Biology subjects

Duan, L.

Publications and source records attributed to Duan, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Activity-gated exocytosis drives myelin remodeling required for adult learning

Myelin remodeling is emerging as a dynamic facet of plasticity in the adult brain. Learning and sensory experience induce remodeling of existing myelin sheaths through incompletely understood mechanisms, leaving its causal contribution to adaptive behaviors unclear. Here, we identify activity-dependent exocytosis in mature oligodendrocytes as a key driver of myelin remodeling. Live-cell imaging reveals that neuronal activity stimulates oligodendrocyte exocytosis. Exocytosis in mature oligodendrocytes drives myelin sheath elongation on optogenetically stimulated axons in adult mice. Disrupting exocytosis in pre-existing myelin, but not newly formed myelin, impairs motor skill acquisition, suggesting that remodeling of pre-existing myelin sheaths is required for learning. These results uncover a cellular mechanism that couples neuronal activity to myelin membrane remodeling and provide a molecular handle to interrogate the function of myelin plasticity across different circuits, behaviors, and neurological disorders.

neuroscience↗

bioRxiv2026

Histone lysine demethylase inhibition is a disease-modifying therapy for hypertrophic cardiomyopathy

RationaleHypertrophic cardiomyopathy (HCM) is a common inherited cardiac disorder characterized by cardiac hypertrophy, fibrosis, arrhythmias, and sudden cardiac death (SCD). Although current therapies primarily target sarcomere dysfunction, the contribution of epigenetic dysregulation to HCM pathogenesis and its therapeutic potential remain poorly understood. ObjectiveTo determine whether pharmacological inhibition of histone lysine demethylases (KDMs) with JIB-04 can prevent or reverse HCM progression and to identify the underlying epigenetic mechanisms. Methods and ResultsWe evaluated the pan-KDM inhibitor JIB-04 in Myh6R403Q/+ mice carrying the murine equivalent of the pathogenic human MYH7 R403Q mutation. JIB-04 prevented disease progression, reduced cardiac hypertrophy and fibrosis, preserved cardiac function, and completely prevented SCD in cyclosporin A- accelerated HCM. JIB-04 also reversed established disease, produced sustained therapeutic benefits after drug withdrawal, and improved cardiac function in aged mice with spontaneous HCM. Bulk RNA sequencing and ATAC-seq demonstrated partial restoration of disease-associated transcriptional programs and chromatin accessibility. Proteomic analyses identified PHF2 (KDM7C) as a candidate target of JIB-04 in both mouse and human HCM hearts. PHF2 knockdown suppressed hypertrophic, inflammatory, and fibrotic gene expression in cardiomyocytes, macrophages, and fibroblasts, respectively. Human HCM hearts exhibited increased expression of multiple JIB-04-sensitive KDMs, including PHF2. In MYH7 R403Q induced pluripotent stem cell- derived cardiomyocytes, JIB-04 normalized disease-associated gene expression, restored connexin-43 membrane localization, and improved mitochondrial respiration. Although prolonged treatment induced reversible hepatomegaly with hepatic lipid accumulation, co-administration of the antioxidant N-acetylcysteine mitigated liver toxicity while preserving the therapeutic efficacy of JIB-04. ConclusionsPharmacological KDM inhibition prevents and reverses HCM through epigenetic remodeling of disease-associated transcriptional and chromatin programs. These findings identify KDM inhibition as a promising therapeutic strategy for HCM, establish PHF2 as a candidate mediator of disease pathogenesis, and support further development of KDM-targeted therapies.

physiology↗

bioRxiv2026

IgG4⁺ plasma cell enrichment and {lambda}-chain-biased BCR remodeling drive low-grade autoimmunity in chronic obstructive pulmonary disease

