Biology subjects

Xu, L.

Publications and source records attributed to Xu, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

EA-PheWAS: Integrating Phenotype Embeddings with PheWAS for Enhanced Gene-Phenotype Discovery

Phenome-wide association studies (PheWAS) enable systematic exploration of relationships between genetic variants and clinical phenotypes derived from electronic health records (EHRs). Conventional regression-based PheWAS treats phenotypes separately and relies on binary phenotype representations, which limits statistical power for rare variants and rare phenotypes and reduces the ability to detect associations with phenotypes that are distributed across clinical codes. To address this limitation, we first developed EmbedPheScan, a phenotype embedding-based prioritization framework that summarizes the phenotypic profiles of rare loss-of-function variant carriers in a continuous embedding space. We then proposed EA-PheWAS by combining these embedding-derived signals with conventional regression-based PheWAS results using the aggregated Cauchy association test. Using the UK Biobank whole-exome sequencing and EHR data, we show that the proposed methods maintain appropriate false-positive control. We then performed genome-wide phenome scans across all genes and across biologically defined gene classes to evaluate EA-PheWAS relative to conventional PheWAS and EmbedPheScan, consistently finding that EA-PheWAS outperformed the other two methods. We illustrate the utility of EA-PheWAS focusing on four genes representing distinct scenarios, including strong-effect disease genes (PKD1, PKD2), genes with large numbers of rare LoF carriers (NF1), and genes with extremely sparse carrier counts (FBN1).

genetics↗

bioRxiv2026

Engineered Vibrio natriegens lysate can replace multiple components of cell culture media

Reducing the cost and environmental impact of cell culture media is an important goal for cultivated meat, the process of generating meat in vitro using proliferating animal cells. While prior approaches have demonstrated the use of microbial lysates to replace expensive animal-based fetal bovine serum (FBS) in media, these formulations still rely on large quantities of growth factors such as fibroblast-like growth factor 2 (FGF2). Here, we demonstrate the use of FGF2-expressing Vibrio natriegens to create whole-cell lysates that replace both FBS and FGF2 in cell culture media for cultivated meat applications. This medium, named "VN40FGF", supports rapid proliferation of immortalized bovine muscle satellite cells (iBSCs) in the absence of supplemented FGF2. Cells grown in VN40FGF maintain phenotype and differentiation capacity. We also demonstrate that engineered V. natriegens can grow in spent cell culture media, further improving sustainability and economics, and reducing potential eutrophication concerns associated with waste disposal. Our approach combines multiple strategies for reducing the total number of media inputs, demonstrating opportunities for more economical and sustainable cell culture, especially for cultivated meats.

bioengineering↗

bioRxiv2026

REST-AKT-SOX2 axis controls neuronal lineage state and Midkine-mediated communication in SHH-medulloblastoma.

Stem/progenitor-like cells are known drivers of tumor progression, chemoresistance, and relapse in Sonic-Hedgehog medulloblastoma (SHH-MB), yet the regulatory mechanisms that sustain these resilient cellular states remain incompletely defined. Here, we identify the RE1-silencing transcription factor (REST) as a key transcriptional regulator that preserves the progenitor compartment in SHH-MB through stabilization of the stemness factor SOX2. Mechanistically, REST activates AKT signaling, which in turn enhances SOX2 protein stability, revealing a REST-AKT-SOX2 axis that supports stem/progenitor identity and ongoing tumor maintenance. Beyond maintaining intrinsic stem-like programs, REST also orchestrates the extrinsic communication network of SHH-MB tumors. Single cell transcriptomic profiling and ligand-receptor interaction mapping highlight Midkine (MDK)-mediated signaling as one of the most upregulated intercellular communication routes in MB. We demonstrate that REST drives this signaling cascade through its control of SOX2. Perturbation of REST or SOX2 results in reduced MDK and its receptor, SDC2 expression, and chromatin immunoprecipitation assays show that SOX2 directly binds and regulates MDK/SDC2 expression, establishing and reinforcing a REST/SOX2 centered transcriptional mechanism that coordinates both progenitor maintenance and cell-cell communication in the malignant compartment. Together, these findings position REST as an integrator of intrinsic progenitor cell programs and extrinsic MDK-mediated signaling in SHH-MB. By linking stemness, communication and potential for therapeutic resistance, the REST-AKT-SOX2-MDK signaling axis emerges as a targetable vulnerability to suppress stem/progenitor driven tumor program in REST-driven SHH-MBs.

