Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 523 records · Page 29Linked to original sources

bioRxiv2025

Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution

Long-read scRNA-seq enables simultaneous, unbiased identification of transcriptomic variants and gene expression but is often limited by low read coverage, restricting genotype-phenotype analyses at single-cell resolution. We systematically evaluated short-read whole-transcriptome amplification (SR-WTA) via Illumina, long-read whole-transcriptome amplification (LR-WTA), and long-read targeted sequencing (LR-Twist) via PacBio for cell typing and genotyping performance. Based on these comparisons, we propose a hybrid strategy and accompanying Snakemake pipeline that integrates SR-WTA with LR-Twist to leverage the strengths of both approaches. SR-WTA provides broad transcriptome coverage, while LR-Twist enriches a 50-gene panel for deeper variant detection. This hybrid approach improves power to link mutational profiles with transcriptional programs at single-cell resolution.

bioinformatics↗

bioRxiv2025

Xanthomonas type III effector XopN targets scaffold protein OsRACK1B to suppress rice immunity

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a major bacterial disease that poses a substantial threat to rice production. Although Xoc deploys a variety of effectors to subvert host defenses, the mechanistic basis of how these effectors modulate plant immune signaling remains largely unclear. Here, we show that XopN suppresses rice immune responses and physically interacts with the rice scaffold protein OsRACK1B. Notably, OsRACK1B expression is induced following Xoc infection in a type III secretion system (T3SS)-independent manner. Functional analyses indicate that OsRACK1B overexpression enhances Xoc resistance, whereas loss-of-function mutants exhibit heightened susceptibility. This increased susceptibility is characterized by compromised immunity, including reduced callose deposition, diminished reactive oxygen species (ROS) accumulation, and attenuated expression of defense-related genes such as OsPBZ1 and OsPAL1. Furthermore, we demonstrate that XopN competes with OsRap2.6 for binding to OsRACK1B, thereby disrupting the formation of the OsRACK1B-OsRap2.6 immune complex. These findings reveal a novel virulence strategy in Xoc and identify promising gene targets for developing disease-resistant rice varieties.

plant biology↗

bioRxiv2025

Lamin B1 Safeguards the B Cell Genome and Shapes Lymphoma Outcome

Lamin B1 is a structural component of the nuclear lamina that participates in diverse cellular processes, including genome regulation and cellular senescence. During adaptive immune responses, B lymphocytes in germinal centres (GCs) undergo clonal expansion and programmed DNA damage at immunoglobulin loci, while simultaneously downregulating Lamin B1. Likewise, Lamin B1 downregulation has been observed in GC-derived lymphomas and myeloid malignancies, yet the functional consequences of Lamin B1 loss during B cell development remain poorly understood. Here, we used in vivo and in vitro B cell models of conditional hypomorphic expression of Lamin B1, which showed elevated DNA damage, altered chromatin accessibility, and disrupted transcriptional profiles. Using sBLISS (in situ labelling and sequencing of double-strand breaks), we identified non-random double-strand break hotspots in both mouse and human GC B cells, depleted of Lamin B1. These breaks are preferentially located near transcriptional start sites (TSSs) and regulatory elements that control translation and mRNA fate, implicating Lamin B1 in protecting fragile regulatory regions. Moreover, low LMNB1 expression correlated with poor clinical outcomes in patients with diffuse large B cell lymphoma (DLBCL). Together, this study reveals a crucial role for Lamin B1 in preserving genomic stability in B cells, underscoring its impact on the pathogenesis of B cell-derived malignancies.

