nils-herrmann/clean_scirepeval huggingface dataset:
Cell-cell communication in gram-positive bacteria.
Venue: Annual Review of Microbiology

In gram-positive bacteria, many important processes are controlled by cell-to-cell communication, which is mediated by extracellular signal molecules produced by the bacteria. Most of these signaling molecules are peptides or modified peptides. Signal processing, in most cases, involves either transduction across the cytoplasmic membrane or import of the signal and subsequent interaction with intracellular effectors. Concentrations of signal in the nanomolar range or below are frequently sufficient for biological activity. The microbial processes controlled by extracellular signaling include the expression of virulence factors, the expression of gene transfer functions, and the production of antibiotics.
Mapping the β-Scorpion Toxin Receptor Site on Voltage-Gated Sodium Channels
Venue: Biophysical Journal

Voltage-gated sodium channels are molecular targets of β-scorpion toxins, which enhance excitability by shifting the voltage dependence of activation to more negative potentials. These effects result from a voltage sensor trapping mechanism, in which toxins trap the voltage sensor in its activated conformation. Determinants of β-scorpion toxin (CssIV) binding and action on sodium channel (Nav1.2) are located in the S1-S2 and S3-S4 extracellular linkers in the voltage-sensing module in domain II. To completely map these regions, we made substitutions for previously unstudied amino acid residues and examined modulation by CssIVE15A, a highly active toxin derivative. Of 11 positions studied in IIS1-S2, only one significantly altered the toxin effect from wild-type by reducing binding to the resting state and almost abolishing trapping activity. In IIS3-S4, five positions surrounding a previously identified key binding determinant, G845, define a hotspot of high impact residues. Three of these substitutions reduced toxin binding and voltage-sensor trapping. The other two, V843A and E844N, increased voltage-sensor trapping approximately 4-fold and decreased apparent EC50. The rate of voltage sensor trapping upon depolarization was unchanged for V843A and increased approximately 2.5-fold for E844N. The rate at which the toxin releases the voltage sensor upon repolarization was increased 2.2-fold for the V843A but was unchanged for E844N. Thus CssIVE15A interacts with a short segment of IIS1-S2 and a broader region of DIIS3-S4. The bidirectional effects of mutations on toxin efficacy suggest that native residues make both positive and negative interactions with the toxin. Substitutions that increase toxin effects do so by increasing affinity of resting channels for the toxin and further increasing the relative affinity of the activated voltage-sensor for the toxin. These results provide further support for the voltage sensor-trapping model.
Bacterial Adhesion and Entry into Host Cells
Venue: Cell

Successful establishment of infection by bacterial pathogens requires adhesion to host cells, colonization of tissues, and in certain cases, cellular invasion-followed by intracellular multiplication, dissemination to other tissues, or persistence. Bacteria use monomeric adhesins/invasins or highly sophisticated macromolecular machines such as type III secretion systems and retractile type IV pili to establish a complex host/pathogen molecular crosstalk that leads to subversion of cellular functions and establishment of disease.
Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics.
Venue: Fems Microbiology Reviews

Lipopeptides constitute a structurally diverse group of metabolites produced by various bacterial and fungal genera. In the past decades, research on lipopeptides has been fueled by their antimicrobial, antitumour, immunosuppressant and surfactant activities. However, the natural functions of lipopeptides in the lifestyles of the producing microorganisms have received considerably less attention. The substantial structural diversity of lipopeptides suggests that these metabolites have different natural roles, some of which may be unique to the biology of the producing organism. This review gives a detailed overview of the versatile functions of lipopeptides in the biology of Pseudomonas and Bacillus species, and highlights their role in competitive interactions with coexisting organisms, including bacteria, fungi, oomycetes, protozoa, nematodes and plants. Their functions in cell motility, leading to colonization of novel habitats, and in the formation and development of highly structured biofilms are discussed in detail. Finally, this review provides an update on lipopeptide detection and discovery as well as on novel regulatory mechanisms and genes involved in lipopeptide biosynthesis in these two bacterial genera.
Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi
Venue: Nature Reviews Microbiology

