nils-herrmann/clean_scirepeval huggingface dataset:
Cercosporamide inhibits bone morphogenetic protein receptor type I kinase activity in zebrafish
Venue: Disease Models & Mechanisms

Zebrafish models are well-established tools for investigating the underlying mechanisms of diseases. Here, we identified cercosporamide, a metabolite from the fungus Ascochyta aquiliqiae, as a potent bone morphogenetic protein receptor (BMPR) type I kinase inhibitor through a zebrafish embryo phenotypic screen. The developmental defects in zebrafish, including lack of the ventral fin, induced by cercosporamide were strikingly similar to the phenotypes caused by renowned small-molecule BMPR type I kinase inhibitors and inactivating mutations in zebrafish BMPRs. In mammalian cell-based assays, cercosporamide blocked BMP/SMAD-dependent transcriptional reporter activity and BMP-induced SMAD1/5-phosphorylation. Biochemical assays with a panel of purified recombinant kinases demonstrated that cercosporamide directly inhibited kinase activity of type I BMPRs [also called activin receptor-like kinases (ALKs)]. In mammalian cells, cercosporamide selectively inhibited constitutively active BMPR type I-induced SMAD1/5 phosphorylation. Importantly, cercosporamide rescued the developmental defects caused by constitutively active Alk2 in zebrafish embryos. We believe that cercosporamide could be the first of a new class of molecules with potential to be developed further for clinical use against diseases that are causally linked to overactivation of BMPR signaling, including fibrodysplasia ossificans progressiva and diffuse intrinsic pontine glioma. This article has an associated First Person interview with the first author of the paper.  Cercosporamide, a metabolite from the fungus Ascochyta aquiliqiae, was identified as a potent bone morphogenetic protein receptor (BMPR) type I kinase inhibitor through a zebrafish embryo phenotypic screen.
Diverse nanostructures underlie thin ultra-black scales in butterflies
Venue: Nature Communications

Recently, it has been shown that animals such as jumping spiders, birds, and butterflies have evolved ultra-black coloration comparable to the blackest synthetic materials. Of these, certain papilionid butterflies have reflectances approaching 0.2%, resulting from a polydisperse honeycomb structure. It is unknown if other ultra-black butterflies use this mechanism. Here, we examine a phylogenetically diverse set of butterflies and demonstrate that other butterflies employ simpler nanostructures that achieve ultra-black coloration in scales thinner than synthetic alternatives. Using scanning electron microscopy, we find considerable interspecific variation in the geometry of the holes in the structures, and verify with finite-difference time-domain modeling that expanded trabeculae and ridges, found across ultra-black butterflies, reduce reflectance up to 16-fold. Our results demonstrate that butterflies produce ultra-black by creating a sparse material with high surface area to increase absorption and minimize surface reflection. We hypothesize that butterflies use ultra-black to increase the contrast of color signals. Nature has developed the ability to produce a wide range of optical effects most notably in the butterfly wing. Here, the authors report on the analysis of the structures responsible for ultra-black coloration across different butterflies and combine this with modelling to identify the key characteristics
How do hoverflies use their righting reflex?
Venue: The Journal of Experimental Biology

When taking off from a sloping surface, flies have to reorient themselves dorsoventrally and stabilize their body by actively controlling their flapping wings. We have observed that righting is achieved solely by performing a rolling manoeuvre. How flies manage to do this has not yet been elucidated. It was observed here for the first time that hoverfly reorientation is entirely achieved within 6 wingbeats (48.8 ms) at angular roll velocities of up to 10×103 deg s−1 and that the onset of their head rotation consistently follows that of their body rotation after a time lag of 16 ms. The insects' body roll was found to be triggered by the asymmetric wing stroke amplitude, as expected. The righting process starts immediately with the first wingbeat and seems unlikely to depend on visual feedback. A dynamic model for the fly's righting reflex is presented, which accounts for the head/body movements and the time lag recorded in these experiments. This model consists of a closed-loop control of the body roll, combined with a feedforward control of the head/body angle. During the righting manoeuvre, a strong coupling seems to exist between the activation of the halteres (which measure the body's angular speed) and the gaze stabilization reflex. These findings again confirm the fundamental role played by the halteres in both body and head stabilization processes.  Hoverfly righting is achieved by performing a rolling manoeuvre; reorientation is achieved within 6 wingbeats and hoverfly head rotation follows that of their body after a time lag of 16 ms.
Antiviral and virucidal effects of curcumin on transmissible gastroenteritis virus in vitro.
Venue: Journal of General Virology

