nils-herrmann/clean_scirepeval huggingface dataset:
Biomineralization of Gold: Biofilms on Bacterioform Gold
Venue: Science

Bacterial biofilms are associated with secondary gold grains from two sites in Australia. 16S ribosomal DNA clones of the genus Ralstonia that bear 99% similarity to the bacterium Ralstonia metallidurans—shown to precipitate gold from aqueous gold(III) tetrachloride—were present on all DNA-positive gold grains but were not detected in the surrounding soils. These results provide evidence for the bacterial contribution to the authigenic formation of secondary bacterioform gold grains and nuggets.
Insect Odorscapes: From Plant Volatiles to Natural Olfactory Scenes
Venue: Frontiers in Physiology

Olfaction is an essential sensory modality for insects and their olfactory environment is mostly made up of plant-emitted volatiles. The terrestrial vegetation produces an amazing diversity of volatile compounds, which are then transported, mixed, and degraded in the atmosphere. Each insect species expresses a set of olfactory receptors that bind part of the volatile compounds present in its habitat. Insect odorscapes are thus defined as species-specific olfactory spaces, dependent on the local habitat, and dynamic in time. Manipulations of pest-insect odorscapes are a promising approach to answer the strong demand for pesticide-free plant-protection strategies. Moreover, understanding their olfactory environment becomes a major concern in the context of global change and environmental stresses to insect populations. A considerable amount of information is available on the identity of volatiles mediating biotic interactions that involve insects. However, in the large body of research devoted to understanding how insects use olfaction to locate resources, an integrative vision of the olfactory environment has rarely been reached. This article aims to better apprehend the nature of the insect odorscape and its importance to insect behavioral ecology by reviewing the literature specific to different disciplines from plant ecophysiology to insect neuroethology. First, we discuss the determinants of odorscape composition, from the production of volatiles by plants (section “Plant Metabolism and Volatile Emissions”) to their filtering during detection by the olfactory system of insects (section “Insect Olfaction: How Volatile Plant Compounds Are Encoded and Integrated by the Olfactory System”). We then summarize the physical and chemical processes by which volatile chemicals distribute in space (section “Transportation of Volatile Plant Compounds and Spatial Aspects of the Odorscape”) and time (section “Temporal Aspects: The Dynamics of the Odorscape”) in the atmosphere. The following sections consider the ecological importance of background odors in odorscapes and how insects adapt to their olfactory environment. Habitat provides an odor background and a sensory context that modulate the responses of insects to pheromones and other olfactory signals (section “Ecological Importance of Odorscapes”). In addition, insects do not respond inflexibly to single elements in their odorscape but integrate several components of their environment (section “Plasticity and Adaptation to Complex and Variable Odorscapes”). We finally discuss existing methods of odorscape manipulation for sustainable pest insect control and potential future developments in the context of agroecology (section “Odorscapes in Plant Protection and Agroecology”).
Photoelectrochemical complexes for solar energy conversion that chemically and autonomously regenerate
Venue: Nature Chemistry

Naturally occurring photosynthetic systems use elaborate pathways of self-repair to limit the impact of photo-damage. Herein, we demonstrate a complex that mimics this process consisting of two recombinant proteins, phospholipids and a carbon nanotube. The components self-assemble into a configuration in which an array of lipid bilayers aggregate on the surface of the carbon nanotube, creating a platform for the attachment of light-converting proteins. The system can disassemble upon the addition of a surfactant and reassemble on its removal over an indefinite number of cycles. The assembly is thermodynamically meta-stable and can only transition reversibly if the rate of surfactant removal exceeds about 10−5 sec−1. Only in the assembled state do the complexes exhibit photoelectrochemical activity. We demonstrate a regeneration cycle that uses surfactant to switch between assembled and disassembled states, resulting in increased photo-conversion efficiency of more than 300% over 168 hours and an indefinite extension of the system's lifetime.
Macrophages employ quorum licensing to regulate collective activation
Venue: Nature Communications

