Biology subjects

Zhong, Z.

Publications and source records attributed to Zhong, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Acetylation of NDUFA13 at K7 Senses OXPHOS Dysfunction to Disrupt Prohibitin Scaffolds and Drive Cristae Remodelling in Heart Failure

Mitochondrial cristae disintegration is a hallmark of heart failure, yet how oxidative phosphorylation (OXPHOS) dysfunction triggers this structural collapse remains unclear. Here we identify acetylation of the complex I subunit NDUFA13 at lysine 7 (K7) as a metabolic sensor coupling OXPHOS dysfunction to cristae remodelling. OXPHOS inhibition drove NDUFA13-K7 hyperacetylation, inducing conformational compaction and translocation to the intermembrane space. Acetylated NDUFA13 competitively engaged PHB2 through its coiled-coil domain, displacing PHB1 and disassembling prohibitin scaffolds. The acetylation-mimetic NDUFA13-K7Q induced cristae fragmentation in vitro, and cardiomyocyte-specific K7Q knock-in mice showed accelerated mortality and cristae loss under pressure overload, accompanied by impaired TCA cycle flux, defective fatty acid oxidation and selective depletion of polyunsaturated cardiolipins. These findings establish NDUFA13-K7 acetylation as a reversible switch converting bioenergetic failure into pathological cristae remodelling and metabolic reprogramming, highlighting therapeutic potential for targeted deacetylation.

cell biology↗

bioRxiv2026

Reconstruction of the gastropod ancestral karyotype reveals lineage-specific chromosomal evolution and adaptations during habitat transitions

Gastropoda is the most diverse class of molluscs, with spectacular adaptive radiations across shallow to deep marine, freshwater, and terrestrial environments, yet the role of chromosomal restructuring behind these habitat transitions remain largely unexplored. This is in part due to most chromosomal genomes available are in the subclasses Caenogastropoda and Heterobranchia, with few representatives from the other four subclasses. Here, we assembled chromosome-level genomes for five representatives from those four subclasses: Vittina coromandeliana (Neritimorpha), Shinkailepas gigas (Neritimorpha), Turbo cornutus (Vetigastropoda), Neomphalus fretterae (Neomphaliones), and Cellana toreuma (Patellogastropoda), and reconstructed the ancestral gastropod karyotype consisting of 20 linkage groups (GLGs) as well as the ancestral karyotype of each subclass. Integrating macrosynteny and phylogenomic analyses across all six subclasses, we show that different lineages have adopted fundamentally different chromosomal strategies to colonize novel habitats: freshwater caenogastropods genomes are characterized by extensive end-to-end fusions, terrestrial heterobranchs by whole genome duplications, freshwater neritimorphs by lineage specific fissions plus fusion with mixing, and deep sea hydrothermal vent vetigastropods by widespread chromosomal restructuring, whereas hydrothermal vent neomphaliones and caenogastropods retain remarkably conserved ancestral karyotypes. Rearrangement breakpoints preferentially reside within topologically associating domains (TADs) rather than at boundaries, preserving higher order chromatin architecture. Functionally, convergent enrichment of the mucin type O glycan biosynthesis pathway in both freshwater and hydrothermal vent lineages is accompanied by lineage specific modifications, enhanced immune modulation in freshwater versus reinforced physicochemical shielding in the deep sea, reflecting divergent adaptive applications of this pathway. Our findings demonstrate that habitat transitions in gastropods are facilitated not by a uniform genomic mechanism, but by a diverse repertoire of lineage specific chromosomal strategies, highlighting the extraordinary genomic flexibility that underpins the remarkable gastropod diversity seen today.

evolutionary biology↗

bioRxiv2026

Hologenomics of xylotrophic bivalves reveals a minimalist, remote-acting evolutionary strategy of wood digestion

