Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Distinct spatial and non-spatial response properties of excitatory narrow-spike and burst-firing neurons in the marmoset auditory cortex

Cell types are the basic units of the cerebral cortex. Broad and narrow spike waveforms (BW and NW) are the primary criteria for classifying putative excitatory and inhibitory cortical neurons, particularly in non-human primates where genetic accessibility is limited. We have classified cell types in the auditory cortex of marmosets using spike waveforms and firing patterns and identified a new type of neuron: the NW-burst neuron. NW-burst neurons are excitatory, as they drive but do not suppress the firing of connected neurons. Furthermore, NW-burst neurons displayed shorter response latencies, lower response variability, smaller receptive fields, stronger correlations between spatial and non-spatial selectivity, and higher decoding accuracy than other neurons. Together, these findings suggest that cortical NW-burst neurons in non-human primates represent a distinct excitatory cell type. Significance StatementClassifying cell types in non-human primates is challenging due to limited genetic tools. Traditionally, neurons with narrow spikes are assumed to be inhibitory. Challenging this view, we analyzed 1,816 high-quality single units in the marmoset auditory cortex and discovered that narrow-spike burst-firing neurons were excitatory. These neurons exhibited shorter response latencies, smaller receptive fields, and higher decoding accuracy. Crucially, they showed a positive correlation between "where" and "what" selectivity, defying the standard trade-off between spatial and non-spatial response properties. These findings reveal a specific excitatory cell type in the auditory cortex of a non-human primate species that integrates sound information with high temporal fidelity and feature selectivity.

neuroscience↗

bioRxiv2026

EBNA1 INHIBITORS REVEAL CDC7 AND POU2F1 AS DIRECT FUNCTIONAL TARGETS IN EBV EPITHELIAL CANCERS

Epstein-Barr virus (EBV) latent infection is causally linked to several epithelial cancers, including endemic forms of undifferentiated nasopharyngeal carcinoma (NPC) and to a subtype of gastric cancer (GC). EBNA1 is the viral-encoded sequence-specific DNA-binding protein required for episome maintenance but also contributes to host-cell survival through multiple mechanisms including binding to host chromosome. We previously developed small molecule inhibitors of EBNA1 DNA-binding that block host cell cycle progression and growth of EBV+ tumors in vivo. However, the underlying molecular mechanisms of EBNA1 function and inhibition have not been completely elucidated. In this study, we employ VK1727 to inhibit EBNA1 DNA-binding to viral and cellular genomes in three EBV+ epithelial tumors (PDX C15, C666-1 and SNU719). We integrate EBNA1ChIP-seq and transcriptomic RNA-seq analyses to identify the cell cycle dependent kinase CDC7 and a stem cell transcription factor POU2F1 as direct functional targets of EBNA1 in these epithelial cancers. EBNA1 binding to CDC7 promoter and POU2F1 intron promotes RNA Pol II-pS5 to initiate transcription of these two genes. We show that CDC7 inhibitor Simurosertib is epistatic, while Bcl2 inhibitor Venetoclax is synergistic with VK1727 in the inhibition of EBV+ epithelial cancer cell proliferation and survival. Our study reveals new functional gene targets and pathways of VK1727 in EBV+ epithelial cancers that provide new biomarkers and combinatorial strategies to treat EBV-driven cancers. IMPORTANCEEBNA1 is essential for EBV latency and tumorigenesis, but its mechanism of action on host gene expression is not yet known. Small molecule inhibitors of EBNA1 DNA-binding block cell cycle progression and inhibit growth of EBV+ tumors. In this study, we use the EBNA1 small molecule inhibitor VK1727 to identify cellular gene targets that are bound by EBNA1 and deregulated by its pharmacological inhibition in EBV+ epithelial cancer cell lines and an NPC PDX mouse model. We identify cycle dependent kinase CDC7 and the stem cell transcription factor POU2F1 as EBNA1 bound and regulated genes important for EBV epithelial cancer proliferation. These findings not only decipher molecular mechanism how VK1727 blocks cell cycle progression and inhibits cell proliferation but also provide two new cellular gene targets and pathways for therapeutic intervention in EBV+ epithelial cancers.

