Communications Biology最新文献

{"title":"Principles of coarse-scale functional organization in occipitotemporal cortex.","authors":"Laura M Stoinski, Talia Konkle, Martin N Hebart","doi":"10.1038/s42003-026-11319-0","DOIUrl":"https://doi.org/10.1038/s42003-026-11319-0","url":null,"abstract":"<p><p>Occipitotemporal cortex (OTC) is known to support visual object processing, yet identifying general principles underlying its coarse-scale functional organization remains challenging. Previously proposed organizational dimensions, such as animacy or real-world size, may not generalize to more diverse, naturalistic stimuli and strong intercorrelations of object properties complicate determining which dimensions, if any, dominate OTC organization. We addressed these challenges through detailed analyses of the cortical topography underlying 15 object properties, using fMRI responses to thousands of natural images, focusing on animacy and size given their established prominence. Our results confirm many characteristics of the purported animacy-size organization, but reveal distinctions that challenge dominant notions of this organization, highlighting the importance of generalizing to large-scale naturalistic data. Beyond animacy and size, many properties could alternatively serve as organizational dimensions, yet none emerges as clearly dominant throughout OTC. Together, our findings reveal a more refined animacy-size organization than previously assumed and highlight challenges of assigning individual principles to account for OTC organization.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149370103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic biomarkers reveal jasmonic and salicylic acid states under field herbivory in Arabidopsis thaliana.","authors":"Atsuki Tomita, Taro Maeda, Natsumi Mori-Moriyama, Yasuyuki Nomura, Yuko Kurita, Makoto Kashima, Shigeyuki Betsuyaku, Yasuhiro Sato, Atsushi J Nagano","doi":"10.1038/s42003-026-11263-z","DOIUrl":"https://doi.org/10.1038/s42003-026-11263-z","url":null,"abstract":"<p><p>Plants coordinate defence against pathogens and herbivores through the crosstalk between salicylic acid (SA) and jasmonic acid (JA) signalling pathways. However, little is known about how plants integrate the phytohormone concentration profiles to shape defence states in complex field environments. Here we show that systematically varying combinatorial SA and JA concentrations in Arabidopsis thaliana reveals 43 distinct combination-specific transcriptional signatures beyond SA-JA antagonism. Leveraging these data, we develop and validate machine-learning-based transcriptomic biomarkers that independently measure the SA and JA response states from gene-expression data. Applying these biomarkers to field-grown A. thaliana shows that SA/JA response states are associated with the abundance and co-occurrence patterns of herbivores on individual plants. Our study provides a strategy for decoding hormonal responses to biotic environments from field transcriptomes, bridging the gap between molecular signalling and ecological dynamics.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149370104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic climate and ecological expansion drive body morphology evolution in fossil and extant neocoleoid cephalopods.","authors":"Chao Wang, Zhou Fang, Bilin Liu, Zhaoxia Ding, Xinjun Chen","doi":"10.1038/s42003-026-11173-0","DOIUrl":"10.1038/s42003-026-11173-0","url":null,"abstract":"<p><p>Cephalopods originated in the Cambrian approximately 500 million years ago, evolving from externally shelled ancestors to forms with diverse morphologies. Despite their morphological diversity, the macroevolutionary patterns and drivers of their diversification remain incompletely understood. Here, we construct a time-calibrated phylogenetic framework for fossil and extant neocoleoid cephalopods and quantify evolutionary rates and morphological disparity over ~490 million years. We identify five peaks in morphological diversification, indicating rapid evolutionary phases during historical periods. Morphological disparity exhibits a time-lagged response to evolutionary rate shifts. Sea surface temperature and ecological factors are macroevolutionary drivers shaping evolutionary rates and morphological disparity. Major environmental perturbations, including the end-Permian and end-Triassic mass extinctions and Early Triassic and Toarcian hyperthermal events, are associated with reduced evolutionary rates, whereas post-Cretaceous conditions correspond to elevated rates driven by ecological release and adaptive radiation. Our results show that cephalopod morphological evolution is governed by coupled environmental and ecological processes that structure evolutionary dynamics over deep time.