BackgroundThis study aimed to elucidate B cell subset pathology in COPD, a poorly characterized area, with a focus on its similarities to and differences from classical autoimmune disorders. MethodsThe single-cell RNA-sequencing (scRNA-seq) data from COPD and autoimmune diseases were obtained from Gene Expression Omnibus (GEO) for comparative analyses of B cell subsets and functions via differentially expressed genes (DEGs), KEGG, protein-protein interaction (PPI), and cell-cell communication analyses. Serum IgG4 was measured by ELISA and correlated with clinical parameters. The peripheral blood B cells were sorted by flow cytometry for single-cell B cell receptor (BCR) sequencing. A v-Abl/Bcl2 pro-B cell line was stimulated with cigarette smoke extract (CSE) to assess abnormal development in vitro. ResultsIn lung tissue, IgG4+ plasma cells were enriched and expressed BCR activation/inflammatory genes and TNF/NF-{kappa}B/MAPK pathways. Serum IgG4 concentrations correlated negatively with pre-and post-bronchodilator FEV1/FVC. B cell interacted with monocytes, macrophages, fibroblasts and endothelial cells via IL-1{beta}/IL-6, integrin and chemokine signalling, contributing to chronic inflammation and remodelling. In peripheral blood, transitional T1 B cells were increased, accompanied by {lambda}-chain enrichment and increased IGLV1-47 usage, as well as enrichment of autoimmune pathways. In the bone marrow, the numbers of pre-B I cells were increased while those of small pre-B III cells were reduced, with altered expression of BCR development genes. CSE stimulation of the pro-B cell line reduced {lambda}5 expression in a concentration-dependent manner. ConclusionsThe autoimmune abnormalities in COPD appear more restricted, although IgG4 antibody generation may contribute to immune-mediated lung damage.

immunology↗

bioRxiv2026

Integration of proteogenomic analyses in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is still lack of clinically molecular subtyping and effective therapeutic strategies. Herein, a total of 46 paired tissue samples of esophageal squamous cell carcinoma (ESCC) were collected and subjected to a systematic proteogenomic evaluation. Consensus assessment of the ESCC-related transcriptomes and TCGA dataset revealed several consensual modes of gene expression related to ESCC specificity, with 8 plasma-detectable hub proteins that could discriminate ESCC from others. Three ESCC molecular subtypes were defined and validated based on proteome data, including pCC1 with activated immune response and best survival outcome, pCC2 as cell cycle subtype with relative worse outcome, and pCC3 with worst outcome that expressed more cell adhesion related proteins. Furthermore, we proposed potential therapeutic strategies for improving survival outcomes in patients with different ESCC molecular subtypes. This integrative proteogenomic analysis provided a novel view of ESCC-dependent molecular information.

cancer biology↗

bioRxiv2026

The Effects of Different Gait Patterns on Knee Joint Biomechanics and Dynamic Stability during Stair Walking in Healthy Adults

ObjectiveTo investigate the effects of different gait patterns on knee joint biomechanics and dynamic stability during stair ascent. MethodsFourteen healthy males were recruited to ascend stairs using two distinct gait patterns: the "single-step" (leading with the same leg) and "cross-step" (alternating legs) strategies. Kinematic and kinetic data were collected synchronously using a Qualisys infrared motion capture system and a Kistler 3D force plate. Dynamic stability was quantified using the Margin of Stability (MOS), and knee joint biomechanics were evaluated using Patellofemoral Joint Stress (PFJS) and other relevant metrics. ResultsThroughout the gait cycle, there was no significant difference in the Medio-Lateral (ML) MOS between the single-step and cross-step patterns (P=0.318). However, in the Anterior-Posterior (AP) direction, the MOS for both patterns remained negative and decreased over time, with the cross-step pattern exhibiting significantly lower AP MOS values than the single-step pattern (P=0.002). At the moment of left foot-off, significant differences were observed in the right knee joint angle, right knee joint moment, net joint moment, effective quadriceps muscle lever arm, Quadriceps Force (QF), the angle between the quadriceps tendon and patellar ligament, Patellofemoral Joint Force (PFJF), patellofemoral joint stress, and patellofemoral contact area (all P<0.001). ConclusionsDuring stair ascent, the cross-step pattern reduces body stability, thereby increasing the risk of backward falls. Furthermore, this pattern increases patellofemoral joint stress, subjecting the knee to greater loading. Therefore, it is recommended to enhance lower limb muscle strength through targeted training to reduce fall risk. Additionally, adopting a more cautious gait strategy (such as the single-step pattern) can help minimize patellofemoral joint loading and mitigate the risk of patellofemoral pain.