microbiology↗

bioRxiv2026

Inhibition of Endocannabinoid Degradation in Astrocytes Reprograms Glial Reactivity and Prevents Seizure Sequelae

BackgroundTemporal lobe epilepsy (TLE) is the most common form of focal epilepsy and is characterized by a pathological cascade of excitotoxicity that leads to neuroinflammation, progressive neuronal loss, and subsequent cognitive decline. Despite its prevalence, effective disease-modifying therapies remain lacking. Previous studies have demonstrated that the endocannabinoid system contributes to epileptic activity. In particular, inactivation of monoacylglycerol lipase (MAGL), the key rate-limiting enzyme responsible for the degradation of the endocannabinoid 2-arachidonoylglycerol (2-AG), an endogenous lipid mediator with anti-inflammatory and neuroprotective properties, suppresses seizures and reduces neuroinflammation. However, the cellular and molecular mechanisms underlying these protective effects remain unclear. MethodsTo dissect the cellular mechanisms underlying MAGL-mediated neuroprotection, we employed a kainic acid (KA)-induced status epilepticus model in mice with global, astrocyte-specific (aKO), and neuron-specific (nKO) deletion of mgll. We combined single-nucleus RNA sequencing (snRNA-seq) to map the transcriptomic landscape of glial responses with pharmacological interventions to validate key signaling pathways, as well as behavioral assays to assess functional recovery. ResultsWe demonstrated that astrocyte-specific, but not neuron-specific, mgll deletion was sufficient to attenuate seizure susceptibility and hippocampal neurodegeneration, thereby recapitulating the protective phenotype observed in global knockouts. Transcriptomic profiling revealed that astrocytic MAGL deficiency fundamentally reshaped the glial response to injury by preventing the transition to pro-inflammatory reactive astrocyte states and suppressing the activation of disease-associated microglia (DAM). Mechanistically, we identified a signaling pathway in which the neuroprotective effects of MAGL inhibition depend on cannabinoid receptor 1 (CB1) activation and are mediated by downstream peroxisome proliferator-activated receptor {gamma} (PPAR-{gamma}) signaling. Either genetic deletion of CB1 or pharmacological blockade of PPAR-{gamma} abolished the protective effects. Furthermore, aKO mice exhibited reduced neuronal loss, preserved synaptic structural integrity and protection against post-seizure cognitive deficits. ConclusionThese findings reveal astrocytic MAGL as a crucial regulatory node in the epileptic brain and demonstrated that enhancing 2-AG signaling in astrocytes orchestrates neuroprotection via CB1-PPAR-{gamma} signaling pathways, thereby attenuating neuroinflammation, preserving synaptic function, and preventing the cognitive comorbidities associated with epilepsy.

neuroscience↗

bioRxiv2026

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

Directly measuring chromatin states alongside transcription is essential for understanding how cell-type-specific regulatory programs are established and maintained in the adult human brain. We present a large-scale single-cell multimodal atlas generated by jointly profiling transcriptome with active (H3K27ac) and repressive (H3K27me3) histone modifications across 18 brain regions. We profile >750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. C_LI

genomics↗

bioRxiv2026

Novel repressors of cambium activity in Arabidopsis

Wood is the greatest reservoir of terrestrial biomass and an essential carbon sink. Formed of xylem, it is derived from the cambium, a meristematic zone within plant stems from which phloem also forms. In Arabidopsis, cell division within the cambium is promoted by three major factors: auxin, cytokinin, and the TDIF-PXY ligand-receptor pair. Meristems and other stem cell populations are typically regulated by a balance between cell division-promoting factors and those that repress cell division to control meristem size, however few factors with cambium-repressing activity are known. Here we combined transcriptomics and transcriptional network analysis, which led to identification of related homeodomain zinc-finger transcription factors, ATHB23, ATHB30, and ATHB34, that repress cambium activity. These factors inhibit cambium activity by directly binding of promoters from a subset of auxin, cytokinin and TDIF-PXY transcriptional target genes, resulting in attenuation of their transcription. Our findings thus reveal a new mechanism underpinning balanced cambium activity.

plant biology↗

bioRxiv2026

Deep learning-enabled speckle reduction for cleared-sample coherent scattering tomography

