Biology subjects

Wang, R.

Publications and source records attributed to Wang, R..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Benchmarking generative scaffold design methods for peptide engineering in TCR-MHC complexes

De novo peptide design at T cell receptor-peptide-major histocompatibility complex (TCR-pMHC) interfaces is a central challenge in computational immunology, with direct implications for vaccine development, cancer immunotherapy, and autoimmune disease. Despite rapid advances in generative protein modeling, there is currently no systematic benchmark evaluating these methods in the highly constrained and immunologically relevant setting of peptide-MHC presentation and TCR recognition. Here, we present two complementary contributions. First, we introduce a multi-stage computational pipeline for peptide design in predefined TCR-pMHC contexts, integrating generative modeling with sequence optimization and structure-based filtering. Second, we establish a benchmark for evaluating generative peptide design methods in TCR-pMHC complexes. Using a curated dataset of high-quality crystal structures deposited after the AlphaFold3 training cutoff, we assess state-of-the-art generative approaches for peptide backbone generation, sequence design, and the enrichment of near-native solutions. We explicitly examine whether different backbone generation strategies respect the geometric constraints of the MHC binding groove and recover native-like peptide conformations. Our results reveal substantial method-dependent differences: some generative strategies fail systematically in the groove-bound peptide setting, whereas others generate physically plausible backbones with varying accuracy and conformational diversity. We further show that enforcing anchor constraints strongly influences peptide conformations at non-anchor positions, highlighting a trade-off between structural accuracy and conformational sampling. To enable fair and reproducible comparison, we introduce a standardized, multi-stage scoring protocol that integrates MHC binding prediction, physics-based energy evaluation, and independent structure prediction confidence metrics to enrich near-native designs from large candidate pools. Together, this work establishes the first comprehensive pipeline and benchmark for generative peptide design at TCR-pMHC interfaces and provides practical guidelines for developing peptide design workflows and evaluating generative models in immunologically constrained protein design settings.

bioinformatics↗

bioRxiv2026

Optimizing broadly neutralizing antibodies via all-atom interaction modeling and pre-trained language models

Antibody optimization is a fundamental challenge, and the identification of antibody-antigen interactions is crucial in the optimization process. However, current methods cannot accurately predict antibody-antigen interactions, providing limited functional guidance to improve the time-consuming and costly traditional optimization techniques. Here, we present InterAb and InterAb-Opt, a unified computational framework that integrates all-atom modeling with antibody language models to predict antibody-antigen interactions and enable antibody optimization. Leveraging the proposed all-atom modeling approach, AtomInter, and pre-trained antibody language models, InterAb outperforms existing methods in predicting antibody specificity and antibody-antigen binding affinity. InterAb successfully identified influenza A virus-binding antibodies from an antibody library and accurately detected high-affinity antibodies in the AIntibody competition. Empowered by the robust functional insights from InterAb, InterAb-Opt was developed to optimize broadly neutralizing antibodies. For R1-32 antibody, biolayer interferometry results reveal that 85%, 80%, 90%, and 67.5% of the 40 InterAb-Opt-optimized antibodies exhibit enhanced binding affinities to wild-type SARS-CoV-2, Lambda, BQ.1.1, and EG.5.1, respectively, with a maximum improvement of up to 96-fold. For the newly emerging BA.2.86 and KP.3, 55% and 52.5% of the optimized antibodies notably transition from non-binding to binding. Neutralization assays demonstrated that the optimized antibodies exhibited enhanced neutralization activity across multiple targets, highlighting the capability of InterAb-Opt in engineering broadly neutralizing antibodies. This technology enables precise analysis of antibody-antigen interactions and optimization of broadly neutralizing antibodies, holding promise for addressing challenges in immune evasion and vaccine design.

bioinformatics↗

bioRxiv2026

Iron Deficiency Drives Sarcopenia in the Elderly: HIF-1α-Mediated Fibro-Adipogenic Progenitor Differentiation Induces Fat Infiltration and Impairs Muscle Function

