bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids
Authors: Machii Nagatoshi , Hatashima Ryo , Niwa Tatsuya , Taguchi Hideki , Kimirei Ismael A. , Mrosso Hillary D. J. , Aibara Mitsuto , Nagasawa Tatsuki , Nikaido Masato 
Published: April 2024

AbstractCichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, “hypertrophied lip” has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.
Sex-peptide targets distinct higher order processing neurons in the brain to induce the female post-mating response
Authors: Nallasivan Mohanakarthik P. , Singh Deepanshu N.D. , Saleh Mohammed Syahir R. S. , Soller Matthias 
Published: April 2024

AbstractSex-peptide (SP) transferred during mating induces female post-mating responses including refractoriness to re-mate and increased oviposition inDrosophila. Yet, where SP target neurons reside, remained uncertain. Here we show that expression of membrane-tethered SP (mSP) in the head or trunk either reduces receptivity or increases oviposition, respectively. Using fragments from large regulatory regions ofSex Peptide Receptor,fruitlessanddoublesexgenes together with intersectional expression of mSP, we identified distinct interneurons in the brain and abdominal ganglion controlling receptivity and oviposition. These interneurons can induce post-mating responses through SP received by mating. Trans-synaptic mapping of neuronal connections reveals input from sensory processing neurons and two post-synaptic trajectories as output. Hence, SP target neurons operate as key integrators of sensory information for decision of behavioural outputs. Multi-modularity of SP targets further allows females to adjust SP-mediated male manipulation to physiological state and environmental conditions for maximizing reproductive success.
Impacts of global warming on fertility of male fishes: evidence from meta-analysis of temperature effects on spermatozoa motility
Authors: Cheng Yu , Wang Jinhai , Alavi Sayyed Mohammad Hadi , Zhang Songpei , Linhartová Zuzana , Roy Deepali Rahi , Shazada Nururshopa Eskander , Dzyuba Borys , Linhart Otomar 
Published: April 2024

AbstractStudies have demonstrated adverse effects of global warming on aquatic ecosystems from the abiotic to the biotic level. In the present work, a meta-analysis study was conducted to elucidate the effects of global warming on spermatozoa functions, which are key determinants of male fertility. We recruited 245 data records from a pool of empirical studies, which includes 20 studies spanning 20 cold- and warm-water fish species, to identify the effects of increased water temperature (IWT) on determinants of sperm fertility in fishes. Data were systematically re-processed and re-analyzed to determine the overall effects of IWT on sperm kinetics such as motility (MOT), duration of motility (DSM), curvilinear velocity (VCL), rectilinear velocity (VSL) and average path velocity (VAP), as well as on enzymatic activities for energy supply (EAES) and antioxidant enzyme activity (ANEA). The standardized mean difference was calculated for each study, with positive values indicating higher performance under IWT. Results showed that (a) the overall effect size for MOT was more negative in cold-water fishes (-1.22) than in warm-water fishes (-0.98). (b) Each 1 °C increase in the activation medium reduced MOT by 1.30% (cold-water fishes) and 3.47% (warm-water fishes). (c) The IWT negatively affected DSM, decreasing it by 10 s (cold-water species) and 5.64 s (warm-water species) per degree of IWT. (d) Spermatozoa velocity (VCL and VSL) was increased by IWT in warm-water species. In conclusion, this study shows that IWT negatively affects sperm motility kinetics, suggesting an impact of global warming on fish reproduction.
Coastal oceanographic connectivity estimates at the global scale
Authors: Assis Jorge , Legrand Terence , Fragkopoulou Eliza , Serrão Ester A. , Araújo Miguel 
Published: April 2024

