Biology subjects

Warren, J.

Publications and source records attributed to Warren, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Ecological and metabolic signatures of biofilm viromes across a national river surveillance network

Benthic biofilms are biogeochemical hotspots in rivers, yet their endogenous viral communities remain poorly resolved at national scales. We analysed 447 biofilm metagenomes from 146 sites within England's River Surveillance Network (RSN), sampled in spring and autumn from 2021 to 2023, integrating viral operational taxonomic units (vOTUs), water-quality gradients, predicted host associations and auxiliary metabolic genes (AMGs). We recovered 38,534 vOTUs, revealing extensive viral novelty, where 93% of the vOTUs could not be assigned to a known family. Viromes were dominated by Caudoviricetes and unclassified lineages and were extremely heterogeneous: no vOTU occurred in more than 8.3% of samples. Season, but not sampling year, structured virome composition (family-level PERMANOVA R2 = 0.050, p = 0.001; year p = 0.08), and within-site turnover between spring and autumn exceeded turnover between years. Bray-Curtis ordination linked virome structure weakly to pH, dissolved organic carbon, conductivity, nitrate-N and dissolved oxygen (envfit R2 [≤] 0.066), while threshold indicator taxa analysis (TITAN) identified vOTUs with abrupt change points along alkalinity, dissolved oxygen, nitrate-N and temperature gradients. Predicted host associations were concentrated in Pseudomonodota, Cyanobacteriota and Bacteroidota, with Microcoleus, Chamaesiphon and Flavobacterium among the dominant host genera. Virus-host networks were modular, and module abundances correlated with water quality variables (dissolved oxygen, pH, nitrate etc.), suggesting that environmental filtering acts partly through host ecology. Predicted virus-host associations formed a sparse network organised around a few highly connected viral lineages. Functional profiling showed that the biofilm virome was dominated by nucleotide metabolism, DNA methylation, phosphate-stress, glycan-modification and photosynthesis-related AMGs, with nrdA/nrdB ribonucleotide reductase as the dominant AMG signal. Few vOTUs (1.2%) were detected as proviruses, although provirus fractions were higher in selected host-linked lineages. Collectively, these results show that river biofilm viromes are seasonally structured ecological communities whose composition, host associations and metabolic potential reflect the physicochemical and biological state of rivers. We propose that biofilm viromes provide a complementary layer of information for understanding river health, microbial ecology and the propagation of anthropogenic pressures in freshwater systems.

microbiology↗

bioRxiv2026

A mitochondrion-like ribosome in an insect endosymbiont

Understanding how the mitochondrion evolved from a bacterial endosymbiont to an organelle is obscured by time and a lack of comparative examples. It is clear that mitochondrial ribosomes are derived from bacterial ribosomes, but it is unclear whether the baroque and idiosyncratic structural changes seen in mitochondrial ribosomes are specifically driven by mitochondrial evolution or simply reflect the syndrome of being a long-term endosymbiont. Here we show that two of the most characteristic features of mitochondrial ribosomes--the acquisition of host proteins and alterations to specific structural regions--are shared by Hodgkinia, an ancient bacterial endosymbiont of cicadas. These results imply that many of the striking changes observed in mitochondrial ribosomes result from their common ancestry as bacterial endosymbionts rather than their uniqueness as mitochondria.

evolutionary biology↗

bioRxiv2026

A Mechanistic Theory Unifying Value and Schema in the Prefrontal Cortex

Animals exhibit behavioural flexibility by making reward-optimal decisions in unfamiliar situations. Computing value from minimal reward feedback requires leveraging known structure in the world. The Prefrontal Cortex (PFC) plays a pivotal role in both value computation and learning world structure, however mechanistic explanations for each---within the frameworks of Reinforcement Learning and Cognitive Maps---are largely distinct. We develop a mechanistic model of PFC that unifies value and structure through behavioural flexibility. In this model, value acts as a control signal that gates structured working memory representations of the current context in order to ultimately control behaviour. This is a significant departure from the conventional perspective of value, in which it is used for action readout. Critically, this model generalises to novel contexts without the need for additional synaptic plasticity. We demonstrate that recurrent neural networks (RNNs) meta-trained with either reinforcement learning or supervised learning recapitulate this exact model on various value-based tasks. These results not only provide a parsimonious explanation of both the value and schema frameworks of PFC function, but also propose a new mechanistic interpretation of the role of PFC in flexible decision making.