cancer biology↗

bioRxiv2025

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

Understanding how distinct neuronal subtypes contribute to Alzheimers disease (AD) pathology remains a major challenge. Patient-derived induced pluripotent stem cell (iPSC) studies have shown neuronal subtype-specific molecular and pathological signatures, yet the underlying metabolic shifts driving this selective vulnerability are not completely understood. Here we present iNeuron-GEM, the first manually curated, genome-scale metabolic network of human neurons that integrates transcriptomic and metabolic knowledge to resolve subtype-specific metabolic states. By coupling iNeuron-GEM with single nucleus RNA sequencing data from post-mortem human cohort studies, ROSMAP and SEA-AD, we capture neuronal subtype-specific metabolic features and fluxes and identify perturbations in lipid and energy metabolism across excitatory and inhibitory neurons. Integrative analysis with NPS-AD data shows overlapping metabolic disruptions in AD and schizophrenia (SCZ), suggesting shared molecular vulnerabilities between neurodegenerative and neuropsychiatric disorders. We also developed a computational pipeline to infer transcriptional regulation of metabolic pathways and identify NR6A1 and NR3C1 as important regulators of lipid dysregulation in AD neurons. Our study establishes iNeuron-GEM as a framework to identify neuronal subtype-specific metabolic vulnerabilities in complex brain disorders.

systems biology↗

bioRxiv2025

NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pH during nitrate uptake in Medicago truncatula

Nitrate is the primary source of nitrogen for plants in most environments. Nitrate uptake from the rhizosphere into root cells is mediated by Nitrate Transporter 2 (NRT2) and NRT1.1 proteins via proton symport, with the apoplast serving as an intermediate compartment. Using a simple root immersion system, we investigated the effects of NRT transporters on external media pH (pHmed) and apoplastic pH (pHapo) in M. truncatula nitrate transporter mutants. Monitoring of pHmed showed that loss of NRT2.1 largely prevented nitrate induced alkalization of the media, while loss of NRT1.1A/B reduced media alkalization only during the initial stages of nitrate uptake, suggesting they have fundamentally different physiological roles. Use of the pH sensitive dye HPTS showed that the pHapo of root cells initially decreased during nitrate uptake, and this required NRT1.1A/B. Unexpectedly, the observed changes in pHmed during nitrate uptake in WT and the mutants were not reflected in pHapo. To explain these discrepancies, we propose a model in which the depletion of protons in the media occurring during nitrate symport is offset by the buffering of protons in the cell wall and the activity of the H+-ATPase, allowing a lower pHapo to be maintained. Such a mechanism would enable efficient nitrate uptake across a range of external pH values.

plant biology↗

bioRxiv2025

Zwitterionic hydrogel designs for conducting polymers enable bioelectronics with suppressed foreign body response

For long-term, continuous operation of implantable biosensors and electrophysiological devices, the foreign body response (FBR) is a major obstacle that needs to be overcome. As the FBR progresses, any implanted device will become damaged and isolated from its physiological environment, due to encapsulation by fibrotic tissue and inflammatory immune cells. To achieve more compatible and low-impedance biointerfaces, conducting polymers, such as PEDOT:PSS, have been extensively explored as ideal materials. However, FBR on such conducting polymers remains an unmet challenge. We report a zwitteronic-hydrogel-based double-network design for PEDOT:PSS that can significantly suppress the FBR by 64%, in addition to improving conductivity by more than one order of magnitude. Surprisingly, the FBR level of this design is even lower than that of the parent zwitteronic hydrogel by 53%. Our further immunological investigations at the histological, cellular, and transcriptomic levels give deeper insights into the unique effects that come from the chemical heterogeneity. Furthermore, chronic electrocardiographic recording in mice demonstrate the benefit of this material design to long-term, implanted electrophysiology, which provides indications for the future development of immunocompatible electronic polymers.

bioengineering↗

bioRxiv2025

Computational Discovery of Core Protein - Targeted Therapeutics Against Ginger Wilt Pathogen Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum poses a severe threat to ginger production worldwide, as no consistently effective control measures exist. Here, we present a comprehensive strategy integrating pangenome analysis, functional enrichment, molecular docking, and state-of-the-art protein structure prediction to identify antibacterial agents targeting this phytopathogen. By prioritizing core, evolutionarily conserved proteins in R. solanacearum, we utilized AutoDock Vina and the recently developed AlphaFold3 to assess the binding affinity and validate protein-ligand interactions of key candidates from commercially available antibacterial pesticides. In vitro antibacterial assays confirmed strong inhibitory effects for several compounds, notably streptomycin sulfate, phellodendrine chloride, chlorogenic acid, and allicin. Our results highlight the power of combining large-scale computational screening with experimental validation for accelerating the discovery of novel antibacterial agents against highly divergent, recalcitrant plant pathogens. ImportanceThe indiscriminate use of broad-spectrum agrochemicals causes pollution and antimicrobial resistance. Our study proposes a targeted strategy against Ralstonia solanacearum by focusing on essential core proteins. This approach aims to develop specific agents that minimize harm to soil microbiota and reduce resistance selection. Our in silico framework aligns with green chemistry, offering a sustainable path for crop protection with a lower environmental footprint.

