Biology subjects

Chen, J.

Publications and source records attributed to Chen, J..

At least 325 records · Page 18Linked to original sources

bioRxiv2025

Fluctuating flooding motivates the facilitation of a wetland invader: a probe into the stress gradient hypothesis

Stress gradient hypothesis proposes that the plant interaction tends to convert from competition to facilitation when facing accelerating stress. The present study aims to explore the interaction between two co-existing wetland plant invaders - Alternanthera philoxeroides and Myriophyllum aquaticum with exposure to flooding stress. Different plant assemblages including monospecific (single individual per species), homospecific (two individuals of same species) and heterospecific (two individuals of different species) treatments were subjected to different flooding regimes including mesic habitat, constant flooding and fluctuating flooding. The plant interaction was evaluated by biomass accumulation, biomass allocation and relative competition intensity index (RCI). We found that the biomass accumulation and allocation of A. philoxeroides were consistent across different treatments of community assemblage and flooding regime, while the root mass, biomass and root mass allocation of M. aquaticum significantly increased at the presence of A. philoxeroides. Moreover, the RCI of M. aquaticum decreased at the presence of A. philoxeroides. Especially, the RCI of M. aquaticum was 0.06 in the homospecific community, while that of M. aquaticum was -0.82 in the heterospecific treatment under fluctuating flooding condition. Overall, Alternanthera philoxeroides facilitated M. aquaticum, especially under fluctuating flooding condition, which complies with the stress gradient hypothesis. The water level drawdown can benefit the impedance of the growth of M. aquaticum and the deceleration of the co-invasion of A. philoxeroides and M. aquaticum.

ecology↗

bioRxiv2025

Assessment of the Genetic Architecture at Early-Stage Drought Tolerance in Wheat Using UAV-Based Multispectral Imaging

Recent advances in unmanned aerial vehicles (UAVs) and multispectral sensor technologies have transformed high-throughput phenotyping as an efficient alternative to traditional approaches. In this study, we employed UAV-based multispectral imaging to monitor early-stage drought stress in wheat. A panel of 221 historical spring wheat cultivars from Pakistan, representing over a century of breeding history, were evaluated under irrigated and drought conditions. UAV flights were conducted twice at early growth stages to capture multispectral imagery, which was processed in Pix4D mapper for image alignment and orthomosaic generation. Plot segmentation and trait extraction were performed in QGIS. Eight drought-responsive vegetative indices (VIs) were analyzed to assess genotypic variation. Significant to highly significant differences were observed among genotypes, treatments, and their interactions across all VIs. Broad-sense heritability estimates were moderate to high for most traits, with predominantly additive gene action. Vegetative indices such as NDVI, GNDVI, EVI, and SAVI showed strong correlations with each other and effectively detected early canopy stress under drought. Principal component analysis based on 23.897K SNPs indicated a mixed genetic population. Genome-wide association studies identified 115 significant QTNs linked to VIs under both conditions, corresponding to 74 loci, including 26 pleiotropic loci. Of these, 10 pleiotropic loci detected under drought were annotated and six putative candidate genes were identified which showed expression in multiple tissues based on transcriptome data. Two genes i.e., TraesCS1D01G217600.1 (HSP70) and TraesCS6D01G254000.1 (ZmMDAR3), showed differential expression pattern among control and drought treatment. These findings highlight the potential of UAV-based phenotyping for early drought detection and provide candidate genes for improving drought tolerance in wheat. Future research should focus on the functional roles of these genes under drought stress.

molecular biology↗

bioRxiv2025

The brain architecture of punishment learning

Learning which actions cause harm is essential for survival, yet how the brain transforms this knowledge into adaptive control of behavior remains unclear. We combined whole-brain analysis, multisite chemogenetic silencing, spatial transcriptomics, and longitudinal calcium imaging to map how punishment learning reorganizes brain networks across scales. Learning reshaped mesoscale community organization into a network anchored by the amygdala, subthalamic-hypothalamic zone, and ventral midbrain tegmentum. These regions contributed distinct components of adaptive avoidance and engaged diverse transcriptional programs across multiple neuronal subclasses. Within this network, the amygdala acted as a hub, partitioning action and outcome information and remapping neural geometry to segregate punished from safe actions. Together, these results identify a multiscale neural architecture through which aversive experience can be transformed into flexible behavioral control.

