Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 433 records · Page 24Linked to original sources

bioRxiv2025

Cell state transitions drive the evolution of disease progression in B-lymphoblastic leukemia

Cancer stem cells (CSCs) are hypothesized to promote tumor progression through innate chemoresistance and self-renewal. CSCs reside in the CD34+/CD38- immunophenotypic subpopulation of acute myeloid leukemia (AML); correspondingly, the size of this subpopulation has a strong negative impact on overall survival. Isolation of CSCs from B-lymphoblastic leukemia (B-ALL) has proven difficult, and the cells of interest apparently are not isolated to the CD34+/CD38- compartment. This may be explained, in part, by temporal variations of CD34 and CD38 expression which result in stochastic cell state transitions (e.g., from CD34+/CD38+ to CD34+/CD38-). We present a mathematical model of these transitions and correlate salient findings with BCR::ABL1 status, minimal residual disease (MRD), and relapse in adult B-ALL. As the CSC hypothesis is well supported in AML, we focus on transitions to and from the hematopoietic stem cell compartment (CD34+/CD38-), which our findings suggest can be estimated from peripheral blood or bone marrow samples. Additionally, we find that BCR::ABL1 positive patient samples are associated with high transition rates into the CD34+/CD38- compartment, including self-renewal. In contrast, BCR::ABL1 negative patient samples have low CD34+/CD38- self-renewal rates and either high CD34+/CD38+ or CD34-/CD38+ incoming rates. High CD34+/CD38- self renewal is also associated with MRD post-induction chemotherapy. We find a lack of observable changes in cell state transitions between diagnosis and relapse specimens. Our analysis provide evidence of de-differentiation transitions to a CD34+/CD38-stem cell-like immunophenotype in leukemia samples collected from B-ALL patients, and the tendency for these transitions is especially strong for B-ALL with BCR::ABL1. The modeling framework used here is a novel, useful tool to infer both prognosis and genotype from routine flow cytometry data. Significance StatementFlow cytometry characterization of B-lymphoblastic leukemia samples (diagnosis, remission, relapse) is used to parameterize a mathematical model of cell state transition rates and stratify patients at risk for post-induction chemotherapy minimal residual disease.

cancer biology↗

bioRxiv2025

Heme-NO dilates arteries via mobilization of NO moieties from a vascular intracellular NO store

Nitrosyl heme (heme-NO) has recently emerged as a surrogate signaling entity for nitric oxide (NO). However, questions remain about how heme-NO signals across the cell membrane. Herein, we test the hypothesis that heme-NO signals as a nitrodilator that vasodilates by mobilizing NO moiety from a nitrodilator-activated intracellular NO store (NANOS) in the vasculature. We identify a novel mechanism for glutathione-catalyzed formation of a model compound, alb-heme-NO, and determine glutathione (GSH) as a ligand in its structure. Heme-NO complexes with plasma proteins in blood and, as such, it is impermeable to red blood cells or the vascular wall. Alb-heme-NO-mediated vasodilation, both in vitro and in vivo, is attenuated by prior depletion of the NANOS and potentiated by NANOS supplementation. Incubation with alb-heme-NO induces efflux of NO moieties from arteries. Additionally, the role of nitrosyl hemoglobin (HbNO) in mediating NO bioactivity export from erythrocytes is challenged. In conclusion, heme-NO functions as an extracellular nitrodilator via activation of the intracellular NANOS.

physiology↗

bioRxiv2025

Nuclear 2'-O-methylation regulates RNA splicing through its binding protein FUBP1

2'-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

molecular biology↗

bioRxiv2025

RBMX2: A Pivotal Regulator Linking Mycobacterium bovis Infection to Epithelial-Mesenchymal Transition and Lung Cancer Progression