Emerging coronaviruses represent serious threats to human and animal health worldwide, and no approved therapeutics are currently available. Here, we used Transmissible gastroenteritis virus (TGEV) as the alpha-coronavirus model, and investigated the antiviral properties of curcumin against TGEV. Our results demonstrated that curcumin strongly inhibited TGEV proliferation and viral protein expression in a dose-dependent manner. We also observed that curcumin exhibited direct virucidal abilities in a dose-, temperature- and time-dependent manner. Furthermore, time-of-addition assays showed that curcumin mainly acted in the early phase of TGEV replication. Notably, in an adsorption assay, curcumin at 40 µM resulted in a reduction in viral titres of 3.55 log TCID50 ml-1, indicating that curcumin possesses excellent inhibitory effects on the adsorption of TGEV. Collectively, we demonstrate for the first time that curcumin has virucidal activity and virtual inhibition against TGEV, suggesting that curcumin might be a candidate drug for effective control of TGEV infection.
Luminance Information Is Required for the Accurate Estimation of Contrast in Rapidly Changing Visual Contexts
Venue: Current Biology

Visual perception scales with changes in the visual stimulus, or contrast, irrespective of background illumination. However, visual perception is challenged when adaptation is not fast enough to deal with sudden declines in overall illumination, for example, when gaze follows a moving object from bright sunlight into a shaded area. Here, we show that the visual system of the fly employs a solution by propagating a corrective luminance-sensitive signal. We use in vivo 2-photon imaging and behavioral analyses to demonstrate that distinct OFF-pathway inputs encode contrast and luminance. Predictions of contrast-sensitive neuronal responses show that contrast information alone cannot explain behavioral responses in sudden dim light. The luminance-sensitive pathway via the L3 neuron is required for visual processing in such rapidly changing light conditions, ensuring contrast constancy when pure contrast sensitivity underestimates a stimulus. Thus, retaining a peripheral feature, luminance, in visual processing is required for robust behavioral responses.
Universal metabolic constraints shape the evolutionary ecology of diving in animals
Venue: Proceedings of The Royal Society B: Biological Sciences

Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. Therefore, we suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode. The steeper scaling relationship between body mass and dive duration in endotherms not only helps explain why the largest extant vertebrate divers are endothermic rather than ectothermic, but also fits well with the emerging consensus that large extinct tetrapod divers (e.g. plesiosaurs, ichthyosaurs and mosasaurs) were endothermic.
Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica
Venue: Marine Drugs

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
Brilliant angle-independent structural colours preserved in weevil scales from the Swiss Pleistocene
Venue: Biology Letters

Extant weevils exhibit a remarkable colour palette that ranges from muted monochromatic tones to rainbow-like iridescence, with the most vibrant colours produced by three-dimensional photonic nanostructures housed within cuticular scales. Although the optical properties of these nanostructures are well understood, their evolutionary history is not fully resolved, in part due to a poor knowledge of their fossil record. Here, we report three-dimensional photonic nanostructures preserved in brightly coloured scales of two weevils, belonging to the genus Phyllobius or Polydrusus, from the Pleistocene (16–10 ka) of Switzerland. The scales display vibrant blue, green and yellow hues that resemble those of extant Phyllobius/Polydrusus. Scanning electron microscopy and small-angle X-ray scattering analyses reveal that the subfossil scales possess a single-diamond photonic crystal nanostructure. In extant Phyllobius/Polydrusus, the near-angle-independent blue and green hues function primarily in crypsis. The preservation of far-field, angle-independent structural colours in the Swiss subfossil weevils and their likely function in substrate matching confirm the importance of investigating fossil and subfossil photonic nanostructures to understand the evolutionary origins and diversification of colours and associated behaviours (e.g. crypsis) in insects.
Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity
Venue: Science Advances

Natural selection on structural color in tarantulas resulted in convergence on color through diverse structural mechanisms. Slight shifts in arrangement within biological photonic nanostructures can produce large color differences, and sexual selection often leads to high color diversity in clades with structural colors. We use phylogenetic reconstruction, electron microscopy, spectrophotometry, and optical modeling to show an opposing pattern of nanostructural diversification accompanied by unusual conservation of blue color in tarantulas (Araneae: Theraphosidae). In contrast to other clades, blue coloration in phylogenetically distant tarantulas peaks within a narrow 20-nm region around 450 nm. Both quasi-ordered and multilayer nanostructures found in different tarantulas produce this blue color. Thus, even within monophyletic lineages, tarantulas have evolved strikingly similar blue coloration through divergent mechanisms. The poor color perception and lack of conspicuous display during courtship of tarantulas argue that these colors are not sexually selected. Therefore, our data contrast with sexual selection that typically produces a diverse array of colors with a single structural mechanism by showing that natural selection on structural color in tarantulas resulted in convergence on similar color through diverse structural mechanisms.
Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin
Venue: Proceedings of the National Academy of Sciences of the United States of America

Green coloration of vertebrates is normally attributed to pigments and structural components inside skin chromatophores cells. However, these components do not account for the vivid blue-green colors of hundreds of species of frogs with sparse chromatophores. Our study shows that green coloration originates in proteins of the serpin superfamily that bind the pigment biliverdin, modulating its absorbance properties. Using a South American treefrog, we demonstrated that these serpins have a clear ecological role in modulating the reflectance properties and rendering animals cryptic in the foliage even in the near-infrared portion of the spectrum. These findings open up exciting research perspectives both in biochemistry and evolution of serpins, as well as in the study of extracellular protein-mediated coloration in vertebrates. Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations—a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism—the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.
Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes
Venue: Animal Behaviour

