bluuebunny/crossref_metadata_2025_split huggingface dataset:
An optimised approach to evaluate variability in gut health markers in healthy adults
Authors: Krüger Kirsten , Myeonghyun Yoou , van der Wielen Nicky , Kok Dieuwertje , Hooiveld Guido J. , Keshtkar Shohreh , Diepeveen-de Bruin Marlies , Balvers Michiel G.J. , Grootte-Bromhaar Mechteld , Mudde Karin , Ly Nhien T.H.N , Vermeiren Yannick , de Groot Lisette C.P.G.M , de Vos Ric C.H. , Gonzales Gerard Bryan , Steegenga Wilma T. , van Trijp Mara P.H. 
Published: July 2024

AbstractDespite advances in gut health research, the variability of important gut markers within individuals over time remains underexplored. We investigated the intra-individual variation of various faecal gut health markers using an optimised processing protocol aimed at reducing variability. Faecal samples from ten healthy adults over three consecutive days demonstrated marker-specific intra-individual coefficients of variation (CV%), namely: stool consistency (16.5%), water content (5.7%), pH (3.9%), total SCFAs (17.2%), total BCFAs (27.4%), total bacteria and fungi copies (40.6% and 66.7%), calprotectin and myeloperoxidase (63.8% and 106.5%), and untargeted metabolites (on average 40%). For thirteen microbiota genera, includingBifidobacteriumandAkkermansia, variability exceeded 30%, whereas microbiota diversity was less variable (Phylogenetic Diversity 3.3%, Inverse Simpson 17.2%). Mill-homogenisation of frozen faeces significantly reduced the replicates CV% for total SCFAs (20.4% to 7.5%) and total BCFAs (15.9% to 7.8%), and untargeted metabolites compared to only faecal hammering, without altering mean concentrations. Our results show the potential need for repeated sampling to accurately represent specific gut health markers. We also demonstrated the effectiveness of optimised preprocessing of stool samples in reducing overall analytical variability.
Endothelial TRPV4/Cx43 Signaling Complex Regulates Vasomotor Tone in Resistance Arteries
Authors: Burboa Pía C. , Gaete Pablo S. , Shu Ping , Araujo Priscila A. , Beuve Annie V. , Durán Walter N. , Contreras Jorge E. , Lillo Mauricio A. 
Published: July 2024

ABSTRACTS-nitrosylation of Cx43 gap junction channels critically regulates communication between smooth muscle cells and endothelial cells. This posttranslational modification also induces the opening of undocked Cx43 hemichannels. However, its specific impact on vasomotor regulation remains unclear. Considering the role of endothelial TRPV4 channel activation in promoting vasodilation through nitric oxide (NO) production, we investigated the direct modulation of endothelial Cx43 hemichannels by TRPV4 channel activation. Using the proximity ligation assay, we identify that Cx43 and TRPV4 are found in close proximity in the endothelium of resistance arteries. In primary endothelial cell cultures from resistance arteries (ECs), GSK-induced TRPV4 activation enhances eNOS activity, increases NO production, and opens Cx43 hemichannels via direct S-nitrosylation. Notably, the elevated intracellular Ca2+levels caused by TRPV4 activation were reduced by blocking Cx43 hemichannels. In ex vivo mesenteric arteries, inhibiting Cx43 hemichannels reduced endothelial hyperpolarization without affecting NO production in ECs, underscoring a critical role of TRPV4/Cx43 signaling in endothelial electrical behavior. We perturbed the proximity of Cx43/TRPV4 by disrupting lipid rafts in ECs using β-cyclodextrin. Under these conditions, hemichannel activity, Ca2+influx, and endothelial hyperpolarization were blunted upon GSK stimulation. Intravital microscopy of mesenteric arteriolesin vivofurther demonstrated that inhibiting Cx43 hemichannels activity, NO production and disrupting endothelial integrity reduce TRPV4-induced relaxation. These findings underscore a new pivotal role of Cx43 hemichannel associated with TRPV4 signaling pathway in modulating endothelial electrical behavior and vasomotor tone regulation.
Multi-species genome-wide CRISPR screens identify conserved suppressors of cold-induced cell death
Authors: Lam Breanna , Kajderowicz Kathrin M. , Keys Heather R. , Roessler Julian M. , Frenkel Evgeni M. , Kirkland Adina , Bisht Punam , El-Brolosy Mohamed A. , Jaenisch Rudolf , Bell George W. , Weissman Jonathan S. , Griffith Eric C. , Hrvatin Sinisa 
Published: July 2024