Abnormal iron metabolism is closely linked to sarcopenia; however, the specific iron metabolism features of fat-infiltrating sarcopenia remain poorly understood. Proteomic sequencing revealed that in skeletal muscle with severe fat infiltration, the expression of iron utilization-related proteins was significantly downregulated, whereas that of iron uptake and storage proteins was markedly upregulated, thereby presenting an abnormal iron deficiency (ID) phenotype. Nevertheless, the mechanism by which ID drives intramuscular fat infiltration has not been fully elucidated. Using clinical samples, aged murine ID models, and in vitro cell assays, this study is the first to demonstrate that ID stabilizes hypoxia-inducible factor-1 (HIF-1), promoting aberrant adipogenic differentiation of fibro-adipogenic progenitors (FAPs), disrupting the homeostatic balance between satellite cells (SCs) and FAPs, exacerbating skeletal muscle fat infiltration, and impairing muscle repair capacity. Notably, treatment with the HIF-1 inhibitor PX478 reversed these pathological alterations and improved muscle function. Collectively, our findings identify the ID-HIF-1-FAPs axis as a key driver of intramuscular fat infiltration, offering a novel therapeutic target for the clinical management of fat-infiltrating sarcopenia.

cell biology↗

bioRxiv2026

Origin-1: a generative AI platform for de novo antibody design against novel epitopes

0Generative artificial intelligence has advanced antibody discovery, yet de novo design of therapeutic antibodies against targets with "zero-prior" epitopes remains a fundamental challenge. We define "zero-prior" epitopes as target sites lacking structural data from any reported antibody-antigen or protein-protein complex involving the target. Here we present Origin-1, a generative AI platform that overcomes this by integrating epitope-conditioned all-atom structure generation, paired complementarity determining region sequence design, and a specialized co-folding-based scoring protocol to select antibody designs predicted to be high-confidence, specific binders with favorable developability. We evaluated Origin-1 on a panel of ten targets selected to have no available protein-protein complex structures and minimal homology ([≤]60% sequence identity) to proteins with known complexes, creating stringent design conditions. In fewer than one hundred design attempts per target, we identified developable, specific antibodies, validated across multiple biophysical and developability assays, for four targets: COL6A3, AZGP1, CHI3L2, and IL36RA, with functional inhibition demonstrated for IL36RA. Cryogenic electron microscopy confirmed the atomic accuracy of our designs, revealing complexes that closely matched the computational models with high structural fidelity (3.0-3.3 [A] resolution; 0.83-0.91 DockQ). Furthermore, we employed AI-guided affinity maturation to optimize a de novo antibody binder against IL36RA, producing functional antagonists with sub-nanomolar affinities and a top EC50 of 12.3 nM. These results demonstrate a framework for targeting epitopes without structural precedent, expanding the programmable therapeutic antibody landscape.

molecular biology↗

bioRxiv2026

Development of Integrin α5β1-targeted PET/NIR imaging probes for glioblastoma intraoperative navigation and intracavity targeted radionuclide therapy

Incomplete extent of tumor resection is the major factor of glioblastoma recurrence, leading to its poor prognosis. Developing therapies that enable the minimal tumor cell remnant during surgical resection is a major challenge to combat this aggressive cancer. This study develops a glioblastoma integrin 5{beta}1-selective peptide binder through series strategy screening and labeling it with 68Ga, indocyanine green (ICG), or 177Lu for efficacious multimodal treatment. This strategy combines positron emission tomography (PET) imaging for preoperative diagnosis, intraoperative NIR-II fluorescence-guided surgery for maximal tumor resection, and followed by intracavity targeted radionuclide therapy for elimination of residual tumor cells. We identified GR, with five arginine mutation, exhibiting superior integrin 5{beta}1 binding affinity and brain penetration. [68Ga]GR demonstrated substantial tumor uptake and prolonged retention time in both mouse models and tissues from glioblastoma patients. The guidance of ICG-GR achieved accurately intraoperative tumor imaging and maximal tumor resection in orthotopic mouse glioblastoma models. Notably, combining intracavity administration of [177Lu]GR following ICG-GR guiding resection markedly inhibited tumor growth and reduced possibility of tumor recurrence compared with surgery alone (unguided or ICG-GR-guided) or unguided surgery followed by [177Lu]GR. Therefore, we have reported the integrin 5{beta}1-targeted radionuclide and optical agents for maximal elimination of tumor cells during surgical resection in glioblastoma patients. HIGHLIGHTSO_LIGR is a glioblastoma-specific peptide with both favorable binding affinity superior brain penetration. C_LIO_LIICG-GR is a glioblastoma-targeted NIR probe enabling maximal surgical resection. C_LIO_LIICG-GR-guided surgery with [177Lu]GR-based adjuvant therapy allows robust elimination of tumor cells. C_LI