Wood constitutes the largest reservoir of biogenic carbon on Earth, yet remarkably few animals can exploit it. While terrestrial wood-feeders like termites rely on highly diverse gut microbiomes, xylotrophic marine bivalves have evolved a fundamentally different approach: a spatially segregated system where intracellular gill symbionts produce enzymes that act remotely within a nearly sterile cecum. However, the genetic and evolutionary basis of this unique symbiosis remains largely elusive. Here, we integrate hologenomics, transcriptomics, and biochemistry of a shallow-water shipworm (Teredo navalis) and a deep-sea borer (Xyloredo sp.). We find that despite diverging approximately 147 million years ago and occupying drastically different habitats, these bivalves maintain a strictly conserved ancestral karyotype and a shared genomic architecture for wood digestion. Our models reveal a clear host-symbiont division of labor. The host genome is specialized for lignin modification and targeted enzyme transport, whereas a highly streamlined symbiont community is responsible for core polysaccharide degradation. Central to this minimalist strategy is a lineage-specific GH5-GH6 dual-catalytic enzyme. By sharing amino acids across proximal binding pockets, this fusion protein unites endo- and exo-cellulase activities, enabling highly synergistic cellulose cleavage without the need for complex microbial communities. Ultimately, our comparative analysis with terrestrial models demonstrates that these marine invertebrates achieve efficient biomass degradation not through microbial expansion, but through extreme functional streamlining and molecular innovation, offering a distinct evolutionary paradigm for marine carbon cycling.

evolutionary biology↗

bioRxiv2026

CMPK2 restricts Mycobacterium tuberculosis replication and regulates macrophage gene expression

Host cell metabolic pathways influence innate immune responses to intracellular pathogens, but the contribution of nucleotide metabolism to antimicrobial defense remains incompletely defined. Here, we identify the mitochondrial nucleoside monophosphate kinase CMPK2 as a regulator of macrophage responses to Mycobacterium tuberculosis (Mtb). Using a targeted genetic screen of candidate host factors, we found that depletion of CMPK2 enhances intracellular Mtb replication in human macrophages. This phenotype was confirmed using both shRNA-mediated knockdown and CRISPR-Cas9-mediated knockout approaches. CMPK2 expression increased following macrophage activation and Mtb infection. Transcriptomic profiling revealed that loss of CMPK2 is associated with broad alterations in gene expression, including reduced expression of genes linked to innate immune and inflammatory responses early after infection. In contrast, myeloid-specific deletion of Cmpk2 in mice did not significantly alter bacterial burden or survival following aerosol Mtb infection, indicating that the contribution of CMPK2 to host defense is context dependent. Together, these findings identify CMPK2 as a host factor that limits Mtb replication in human macrophages and shapes innate immune gene expression programs.

immunology↗

bioRxiv2026

HESTIA: Scalable Multimodal Integration of Histology and High-Resolution Spatial Transcriptomics for Robust Spatial Domain Identification

Spatial omics has revolutionized molecular biology by providing invaluable insights into how native tissue microenvironments regulate cellular functions and disease mechanisms. Accurately capturing this structural complexity and decoding the underlying biological processes requires effectively integrating data from multiple modalities. However, transitioning to subcellular resolutions introduces massive data scales and severe transcriptomic sparsity, which challenge current analytical frameworks. To address this, we present HESTIA (Histology-Enhanced Scalable cross-Resolution inTegration for spatial trAnscriptomics), a highly efficient multimodal algorithm designed for identifying spatial domains in large-scale, high-resolution spatial omics data. By circumventing memory-intensive computations, HESTIA efficiently processes massive datasets on which existing algorithms fail due to memory constraints. HESTIA outperforms current multimodal methods in clustering accuracy and spatial continuity, accurately delineating fine structural boundaries. Furthermore, applying HESTIA to large-scale pathological samples successfully dissects clinically relevant intratumoral heterogeneity and maps distinct immune microenvironments in lung and colorectal cancers.

bioinformatics↗

bioRxiv2026

OpenBase: a universal framework for high-accuracy single-molecule detection of diverse non-canonical DNA bases using nanopore sequencing

Nanopore sequencing holds great potential for the direct detection of non-canonical DNA bases from electrical signals, yet current approaches remain limited to a few classical epigenetic marks. Here we present OpenBase, an open and universal framework that standardizes training-data generation and deep learning based-modeling for single-molecule identification of diverse non-canonical DNA bases. OpenBase transforms nanopore sequencing into a broadly accessible platform for exploring the chemical diversity of DNA.