SummaryCells must adapt to environmental changes to maintain homeostasis. One of the most striking environmental adaptations is entry into hibernation during which core body temperature can decrease from 37°C to as low at 4°C. How mammalian cells, which evolved to optimally function within a narrow range of temperatures, adapt to this profound decrease in temperature remains poorly understood. In this study, we conducted the first genome-scale CRISPR-Cas9 screen in cells derived from Syrian hamster, a facultative hibernator, as well as human cells to investigate the genetic basis of cold tolerance in a hibernator and a non-hibernator in an unbiased manner. Both screens independently revealed glutathione peroxidase 4 (GPX4), a selenium-containing enzyme, and associated proteins as critical for cold tolerance. We utilized genetic and pharmacological approaches to demonstrate that GPX4 is active in the cold and its catalytic activity is required for cold tolerance. Furthermore, we show that the role of GPX4 as a suppressor of cold-induced cell death extends across hibernating species, including 13-lined ground squirrels and greater horseshoe bats, highlighting the evolutionary conservation of this mechanism of cold tolerance. This study identifies GPX4 as a central modulator of mammalian cold tolerance and advances our understanding of the evolved mechanisms by which cells mitigate cold-associated damage—one of the most common challenges faced by cells and organisms in nature.
Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020
Authors: Richard Gautier , Hervé Séverine , Chastagner Amélie , Quéguiner Stéphane , Beven Véronique , Hirchaud Edouard , Barbier Nicolas , Gorin Stéphane , Blanchard Yannick , Simon Gaëlle 
Published: July 2024

AbstractSwine influenza A viruses (swIAV) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022. Molecular subtyping revealed a marked increase in H1avN2 cases from 2020 onwards, altering the previously stable subtypes’ distribution. Whole-genome sequencing and phylogenetic analyses of H1av(1C) strains identified ten circulating genotypes, including five new genotypes, marked by a significant predominance of the H1avN2#E genotype. It was characterized by an HA-1C.2.4, an N2-Gent/84, and internal protein-encoding genes belonging to a newly defined genogroup within the Eurasian avian-like (EA) lineage, the EA-DK subclade. H1avN2#E emerged in Brittany, the country’s most pig-dense region, and rapidly became the most frequently detected swIAV genotype across France. This drastic change in the swIAV lineages proportions at a national scale was unprecedented, making H1avN2#E a unique case for understanding swIAV evolution and spreading patterns. Phylogenetic analyses suggested an introduction of the H1avN2#E genotype from a restricted source, likely originating from Denmark. It spread rapidly with low genetic diversity at the start of the epizootic in 2020, showing increasing diversification in 2021 and 2022, and exhibiting reassortments with other enzootic genotypes. Amino acid sequence alignments of H1avN2#E antigenic sites revealed major mutations and deletions compared to vaccine 1C strain (HA-1C.2.2) and previously predominant H1avN1 strains (HA-1C.2.1). Antigenic cartography confirmed significant antigenic distances between H1avN2#E and other 1C strains, suggesting the new genotype escaped from the swine population preexisting immunity. Epidemiologically, the H1avN2#E virus exhibited epizootic hallmarks with more severe clinical outcomes compared to H1avN1 viruses. These factors likely contributed to the spread of H1avN2#E within the pig population. The rapid rise of H1avN2#E highlighted the dynamic nature of swIAV genetic and antigenic diversity, underscoring the importance of adapted surveillance programs to support risk assessment in the event of new outbreaks. This also demonstrate the need to strengthen biosecurity measures when receiving pigs in a herd and to limit trading of swIAV-excreting live swine between European countries.
Spotted hyena gut cross-talks: Symbionts modulate mucosal immunity
Authors: Soares Susana P. V. , Jarquín-Díaz Victor Hugo , Veiga Miguel M. , Karl Stephan , Czirják Gábor Á. , Weyrich Alexandra , Metzger Sonja , East Marion L. , Hofer Heribert , Heitlinger Emanuel , Benhaiem Sarah , Ferreira Susana C. M. 
Published: July 2024