cancer biology↗

bioRxiv2026

EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

Mitochondria possess their own mRNA translation system, mediated by specialized mitoribosomes. Dysregulation of mitochondrial translation disrupts metabolic homeostasis and is linked to various pathologies, including metabolic syndromes, neurological disorders, and cardiac diseases. Using CRISPR/Cas9 screening, we identified EOLA1 (endothelial-overexpressed lipopolysaccharide-associated factor 1) as a novel mitochondrial matrix protein essential for metabolic homeostasis. Knockout of Eola1 severely affects mitochondrial translation and consequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 physically interacts with mitochondrial 12S ribosomal RNA (12S mt-rRNA) and the mitochondrial Tu translation elongation factor (TUFM), facilitating efficient translation elongation of mitochondrial-encoded mRNAs. Furthermore, genetic ablation of Eola1 in mice induced severe cardiac dysfunction, demonstrating its indispensable role in maintaining heart function through mitochondrial translation control. Together, our findings establish EOLA1 as a key regulator of mitochondrial translation via its interactions with 12S mt-rRNA and TUFM, highlighting its importance in cellular metabolism and a potential role in cardiac disease pathogenesis.

molecular biology↗

bioRxiv2026

High performance sorting of motor unit action potentials with EMUsort

Understanding how neural signals control muscle activity during behavior is a key challenge in motor neuroscience. To this end, recent advances in intramuscular multielectrode arrays have enabled high-quality multichannel recordings of many motor unit action potentials (MUAPs) in freely moving subjects. However, identifying individual MUAP events within multichannel recordings is a significant challenge for existing spike sorting methods, which are typically optimized for identifying action potentials from neurons in the brain. To overcome this challenge, we developed the Enhanced Motor Unit sorter (EMUsort), an extension of Kilosort4 (KS4) that achieves high-performance MUAP spike sorting. We applied EMUsort to high-resolution intramuscular recordings from rat forelimb during locomotion and monkey forelimb during a reaching task. EMUsort improves upon prior methods by addressing key challenges encountered with MUAP datasets, including: 1) long time delays across electrodes due to propagation along muscle fibers, 2) more complex waveform shapes compared to neuronal action potentials, and 3) a high degree of MUAP overlap due to cumulative motor unit recruitment. We compared EMUsort to existing spike sorting methods quantitatively using simulated datasets that closely emulated the rat and monkey datasets we recorded. EMUsort provided median error rate reductions of 67.5% and 49.9% during periods of high motor unit activation for the rat and monkey datasets, respectively. In sum, EMUsort provides a substantial improvement to MUAP spike sorter accuracy, especially during regions of high MUAP overlap, in an easy-to-use software package.

neuroscience↗

bioRxiv2026

DNA sequence quantitatively encodes CTCF-binding affinity at genome scale

CTCF is a central architectural protein that shapes 3D genome organization through sequence-specific DNA binding, but how DNA sequence quantitatively determines CTCF-binding strength remains poorly understood. Progress has been hampered by the lack of large, high-quality measurements of binding affinity. Here, we experimentally determine in vitro CTCF-binding affinity for 276,765 DNA sequences derived from the human genome, generating a comprehensive quantitative landscape of CTCF-DNA interactions. Leveraging these data, we develop DeepCTCF, a deep learning model that predicts CTCF-binding strength directly from DNA sequence and enables quantitative interpretation of CTCF motif grammar. Using this framework, we systematically dissect how specific sequence features modulate CTCF-binding affinity and generate quantitative predictions for disease-associated variants that alter CTCF binding. Together, this study defines general principles by which DNA sequence encodes CTCF-binding affinity and provides a quantitative framework for interpreting regulatory sequence variation. TeaserMapping how DNA encodes CTCF binding reveals quantitative rules across over 1{per thousand} of the human genome.

