nils-herrmann/clean_scirepeval huggingface dataset:
Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases.
Venue: Gene

The epithelial sodium channel (ENaC) is composed of three homologous subunits and allows the flow of Na(+) ions across high resistance epithelia, maintaining body salt and water homeostasis. ENaC dependent reabsorption of Na(+) in the kidney tubules regulates extracellular fluid (ECF) volume and blood pressure by modulating osmolarity. In multi-ciliated cells, ENaC is located in cilia and plays an essential role in the regulation of epithelial surface liquid volume necessary for cilial transport of mucus and gametes in the respiratory and reproductive tracts respectively. The subunits that form ENaC (named as alpha, beta, gamma and delta, encoded by genes SCNN1A, SCNN1B, SCNN1G, and SCNN1D) are members of the ENaC/Degenerin superfamily. The earliest appearance of ENaC orthologs is in the genomes of the most ancient vertebrate taxon, Cyclostomata (jawless vertebrates) including lampreys, followed by earliest representatives of Gnathostomata (jawed vertebrates) including cartilaginous sharks. Among Euteleostomi (bony vertebrates), Actinopterygii (ray finned-fishes) branch has lost ENaC genes. Yet, most animals in the Sarcopterygii (lobe-finned fish) branch including Tetrapoda, amphibians and amniotes (lizards, crocodiles, birds, and mammals), have four ENaC paralogs. We compared the sequences of ENaC orthologs from 20 species and established criteria for the identification of ENaC orthologs and paralogs, and their distinction from other members of the ENaC/Degenerin superfamily, especially ASIC family. Differences between ENaCs and ASICs are summarized in view of their physiological functions and tissue distributions. Structural motifs that are conserved throughout vertebrate ENaCs are highlighted. We also present a comparative overview of the genotype-phenotype relationships in inherited diseases associated with ENaC mutations, including multisystem pseudohypoaldosteronism (PHA1B), Liddle syndrome, cystic fibrosis-like disease and essential hypertension.
Microtubule catastrophe and rescue.
Venue: Current Opinion in Cell Biology

Microtubules are long cylindrical polymers composed of tubulin subunits. In cells, microtubules play an essential role in architecture and motility. For example, microtubules give shape to cells, serve as intracellular transport tracks, and act as key elements in important cellular structures such as axonemes and mitotic spindles. To accomplish these varied functions, networks of microtubules in cells are very dynamic, continuously remodeling through stochastic length fluctuations at the ends of individual microtubules. The dynamic behavior at the end of an individual microtubule is termed 'dynamic instability'. This behavior manifests itself by periods of persistent microtubule growth interrupted by occasional switching to rapid shrinkage (called microtubule 'catastrophe'), and then by switching back from shrinkage to growth (called microtubule 'rescue'). In this review, we summarize recent findings which provide new insights into the mechanisms of microtubule catastrophe and rescue, and discuss the impact of these findings in regards to the role of microtubule dynamics inside of cells.
Energy transfer and trapping in photosystem I.
Venue: Biochimica et Biophysica Acta

The primary processes in all photosynthetic systems involve the absorption of energy from (sun) light by chromophores in a light harvesting antenna, and the subsequent transfer of this energy to a reaction centre (RC) site where the energy is `trapped' by means of a stable charge separation. Photosystem (PS) I is one of two such photosystems in oxygenic photosynthesis. When co-operating with PS II it uses the energy of light to transfer electrons from plastocyanin or soluble cytochrome c6 to ferredoxin and eventually to NADP. In an alternative pathway, the electrons from ferredoxin are transferred back to plastocyanin via the cytochrome b6f complex. This cyclic electron transport, which does not require the input of free energy by PS II, results in a transmembrane electrochemical gradient that can be used to produce ATP. In plants and green algae the PS I complex consists of two separable functional units: the PS I core, and the light harvesting complex (LHC) I peripheral antenna. The PS I complex in cyanobacteria does not possess the peripheral LHCI antenna, but since the PS I core complexes of cyanobacteria bear a large resemblance to the core complex of plants, a direct comparison of the energy transfer and trapping properties of these complexes is justi¢ed .
Adaptations of metabolism for freeze tolerance in the gray tree frog, Hyla versicolor
Venue: Canadian Journal of Zoology