neuroscience↗

bioRxiv2026

Chromosome-scale Juglans genomes focus fungal defense gene divergence in gene presence and absence instead of copy number

Butternut (Juglans cinerea) is a North American hardwood in steep decline, driven largely by an introduced fungal pathogen that causes butternut canker disease. Tolerance exists within the genus, with the Asian Juglans ailantifolia comparatively tolerant and hybridizing readily with J. cinerea, yet the genomic basis of that difference is poorly resolved. Chromosome-scale reference genomes are presented for J. ailantifolia and for a second J. cinerea accession from the species primary range, with independent scaffolding and uniform annotation across all compared assemblies. Gene family evolution was assessed across twelve Juglandaceae genomes, one per species, and a four accession pangenome was built from J. ailantifolia and J. mandshurica representing section Cardiocaryon and two J. cinerea accessions, Brenton and New Brunswick, representing section Trachycaryon. Neither J. cinerea accession is a putative tolerant selection, so their contrast provides a null against which section-level differences are calibrated. Spanning two sections separated by approximately 30 My, the pangenome partitions many tandem arrays by accession instead of by gene, so copy number is interpreted after merging homology nodes representing the same gene. Section-level variation resides primarily in gene presence and absence, where pathogenesis-related proteins, cysteine-rich receptor-like kinases, wall-associated kinases and lectin-domain receptor kinases are over-represented in the lineage-specific complement of both sections, indicating rapid bidirectional turnover. A smaller set of families is asymmetric, with chitinases and chitin-binding proteins and NB-LRR receptors biased toward the tolerant section and dehydrins, pectin-modifying enzymes and the CBF regulon toward the susceptible one. The largest copy number difference in the dataset separates the two conspecific accessions, at a senescence-associated cysteine protease. The two butternuts are further distinguished by their demographic histories and by the functional composition of their accession-specific gene content: the northern New Brunswick accession retains lower heterozygosity, a distinct coalescent trajectory, and enrichment for calcium transport across channels, pumps and homeostasis, for salt stress response regulation, and for raffinose family oligosaccharide biosynthesis, spanning both the perception and the cryoprotective effectors of freezing tolerance. These findings support recognition of the northern population as a cryptic glacial refugium and a conservation priority.

genomics↗

bioRxiv2026

Behavioural and neural mechanisms for stochastic choices in mixed strategy games

Adaptive behaviour usually requires exploiting regularities in the environment, but in competitive settings the opposite can be true: predictable choice patterns can be exploited by others, making unpredictability itself advantageous. How neural circuits generate such strategic variability remains poorly understood. Here, we trained mice to play a zero-sum game against an opponent that exploited statistical regularities in their choices and rewards, and tracked their behaviour and dorsal cortical dynamics across learning. Using a hidden Markov model, we found that mice transitioned from structured, predictable strategies towards a near-optimal stochastic strategy as they learned. Applying the same framework to monkeys playing the same game identified a shared stochastic strategy across species, despite differences in how it was deployed. Cortex-wide imaging revealed that stochastic choices were associated with reduced representation of reward history, while immediate reward signals remained robust. Critically, while the strength of cortical reward signals predicted subsequent choice during reward-guided behaviour, this relationship was abolished during stochastic behaviour. Thus, adaptive stochasticity does not simply arise from a loss of reward information, but from selectively decoupling reward from future choice. These results reveal a neural mechanism through which animals suppress otherwise useful reward-guided structure to generate adaptive unpredictability in competitive environments.

neuroscience↗

bioRxiv2026

lncRNA MANCR isoforms selectively mediate multiple levels of epigenomic and P53-responsive transcriptional control in triple negative breast cancer