Clearing Assisted Scattering Tomography (CAST) extends coherent scattering tomography to whole-brain imaging, enabling visualization of fine-scale brain-wide connectivity. As a coherent optical tomography modality, CAST is inherently affected by speckle noise, which degrades image quality and limits quantitative analysis. However, existing speckle reduction methods developed for optical coherence tomography (OCT) are not directly transferable to CAST images due to differences in sample and noise statistics. Here, we present a learning-based cleared-sample speckle reduction network, termed CLEAR Net, specifically designed for CAST imaging, which effectively suppresses speckle noise in whole-brain white matter images while preserving fine structural details. We quantitatively benchmarked CLEAR Net against representative speckle reduction algorithms on CAST datasets and further evaluated its generalizability using publicly available ophthalmic datasets.

bioengineering↗

bioRxiv2026

CTLA-4 inhibitors drive colitis through metabolic reprogramming-mediated Treg/Th17 imbalance

Immune checkpoint inhibitors (ICIs), especially CTLA-4 inhibitors (CTLA-4), exhibit a high incidence of colitis as an immune-related adverse event (irAE) during cancer treatment, severely limiting patient benefit. Clinically, both treatment interruption and existing intervention drugs for ICI-mediated colitis may compromise antitumor efficacy. However, there is inadequate research on the pathogenesis of ICI-mediated colitis, with findings often conflicting. Here, we first established multiple clinically relevant animal models, including an immuno-humanized ICI-mediated colitis model. Through time-series transcriptomics, we discovered that CTLA-4-induced colonic toxicity exhibits characteristics ranging from early metabolic reprogramming represented by glycolysis to later immune disorders represented by Th17 responses. By targeting colonic CTLA-4+ T cells, CTLA-4 blocked CD80/CD86-CTLA-4 interaction, thereby activating the PI3K-AKT-mTOR pathway. Subsequently, mTOR mediated metabolic reprogramming in T cells, shifting them from Treg-biased oxidative phosphorylation to Th17-biased glycolysis. The colonic toxicity of CTLA-4 has also been demonstrated to depend on the PI3K-AKT-mTOR pathway, glycolysis, and Th17 responses. Notably, metformin significantly relieved ICI-mediated colitis by inhibiting mTOR without impeding antitumor efficacy. Collectively, these findings highlighted the metabolic-immune axis in the colonic toxicity of ICI and provided a clinically superior intervention strategy.

pharmacology and toxicology↗

bioRxiv2026

Bacteria-herpesvirus interaction reveals a proviral role of ISGylation in promoting herpesvirus capsid assembly

Herpesviruses are common pathogens of the oral cavity, yet how they interact with other oral microbes are poorly understood. Using murine gamma-herpesvirus 68 (MHV68) as a model for human gamma-herpesviruses, we discover that ISGylation is hijacked to facilitate viral capsid assembly and lytic replication. Co-infection with the oral Aggregatibacter actinomycetemcomitans (A.a.) and MHV68 synergistically induced interferon-stimulated gene 15 (ISG15) expression and global ISGylation. Proteomic profiling revealed viral structural proteins as the dominant targets of ISGylation in MHV68-infected cells. Genetic ablation of ISGylation, using ISGylation-resistant recombinant MHV68 and ISG15-deficient mouse embryonic fibroblasts (MEFs), demonstrated that ISGylation of the major capsid protein ORF25 is required for efficient capsid assembly and maturation into the infectious C-type virions. Strikingly, introduction of a de novo ISGylation site into the ISGylation-resistant MHV68 was sufficient to restore ISGylation, capsid assembly, and virion maturation. Consistent with these findings, A.a. failed to enhance MHV68 lytic replication in ISG15-deficient MEFs. Extending this mechanism to representative herpesviruses, we showed that ISGylation of major capsid proteins is broadly required for efficient lytic replication. Together, these findings uncover a previously unrecognized strategy by which herpesviruses exploit an ISG15 innate immune effector, amplified by microbial co-infection, to promote virion biogenesis and productive infection.