Tuberculosis (TB) is a complex disease that arises from the dynamic interplay among the pathogen, host, and environmental factors. In 2022, TB affected approximately 10.6 million people worldwide, resulting in 1.3 million deaths. In regions with a high burden of zoonotic TB, Mycobacterium bovis (M. bovis) accounts for nearly 10% of human TB cases. The immune evasion strategies and latent nature of Mycobacterium tuberculosis (M. tb) pose significant challenges to understanding the host immune response to TB infection. In this study, we identify RNA-binding motif protein X-linked 2 (RBMX2) as a novel host factor that may facilitate M. bovis infection. However, the molecular mechanisms and functional roles of RBMX2 during M. bovis infection remain poorly understood. Our findings show that RBMX2 is significantly upregulated across multiple cell types following infection, including embryonic bovine lung (EBL) cells, bovine macrophage (BoMac) cells, bovine pulmonary alveolar primary cells, and human alveolar epithelial cells (A549). Using a combination of global transcriptomic sequencing, proteomic profiling, cell adhesion assays, ChIP-PCR, and Western blotting, we demonstrate that RBMX2 suppresses cell adhesion and tight junction formation in EBL cells while promoting M. bovis adhesion and invasion through activation of the p65 signaling pathway. Importantly, integrated analyses of transcriptomic, proteomic, and metabolomic data reveal that RBMX2 plays a key role in regulating epithelial-mesenchymal transition (EMT), a cellular process closely associated with cancer progression. To further explore the potential link between RBMX2 and cancer, we analyzed the TIMER2.0 database and found elevated RBMX2 expression in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues compared to normal lung tissues. These findings were corroborated by immunofluorescence staining. Using an M. bovis-infected BoMac-induced EBL-EMT model, we show that RBMX2 promotes EMT through activation of the p65/MMP-9 pathway following infection. Additionally, we validated the EMT process in human lung epithelial cancer cells (H1299), further supporting the involvement of RBMX2 in this transition. Collectively, our study identifies RBMX2 as a novel host factor that may enhance M. bovis infection and drive infection-induced EMT. These findings provide new insights into the molecular mechanisms underlying TB pathogenesis and suggest that RBMX2 could serve as a potential target for the development of TB vaccines and therapeutic strategies against TB-associated lung cancer.

microbiology↗

bioRxiv2025

Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis

BackgroundErythroid cells can be generated from hematopoietic stem and progenitor cells (HSPC) derived from various sources; however, few studies decode ex vivo human erythropoiesis for the discrepancies at single-cell multi-omics resolution and uncover the underlying restraints for erythrocyte regeneration. ResultsWe deciphered ex vivo human erythropoiesis at two differentiation states from three sources at single-cell chromatin accessibility and transcriptomes level. We identified detrimental myeloid differentiation tendencies during early differentiation. These tendencies were linked to low glutamine activity in cord blood- and iPSC-derived erythropoiesis. The erythroid progenitor differentiation is restricted by cell cycle and hypoxia signaling deficiencies, which are pronounced in the iPSC-derived erythropoiesis. We delineated the erythroid differentiation trajectory of various ex vivo erythropoiesis systems, and revealed a distinct roadmap from HSC to orthochromatic erythroblast with unprecedented resolution. The integrative analysis of single-cell chromatin accessibility and transcriptome across developmental stages uncovered a dynamic coordination, and highlighted the pivotal role of chromatin accessibility and associated enhancers in regulating ex vivo erythropoiesis. Cell-cell communications in the ex vivo erythropoiesis system were not as well established as those in the BM, suggesting that modulating cell-cell communication signals in distinct ex vivo erythropoiesis system may facilitate erythrocyte regeneration. ConclusionsThis study comprehensively characterized the discrepancies and constraints in ex vivo human erythropoiesis at single-cell multi-omics resolution, offering novel strategies to overcome these constraints. These insights are critical for advancing functional erythrocyte generation and have significant implications for clinical applications.

developmental biology↗

bioRxiv2025

The Gut Microbiome and Butyrate Differentiate Clostridioides difficile Colonization and Infection in Children

