Biology subjects

Zhang, J.

Publications and source records attributed to Zhang, J..

At least 253 records · Page 14Linked to original sources

bioRxiv2026

Exercise-induced Sweat Promotes Wound Healing in Diabetic Foot Ulcers

Persistent hyperglycemia impairs wound healing in diabetic patients, and severe cases may even lead to disability or death. Glycemic control alone cannot effectively prevent the occurrence of diabetic foot ulcers, a serious complication of diabetes. However, safe, efficient, and cost-effective therapies remain unavailable and are urgently needed. Using a novel sports medicine paradigm, we predicted, based on reverse-transcriptomics, that exercise-induced sweat has the potential to promote would healing in diabetic foot ulcers. Subsequent animal experiments demonstrated that sweat can indeed promote re-epithelialization and collagen deposition, upregulate the expression of the proliferation marker Ki-67, the angiogenesis marker CD31, and -SMA, and significantly accelerate wound healing in a mouse model of diabetic foot ulcers. This study provides a new direction for sports medicine and offers a novel therapeutic strategy for patients with diabetic foot ulcers.

zoology↗

bioRxiv2026

Interrogating the Escherichia coli epitranscriptome via CRISPR interference and Nanopore native RNA sequencing

Epitranscriptomics has recently gained significant momentum due to technological advances and translational applications, however, studies on bacterial RNA modifications remain limited. Bacterial RNA remains notoriously prone to degradation and methodologies to investigate the epitranscriptome are challenging. Prior research has shown RNA modifications modulate antimicrobial resistance, virulence and pathogenicity. This research employed CRISPR interference to knock down five known Escherichia coli rRNA modification genes (rlmF, rlmJ, rluD, rsmF and rsmG) in three E. coli strains. These isolates underwent growth curves, proteome analysis and native RNA sequencing CRISPRi adequately silenced the majority of RNA modification genes in E. coli (>80% reduction). Significant growth delays were associated with rlmF, rsmF and rsmG repression. Unique protein pathways corresponding with RNA modification loss were found for rlmJ (TreB, XylF), rluD (CysH, HycB, PutP, TrpB), rsmF (EvgA) and rsmG (OppC). Known rRNA modification sites for rluD ({Psi}) and rsmG (m7G) were detected from analysis of nanopore electrical signal, however, only a weak signal was apparent for m6A (rlmF, rlmJ) and m5C (rsmF) modifications. The inhibition of rRNA modifications resulted in mRNA modification changes including for genes ompC, cspC, dbhA, dbhB and secY. Our work provides an approach for unravelling the epitranscriptome of E. coli and gain insight into its functional role.

microbiology↗

bioRxiv2026

Learning latent conformational landscapes encoded in cryo-EM

A protein populates a landscape of structural states, abundant snapshots of which are sampled in every cryo-EM experiment. Current analysis averages these snapshots into single density maps or partitions them into discrete classes, discarding the continuous dynamics encoded in the data. Continuous latent-space methods offer a promising alternative, yet whether their learned representations are physically grounded remains unresolved. Here, we realize cryo-EM as structural landscape microscopy, in which latent density directly reflects the probabilistic distribution of molecular states. A central question is whether such a landscape reflects physical reality. For integrin v{beta}8, the learned landscape shows strong agreement with independently derived molecular dynamics simulations, supporting its physical plausibility. We then apply the landscape to structural states that conventional cryo-EM cannot resolve. For LIS1-mediated dynein activation, the landscape reveals a spectrum of states from dominant conformations to low-population intermediates defined by distinct binding modes, including a previously unresolved state. For the KCTD5/CUL3NTD/G{beta}{gamma} complex, the landscape resolves continuous conformational pathways directly from experimental data. Probability-guided particle selection further improves reconstruction quality.