biophysics↗

bioRxiv2026

A tunnel microtract organ for T cell progenitor homing is formed by neural crest morphogenesis via Sox10-Cdc42 axis

Thymic colonization by T cell progenitors (TCPs) is essential for adaptive immunity, yet the guiding tissues remain elusive. Here, we unveiled a tunnel microtract (TMT) as an organ indispensable in TCPs homing in both zebrafish and mouse. Disruption of TMT leads to compromised T cell development. Specifically, the zebrafish TMT were positioned bilaterally beneath the fifth branchial levator muscle, connecting the thymus and kidney. They are semi-coiled, non-vascular, non-lymphatic tubes of epithelial signatures. Impressively, Sox10 activates Cdc42 to promote F-actin remodeling in neural crest cells (NCCs), leading to precise elongation and tight packaging of a low-permeability TMT. Remarkably, a homologous CD34 TMT was observed in mice, which bilaterally enveloped the embryonic thymus and extended into the thyroid cartilage. Sox10-Cdc42 signalling functioned recapitulatively in NCC morphogenesis during its construction. These findings establish TMT as an unappreciated NCC-derived organ in TCPs homing, with implications in T cell development and immune disorders.

developmental biology↗

bioRxiv2026

Multiomic Spatial Imaging Assay (MSIA) -- A High-plex In Situ Detection Method for mRNAs, Proteins, and Protein-Protein Interactions using Manual And Semi-Automated Workflows

We report Multiomics Spatial Image Analysis (MSIA), a suite of technologies that include streamlined manual and semi-automated workflows to image 100s of RNAs from fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, contextualize RNAs with select protein markers including imaging synaptic protein interactions, a data analysis pipeline that includes corrections for chromatic aberration, algorithms for image stitching, deep learning models for image analysis (cell segmentation and RNA dot detection using hundreds of RNAscope images) from multiple stain-image cycles and proof of concept for a language model trained on extensive Parkinsons Disease (PD) literature. We used the language model to identify potential new biomarkers that were confirmed in MPTP-treated mouse model of PD. Furthermore, by incorporating more stain-image cycles alongside an additional fluorescent channel and advanced error-correcting decoding schemes, the MSIA workflow demonstrates the scalability to potentially quantify over 1,000 genes.

neuroscience↗

bioRxiv2026

Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure

Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure. ImportanceWidespread fungicide use contaminates ecosystems worldwide, but the biological pathways underlying their effects on humans and other animals are not well understood. Using zebrafish (Danio rerio), we found that short-term exposure to the fungicide azoxystrobin was associated with changes in the gut microbiome, liver gene activity, and liver changes. Exposure produced dose- and sex-dependent shifts in microbial communities, including changes in predicted microbial functions involved in chemical metabolism, bacterial motility and defense. Compositional changes in the microbiome correlated with gene-expression changes consistent with stress and altered metabolism in exposed fish, suggesting that exposure induced disruption may contribute to exposure impact to the host. These results highlight a potential role for the microbiome in mediation of the impacts of azoxystrobin on host physiology. As such microbial based interventions could be a viable strategy to mitigate exposure impacts on health.

microbiology↗

bioRxiv2026

HIV-producing resting T cells monopolize virus production, associated PANoptosis, and persistence in lymphoid tissue