Background and AimsSymptomatic Clostridioides difficile infection (CDI) can cause significant morbidity and mortality. Conversely, patients can be colonized with toxigenic C. difficile in the absence of symptoms, termed asymptomatic colonization. We previously demonstrated that the presence and function of C. difficile toxins do not differentiate between asymptomatic colonization and CDI in children, suggesting the influence of other factors. This study aimed to interrogate the intestinal microbiome and butyrate in stool samples from children with CDI and asymptomatic colonization. MethodsDesign: Case-control study Setting: Tertiary care childrens hospital Participants and measures: Asymptomatic children had stool tested for C. difficile by nucleic-acid amplification-based testing (NAAT) and were considered colonized if positive (N=50). Residual stool was also obtained from symptomatic children who tested positive for C. difficile by NAAT (N=55). The microbiome was assessed via 16S rRNA sequencing and butyrate via liquid chromatography-mass spectrometry. ResultsCompared to clinical co-variates and comorbidities, C. difficile symptom status (i.e., asymptomatic colonization versus symptomatic CDI) demonstrated the strongest differential abundance association on gut microbes. Symptomatic CDI was associated with increased abundance of Escherichia/Shigella (Benjamini-Hochberg adjusted q=3.94x10-5), Haemophilus (q=0.022), and Gemella (q=0.085), and depleted abundance of gut commensals such as Faecalibacterium (q=0.041), Blautia (q=0.041), and Bifidobacterium (q=0.063). We also observed depletion in the abundance of microbial butyrate producers and fecal butyrate in participants with symptomatic CDI versus asymptomatic colonization. ConclusionThe gut microbiota and butyrate differ between participants with asymptomatic C. difficile colonization and symptomatic CDI, suggesting their potential role in symptom development.

microbiology↗

bioRxiv2025

The Promotive Effect of Ocean Literacy on Marine Conservation Behavior: A Qualitative Study Based on Chinese University Students

IntroductionOcean literacy is crucial in shaping marine conservation behaviors among Chinese university students. This study explores the intricate relationship between ocean literacy and pro-environmental behaviors, emphasizing the roles of emotional connections, cultural significance, and educational experiences. By examining the multidimensional aspects of ocean literacy, the research seeks to identify key factors that influence conservation actions and the practical application of marine knowledge. MethodsUtilizing qualitative methodologies, this study conducted semi-structured interviews with 16 Chinese university students to delve into their perceptions and interactions with the marine environment. The interviews explored various dimensions such as oceanic knowledge, environmental beliefs, value orientations, and actions related to marine conservation. NVivo software was used for data analysis, allowing for the identification of key themes through a rigorous coding process. The studys analysis also included a moderated mediation model to examine how educational experiences influence the relationship between ocean literacy and conservation behaviors. ResultsThe findings reveal that ocean literacy among university students comprises key components such as scientific knowledge, environmental ethics, conservation action, policy understanding, and critical thinking. Significant gaps in marine knowledge were observed, alongside strong emotional and cultural connections to the ocean, which significantly mediate the relationship between ocean literacy and conservation behaviors. Educational experiences further moderated these effects, highlighting the need for enhanced marine education. ConclusionThis study underscores the necessity of integrating comprehensive educational strategies with emotional and cultural engagement to effectively promote marine conservation behaviors. The results advocate for educational reforms that incorporate practical and interactive learning approaches, aimed at deepening students understanding and involvement in marine conservation. Strengthening these educational frameworks can significantly enhance ocean literacy and foster proactive environmental stewardship among university students.

scientific communication and education↗

bioRxiv2025

Exploring Population Differences in the Human Gut Microbiome: from Microbial Abundance to Single Nucleotide Polymorphisms

The human gut microbiota exhibits significant diversity across populations, influenced by factors such as geography, diet, and lifestyle, particularly between the Han Chinese and non-Chinese populations. While previous studies have predominantly focused on the taxonomic abundance of the gut microbiome, the impact of single nucleotide polymorphisms (SNPs) in driving population-specific differences remains largely underexplored. In this study, we systematically investigated gut microbial differences between the Han Chinese and non-Chinese populations using the Human Gut Microbiome Reference Genome Catalog (HGMRGC). HGMRGC includes 271,480 non-redundant genomes from 5,785 prokaryotic species, which was generated by metagenomic sequencing data from 9,320 publicly available samples across 22 countries and 3,584 newly sequenced samples from Han Chinese individuals across 29 provinces and regions in China. We observed geography was the primary driver of microbial variation of abundance and SNPs. We identified 625 novel population-specific genome clusters from HGMRGC with functional differences in carbohydrate utilization and 126 species exhibiting distinct prevalence related to vitamin biosynthesis, antibiotic resistance, and carbohydrate metabolism. Beta diversity analysis highlighted significant inter-population differences in both microbial abundance and SNPs, while alpha diversity analysis revealed that non-Chinese populations exhibited higher diversity in microbial abundance, and Han Chinese populations displayed greater diversity in SNPs. These results provide valuable insights into population-specific microbial diversity, laying the groundwork for future research on its functional and health implications.