Biochemical adaptations allowing the natural survival of extracellular freezing were examined in the gray tree frog, Hyla versicolor. Laboratory-reared immature adults froze between −1 and −1.5 °C and survived 5 days of freezing at −2 °C as well as repeated rapid bouts of freeze–thaw. Measurements of ice content showed 41.5% of total body water frozen. Glycerol accumulated as the cryoprotectant in sexually mature adult H. versicolor (423 μmol/mL in blood) while both glycerol and glucose accumulated in immature adults (16.3 ± 6.8 and 25.9 ± 11.6 μmol/mL in blood, respectively). Cryoprotectant synthesis was freezing stimulated only and did not occur over long-term cold acclimation at 0 to 1 °C. Cryoprotectant synthesis was correlated with a 203% increase in liver total phosphorylase activity and an increase in phosphorylase a content from 40 to 60%. Activities of 15 other enzymes of intermediary metabolism were determined in liver and leg muscle; activities of most enzymes increased with freezing exposure a...
Ultrastructure and geographic distribution of the genus Paradermamoeba (Gymnamoebia, Thecamoebidae)
Venue: European Journal of Protistology

The genus Paradermamoeba includes two species with a distinct and unusually thick cell coat. This coat consists of densely packed helical glycostyles, up to 520 nm in length. Perhaps due to the impenetrable properties of the cell coat, we were unable to achieve satisfactory quality of EM fixation in these species until recently. In this study the treatment of cells with dilute Triton X-100 detergent prior to fixation has improved preservation of the ultrastructure of both Paradermamoeba species. Paradermamoeba valamo has an unusual central nucleolus consisting of densely packed fibrils of nucleolar material. A newly isolated strain of P. levis from a UK pond, Priest Pot, forms rounded, single-walled cysts. Both species have enigmatic trichocyst-like bodies in the cytoplasm. Despite the presence of a thick and highly differentiated cell coat, dictyosomes in both species are few and are not more developed than in many other species of gymnamoebae. Neither ultrastructure nor LM morphology indicates the phylogenetic position of Paradermamoeba. It seems that the family Thecamoebidae is a heterogeneous assemblage of unrelated genera. Recent isolation of both P. valamo and P. levis in Switzerland and in the UK indicates the wide distribution of both species in Europe.
Structure, mechanism and mechanical properties of pupal attachment in Greta oto (Lepidoptera: Nymphalidae: Ithomiinae)
Venue: Entomological Science

The structure and mechanism of pupal attachment are described for the nymphalid Greta oto using electron microscopy, and high‐speed and time‐lapse photography. The cremaster is composed of a 3‐D array of hooked setae that engage with silk fibers spun into layers in a pad on the lower leaf surface. Each seta comprises a shaft terminating in a strongly curved hook, tipped with two lateral barbs. These hook into the silk pad, which is densely laid and built‐up in the central portion, flattening out peripherally. Time‐lapse photography showed that silk pad construction by fifth instar larvae is completed in four distinct spinning movements, producing a random fiber arrangement. It is proposed that such a fiber arrangement provides isotropic strength, giving greater flexibility to the attachment. The cremaster is attached to the silk pad by a series of lateral movements of the pupa's posterior abdomen. This movement, together with the shape of the setal hooks, is thought to be integral to the attachment process. Tensile loading tests showed that attachment failure is due to the breakage of the silk pad, which undergoes gradual destruction before releasing the cremaster. The attachment was found to have high tensile strength and fracture toughness, both of which suggest that it has evolved for the dual purpose of preventing the pupa being pulled from the leaf by a predator and preventing the attachment being weakened by wind, which causes the pupa to swing.
Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinoceros
Venue: Scientific Reports