microbiology↗

bioRxiv2026

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome

Orphan genes - genes lacking detectable homologs outside a species - are widespread in microbial genomes and are thought to contribute to their adaptation and molecular innovation. However, not all predicted orphan genes may represent novel functional coding sequences. False positive orphan genes, also called spurious orphan genes, can arise from gene prediction errors. We reason that orphan genes lacking detectable expression are more likely to be spurious. To test this, we combined large-scale metatranscriptomic profiling of the human gut microbiome with machine learning to distinguish expressed orphan genes from spurious ones and to compare them with conserved genes found in multiple species. Using nearly 5,000 metatranscriptome libraries, we identified [~]218,000 orphan genes supported by expression evidence, while [~]330,000 predicted orphan genes lacked detectable expression, and were classified as spurious. We extracted 154 features for sequence, structural, and evolutionary properties for each gene and trained XGBoost classifiers while accounting for genomic representation. The models achieved an area under the receiver operating characteristic curve (AUC) of 0.82 in distinguishing expressed orphan genes from spurious orphan genes and an AUC of 0.93 in distinguishing expressed orphan genes from conserved genes. SHAP-based interpretation revealed clear biological signals. Particularly, expressed orphans were present in more genomes than spurious ones and expressed orphan genes were shorter than conserved genes. This work improves orphan gene discovery and suggests that expressed orphan genes differ systematically from conserved genes and spurious orphan genes in sequence composition, structural constraints, and evolutionary signals. Significance statementSpecies-specific genes, also called orphan genes, are abundant in bacterial genomes and have the potential to drive evolutionary innovation. However, the study of orphan genes is confounded by annotation errors that produce spurious gene predictions. Here, we leveraged nearly 5,000 metatranscriptomes from the human gut microbiome and implemented machine learning models to distinguish expressed orphan genes from non-expressed, likely spurious, genes and conserved genes. We show that a substantial fraction of predicted orphan genes lacks expression support and they exhibit distinct sequence and evolutionary signatures from expressed orphans. By integrating expression evidence with sequence-, structure-, and evolution-based features, our work refines orphan gene catalogs. This work improves the reliability of orphan gene discovery and provides new insights into the biological characteristics of orphan genes in human microbial communities.

genomics↗

bioRxiv2026

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

bioRxiv2026

SENOMORPHIC EFFECT OF GENETIC AND CHEMICAL PARTIAL REPROGRAMMING

Partial reprogramming has emerged as a promising strategy to ameliorate aging phenotypes, yet its cellular targets and mechanisms remain poorly defined. Cellular senescence is a central hallmark of aging and a plausible mediator of reprogramming-induced rejuvenation. Here we show that genetic and chemical partial reprogramming act directly on senescent cells without restoring proliferative capacity. OSKM expression or a reduced two-compound regimen, tranylcypromine and RepSox (2c), attenuates senescence-associated secretory activity, restores mitochondrial homeostasis and apoptotic priming, and improves functional and inflammatory parameters in aged mice, establishing senomorphic, identity-preserving reprogramming as a potentially safer aging intervention.

cell biology↗

bioRxiv2026

Villin-SNAP25 interaction regulates insulin secretion downstream of ICA512 signaling