The gut microbiome is structured by social groups in a variety of host taxa. Whether this pattern is driven by relatedness, similar diets or shared social environments is under debate because few studies have had access to the data necessary to disentangle these factors in wild populations. We investigated whether diet, relatedness or the 1 m proximity network best explains differences in the gut microbiome among 45 female colobus monkeys in eight social groups residing at Boabeng-Fiema, Ghana. We combined demographic and behavioural data collected during May – August 2007 and October 2008 – April 2009 with 16S rRNA sequencing of faecal samples collected during the latter part of each observation period. Depending on the beta diversity index, social group identity explained 19–28% of the variation in gut microbiome beta diversity. When comparing the predictive power of dietary dissimilarity, relatedness and connectedness in the 1 m proximity network, the models with social connectedness received the strongest support, even in our analyses that excluded within-group dyads. This novel finding indicates that microbes may be transmitted during intergroup encounters, which could occur either indirectly via shared environments or directly via social contact. Lastly, some of the gut microbial taxa that appear to be transmitted via 1 m proximity are associated with digestion of plant material. Further research is needed to investigate whether this type of gut microbe transmission yields health benefits, which could provide an incentive for the formation and maintenance of social bonds within and between social groups.
Broadband omnidirectional light reflection and radiative heat dissipation in white beetles Goliathus goliatus.
Venue: Soft Matter

Structural whiteness, stemming from biologically evolutionarily refined structures, provides inspiration for designing promising, reflectance-based materials. White beetles Goliathus goliatus, which can survive in high-temperature-equatorial forests, may suggest undiscovered new physical mechanisms for thermoregulation. Their scales' whiteness is created by the exquisite shell/hollow cylinder structure with two thermoregulatory effects, contributing to a lower equilibrium temperature of elytra under direct sunlight. In the visible regime, they enhance the broadband omnidirectional reflection significantly by synergetic structural effects originating from the thin-film interference, Mie resonance and total reflection. In the mid-infrared (MIR) regime, white scales act as antireflective layers to increase the emissivity in the MIR range, enabling the elytra to reradiate heat to the environment and help the beetles reduce their temperature by as much as ∼7.8 °C in air. These biological strategies for thermoregulation could provide new approaches for bioinspired coatings towards passive radiative cooling.
Juvenile social dynamics reflect adult reproductive strategies in bottlenose dolphins
Venue: Behavioral Ecology

The juvenile period is a challenging life-history stage, especially in species with a high degree of fission–fusion dynamics, such as bottlenose dolphins, where maternal protection is virtually absent. Here, we examined how juvenile male and female bottlenose dolphins navigate this vulnerable period. Specifically, we examined their grouping patterns, activity budget, network dynamics, and social associations in the absence of adults. We found that juveniles live in highly dynamic groups, with group composition changing every 10 min on average. Groups were generally segregated by sex, and segregation was driven by same-sex preference rather than opposite-sex avoidance. Juveniles formed strong associations with select individuals, especially kin and same-sex partners, and both sexes formed cliques with their preferred partners. Sex-specific strategies in the juvenile period reflected adult reproductive strategies, in which the exploration of potential social partners may be more important for males (which form long-term alliances in adulthood) than females (which preferentially associate with kin in adulthood). Females spent more time alone and were more focused on foraging than males, but still formed close same-sex associations, especially with kin. Males cast a wider social net than females, with strong same-sex associations and many male associates. Males engaged in more affiliative behavior than females. These results are consistent with the social bonds and skills hypothesis and suggest that delayed sexual maturity in species with relational social complexity may allow individuals to assess potential associates and explore a complex social landscape without the risks associated with sexual maturity (e.g., adult reproductive competition; inbreeding).
Character Displacement Promotes Cooperation in Bacterial Biofilms
Venue: Current Biology

Resource competition within a group of cooperators is expected to decrease selection for cooperative behavior but can also result in diversifying selection for the use of different resources, which in turn could retard the breakdown of cooperation. Diverse groups are likely to be less susceptible to invasion by noncooperating social cheats: First, competition repression resulting from character displacement may provide less of a selective advantage to cheating; second, cheats may trade off the ability to exploit cooperators that specialize in one type of resource against cooperators that specialize in another ; third, diverse communities of any kind may have higher invasion resistance because there are fewer resources available for an invader to use . Furthermore, diverse groups are likely to be more productive than clonal groups if a wider range of total resources are being used . We addressed these issues by using the cooperative trait of biofilm formation in Pseudomonas fluorescens. Character displacement through resource competition evolved within biofilms; productivity increased with increasing character displacement, and diverse biofilms were less susceptible to invasion by cheats. These results demonstrate that diversification into different ecological niches can minimize selection against cooperation in the face of local resource competition.