microbiology↗

bioRxiv2025

Gap-free genomes and transcriptomes uncover race-specific effectors in watermelon wilt pathogen Fusarium oxysporum f. sp. niveum

Watermelon (Citrullus lanatus L.) is one of the worlds most economically important fruit crops, yet it is susceptible to devastating diseases such as vascular wilt caused by Fusarium oxysporum f. sp. niveum (Fon), with limited effective control measures. Fon evolves rapidly in the field to overcome host resistance and global watermelon production is constantly threatened by new pathogenic races. High-quality genomic resources are key to understanding the molecular mechanisms underlying Fon virulence evolution for disease management. Here, we de novo assembled and annotated gapless genomes of three physiological races of Fon (race 1, 2, and 3), and dissected the mechanisms behind their distinctive virulence through comparative genomics and transcriptomics. Whole-genome alignments identified core and accessory chromosomes in Fon where each race carried a unique set of accessory chromosomes or regions. Comparative transcriptomics of Fon infection revealed distinctive temporal patterns of gene expression even among core gene families, particularly those related to cell wall degradation enzymes. Effectoromic prediction and comparative analysis in three gap-free genomes identified 13 race-specific effectors (RSEs) in FonR3, one (FonRSE1) of which was a critical virulence factor of FonR3 on watermelon as demonstrated via functional experiments. The gap-free genome assemblies and annotations, and the RSEs are valuable resources for studying Fon pathobiology and genome evolution, adding in the design of improved disease control strategies.

genomics↗

bioRxiv2025

Spatial Metagene Discovery and Associated Molecular Pattern Characterization in Spatial Transcriptomics and Multi-Omics using SEPAR

Spatially resolved transcriptomics (SRT) has transformed biomedical research by enabling gene expression profiling at near- or sub-cellular resolution while preserving spatial context. However, interpreting SRT data to understand cellular and gene organization remains challenging. Current methods focus on identifying global spatial domains across all genes, but often miss localized structures driven by specific gene subsets. Here, we introduce SEPAR, an unsupervised computational framework designed to analyze SRT data using a limited number of spatial metagenes and their expression patterns. SEPAR integrates gene activity and spatial neighborhood relationships to summarize gene expression per spot/- cell, decomposing data into contributions from spatial metagenes. It supports downstream analyses, including metagene expression pattern-specific gene identification, spatially variable gene (SVG) detection, spatial domain delineation, and gene expression refinement. Applied to diverse datasets, SEPAR demonstrates high efficacy. Gene sets linked to spatial metagene patterns are enriched with meaningful cell types and gene ontologies. SVGs are detected with higher accuracy, and gene refinement enhances biological signals, improving correlation analysis of functionally related genes. In spatial multi-omics data, SEPAR excels at revealing strong correlations between co-localized molecules in spatial CITE-seq data and identifies coordinated gene-peak relationships in MISAR-seq data, offering insights into spatial molecular interactions.

bioinformatics↗

bioRxiv2025

Specialized Pro-Resolving Mediator loaded Extracellular Vesicles Mitigate Pulmonary Inflammation