Extracellular vesicles (EVs) are produced by all domains of life. In Gram-negative bacteria, EVs are produced by the pinching off of the outer membrane; however, how EVs escape the thick cell walls of Gram-positive bacteria, mycobacteria and fungi is still unknown. Nonetheless, EVs have been described in a variety of cell-walled organisms, including Staphylococcus aureus, Mycobacterium tuberculosis and Cryptococcus neoformans. These EVs contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes, and have important roles in microbial physiology and pathogenesis. In this Review, we describe the current status of vesiculogenesis research in thick-walled microorganisms and discuss the cargo and functions associated with EVs in these species.
Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival.
Venue: Ecology

The dynamics of forest ecosystems depend largely on the survival of seedlings in their understories, but seedling survival is known to be limited by preemption of light and soil resources by overstory trees. It has been hypothesized that "common mycorrhizal networks," wherein roots of seedlings are linked to overstory trees by symbiotic mycorrhizal fungi, offset some or all of the negative effects of trees on seedlings. Here we report the results of an unambiguous experimental test of this hypothesis in a monodominant Pinus radiata forest. We also tested the hypothesis that adaptive differentiation among plant populations causes local plant genotypes to respond more positively to mycorrhizal networks than nonlocal plant genotypes. Our results demonstrate large positive effects of overstory mycorrhizal networks on seedling survival, along with simultaneous negative effects of tree roots, regardless of whether plant genotypes were locally derived. Physiological and leaf-chemistry measurements suggest that seedlings connected to common mycorrhizal networks benefited from increased access to soil water. The similar magnitude of the positive and negative overstory effects on seedlings and the ubiquity of mycorrhizal networks in forests suggest that mycorrhizal networks fundamentally influence the demographic and community dynamics of forest trees.
Anemonefish symbiosis: vulnerability and resistance of fish to the toxin of the sea anemone.
Venue: Toxicon

Protein toxins (20 kD molecular mass) causing lysis of human erythrocytes were isolated from sea anemones (Heteractis magnifica, Madang, Papua New Guinea, and Entacmaea quadricolor, Red Sea), which host anemonefish (Amphiprion sp.). These toxins are also ichthyotoxic. Freshwater and marine fish exposed to toxin concentrations of 0.5 micrograms/ml water were killed within 2 hr and exhibited extensive pathological alterations of the gill filaments. Amphiprion species, e.g. clarkii and percula, which live in the sea anemones Heteractis crispa and Stichodactyla mertensii, were highly vulnerable to the Heteractis magnifica toxin, whereas A. percula from the sea anemone H. magnifica proved to be toxin resistant. However, another species, A. perideraion also living in H. magnifica, was highly sensitive to the toxin. The two toxins exhibited cross-reactivity: Amphiprion, resistant to H. magnifica toxin, was also resistant to Entacmaea quadricolor toxin; but all fish were killed by other membrane-active substances such as gramicidin, saponin and latrunculin. The results of the study indicate that resistance to toxins secreted by the sea anemone has evolved in some Amphiprion species, but it is not an essential or a major factor in the anemonefish symbiosis. The skin's mucus layer seems to provide protection from nematocyst discharge.
UV protective coatings: A botanical approach
Venue: Progress in Organic Coatings

Solar UV radiation is harmful to many biological systems, as well as all kind of technical applications. UV protective coatings are commonly utilised to shield many susceptible substances. In an attempt to learn from nature we demonstrate that for the Pinus mugo subsp. mugo (dwarf mountain pine) the cuticular wax layer provides UV protection. This biological coating contains chromophores that absorb UV radiation in such a way that it removes the most harmful UV-B and UV-A from the solar spectrum received by the plant and does not lower the received PAR (photosynthetically active radiation). In addition, the P. mugo grown at high elevations in the Alps has a cuticular wax coat that also contains fluorsphores, which convert the harmful solar UV into blue light. This additional blue light can be utilised for photosynthesis in low-light conditions, which gives the P. mugo ecological advantage over other Alpine species. The principle of turning useless or even harmful radiation into useful energy sets an example for new biological based coatings.
Evolutionary aspects of intestinal bicarbonate secretion in fish.
Venue: Comparative Biochemistry and Physiology A-molecular & Integrative Physiology