Long noncoding RNAs (lncRNAs) are important regulators of gene expression and are frequently dysregulated in cancer. The mitotically associated lncRNA MANCR is highly expressed in aggressive cancers and contributes to genomic instability in triple-negative breast cancer (TNBC), but the molecular mechanisms underlying its activity remain poorly defined. Here we integrate computational and experimental approaches to examine the structure and regulatory interactions of MANCR isoforms. Analysis of transcriptomic datasets revealed tumor-type-specific expression patterns for seven MANCR isoforms in breast cancer cell lines. Computational prediction of RNA secondary structures identified conserved structural features across isoforms, suggesting potential functional specialization. We identify p53 as a MANCR-interacting protein through computational docking and RNA immunoprecipitation sequencing (RIP-seq) and demonstrate that MANCR depletion reduces p53-dependent transcriptional activity. Chromatin isolation by RNA purification sequencing (ChIRP-seq) revealed 1, 250 genomic regions associated with MANCR, including enrichment of p53 consensus motifs and GC-rich sequence elements. Motif analysis further identified candidate sequence features associated with MANCR-occupied chromatin regions. Computational prediction of RNA-miRNA interactions identified multiple potential miRNA binding sites across MANCR isoforms, including miR-6756-5p, which targets the androgen receptor (AR). Consistent with this prediction, AR expression decreased following MANCR knockdown in TNBC cells. Together, these results suggest that MANCR isoforms may contribute to transcriptional regulation in TNBC through interactions with chromatin, p53 signaling pathways, and potential miRNA regulatory networks. One Sentence SummaryMitotically-associated lncRNA (MANCR) is prevalent in aggressive cancers interacting with DNA, P53, and miRNAs, to mediate multiple levels of epigenetic transcriptional control in triple negative breast cancer.

cancer biology↗

bioRxiv2026

Acute degron-mediated RUNX1 loss reprograms enhancer activity to epigenetically drive epithelial destabilization and initiate cancer hallmarks

The RUNX1 transcription factor mediates cell-type specific gene expression. RUNX1 suppression and perturbations are recurrently associated with breast tumor initiation and progression. However, the mechanisms governing the dual roles of RUNX1 in sustaining the mammary epithelial phenotype while epigenetically suppressing initiation of cancer-compromised gene expression are poorly understood. To address this, we used the power of degron-mediated acute, selective, and complete RUNX1 ablation in human mammary epithelial cells. RUNX1 mediates promoter and distal enhancer-driven expression of a gene cohort. Dynamic epigenomic responsiveness upon RUNX1 ablation reveals a rapid and selective decrease in chromatin accessibility and H3K27ac at RUNX1-bound enhancers, but not promoters. While differentially initiated and expressed genes contacted by RUNX1-bound enhancers are enriched in pathways involved in epithelial maintenance and stemness, genes with RUNX1-promoter occupancy support DNA damage responsiveness. Modified cell morphology, metabolic control, increased breast cancer stemness, plasticity, anchorage-independent survival, chemoresistance, and perturbed DNA damage reactivity are observed upon RUNX1 ablation. Together, these findings define RUNX1 as an epigenetic tumor suppressor that maintains epithelial cell state by preserving enhancer activity and preventing gene expression associated with hallmarks of cancer.

cancer biology↗

bioRxiv2026

Cardiac REDD1 alters glucose and fatty acid metabolic gene expression via an mTORC1-independent, PPAR alpha-dependent mechanism and drives hypertrophic growth