bioinformatics↗

bioRxiv2025

Structural mechanisms of pump assembly and drug transport in the AcrAB-TolC efflux system

Tripartite multidrug efflux pumps that span the cell envelope are essential for antibiotic resistance in Gram-negative bacteria. Here, we report cryo-EM structures of two endogenous efflux complexes from Escherichia coli: a TolC-YbjP subcomplex at 3.56 [A] resolution and the complete TolC-YbjP-AcrABZ pump at 3.39 [A]. Structural analysis reveals that YbjP, a previously uncharacterized lipoprotein, binds TolC in a 3:3 stoichiometry, bridging the TolC protomers at their equatorial domain. Clear density of the mature YbjPs N-terminal Cys19 indicates that YbjP is anchored to the outer membrane by an N-terminal lipid moiety. Notably, YbjP remains bound as TolC undergoes AcrA-induced opening, suggesting that this accessory protein accommodates the conformational change. The AcrB trimer simultaneously presents three distinct conformational states (L, T, O), capturing a complete transport cycle. These high-resolution structures provide insights into the architecture and mechanism of clinically relevant efflux machinery, identifying YbjP as a previously unrecognized structural component that contributes to TolC positioning and may assist in its membrane localization.

biophysics↗

bioRxiv2025

Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification

Seasonal influenza viruses undergo continuous antigenic drift due to mutations in the hemagglutinin (HA) protein, rendering vaccines ineffective and posing a significant global public health challenge. Existing computational models can predict antigenic relationships but generally lack interpretability, making it difficult to reveal the molecular determinants driving antigenic changes. To address this, we developed PREDAC-Transformer, an end-to-end deep learning framework that integrates sequence, physicochemical, and evolutionary features, and employs a self-attention mechanism to capture long-range dependencies relevant to antigenicity. More importantly, we introduce the integrated antigenicity score, which combines attention-based attribution with information-theoretic metrics to provide continuous quantification and ranking of the antigenic contributions of individual amino acid site. Our results demonstrate that PREDAC-Transformer not only significantly improves the accuracy of antigenic relationship prediction but also successfully recapitulates major historical antigenic cluster transitions. Using integrated antigenicity score, we systematically identified two classes of key sites: global key sites with sustained impact on antigenic evolution, and cluster-transition determining sites that drive cluster transitions. These sites include most canonical epitopes and reveal additional functional residues previously overlooked, which may influence immune escape via cooperative effects or glycosylation. Collectively, these findings advance our understanding of influenza antigenic evolution and provide novel insights for refining computational models. PREDAC-Transformer achieves high-precision prediction while attributing antigenic differences to individual residues, thereby linking viral genomic variation, antigenic change, and public health decision-making. This framework has the potential to reduce experimental burdens in influenza surveillance and assist in vaccine strain recommendation, thereby supporting global influenza control efforts.

bioinformatics↗

bioRxiv2025

Recruitment of the outer-membrane lipoprotein DolP to thedivision site via cardiolipin-mediated diffusion-stateswitching

In diderm bacteria, the outer membrane (OM) must invaginate in step with septal peptidoglycan (PG) remodeling during cytokinesis. One OM lipoprotein, DolP, has been shown to localize at the cell division site and to facilitate the daughter cell separation. Yet how DolP is recruited to the division site remains unclear at the molecular level. Here, we show that DolP arrives concomitantly with the late divisome protein FtsN. Utilizing single-particle tracking Photoactivated Localization Microscopy (spt-PALM), we investigated the dynamics of individual DolP molecules in living Escherichia coli cells. Single-molecule analysis revealed two diffusion states: a diffusive state across the cell envelope and a previously underappreciated immobile state enriched at the septal and polar regions. Importantly, DolP does not comigrate with the processive FtsW-FtsI-FtsN complex. Mutations of the cardiolipin-binding surface caused loss of mid-cell enrichment and reduced the immobile fraction. Cardiolipins preference for high negative curvature enriches it at the division site, creating a trapping environment for DolP. Additionally, the active septal constriction but not the late divisome proteins recruit DolP. Together, these findings indicate that cardiolipin-mediated immobilization underlies DolPs septal enrichment.