molecular biology↗

bioRxiv2026

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1

RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA (lncRNA) and regulates RNA processing, stability, and translation. RNA modifications are not well characterized in multiple myeloma (MM), a plasma cell malignancy characterized by relapse and disease progression, and the contribution of m6A-modified lncRNAs to the disease remains unclear. Here, we define the RNA modification landscape of MM by combining mass spectrometry, Nanopore Direct RNA sequencing, and methylated RNA immunoprecipitation sequencing. We identify 20 RNA modification types and > 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival.

cancer biology↗

bioRxiv2026

Understanding the impact of sodium sulfide on the invasive growth of wine yeast

Yeasts ability to invade surfaces has important implications for infections and food contamination. Invasive growth in yeast is influenced by genetic and environmental factors. In this exploratory study, we used a systematic experimental design to identify conditions under which sulfide-induced invasive growth can be reliably observed and quantified and investigated the effects of sulfide, gene deletions, and environmental conditions on the invasive behaviour of the wine yeast strain AWRI 796. Sulfide enhanced invasion in the (parent) AWRI 796 strain under nitrogen-limiting conditions, although its effect was obscured by experimental variability and pre-culture conditions. Genetic factors had a major effect on the overall invasive phenotype, with deletion of key genes suppressing invasion. Most gene-deletion mutants did not significantly affect how the colony responded to sulfide. In addition to sulfide and genotype, environmental conditions also influenced invasive behaviour. The pre-2xSLAD pre-culture condition was best for detecting sulfide-induced growth, and later plate washing time and decreased nutrient levels enhanced invasiveness. Our experimental design and findings provide a framework for understanding the determinants of yeast invasiveness, which may inform future studies on filamentous yeast behaviour.

microbiology↗

bioRxiv2026

Domain classification of archaeal proteomes reveals conserved fold repertoire

Archaea represent one of the three domains of cellular life and yet account for fewer than 1% of experimentally determined protein structures, leaving the extent of their structural novelty unknown. Here we present a systematic domain-level classification of 124,075 proteins from 65 archaeal classes spanning 21 phyla and all major lineages, using both AFDB and newly predicted AlphaFold3 structures classified against the Evolutionary Classification of protein Domains (ECOD). We assigned 204,758 domains, of which 76.8% received high-confidence classifications, spanning 987 ECOD X-groups; 40% of known structural diversity within a single domain of life. Clustering by Foldseek recovered structural relationships for 63% of domains that are singletons by sequence comparison. To characterize the 21% of proteins lacking high-confidence classification, we applied successive filters for structure prediction confidence, protein length, and structural cluster context, reducing 8,452 domain-free proteins to a small number of well-folded structural orphans (less than 0.1% of the dataset). The unclassified fraction is dominated by sub-threshold matches to known folds (14% of all proteins) and low-confidence structure predictions (5%), not by novel structures. These results demonstrate that the protein fold repertoire at the single-domain level is broadly conserved across the deepest phylogenetic distances in cellular life, and that the gap between archaeal and well-characterized proteomes reflects classification sensitivity for divergent sequences rather than unexplored structural diversity.

bioinformatics↗

bioRxiv2026

OpenAc4C: A gateway to decode the landscape, regulation and pathogenesis of N4-acetylcytidine (ac4C) epitranscriptome

N4-acetylcytidine (ac4C) is an ancient and highly conserved chemical marker found in all domains of life. Recent advancements in sequencing techniques have enabled the functional analysis of ac4C occurrence by accurately capturing its locations and levels, shedding light on its significant regulatory potential and emerging role in diseases. The OpenAc4C, the first comprehensive knowledgebase exclusively designed for unraveling the ac4C epitranscriptome across diverse species, spanning vertebrates, mammals, insects, fungi, plants, bacteria, archaea, and viruses. By mining a large array of ac4C epitranscriptome datasets with deep learning-based pipelines, OpenAc4C features a collection of 536,745 ac4C sites identified from four distinct next-generation sequencing (NGS)-based techniques, alongside novel insights from Oxford Nanopore direct RNA sequencing (ONT)-based samples, encompassing a total of 33 species. Beyond the ac4C landscape, a total of 536,986 ac4C-affecting variants were identified in seven species. Among them, 4,766 pathogenic ac4C-SNPs may drive ac4C dysregulation with implications for disease pathogenesis. In addition, OpenAc4C offers a user-friendly graphical interface and a web-based analysis platform for comprehensive querying and interactive exploration of the database collections. Together, OpenAc4C will serve as a valuable integrated resource to facilitate studies of ac4C modification. It is freely accessible at: www.rnamd.org/ac4cportal.