AbstractThe intestinal mucosa is at the front line of host-microbiome interactions, but little is known about these interactions within natural populations. Here, we non-invasively investigated associations between the gut microbiome and mucosal immune measures while controlling for host, social, and ecological factors in 199 samples of 158 wild spotted hyenas (Crocuta crocuta) in the Serengeti National Park, Tanzania. We profiled the microbiome composition, including bacteria, fungi and parasites, using a multi-amplicon approach, and measured faecal immunoglobulin A and mucin. Probabilistic models indicated that both immune measures predict microbiome similarity among individuals in an age-dependent manner. The strength of the association effect varied, being strongest within bacteria, intermediate within parasites, and weakest within fungi communities. Machine learning regression accurately predicted both measures and identified the taxa driving these associations: symbiotic bacteria reported in humans and laboratory mice, unclassified bacteria, a hookworm, host DNA likely reflecting inflammation, and diet. Our findings indicate a complex interplay between the host, its environment and symbionts. These findings increase our knowledge of the gut microbiome in natural populations, which harbour highly dynamic and diverse eukaryotes under the influence of unpredictable environmental factors and where selection is not artificially biased.
Environmental stiffness regulates neuronal maturation via Piezo1-mediated TTR activity
Authors: Kreysing Eva , Gautier Hélène , Humphrey Robert , Mooslehner Katrin , Muresan Leila , Haarhoff Daniel , Mukherjee Sudipta , Zhao Xiaohui , Winkel Alexander , Dimitracopoulos Andrea , Pillai Eva K. , Káradóttir Ragnhildur Thóra , Franze Kristian 
Published: July 2024

AbstractDuring brain development, neurons extend axons to connect to their target cells while initiating a maturation process, during which neurons start expressing voltage-gated ion channels, form synapses, express synaptic transmitters and receptors, and start communicating via action potentials. Little is known about external factors regulating this process. Here, we identified environmental mechanics as an important regulator of neuronal maturation, and a molecular pathway linking tissue stiffness to this process. Using patch clamp electrophysiology, calcium imaging and immunofluorescence, we found that neurons cultured on stiffer substrates showed a delay in voltage-gated ion channel activity, spontaneous and evoked action potentials, and synapse formation. RNA sequencing and CRISPR/Cas9 knockdown strategies revealed that the mechanosensitive ion channel Piezo1 supresses transthyretin (TTR) expression on stiffer substrates, slowing down synaptic receptor expression and consequently electrical maturation. Stiffening of brain tissue inXenopus laevisembryos also resulted in a significant delay of synaptic activityin vivo. Our data indicate that environmental stiffness represents a fundamental regulator of neuronal maturation, which is important for the development of normal circuitry in the brain, and potentially for neurodevelopmental disorders.
Exploring the impacts of human breast milk functional lipidome on infant health and growth outcomes in early life using lipid bioinformatics
Authors: Ganeshalingam Moganatharsa , Cheema Sukhinder , Wagner Carol L. , Pham Thu Huong , Enstad Samantha , Andrews Chloe , Grapov Dmitry , Esposito Flavia , Sen Sarbattama , Thomas Raymond 
Published: July 2024

AbstractHuman breast milk lipidome is complex, and how changes in the functional lipid metabolism converge systematically to alter infants’ health outcomes is poorly understood. We used human breast milk and infant-mother dyads as a test system to demonstrate how the application of improved lipid bioinformatics can be effective in discerning systematic changes in functional lipid metabolism providing novel discoveries of how lactational programming in early life can influence infant health and growth outcomes. The study consisted of 40 mother-infant dyads where breast milk, maternal diet, infant anthropometrics [fat mass index (FMI), length z score, BMI z score, fat-free mass index (FFMI)], and infant atopic disease outcome (ear infection, cold, wheezing, diarrhea, and eczema) were collected at one and four months postpartum. Integrated Lipid Bioinformatics analyses were conducted using XLSTAT, Metaboanalyst 5.0. R software, Lipid Search, Xcalibur, and Cytoscape software. The results showed breast milk lipidome ordinated into distinct clusters based on maternal BMI status, and differences in developmental and atopic disease outcomes following redundancy analysis. Specifically, lipids from obese mothers clustered with FMI and eczema, while lipids from non-obese mothers clustered with FFM and wheezing. Receiver operating analysis was effective in identifying potential lipid biomarkers that were significantly associated with infant FMI, FFMI, and eczema during early life. Sphingolipid and glycerophospholipid pathways were significantly associated with the altered breast milk lipidome impacting infant development and atopic disease outcome during the first year of life. The findings following the advanced lipid bioinformatics suggest that the breastmilk functional lipid metabolism appears to play a key role in lipid-mediated lactational programming influencing development and atopic disease outcome, and present opportunities for potential dietary intervention in early life.
Evolution of a central dopamine circuit underlies adaptation of light-evoked sensorimotor response in the blind cavefish,Astyanax mexicanus
Authors: Kozol RA , Canavan A , Tolentino B , Keene AC , Kowalko JE , Duboué ER 
Published: July 2024