Experiments compared intestinal HCO3- secretion in the intestine of marine teleost Gulf toadfish, Opsanus beta, to representatives of early chondrostean and chondrichthyan fishes, the Siberian sturgeon, Acipenser baerii, and white-spotted bamboo shark, Chiloscyllium plagiosum, respectively. As seen in marine teleosts, luminal HCO3- concentrations were 10-fold plasma levels in all species when exposed to hyperosmotic conditions. While intestinal water absorption left Mg2+ and SO4(2-) concentrated in intestinal fluids up to four-fold ambient seawater concentrations, HCO3- was concentrated up to 50 times ambient levels as a result of intestinal HCO3- secretion. Reduced luminal Cl- concentrations in the intestine of all species suggest that HCO3- secretion also occurs via Cl-/HCO3- exchange in chondrostean and chondrichthyan fishes. Sturgeon began precipitating carbonates from the gut after only 3 days at 14 per thousand, a mechanism utilized by marine teleosts to reduce intestinal fluid osmolality and maintain calcium homeostasis. Analysis of published intestinal fluid composition in the cyclostome Lampetra fluviatilis reveals that this species likely also utilize intestinal HCO3- secretion for osmoregulation. Analysis of existing cyclostome data and our results indicate that intestinal Cl-/HCO3- exchange plays an integral role in maintaining hydromineral balance not only in teleosts, but in all fish (and perhaps other animals) with a need to drink seawater.
FEEDING BEHAVIOR OF THE HUMPBACK WHALE, MEGAPTERA NOVAEANGLIAE, IN THE WESTERN NORTH ATLANTIC
Venue: Fishery Bulletin

Observations on the feeding behavior of the humpback whale, Megapteranovaeangliae, were made from aerial and surface platforms fTom 1977 to 1980 in the continental shelf waters of the north­ eastern United States. The resulting catalog of behaviors includes two principal categories: Swim­ ming/lunging behaviors and bubbling behaviors. A behavior from a given category may be used independently or in association with others, and by individual or groups of humpbacks. The first category includes surface lunging, circular swimming/thrashing, and the "inside loop" behavior. In the second category, a wide variety of feeding-associated bubbling behaviors are described, some for the first time. The structures formed by underwater exhalations are of two major types: 1) bubble cloud-a single, relatively large (4-7m diameter), dome-shaped cloud formed of small, uniformly sized bubbles; and 2) bubble column-a smaller (1-1.5 m diameter) structure composed of larger, randomly sized bubbles, used in series or multiples. Both basic structures are employed in a variety of ways. Many of these behaviors are believed to be utilized to maintain naturally occurring concentrations of prey, which have been identified as the American sand lance, Ammodytes americanus, and occasionally as herring, Clupea harengus. This paper reports on the feeding behavior of the humpback whale, Megaptera novaeangliae, in the continental shelf waters of the northeastern United States. We describe several feeding be­ haviors reported for the first time, as well as a number of behaviors known from other areas but not previously reported for these waters. Our col­ lective observations provide the beginning of a more complete catalog than has previously been available.
Theoretical and experimental studies of energy exchange from jackrabbit ears and cylindrically shaped appendages.
Venue: Biophysical Journal

Convection properties of jackrabbit ears were examined in a wind tunnel and in the field in an attempt to study the possible thermal role of the large ears. This work was part of a study on energy exchange of appendages. Cylindrical copper models of various shapes, aluminum castings of domestic and jackrabbit ears, and an amputated jackrabbit ear were studied in a wind tunnel (a) to define the range for convective heat loss for appendages of various shapes, and (b) to study the effect on convection of model shape and orientation to the wind. Shape, i.e. length and closure, proved important. Orientation to the wind produced no consistent or significant variation in the convection coefficient. The convection coefficients from the ear castings fell within the range generated from the cylindrical models. The convection coefficients for the amputated rabbit ear fell partially within the range. Net thermal radiation loss at midday from the jackrabbit ears was found to be small. Convection from the ears, however, could account for the loss of over 100% of the animal's metabolic heat at an air temperature of 30 degrees C. If air temperature exceeds body temperature, the animal must either store heat or resort to the evaporation of water.
The jump of the click beetle (Coleoptera: Elateridae)—energetics and mechanics
Venue: Journal of Zoology