MotivationOceanographic connectivity driven by ocean currents is critical in determining the distribution of marine biodiversity. It mediates the genetic and individual exchange between populations, from structuring dispersal barriers that promote long-term isolation to enabling long-distance dispersal that underpins species expansion and resilience against climate change. Despite its significance, comprehensive estimates of oceanographic connectivity on a global scale remain unavailable, while traditional approaches, often simplistic, fail to capture the complexity of oceanographic factors contributing to population connectivity. This gap hinders a deeper understating of species’ dispersal ecology, survival, and evolution, ultimately precluding the development of effective conservation strategies aimed at preserving marine biodiversity. To address this challenge, we present a comprehensive dataset of connectivity estimates along the world’s coastlines, known for their rich marine biodiversity. These estimates are derived from a biophysical modelling framework that combines high-resolution ocean current data with graph theory to predict multi-generational stepping-stone connectivity. Alongside, we provide coastalNet, an R package designed to streamline access, analysis, and visualization of connectivity estimates. This tool enhances the utility and application of the data, adhering to the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. The dataset and package set a new benchmark for research in oceanographic connectivity, allowing a better exploration of the complex dynamics of coastal marine ecosystems.Main types of variables containedPairwise connectivity estimates (probability and time) between coastal sites.Spatial location and grainGlobal, equal-area hexagons with 8.45 km edge length.Time period and grainDaily, from 2000 to 2020.Major taxa and level of measurementCoastal marine biodiversity.Software formatA package of functions developed for R software.
Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities
Authors: Emelianova Katie , Hawranek Anna-Sophie , Eriksson Mimmi C. , Wolfe Thomas M. , Paun Ovidiu 
Published: April 2024

SummaryPhenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalisandD. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species.Significance statementThis study highlights the role of phenotypic plasticity in the persistence and distribution of sibling allopolyploid marsh orchids (Dactylorhiza majaliss.l.). By examining gene expression and the diversity of root mycobiome across reciprocal transplantations in native environments, we uncover high plasticity that facilitates adaptation and gene flow, thereby promoting both diversification and homogenization. These findings underscore the importance of plasticity in the establishment and long-term survival of allopolyploid species across the landscape.
Inferring species interactions from co-occurrence networks with environmental DNA metabarcoding data in a coastal marine food-web
Authors: Boyse Elizabeth , Robinson Kevin P. , Carr Ian M. , Beger Maria , Goodman Simon J. 
Published: April 2024

AbstractImproved understanding of biotic interactions is necessary to accurately predict the vulnerability of ecosystems to climate change. Recently, co-occurrence networks built from environmental DNA (eDNA) metabarcoding data have been advocated as a means to explore interspecific interactions in ecological communities exposed to different human and environmental pressures. Co-occurrence networks have been widely used to characterise microbial communities, but it is unclear if they are effective for characterising eukaryotic ecosystems, or whether biotic interactions drive inferred co-occurrences. Here, we assess spatiotemporal variability in the structure and complexity of a North Sea coastal ecosystem inferred from co-occurrence networks and food webs using 60 eDNA samples covering vertebrates and other eukaryotes. We compare topological characteristics and identify potential keystone species,i.e., highly connected species, across spatial and temporal subsets, to evaluate variance in community composition and structure. We find consistent trends in topological characteristics across co-occurrence networks and food webs, despite trophic interactions forming a minority of significant co-occurrences. Known keystone species in food webs were not highly connected in co-occurrence networks. The lack of significant trophic interactions detected in co-occurrence networks may result from ecological complexities such as generalist predators having flexible interactions or behavioural partitioning, as well as methodological limitations such as the inability to distinguish age class with eDNA, or co-occurrences being driven by other interaction types or shared environmental requirements. Deriving biotic interactions with co-occurrence networks constructed from eDNA requires further validation in well-understood ecosystems, and improved reporting of methodological limitations, such as species detection uncertainties, which could influence inferred ecosystem complexity.
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data
Authors: Kelly Katherine , Scherer Michael , Braun Martina Maria , Lutsik Pavlo , Plass Christoph 
Published: April 2024

AbstractEpigenetic heterogeneity is a fundamental property of biological systems, and is recognized as a potential driver of tumor plasticity and therapy resistance. Single-cell epigenomics technologies have been widely employed to study epigenetic variation between – but not within – cellular clusters. We introduce epiCHAOS: a quantitative metric of cell-to-cell heterogeneity, applicable to any single-cell epigenomics data type. After validation in synthetic datasets, we applied epiCHAOS to investigate global and region-specific patterns of epigenetic heterogeneity across diverse biological systems. EpiCHAOS provides an excellent approximation of stemness and plasticity in development and malignancy, making it a valuable addition to single-cell cancer epigenomics analyses.
Biodetection of an odor signature in white-tailed deer associated with infection by chronic wasting disease prions
Authors: Golden Glen J. , Ramirez Elizabeth A. , Stevens Hayley N. , Bourbois Jennifer , Grove Daniel , Bowen Richard A. , DeLiberto Thomas J. , Kimball Bruce A. 
Published: April 2024