neuroscience↗

bioRxiv2025

Observations of anisotropic paramagnetic and diamagnetic susceptibility in the primate brain

Bulk magnetic susceptibility in the brain white matter is known to be diamagnetic and anisotropic due to the ordered myelin lipids. While paramagnetic iron is widely present in the brain, it is typically not considered to contribute to anisotropy. Using experimental MRI and computational techniques, this study explores the competing contribution of diamagnetic and paramagnetic substances to the susceptibility anisotropy. Multi-echo gradient-echo imaging and diffusion-weighted imaging data from a paraformaldehyde-fixed post-mortem chimpanzee (Pan troglodytes verus) brain was analyzed. A computational method, DECOMPOSE-QSM, was used to separate paramagnetic susceptibility and diamagnetic susceptibility components. As expected, diamagnetic components showed significant anisotropy; unexpectedly, paramagnetic components also exhibited strong anisotropy in deep gray matter and parts of white matter. This may arise from the geometric arrangement of iron-rich cellular compartments, such as oligodendrocytes, astrocytes, and microglia, along nerve fibers. This method enables further exploration of tissue-specific contributions to susceptibility anisotropy.

neuroscience↗

bioRxiv2025

Structural basis for BCL7B-mediated ncBAF-nucleosome engagement

The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble nucleosomes to regulate gene expression and chromatin structure dependent on ATP hydrolysis energy. While the chromatin engagement mechanisms of cBAF and PBAF have been structurally resolved, the molecular architecture governing ncBAF interaction with chromatin remains elusive. In this study, by integrating cryo-electron microscopy, biochemical assays and cross-linking mass spectrometry, we resolved the conformational transition of ncBAF-nucleosome complexes from nucleotide-free to nucleotide-bound states. Our analyses establish BCL7 proteins as dynamic molecular tethers connecting the ARP module to the nucleosomal acidic patch and demonstrate that BCL7B promotes ncBAF-mediated nucleosome remodeling, with BRG1-catalyzed ATP hydrolysis triggering conformational changes that modulate BCL7-mediated histone association. Structurally and biochemically, we further demonstrate that {beta}-actin within the BCL7-containing ARP module retains ATP hydrolysis activity, rendering its exposed pointed end structurally compatible with incorporation into the barbed end of nuclear actin filaments, which provides a potential molecular basis for coordinating nuclear actin networks with chromatin remodeling. Collectively, our findings unravel a dynamic role of BCL7 in regulating ncBAF-mediated chromatin remodeling and establish a distinct chromatin engagement mode of ncBAF from that of cBAF/PBAF.

molecular biology↗

bioRxiv2025

Spatio-Temporal Multi-Omics Profiling of Mechanisms and Biomarkers in Inhaled Drug-Induced Lung Toxicity

Comprehensive understanding and early detection of drug-induced lung toxicity remain critical challenges in respiratory drug development. In this study, we propose a multi-omics framework that integrates spatial and temporal tissue-specific transcriptomic signatures with proteomics from minimally invasive biofluids to understand mechanisms and identify safety biomarkers associated with lung toxicity. Using this framework, we identified a panel of candidate biomarkers in bronchoalveolar lavage fluid and plasma, including LCN2/NGAL, RETNLA, SP-D, SPP1/osteopontin, and MMP7, that correlate with histopathological features (e.g., inflammation and epithelial remodeling). We confirmed that these molecular biomarkers were consistently dysregulated across a range of inhaled lung toxicants, human disease (IPF), and environmental exposures (smoke, Alternaria), demonstrating broad applicability across different toxic exposures and translatability. Collectively, this study establishes a robust workflow for mechanism-guided biomarker discovery and proposes a panel of candidates for monitoring drug-induced lung injury in humans.