genomics↗

bioRxiv2026

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

bioRxiv2025

CyTOF-based profiling of circulating tumor cells predicts aggressiveness and therapy response in SCLC liquid biopsies at a personalized level

Small-cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma characterized by high numbers of circulating tumor cells (CTCs). We applied CyTOF and a 20-marker antibody panel to detect and phenotype CTCs directly in liquid biopsies of 51 SCLC patients (treatment-naive, chemotherapy and immunotherapy-treated, and tarlatamab-treated), of which a subset were longitudinally tracked. Unsupervised clustering revealed distinct cell populations enriched in patient liquid biopsies compared to those from healthy donors. Further analysis identified CTC populations of the three established SCLC subtypes driven by the high expression of ASCL1, NeuroD1, and POU2F3 transcription factors respectively. Significant differences in CTC EMT markers, established therapeutic targets (e.g. DLL3), and subtype heterogeneity were observed between naive versus treated samples. Changes in subtype proportions were observed in longitudinally tracked samples in both treatment modalities. Our study demonstrates the utility of CyTOF for high-resolution CTC profiling, offering dynamic insights into CTC heterogeneity, treatment response, and resistance mechanisms. HighlightsO_LICTCs can be detected, subtyped and phenotyped in SCLC liquid biopsies using CyTOF C_LIO_LICTC subtypes and EMT states are differentially associated with treatment modality C_LIO_LICTC DLL3 levels and epithelial features increase following anti-DLL3 BiTE therapy C_LIO_LICyTOF CTC subtyping can predict disease aggressiveness C_LIO_LILongitudinal tracking reveals CTC plasticity and therapy response correlations C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/694669v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@384cbcorg.highwire.dtl.DTLVardef@35dd37org.highwire.dtl.DTLVardef@4e7d61org.highwire.dtl.DTLVardef@1098e4f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Torsins Organize CLCC1 Assembly to Safeguard ER Bilayer and Lipid Homeostasis

The TMEM41B scramblase and its regulatory partner CLCC1 initiate lipid flux by equilibrating newly-synthesized phospholipids across the endoplasmic reticulum (ER) bilayer, a fundamental process required for diverse events ranging from membrane biogenesis to bulk lipid supply. Loss of CLCC1/TMEM41B causes ER bilayer imbalance, inducing giant ER-enclosed lipid droplets (geLDs) and driving rapid progression into severe MASH. Here we identify CLCC1 as the long-missing client of the lumenal Torsin ATPases, which selectively engage oligomerized CLCC1 at sites of ER bilayer imbalance. Hepatic TorsinA inactivation triggers geLD formation amid disrupted lipoprotein biogenesis and severe MASH, closely phenocopying CLCC1/TMEM41B deficiency. Mechanistically, Torsins act as foldases that drive CLCC1 oligomerization for its recruitment to imbalanced bilayers. Remarkably, ectopic CLCC1 expression reverses cellular and systemic lipid disorders arising from hepatic TorsinA deficiency. Hence, Torsin ATPases emerge as fundamental regulators that organizes CLCC1 and the downstream TMEM41B scramblase to govern lipid partitioning and membrane homeostasis.