microbiology↗

bioRxiv2025

DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification

DNA barcoding is a powerful tool for exploring biodiversity, and DNA language models have significantly facilitated its construction and identification. However, since DNA barcodes come from a specific region of mitochondrial DNA and there are structural differences between DNA barcodes and reference genomes used to train existing DNA language models, it is difficult to directly apply the existing DNA language models to the DNA barcoding task. To address this, this paper introduce DNACSE (DNA Contrastive Learning for Sequence Embeddings), an unsupervised noise contrastive learning framework designed to fine-tune the DNA language foundation model while enhancing the distribution of the embedding space. The results demonstrate that DNACSE outperforms direct usage of DNA language models in DNA barcoding-related tasks. Specifically, in fine-tuning and linear probe tasks, it achieves accuracy rates of 99.17% and 98.31%, respectively, surpassing the current state-of-the-art BarcodeBERT by 6.44% and 6.44%. In zero-shot clustering tasks, it raises the Adjusted Mutual Information (AMI) score to 92.25%, an improvement of 8.36%. In addition, zero-shot benchmarking and genomic benchmarking tests are evaluated, indicating that DNACSE enhances the performance of DNA language models in generalized genomic tasks. In summary, DNACSE has demonstrated excellent performance in DNA barcode species classification by making full use of multi-species information and DNA barcode information, providing a feasible way to further explore and protect biodiversity. The code repository is available at https://github.com/Kavicy/DNACSE.

bioinformatics↗

bioRxiv2025

Symmetric brain-liver circuits mediate lateralized regulation of hepatic glucose output

Neural lateralization is well recognized in the control of contralateral somatic movement, yet its relevance to visceral organ regulation remains poorly understood. This study aimed to determine whether the central nervous system exerts lateralized control over hepatic glucose metabolism and to localize the site of peripheral sympathetic crossover to the liver. Pseudorabies virus (PRV) tracing revealed bilateral projections from the lateral paragigantocellular nucleus (LPGi) with preferential innervation of the contralateral hepatic lobes. Unilateral LPGi activation elevated systemic glucose by enhancing glycogenolysis and gluconeogenesis specifically in contralateral lobes, whereas bilateral activation produced additive effects. Following unilateral hepatic denervation, contralateral LPGi activation induced metabolic compensation in the remaining innervated lobes, characterized by increased norepinephrine release, glucose production, and glycogen depletion. Whole-mount tissue clearing and dual viral tracing localized the sympathetic crossover to the porta hepatis. Developmental analysis showed that lobar-specific innervation along the vasculature emerges by postnatal week 2. These findings demonstrate that the brainstem can exert lobe-specific, lateralized control of hepatic glucose metabolism via bilaterally projecting brain - liver sympathetic pathways. This contralateral regulation arises from a peripheral decussation at the porta hepatis, and the compensatory activation observed after denervation reveals an intrinsic neuroadaptive mechanism that helps safeguard systemic glucose homeostasis. HighlightsO_LIBrain-liver sympathetic projections exhibit predominant contralateral innervation C_LIO_LIUnilateral LPGi activation drives glucose production in contralateral hepatic lobes C_LIO_LIUnilateral denervation augments contralateral LPGi-mediated metabolic compensation C_LIO_LISympathetic crossover to the liver localizes at the porta hepatis C_LI

neuroscience↗

bioRxiv2025

TMEM100 attenuates NF-κB activation via disrupting the PRDX1-GNAI2 complex to alleviate acute lung injury