systems biology↗

bioRxiv2025

B-cell follicles of lymphatic tissues act as a critical microanatomical niche for sustained viral replication, virus-host interaction and damage during chronic SIV infection

Most people living with HIV-1 (HIV) are diagnosed during the chronic stage of infection, at which point viral setpoint has been established and a substantial immunopathologic damage in the secondary lymphatic tissues (LTs) has been induced. To better characterize virus-host interaction and immunopathologic damage in LTs, we investigated viral spatial distribution patterns and the corresponding LT structural alterations in SIV chronically infected rhesus macaques. Using RNAscope in-situ hybridization (RNAscope) and a combination of CODEX with RNAscope (Comb-CODEX-RNAscope), we demonstrated that in chronic infection, SIV viral RNA (vRNA) is predominantly resides within B-cell follicles with minimal presence in T-cell zones, and there is significant B-cell follicular damage, encompassing follicular hyperplasia, fibrosis, and disintegration of the germinal center. Our results reveal that the B-cell follicles act as a critical microanatomical niche for sustained viral replication, virus-host interaction and tissue damage during SIV chronic infection.

immunology↗

bioRxiv2025

Integrative analysis of GTEx data reveals that systemic transcriptomes correlate with human spermatogenic dysfunction

Declining of male fertility may stem from intrinsic testicular dysfunction or systemic influences from other tissues. However, beyond the hypothalamic-pituitary-testis axis, little is known about which organs interact with the testes or whether they affect spermatogenic capacity. To investigate this, we analyzed GTEx open-access data, comparing transcriptomic profiles across various tissues in men with high and low testicular spermatogenic activity. Our findings reveal significant associations between testicular function and the pituitary gland, adrenal gland, lungs, liver, and key brain regions involved in neuroendocrine regulation, including the amygdala, substantia nigra, anterior cingulate cortex, and frontal cortex. These results suggest potential extragonadal pathways that modulate male fertility, highlighting candidate biomarkers for testicular dysfunction and novel therapeutic targets for infertility intervention.

developmental biology↗

bioRxiv2025

Distinct Programs Drive Organ Development and Regeneration

A prevailing paradigm in stem cell and developmental biology posits that regeneration is a recapitulation of embryonic programs, yet the molecular logic underlying these processes remains unclear. Here, using the mammary gland as a model, we identified a novel intermediate cell state essential for basal-to-luminal differentiation during regeneration. The transcription factor Pou2f3 is a master regulator of this state, critical for regeneration but dispensable for organ physiology. Mechanistically, we found that POU2F3 functions as a transcriptional repressor that drives lineage conversion by restricting chromatin accessibility of basal genes rather than by directly activating luminal programs. Furthermore, we uncovered a POU2F3-TNF feedback loop that maintains epithelial homeostasis, where TNF signaling suppresses Pou2f3 to inhibit differentiation, and loss of luminal cells relieves this repression to trigger regeneration. Strikingly, cell fate is governed by signaling pathways essential for cell-cell communication during development, but by Pou2f3-dependent chromatin remodeling for rapid response and injury repair. We validate the regeneration-specific requirement for Pou2f3 in mammary gland and further demonstrate analogous regeneration defects in prostate and pancreas. These findings challenge the long-held assumption that regeneration recapitulates development and establish a framework for understanding context-specific mechanisms of tissue plasticity, with implications for regenerative medicine and epithelial biology.