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13736915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FAK- and TGF-β1-dependent biomechanical alterations in microvascular endothelial cells exposed to fluid shear stress gradients.","authors":"Julio César Sánchez-Rendón, Erva Keskin, Nadine Oder, Annalena Reuss, Eleftheria Michalaki, Gerald G Fuller, Alexander Dunn, Effie E Bastounis","doi":"10.1038/s42003-026-11283-9","DOIUrl":"10.1038/s42003-026-11283-9","url":null,"abstract":"<p><p>Endothelial cells (EC) form a dynamic monolayer barrier that regulates vascular permeability and is highly sensitive to mechanical cues, including shear stresses (SS) generated by blood flow. While spatial shear stress gradients (SSG) are linked to vascular pathologies such as atherosclerosis, their direct effects on cellular biomechanics across EC subtypes remain underexplored. Here, using an impinging flow device compatible with videomicroscopy, we demonstrate that exposure of two EC types to SSG causes an immediate and sustained two-fold decrease in migration speed, accompanied by enhanced coordination of collective motion and directional migration against the flow. Concurrently, EC traction and monolayer stresses increase acutely upon flow onset and continue to rise linearly over time. Mechanistically, FAK-mediated mechanotransduction governs flow-opposed migration, whereas the time-dependent increase in traction depends on TGF-β1 signaling and actomyosin contractility. Together, these findings identify SSG as key regulators of EC mechanics, collective dynamics, and signaling, with important implications for vascular disease diagnostics and therapeutics.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13731646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149318733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Widening the BRCAness therapeutic window for its synthetic lethality effects with PARP inhibitors.","authors":"Anthony Fernandez, Yuvika Salman, Roxanne Castillo, Carlotta Glackin, Binghui Shen","doi":"10.1038/s42003-026-11257-x","DOIUrl":"10.1038/s42003-026-11257-x","url":null,"abstract":"<p><p>This review examines the expanding role of PARP inhibitors in cancer therapy, moving beyond the traditional model of single-strand break repair inhibition and BRCA-dependent synthetic lethality. We highlight emerging evidence that PARP inhibitors induce cytotoxicity through replication-associated DNA damage, including defects in Okazaki fragment maturation and replication gap accumulation. By integrating recent mechanistic insights with findings from CRISPR-based screens, we outline how disruptions in DNA replication and repair pathways define a broader BRCAness phenotype. We further emphasize the clinical implications of these discoveries, including novel combination strategies that extend the therapeutic applicability of PARP inhibitors beyond prevailing treatment regimens.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13728100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149318734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pole-to-pole LOV-domain receptor diversity points to an early stramenopile origin and global dominance of aureochromes.","authors":"Melissa Misir, Peter G Kroth, Sylke Wohlrab","doi":"10.1038/s42003-026-11067-1","DOIUrl":"10.1038/s42003-026-11067-1","url":null,"abstract":"<p><p>Light regimes are a fundamental environmental cue for marine organisms. Yet molecular adaptations of photoreceptors to the extreme seasonality of polar regions remain poorly understood. We demonstrate that the diversity of candidate blue-light-sensing LOV-domain proteins increases at higher latitudes. We identify aureochromes, blue-light-sensitive transcription factors unique to stramenopiles, as the most frequent LOV-domain receptors across ocean latitudes. Phylogenetic reconstructions reveal early aureochrome diversification in the stramenopile lineage, originating in a heterotrophic ancestor before photosynthesis was acquired. This challenges the assumption that aureochromes are restricted to phototrophs, suggesting an ancestral role in spectral light signaling. We find that, despite changes in light quality and photoperiod by latitude, diatom aureochrome domain architecture remains conserved. This implies adaptation through regulatory tuning, such as altered expression dynamics or post-translational control. Our results emphasise the importance of spectral-light sensing in polar oceans and link the widespread dominance of aureochromes to their ancient origin and conservation.