conceptual difficulties. A focus on niche construction and ecosystem engineering, however, could provide new insights and methods for conservation biology. Many organisms modulate the availability of resources to other species by causing state changes in biotic or abiotic materials (ecosystem engineering), in the process frequently changing the selection to which the ecosystem engineers and other organisms are exposed (niche construction). We describe growing evidence that organisms have significant nontrophic impacts on ecosystem structure, function, and biodiversity, and outline established means of identifying key species involved in niche construction. On the basis of this engineering perspective, we propose a number of measures that could be employed to enhance conservation efforts.
Freeze tolerance and intolerance as strategies of winter survival in terrestrially-hibernating amphibians.
Venue: Comparative Biochemistry and Physiology Part A: Physiology

The ability to tolerate extracellular freezing as an adaptation for winter survival was tested in seven species of terrestrially-hibernating amphibians found in eastern Canada. All species had only moderate supercooling abilities, with whole animal supercooling points of -1.5 to -3 degrees C. Two salamander species, Plethodon cinereus and Ambystoma laterale, and the toad, Bufo americanus, were freezing intolerant and were killed when frozen for 24 hr at temperatures just below their supercooling points. The major winter strategy of these animals appears to behavioural avoidance of subzero temperatures. Four species of frogs Rana sylvatica, Hyla versicolor, Hyla crucifer and Pseudacris triseriata, survived extracellular freezing at moderate subzero temperatures (-2 to -4 degrees C) for periods of time ranging up to 2 weeks. All four frog species accumulated low molecular weight carbohydrates as cryoprotectants, glycerol being the major cryoprotectant in adult H. versicolor, while immature adults of this species as well as the other three species all produced high levels of glucose as the cryoprotectant.
Cryo-EM Model of the Bullet-Shaped Vesicular Stomatitis Virus
Venue: Science

VSV in 3D Rhabdoviruses are a family of negative-stranded RNA viruses that includes rabies virus, which have a characteristic bullet shape. Though structures of individual rhabdovirus proteins have been reported, how these are organized into a bullet shape has remained unclear. Now, Ge et al. (p. 689) report a cryo-electron microscopy structure of a model rhabdovirus, vesicular stomatitis virus. The structural data and examination of mutants allows modeling of virion assembly. The structure of a negative-strand RNA virus suggests how bullet-shaped rhabdoviruses assemble. Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo–electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer.
Deconstruction for Reconstruction: The Role of Proteolysis in Neural Plasticity and Disease
Venue: Neuron

The brain changes in response to experience and altered environment. This neural plasticity is largely mediated by morphological and functional modification of synapses, a process that depends on both synthesis and degradation of proteins. It is now clear that regulated proteolysis plays a critical role in the remodeling of synapses, learning and memory, and neurodevelopment. Here, we highlight the mechanisms and functions of proteolysis in synaptic plasticity and discuss its alteration in disease states.
Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics
Venue: Proceedings of The Royal Society B: Biological Sciences

Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems.
Wet but not slippery: boundary friction in tree frog adhesive toe pads
Venue: Journal of the Royal Society Interface

Tree frogs are remarkable for their capacity to cling to smooth surfaces using large toe pads. The adhesive skin of tree frog toe pads is characterized by peg-studded hexagonal cells separated by deep channels into which mucus glands open. The pads are completely wetted with watery mucus, which led previous authors to suggest that attachment is solely due to capillary and viscous forces generated by the fluid-filled joint between the pad and the substrate. Here, we present evidence from single-toe force measurements, laser tweezer microrheometry of pad mucus and interference reflection microscopy of the contact zone in Litoria caerulea, that tree frog attachment forces are significantly enhanced by close contacts and boundary friction between the pad epidermis and the substrate, facilitated by the highly regular pad microstructure.
Iridescent Colors of Hummingbird Feathers
Venue: Journal of the Optical Society of America