The West African Gaboon viper (Bitis rhinoceros) is a master of camouflage due to its colouration pattern. Its skin is geometrically patterned and features black spots that purport an exceptional spatial depth due to their velvety surface texture. Our study shades light on micromorphology, optical characteristics and principles behind such a velvet black appearance. We revealed a unique hierarchical pattern of leaf-like microstructures striated with nanoridges on the snake scales that coincides with the distribution of black colouration. Velvet black sites demonstrate four times lower reflectance and higher absorbance than other scales in the UV – near IR spectral range. The combination of surface structures impeding reflectance and absorbing dark pigments, deposited in the skin material, provides reflecting less than 11% of the light reflected by a polytetrafluoroethylene diffuse reflectance standard in any direction. A view-angle independent black structural colour in snakes is reported here for the first time.
Most fertilizing mouse spermatozoa begin their acrosome reaction before contact with the zona pellucida during in vitro fertilization
Venue: Proceedings of the National Academy of Sciences of the United States of America

To fuse with oocytes, spermatozoa of eutherian mammals must pass through extracellular coats, the cumulus cell layer, and the zona pellucida (ZP). It is generally believed that the acrosome reaction (AR) of spermatozoa, essential for zona penetration and fusion with oocytes, is triggered by sperm contact with the zona pellucida. Therefore, in most previous studies of sperm–oocyte interactions in the mouse, the cumulus has been removed before insemination to facilitate the examination of sperm–zona interactions. We used transgenic mouse spermatozoa, which enabled us to detect the onset of the acrosome reaction using fluorescence microscopy. We found that the spermatozoa that began the acrosome reaction before reaching the zona were able to penetrate the zona and fused with the oocyte's plasma membrane. In fact, most fertilizing spermatozoa underwent the acrosome reaction before reaching the zona pellucida of cumulus-enclosed oocytes, at least under the experimental conditions we used. The incidence of in vitro fertilization of cumulus-free oocytes was increased by coincubating oocytes with cumulus cells, suggesting an important role for cumulus cells and their matrix in natural fertilization.
Functional anatomy of the valves in the ambulacral system of sea urchins (Echinodermata, Echinoida)
Venue: Zoomorphology

SummaryThe water vascular system of sea urchins is examined with special reference to the valves positioned between the radial vessel and the ampullae of the tube feet. The lips of the valve protrude into the ampulla. Thus the valve functions mainly like a check valve that allows the unidirectional flow of fluid towards the ampulla. Each ampulla-tube foot compartment acts as a semi-autonomous hydraulic system. The lumina of the ampulla and the tube foot are lined with myoepithelia except for the interconnecting channels that pierce the ambulacral plate. The contraction of the ampulla results in an increasing hydraulic pressure that protrudes the tube foot, provided that the valve is closed. The retraction of the tube foot results in a backflow of fluid independent of the condition of the valve. The lips of the valve are folds of the hydrocoel epithelium. The pore slit lies in the midline. The perradial faces of the lips are covered with the squamous epithelium of the lateral water vessel. The ampullar faces are specialized parts of the ampulla myoepithelium. Turgescent cells which form incompressible cushions take the place of the support cells. The valve myocytes run parallel to the pore slit and form processes that run along the base of the ampulla and the perradial channel up to the podial retractor muscle. The findings lead to the hypothesis of multiple control of the ampulla-tube foot system: (1) The mutual activity of the ampulla and the tube foot is indirectly controlled by the lateral and podial nerves which release transmitter substances that diffuse through the connective tissue up to the muscle layers. (2) A muscle-to-muscle conduction causes the simultaneous contraction of the ampulla or the podial retractor muscles. (3) The valve muscles are directly controlled by the processes of the valve myocytes which make contact with the podial retractor. In extreme conditions a backflow of hydrocoel fluid towards the radial water vessel occurs.
Allometry of Alarm Calls: Black-Capped Chickadees Encode Information About Predator Size
Venue: Science

Many animals produce alarm signals when they detect a potential predator, but we still know little about the information contained in these signals. Using presentations of 15 species of live predators, we show that acoustic features of the mobbing calls of black-capped chickadees (Poecile atricapilla) vary with the size of the predator. Companion playback experiments revealed that chickadees detect this information and that the intensity of mobbing behavior is related to the size and threat of the potential predator. This study demonstrates an unsuspected level of complexity and sophistication in avian alarm calls.
Bioinspired synthesis of mesoporous silicas
Venue: Current Opinion in Solid State & Materials Science