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/703840v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@167c265org.highwire.dtl.DTLVardef@10ba2beorg.highwire.dtl.DTLVardef@e97e06org.highwire.dtl.DTLVardef@150c07c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic:C_FLOATNO In chronic HIV infection, HIV is produced before antiretroviral therapy (ART) by resting CD4+ T cells in lymphoid tissue germinal centers. Virus production is associated with destruction of T cells, follicular dendritic cells (FDCs), and B cells required for humoral immune responses by PANoptosis (apotosis, pyroptosis and necroptosis) mediated by the PANoptosome, a cellular structure that incorporates cell contents and programmed cell death pathways in a nodal latticework that mediates cell emptying and disruption in progressive stages indicated by the numbers. During ART, persistent HIV-producing resting T cells represent an immediate source of virus for infection rebound on treatment interruption. C_FIG Activated CD4+ T cells have long been considered the principal source of HIV production before treatment and reactivated latently infected cells the source of virus rebound on treatment interruption, based largely on studies of peripheral blood T cells. Here we show before ART in the lymphoid tissue reservoir that HIV-producing resting CD4+ T cells are essentially the sole source of virus production in germinal centers. Virus is produced in infection complexes of virus bearing follicular dendritic cells (FDCs) that induce high multiplicity multi-HIV-DNA copy infections in overlying resting T cells. HIV production is associated with destruction by PANoptosis (pyroptosis, necroptosis and apoptosis) of interacting antibody-producing populations of FDCs, T cells and B cells. PANoptosis is mediated by the PANoptosome, visualized and defined here as a cellular structure incorporating cytoplasmic and nuclear contents and programmed cell death pathway components in a nodal latticework that executes cell emptying and disruption. During ART, HIV-producing resting T cells persist in lymphoid tissues when virus is undetectable in peripheral blood. These HIV-producing resting T cells that persist during ART represent an immediate source of virus to reignite infection on treatment interruption and are thus identified as an important new target for functional cure strategies.

microbiology↗

bioRxiv2026

Structural insights into the recognition and catalysis of tRNA by human NSUN2

The human RNA m5C methyltransferase NSUN2 catalyzes site-specific cytosine methylation across diverse RNA substrates and thereby regulates a wide range of biological and physiological processes. However, the molecular basis by which NSUN2 achieves broad substrate recognition while maintaining catalytic specificity has remained unclear. Here we determine structures of human NSUN2 in both substrate-free and substrate-bound states using X-ray crystallography and cryo-electron microscopy. Structures of NSUN2 in complex with multiple tRNA substrates reveal a structure-first, sequence-tolerant strategy in which NSUN2 actively remodels tRNA architecture, exposing the buried target cytosine and positioning it within the catalytic pocket for methyl transfer. This recognition strategy enables NSUN2 to accommodate diverse tRNA substrates through a largely conserved interaction interface. Guided by these structural insights, we identify a small-molecule inhibitor that suppresses NSUN2 activity and cancer cell proliferation. Together, our findings define the molecular principles underlying NSUN2-mediated RNA m5C modification and provide a structural foundation for targeting NSUN2 in cancers.

molecular biology↗

bioRxiv2025

Integrating Millions of Years of Evolutionary Information into Protein Structure Models for Function Prediction

BackgroundUnderstanding life processes relies on accurate protein function prediction, fundamentally requiring the integration of evolutionary information encoded in sequences with spatial characteristics from 3D structures. Existing approaches often face limitations, however, by either over-relying on sequence, using simplified structural representations instead of fine-grained spatial details, or failing to capture the synergistic relationship between sequence and structure, compounded by challenges in acquiring annotated data. ResultsTo address these issues, we propose a novel contrast-aware pre-training framework, ESMSCOP. ESMSCOP leverages a state-of-the-art protein language model to harness evolutionary insights embedded in sequences, and introduces a new encoder to fuse topological and fine-grained spatial structural features. By employing a contrastive pre-training strategy with auxiliary supervision, ESMSCOP effectively bridges the sequence-structure gap, yielding rich and informative representations. ConclusionsExtensive experiments conducted on multiple benchmark datasets demonstrate that ESMSCOP achieves superior performance in protein function prediction tasks compared to existing methods. Furthermore, it shows strong performance even when utilizing relatively less pre-training data compared to some large-scale models.

bioinformatics↗

bioRxiv2025

Nurture over nature in new Micromonospora spp. strains metabolism: multi-omics analyses reveal fermentation conditions as the dominant driver over phylogeny

