nils-herrmann/clean_scirepeval huggingface dataset:
Deciphering links between bacterial interactions and spatial organization in multispecies biofilms
Venue: The ISME Journal

Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.
Discovery of os cordis in the cardiac skeleton of chimpanzees (Pan troglodytes)
Venue: Scientific Reports

Cardiovascular diseases, especially idiopathic myocardial fibrosis, is one of the most significant causes of morbidity and mortality in captive great apes. This study compared the structure and morphology of 16 hearts from chimpanzees (Pan troglodytes) which were either healthy or affected by myocardial fibrosis using X-ray microtomography. In four hearts, a single, hyperdense structure was detected within the right fibrous trigone of the cardiac skeleton. High resolution scans and histopathology revealed trabecular bones in two cases, hyaline cartilage in another case and a focus of mineralised fibro-cartilaginous metaplasia with endochondral ossification in the last case. Four other animals presented with multiple foci of ectopic calcification within the walls of the great vessels. All hearts affected by marked myocardial fibrosis presented with bone or cartilage formation, and increased collagen levels in tissues adjacent to the bone/cartilage, while unaffected hearts did not present with os cordis or cartilago cordis. The presence of an os cordis has been described in some ruminants, camelids, and otters, but never in great apes. This novel research indicates that an os cordis and cartilago cordis is present in some chimpanzees, particularly those affected by myocardial fibrosis, and could influence the risk of cardiac arrhythmias and sudden death.
Thoracic scales of moths as a stealth coating against bat biosonar
Venue: Journal of the Royal Society Interface

Many moths are endowed with ultrasound-sensitive ears that serve the detection and evasion of echolocating bats. Moths lacking such ears could still gain protection from bat biosonar by using stealth acoustic camouflage, absorbing sound waves rather than reflecting them back as echoes. The thorax of a moth is bulky and hence acoustically highly reflective. This renders it an obvious target for any bat. Much of the thorax of moths is covered in hair-like scales, the layout of which is remarkably similar in structure and arrangement to natural fibrous materials commonly used in sound insulation. Despite this structural similarity, the effect of thorax scales on moth echoes has never been characterized. Here, we test whether and how moth thorax scales function as an acoustic absorber. From tomographic echo images, we find that the thin layer of thoracic scales of diurnal butterflies affects the strength of ultrasound echoes from the thorax very little, while the thorax scales of earless moths absorbs an average of 67 ± 9% of impinging ultrasonic sound energy. We show that the thorax scales of moths provide acoustic camouflage by acting as broadband (20–160 kHz) stealth coating. Modelling results suggest the scales are acting as a porous sound absorber; however, the thorax scales of moths achieve a considerably higher absorption than technical fibrous porous absorbers with the same structural parameters. Such scales, despite being thin and lightweight, constitute a broadband, multidirectional and efficient ultrasound absorber that reduces the moths' detectability to hunting bats and gives them a survival advantage.
Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis
Venue: Nature Chemistry

Type II polyketide synthases (PKSs) are multi-enzyme complexes that produce secondary metabolites of medical relevance. Chemical backbones of such polyketides are produced by minimal PKS systems that consist of a malonyl transacylase, an acyl carrier protein and an α/β heterodimeric ketosynthase. Here, we present X-ray structures of all ternary complexes that constitute the minimal PKS system for anthraquinone biosynthesis in Photorhabdus luminescens . In addition, we characterize this invariable core using molecular simulations, mutagenesis experiments and functional assays. We show that malonylation of the acyl carrier protein is accompanied by major structural rearrangements in the transacylase. Principles of an ongoing chain elongation are derived from the ternary complex with a hexaketide covalently linking the heterodimeric ketosynthase with the acyl carrier protein. Our results for the minimal PKS system provide mechanistic understanding of PKSs and a fundamental basis for engineering PKS pathways for future applications. The invariable core of a type II polyketide synthase has been characterized using X-ray crystallography, simulations, mutagenesis experiments and functional assays. The characterization of the ternary acyl carrier protein complexes provides a mechanistic understanding of the reactivity and could inform future engineering of this complex biosynthetic machinery.
Dynamic, Non-binary Specification of Sexual State in the C. elegans Nervous System
Venue: Current Biology