Recent years have witnessed rapid growth in the number of new investigations at the interface of materials chemistry and biology. This review highlights the recent developments in the studies of protein-mediated silica biomineralization in diatoms and the “downscaling” and “upscaling” models derived thereof, as well as the recent progress in the fabrication of artificial silicas with novel pore structures and morphologies at different length scales based on these new insights into biosilica formation.
Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria.
Venue: Science

Abundant, micrometer-scale, spherical aggregates of 2- to 5-nanometer-diameter sphalerite (ZnS) particles formed within natural biofilms dominated by relatively aerotolerant sulfate-reducing bacteria of the family Desulfobacteriaceae. The biofilm zinc concentration is about 10(6) times that of associated groundwater (0.09 to 1.1 parts per million zinc). Sphalerite also concentrates arsenic (0.01 weight %) and selenium (0.004 weight %). The almost monomineralic product results from buffering of sulfide concentrations at low values by sphalerite precipitation. These results show how microbes control metal concentrations in groundwater- and wetland-based remediation systems and suggest biological routes for formation of some low-temperature ZnS deposits.
Skin and Aestivational Cocoon of the Aquatic Amphibian, Siren intermedia Le Conte
Venue: Copeia

The skin of Siren intermedia is fully metamorphosed, amphibian-like, and specialized in its cocoon-producing function. During aestivation in burrows in the bottoms of dry ponds, epidermal and dermal skin glands secrete a cocoon which covers the entire body except the mouth. This structure, remarkably like the cocoons of African lungfishes, retards desiccation and permits sirens to remain in periodically dry, aquatic environments. This adaptive strategy may be alternative to that of avoiding drought by overland movement to nearby water.
Mechanics without muscle: biomechanical inspiration from the plant world.
Venue: Integrative and Comparative Biology

Plant and animal biomechanists have much in common. Although their frame of reference differs, they think about the natural world in similar ways. While researchers studying animals might explore airflow around flapping wings, the actuation of muscles in arms and legs, or the material properties of spider silk, researchers studying plants might explore the flow of water around fluttering seaweeds, the grasping ability of climbing vines, or the material properties of wood. Here we summarize recent studies of plant biomechanics highlighting several current research themes in the field: expulsion of high-speed reproductive projectiles, generation of slow movements by shrinking and swelling cell walls, effects of ontogenetic shifts in mechanical properties of stems, flexible reconfiguration and material properties of seaweeds under crashing waves, and the development of botanically-inspired commercial products. Our hope is that this synopsis will resonate with both plant and animal biologists, encourage cross-pollination across disciplines, and promote fruitful interdisciplinary collaborations in the future.
Bug juice: harvesting electricity with microorganisms
Venue: Nature Reviews Microbiology

It is well established that some reduced fermentation products or microbially reduced artificial mediators can abiotically react with electrodes to yield a small electrical current. This type of metabolism does not typically result in an efficient conversion of organic compounds to electricity because only some metabolic end products will react with electrodes, and the microorganisms only incompletely oxidize their organic fuels. A new form of microbial respiration has recently been discovered in which microorganisms conserve energy to support growth by oxidizing organic compounds to carbon dioxide with direct quantitative electron transfer to electrodes. These organisms, termed electricigens, offer the possibility of efficiently converting organic compounds into electricity in self-sustaining systems with long-term stability.
Intracellular invasion of green algae in a salamander host
Venue: Proceedings of the National Academy of Sciences of the United States of America