BackgroundRegulated in development and DNA damage 1 (REDD1) is a highly inducible molecule that plays a role in numerous physiological and pathophysiological processes. It is a well-established negative regulator of mammalian target of rapamycin complex 1 (mTORC1), which is critical for maintaining elevated fatty acid-to-glucose oxidation ratio in the heart. In addition, REDD1 deletion results in hyperglycemia, suggesting that REDD1 is critical for tissue glucose metabolism. The role of REDD1 in regulating cardiac glucose and/or fatty acid metabolism in response to physiologic or pathophysiologic cues, however, remains unexplored. MethodsHerein, we utilize AC16 cardiomyocytes with REDD1 deletion, as well as mice with global or cardiomyocyte-specific deletion of Redd1, and their respective controls. We also subject these mice cardiac pressure overload using transverse aortic constriction (TAC) for 2 weeks or sham operation as a control. To examine the molecular regulators of glucose oxidation, we utilized qPCR and western blotting to evaluate pyruvate dehydrogenase (PDH) kinase (PDK) and phospho-PDH (pPDH) levels, respectively. We also directly measured PDH activity and glucose-driven cellular respiration. To investigate the complete REDD1-dependent transcriptome and metabolome, we performed RNA-sequencing (RNA-Seq) and untargeted metabolomics, respectively. To determine if the observed gene expression changes were dependent upon transcription factor peroxisome proliferator-activated receptor alpha (PPAR), we utilized an established pharmacologic PPAR inhibitor, GW6471. Here, we measured PPAR activity directly, as well as the expression of its target genes. In order to determine if our observed effects were mTORC1-dependent, we utilized mTORC1-specific inhibitor, everolimus. Finally, we measured cardiac hypertrophy using gravimetric analyses (heart weight (HW)-to-body weight (BW) or HW-to-tibia length (TL) ratios) and histological analyses of cardiomyocyte cross sectional area (CSA). We also measured mRNA and protein levels of pathological hypertrophic markers Natriuretic Peptide B (Nppb) and Cardiac Ankyrin Repeat Protein (CARP), respectively. ResultsOur data demonstrate that physiological levels of glucose induce REDD1 expression in cardiomyocytes. Further, we show that in cardiomyocytes or the hearts of mice with REDD1 deletion, there is elevated PDK4 expression, as well as increased levels of pPDH (S300 and/or S293) and reduced PDH activity. Interestingly, everolimus treatment has no effect on these alterations. In vitro, we also observe elevated glycolysis and glycolytic capacity, and reduced maximal respiratory capacity (MRC) in the presence of glucose. Interestingly, our RNA-Seq data reveals the upregulation of genes involved in fatty acid catabolism. Further, we demonstrate that PPAR activity is enhanced, and everolimus treatment also has no effect on this parameter. Additionally, we show that treatment of cardiomyocytes with GW6471 normalizes the expression of its target genes (PDK4, ACSL1) and levels of pPDH (S300), that are elevated in cells with REDD1 deletion. Finally, we observe elevated REDD1 in the hearts of mice following TAC. Moreover, we show reduced HW/BW, HW/TL, cardiomyocyte CSA, and levels of cardiac Nppb and CARP in mice with cardiomyocyte Redd1 deletion subjected to TAC versus controls also subjected to TAC. Importantly, TAC-induced reductions in cardiac Pdk4 and pPDH (S293 and S300), are normalized to control levels in mice with Redd1 deletion subjected to TAC. ConclusionsTogether, our findings suggest that physiological glucose-induced and pathological pressure overload-induced REDD1 is required for enhancing glucose oxidation and suppressing fatty acid oxidation in cardiomyocytes. In this way, REDD1 supports cardiac hypertrophic growth. We also outline a mechanism whereby REDD1 inhibits PPAR activity, thereby inhibiting the expression of its target genes, including PDK4 and those involved in fatty acid oxidation. Finally, we demonstrate that these effects are independent of REDD1s ability to inhibit mTORC1.

cell biology↗

bioRxiv2026

Resolving eukaryotic river biofilm communities using long-read sequencing for biomonitoring