cancer biology↗

bioRxiv2026

UBL3 UBL domain exhibits distinct helix-centered dynamic control among ubiquitin-like proteins

Ubiquitin-like protein 3 (UBL3) is a post-translational modifier that sorts proteins into small extracellular vesicles and regulates the trafficking of disease-associated proteins such as -synuclein. The structural and dynamic features of the UBL domain that underlie these functions, however, remain poorly understood. Here we performed in silico structural dynamics analysis of the UBL3 UBL domain using an NMR structure ensemble combined with anisotropic network modeling (ANM) and perturbation response scanning (PRS). Principal component analysis and residue-wise fluctuation analysis consistently revealed high flexibility in the C-terminal region of UBL3. Comparative ANM analysis across 20 ubiquitin-like proteins (UBLs) further showed that C-terminal flexibility is a conserved yet variable property within the UBL family. PRS analysis demonstrated that residues forming the central -helix of the {beta}-grasp fold exert greater dynamic control over collective motions than {beta}-sheet residues. Notably, UBL3 displayed the highest helix/sheet PRS effectiveness ratio among all UBLs analyzed, highlighting the prominent dynamic contribution of helix residues in this domain. Together, these results provide a structural basis for understanding UBL3-dependent protein interactions and disease-related mechanisms, and suggest that helix-centered dynamic control in the UBL domain may represent a potential target for modulating UBL3 function.

bioinformatics↗

bioRxiv2026

Looplook: An integrative suite for target assignment and functional annotation of chromatin interactions empowered by expression-aware refinement and connected components clustering

Deciphering target genes regulated by cis-regulatory elements (CREs) is critical for translating genetic and epigenomic findings into clinically actionable insights. However, linking distal CREs to their cognate target genes remains a fundamental challenge due to the limited availability of computational tools for spatial annotation and the oversimplified assignments inherent to conventional topology-only strategies. A flexible framework that integrates 3D proximity with transcriptional output is urgently needed. To address these limitations, we develop looplook, an integrated computational framework that bridges 3D chromatin topology with functional genomics to enable accurate, flexible, and user-driven CRE-target gene assignment. Looplook provides four core capabilities: (1) robust consensus building for denoising and consolidating replicated or multi-source chromatin loops by employing connected component clustering; (2) bidirectional spatial annotation between 3D chromatin loops and diverse linear genomic features, offering optional graph-based high-order discovery and a linear fallback for gapless network resolution; (3) an expression- or chromatin-aware refinement algorithm that selectively retains functional loops; and (4) automated downstream functional profiling seamlessly integrated with customizable multi-track visualization. Through case studies of the FOSL2 and BRD4 cistromes in liposarcoma cells, we demonstrate that looplook outperforms conventional linear annotation methods by integrating chromatin interactions with expression data and chromatin profiles, offering a powerful and valuable framework for distilling experimental omics data into functionally interpretable high-order gene regulation networks. looplook is freely available as an open-source R package, with source code and documentation hosted on GitHub, and will be distributed via the Bioconductor repository.

bioinformatics↗

bioRxiv2026

The structure-interaction model of polymyxin lipopeptides with human oligopeptide transporter 2

Multidrug-resistant (MDR) Gram-negative bacteria pose a critical global health threat, while polymyxins remain a last-line therapy. However, their clinical use is limited by nephrotoxicity. Human oligopeptide transporter 2 (hPepT2) is a membrane transporter mediating the reabsorption of polymyxins in renal cells and contributes to their nephrotoxicity, but the molecular basis of their interaction remains unclear. Here, we investigated the structure-interaction relationship (SIR) of polymyxins with hPepT2 by integrating computational, chemical, and cell biology approaches. Bioinformatic modelling predicted an outward-facing hPepT2 structure and a potential transport pathway, with polymyxins interacting at the lateral opening, particularly E214, D215, D317, D342, and E622. Transporter mutagenesis and molecular analyses confirmed that D215 is critical for polymyxin binding, while other residues influence transporter turnover and/or expression. We subsequently synthesised polymyxin analogues with modifications at Dab1, Dab3, Dab5, and Dab9 of polymyxins, which reduced interactions with hPepT2. Notably, alanine substitution at Dab3 reduced nephrotoxicity in mice while retaining antibacterial activity. Overall, this proof-of-concept study demonstrates that the hPepT2-polymyxin SIR model provides a viable strategy for developing novel, safer lipopeptide antibiotics.

biochemistry↗

bioRxiv2026

Transcriptional landscape of cardiac-specific Gpx4 deletion recapitulates human cardiomyopathy