AbstractChronic wasting disease (CWD) has become a major concern among those involved in managing wild and captive cervid populations. CWD is a fatal, highly transmissible spongiform encephalopathy caused by an abnormally folded protein, called a prion. Prions are present in a number of tissues, including feces and urine in CWD infected animals, suggesting multiple modes of transmission, including animal-to-animal, environmental, and by fomite. CWD management is complicated by the lack of practical, non-invasive, live-animal screening tests. We previously demonstrated that ferrets were able to detect and discriminate fecal samples from ducks infected or not infected with avian influenza virus based on odor. That work clearly predicted that animal biodetectors can be trained to identify populations and/or individuals infected with CWD via detection of fecal odors. Such a tool may also prove useful in identifying potentially infected live animals, carcasses, urine, feces, and contaminated environments. Toward this goal, dogs were trained to detect and discriminate CWD infected individuals from non-infected deer in a laboratory setting. Dogs were tested with novel panels of fecal samples demonstrating the dogs’ ability to generalize a learned odor profile to novel odor samples based on infection status. Additionally, dogs were transitioned from alerting to fecal samples to an odor profile that consisted of CWD infection status with a different odor background using different sections of gastrointestinal tracts. These results indicated that canine biodetectors can discriminate the specific odors emitted from the feces of non-infected versus CWD infected white-tailed deer as well as generalizing the learned response to other tissues collected from infected individuals. These findings suggest that the health status of wild and farmed cervids can be evaluated non-invasively for CWD infection via monitoring of volatile metabolites thereby providing an effective tool for rapid CWD surveillance.
Finding Fluorescence: Utilizing community science to document novel biofluorescence occurrences and encourage community engagement in science
Authors: Burke Hannah , Serrano Lauren , Lemmon Emily , Whitcher Courtney 
Published: April 2024

AbstractFluorescence, a form of photoluminescence, is the emission of light at a longer wavelength by a substance when exposed to shorter-wavelength energy. Biofluorescence, which can be observed in living organisms, involves the absorption of light at one wavelength and re-emission at a longer wavelength due to fluorophores in specialized cells or structures. While initially studied in marine organisms, attention has shifted to exploring biofluorescence in terrestrial organisms, revealing roles in reproduction, camouflage, communication, and prey attraction across phyla. Community science databases engage the public in data collection, fostering scientific discovery and strengthening the science-society connection. Such databases have become valuable tools and have aided scientists in understanding the natural history of many different traits in organisms. This paper introducesFinding Fluorescence, the first biofluorescence-based community science website established in 2020 to gather public observations of biofluorescent organisms. The study presents at least 15 novel biofluorescence accounts spanning five phyla, 15 families, and 15 species. The observations collected fromFinding Fluorescencecontribute to our understanding of fluorescence in organisms and provide insight into possible ecological functions. We emphasize the importance of community engagement in scientific exploration and encourage future studies to incorporate such aspects into their research.
Treg fitness as a biomarker for disease activity in Juvenile Idiopathic Arthritis
Authors: Attrill Meryl H. , Shinko Diana , Viveiros Telma Martins , Milighetti Martina , de Gruijter Nina M. , Jebson Bethany , Kartawinata Melissa , Rosser Elizabeth C. , Wedderburn Lucy R. ,   CHARMS study,   JIAP study, Pesenacker Anne M. 
Published: April 2024

AbstractJuvenile Idiopathic Arthritis (JIA) is an autoimmune condition characterised by persistent flares of joint inflammation. However, no reliable biomarker exists to predict the erratic disease course. Normally, regulatory T cells (Tregs) maintain immune tolerance, with altered Tregs associated with autoimmunity. Treg signatures have shown promise in monitoring other autoimmune conditions, therefore a Treg gene and/or protein signature could offer novel biomarker potential for predicting disease activity in JIA.Machine learning on our nanoString Treg gene signature on peripheral blood (PB) Tregs generated a model to distinguish active JIA (active joint count, AJC≥1) Tregs from healthy controls (HC, AUC=0.9875). Biomarker scores from this model successfully differentiated inactive (AJC=0) from active JIA PB Tregs. Moreover, scores correlated with clinical activity scores (cJADAS), and discriminated subclinical disease (AJC=0, cJADAS≥0.5) from remission (AUC=0.8980, Sens=0.8571, Spec= 0.8571).To investigate altered Treg fitness in JIA by protein expression, we utilised spectral flow cytometry and unbiased analysis. Three Treg clusters were increased in active JIA PB, including CD226highCD25loweffector-like Tregs and CD39-TNFR2-Helioshigh, while a 4-1BBlowTIGITlowID2intermediateTreg cluster predominated in inactive JIA PB (AJC=0). The ratio of these Treg clusters correlated to cJADAS, and higher ratios could predict inactive individuals that flared by 6-month follow-up.Thus, we demonstrate altered Treg signatures and subsets as an important factor, and useful biomarker, for disease progression versus remission in JIA, revealing genes and proteins important in Treg fitness. Ultimately, PB Treg fitness measures could serve as routine biomarkers to guide disease and treatment management to sustain remission in JIA.
The nuclear sulfenome ofArabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols
Authors: Smet Barbara De , Yang Xi , Plskova Zuzana , Castell Carmen , Fernandez-Fernandez Alvaro , Dard Avilien , Mhamdi Amna , Vertommen Didier , Chan Kai Xun , Pyr dit Ruys Sébastien , Messens Joris , Kerchev Pavel I. , Breusegem Frank Van 
Published: April 2024