The reflectance spectra of iridescent hummingbird feathers were measured spectrophotometrically for many species, and the structure of the iridescent parts of such feathers investigated by electron microscopy. In the direction normal to the iridescent feather surfaces the structure is found to be periodic in optical dimensions. It consists of stacks of 7–15 elliptical platelets of a material with refractive index ~2, each containing a structurally reinforced air gap. To interpret the reflectance spectra in terms of the surface structures, a theory is given of reflection coefficients of stratified media with analytic refractive-index variations. The theory is applied to the iridescence of hummingbird feathers and accounts quantitatively for the iridescent colors as interference colors by reflection from the observed feather structures.
On the Utility of the Saw of the Sawfish
Venue: Copeia

cheeks and opercles silvery, the latter with bluish reflections; snout entirely transparent except at tip where there is some duskiness that extends a short way backward on sides. The colors have changed very little but there is no longer any silver on the opercles, which are black due to the black lining of the gill-cavity showing through the transparent bones. The specimen agrees with the excellent description of the type in all characters not mentioned above.
The lantern shark's light switch: turning shallow water crypsis into midwater camouflage
Venue: Biology Letters

Bioluminescence is a common feature in the permanent darkness of the deep-sea. In fishes, light is emitted by organs containing either photogenic cells (intrinsic photophores), which are under direct nervous control, or symbiotic luminous bacteria (symbiotic photophores), whose light is controlled by secondary means such as mechanical occlusion or physiological suppression. The intrinsic photophores of the lantern shark Etmopterus spinax were recently shown as an exception to this rule since they appear to be under hormonal control. Here, we show that hormones operate what amounts to a unique light switch, by acting on a chromatophore iris, which regulates light emission by pigment translocation. This result strongly suggests that this shark's luminescence control originates from the mechanism for physiological colour change found in shallow water sharks that also involves hormonally controlled chromatophores: the lantern shark would have turned the initial shallow water crypsis mechanism into a midwater luminous camouflage, more efficient in the deep-sea environment.
Adaptable Defense: A Nudibranch Mucus Inhibits Nematocyst Discharge and Changes With Prey Type
Venue: The Biological Bulletin

Nudibranchs that feed on cnidarians must defend themselves from the prey’s nematocysts or risk their own injury or death. While a nudibranch’s mucus has been thought to protect the animal from nematocyst discharge, an inhibition of discharge by nudibranch mucus has never been shown. The current study investigated whether mucus from the aeolid nudibranch Aeolidia papillosa would inhibit nematocyst discharge from four species of sea anemone prey. Sea anemone tentacles were contacted with mucus-coated gelatin probes, and nematocyst discharge was quantified and compared with control probes of gelatin only. Mucus from A. papillosa inhibited the discharge of nematocysts from sea anemone tentacles. This inhibition was specifically limited to the anemone species on which the nudibranch had been feeding. When the prey species was changed, the mucus changed within 2 weeks to inhibit the nematocyst discharge of the new prey species. The nudibranchs apparently produce the inhibitory mucus rather than simply becoming coated in anemone mucus during feeding. Because of the intimate association between most aeolid nudibranchs and their prey, an adaptable mucus protection could have a significant impact on the behavior, distribution, and life history of the nudibranchs.
Effect of blood removal and infusion on gull salt gland secretion
Venue: Journal of Comparative Physiology B-biochemical Systemic and Environmental Physiology

Summary1.The effect of blood removal and addition on salt gland secretion was studied in freshwater and seawater acclimated gulls,Larus glaucescens.2.In contrast to published reports that blood removal decreased and blood infusion increased salt gland secretion in ducks, neither blood removal nor addition had an effect on concentration or volume of salt gland secretion in gulls.
Defoliation of interior Douglas-fir elicits carbon transfer and stress signalling to ponderosa pine neighbors through ectomycorrhizal networks
Venue: Scientific Reports

Extensive regions of interior Douglas-fir (Pseudotsuga menziesii var. glauca, IDF) forests in North America are being damaged by drought and western spruce budworm (Choristoneura occidentalis). This damage is resulting from warmer and drier summers associated with climate change. To test whether defoliated IDF can directly transfer resources to ponderosa pine (Pinus ponderosae) regenerating nearby, thus aiding in forest recovery, we examined photosynthetic carbon transfer and defense enzyme response. We grew pairs of ectomycorrhizal IDF ‘donor’ and ponderosa pine ‘receiver’ seedlings in pots and isolated transfer pathways by comparing 35 μm, 0.5 μm and no mesh treatments; we then stressed IDF donors either through manual defoliation or infestation by the budworm. We found that manual defoliation of IDF donors led to transfer of photosynthetic carbon to neighboring receivers through mycorrhizal networks, but not through soil or root pathways. Both manual and insect defoliation of donors led to increased activity of peroxidase, polyphenol oxidase and superoxide dismutase in the ponderosa pine receivers, via a mechanism primarily dependent on the mycorrhizal network. These findings indicate that IDF can transfer resources and stress signals to interspecific neighbors, suggesting ectomycorrhizal networks can serve as agents of interspecific communication facilitating recovery and succession of forests after disturbance.
Mechanism of infrared detection and transduction by beetle Melanophila Acuminata
Venue: Journal of Bionic Engineering