Glutathione peroxidase 4 (GPX4) is an antioxidant enzyme important for the reduction of toxic lipid peroxide products. Previous studies revealed the importance of mouse Gpx4 in protecting cardiomyocytes from ferroptosis and, subsequently, the development of cardiovascular disease. In this paper, we investigate the transcriptional consequences of cardiac-specific deletion of Gpx4 in mice and compare this response with that observed in human cardiomyopathy. The findings in this study highlight the importance of GPX4 in maintaining both structural and functional stability of the heart and identify key pathway changes resulting from excessive ferroptosis in cardiac tissue. By overlapping common transcriptional programs perturbed in this animal model and human cardiomyopathy, our findings identify putative mechanisms through which ferroptosis contributes to the development and progression of heart disease. These studies may help guide future cardiovascular therapeutics targeting ferroptosis-dependent pathways.

genomics↗

bioRxiv2026

Distribution, assembly and mechanism of GluN1/GluN3A excitatory glycine receptors

NMDA receptors play key roles in brain development, plasticity and diseases. While glutamate and glycine co-gated GluN2-containing NMDARs have been extensively characterized, little is known regarding GluN3A-containing NMDARs that form receptors gated by glycine only. Here, combining native purification, mass spectrometry, cryo-EM and electrophysiology, we provide key insights on the molecular logic of GluN3A-NMDARs. We demonstrate that native GluN3A receptors account for a sizeable fraction of total NMDARs, are enriched at extrasynaptic compartments in the adult brain, and assemble specifically as diheteromeric GluN1/GluN3A excitatory glycine receptors (eGlyRs) rather than as triheteromeric GluN1/GluN2/GluN3A receptors. The architecture of eGlyRs reveal splayed and loosely packed extracellular domains, strikingly different from conventional GluN1/GluN2 receptors. Through back-and- forth structural and functional validations, we demonstrate how the combined effects of a weak ligand-binding domain (LBD) dimer interface and high intrinsic mobility of the N-terminal domains (NTDs) shape the atypical gating of eGlyRs. These findings illuminate GluN3A-NMDAR physiology and mechanism, with implications for neuronal signaling and pharmacology.

neuroscience↗

bioRxiv2026

Light Chain Dominant Quaternary Epitope Recognition and IgG3 Switching Drive Broad Dengue and Zika Virus Neutralization

Defining how antibodies achieve broad neutralization across antigenically related flaviviruses is essential for rational therapeutics and vaccine design. Here, we describe 3A06, a human monoclonal antibody that neutralizes dengue virus (DENV) serotypes 1-3 and zika virus (ZIKV). Notably, subclass switching to IgG3 exhibits expanded neutralizing activity against all four DENV serotypes. High-resolution cryo-electron microscopy (cryo-EM) analysis of 3A06 Fab bound to chimeric ZIKV virions shows that 3A06 engages a quaternary epitope spanning three E protomers. Functional analyses identify a major functional contribution from the light-chain, where somatic hypermutations are critical for neutralization potency, and reversion of improbable mutations substantially reduces neutralization and increases antibody dependent enhancement (ADE) at sub-neutralizing concentrations. Cryo-EM analyses of intact IgG3 in complex with chimeric DENV2 and DENV4 show that the conformational clexibility and extended IgG3 Fc-hinge enable bivalent engagement across E-protein rafts in multiple concigurations, overcoming geometrical constraints that limit binding in the IgG1 format. Together, these results define a distinct mode of epitope recognition relative to previously characterized E-dimer epitope (EDE)-specific broadly neutralizing antibodies (bnAbs), and demonstrate how IgG3 subclass architecture can expand virus neutralization breadth. These insights inform the rational engineering of antibodies and vaccines targeting quaternary epitopes on flaviviruses to overcome viral diversity.

immunology↗

bioRxiv2026

Neutrophil-targeted delivery of circSCMH1 unlocks an acute anti-thromboinflammatory function to restore microvascular perfusion in stroke