Some aspects of the energetics and mechanics of two jumps made by a single specimen of Athous haemorrhoidalis (Fab.) are considered. In the first jump, the 40 mg beetle had a take-off velocity of 2–4 m/s and the jumping action occurred in about 064 ms; in the second jump, the take/off velocity was 2–26 m/s and the jumping action took about 0–53 ms. Energy budgets have been constructed in two different ways for each jump, and the total energy involved in each case was estimated to lie between 1–6 × 10−4 J and 3–8 × 10−4 J. Power output during the jumping action (a “catapult”) lay between 80 × 103 W/kg muscle and 180 × 103 W/kg muscle, whilst power output during the energy storing pre-jump period (of about 0–4 s) was at least 130 W/kg muscle (at over 25°C). Forces and tensile stresses in the jumping muscles and their apodemes have also been calculated. The method of jumping appears to be fairly inefficient in that only about 50–60% of the energy expended in the jumping action is energy of translation, which actually raises the beetle.
A single touch can provide sufficient mechanical stimulation to trigger Venus flytrap closure
Venue: PLOS Biology

The carnivorous Venus flytrap catches prey by an ingenious snapping mechanism. Based on work over nearly 200 years, it has become generally accepted that two touches of the trap’s sensory hairs within 30 s, each one generating an action potential, are required to trigger closure of the trap. We developed an electromechanical model, which, however, suggests that under certain circumstances one touch is sufficient to generate two action potentials. Using a force-sensing microrobotic system, we precisely quantified the sensory-hair deflection parameters necessary to trigger trap closure and correlated them with the elicited action potentials in vivo. Our results confirm the model’s predictions, suggesting that the Venus flytrap may be adapted to a wider range of prey movements than previously assumed.
Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods
Venue: Current Biology

Transparent zooplankton and nekton are often nearly invisible when viewed under ambient light in the pelagic zone [1-3]. However, in this environment, where the light field is directional (and thus likely to cause reflections), and under the bioluminescent searchlights of potential predators, animals may be revealed by reflections from their body surface [4-7]. We investigated the cuticle surfaces of seven species of hyperiids (Crustacea; Amphipoda) using scanning electron microscopy and found two undocumented features that may reduce reflectance. We found that the legs of Cystisoma spp. (n = 5) are covered with an ordered array of nanoprotuberances 200 ± 20 nm SD in height that function optically as a gradient refractive index material [6, 8, 9]. Additionally, we observed that Cystisoma and six other species of hyperiids are covered with a monolayer of homogenous spheres (diameters ranging from 52 ± 7 nm SD on Cystisoma spp. to 320 ± 15 nm SD on Phronima spp.). Optical modeling using effective medium theory and transfer matrix methods demonstrated that both the nanoprotuberances and the monolayers reduce reflectance by as much as 100-fold, depending on the wavelength and angle of the incident light and the thickness of the gradient layer. Even though we only consider surface reflectance and not internal light scattering, our study demonstrates that these nanoprotuberances and spheres can improve crypsis in a featureless habitat where the smallest reflection can render an animal vulnerable to visual predation.
Bioactive Molecular Networking for Mapping the Antimicrobial Constituents of the Baltic Brown Alga Fucus vesiculosus
Venue: Marine Drugs