Pancreatic islet {beta}-cells step-up insulin production and secretion in response to the elevation of blood glucose levels. ICA512/PTPRN is a transmembrane cargo of the insulin secretory granules (SGs). Upon SG exocytosis, its Ca2+/calpain mediated cleavage at the plasma membrane generates an ICA512-cleaved cytosolic fragment (ICA512-CCF) which as a decoy phosphatase prolongs phospho-STAT5/3 activities, thereby enhancing the transcription of mRNAs for SG cargoes, including insulin and its own, to replenish SG stores. In addition, ICA512 positively regulates the expression of F-actin modifier villin. Villin, in turn, modulates the size of actin cages surrounding cortical SGs, hence regulating SG mobility and exocytosis. Here we show that villin controls the number of SG docking sites for exocytosis by directly interacting at low glucose with the t-SNARE SNAP-25, thus restricting in this condition SG access to fusion sites and insulin release. Replacement of ICA512-CCF N-terminal ubiquitin-acceptor lysine 609 (K609) with valine (V) stabilized ICA512-CCF in insulinoma cells and homozygous ICA512K609V mice and enhanced the levels of phospho-STAT5/3 and villin. In ICA512K609V female mice these molecular traits correlated with reduced body weight, improved insulin sensitivity, reduced basal insulin secretion and onset time for glucose stimulated insulin secretion. Taken together, these data demonstrates that SG exocytosis induced ICA512 retrograde signaling acts in concert with the novel SNARE complex regulator villin to plastically adapt {beta}-cell actin cytoskeleton and access to SG docking sites for optimal control of insulin secretion in response to variations in extracellular glucose levels. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/699220v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@37d835org.highwire.dtl.DTLVardef@5389f1org.highwire.dtl.DTLVardef@855d98org.highwire.dtl.DTLVardef@1c3c639_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Model of ICA512 and STAT3/5-dependent regulation of -cell function. At basal conditions, villin limits secretory granule (SG) docking by interacting with SNAP-25, restricting insulin release (1). Increased metabolic load triggers hyperglycemia-induced ICA512 processing and growth factor-mediated STAT3/5 phosphorylation (2-4), enhancing ISG mRNAs, granule biogenesis, and villin expression (5,6). Villin modulates SNARE protein availability, controlling SG docking and secretion. Together, ICA512 retrograde signaling and villin-mediated SNARE regulation dynamically remodel the -cell actin cytoskeleton, adjusting SG docking site access to ensure appropriate insulin secretion in response to fluctuating glucose levels. C_FIG

cell biology↗

bioRxiv2026

Structure of HIV-1 Env glycoprotein on virions reveals an alternative fusion subunit organization and native membrane coupling

An effective vaccine for Human Immunodeficiency Virus type-1 (HIV-1) has yet to be developed, and detailed characterization of functional Env glycoprotein, the primary antigenic target on virions, has remained elusive. While engineered Env trimers recapitulate many aspects of functional Env, key differences in antigenicity and dynamic behavior have been reported. Here, cryo-electron tomography and subtomogram averaging of HIV-1 virus-like particles (VLPs) revealed conformational differences in critical membrane-proximal regions compared to soluble Envs. Hydrogen/Deuterium-Exchange Mass Spectrometry and Molecular Dynamics captured dynamic profiles of membrane-bound Env and identified critical interactions with membrane. We show that disruption of the viral membrane results in relaxation of Env to a form that resembles engineered, soluble trimers. Additionally, Env from mature and immature VLPs exhibit only minor conformational differences, while surface clustering on virions changes significantly. These studies provide new insights into the essential role the membrane plays in maintaining Env in its native conformational form.

biochemistry↗

bioRxiv2026

High gene flow in Atlantic vent shrimp species with multiple ridge colonizations by ecotypic lineages with contrasting symbioses

Conservation concerns regarding potential mineral extraction near deep-sea hydrothermal vents have emphasised the need for a better understanding of the contemporary connectivity of various vent-endemic species, accounting for the specifics of their life-history traits and habitat requirements. Rimicaris shrimps are a major component of vent communities in the Atlantic Ocean, both along the Mid-Atlantic Ridge (MAR) and at the Mid-Cayman Spreading Center (MCSC). Using ddRAD sequencing, we examined the genetic differentiation of three Atlantic Rimicaris species to better understand their past and present migration pathways and the possible demographic history that led to their current distribution and ecology. Rimicaris exoculata and R. chacei inhabit the MAR and exhibit widespread gene flow along the ridge with no areas of restricted connectivity. R. hybisae occurs at the MCSC and exhibits almost no genetic difference with its congeneric from the MAR, R. chacei, despite the geographic distance between them and their contrasting ecologies and morphologies. Demographic inferences support a scenario of a very recent (less than 2000 generations) separation between MCSC and MAR shrimp populations, followed by a rapid expansion in both regions, possibly triggered by symbiotic development. Analyses further suggest recent or ongoing secondary contacts involving two-way migration, which is more pronounced from the MCSC towards the MAR. All together these results suggest that R. chacei and R. hybisae represent distinct forms of the same species, which we hereby synonymise as R. chacei, highlighting their morphological plasticity in relation to symbiosis.