ObjectivesFutile recanalization (FR) after endovascular thrombectomy (EVT) is driven by neutrophil-mediated thromboinflammation, yet conventional neuroprotectants fail to address the spatiotemporal complexity of stroke injury. This study aimed to identify the clinical link between circSCMH1, traditionally viewed as a late-stage repair molecule, and FR, while evaluating its hyperacute anti-inflammatory potential via a neutrophil-targeted delivery system. MethodsWe analyzed thrombi and plasma from LVO-AIS patients stratified by functional outcomes. We engineered neutrophil-targeted lipid nanoparticles (circSCMH1@pepLNP) for delivery in a mouse transient middle cerebral artery occlusion model. Therapeutic outcomes were evaluated through infarct volume measurement, histological assessment of NETosis, and intravital two-photon microscopy to monitor real-time neutrophil dynamics and capillary stalling. ResultsClinical analyses showed circSCMH1 was significantly downregulated in FR patients, with its levels negatively correlated with NET burden. Furthermore, circSCMH1-negative neutrophils exhibited a higher propensity for NETosis within the thrombus microenvironment. In mice, circSCMH1@pepLNP achieved specific neutrophil delivery, significantly reduced infarct volume, and suppressed the expression of citrullinated histone H3 and neutrophil elastase. Intravital two-photon and laser speckle imaging further confirmed that this intervention attenuated neutrophil adhesion, increased migratory velocity, and alleviated capillary stalling, thereby restoring cortical microvascular perfusion. ConclusionsOur findings associate neutrophil-specific circSCMH1 downregulation with clinical FR in LVO-AIS. Targeted intracellular delivery reveals an acute anti-thromboinflammatory function that complements established reparative properties, proposing a novel adjunctive approach for EVT to address the spatiotemporal complexity of stroke and improve clinical outcomes.

neuroscience↗

bioRxiv2026

Reduced Prefrontal PRDM2 Increases Stress-Induced Reinstatement Across Sexes via a dmPFC-Nucleus Accumbens Pathway

Stress is a major driver of relapse in alcohol use disorder (AUD), partly through stress-induced dysregulation of prefrontal cortex (PFC) circuits that govern executive control, craving regulation, and adaptive behavioral responses. Such dysfunction may be partly driven by epigenetic regulation of transcriptional programs that shape PFC responses to stress. Here, we investigated the role of the histone methyltransferase PRDM2 in stress-induced relapse to alcohol seeking. Analysis of postmortem human tissue showed that PRDM2 expression in the PFC was reduced in both men and women with AUD compared with control individuals. To examine the functional significance of this reduction in alcohol-related behaviors, we used viral-mediated knockdown of Prdm2 in the dorsomedial prefrontal cortex (dmPFC) of male and female rats. Prdm2 knockdown increased vulnerability to stress-induced reinstatement of alcohol seeking in both sexes, without altering pain sensitivity or being influenced by estrous cycle stage. To determine whether this effect was mediated through specific prefrontal output pathways, we selectively reduced Prdm2 expression in dmPFC neurons projecting to the nucleus accumbens (NAc). Projection-specific knockdown also increased stress-induced reinstatement of alcohol seeking in male and female rats in a shock intensity-dependent manner. Together, these findings suggest that reduced PRDM2 expression in the PFC contribute to stress-induced relapse-like behavior and identify the dmPFC-NAc projection as a circuit through which PRDM2 influences alcohol seeking.

neuroscience↗

bioRxiv2026

Network reorganization distinguishes vulnerability and resilience to observational fear

Individuals vary widely in their responses to stress and threat, with some developing persistent fear after adverse experiences while others remain resilient. Such variability also extends to social contexts, where individuals can acquire information about danger by observing others in distress through observational fear learning. The neural mechanisms underlying individual differences in responses to socially conveyed threat remain poorly understood. Here, we examined how variability in OFL relates to large-scale brain network organization. Rats observed conspecifics receiving tone-shock pairings and were later tested for fear responses to the conditioned stimulus. Behavioral analysis revealed two phenotypes: observational-susceptible rats displaying robust freezing and observational-resilient rats showing freezing levels comparable to controls. Despite these differences, both groups exhibited elevated corticosterone responses, indicating that socially conveyed threat was detected across animals. Brain-wide c-Fos mapping across 84 regions combined with graph-theoretical analysis revealed distinct network architectures associated with each phenotype. These findings suggest that susceptibility and resilience to socially acquired fear emerge from differences in distributed brain network organization.

neuroscience↗

bioRxiv2026

Identifying genetic regulations on immune cell type proportions and their impacts on autoimmune diseases