cell biology↗

bioRxiv2025

Epithelial FOXP3 Drives Pancreatic Fibrosis through O-glycosylated IL-6

BACKGROUND & AIMSThe transcription factor FOXP3, known for specifying regulatory T cell fate, is unexpectedly expressed in the epithelium of precancerous pancreatic lesions. Here we investigate its non-immune role in initiating pancreatic fibrosis, a process driving therapeutic resistance and organ failure in pancreatic ductal adenocarcinoma (PDAC) with unknown origins in early neoplasia. METHODSUsing human tissues and genetically engineered mouse models, we analysed FOXP3 expression in premalignant lesions. We employed epithelial-specific FOXP3 knockout and knock-in strategies to determine its functional impact on fibrogenesis and neoplasia progression. Mechanistic studies included chromatin immunoprecipitation, glycomic analyses, and signalling assays. RESULTSFOXP3 was consistently expressed in the epithelial compartment of human and murine precancerous pancreas. Epithelial-specific deletion of FOXP3 attenuated pancreatic fibrosis and delayed neoplasia, whereas its knock-in induced spontaneous stromal activation and accelerated PanIN progression. Mechanistically, epithelial FOXP3 directly transactivated the glycosyltransferase GALNT1. GALNT1, in turn, mediated O-glycosylation of interleukin (IL)-6, which was essential for its rapid secretion. CONCLUSIONSOur study establishes epithelial-derived FOXP3 as a master regulator of early pancreatic fibrocarcinogenesis. It drives a glycosylation-dependent amplification loop for IL-6 signalling, orchestrating sustained stromal activation. This pathway represents a promising target for intercepting pancreatic fibrosis and carcinogenesis at its origin.

cancer biology↗

bioRxiv2025

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

Functional annotation of proteins from extreme environments represents a major bottleneck for bioresource discovery, as a vast reservoir of functional dark matter defies existing homology-based methods. We demonstrate that environmental pressures impart conserved physicochemical energy signatures that co-determine protein function with sequence and structure. Here we developed ACCESS, a multimodal graph neural network employing hierarchical contrastive learning with a tailored label-sample co-embedding to fuse energy, sequence, and structural information and overcome homology scarcity. ACCESS surpasses state-of-the-art methods including BLASTp and CLEAN in annotating low-identity enzymes. Applied to extreme environmental metagenomics, we constructed a function map of extremophile enzymes to expand the biocatalyst library, pinpointed functionally critical residues to guide rational design, and enabled large-scale, function-based macro-evolutionary analyses. This paradigm transcends the limitations of homology, illuminating protein dark matter and accelerating the exploration of the biospheres functional diversity for applications in biotechnology and therapeutic development.

bioinformatics↗

bioRxiv2025

Identification of gingipains in glioblastoma tumors and evidence that P. gingivalis infection drives IL-6 and PD-L1 expression in glioma cells

Glioblastoma multiforme (GBM), a highly aggressive brain tumor that accounts for approximately 60% of all gliomas and 48% of primary central nervous system malignancies, is incurable and poorly understood, with a median survival of only 15 months after diagnosis. Thus, there is an urgent need to understand GBM pathogenesis in order to develop an effective treatment. Recent research has revealed frequent Alzheimers disease (AD) pathology in the brains of patients with GBM, i.e., amyloid beta (A{beta}) and hyperphosphorylated tau (pTau), indicating that GBM and AD may share some unknown environmental risk. Since chronic periodontitis (CP), and specifically Porphyromonas gingivalis (P. gingivalis), a keystone bacterial pathogen in CP, have emerged as risk factors for both AD and GBM, we investigated whether P. gingivalis gingipain virulence factors could be identified in GBM tissue samples and whether P. gingivalis infection affects glioma cell behavior. Using immunohistochemistry on tissue microarrays (70 GBM cores from 35 patients; 34 cerebral tissue cores from 17 patients), we quantified the presence of arginine-gingipain B (RgpB) and lysine-gingipain (Kgp) antigens. Both gingipains showed significantly elevated staining in GBM samples compared to controls (**p < .01, ****p < .0001, respectively), with Kgp levels notably higher than RgpB within GBM tissue (****p < .0001). In functional assays using U251 glioma cells, P. gingivalis infection induced robust, dose-dependent IL-6 secretion (peaking at MOI 5), increased PD-L1 expression by 30% (*p = .036), and significantly enhanced cell invasiveness (**p < .01) in a viability-dependent manner. These findings demonstrate that P. gingivalis gingipains are present at elevated levels in GBM tissue and that P. gingivalis infection reprograms glioma cells to adopt an immunosuppressive, invasive phenotype through upregulation of the IL-6/PD-L1 axis, suggesting a potential microbial contribution to GBM pathogenesis and immune evasion. Key pointsO_LIGlioblastoma multiforme (GBM) patients have frequent Alzheimers disease (AD) neuropathological changes in the tumor-adjacent cortex, indicating that GBM tumors may share some environmental risk factors with AD. C_LIO_LIThis study identifies gingipain antigens in GBM tissue samples at significantly elevated levels compared to healthy controls, suggesting that P. gingivalis infection may be an environmental risk factor for both AD and GBM. C_LIO_LIIn in vitro experiments, P. gingivalis infection of the human glioma cell line U251 upregulated IL-6 secretion and PD-L1 expression, and significantly increased cell invasiveness compared to uninfected cells. C_LI