Specialized pro-resolving mediators (SPMs), including lipoxins derived from arachidonic acid and resolvins, protectins, and maresins derived from docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), orchestrate the active resolution of inflammation. These SPMs are biosynthesized through the coordinated interaction of various cells in a process known as transcellular biosynthesis, involving the sequential action of cyclooxygenase-2 (COX-2), 5-lipoxygenase (5-LOX), 12-lipoxygenase (12-LOX), and/or 15-lipoxygenase (15-LOX) enzymes. Additionally, Aspirin-triggered Resolvins are produced by acetylated COX-2, along with various lipoxygenases. Although SPMs regulate various cellular processes to actively resolve inflammation, their in vivo levels are typically low. To address this limitation, we engineered a multigene expression vector that co-expresses COX-2, 5-LOX, and 15-LOX, potentiating the synthesis of various SPMs. HEK293T cells transfected with this vector and cultured with fatty acid-free BSA-complexed DHA, EPA, and aspirin, successfully mimicked both transcellular and aspirin-triggered biosynthesis of Resolvins. These Resolvins are packaged into extracellular vesicles, which significantly inhibited neutrophil adhesion to endothelial cells, preserved endothelial monolayer barrier integrity, suppressed NF-{kappa}B reporter activity, and enhanced macrophage efferocytosis in vitro. Notably, post-injury administration of Resolvin-loaded EVs mitigated pulmonary inflammation in LPS-treated mice without causing systemic or pulmonary toxicity. In summary, we report a novel cell-based platform for generating Resolvin-loaded EVs that mitigate pulmonary inflammation in mouse models, underscoring their potential for treating other acute inflammatory diseases.

synthetic biology↗

bioRxiv2025

Enhancing variant detection in complex genomes: leveraging linked reads for robust SNP, Indel, and structural variant analysis

Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is essential for comprehensive genomic analysis. While short-read sequencing performs well for SNP and INDEL detection, it remains limited in resolving SVs, particularly in complex genomic regions, due to its short read length. Linked-read sequencing technologies, such as single-tube Long Fragment Read (stLFR), partially address this limitation by incorporating molecular barcodes to provide long-range information. In this study, we evaluate conventional paired-end linked reads (PE100_stLFR) and explore a conceptual extension: long single-end barcoded reads of 500 bp (SE500_stLFR) and 1000 bp (SE1000_stLFR). We developed_stLFR-sim, a Python-based simulator that reproduces the_stLFR workflow and enables realistic benchmarking. Using a high-quality T2T assembly of HG002, we generated multiple datasets across 12 sequencing configurations. SVs were called using Aquila_stLFR (v2) and benchmarked against the Genome in a Bottle (GIAB) HG002 SV truth set with Truvari. We show that simulated PE100_stLFR closely matches real data, validating the simulation framework. Increasing read length consistently improves SV detection accuracy, with SE1000_stLFR achieving the best performance and approaching long-read methods while outperforming short-read and pangenome-based approaches. Collectively, our results highlight the strong potential of long single-end barcoded reads for improving SV detection, and suggest that even modest increases in read length, when combined with barcode information, can provide a cost-effective and practical strategy for enhancing future sequencing technologies and SV discovery.

bioinformatics↗

bioRxiv2025

Novel multi-transmitter calyx-like giant synapse revealed in the extended amygdala

We have discovered a highly specialized innervation of the forebrain by pituitary adenylate cyclase activating polypeptide (PACAP) immunohistochemistry originating from the brain stem that uses glutamate, acetylcholine and PACAP and other peptides as neurotransmitters. The parent neurons of the axons are in the Kolliker-Fuse nucleus and their terminals form calyx-like multi-release site synapses in the rodent forebrain extended amygdala similar to the calyx of Held in the auditory brain stem. The latter is a giant, excitatory, cup-like axo-somatic high-fidelity synapse. The PACAP-positive terminals also form enveloping axo-somatic specialization with mixed glutamatergic and cholinergic molecular identities, co-expressing VGluT1, VGluT2, VAChT, and the neuropeptides PACAP, CGRP, and neurotensin, together with calretinin in the presynaptic compartment. We identified a distinct neuronal subpopulation in the pontine Kolliker-Fuse region of the parabrachial complex that gives rise to these calyceal terminals, which engulf PKC/GluD1 somata in the capsular central amygdala and oval bed nucleus of the stria terminalis. Strikingly, GluD1 immunolabeling is concentrated at axo-somatic contact zones apposed to VAChT presynaptic vesicle clusters zones but is absent from postsynaptic densities of conventional type I synapses within the same terminals. The results demonstrate a previously unrecognized multimodal calyx-like synapse in the forebrain, with parallel fast ionotropic and modulatory peptidergic neurotransmission mechanisms, which is a substrate for high-fidelity signal transmission within viscerosensory -emotional circuits. Significance StatementA high-fidelity axo-somatic glutamatergic synapse is exemplified by the calyx of Held in the auditory brainstem, but is unknown in the forebrain. Here we reveal a multimodal calyceal synapse in the extended amygdala formed by glutamatergic afferents of the pontine Kolliker-Fuse nucleus that contain also several neuropeptides. These giant terminals co-package glutamate, acetylcholine, PACAP, CGRP and neurotensin. They envelop select PKC/GluD1 neurons in the capsular central amygdala and oval BNST. These unique forebrain synapses link viscerosensory input from the hindbrain to limbic autonomic centers. Such high-fidelity multimodal transmission is likely to underlie the precise synchronization of emotional and homeostatic control circuits.