Biological sex in animals is often considered a fixed, individual-level characteristic. However, not all sex-specific features are static: for example, C. elegans males (XO) can sometimes exhibit hermaphrodite (XX)-like feeding behavior [1, 2]. (C. elegans hermaphrodites are somatic females that transiently produce self-sperm.) Essentially all somatic sex differences in C. elegans are governed by the master regulator tra-1, whose activity is controlled by chromosomal sex and is necessary and sufficient to specify the hermaphrodite state . One aspect of this state is high expression of the chemoreceptor odr-10. In hermaphrodites, high odr-10 expression promotes feeding, but in males, low odr-10 expression facilitates exploration . However, males suppress this sex difference in two contexts: juvenile males exhibit high odr-10 expression and food deprivation activates odr-10 in adult males [4-6]. Remarkably, we find that both of these phenomena require tra-1. In juvenile (L3) males, tra-1 is expressed in numerous neurons; this expression diminishes as individuals mature into adulthood, a process that requires conserved regulators of sexual maturation. tra-1 remains expressed in a small number of neurons in adult males, where it likely has a permissive role in odr-10 activation. Thus, the neuronal functions of tra-1 are not limited to hermaphrodites; rather, tra-1 also acts in the male nervous system to transiently suppress a sexual dimorphism, developmentally and in response to nutritional stress. Our results show that the molecular and functional representation of sexual state in C. elegans is neither static nor homogeneous, challenging traditional notions about the nature of biological sex.
Life cycle of a cyanobacterial carboxysome
Venue: Science Advances

Single cell and organelle measurements reveal activity dynamics and degradation of the carbon-fixing cyanobacterial carboxysome. Carboxysomes, prototypical bacterial microcompartments (BMCs) found in cyanobacteria, are large (~1 GDa) and essential protein complexes that enhance CO2 fixation. While carboxysome biogenesis has been elucidated, the activity dynamics, lifetime, and degradation of these structures have not been investigated, owing to the inability of tracking individual BMCs over time in vivo. We have developed a fluorescence-imaging platform to simultaneously measure carboxysome number, position, and activity over time in a growing cyanobacterial population, allowing individual carboxysomes to be clustered on the basis of activity and spatial dynamics. We have demonstrated both BMC degradation, characterized by abrupt activity loss followed by polar recruitment of the deactivated complex, and a subclass of ultraproductive carboxysomes. Together, our results reveal the BMC life cycle after biogenesis and describe the first method for measuring activity of single BMCs in vivo.
Biosynthetic origin of benzoquinones in the explosive discharge of the bombardier beetle Brachinus elongatulus
Venue: Naturwissenschaften

Bombardier beetles are well-known for their remarkable defensive mechanism. Their defensive apparatus consists of two compartments known as the reservoir and the reaction chamber. When challenged, muscles surrounding the reservoir contract sending chemical precursors into the reaction chamber where they mix with enzymes resulting in an explosive discharge of a hot noxious chemical spray containing two major quinones: 1,4-benzoquinone and 2-methyl-1,4-benzoquinone (toluquinone). Previously, it has been speculated that the biosynthesis of all benzoquinones originates from one core precursor, 1,4-hydroquinone. Careful ligation of the base of the reservoir chamber enabled us to prevent the explosive reaction and sample untransformed reservoir fluid, which showed that it accumulates significant quantities of 1,4-hydroquinone and 2-methyl-1,4-hydroquinone. We investigated the biosynthetic mechanisms leading to quinone formation by injecting or feeding Brachinus elongatulus beetles with stable-isotope-labeled precursors. Chemical analysis of defensive secretion samples obtained from 1,4-hydroquinone-d6-administered beetles demonstrated that it underwent conversion specifically to 1,4-benzoquinone. Analogously, results from m-cresol-d8 injected or fed beetles confirmed that m-cresol is metabolized to 2-methyl-1,4-hydroquinone, which is then oxidized to 2-methyl-1,4-benzoquinone in the hot spray. Our results refute the previous claim that 1,4-hydroquinone is the precursor of all substituted benzoquinones in bombardier beetles and reveal that they are biosynthetic products of two independent pathways. Most likely, the aforementioned biosynthetic channel of hydroxylation of appropriate phenolic precursors and subsequent oxidation is not restricted to bombardier beetles; it could well be a general pathway that leads to the formation of all congeners of benzoquinones, one of the most widely distributed groups of defensive compounds in arthropods.
Wild hummingbirds discriminate nonspectral colors
Venue: Proceedings of the National Academy of Sciences of the United States of America