neuroscience↗

bioRxiv2025

Analysis of SIV Spatiotemporal Dissemination Patterns in Rhesus Macaques During Early Rectal Transmission Demonstrates Systemic Infection Does Not Require Viral Local Amplification at the Entry Portal

Receptive anal sex is a dominant mode of HIV-1 (HIV) transmission, especially among men who have sex with men (MSM). However, the early events during HIV rectal transmission are not well understood and many questions remain, such as, does virus local amplification at the entry portal require for viral distal seeding? What is the spatiotemporal dissemination pattern across whole body? How do three viral forms, i.e., cell-free virus (VCF), cell-associated virus (VCA), and follicular dendritic cell-trapped virus (VFDC), evolve during early infections? To close this knowledge gap, we comprehensively examined rectum, draining lymph nodes (dLN) and distal lymph nodes (disLN), as well as non-lymphoid organs of brain, lungs, and liver of Indian rhesus macaques (RMs) at the early time points following intrarectal SIVmac251 inoculation (1, 2, 3, 4, 6, 10 14, 28 day post inoculation, dpi). Our findings demonstrated SIV rapidly disseminates to distant tissues and organs (<=1 dpi) and virus local amplification in rectum and dLN is not required for viral distal seeding for the establishment of systemic infection, viral forms shift from VCF and VCA to VFDC accompanying from T cell zones into B cell follicles. Collectively, these findings indicate that an effective HIV vaccine needs to induce immune protection both locally at sites of viral entry and systemically.

immunology↗

bioRxiv2025

Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes

Progressive {beta}-cell dysfunction precedes the onset of type 1 diabetes (T1D), yet the molecular mechanisms driving early T1D development remain poorly understood. Although single-cell RNA-sequencing has uncovered transcript-level changes in human islet cells, it offers limited insight into the heterogeneity of distinct islet microenvironments. Here, we applied a single-islet proteomics workflow to profile intra-donor islet heterogeneity in three stage 1 T1D cases with matched non-diabetic controls and define in situ protein signatures of pseudo-temporal islet dysfunction. Intra-donor analyses of [~]100 individual islets per donor revealed highly consistent proteomic patterns reflecting pseudo-time progression of islet immune responses and {beta}-cell dysfunction. Several pathways, including extracellular matrix remodeling and mRNA processing, were identified as closely associated with progressive islet immune activation and loss of {beta}-cell function. These findings provide robust proteome-wide evidence of the progression of islet dysfunction, offer a valuable resource for investigating early mechanisms of T1D pathogenesis-- including novel candidates for functional studies--and underscore the utility of single-islet spatial proteomics for examining islet heterogeneity in T1D.

systems biology↗

bioRxiv2025

N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis

N6-methyladenosine (m6A) is an abundant modification of mRNA with important regulatory roles in normal and malignant hematopoiesis. We previously reported that in human erythroid leukemia (HEL) cells, m6A mRNA marking selectively regulates translation of essential erythropoiesis genes required for in vitro differentiation and human erythroid colony formation. Here, we further investigated the timing and nature of requirement for m6A-methyltransferase (MTase) activity during human erythropoiesis, using a standardized in vitro erythroid differentiation assay for hHSPCs. We identified two critical m6A regulated developmental windows in BFU-E and during the transition from CFU-E to proerythroblasts. These windows of m6A-MTase requirement coincide with rising global m6A levels, which peak in proerythroblasts. After proerythroblast formation, however, m6A -MTase activity is dispensable for differentiation, proliferation, and survival. In BFU-E, m6A-MTase promotes proliferation but is dispensable for differentiation, while, in CFU-E, both m6A -MTase and the YTHDF family of m6A readers are essential for differentiation to proerythroblasts. Mechanistically, in CFU-E, m6A MTase activity enhances translation of ribosomal and oxidative phosphorylation (OXPHOS) genes, thereby elevating global protein synthesis rates and enabling efficient erythroblast formation. We propose that this form of translational regulation by m6A emerged as an evolutionary adaptation to meet the high translational demands of human erythropoiesis.