bioinformatics↗

bioRxiv2026

Celastrol alleviates SGLT2 inhibitor-induced diabetic hyperketonemia by inhibiting hepatic ketogenesis

SGLT2 inhibitor (SGLT2i)-induced diabetic hyperketonemia is a life-threatening acute complication of diabetes. While Celastrol has been reported to exert beneficial effects on obesity; its potential role in ketogenesis remains unclear. In this study, Celastrol administration significantly attenuates the fasting-induced elevation of blood {beta}-hydroxybutyrate. Moreover, a 7-day course of Celastrol (1 mg/kg/day) leads to reductions in body weight and fat mass. Mechanistically, Celastrol specifically downregulates HMGCS2 expression and suppressess hepatic ketogenesis through inhibiting PPAR expression in the short term ([≤] 2 days). However, after prolonged treatment for 7 days, Celastrol modulates both PPARand serum free fatty acids (FFAs) levels. Furthermore, anti-ketogenic effect of Celastrol is abolished in Ppar{square} /{square} mice. Importantly, Celastrol effectively ameliorates SGLT2i-induced hyperketonemia. In summary, Celastrol curbs hepatic ketone overproduction in a PPAR-dependent manner, indicating its protective potential against SGLT2i-induced hyperketonemia.

molecular biology↗

bioRxiv2026

FAM134B isoform 2/RETREG1-2 defines a calnexin-TOLLIP-coupled ER-phagy pathway that restricts Ebola virus glycoprotein and is antagonized by VP40 through macro-autophagy

Selective autophagy of the endoplasmic reticulum (ER-phagy) is critical for ER proteostasis and host defense, yet how ER quality-control pathways interface with ER-phagy to restrict viral glycoproteins remains poorly defined. Previously, the 1st known ER-phagy receptor gene RETREG1 (RETR1)/FAM134B gene was reported to restrict Ebola virus (EBOV) replication in vivo by inhibiting the viral glycoprotein (GP) and viral protein 40 kDa (VP40) expression, but this mechanism remains unknown. Here, we identify the truncated RETR1/FAM134B isoform 2 (RETR1-2), but not its full-length protein RETR1, as an ER-phagy receptor that targets EBOV-GP for degradation. RETR1-2 broadly triggers GP degradation across ebolavirus species but not Marburg virus and inhibits EBOV replication. Mechanistically, RETR1-2 recognizes EBOV-GP via its luminal domain, undergoes GP-induced oligomerization, and directs GP-containing ER membranes to lysosomes through canonical macro-autophagy. Using unbiased mass spectrometry, we identified TOLLIP as the key cytoplasm adaptor for RETR1-2, which also requires cooperation with the ER chaperone calnexin for EBOV-GP degradation. Notably, the PI3P-binding C2 domain of TOLLIP mediates its interaction with RETR1-2, and the EBOV-GP degradation occurs independently of ubiquitination, revealing an unexpected role for TOLLIP in ER-phagy. Furthermore, EBOV-VP40 antagonizes this pathway by selectively targeting RETR1-2 for macroautophagic degradation independently of TOLLIP, thereby restoring GP expression and viral infectivity. Nevertheless, RETR1-2 reciprocally degrades VP40 via a similar mechanism. Together, these findings define a calnexin-TOLLIP-RETR1-2 axis that links ER quality control to ER-phagy-mediated antiviral restriction and uncover a reciprocal host-virus arms race centered on selective macro-autophagy.

microbiology↗

bioRxiv2026

TXNDC15 modulated quality control at the endoplasmic reticulum shapes ciliogenesis