Acute lung injury (ALI) is a severe and diffuse inflammatory disorder of interstitial lung. Emerging evidence suggests that TMEM100 is closely associated with lung development and function. However, its role in ALI remains unclear. In this study, we observed a significant downregulation of TMEM100 expression in both mouse lung tissues with ALI and lipopolysaccharide (LPS)-induced pulmonary vascular endothelial cells (PVECs). Overexpression of TMEM100 markedly attenuates LPS-induced lung injury and inflammation, while also restoring the imbalance between proliferation and apoptosis in PVECs. Mechanistically, TMEM100 interacts with both PRDX1 and GNAI2, disrupting the PRDX1-GNAI2 complex and thereby inhibiting LPS-induced NF-{kappa}B activation, which contributes to its anti-inflammatory effects. These findings highlight the protective role of TMEM100 in endotoxin-induced ALI and provide a theoretical basis for understanding its biological functions and potential applications in ALI gene therapy.

immunology↗

bioRxiv2025

Integrated multi-omic and functional evidence uncover substantial strain-specific divergence in zebrafish

The zebrafish (Danio rerio) is a foundational vertebrate model in biomedical and developmental research, yet genetic divergence among laboratory strains remains an underappreciated source of biological and experimental variation. Among these, the AB and Tubingen (TU) strains are used globally, forming the basis for most zebrafish-based discoveries. Here, we integrated long- and short-read sequencing, ATAC-seq, Hi-C, transcriptomics, and functional assays to generate a comprehensive multi-omic comparison of these two strains. Our analyses revealed substantial genomic and regulatory divergence, including a 62-bp insertion in the asmt promoter that elevates transcription and alters melatonin biosynthesis, driving strain-specific circadian phenotypes. We also identify a non-synonymous variant (mybbp1aG2612C) associated with heightened immune responsiveness. Together, these findings construct the first genome-wide atlas of functional variation between zebrafish strains, illuminating how hidden genetic differences can shape phenotype, regulatory architecture, and experimental reproducibility in this essential vertebrate model.

genomics↗

bioRxiv2025

Spatial genome reorganization is associated with chromosomal breakage regions and karyotype changes induced by programmed DNA elimination

Programmed DNA elimination (PDE) is a notable exception to genome integrity, characterized by significant DNA loss during development. In many nematodes, PDE is initiated by DNA double-strand breaks (DSBs), which lead to chromosome fragmentation and subsequent DNA loss. However, the mechanism of nematode programmed DNA breakage remains largely unclear. Interestingly, in the human and pig parasitic nematode Ascaris, no conserved motif or sequence structures are present at chromosomal breakage regions (CBRs), suggesting the recognition of CBRs may be sequence-independent. Using Hi-C, we revealed that Ascaris CBRs engage in three-dimensional (3D) interactions before PDE, indicating that physical contacts between break regions may contribute to the PDE process. The 3D interactions are established in both Ascaris male and female germlines, demonstrating inherent genome organization associated with the CBRs and to-be-eliminated sequences. In contrast, in the unichromosomal horse parasite Parascaris univalens, transient pairwise interactions between neighboring CBRs that will form the ends of future somatic chromosomes were observed only during PDE. Intriguingly, we found that Ascaris PDE, which converts 24 germline chromosomes into 36 somatic ones, induces specific compartmentalization changes. Remarkably, Parascaris PDE generates the same set of 36 somatic chromosomes, and the 3D compartment changes following PDE are consistent between the two species. Overall, our findings suggest that CBRs spatially demarcate the retained and eliminated DNA and may contribute to their spatial organization during Ascaris PDE. We also demonstrated that the 3D genome reorganization of the somatic chromosomes in these nematodes following PDE is evolutionary and developmentally conserved.