evolutionary biology↗

bioRxiv2025

STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis

As the leading contributor to cancer-related mortality, metastasis often evades detection until advanced stages, underscoring the critical need for early predictive biomarkers. Neutrophils are naturally circulating sentinels that have been implicated in pioneering pre-metastatic niche formation in distant organs. Nevertheless, their heterogeneity within evolving metastatic microenvironments remains poorly characterized. Here, through dynamically delineating neutrophil subsets via single-cell transcriptomics, we identified a conserved feature of lung metastasis in breast cancer and other cancer models. Among the core genes, a cell surface marker, STEAP4, was selected and validated to indicate lung metastases at both RNA and protein levels. In both humans and mice, these STEAP4+ neutrophils were detectable not only in lung metastatases but also in the circulation. Clinically, the abundance of circulating STEAP4+ neutrophils robustly discriminates patients with lung metastasis from those with localized primary tumor. Our findings uncover STEAP4+ neutrophils as a promising biomarker and lay the groundwork for a non-invasive, blood-based diagnostic strategy for metastatic disease.

cancer biology↗

bioRxiv2025

Discovery of a chemosynthetic community at the serpentinite-hosted seep on the Quaker Seamount, Mariana Forearc

Deep-sea chemosynthesis-based ecosystems in the Mariana Region include hydrothermal vents on the Mariana Arc and in the Mariana Back-Arc, and serpentinite-hosted seeps on the Mariana Forearc - with the latter being by far the least studied. Here, we surveyed the biodiversity of the serpentine seep on the Quaker Seamount. At first glance, the area appears to be devoid of megafauna, but examination of the carbonates revealed dense aggregations of animals dominated by the limpets Bathyacmaea and Pyropelta on brucite-carbonate chimney structures exhibiting visible fluid venting. Sorting of recovered material yielded a total of 14 species and together with an observation of a Munidopsis squat lobster we report a total of 15 species; six of these are considered endemics of chemosynthetic ecosystems. The occurrence of taxa such as the snail Lurifax cf. japonicus and the limpet Pyropelta ryukyuensis, otherwise only known from distant vents in the Izu-Ogasawara Arc and Okinawa Trough off Japan, strengthens the hypothesis that serpentine seeps may function as dispersal stepping-stones across arc and back-arc systems.

ecology↗

bioRxiv2025

Concreteness shapes semantic representations in bilingual brains

Behavioral studies show that humans process concrete words more similarly across languages than abstract words. This suggests that in bilingual brains, semantic representations may be more similar across languages for concrete concepts than for abstract concepts, but existing neuroimaging evidence is inconclusive. Here, we analyzed functional magnetic resonance imaging (fMRI) data from fluent Chinese-English bilinguals who read several hours of naturalistic narratives in both languages. We used encoding models to estimate voxelwise tuning towards concrete and abstract concepts in each language separately. We then quantified the similarity of cortical semantic representations across languages. First, we find that the cortical organization of concreteness tuning is consistent across languages. Second, semantic representations are similar across languages for both concrete-tuned voxels and abstract-tuned voxels. Third, we find that for abstract concepts, cross-language similarity of semantic representations may be driven by emotionality. Overall, these findings reveal how concreteness affects semantic representations in bilingual brains.

neuroscience↗

bioRxiv2025

Reconstructing physiological oxygen gradients reveals the role of hypoxia in colon epithelial organization

Oxygen gradients organize tissue architecture and metabolism1,2, yet their precise spatial profiles and mechanistic roles remain poorly understood because both in vivo measurement and in vitro control are technically challenging3,4. Here, we quantify the oxygen landscape of the mammalian intestine using microscale sensors, revealing a steep luminal-basal gradient of approximately 10-60 {micro}M mm-1 that collapses under antibiotic perturbation. We then recreate this physiological range ex vivo with a submerged chemostat microfluidic platform that fixes the oxygen boundary condition by coupling an oxygen-permeable PDMS chip to an external scavenger reservoir and integrating embedded optical sensors for real-time readout. This architecture suppresses ambient oxygen ingress and sustains programmable gradients of 10-20 {micro}M mm-1 across three-dimensional colorectal cancer organoid cultures while remaining compatible with live imaging and endpoint retrieval. The platform bridges quantitative in vivo oxygen mapping with controlled ex vivo modeling, establishing a generalizable approach to interrogate how spatial oxygen dynamics govern epithelial organization and disease progression.

bioengineering↗