The genus Micromonospora, a key member of the actinomycetes, has demonstrated considerable potential for natural product biosynthesis. In this study, we isolated 15 Micromonospora spp. strains from desert soil and marine sediment samples, eight of which represent four novel species. To explore the biosynthetic capacity of this genus, we performed an integrated analysis of Micromonospora reference genomes. Pan-genomic analysis further unveiled the core biosynthetic characteristics of the genus responsible for producing terpenes and polyketides. Further multi-omics investigation, combining genomic and metabolomic data, uncovered a positive correlation between phylogenetic relationships and biosynthetic potential, alongside a decoupling of metabolic profiles. Notably, metabolomic findings emphasized the dominant influence of culture conditions on the expression of biosynthetic capabilities. Overall, our study provides a comprehensive elucidation of the biosynthetic potential of the genus Micromonospora and highlights the value of investigating novel strains and applying diverse cultivation strategies in natural product discovery. ImportanceOur study provides a comprehensive genomic and metabolomic elucidation of the significant biosynthetic potential within the genus Micromonospora. It reveals a core biosynthetic capacity for terpenes and polyketides that is phylogenetically linked, whereas the resulting natural product repertoire is subject to strong modulation by cultivation conditions. These findings underscore the critical importance of exploring novel species and employing diverse cultivation strategies to unlock the full potential of microbial resources for natural product discovery.

microbiology↗

bioRxiv2025

Integrative genomic insights into parallel local adaptation to Danxia and Karst edaphic islands in the endangered tree Firmiana danxiaensis

Uncovering the genetic basis of local adaptation is a central goal in evolutionary biology. Edaphic islands, such as Karst (KL) and Danxia (DL) landforms, provide ideal natural laboratories for this endeavor. However, the mechanisms underlying parallel adaptation to contrasting edaphic extremes within a single species remain poorly understood. Firmiana danxiaensis, an endangered tree endemic to both KL and DL in the Nanling Mountains, offers a rare opportunity to address this question. We integrated a chromosome-level genome assembly, population genomic analysis of 225 individuals from 20 populations across its entire range, and genotype-environment association (GEA) with high-resolution soil and climate data. The relatively large genome of F. danxiaensis (1.51 Gb) reveals two ancient whole-genome duplications and a Quaternary burst of LTR retrotransposons, which, together with significant expanded drought-related transcription factor (TF) families, together constitute its genomic basis of adaptation. Population structure resolved four genetic lineages with distinct demography and inbreeding patterns. GEA identified stronger local adaptation in DL than KL, driven mainly by soil factors (e.g., cadmium, zinc), while climate variables (e.g., Bio9, Bio11) predominated in KL. Despite these divergent drivers, drought stress and elevated metal ion acted as major selective pressures in both landforms. Furthermore, six key TFs (e.g., NAC090, bHLH42, MAPKKK20) under both local adaptation and positive selection in DL are involved in drought response and metal ion binding, facilitating survival in stressful habitats. Our findings provide novel insights into parallel local adaptation to contrasting edaphic islands and offer concrete genomic guidance for the conservation of F. danxiaensis. Significance statementThe genetic basis of parallel local adaptation to contrasting environments remains unclear. Using the endangered tree Firmiana danxiaensis, we uncover genomic mechanisms enabling its adaptation to both Karst and Danxia edaphic islands. We demonstrate that adaptation is primarily driven by soil factors in Danxia and climate in Karst, generating divergent genomic signatures yet converge on drought response. These findings establish a framework for understanding parallel local adaptation and offer concrete genomic guidance for conservation.

evolutionary biology↗

bioRxiv2025

OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section

Spatial transcriptomics enables in situ mapping of gene expression, yet no current platform provides single-cell, same-section integration with metabolomics, limiting direct links between transcriptional programsand metabolic phenotypesin native tissue. We present OpenFISH, a rapid, imaging-based spatial transcriptomics method operable on standard microscopes, requiring no proprietary hardware, and fully compatible with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). OpenFISH resolves hundreds of transcripts at subcellular resolution within 24 h and can be performed after MALDI-MSI, preserving metabolite distributions for cell-accurate co-registration on the same section. In mouse brain, integration with MALDI-MSI resolved metabolic heterogeneity at the level of individual cells. OpenFISH also quantified cell type-specific transcriptional activation of transposable elements after systemic lipopolysaccharide (LPS) challenge and detected disrupted spatial organization of D1 striatal neurons in Reeler mutants. Benchmarking showed performance comparable to or exceeding commercial platforms at [~]0.5% of per-sample cost. By enabling same-section, near-single-cell co-mapping of transcripts and metabolites in an accessible workflow, OpenFISH provides a scalable framework for high-content spatial multi-omics across neuroscience, immunology, cancer biology, and beyond.