genomics↗

bioRxiv2025

Argonautes and small RNAs associated with nematode programmed DNA elimination

Programmed DNA elimination (PDE) selectively removes DNA in pre-somatic cells to form the somatic genome during development. Our mechanistic understanding of PDE is mainly based on studies in the single-cell ciliates, where small RNAs and transposases are involved. In contrast, the mechanism(s) of metazoan PDE remains largely unknown. In the parasitic nematode Ascaris, PDE removes and remodels all germline chromosome ends and partitions fused germline chromosomes into somatic chromosomes, resulting in dramatic karyotype changes. Here, we identified two Ascaris Argonautes, AsWAGO-2 and AsWAGO-3, associated with retained or eliminated chromosome regions, respectively, during PDE mitoses. AsWAGO-3 siRNAs target primarily genes. However, a subset of AsWAGO-3 siRNAs targets repeats within the eliminated regions and located in the middle of chromosomes. These chromosome regions are derived from the fusion of the ends of ancestral chromosomes. In contrast, AsWAGO-2 and its associated siRNAs are transiently enriched on retained chromosomes during elimination mitoses. Overall, our data reveal a link between Ascaris WAGOs, their siRNAs, and PDE, identifying small RNA pathways that selectively distinguish retained and eliminated DNA. We suggest that AsWAGO-3 associated small RNAs targeting the interior of select chromosomes may be a response to the fusions of germline chromosomes.

molecular biology↗

bioRxiv2025

YAP1 defines an emergent, plastic population of relapsed small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by rapid onset of chemoresistance and poor clinical outcomes. Transcriptional heterogeneity among treatment-naive SCLC tumors underlies four transcriptional subtypes, each with distinct clinical vulnerabilities. Though previously hypothesized to delineate a distinct subtype, expression of YAP1 is largely absent from treatment-naive, pure SCLC. To characterize relapsed SCLC, circulating tumor DNA, circulating tumor cells, and core needle biopsies from SCLC patients and preclinical models following resistance to standard-of-care therapies were analyzed. In contrast to treatment-naive SCLC, these analyses reveal an emergent YAP1-positive cell population that coincides with treatment resistance. These YAP1-positive cells exhibit characteristics of drug tolerant persister cells, including senescence, stemness, and plasticity, as YAP1 positive cells largely abandon features characteristic of SCLC to adopt those of large-cell neuroendocrine carcinoma (LCNEC). As a result of this SCLC-like to LCNEC-like evolution, YAP1-positive cells lack several clinically relevant SCLC surface targets (i.e., DLL3, SEZ6), but are enriched for others (i.e., B7-H3, TROP2). We propose a model where YAP1 expressing cells emerge with SCLC treatment resistance and characterize a tenacious subpopulation capable of diverging from the treatment naive lineage and adopting features to evade therapeutic response.

cancer biology↗

bioRxiv2025

Wearable Focused Ultrasound Neuromodulation and Electrophysiological Recording Patch for REM Sleep Enhancement

The rise in sleep disease affecting the general population globally in the past decade has been detrimental to individually and socioeconomically. As of now, approaches often are temporary through medication, permanently using invasive implants with surgical complications or neuromodulation therapy. However, non-invasive, state-dependent neuromodulation during sleep is technically challenging, especially with the lack of flexibility, comfortability and robustness for sleep conditions. Here, we introduce a Non-invasive Electrophysiological Recording and Ultrasound Neuromodulation Sleep Patch (NEUSLeeP) in delivering focused ultrasound stimulation to the subthalamic nucleus (STN) overnight with simultaneous stable polysomnography recording. Our sleep patch integrates a custom eight-channel concentric ring transducer array with real-time electroencephalography (EEG), electrooculography (EOG), electromyography (EMG) recording, and individualized line-of-sight targeting to sonicate deep brain areas while preserving mobility. Our platform operated safely and comfortably across the two-nights sleep study. Stimulation of the left STN was delivered every 90 minutes throughout the night and was associated with a 25% increase in REM (Rapid Eye Movement) sleep duration and a 43 minutes reduction in REM sleep latency compared to a sham night in a study of 26 subjects. Blood Oxygen Level Dependent (BOLD) signal attenuation in functional Magnetic Resonance Imaging (fMRI) was localized primarily to a left ipsilateral basal-ganglia-midbrain-temporal circuit, consistent with selective network modulation rather than global arousal changes. Overall, NEUSLeeP demonstrates feasibility by (i) a light weight and wearable ultrasound neuromodulation and sleep recording during natural sleep; (ii) establishing a potential mechanism relating targeted ultrasound stimulation of STN/sleep networks to REM enhancement.

bioengineering↗