cell biology↗

bioRxiv2025

A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability

Recent studies have revealed many alternative exons differentially spliced across diverse neuron types in the mammalian brain, but their links to neuronal physiology remain unclear. Here we characterize a deeply conserved microexon E35a in Ank3 encoding ankyrin-G (AnkG), a multifaceted adaptor protein best known as a master organizer of the axon initial segment (AIS) and as a leading genetic risk factor for bipolar disorder. E35a is predominantly skipped in cortical glutamatergic neurons but included in cortical GABAergic neurons and cerebellar neurons, which is dictated by multiple neuronal splicing factors. In E35a-deletion mice we generated, interneurons show increased excitability and somatic Ca2+ activity, without disruption in AIS. Biochemical analyses suggest that E35a inclusion facilitates AnkG interaction with a protein complex involving inositol trisphosphate receptors (InsP3Rs) important for intracellular Ca2+ signaling. Alternative splicing therefore allows AnkG to modulate neuron type-specific excitability in addition to its ubiquitous pan-neuronal role in organizing the AIS.

neuroscience↗

bioRxiv2025

Exudate-Guided Janus Trilayer Bioelectronic Dressing for Multimodal Sensing and Therapy of Chronic Wounds

Chronic wound treatment remains challenging because conventional dressings and systemic therapies typically lack real-time adaptability to the dynamic changes in the wound microenvironment. Here, we report a breathable self-adhesive multifunctional wound dressing based on a gradient-wettable Janus trilayer fibrous membrane, which integrates real-time biochemical sensing, on-demand drug release, and low-voltage electrical stimulation therapy simultaneously. The dressing features a vertically integrated trilayer architecture with hierarchical partitioning, where the three vertically stacked layers integrate a multiplex electrochemical sensor array (glucose, lactate, pH), a silver-sulfadiazine drug reservoir, and stimulation electrodes. Specifically, a hydrophilic sensing layer, intermediate drug-storage layer, and hydrophobic adhesivelayer are assembled to achieve spatially resolved functionalities. The membranes gradient wettability and asymmetric porous structure enable directional exudate transport, thereby triggering stepwise activation of sensing, drug release, and electrical stimulation in a spatiotemporally controlled manner. The dressing is thin, breathable, stretchable, self-adhesive and biocompatible, enabling conformal contact and stable signal acquisition on deformable skin without tapes. This design ensures continuous bio-signal monitoring while maintaining a favorable wound healing microenvironment. Preclinical tests demonstrate its effectiveness in promoting wound closure, reducing infection, and providing continuous wound status monitoring. This integrated system offers a promising approach for next-generation wound care and regenerative medicine.

bioengineering↗

bioRxiv2025

A transition zone enriched WIF1⁺ basal cell subtype is associated with benign prostatic hyperplasia

ABSTRACT/SUMMARYThe cellular composition and disease susceptibilities of the distinct zones of the human prostate remain incompletely understood. Through extensive single-cell RNA sequencing (scRNA-seq) of benign regions from prostatectomy specimens, we identified a basal cell population expressing WIF1, VCAN, and NRG1, among other genes, that was significantly enriched in the transition zone (TZ). Benign prostatic hyperplasia (BPH) is a common condition that causes widespread morbidity and is nearly exclusively localized to the TZ. Analysis of previously published scRNA-seq datasets further confirmed that WIF1+ basal cells were significantly enriched in BPH compared to normal prostate. Pathway and cell-cell communication analyses revealed that this basal subtype is associated with programs related to cell proliferation, epithelial-mesenchymal transition (EMT), angiogenesis, and hormone response. Together, the molecular signature, zonal distribution, and pathway enrichment suggest that TZ-enriched WIF1+ basal cells may contribute to BPH pathogenesis by promoting epithelial and stromal remodeling.

cell biology↗

bioRxiv2025

A transcription factor-responsive enhancer discovery platform for targeted immunotherapy

Synthetic enhancers with high specificity are crucial for therapeutic gene control. However, experimental screens and machine learning-guided design typically require context-specific datasets, limiting generalizability. Because transcription factor (TF) activity reflects cellular state, TF-responsive enhancer libraries offer a universal starting point. Here, we developed TREND (transcription factor-responsive enhancer discovery), a massively parallel reporter assay of [~]2.7 million enhancer-barcode constructs representing 57,715 designs. TREND covers 1,068 motif-annotated proteins, including 729 confirmed TFs across 49 DNA-binding domain families. Applied to ovarian cancer, TREND identified enhancers that discriminate cancer from normal epithelial cells. These enhancers enabled protein-interaction-based AND-gate circuits with reduced OFF-state leakage and amplified ON-state output, driving tumor-restricted expression of combinatorial immune effectors and robust antitumor responses in murine ovarian cancer models. TREND also identified T-cell activation-responsive enhancers with greater inducibility and lower basal activity than conventional NFAT-motif-based elements. Together, TREND provides a generalizable framework for context-specific enhancer discovery and therapeutic gene regulation.