The brown alga Fucus vesiculosus is common to the intertidal zones of the Baltic Sea, where it is exposed to high fouling pressures by microorganisms. Our previous studies showed, repeatedly, the consistent antimicrobial activity of F. vesiculosus crude extracts against human pathogens, while untargeted metabolomics analyses have revealed a variety of metabolites. In this study, we applied the UPLC-QToF-MS/MS-based “bioactive molecular networking” (BMN) concept on the most bioactive n-hexane and n-butanol subextracts of Baltic F. vesiculosus coupled with in silico dereplication tools to identify the compounds responsible for antimicrobial activity. The first antimicrobial cluster identified by BMN was galactolipids. Our targeted isolation efforts for this class led to the isolation of six monogalactosyldiacylglycerol (MGDG) derivatives (1–6) and one digalactosyldiacylglycerol (DGDG, 7). The MGDGs 5 and 6 and the DGDG 7 exhibited activity against Staphylococcus aureus. The second compound class with high bioactivity was phlorotannins. In particular, phlorethol-type phlorotannins showed high correlations with antimicrobial activity based on the BMN approach, and two phlorotannins (8–9) were isolated. This study shows that antimicrobial components of F. vesiculosus reside in the algal cell walls and membranes and that BMN provides a complementary tool for the targeted isolation of bioactive metabolites.
Metabolic rate in common shrews is unaffected by temperature, leading to lower energetic costs through seasonal size reduction
Venue: Royal Society Open Science

Small endothermic mammals have high metabolisms, particularly at cold temperatures. In the light of this, some species have evolved a seemingly illogical strategy: they reduce the size of the brain and several organs to become even smaller in winter. To test how this morphological strategy affects energy consumption across seasonally shifting ambient temperatures, we measured oxygen consumption and behaviour in the three seasonal phenotypes of the common shrew (Sorex araneus), which differ in size by about 20%. Body mass was the main driver of oxygen consumption, not the reduction of metabolically expensive brain mass. Against our expectations, we found no change in relative oxygen consumption with low ambient temperature. Thus, smaller body size in winter resulted in significant absolute energy savings. This finding could only partly be explained by an increase of lower cost behaviours in the activity budgets. Our findings highlight that these shrews manage to avoid one of the most fundamental and intuitive rules of ecology, allowing them to subsist with lower resource availability and successfully survive the harsh conditions of winter.
The jumping mechanism of flea beetles (Coleoptera, Chrysomelidae, Alticini), its application to bionics and preliminary design for a robotic jumping leg.
Venue: ZooKeys

Flea beetles (Coleoptera, Chrysomelidae, Galerucinae, Alticini) are a hyperdiverse group of organisms with approximately 9900 species worldwide. In addition to walking as most insects do, nearly all the species of flea beetles have an ability to jump and this ability is commonly understood as one of the key adaptations responsible for its diversity. Our investigation of flea beetle jumping is based on high-speed filming, micro-CT scans and 3D reconstructions, and provides a mechanical description of the jump. We reveal that the flea beetle jumping mechanism is a catapult in nature and is enabled by a small structure in the hind femur called an 'elastic plate' which powers the explosive jump and protects other structures from potential injury. The explosive catapult jump of flea beetles involves a unique 'high-efficiency mechanism' and 'positive feedback mechanism'. As this catapult mechanism could inspire the design of bionic jumping limbs, we provide a preliminary design for a robotic jumping leg, which could be a resource for the bionics industry.
Herbivory meets fungivory: insect herbivores feed on plant pathogenic fungi for their own benefit.
Venue: Ecology Letters

Plants are regularly colonised by fungi and bacteria, but plant-inhabiting microbes are rarely considered in studies on plant-herbivore interactions. Here we show that young gypsy moth (Lymantria dispar) caterpillars prefer to feed on black poplar (Populus nigra) foliage infected by the rust fungus Melampsora larici-populina instead of uninfected control foliage, and selectively consume fungal spores. This consumption, also observed in a related lepidopteran species, is stimulated by the sugar alcohol mannitol, found in much higher concentration in fungal tissue and infected leaves than uninfected plant foliage. Gypsy moth larvae developed more rapidly on rust-infected leaves, which cannot be attributed to mannitol but rather to greater levels of total nitrogen, essential amino acids and B vitamins in fungal tissue and fungus-infected leaves. Herbivore consumption of fungi and other microbes may be much more widespread than commonly believed with important consequences for the ecology and evolution of plant-herbivore interactions.