developmental biology↗

bioRxiv2025

Improved marker detection for rare population in single-cell transcriptomics through text mining-inspired scoring approach

Accurate identification of cell types and states is a crucial step when analysing single cell RNA-seq data. Inaccurate cell type annotation leads to spurious results and biological interpretations in subsequent analyses. Cell type identification is traditionally done using established marker genes of each cell population. However, many existing methods do not perform well for imbalanced cell populations, which often occurs in the presence of rare cell types. Most existing methods tend to be biased towards the dominant cell populations or highly expressed genes, leading to inaccurate results. Here, we introduce the package smartid, which accurately identifies markers from even imbalanced data across batches by employing a modified Term Frequency-Inverse Document Frequency approach with Gaussian Mixture Model. smartid is also a gene-set scoring method which is able to distinguish the target group of interest. smartid is implemented in R and is freely available on Bioconductor at https://bioconductor.org/packages/release/bioc/html/smartid.html.

bioinformatics↗

bioRxiv2025

Structural and Functional Insights into HBx-Smc6 Targeting for HBV Inhibition

The hepatitis B virus (HBV) X protein (HBx) is a multifunctional regulator essential for HBV replication and HBV-associated hepatocarcinogenesis. Despite its central role, the molecular basis of HBx function has remained elusive. Here, we present the first cryo-electron microscopy structure of the human HBx-CRL4-Smc5/6 complex at 3.1 [A] resolution. In this reconstituted ten-subunit assembly, HBx adopts a Zn2 {square}-stabilized Y-shaped architecture that simultaneously engages the DDB1 and the Smc6 subunit. A composite helix-turn-helix (HTH) pocket in HBx accommodates a conserved "Leucine Key" motif (LRCKL) on Smc6, forming a critical interface essential for complex stability and function. Molecular docking and biochemical validation reveal that the compound Tranilast binds this HTH pocket, disrupts the HBx-Smc6 interaction, and suppresses HBV replication. These findings define the structural mechanism by which HBx counteracts host restriction and establish the HBx-Smc6 interface as a previously unrecognized and druggable target for antiviral intervention.

cell biology↗

bioRxiv2025

A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present "simplified 5PSeq" (s5PSeq), a streamlined protocol for profiling 5 monophosphorylated (5P) mRNA degradation intermediates that reflect ribosome dynamics in vivo. By capturing antibiotic-induced, context-specific ribosome stalling events, s5PSeq provides a molecular proxy for bacterial growth inhibition--offering a molecular phenotypic readout without the need for culturing. s5PSeq reduces library preparation time to under four hours and incorporates a novel rRNA blocking strategy. We demonstrated its clinical utility by identifying erythromycin-resistant and sensitive Clostridioides difficile clinical isolates. Combining s5PSeq with real-time nanopore sequencing enables fast AMR diagnosis with as few as 3000 reads. In addition to simplifying the study of 5P co-translational mRNA decay, our work suggests that utilizing information-rich phenotypic molecular readouts can significantly improve AMR diagnostics. HighlightsO_LIs5PSeq is a streamlined protocol for profiling 5P mRNA degradation intermediates. C_LIO_LIContext-specific ribosome stalls can be used to assess phenotypic antimicrobial sensitivity at the molecular level. C_LIO_LIBlocking rRNA sequencing at the ligation step streamlines library preparation and lowers costs and hands-on time. C_LIO_LIIntegration with nanopore sequencing allows same-day antimicrobial sensitivity testing in species with 5-3 exonuclease. C_LI

microbiology↗