At the endoplasmic reticulum (ER), membrane protein quality control is tightly regulated to ensure excess subunits are recognized and degraded to protect cellular homeostasis. Using genome wide CRISPR screens, we identified a factor of unknown function, thioredoxin domain containing protein 15 (TXNDC15), and showed that it regulates membrane protein stability by tuning the activity of the E3-ubiquitin ligase, MARCHF6. TXNDC15 modulates MARCHF6 in two opposing ways: first, it enhances the binding, ubiquitination, and degradation of membrane protein subunits with soluble cytosolic domains; and second, it prevents the inappropriate recruitment and ubiquitination of subunits with globular lumenal domains. Patient mutations to TXNDC15 that cause the ciliopathy Meckel-Gruber syndrome, disrupted its binding to MARCHF6, allowing degradation of critical ciliary proteins as they transit through the ER leading to defects in ciliogenesis. The regulatory function of TXNDC15 therefore exemplifies how protein quality control maintains the integrity of the proteome to prevent disease.

molecular biology↗

bioRxiv2026

State-Dependent Organization of Microscale Functional Circuitry in Visual Cortex

How the cortex organizes directed functional interactions among individual neurons and how this microscale circuitry maps onto cell types and the underlying anatomy remains poorly understood. Here, we construct one of the largest single-neuron-resolution directed functional circuit maps in mouse visual cortex from calcium imaging of more than 57,000 active neurons across four visual areas and five cortical layers. We infer directed connections with a time-aware causal-inference method (CITS) that is specifically designed for neural time-series. In the co-registered electron-microscopy connectome, CITS-inferred pairs are 3.6-fold more likely to be synaptically connected than unconnected pairs, which is significantly more than Granger causality (1.1-fold) or lagged correlation (1.6-fold). We found that our inferred functional circuits organization aligns with synaptic connectivity at areal, laminar, and cell-type levels. Among intra-areal connections, anterolateral area (AL) had the highest density, and among inter-areal connections, the AL{leftrightarrow}rostrolateral area (RL) axis formed the strongest pathway. At the cell-type level, layer 6 recurrence dominated the aggregate network in low arousal, whereas layer 6-to-layer 5 output connections dominated in high arousal. Spatial extent expanded with inter-neuron distance in high arousal, for both excitatory-to-excitatory and excitatory-to-inhibitory connections. Finally, in stimulusdriven response prediction, neuron pairs with stronger functional connections exhibited more similar predictive performance in both high-arousal and low-arousal states, with performance varying by layer and cell type. Overall, our findings establish, at single-neuron resolution, the multi-scale organization of directed functional circuitry in mouse visual cortex across brain states.

neuroscience↗

bioRxiv2026

A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers

Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

molecular biology↗

bioRxiv2026

ASFV early protein p30 suppresses antiviral type I IFN induction by targeting TRIM21 and RIG-I like receptor signaling adaptor MAVS

African swine fever (ASF) is a highly pathogenic disease caused by the African swine fever virus (ASFV) infection, which can affect pigs of all ages and breeds, posing significant threat to the global pig farming industry. The ASFV p30 protein is an early-expressed viral structural protein; however, its function is not fully understood. In this study, the interaction of viral p30 with host TRIM21 was identified. The ectopic TRIM21 inhibited ASFV replication, while knockdown or knockout of TRIM21 promoted ASFV replication. Further, p30 was found to interact with RIG-I-like receptor (RLR) signaling adaptor MAVS, and during ASFV infection, p30-TRIM21-MAVS interacted with each other. Mechanistically, TRIM21 activated the K27 polyubiquitination of MAVS to induce IRF3 mediated type I interferon (IFN) production, whereas p30 counteracted TRIM21 activated MAVS K27 polyubiquitination to evade RLR signaling mediated antiviral IFN induction. In summary, our study revealed a novel function of ASFV p30, and provided new insights into the immune evasion of ASFV.

immunology↗

bioRxiv2026

Species-specific regulation of porcine STING stability and antiviral signaling via its K61 mediated K48 ubiquitination and proteasome degradation