Macrophage-initiated inflammation is tightly regulated to eliminate threats such as infections while suppressing harmful immune activation. However, individual cells’ signaling responses to pro-inflammatory cues are heterogeneous, with subpopulations emerging with high or low activation states. Here, we use single-cell tracking and dynamical modeling to develop and validate a revised model for lipopolysaccharide (LPS)-induced macrophage activation that invokes a mechanism we term quorum licensing. The results show that bimodal phenotypic partitioning of macrophages is primed during the resting state, dependent on cumulative history of cell density, predicted by extrinsic noise in transcription factor expression, and independent of canonical LPS-induced intercellular feedback in the tumor necrosis factor (TNF) response. Our analysis shows how this density-dependent coupling produces a nonlinear effect on collective TNF production. We speculate that by linking macrophage density to activation, this mechanism could amplify local responses to threats and prevent false alarms. Macrophage activation is tightly regulated to maintain immune homeostasis, yet activation is also heterogeneous. Here, the authors show that macrophages coordinate activation by partitioning into two phenotypes that can nonlinearly amplify collective inflammatory cytokine production as a function of cell density.
The most versatile of all reactive intermediates?
Venue: Nature Chemical Biology

The iron(II)- and 2-oxoglutarate-dependent oxygenases catalyze varied oxidative reactions. Spectroscopic analyses on the catalytic cycle of the chlorinating enzyme CytC3 reveal the presence of chloride–iron(IV)–oxo complexes, expanding the scope of chemistry known to be catalyzed by non-heme iron-oxo species.
Cloning, characterization and expression of escapin, a broadly antimicrobial FAD-containing l-amino acid oxidase from ink of the sea hare Aplysia californica
Venue: The Journal of Experimental Biology

A 60 kDa monomeric protein isolated from the defensive purple ink secretion of the sea hare Aplysia californica was cloned and sequenced, and is the first sea hare antimicrobial protein to be functionally expressed in E. coli. Sequence analysis suggested that this protein is a flavin-containing l-amino acid oxidase (LAAO), with one predicted potential glycosylation site, although the glycosylation could not be experimentally confirmed. This protein, which we call `escapin', has high sequence similarity to several other gastropod proteins. Escapin was verified by NMR, mass spectroscopy and HPLC to have FAD as its flavin cofactor. Escapin's antimicrobial effects, bacteriostasis and bactericidal, were determined using a combination of two assays: (1) incubation of bacteria on solid media followed by assessment of inhibition by direct observation of zones of inhibition or by turbidity measurements; and (2) incubation of bacteria in liquid media followed by counting viable colonies after growing on agar plates. Native escapin inhibited the growth of Gram-positive and Gram-negative bacteria, including marine bacteria (Vibrio harveyii and Staphylococcus aureus) and pathogenic bacteria (Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa). Escapin also inhibited the growth of yeast and fungi, with different efficacies. Escapin's antimicrobial activity was concentration dependent and did not decrease when stored for more than 5 months at room temperature. Escapin was bacteriostatic and not bactericidal in minimal media (e.g. salt media) with glucose, yeast extract, and a mixture of 20 amino acids each at 50 μmol l-1, but was bactericidal in media enriched with Tryptone Peptone. Escapin was also strongly bactericidal in media with l-lysine at concentrations as low as 3 mmol l-1 and slightly bactericidal in 50 mmol l-1 l-arginine, but not in most other amino acids even at 50 mmol l-1. Escapin had high oxidase activity (producing hydrogen peroxide) with either l-arginine or l-lysine as a substrate and little to no oxidase activity with other l-amino acids. Hydrogen peroxide alone (without escapin or amino acids) was strongly bacteriostatic but poorly bactericidal, similar in this respect to l-arginine but different from l-lysine in the presence of escapin. Together these results suggest that there are multiple mechanisms to escapin's antimicrobial effects, with bacteriostasis resulting largely or entirely from the effects of hydrogen peroxide produced by escapin's LAAO activity, but bactericidal effects resulting from lysine-dependent mechanisms not directly involving hydrogen peroxide. Recombinant escapin expressed in bacteria was also active against Gram-positive and Gram-negative bacteria, suggesting that glycosylation is not essential for antimicrobial activity.
Biosensing of opioids using frog melanophores.
Venue: Biosensors and Bioelectronics