Freshwater biofilms host diverse microbial eukaryotic communities that are central to ecosystem functioning and serve as key indicators of water quality. Molecular biomonitoring approaches based on environmental DNA (eDNA) sequencing are increasingly used to characterise these communities, offering scalable alternatives to traditional microscopy-based assessments. Understanding how DNA sequencing methods influence the observed community composition and diversity is essential for ensuring accurate ecological interpretation. Here, we compared short-read Illumina and long-read Pacific Biosciences sequencing of the 18S rRNA gene, alongside a trimmed long-read dataset (restricted to the Illumina-primed region), to evaluate how read length and sequencing platform affect community profiling in river biofilms from seven English rivers sampled across three timepoints. Distinct community patterns were observed between the sequencing approaches, with PERMANOVA revealing significant differences in beta diversity (p = 0.001) and modest effect sizes (R2 = 3.8-8.3%). While the long and trimmed datasets produced nearly identical community structures, both diverged strongly from the short-read data, suggesting that short-read sequencing captures a systematically different subset of taxa than long-read sequencing. Long-read sequencing significantly improved taxonomic resolution of the 18S rRNA gene, particularly at the genus and species levels, enabling detection of lineages that were unresolvable in short-read data. However, comparisons of paired long- and trimmed-read ASVs indicated that trimming can increase taxonomic mismatches at finer ranks, likely due to reduced sequence length rather than sequencing platform bias. Collectively, our results demonstrate that sequencing strategy significantly influences inferred community composition and taxonomic precision. Long-read sequencing provides a more robust representation of community diversity, whereas trimmed analyses reveal how shorter amplicons may contribute to misidentification. These findings emphasise the importance of considering read length when interpreting eDNA-based assessments using the 18S rRNA gene and support the adoption of long-read sequencing for high-resolution biomonitoring applications.

molecular biology↗

bioRxiv2026

Identification of clofibric acid as a SYVN1 ligand for PROTAC development

Targeted protein degradation (TPD) is an emerging therapeutic modality for numerous diseases. PROteolysis-TArgeting Chimeras (PROTACs) represent a potentially generalizable strategy to achieve TPD. A PROTAC is composed of a ligand for a protein of interest, a linker and a ligand for E3 ligase. As such, PROTACs can bring the E3 ligase into the close proximity of a protein target leading to polyubiquitination followed by target protein degradation. While the human genome encodes over 600 E3 ligases, only a handful of them have been harnessed for developing PROTACs. In order to expand the repertoire of E3 ligases for PROTAC development, we developed clickable photoaffinity probes based on clinically used drugs and metabolites to identify potential E3 ligases as the targets. In this paper, we report the discovery of clofibric acid with a molecular weight of only 214 Daltons as a ligand for synoviolin (SYVN1). We demonstrate its utility by developing clofibric acid-based BRD4 PROTACs. The linker length and architecture play a critical role in target degradation efficiency. The clofibric acid-derived BRD4 PROTACs achieve selective BRD4 degradation in a SYVN1-dependent manner. Our findings establish clofibric acid as a robust addition to the TPD toolbox, offering a novel E3 ligase recruitment strategy for the development of next-generation degraders. TOC Graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/701774v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@776850org.highwire.dtl.DTLVardef@1616bd0org.highwire.dtl.DTLVardef@ed3e03org.highwire.dtl.DTLVardef@18271e7_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

A frontal motor circuit for economic decisions and actions

Flexible behaviour requires transforming abstract cognitive representations, such as value preferences, into concrete motor actions. During economic decision-making, individuals evaluate options to guide choices and then transform these choices into specific actions to obtain rewards. Understanding how neural circuits convert these abstract economic decisions into spatial actions remains challenging because decision formation and motor planning are typically intertwined. Here we introduce a mouse task that temporally dissociates value-guided decisions from spatial action planning, and show that a frontal motor network implements the transformation across decision stages through dynamic circuit reconfiguration. Using cortex-wide imaging and optogenetic perturbations, we identified a frontal motor circuit that was causally required for both abstract and motor stages of choice. During the abstract decision stage, neurons in this circuit encoded option values and economic choices independently of sensorimotor contingencies, and unilateral silencing impaired decisions without spatial bias. In contrast, during spatial planning, value and spatial signals were non-linearly integrated to guide action selection, and unilateral silencing produced an ipsilateral bias. A dynamical model captured this transformation, predicting a mode switch from cooperative interhemispheric maintenance of economic choice to competitive, lateralized control of actions, which we validated with simultaneous bilateral recordings. These findings demonstrate how frontal motor circuits reconfigure their interactions to bridge abstract cognition and concrete actions, providing a circuit-level mechanism for flexible, value-guided behaviour.

neuroscience↗

bioRxiv2025

An IL-21R hypomorph circumvents functional redundancy to define STAT1 signaling in germinal center responses