The cGAS-STING pathway has been widely recognized as a critical DNA-sensing pathway that plays a broad-spectrum antiviral role. Livestock, especially pigs, represents one of the most important meat sources. In this study, we identified a key lysine 61 (K61) of porcine STING (pSTING) that plays an essential role in its degradation and antiviral signaling in a species-specific manner, with K61 as the major lysine of pSTING for K48-linked ubiquitination. After virus infection, pSTING recruits the E3 ligase, RNF5, which specifically assembles a K48-linked ubiquitin chain at K61, thereby mediating pSTING proteasomal degradation and reducing its antiviral activity. Meanwhile, the deubiquitylation of K61 is mediated mainly by deubiquitinase USP20, which enhances the stability and antiviral activity of pSTING. Together, given the relatively few lysine numbers in livestock STINGs and species-specific K61 regulation of pSTING stability and antiviral function, the K61 and its specific regulatory enzymes of pSTING could serve as potential targets for breeding of antiviral pigs and design of antiviral drugs, respectively.

immunology↗

bioRxiv2026

Bimodal Coupling Optimization in Biological Rhythms: Balancing Energy Efficiency and Functional Demand

Biological rhythms are governed by intricate interactions among oscillatory subsystems, yet how they balance functional demands and energy efficiency remains unclear. We present a bimodal coupling optimization strategy where physiological systems dynamically alternate between synchronized (energy-saving) and desynchronized (function-priority) coupling modes. By employing the water-filling principle developed in communications engineering, we prove synchronized heart rate(HR)-respiration oscillations maximize energy efficiency (oxygen uptake per cardiac work). Then, system modeling confirms task/stress-induced oxygen demands enhance oxygen uptake at the cost of desynchronization and reduced efficiency. Experiments reveal a 70.36% decrease in HR-respiration synchronization during arithmetic versus relaxation, enabling 4.43% higher oxygen uptake but with 11.38% lower energy efficiency. This bimodal coupling optimization strategy is also evident in pancreatic islets, with their insulin/glucagon oscillator alternating between in-phase (energy-saving) and anti-phase (rapid glucose reduction) coupling. This framework, integrating engineering and life sciences, reveals a universal regulatory principle for biological oscillatory systems.

systems biology↗

bioRxiv2026

Hormonal stimulation induces broader decidualization responses than cAMP alone in 3D human endometrial organoids

The human endometrium undergoes cyclic, hormone-driven remodeling that establishes a transient window of receptivity required for embryo implantation, placentation, and maintenance of pregnancy. Decidualization of endometrial stromal cells is a central component of this process and can be induced in vitro using cAMP alone or in combination with ovarian steroid hormones (EPC: estradiol, progesterone, and cAMP). Although cAMP activates the core decidual transcriptional program, whether hormone supplementation induces a more physiologically relevant response remains unclear, particularly in 3D endometrial organoid (Endo-organoid) models which have emerged as a new alternative methodology (NAM). Here, we compared morphological and transcriptomic responses of human endometrial stromal cell-derived Endo-organoids undergoing decidualization induced by cAMP or EPC stimulation. EPC-treated Endo-organoids exhibited enhanced structural remodeling and more advanced morphological transformation compared with cAMP-treated organoids. RNA-seq analysis revealed substantial overlap in canonical decidual gene expression between the two conditions, but EPC induced broader transcriptional and pathway-level changes, including enrichment of metabolic, stress-response, and differentiation-related processes. Together, these findings demonstrate that while cAMP activates the core decidual program, EPC elicits a broader and more physiologically relevant decidualization response in 3D human Endo-organoids, providing guidance for optimizing Endo-organoids to study endometrial receptivity, implantation, and early pregnancy success.

physiology↗

bioRxiv2026

Genetic influences on food liking and food preference patterns in young adults: a genome-wide association study