Spectacular color changes of fishes, frogs and other lower vertebrates are due to the motile activities of specialized pigment containing cells. Pigment cells are interesting for biosensing purposes since they provide an easily monitored physiological phenomenon. Melanophores, containing dark brown melanin pigment granules, constitute an important class of chromatophores. Their melanin-filled pigment granules may be stimulated to undergo rapid dispersion throughout the melanophores (cells appear dark), or aggregation to the center of the melanophores (cells appear light). This simple physiological response can easily be measured in a photometer. Selected G protein coupled receptors can be functionally expressed in cultured frog melanophores. Here, we demonstrate the use of recombinant frog melanophores as a biosensor for the detection of opioids. Melanophores were transfected with the human opioid receptor 3 and used for opiate detection. The response to the opioid receptor agonist morphine and a synthetic opioid peptide was analyzed by absorbance readings in an aggregation assay. It was shown that both agonists caused aggregation of pigment granules in the melanophores, and the cells appeared lighter. The pharmacology of the expressed receptors was very similar to its mammalian counterpart, as evidenced by competitive inhibition by increasing concentrations of the opioid receptor inhibitor naloxone. Transfection of melanophores with selected receptors enables the creation of numerous melanophore biosensors, which respond selectively to certain substances. The melanophore biosensor has potential use for measurement of substances in body fluids such as saliva, blood plasma and urine.
Dew condensation on desert beetle skin
Venue: European Physical Journal E

Some tenebrionind beetles inhabiting the Namib desert are known for using their body to collect water droplets from wind-blown fogs. We aim to determine whether dew water collection is also possible for desert insects. For this purpose, we investigated the infra-red emissivity, and the wetting and structural properties, of the surface of the elytra of a preserved specimen of Physasterna cribripes (Tenebrionidæ) beetle, where the macro-structure appears as a series of “bumps”, with “valleys” between them. Dew formation experiments were carried out in a condensation chamber. The surface properties (infra-red emissivity, wetting properties) were dominated by the wax at the elytra surface and, to a lower extent, its micro-structure. We performed scanning electron microscope on histological sections and determined the infra-red emissivity using a scanning pyrometer. The emissivity measured (0.95±0.07 between 8–14μm) was close to the black body value. Dew formation occurred on the insect’s elytra, which can be explained by these surface properties. From the surface coverage of the condensed drops it was found that dew forms primarily in the valleys between the bumps. The difference in droplet nucleation rate between bumps and valleys can be attributed to the hexagonal microstructure on the surface of the valleys, whereas the surface of the bumps is smooth. The drops can slide when they reach a critical size, and be collected at the insect's mouth.
A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus
Venue: BMC Biology

BackgroundAttine ants live in an intensely studied tripartite mutualism with the fungus Leucoagaricus gongylophorus, which provides food to the ants, and with antibiotic-producing actinomycete bacteria. One hypothesis suggests that bacteria from the genus Pseudonocardia are the sole, co-evolved mutualists of attine ants and are transmitted vertically by the queens. A recent study identified a Pseudonocardia-produced antifungal, named dentigerumycin, associated with the lower attine Apterostigma dentigerum consistent with the idea that co-evolved Pseudonocardia make novel antibiotics. An alternative possibility is that attine ants sample actinomycete bacteria from the soil, selecting and maintaining those species that make useful antibiotics. Consistent with this idea, a Streptomyces species associated with the higher attine Acromyrmex octospinosus was recently shown to produce the well-known antifungal candicidin. Candicidin production is widespread in environmental isolates of Streptomyces, so this could either be an environmental contaminant or evidence of recruitment of useful actinomycetes from the environment. It should be noted that the two possibilities for actinomycete acquisition are not necessarily mutually exclusive.ResultsIn order to test these possibilities we isolated bacteria from a geographically distinct population of A. octospinosus and identified a candicidin-producing Streptomyces species, which suggests that they are common mutualists of attine ants, most probably recruited from the environment. We also identified a Pseudonocardia species in the same ant colony that produces an unusual polyene antifungal, providing evidence for co-evolution of Pseudonocardia with A. octospinosus.ConclusionsOur results show that a combination of co-evolution and environmental sampling results in the diversity of actinomycete symbionts and antibiotics associated with attine ants.
Physiological ecology of nest construction and protein flow in pre-emergence colonies of Polistes chinensis (Hymenoptera Vespidae): effects of rainfall and microclimates
Venue: Ethology Ecology & Evolution