Interleukin-21 receptor engagement initiates a Janus Kinase (JAK) - signal transducer and activator of transcription (STAT) signalling cascade that activates several STAT proteins that drive the germinal center response. However, the relative effects of IL-21 on individual STAT proteins during the differentiation of T follicular helper cells and germinal center B cells has been difficult to distinguish. Here, we characterise a novel mutation in the interleukin-21 receptor (IL-21REINS) that creates a unique defect in the activation of STAT1. Our findings provide evidence that IL-21 mediated activation of STAT1 has a nonredundant role in the differentiation of T follicular (Tfh) cells following T dependent immunisation. IL-21REINS Tfh cells were even more impaired than Tfh cells genetically deficient in IL-21R, questioning our current understanding of the role of IL-21 derived from protein knockout mice. The observation that functional compensation fails in the presence of the IL-21R hypomorph provides insight into how underlying compensation can impact our interpretation of a complex biological system.

immunology↗

bioRxiv2025

River biofilm bacteria as sentinels of national-scale freshwater ecosystems

Freshwaters face increasing pressures from chemical, hydrological, and climatic changes, yet tools for assessing their condition remain limited. River biofilms, composed of diverse microbial communities, integrate environmental signals over space and time, making them sensitive indicators of river health. Using 16S rRNA gene sequencing of more than 1,600 biofilms collected across a national river network, we quantified bacterial diversity and community composition and applied network analysis to identify ecologically cohesive sub- communities with keystone taxa underpinning community stability. Alkalinity, dissolved oxygen, nitrate-nitrogen, and temperature were among the principal gradients shaping community composition. Threshold indicator analyses identified taxa with breakpoints along these gradients, revealing interpretable ecological thresholds. Our results demonstrate the potential for microbiome-based monitoring frameworks that complement existing biotic indices, enabling early detection of ecological changes and supporting the integration of genomic indicators into routine ecosystem assessment. This scalable approach offers a powerful strategy for managing freshwaters under accelerating anthropogenic pressures.

ecology↗

bioRxiv2025

NAB2-STAT6 Fusion Proteins Drive Nuclear Condensate Formation and Transcriptional Reprogramming in Solitary Fibrous Tumors

Solitary fibrous tumor (SFT) is a rare and aggressive sarcoma driven by NAB2-STAT6 gene fusions, yet effective targeted therapies remain unavailable. Here, we report that the NAB2ex4-STAT6ex2 fusion variant forms nuclear condensates via liquid-liquid phase separation (LLPS) in engineered fibroblast models and primary SFT cells. These condensates co-localize with BRD4S and EGR1, key transcriptional regulators, and are functionally active, driving widespread transcriptional reprogramming. Treatment with Mithramycin A, a compound that disrupts EGR1-DNA interactions, dissolves NAB2-STAT6 condensates and reverses their aberrant gene expression and chromatin binding signatures. Our findings uncover a previously unrecognized role for NAB2-STAT6 in condensate-mediated oncogenic signaling and provide a mechanistic rationale for condensate-targeted therapy in SFT.

cancer biology↗

bioRxiv2025

Unlocking River Biofilm Microbial Diversity: A Comparative Analysis of Sequencing Technologies

Freshwater ecosystems are under increasing pressure from pollution, habitat degradation, and climate change, highlighting the need for reliable biomonitoring approaches to assess ecosystem health and identify the causes of biodiversity and ecosystem service loss. Characterisation of freshwater microbiomes has the potential to be an important tool for understanding freshwater ecology, ecosystem health and ecosystem function. High-throughput sequencing technologies, such as Illumina short-read and Pacific Biosciences long-read sequencing, are widely used for microbial community analysis. However, the relative performance of these approaches for monitoring freshwater microbiomes has not been well explored. In this study, we compared the performance of long- and short-read sequencing approaches to assess archaeal and bacterial diversity in 42 river biofilm samples across seven distinct river sites in England by targeting the 16S ribosomal RNA gene. Our findings demonstrated that longer reads generated by PacBio sequencing provide a higher taxonomic resolution, enabling the classification of taxa that remained unassigned in the short-read Illumina datasets. This enhanced resolution is particularly beneficial for biodiversity assessments because it improves species-level identification, which is crucial for ecological monitoring. Despite this, both sequencing methods produced comparable bacterial community structures regarding taxon relative abundance, suggesting that the sequencing approach does not profoundly affect the comparative assessment of community composition. However, while Illumina offers higher throughput and cost efficiency, PacBios ability to resolve complex microbial communities highlights its potential for studies requiring precise taxonomic identification.