Genetic variation contributes to individual differences in food liking and dietary behaviour. Genome-wide association studies (GWAS) have identified genetic variants associated with these traits, but most evidence comes from middle-aged and older populations. Young adulthood is a key life stage during which long-term dietary habits develop, yet the genetic basis of food liking during this period remains largely unexplored. We conducted GWAS of 97 food-liking traits and two derived principal components (PCs) in 2,784 young adults (aged 25) from the Avon Longitudinal Study of Parents and Children. The PCs captured broader plant-based/seafood (PC1) and meat-based (PC2) food preference patterns. GWAS identified 16 genome-wide significant associations across 14 individual food-liking traits and one food preference pattern (PC1). Cross-trait analyses showed that several variants were associated liking for multiple foods. For example, the lentil-associated variant rs76659918 was associated with PC1 and with liking for avocado, honey, plain yogurt, chilli peppers, aubergines, and black olives, whereas burger- and steak-associated variants were linked to multiple meat-based foods and PC2. Exploratory analyses showed that TAS2R38 bitter-sensitive alleles were associated with lower liking for Brussels sprouts, with limited evidence for associations with other traits. Comparison with food liking GWAS from the UK Biobank (aged 37-73) showed limited replication, with robust evidence only for the grapefruit juice-associated variant rs2264192. This study identifies genetic variants associated with food liking in young adulthood and suggests that genetic influences operate at both the level of individual foods and broader food preference patterns.

genetics↗

bioRxiv2026

Suppressing Transfer of Antibiotic Resistance by a Small RNA Virus

The global rise of antimicrobial resistance (AMR) demands innovative strategies to limit the spread of multidrug-resistant bacteria. Conjugative plasmids, particularly those in the incompatibility group P (IncP), play a central role in disseminating resistance genes across diverse bacterial species via their encoded Type IV secretion systems (T4SS). Here, we characterize the single-stranded RNA bacteriophage (ssRNA phage) PRR1, which selectively targets AMR ESKAPEE pathogens carrying the IncP plasmid RP4, and assess its ability to inhibit conjugation. Using cryo-electron microscopy, we first resolved the mature PRR1 virion at 3.45 [A] resolution revealing two phage maturation protein (Mat)-RNA interactions within the 3 untranslated region (UTR) - a conserved interaction (Mat-U1) and a novel interaction (Mat-V1) for ssRNA phages. To characterize the PRR1-RP4 pilus interaction, we performed alanine-scanning mutagenesis and pinpointed four critical TrbC pilin residues (S12, W13, S72, and R77) for infection. Computational modeling revealed that these residues are located near the termini of the pilin at the phage-pilus interface. Notably, native and non-infectious, UV-crosslinked PRR1 were sufficient to block RP4 transfer, indicating conjugation inhibition does not require a complete infection cycle. Finally, combining PRR1 and antibiotic treatment yielded nine unique phage-resistant mutants within T4SS-associated genes on the RP4 plasmid. Eight of these mutants nearly abolished conjugation, while the trbE frameshift mutant retained [~]30% of wild-type efficiency, which is pivotal to clarifying the relationship between phage infection and pilus function. Collectively, these results establish ssRNA phages as specific T4SS plasmid targeting agents and underscore their potential to limit horizontal gene transfer in AMR pathogens. IMPORTANCEAntimicrobial resistance (AMR) spreads rapidly through horizontal gene transfer, largely driven by conjugative plasmids. Despite their central role, few strategies exist to directly block plasmid transfer. Here, we show that the IncP plasmid-dependent ssRNA phage PRR1 can inhibit the spread of antibiotic resistance genes by targeting the RP4 T4SS pilus. Structural and mutational analyses reveal previously unrecognized RNA packaging interactions and identify four pilin residues critical for infection. Remarkably, non-infectious PRR1 particles alone are sufficient to block conjugation, offering inhibition without the selective pressure from phage replication. Almost all PRR1-resistant RP4 mutants lost or had severely reduced plasmid transfer, while the remaining mutant is critical for studying the link between T4SS function and phage infection. These results highlight ssRNA phages as precise agents for limiting AMR gene dissemination.

microbiology↗