Genetic regulation of immune cell composition plays a crucial role in the etiology of complex diseases, yet remains poorly understood. We propose a unified analytical framework that integrates genome-wide association studies (GWAS) of cell type proportions with cell-type-wide association studies (cWAS) to systematically characterize both the genetic regulation of immune cell composition and its downstream effects on disease risk. Using single-cell RNA sequencing data from the OneK1K cohort, we conducted a GWAS of immune cell-type proportions with a depth-weighted quasi-binomial model designed for bounded, overdispersed traits. We identified 47 genome-wide significant loci influencing eight fine-labeled immune cell subtypes. Leveraging these identified genetic effects, we further imputed genetically regulated proportions (GRPs) using polygenic risk score (PRS)-based imputation and assessed their associations with complex diseases through cWAS. We identified five significant cell type-disease associations, including two with type 1 diabetes, two with Crohns disease, and one with ulcerative colitis. Together, our results demonstrate that cell type proportions observed in scRNA-seq can reveal regulatory loci and offer insights into how genetic variations regulate immune cell type proportions to affect disease risk. Although we focused on immune single-cell data, our framework is applicable to other tissues or cellular compositions as scRNA-seq datasets expand. Author SummaryGenome-wide association studies (GWASs) have uncovered many disease-associated signals, yet most lie in noncoding regions and are difficult to interpret. Mapping GWAS signals to the relevant cell types is therefore important for better understanding the biological mechanisms that drive disease. A major challenge is that observed gene expression and measured cell-type proportions can be influenced by environmental factors and disease status. In contrast, genotypes are less affected by these factors, making them more reliable for interpreting factors of diseases. Moreover, the cell-type proportions are bounded and often skewed, so standard GWAS models that rely on Gaussian assumptions may lose power. To address this, we developed a quasi-binomial approach that better matches the data and improves discovery while controlling false positives. In real data, our method identified more genetic loci associated with cell-type proportions than a traditional linear model. To further investigate how genetic variation regulates immune cell composition to influence disease risk, we integrated our results with disease GWAS summary statistics to identify immune cell types that may contribute to disease susceptibility. Together, our results link disease-associated GWAS signals to specific immune cell types and provide insights into the cellular mechanisms that may underlie these diseases.

genetics↗

bioRxiv2026

HuR inhibition attenuates hypertension and fibrosis in chronic kidney disease

BackgroundElevated RNA-binding protein HuR has been reported in patients with chronic kidney disease (CKD), but its specific pathogenic role remains unclear. Here, we investigated HuR involvement in progressive CKD induced by deoxycorticosterone acetate (DOCA) plus angiotensin II (Ang II) in mice and evaluated the therapeutic efficacy and mechanisms of the HuR inhibitor KH3. MethodsAdult male mice underwent uninephrectomy and were subjected to DOCA + Ang II infusion with 1% NaCl in drinking water. Mice were then treated with KH3 or vehicle for 3 weeks. Control mice received saline injections without DOCA and Ang II infusion. ResultsDOCA + Ang II infusion markedly increased HuR expression in circulating exosomes and kidney tissues, which was attenuated by KH3. KH3 halted the progression of albuminuria and improved renal function, and reduced kidney hypertrophy and glomerular and tubulointerstitial fibrosis compared with untreated DOCA + Ang II mice. These improvements were associated with reduced podocyte and tubular injury. KH3 also decreased renal macrophage infiltration and suppressed NF-{kappa}Bp65, Nox2, AKT phosphorylation, TGF-{beta}1, and Wisp1, consistent with reduced inflammation, oxidative stress, and fibrosis. In addition, KH3 partially lowered arterial blood pressure in DOCA + Ang II-infused mice, an effect that may involve suppression of SGLT2-associated profibrotic vascular responses, as supported by studies in cultured VSMCs and mesenteric resistance arteries. ConclusionsHuR is upregulated in DOCA + Ang II-induced renal and vascular injury and contributes to hypertensive, inflammatory, oxidative, and fibrotic responses in CKD. Pharmacologic inhibition of HuR-RNA interactions represents a promising therapeutic strategy for CKD. NOVELTY AND RELEVANCEO_ST_ABSWhat Is New?C_ST_ABSThis study identifies the RNA-binding protein HuR (ELAVL1) as a previously unrecognized upstream post-transcriptional regulator of blood pressure in hypertensive chronic kidney disease. We demonstrate for the first time that pharmacologic disruption of HuR-RNA interactions lowers arterial blood pressure in vivo. In addition, we uncover a novel HuR-SGLT2-vascular smooth muscle cell (VSMC) signaling axis, revealing that HuR regulates inducible vascular SGLT2 expression and Ang II-mediated vasoconstrictive responses. What Is Relevant?Hypertension in CKD arises from integrated renal and vascular dysfunction that is incompletely controlled by current therapies. Our findings are highly relevant because we identify HuR as a nodal post-transcriptional regulator that coordinates renal injury, vascular inflammation, and smooth muscle contractility, rather than acting within a single cell type or signaling pathway. Clinical and Pathophysiological ImplicationThese data support a model in which HuR-driven RNA regulatory programs amplify Ang II-dependent vascular hypercontractility and hypertension in CKD. Therapeutic targeting of HuR-RNA interactions represents a novel antihypertensive strategy that may complement renin-angiotensin-aldosterone system (RAAS) blockade and provides mechanistic insight into the blood pressure-lowering and vascular protective effects of SGLT2 inhibitors, including in non-diabetic CKD.