neuroscience↗

bioRxiv2025

Effects of amendments on remediation of heavy metal contaminated soil and accumulation of Cd and Pb in potato

With the development of agriculture and industry, a large amount of heavy metals are loaded into the soil, posing a high ecological and public health risk. Many methods have been proposed to repair heavy metal contaminated soil, such as electroremediation, chemical washing, phytoremediation and in situ fixation. In the above methods, the application of passivators to in-situ immobilization of heavy metals is an environmentally friendly and cost-effective choice. The effects of different amendments on the improvement of heavy metal contaminated soil and the accumulation of Cd and Pb in potato plants were investigated by using attapulgite, diatomite and humic acid as materials.The results showed that soil pH, organic matter content and cation exchange capacity increased after the application of amendments. Under the treatment of attapulgite+humic acid, the soil pH, organic matter content and cation exchange capacity were increased by 0.57units, 10.0 mg/kg and 7.28cmol/kg, respectively, compared with the control. The content of soil hydrolyzable nitrogen increased, and the content of available phosphorus decreased. The application of amendments increased soil enzyme activity; effectively reduce the bioavailability of Cd and Pb in soil ; under the treatment of attapulgite+humic acid, the contents of Cd and Pb in potato plants decreased by 85.50%and 55.54%respectively, and the contents of Cd and Pb in potato tubers decreased to 0.08 mg/kg and 1.41 mg/kg respectively. The application of amendments affected the accumulation and transport of heavy metals Cd and Pb in potato plants to a certain extent and promoted the transformation of Cd and Pb from acid-soluble and reduced states to oxidized and residual states.

ecology↗

bioRxiv2025

High-throughput Monoclonal Antibody Screening from Immunized Rabbits via Droplet Microfluidics

The discovery of monoclonal antibodies (mAbs) is critical to advancing therapeutics, diagnostics, and biomedical research. While mouse-derived mAbs dominate current applications, their limitations--short serum half-life, human immunogenicity, and restricted recognition of human-specific antigens--underscore the need for alternative sources. Rabbit-derived mAbs have been gaining significant traction with their superior antigen-binding affinity, broader epitope diversity, and higher yield potential. However, the absence of well-defined surface markers on rabbit B cells has hindered efficient enrichment strategies, limiting the exploration of this valuable antibody repertoire. In this study, we present an integrated workflow that combines magnetic negative selection with high-throughput droplet microfluidics to overcome these barriers. By optimizing a pan B cell enrichment protocol using a tailored antibody cocktail, we achieved a notable boost in IgG secretion and B cell enrichment. Through two complementary droplet-encapsulated assays using particle aggregation for soluble antigens and reporter cells for membrane-bound antigens, we identified target cells capable of secreting high-affinity IgGs. Subsequent sequencing, in vitro antibody production and characterization confirmed the high affinity rate of the discovered antibodies, outperforming rates previously reported. The use of droplet microfluidics streamlines the analysis of rabbit IgG repertoires, providing a robust platform for rabbit single B cell antibody discovery with promising applications in precision medicines and diagnostics.