AbstractPartial reduction of oxygen during energy generating metabolic processes in aerobic life forms results in the production of reactive oxygen species (ROS). In plants, ROS production is heightened during periods of both abiotic and biotic stress, which imposes a significant overload on the antioxidant systems. Hydrogen peroxide (H2O2) holds a central position in cellular redox homeostasis and signalling, playing an important role by oxidising crucial cysteines to sulfenic acid (-SOH), considered as a biologically relevant post-translational modification (PTM). Until now, the role of the nucleus in the cellular redox homeostasis has been relatively underexplored. The regulation of histone-modifying enzymes by oxidative PTMs on redox-active cysteines or tyrosine residues is particularly intriguing as it allows the integration of redox signalling mechanisms with chromatin control of transcriptional activity. One of the most extensively studied histone acetyltransferases is the conserved GENERAL CONTROL NONDEPRESSIBLE 5 (GCN5) complex. This study investigated the nuclear sulfenome inArabidopsis thalianaby expressing a nuclear variant of the Yeast Activation Protein-1 (YAP) probe, identifying 225 potential redox-active nuclear proteins subject to sulfenylation. Mass spectrometry analysis further confirmed the sulfenylation of GCN5 at specific cysteine residues, with their functional significance and impact on the protein-protein interaction network assessed through cysteine-to-serine mutagenesis.HighlightProtein cysteine thiols are post-translationally modified under oxidative stress. Through thein vivocapturing of nuclear proteins undergoing sulfenylation inArabidopsis, we highlight the functionality of particular cysteines in the histone acetyltransferase GCN5.
StomaVision: stomatal trait analysis through deep learning
Authors: Wu Ting-Li , Chen Po-Yu , Du Xiaofei , Wu Heiru , Ou Jheng-Yang , Zheng Po-Xing , Wu Yu-Lin , Wang Ruei-Shiuan , Hsu Te-Chang , Lin Chen-Yu , Lin Wei-Yang , Chang Ping-Lin , Ho Chin-Min Kimmy , Lin Yao-Cheng 
Published: April 2024

SummaryStomaVision is an automated tool designed for high-throughput detection and measurement of stomatal traits, such as stomatal number, pore size, and closure rate. It provides insights into plant responses to environmental cues, streamlining the analysis of micrographs from field-grown plants across various species, including monocots and dicots. Enhanced by a novel collection method that utilizes video recording, StomaVision increases the number of captured images for robust statistical analysis. Accessible via an intuitive web interface at <https://stomavision.streamlit.app/> and available for local use in a containerized environment at <https://github.com/YaoChengLab/StomaVision>, this tool ensures long-term usability by minimizing the impact of software updates and maintaining functionality with minimal setup requirements. The application of StomaVision has provided significant physiological insights, such as variations in stomatal density, opening rates, and total pore area under heat stress. These traits correlate with critical physiological processes, including gas exchange, carbon assimilation, and water use efficiency, demonstrating the tool’s utility in advancing our understanding of plant physiology. The ability of StomaVision to identify differences in responses to varying durations of heat treatment highlights its value in plant science research.Plain language summaryStomaVision is a tool that automatically counts and measures tiny openings on plant leaves, helping us learn how plants deal with their surroundings. It is easy to use and works well with various plant species. This tool helps scientists see how plants change under stress, making plant research easier and more accurate.