pathology↗

bioRxiv2026

Super-resolution single-cell spatial atlas of plant de novo regeneration

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com.

cell biology↗

bioRxiv2026

A Lightweight Dual-Attention Neural Network for In-Situ Hyperspectral Classification of Microalgae

Accurate monitoring of microalgae is essential for assessing marine ecological health and preventing harmful algal blooms in ocean engineering. Current in situ identification methods often suffer from limited discriminative feature extraction and inadequate adaptation to complex underwater imaging conditions. This study introduces a lightweight dual-attention neural network, termed ANMM, designed for real-time, in situ hyperspectral classification of microalgae within integrated underwater monitoring systems. The model strengthens a deepened AlexNet backbone with multi-head latent attention (MLA) and multi-head self-attention (MSA) mechanisms, which jointly enhance local feature refinement and global spectral dependency modeling. An early-stopping strategy is further incorporated to prevent overfitting and ensure robust generalization. Evaluated on a custom dataset of field-collected fluorescence spectra, the model achieves a classification accuracy of 98.91%, outperforming several state-of-the-art deep-learning counterparts. With a compact parameter size of 16.34 M and low-latency inference on edge hardware, the system demonstrates strong potential for deployment on embedded underwater sensing platforms. This work provides a practical and efficient AI-driven solution for continuous marine microalgae monitoring, supporting advances in ocean observation technology and ecological engineering.

microbiology↗

bioRxiv2026

Development of KASP Molecular Markers and Construction of Fingerprinting for Cowpea (Vigna unguiculata (L.) Walp) unguiculata Based on ddRAD-Seq

Cowpea (Vigna unguiculata (L.) Walp.) is a globally important legume crop. However, the scarcity of efficient molecular markers has hindered molecular breeding efforts and the protection of plant breeders rights. In this study, we employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to characterize the genetic diversity of 19 core cowpea germplasm accessions. We generated 791,621 SNPs, from which 13,469 high-quality SNPs were filtered. Population structure and phylogenetic analyses revealed that these accessions cluster into three distinct groups. To facilitate cost-effective and rapid genotyping, we developed a panel of KASP (Kompetitive Allele Specific PCR) markers. Through rigorous screening for polymorphism and stability, we identified six core KASP markers located in exonic regions. These six markers alone were sufficient to discriminate all 19 accessions. Based on these core markers, we constructed a unique DNA fingerprinting profile and assigned specific QR codes for each accession. This study demonstrates that extracting core KASP markers from ddRAD-seq data is a powerful strategy for germplasm identification. The developed fingerprinting system provides a robust, low-cost tool for seed purity testing, variety authentication, and marker-assisted selection in cowpea breeding programs.

plant biology↗

bioRxiv2026

Deep learning enables quantitative subcellular analysis of plant-microbe interfaces

Specialized host-microbe interfaces are central to cellular interactions in plants. Intracellular structures such as haustoria formed by filamentous pathogens mediate nutrient exchange and effector delivery to host cells. Despite their biological importance, the lack of quantitative frameworks has largely confined the study of these interfaces to qualitative observations, limiting our ability to compare infection strategies, cellular responses, and spatial organization across cells and tissues. Here, we present HFinder, a deep learning-based framework for automated detection, segmentation, and quantitative analysis of plant-microbe interfaces in confocal images. Using an object-centric deep learning approach, HFinder enables robust identification of haustoria, microbial hyphae, and host organelles across diverse imaging conditions and pathosystems. We demonstrate that this framework supports quantitative analyses of subcellular processes at host-microbe interfaces, including effector secretion, perturbation of host cellular processes, and immune receptor accumulation at haustoria. HFinder provides a practical and scalable solution for the systematic digitalization of plant infection imaging data and establishes a general framework for quantitative studies of cellular dynamics at host-microbe contact zones.

cell biology↗