The amount of oral secretion, which mostly consists of proteinaceous materials, used for the construction and maintenance of nests by foundresses of Polistes chinensis was analysed in 95 field nests (1994–1996). The amounts always exceeded 50% of mean percent secretion to total the dry nest weights, and it was greater in nests built at sites exposed to direct rainfall than in those at sheltered sites. Further, exposed nests built in 1995 (a rainy year) were much smaller than those of 1994 and 1996, and the amount of secretion in that year was much greater than in the other years. The nitrogen content of adult workers, immatures, those left inside cells and the oral secretion in nests of 1996 showed that 10–20% of total protein resources brought in during the founding phase may be devoted to producing the secretion. The results suggest that the foundresses may regulate the amounts of oral secretion used for such purposes in response to environmental conditions.
EVOLUTIONARY SIGNIFICANCE OF AWN LENGTH VARIATION IN A CLONAL GRASS OF FIRE-PRONE SAVANNAS
Venue: Ecology

We investigated the selective advantage of continuous variation of awn length in the clonal grass Hyparrhenia diplandra (Poaceae) in a West African tropical savanna (Ivory Coast) that burns every year. This species is apomictic, so all seeds produced by one mother plant have the same genotype. H. diplandra produces diaspores with a hygroscopic awn whose length varies within and among plants. In other grass species, awns play a significant role in secondary dispersal on the ground and in seed burial. Using an experimental approach, we quantified (1) the environmental and genetic components of awn length variation, (2) the influence of awn length variation on seed burial depth, (3) the effect of awn length on seed germination and seedling survival rates in burned and unburned plots, and (4) the potential role of fire intensity in selecting diaspores with different awn lengths. Awn length varied from 35 to 70 mm and was highly heritable (h2 = 0.63). Variation within individuals was not related to flowering p...
Individually recognizable scent marks on flowers made by a solitary bee
Venue: Animal Behaviour

The marking of flowers with ephemeral scent is an underappreciated but vital element in the foraging behaviour of social bees. Using observational and experimental data, we tested whether a solitary bee (female Anthophora plumipes) uses scent marking while foraging on flowers of Cerinthe major in Portugal. Females used scent marks with at least two components that differed in their volatility and, furthermore, recognized the marks of different individuals. A very short-term component (<3 min) was attractive, resulting in the observed high level of immediate revisits: this component appeared to be adjusted according to the foraging needs of the moment. A longer-term component (<30 min) was initially repellent and matched the rate of nectar renewal; it, or the response to it, also appeared to be adjusted to the perceived level of nectar reward. There may be even longer-term effects associated with the specific foraging areas of individual bees. Observed differences in the way in which individuals responded to scent marks indicate that they may play a role as part of a dominance or exclusion mechanism among females.
Nanoscale chemical tomography of buried organic–inorganic interfaces in the chiton tooth
Venue: Nature