The association between embryos of the spotted salamander (Ambystoma maculatum) and green algae (“Oophila amblystomatis” Lamber ex Printz) has been considered an ectosymbiotic mutualism. We show here, however, that this symbiosis is more intimate than previously reported. A combination of imaging and algal 18S rDNA amplification reveals algal invasion of embryonic salamander tissues and cells during development. Algal cells are detectable from embryonic and larval Stages 26–44 through chlorophyll autofluorescence and algal 18S rDNA amplification. Algal cell ultrastructure indicates both degradation and putative encystment during the process of tissue and cellular invasion. Fewer algal cells were detected in later-stage larvae through FISH, suggesting that the decline in autofluorescent cells is primarily due to algal cell death within the host. However, early embryonic egg capsules also contained encysted algal cells on the inner capsule wall, and algal 18S rDNA was amplified from adult reproductive tracts, consistent with oviductal transmission of algae from one salamander generation to the next. The invasion of algae into salamander host tissues and cells represents a unique association between a vertebrate and a eukaryotic alga, with implications for research into cell–cell recognition, possible exchange of metabolites or DNA, and potential congruence between host and symbiont population structures.
Carbon storage in US wetlands
Venue: Nature Communications

Wetland soils contain some of the highest stores of soil carbon in the biosphere. However, there is little understanding of the quantity and distribution of carbon stored in our remaining wetlands or of the potential effects of human disturbance on these stocks. Here we use field data from the 2011 National Wetland Condition Assessment to provide unbiased estimates of soil carbon stocks for wetlands at regional and national scales. We find that wetlands in the conterminous United States store a total of 11.52 PgC, much of which is within soils deeper than 30 cm. Freshwater inland wetlands, in part due to their substantial areal extent, hold nearly ten-fold more carbon than tidal saltwater sites—indicating their importance in regional carbon storage. Our data suggest a possible relationship between carbon stocks and anthropogenic disturbance. These data highlight the need to protect wetlands to mitigate the risk of avoidable contributions to climate change.
Muscle moment arms of pelvic limb muscles of the ostrich (Struthio camelus)
Venue: Journal of Anatomy

Muscle moment arms were measured for major muscles of the pelvic limb of the ostrich (Struthio camelus) in order to assess specific functional behaviour and to apply this to locomotor performance. Pelvic limbs of six juvenile ostriches were used for this study. The tendon travel technique was used to measure moment arms of 21 muscles at the hip, knee, ankle and metatarsophalangeal joints throughout the ranges of motion observed during level running. Six of the 21 muscles measured were found to have moment arms that did not change with joint angle, whilst the remainder all demonstrated angle‐dependent changes for at least one of the joints crossed. Moment arm lengths tended to be longest for the large proximal muscles, whilst the largest relative changes were found for the moment arms of the distal muscles. For muscles where moment arm varied with joint angle: all hip muscles were found to have increasing moment arms with extension of the joint, knee flexors were found to have moment arms that increased with extension, knee extensor moment arms were found to increase with flexion and ankle extensor moment arms increased with extension. The greatest relative changes were observed in the flexors of the metatarsophalangeal joint, for which a three‐fold increase in moment arm was observed from flexion to full extension. Changes in muscle moment arm through the range of motion studied appear to optimize muscle function during stance phase, increasing the effective mechanical advantage of these muscles.
Biomimetic structure design — a possible approach to change the brittleness of ceramics in nature☆
Venue: Materials Science and Engineering: C

Based on the analysis on structure of natural biomaterials, two kinds of ceramic composites with high toughness have been designed and prepared: one is fibrous monolithic Si3N4/BN composite imitating bamboos or trees in structure, the other is laminated Si3N4/BN composite imitating nacre in structure. Plastic forming methods, including extrusion and roll compaction, respectively, followed by hot-pressed sintering are used to prepare these two materials with particular structures. Both of the two composites have high values of fracture toughness and work of fracture: fracture toughness are 24 MPa m1/2 and 28 MPa m1/2, respectively, for fibrous monolithic and laminated Si3N4/BN composites, and works of fracture are both more than 4000 J/m2. The load-displacement curves reveal that these two materials with biomimetic structure exhibit non-brittle feature when applied load to fracture. Through analysis on fractographs of the materials, it is revealed that high toughness comes from the synergistic toughening among multi-level toughening mechanisms in different scales: weak interfaces, whiskers and elongated grains toughening in ceramic matrix cells.