molecular biology↗

bioRxiv2025

Influence of Housing, Sex, and Sampling Location on Taxonomy and Function of Adult Zebrafish Microbiomes

The zebrafish (Danio rerio) has emerged as an important animal model for the study of host-microbiome interactions. However, information on how variation in experimental parameters contribute to microbiome structure and function in adult zebrafish is limited which complicates experimental design, interpretation of results, and may reduce reproducibility. Here we quantified the impact of two potential sources of microbiome variation - housing strategy and sampling location - on microbial diversity of adult zebrafish using 16S rRNA amplicon sequencing. Our findings indicate that housing strategy significantly impacts gut microbiome diversity in adult fish with the highest similarity between individuals co-housed on recirculating water systems. Microbiome acclimation after housing transfer took between 14- and 21-days. Significant variation in microbiome composition was also observed across sampling sites. As in humans, fecal and intestinal microbial communities were similar and varied by sex, however each body site sampled possessed a small site-specific microbial community signature. Consistently, imputed function of these communities showed that gene family diversity is also predicted to vary by body site particularly between gut and non-gut locations. Together our work demonstrates that housing, sex, and sampling strategy all significantly impact microbial community composition and highlight the need for community wide discussions on best practices and reporting standards for adult zebrafish microbiome studies.

microbiology↗

bioRxiv2025

Drp1 Proteins Released from Hydrolysis-driven Scaffold Disassembly Trigger Nucleotide-dependent Membrane Remodeling to Promote Scission

Dynamin-related protein (Drp1) drives mitochondrial fission, dysregulation of which leads to neurodegenerative, metabolic, and apoptotic disorders. The precise mechanism of fission completion is unclear. One prevailing model is based on GTP-driven assembly of Drp1 helices that increase confinement via force generation. However, constriction to nanoscopic tubule radii appears necessary but not sufficient for scission. The other is based on GTP-driven disassembly of a constricting Drp1 scaffold that drives a membrane disturbance, but the relation of disassembly to scission and GTP hydrolysis remain uncertain. Elucidation of mitochondrial fission is complicated by the multiple time-involved in the dynamics of mechanoenzyme activity, oligomer disassembly, and membrane remodeling. Using machine learning, synchrotron x-ray scattering, and a theoretical model, our data support a model where progressive GTP hydrolysis enable free Drp1s to increase their capacity for inducing membrane negative Gaussian curvature (NGC). Furthermore, we identify and Drp1 variants that diminish this progressive capacity. Machine learning reveals that predicted NGC-generating sequences of the Drp1 oligomer are not in contact with the confined lipid tube, that scission-enhancing membrane remodeling is triggered by free Drp1 released upon disassembly. TeaserFree Drp1 released from disassembly of oligomeric Drp1 constrictase promotes GTP-hydrolysis dependent mitochondrial scission.

biophysics↗

bioRxiv2025

A global P-Process map to avoid P-value abuse

P-abuse is serious in difference identification analysis of data. How to avoid P-abuse is a huge challenge. Here, we evolve P-value (a single value) to P-Process (a global landscape of P-values under different sample size) to help researchers correctly recognize and use p-value. We observed -ln(P-Process) after rotation has very similar morphology with Wiener Process (or Brownian motion). Based on this property, for any sample size, we estimated the 95% fluctuation range of P-value and further estimated how many samples (N95()) could make sure 95% of P-values less than the given significant level . Tests proved that the estimation obtains a good performance with only a small number of samples in each group. For broader accessibility, a free web-service, P-Process Map, is available online to show the whole landscape of P-Process. At the end of the article, we explained 10 of the most typical P-abuse problems which can be easily voided by using P-Process. This "rethinking" of P-value from a higher position, which is profoundly different from the way we have seen this for the past century, would yield a new era - 2P era in which hypothesis testing is strongly required to evolve from P-value to P-Process.

bioinformatics↗

bioRxiv2025

5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for click chemistry labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.

cell biology↗