Birds have four color cone types in their eyes, compared to three in humans. In theory, this enables birds to discriminate a broad range of colors, including many nonspectral colors. Nonspectral colors are perceived when nonadjacent cone types (sensitive to widely separated parts of the light spectrum) are predominantly stimulated. For humans, purple (stimulation of blue- and red-sensitive cones) is a nonspectral color; birds’ fourth color cone type creates many more possibilities. We trained wild hummingbirds to participate in color vision tests, which revealed that they can discriminate a variety of nonspectral colors, including UV+red, UV+green, purple, and UV+yellow. Additionally, based on an analysis of ∼3,300 plumage and plant colors, we estimate that birds perceive many natural colors as nonspectral. Many animals have the potential to discriminate nonspectral colors. For humans, purple is the clearest example of a nonspectral color. It is perceived when two color cone types in the retina (blue and red) with nonadjacent spectral sensitivity curves are predominantly stimulated. Purple is considered nonspectral because no monochromatic light (such as from a rainbow) can evoke this simultaneous stimulation. Except in primates and bees, few behavioral experiments have directly examined nonspectral color discrimination, and little is known about nonspectral color perception in animals with more than three types of color photoreceptors. Birds have four color cone types (compared to three in humans) and might perceive additional nonspectral colors such as UV+red and UV+green. Can birds discriminate nonspectral colors, and are these colors behaviorally and ecologically relevant? Here, using comprehensive behavioral experiments, we show that wild hummingbirds can discriminate a variety of nonspectral colors. We also show that hummingbirds, relative to humans, likely perceive a greater proportion of natural colors as nonspectral. Our analysis of plumage and plant spectra reveals many colors that would be perceived as nonspectral by birds but not by humans: Birds’ extra cone type allows them not just to see UV light but also to discriminate additional nonspectral colors. Our results support the idea that birds can distinguish colors throughout tetrachromatic color space and indicate that nonspectral color perception is vital for signaling and foraging. Since tetrachromacy appears to have evolved early in vertebrates, this capacity for rich nonspectral color perception is likely widespread.
Three-dimensional scaling laws of cetacean propulsion characterize the hydrodynamic interplay of flukes' shape and kinematics

Cetaceans convert dorsoventral body oscillations into forward velocity with a complex interplay between their morphological and kinematic features and the fluid environment. However, it is unknown to what extent morpho-kinematic features of cetaceans are intertwined to maximize their efficiency. By interchanging the shape and kinematic variables of five cetacean species, the interplay of their flukes morpho-kinematic features is examined by characterizing their thrust, power and propulsive efficiency. It is determined that the shape and kinematics of the flukes have considerable influence on force production and power consumption. Three-dimensional heaving and pitching scaling laws are developed by considering both added mass and circulatory-based forces, which are shown to closely model the numerical data. Using the scaling relations as a guide, it is determined that the added mass forces are important in predicting the trend between the efficiency and aspect ratio, however, the thrust and power are driven predominately by the circulatory forces. The scaling laws also reveal that there is an optimal dimensionless heave-to-pitch ratio h* that maximizes the efficiency. Moreover, the optimal h* varies with the aspect ratio, the amplitude-to-chord ratio and the Lighthill number. This indicates that the shape and kinematics of propulsors are intertwined, that is, there are specific kinematics that are tailored to the shape of a propulsor in order to maximize its propulsive efficiency.
Temporal Signatures of Criticality in Human Cortical Excitability as Probed by Early Somatosensory Responses
Venue: The Journal of Neuroscience

Brain responses vary considerably from moment to moment, even to identical sensory stimuli. This has been attributed to changes in instantaneous neuronal states determining the system's excitability. Yet the spatiotemporal organization of these dynamics remains poorly understood. Here we test whether variability in stimulus-evoked activity can be interpreted within the framework of criticality, which postulates dynamics of neural systems to be tuned toward the phase transition between stability and instability as is reflected in scale-free fluctuations in spontaneous neural activity. Using a novel noninvasive approach in 33 male human participants, we tracked instantaneous cortical excitability by inferring the magnitude of excitatory postsynaptic currents from the N20 component of the somatosensory evoked potential. Fluctuations of cortical excitability demonstrated long-range temporal dependencies decaying according to a power law across trials, a hallmark of systems at critical states. As these dynamics covaried with changes in prestimulus oscillatory activity in the alpha band (8-13 Hz), we establish a mechanistic link between ongoing and evoked activity through cortical excitability and argue that the co-emergence of common temporal power laws may indeed originate from neural networks poised close to a critical state. In contrast, no signatures of criticality were found in subcortical or peripheral nerve activity. Thus, criticality may represent a parsimonious organizing principle of variability in stimulus-related brain processes on a cortical level, possibly reflecting a delicate equilibrium between robustness and flexibility of neural responses to external stimuli.  Variability of neural responses in primary sensory areas is puzzling, as it is detrimental to the exact mapping between stimulus features and neural activity. However, such variability can be beneficial for information processing in neural networks if it is of a specific nature, namely, if dynamics are poised at a so-called critical state characterized by a scale-free spatiotemporal structure. Here, we demonstrate the existence of a link between signatures of criticality in ongoing and evoked activity through cortical excitability, which fills the long-standing gap between two major directions of research on neural variability: the impact of instantaneous brain states on stimulus processing on the one hand and the scale-free organization of spatiotemporal network dynamics of spontaneous activity on the other.
Snapping mechanics of the Venus flytrap (Dionaea muscipula)
Venue: Proceedings of the National Academy of Sciences of the United States of America