molecular biology↗

bioRxiv2025

Interaction of the mitochondrial calcium/proton exchanger TMBIM5 with MICU1

Ion transport within mitochondria influences their structure, energy production, and cell death regulation. TMBIM5, a conserved calcium/proton exchanger in the inner mitochondrial membrane, contributes to mitochondrial structure, ATP synthesis, and apoptosis regulation. The relationship of TMBIM5 with the mitochondrial calcium uniporter complex formed by MCU, MICU1-3, and EMRE remains undefined. We generated Tmbim5-deficient Drosophila that exhibit disrupted cristae architecture, premature mitochondrial permeability transition pore opening, reduced calcium uptake, and mitochondrial swelling - resulting in impaired mobility and shortened lifespan. Crossing these with flies lacking mitochondrial calcium uniporter complex proteins was generally detrimental, but partial MICU1 depletion ameliorated the Tmbim5-deficiency phenotype. In human cells, MICU1 rescues morphological defects in TMBIM5-knockout mitochondria, while TMBIM5 overexpression exacerbates size reduction in MICU1-knockout mitochondria. Both proteins demonstrated opposing effects on submitochondrial localization and coexisted in the same macromolecular complex. Our findings establish a functional interplay between TMBIM5 and MICU1 in maintaining mitochondrial integrity, with implications for understanding calcium homeostasis mechanisms.

cell biology↗

bioRxiv2025

ARGContextProfiler: Extracting and Scoring the Genomic Contexts of Antibiotic Resistance Genes using Assembly Graphs

Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibiotic resistance genes (ARGs). Several tools, databases, and algorithms are now available to facilitate the identification of ARGs in metagenomic sequencing data; however, direct annotation of short-read data provides limited contextual information. Knowledge of whether an ARG is carried in the chromosome or on a specific mobile genetic element (MGE) is critical to understanding mobility, persistence, and potential for co-selection. Here we developed ARGContextProfiler, a pipeline designed to extract and visualize ARG genomic contexts. By leveraging the assembly graph for genomic neighborhood extraction and validating contexts through read mapping, ARGContextProfiler minimizes chimeric errors that are a common artifact of assembly outputs. Testing on real, synthetic, and semi-synthetic data, including long-read sequencing data from environmental samples, demonstrated that ARGContextProfiler offers superior accuracy, precision, and sensitivity compared to conventional assembly-based methods. ARGContextProfiler thus provides a powerful tool for uncovering the genomic context of ARGs in metagenomic sequencing data, which can be of value to both fundamental and applied research aimed at understanding and stemming the spread of AR. The source code of ARGContextProfiler is publicly available at GitHub.

bioinformatics↗

bioRxiv2025

AIPAMPDS: an AI platform for antimicrobial peptide design and screening

Antimicrobial resistance (AMR) presents a pressing global health crisis, particularly in the post-pandemic era, underscoring the urgent need for innovative therapeutics. Antimicrobial peptides (AMPs) hold promises for combating multidrug-resistant infections but are hindered by challenges in clinical translation, including limited hemocompatibility and inefficient design processes. To overcome these obstacles, we developed AIPAMPDS, an AI-driven computational platform that integrates a deep generative model with multi-stage screening to design highly active, non-haemolytic AMPs. The platform features two key modules: (1) a Generative Pre-trained Transformer (GPT)-based framework for target-specific AMP generation, enabling rapid exploration of novel peptide sequences, and (2) a multi-neural network screening pipeline for dual evaluation of antimicrobial activity and toxicity. By systematically evaluating both AI-generated and natural candidate AMPs, we identified ten lead peptides for experimental validation, of which 90% exhibited negligible haemolytic activity while maintaining robust antimicrobial potency. AIPAMPDS bridges computational design and therapeutic application, significantly advancing AMP discovery and providing a powerful tool for next-generation antimicrobial development. The platform is freely accessible via a web server at https://amps.pianlab.cn/AIPAMPDS/. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/644774v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14e9a20org.highwire.dtl.DTLVardef@168e811org.highwire.dtl.DTLVardef@5bd9beorg.highwire.dtl.DTLVardef@344c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