synthetic biology↗

bioRxiv2025

Swine wastewater drives dissemination of high-risk blaNDM-positive Escherichia coli clones

Swine wastewater can accelerate the spread of antibiotic-resistant bacteria among animals, the environment, and humans. Therefore, the molecular epidemiological characteristics of carbapenemase-producing E. coli isolates from swine wastewater was investigated. In this study, a total of 100 no-cloning carbapenemase-producing (blaNDM-1, blaNDM-5 and blaOXA-48-like) E. coli isolates were recovered from 316 swine wastewater samples collected from 29 swine farm in Shandong, China. Of which, two isolates that co-harbored blaOXA-48-like and mcr-1, as well as five isolates that co-harbored blaNDM-5 and tet(X4). All isolates were multidrug-resistant (MDR), with a majority exhibiting resistance to meropenem, ciprofloxacin, imipenem and gentamicin. Whole genome sequencing (WGS) analysis indicated that these isolates were belonged to 12 distinct sequence types (STs), with the most prevalent STs being ST10 and ST5299. Additionally, Phylogenomic analysis revealed that clonal spread of blaNDM-positive ST10 E. coli isolates at swine wastewater in multiple cities, including Binzhou, Dezhou, Heze and Weihai. Meanwhile, a notable divergence in SNPs was observed in isolates from this study and public database, which indicates that these blaNDM-positive E. coli isolates have high genetic diversity. In addition, WGS analysis further revealed that blaNDM co-existed with other antibiotic resistance genes, conferring resistance to twelve classes of antimicrobials. This study underscores the importance of surveillance for blaNDM-harboring microbes in swine wastewater, and continuous monitoring in swine wastewater is essential for ensure human and environmental health. IMPORTANCEThe study described the NDM-positive E. coli strains isolated from swine wastewater, where it was associated with antibiotic exposure. Notably, swine wastewater was increasingly considered to be related to CRE hosts. Pathogens originating from this source can be transmitted to humans via direct and indirect contact, as well as through the ingestion or inhalation of contaminated water or aerosols. In addition, under the selective pressure of antibiotics, the co-harbored of blaOXA-48-like and mcr-1, blaNDM-5 and tet(X4) genes within the same host bacterium signifies the emergence of an extremely MDR pathogen, posing a grave threat to public health. Consequently, the monitoring of blaNDM in swine wastewater is critical for containing the transmission and persistence of carbapenem-resistant pathogens.

microbiology↗

bioRxiv2025

Decoding the fibroblast/mast cell signaling pathway of acupuncture

Acupuncture has been practiced for thousands of years with documented therapeutic effects, yet its underlying biological mechanisms remain poorly understood. Here, we show that acupuncture stimulation converts local mechanical forces into neuronal signals through defined cellular interactions, establishing a causal axis that links micro-level events at the ST36 acupoint to systemic therapeutic effects. We demonstrate that acupuncture needle manipulation transmits mechanical tension through collagen fibers to local fibroblasts, which subsequently secrete stem cell factor (SCF) and interleukin-33 (IL-33) in the acupoint. SCF recruits mast cells, while IL-33 induces their activation and the release of neuromodulatory molecules. These molecules then engage the nervous system, as evidenced by c-fos expression in the lumbar dorsal horn, demonstrating the transmission of acupuncture-induced peripheral signals into central circuits. Together, these findings define a functional axis linking needle-evoked stimulation to neuronal activation and provide a mechanistic framework for understanding the biological basis of acupuncture and for its evidence-based refinement.

cell biology↗