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13737086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of 515 human proteomes defines plasma extracellular vesicle core composition, corona and coisolated networks.","authors":"Ana Sofia Carvalho, Juan M Falcón-Pérez, Hans Christian Beck, Rune Matthiesen","doi":"10.1038/s42003-026-11038-6","DOIUrl":"10.1038/s42003-026-11038-6","url":null,"abstract":"<p><p>Plasma extracellular vesicles (EVs) are promising liquid biopsy biomarkers, yet their proteomic profiling remains confounded by massive co-isolation. Here, we resolve this heterogeneity through a meta-analysis of 515 human plasma EV proteomes. We demonstrate that the reproducible core proteome is overwhelmingly governed by predictable, surface-charge-driven mass-action that dynamically mirrors synthetic nanoparticle corona formation. By quantitatively decomposing the core isolate against pan-synthetic coronas and agonist-induced platelet EVs, we trace the core isolate to three main mechanistic origins: an electrostatic plasma corona, ex vivo platelet vesiculation and biological macromolecular co-isolates. Crucially, the residual vesicular cargo strongly correlates with thrombin-induced platelet degranulation, indicating that phlebotomy-induced trauma contribute to the bulk signal. We provide a modular atlas that mathematically distinguishes biophysical coronas from these cellular co-isolates, establishing a new framework for interpreting biological origin in plasma EV proteomics.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13722686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149295396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developmental and genetic modulation of evidence integration dynamics in zebrafish sensorimotor decision-making.","authors":"Roberto Garza, Ahmed El Hady, Armin Bahl","doi":"10.1038/s42003-026-11264-y","DOIUrl":"10.1038/s42003-026-11264-y","url":null,"abstract":"<p><p>Animals integrate information over time and maintain persistent internal representations of cues to guide decision-making. How the underlying behavioral algorithms of individual animals depend on factors such as experience, developmental stage, or genotype remains poorly understood. Drift-diffusion models provide a powerful theoretical framework to describe and predict performance metrics across a wide range of species. The stochastic nature of these models and the typically limited throughput of most experimental designs challenge the automatic inference of latent variables. Here, we combine high-throughput behavioral assays in larval zebrafish with drift-diffusion modeling, revealing that larvae progressively develop more persistent, self-reinforcing integration dynamics during early development. This effect is reduced in fish carrying mutations in genes linked to human epilepsy and schizophrenia. Our results show that behavior-based drift-diffusion modeling can offer a scalable, automated approach to generate experimentally testable hypotheses about the algorithmic implementation of sensorimotor integration in health and disease.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13723567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149318732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data.","authors":"Engy M T Nasr, Nikolaos Pechlivanis, Nikolaos Strepis, Pierre Amato, Matthias Bernt, Anshu Bhardwaj, Daniel Blankenberg, Daniela Brites, Fabio Cumbo, Katherine T Do, Emanuele Ferrari, Timothy J Griffin, Björn A Grüning, Saskia Hiltemann, Cameron J Hyde, Pratik D Jagtap, Ashwani Kumar, Muneer A Malla, Subina Mehta, Kimberly L Métris, Saim Momin, Tiffanie Nelson, Asime J Oba, Christina Pavloudi, Raphaëlle Péguilhan, Gareth R Price, Fotis Psomopoulos, Nedeljka Rosic, Michael C Schatz, Valerie Claudia Schiml, Cléa Siguret, Nicola Soranzo, Andrew P Stubbs, Peter van Heusden, Mustafa Vohra, Paul F Zierep, Bérénice Batut","doi":"10.1038/s42003-026-10750-7","DOIUrl":"10.1038/s42003-026-10750-7","url":null,"abstract":"<p><p>The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community ( microbiology.usegalaxy.org , .eu , .org.au , . fr ).</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13720100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149295420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aberrant RNA sensing and host-specific immunopathology in highly pathogenic influenza infections.","authors":"Ayushi Amin Dey, Aashi Patel, Anantika Chandra, Sannula Kesavardhana","doi":"10.1038/s42003-026-11027-9","DOIUrl":"10.1038/s42003-026-11027-9","url":null,"abstract":"<p><p>Innate immune activation is critical for mounting protective host immune responses against viral infections. Viruses have evolved mechanisms to counteract host innate immune responses and restrict host defence. Intriguingly, growing evidence suggests that RNA viruses of zoonotic origin, particularly influenza viruses, trigger dysregulated innate immune activation leading to excessive inflammation and cellular damage. However, the host and viral mechanisms underlying the dysregulated innate immune responses that cause severe immunopathology remain to be fully unravelled. In this review, we discuss how aberrant RNA sensing contributes to innate immune responses during highly pathogenic influenza infections. We also discuss perspectives on influenza viral polymerase compatibility with host factors and species-specific RNA-sensing mechanisms as critical determinants of the pathological outcome during highly pathogenic influenza infections.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13720091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149295354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}