The Melanophila acuminata beetle is attracted to forest fires via a pair of infrared sensory organs composed of sensilla. Our histological work showed that each sensillum contains lipid layers surrounding a protein layer and a unique polysaccharide base that is associated with a neuron to each sensillum. Infrared microscopy showed that the protein region maximally absorbs infrared radiation at 3 μm wavelength and at 10 μm, which corresponds to the known radiation produced by forest fires at 3 μm. Mathematical calculations showed that the physical properties of the sensilla are such that the expected temperature rise is insufficient for transduction of the infrared signal through mechanical means or as a thermal receptor as previously thought; hence the protein plays the pivotal role in perception of single photons and transmission of the signal within the sensilla.
Functional morphology and movements of the proboscis of Lepidoptera (Insecta)
Venue: Zoomorphology

SummaryThe mouthparts of Lepidoptera were investigated in a number of species by morphological and cinematographical methods. Both the galeae (which compose the proboscis) and the basal maxillary components (stipites) were studied in the resting position, in motion, and during feeding. In the resting position the proboscis is coiled so tightly that the surfaces of the consecutive coils are in close contact and the outermost coil touches the ventral side of the head. Cuticular processes of the galeal wall interlock between the coils in this position. In the investigated species they occur on the galeal wall and on the ventral side of the head in varying number and distribution. By the extension of the basal galeal joint, the coiled proboscis is released from its resting position and is elevated continuously. It uncoils in 3–5 steps which effect the entire length simultaneously. Each uncoiling step occurs synchronously with a compression of the stipital tubes on either side of the body. These compression movements pump hemolymph into the galeae. In all investigated Lepidoptera the uncoiled proboscis shows a distinct downward bend at a certain point which is also detectable in anaesthetized or freshly killed animals in some species. This feeding position and the movements of the uncoiled proboscis are similar in all species despite the intrinsic galeal muscles being variously arranged in the galeal lumen in different Lepidoptera. When comparing cross-sections through corresponding regions of coiled and uncoiled proboscises, the curvatures of the dorsal galeal walls remain unchanged. Coiling of the proboscis starts at the tip and progresses to the base. After coiling the proboscis tightly beneath the head, the diameter of the spiral widens due to its elastic properties until the proboscis props itself against the ventral side of the head. This elastic effect combined with the interlocking cuticular processes seems to be responsible for the resting position of the proboscis.
Revisiting synchronous gamete release by fucoid algae in the intertidal zone: fertilization success and beyond?
Venue: Integrative and Comparative Biology

In the marine environment, both external fertilization and settlement are critical processes linking adult and early juvenile life-history phases. The success of both processes can be tightly linked in organisms lacking a larval dispersive phase. This review focuses on synchronous gamete release (= spawning) in fucoid algae. These brown macroalgae are important components of temperate intertidal ecosystems in many parts of the world, and achieve synchronous gamete release by integrating various environmental signals. Photosynthesis-dependent sensing of boundary-layer inorganic carbon fluxes, as well as blue light and green light signals, possibly perceived via a chloroplast-located photoreceptor(s), are integrated into pathways that restrict gamete release to periods of low water motion. Avoidance of turbulent and/or high flow conditions in the intertidal zone allows high levels of fertilization success in this group. Temporal patterns and synchrony of spawning in natural populations are reviewed. Most species/populations have a more or less semilunar periodicity, although phase differences occur both between and within species at different geographical locations, raising the possibility that tidal and diurnal cues are more important than semilunar cues in entraining the response. The ecological and evolutionary role(s) of synchronous spawning in the intertidal zone are considered, particularly with regard to hybridization/reproductive isolation in species complexes, and reproductive versus recruitment assurance in the intertidal zone, where synchronous spawning during calm periods may be important for recruitment assurance in addition to fertilization success. Ways in which the roles of spawning synchrony could be tested in closely related species with contrasting mating systems (outcrossing versus selfing) are discussed.