Biological organisms possess an unparalleled ability to control the structure and properties of mineralized tissues. They are able, for example, to guide the formation of smoothly curving single crystals or tough, lightweight, self-repairing skeletal elements. In many biominerals, an organic matrix interacts with the mineral as it forms, controls its morphology and polymorph, and is occluded during mineralization. The remarkable functional properties of the resulting composites—such as outstanding fracture toughness and wear resistance—can be attributed to buried organic–inorganic interfaces at multiple hierarchical levels. Analysing and controlling such interfaces at the nanometre length scale is critical also in emerging organic electronic and photovoltaic hybrid materials. However, elucidating the structural and chemical complexity of buried organic–inorganic interfaces presents a challenge to state-of-the-art imaging techniques. Here we show that pulsed-laser atom-probe tomography reveals three-dimensional chemical maps of organic fibres with a diameter of 5–10 nm in the surrounding nano-crystalline magnetite (Fe3O4) mineral in the tooth of a marine mollusc, the chiton Chaetopleura apiculata. Remarkably, most fibres co-localize with either sodium or magnesium. Furthermore, clustering of these cations in the fibre indicates a structural level of hierarchy previously undetected. Our results demonstrate that in the chiton tooth, individual organic fibres have different chemical compositions, and therefore probably different functional roles in controlling fibre formation and matrix–mineral interactions. Atom-probe tomography is able to detect this chemical/structural heterogeneity by virtue of its high three-dimensional spatial resolution and sensitivity across the periodic table. We anticipate that the quantitative analysis and visualization of nanometre-scale interfaces by laser-pulsed atom-probe tomography will contribute greatly to our understanding not only of biominerals (such as bone, dentine and enamel), but also of synthetic organic–inorganic composites.
Cold-stable eye lens crystallins of the Antarctic nototheniid toothfish Dissostichus mawsoni Norman
Venue: The Journal of Experimental Biology

The eye lenses of the Antarctic nototheniid fishes that inhabit the perennially freezing Antarctic seawater are transparent at –2°C, whereas the cold-sensitive mammalian and tropical fish lenses display cold-induced cataract at 20°C and 7°C, respectively. No cold-cataract occurs in the giant Antarctic toothfish Dissostichus mawsoni lens when cooled to temperatures as low as –12°C, indicating highly cold-stable lens proteins. To investigate this cold stability, we characterised the lens crystallin proteins of the Antarctic toothfish, in parallel with those of the sub-tropical bigeye tuna Thunnus obesus and the endothermic cow Bos taurus, representing three disparate thermal climes (–2°C, 18°C and 37°C, respectively). Sizing chromatography resolved their lens crystallins into three groups,α /βH, β and γ, with γ crystallins being the most abundant (>40%) lens proteins in fish, in contrast to the cow lens where they comprise only 19%. The upper thermal stability of these crystallin components correlated with the body temperature of the species. In vitro chaperone assays showed that fish α crystallin can protect same-species γ crystallins from heat denaturation, as well as lysozyme from DTT-induced unfolding, and therefore are small Heat Shock Proteins (sHSP) like their mammalian counterparts. Dynamic light scattering measured an increase in size of αγ crystallin mixtures upon heating, which supports formation of the αγ complex as an integral part of the chaperone process. Surprisingly, in cross-species chaperone assays, tunaα crystallins only partly protected toothfish γ crystallins, while cow α crystallins completely failed to protect, indicating partial and no αγ interaction, respectively. Toothfish γ was likely to be the component that failed to interact, as the supernatant from a cowα plus toothfish γ incubation could chaperone cow γ crystallins in a subsequent heat incubation, indicating the presence of uncomplexed cow α. This suggests that the inability of toothfish γ crystallins to fully complex with tuna α, and not at all with the cowα crystallins, may have its basis in adaptive changes in the protein that relate to the extreme cold-stability of the toothfish lens.
A Novel Vertebrate Eye Using Both Refractive and Reflective Optics
Venue: Current Biology

Sunlight is attenuated rapidly in the ocean, resulting in little visually useful light reaching deeper than approximately 1000 m in even the clearest water. To maximize sensitivity to the relatively brighter downwelling sunlight, to view the silhouette of animals above them, and to increase the binocular overlap of their eyes, many mesopelagic animals have developed upward-pointing tubular eyes. However, these sacrifice the ability to detect bioluminescent and reflective objects in other directions. Thus, some mesopelagic fish with tubular eyes extend their visual fields laterally and/or ventrally by lensless ocular diverticula, which are thought to provide unfocused images, allowing only simple detection of objects, with little spatial resolution. Here, we show that a medial mirror within the ventrally facing ocular diverticulum of the spookfish, Dolichopteryx longipes, consisting of a multilayer stack derived from a retinal tapetum, is used to reflect light onto a lateral retina. The reflective plates are not orientated parallel to the surface of the mirror. Instead, plate angles change progressively around the mirror, and computer modeling indicates that this provides a well-focused image. This is the first report of an ocular image being formed in a vertebrate eye by a mirror.