AbstractAdaptive behaviors emerge in novel environments through functional changes in neural circuits. While relationships between circuit function and behavior have been well studied, how evolution shapes those circuits and leads to behavioral adpation is poorly understood. The Mexican cavefish, Astyanax mexicanus, provides a unique genetically amendable model system, equipped with above ground eyed surface fish and multiple evolutionarily divergent populations of blind cavefish that have evolved in complete darkness. These differences in environment and vision provide an opprotunity to examine how a neural circuit is functionally influenced by the presence of light. Here, we examine differences in the detection, and behavioral response induced by non visual light reception. Both populations exhibit photokinetic behavior, with surface fish becoming hyperactive following sudden darkness and cavefish becoming hyperactive following sudden illumination. To define these photokinetic neural circuits, we integrated whole brain functional imaging with ourAstyanaxbrain atlas for surface and cavefish responding to light changes. We identified the caudal posterior tuberculum as the central modulator for both light or dark stimulated photokinesis. To unconver how spatiotemporal neuronal activity differed between surface fish and cavefish, we used stable pan-neuronal GCaMPAstyanaxtransgenics to show that a subpopulation of darkness sensitve neurons in surface fish are now light senstive in cavefish. Further functional analysis revealed that this integrative switch is dependent on dopmane signaling, suggesting a key role for dopamine and a highly conserved dopamine circuit in modulating the evolution of a circuit driving an essential behavior. Together, these data shed light into how neural circuits evolved to adapte to novel settings, and reveal the power ofAstyanaxas a model to elucidate mechanistic ingiths underlying sensory adaptation.Abstract Figure
Evaluation of Methodologies in Anti-nephrin Autoantibody Detection
Authors: Liu Pan , Liu Shuping , Dalal Vidhi , Lane Jerome , Gessaroli Elisa , Forte Eleonora , Gallon Lorenzo , Jin Jing 
Published: July 2024

ABSTRACTRecent studies discovered the prominent presence of anti-nephrin autoantibodies in minimal change disease, steroid-sensitive nephrotic syndrome and/or post-transplant recurrent focal segmental glomerulosclerosis (FSGS). However, widely different, and often unconventional autoantibody detection methods were used among these studies, making it challenging to assess the pathogenic role for the antibodies. Here we examined methods of conventional ELISA, magnetic on-beads ELISA, immunoprecipitation-immunoblotting (IP-IB), and cell- and tissue-based antibody assays with 127 plasma samples of kidney and non-kidney diseases. On the antigen side, we compared commercially available recombinant human nephrin extracelluar domain (ECD) produced from human or mouse cell lines, as well as lab-made full length, ECD, and series of ECD truncates for measuring autoantibody reactivity and specificity. Surprisingly, different assay methods and different antigen preparations led to observation of assay-specific false-positive and false-negative results. In general, a set of tests that combines magnetic beads-enhanced ELISA, followed by IP-IB, and epitope mapping showed the most robust results for anti-nephrin autoantibodies, detected in two primary FSGS patients among all cases tested. It is interesting to note that cell/tissue-based results, also supported by antigen truncation studies, clearly suggest steric hindrance of reactive epitopes, as in full length nephrin that forms compact self-associated complexes. In conclusion, anti-nephrin positivity is rare among the tested patients (2/127), including those with FSGS (2/42), and autoantibody results can be affected by the choice of detection methods.
Coordinate control of the RNA polymerase II transcription cycle by CDK9-dependent, tripartite phosphorylation of SPT5
Authors: Sun Rui , Fisher Robert P. 
Published: July 2024