The rapid closure of the carnivorous Venus flytrap (Dionaea muscipula) snap-trap incorporates snap-buckling instability as a speed boost. The trap actuation principles required to overcome the involved energy barrier, as determined by the double-lobe curvature, have remained speculative until now. Here we used 3D digital image correlation for the analysis of trap deformation during closure for both the outer and the inner trap surfaces. Accompanying biomechanical and physiological experiments revealed that successful snapping relies on full trap hydration. In combination with FEM simulations elucidating the mechanical contribution of the various trap tissues to the motion, we show that the trapping mechanics incorporate an elaborate interplay between swelling/shrinking processes of the various tissue layers and the release of trap-internal prestress. The mechanical principles for fast snapping in the iconic Venus flytrap are not yet fully understood. In this study, we obtained time-resolved strain distributions via three-dimensional digital image correlation (DIC) for the outer and inner trap-lobe surfaces throughout the closing motion. In combination with finite element models, the various possible contributions of the trap tissue layers were investigated with respect to the trap’s movement behavior and the amount of strain required for snapping. Supported by in vivo experiments, we show that full trap turgescence is a mechanical–physiological prerequisite for successful (fast and geometrically correct) snapping, driven by differential tissue changes (swelling, shrinking, or no contribution). These are probably the result of the previous accumulation of internal hydrostatic pressure (prestress), which is released after trap triggering. Our research leads to an in-depth mechanical understanding of a complex plant movement incorporating various actuation principles.
Information can explain the dynamics of group order in animal collective behaviour
Venue: Nature Communications

Animal groups vary in their collective order (or state), forming disordered swarms to highly polarized groups. One explanation for this variation is that individuals face differential benefits or costs depending on the group’s order, but empirical evidence for this is lacking. Here we show that in three-spined sticklebacks ( Gasterosteus aculeatus ), fish that are first to respond to an ephemeral food source do so faster when shoals are in a disordered, swarm-like state. This is because individuals’ visual fields collectively cover more of their environment, meaning private information is more readily available in disordered groups. Once social information becomes available, however, the arrival times of subsequent group members to the food are faster in more ordered, polarized groups. Our data further suggest that first responding individuals (those that benefit from group disorder) maintain larger differences in heading angle to their nearest neighbours when shoaling, thereby explaining how conflict over whether private or social information is favoured can drive dynamic changes in collective behaviour. In animal groups, the degree of alignment of individuals could have different benefits and costs for individuals depending on their reliance on private or social information. Here the authors show that in shoals of three-spined sticklebacks, some individuals reach resources faster when groups are disordered, a state which favours reliance on privately acquired information, while other individuals reach resources faster when groups are ordered, allowing them to exploit social information more effectively.
Curvature-induced stiffening of a fish fin
Venue: Journal of the Royal Society Interface

How fish modulate their fin stiffness during locomotive manoeuvres remains unknown. We show that changing the fin's curvature modulates its stiffness. Modelling the fin as bendable bony rays held together by a membrane, we deduce that fin curvature is manifested as a misalignment of the principal bending axes between neighbouring rays. An external force causes neighbouring rays to bend and splay apart, and thus stretches the membrane. This coupling between bending the rays and stretching the membrane underlies the increase in stiffness. Using three-dimensional reconstruction of a mackerel (Scomber japonicus) pectoral fin for illustration, we calculate the range of stiffnesses this fin is expected to span by changing curvature. The three-dimensional reconstruction shows that, even in its geometrically flat state, a functional curvature is embedded within the fin microstructure owing to the morphology of individual rays. As the ability of a propulsive surface to transmit force to the surrounding fluid is limited by its stiffness, the fin curvature controls the coupling between the fish and its surrounding fluid. Thereby, our results provide mechanical underpinnings and morphological predictions for the hypothesis that the spanned range of fin stiffnesses correlates with the behaviour and the ecological niche of the fish.