molecular biology↗

bioRxiv2025

National-scale biogeography and function of river and stream bacterial biofilm communities

Biofilm-dwelling microorganisms coat the surfaces of stones in river and stream ecosystems, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning1,2. Flowing water (lotic) ecosystems are under pressure from a wide range of interacting stressors including changes in land use, chemical pollution, and climate3. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are limited by a lack of understanding of their taxonomic composition and physicochemical drivers across large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England, analogous to other large-scale efforts to understand microbial biogeography across diverse environments4,5,6,7. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across Englands extensive river network, revealing substantial taxonomic novelty, with [~]20% of the MAGs representing novel genera. We demonstrated that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and play a significant role in nutrient cycling with the potential for contaminant transformation. Environmental drivers, most notably geology, land cover, and nutrients, explained up to 90% of the variation in community composition. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.

ecology↗

bioRxiv2025

MassVision: An Open-Source End-to-End Platform for AI-Driven Mass Spectrometry Image Analysis

Mass spectrometry imaging (MSI) combines spatial and spectral data to reveal detailed molecular compositions within biological samples. Despite their immense potential, MSI workflows are hindered by the complexity and high dimensionality of the data, making their analysis computationally intensive and often requiring expertise in coding. Existing tools frequently lack the integration needed for seamless, scalable, and end-to-end workflows, forcing researchers to rely on local solutions or multiple platforms, hindering efficiency and accessibility. We introduce MassVision, a comprehensive soft-ware platform for MSI analysis. Built on the 3D Slicer ecosystem, MassVision integrates MSI-specific functionalities while addressing general user requirements for accessibility and usability. Its intuitive interface lowers barriers for researchers with varying levels of computational expertise, while its scalability supports high-throughput studies and multi-slide datasets. Key functionalities include visualization, co-localization, dataset curation, dataset merging, spectral and spatial preprocessing, AI model training, and AI deployment on full MSI data. We detail the workflow and functionalities of MassVision and demonstrate its effectiveness through different experimental use cases such as exploratory data analysis, ion identification, and tissue-type classification, on in-house and publicly available data from different MSI modalities. These use cases underscore the MassVisions ability to seamlessly integrate MSI data handling steps into a single platform, and highlight its potential to reveal new insights and structures when examining biological samples. By combining cutting-edge functionality with user-centric design, MassVision addresses longstanding challenges in MSI data analysis and provides a robust tool for advancing the users ability to achieve biologically-meaningful insights from MSI data.

bioinformatics↗

bioRxiv2024

The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing

Primary sclerosing cholangitis (PSC) is a chronic progressing cholestatic disease that often co-occurs with inflammatory bowel disease (PSC-IBD). PSC-IBD affecting the colon (PSC-UC) is likened clinically to ulcerative colitis (UC), however differences include a right colon dominance, less severe inflammatory presentation and a greater lifetime risk of colorectal cancer. To understand the basis of clinical differences, we combine single-cell mRNA and antigen receptor sequencing, 16S ribosomal DNA analysis and spatial transcriptomics on biopsies from multiple colon regions of both PSC-UC and UC patients in remission or at the time of relapse. We discover disease-specific cell and microbial profiles between these cohorts, highlighting a distinct landscape in the right colon of PSC-UC patients and an epithelial-endothelial cell state that may contribute to intestinal permeability in UC. We show the expansion of an activated mast cell state in both diseases during flare, and demonstrate the requirement of TMEM176B in sustaining this activated state. Together this work demonstrates that PSC-UC and UC are distinct diseases with common cell mechanisms during inflammation, providing cellular and microbial insights to improve treatment of both patient cohorts.

cell biology↗