SUMMARYThe RNA polymerase II (RNAPII) transcription cycle is regulated throughout its duration by reversible protein phosphorylation. The elongation factor SPT5 contains two regions targeted by cyclin-dependent kinase 9 (CDK9) and previously implicated in promoter-proximal pausing and termination: the linker between KOWx-4 and KOW5 domains and carboxy-terminal repeat (CTR) 1, respectively. Here we show that phosphorylations in the KOWx-4/5 linker, CTR1 and a third region, CTR2, coordinately control pause release, elongation speed and RNA processing. Pausing was increased by mutations preventing CTR1 or CTR2 phosphorylation, but attenuated when both CTRs were mutated. Whereas mutating CTR1 alone slowed elongation and repressed nascent transcription, simultaneous mutation of CTR2 partially reversed both effects. Nevertheless, mutating both CTRs led to aberrant splicing, dysregulated termination and diminished steady-state mRNA levels, and impaired cell proliferation more severely than did either single-CTR mutation. Therefore, tripartite SPT5 phosphorylation times pause release and regulates RNAPII elongation rates positively and negatively to ensure productive transcription and cell viability.
Climatic determinants of plant phenology in vernal pool habitats
Authors: Hendrickson Brandon Thomas , Heckel Aubrie , Martin Robert , Sexton Jason 
Published: July 2024

AbstractVernal pool plants are small, colorful, and specialized to both desiccated and inundated conditions that distinguish the ephemeral wetlands in which they grow. These species germinate rapidly in response to the first rain and grow quickly to take advantage of available water supplies. The floral phenology of vernal pool plant species is little understood despite being a crucial developmental stage for producing seeds and determining population growth rates. The current study focuses on two vernal pool plants,Limnanthes douglasiissp.rosea(meadowfoam), a vernal pool specialist, andTrifolium variegatum(whitetip clover), a generalist vernal pool associate, and characterizes their phenology in response to interannual climate variation. We recorded phenology and climate data over seven years during a period of highly variable precipitation and temperature patterns, which serve as a robust dataset for quantifying the relationship of floral phenology with various climatic factors. We found that warmer and drier environmental conditions occurring during early growth periods were strongly associated with advanced floral phenology later in the life cycle for both species. Over the seven-year dataset, which was increasingly warm and dry, phenology advanced by 4.7 days per year for meadowfoam and 5.6 days per year for whitetip clover, respectively. The floral duration of the habitat specialist was influenced by microtopographic features of vernal pools, whereas no such patterns were observed for the habitat generalist. Finally, warmer and drier conditions were associated with reduced occupancy rates of both focal species within vernal pools. To our knowledge, this is the first study quantifying the relationship between vernal pool floral phenology and climate, offering insights into how phenology may shift in response to modern climate change.
Prediction of protein subcellular localization in single cells
Authors: Zhang Xinyi , Tseo Yitong , Bai Yunhao , Chen Fei , Uhler Caroline 
Published: July 2024

AbstractThe subcellular localization of a protein is important for its function and interaction with other molecules, and its mislocalization is linked to numerous diseases. While atlas-scale efforts have been made to profile protein localization across various cell lines, existing datasets only contain limited pairs of proteins and cell lines which do not cover all human proteins. We present a method that uses both protein sequences and cellular landmark images to performPredictions ofUnseenProteins’Subcellular localization (PUPS), which can generalize to both proteins and cell lines not used for model training. PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images for protein localization prediction. The protein sequence input enables generalization to unseen proteins and the cellular image input enables cell type specific prediction that captures single-cell variability. PUPS’ ability to generalize to unseen proteins and cell lines enables us to assess the variability in protein localization across cell lines as well as across single cells within a cell line and to identify the biological processes associated with the proteins that have variable localization. Experimental validation shows that PUPS can be used to predict protein localization in newly performed experiments outside of the Human Protein Atlas used for training. Collectively, PUPS utilizes both protein sequences and cellular images to predict protein localization in unseen proteins and cell lines with the ability to capture single-cell variability.