bioinformatics↗

bioRxiv2026

Dormant Bacteria's Fatal Attraction to RNA Bacteriophages

Phages are the most abundant biological entities on Earth, yet RNA phages are strikingly scarce compared to their DNA counterparts--a long-standing mystery in phage biology. Here, we use dsRNA phage phiYY as a model to demonstrate that while RNA phages efficiently infect growing bacteria, they are gradually eliminated inside dormant bacteria through weak and time-dependent ROS-mediated damage. The RNA phages decline over days rather than through immediate clearance inside dormant bacteria. Accordingly, scavenging ROS with mannitol or overexpressing ROS degradation enzymes AhpB/TrxB2 rescues RNA phages from elimination. Crucially, because the underlying ROS-mediated RNA damage is minimal, RNA phage survival hinges on genomic redundancy. In single-phage infections, the lone RNA genome is highly vulnerable to cumulative damage and is eventually inactivated. In contrast, during co-infection by multiple RNA phages, the presence of multiple genome copies provides functional redundancy, thereby allowing a fraction of RNA phages to survive inside dormant bacteria. Given that most environmental bacteria are dormant and subject to heterogeneous phage infection, this copy number-dependent vulnerability offers a possible explanation for the scarcity, but not perish, of RNA phages in nature.

microbiology↗

bioRxiv2026

Density-dependent facilitation of livestock by small mammal ecosystem engineers

Small mammals and large herbivores have co-evolved in grasslands for millions of years, yet how they interplay remains unclear. Although large herbivores can significantly affect the smaller ones, the reversal effect is largely unknown. On the Qinghai-Tibetan Plateau, plateau pikas (Ochotona curzoniae) are often considered pests that compete with livestock at high densities. Using field experiments, we show that the presence of pikas facilitates weight gains of yaks (Bos grunniens) by improving vegetation composition at a moderate density level. Compared to the pika-present treatment, pika removal dramatically increased cover of the poisonous Stellera forbs by two-fold, reducing the abundance and protein content of palatable grasses and sedges, yak foraging efficiency, and yak weight gain by up to 42%. Notably, we found a humped relationship between yak weight gains and pika burrow densities in the pika-present plots; the facilitative effect of pikas on yaks was highest at about 200 burrows/ha, but shifted to a competitive effect at pika densities exceeding 400 burrows/ha. These results provide the first empirical evidence that maintaining a moderate density of small mammalian herbivores can benefit growth performance of livestock by improving vegetation composition. Our study highlights the significance of moderate populations of ecosystem-engineering small mammals in sustaining pastoral productivity in rangelands.

ecology↗

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

KCC2 Activation Reverses Neurophysiological and Behavioral Deficits in Female Rett Mice

Rett syndrome is an X-linked neurodevelopmental disorder resulting from mutations in the MeCP2 gene, leading to intellectual disability, impaired motor coordination, decreased sociability, and seizures. Central to the underlying pathophysiology are deficits in synaptic inhibition, which are mediated by hyperpolarizing GABAAR currents. These events develop postnatally and are dependent upon increased neuronal Cl- extrusion mediated by SLC12A5 (KCC2). Therefore, we tested whether its activation modifies the disease phenotypes evident in female MeCP2+/- mice, using OV350, a direct activator of KCC2. OV350 rapidly induced a sustained reduction in EEG power, accompanied by a decrease in the severity of epileptic discharges. Increased motor coordination, sociability, and spatial memory were also observed. Deficits in KCC2 phosphorylation were also seen in MeCP2+/- mice, consistent with reductions in its activity that were also ameliorated by OV350. Thus, KCC2 activation may be efficacious in limiting the impact of Rett syndrome and other neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Decoding the Valence of Developmental Social Behavior: Dopamine Governs Social Motivation Deficits in Autism

The social motivation theory posits that core social deficits in autism spectrum disorder (ASD) arise from impaired social valence assignment during the social critical period, yet the specific dopaminergic mechanisms governing this process remain unclear. We combined high-resolution behavioral sequencing (Social-seq) with fiber photometry to resolve nucleus accumbens (NAc) dopamine during naturalistic juvenile interactions. Sex-divergent social strategies emerged: males exhibited peer play-dominant interactions with action-contingent dopamine release, while females favored environmental exploration with attenuated social dopamine. Shank3-deficient juveniles exhibited a triad of dopaminergic dysregulation -- blunted signaling during social investigation, pathological inversion during active play, and hyper-responsive to non-social stimuli -- recapitulating ASD-like phenotypes. Closed-loop activation of dopamine during play rescued social deficits, establishing a causal link between phasic dopaminergic signaling and social motivation. These findings identify NAc dopamine as a dynamic encoder of social valence and suggest that temporally precise modulation of dopaminergic circuits may offer therapeutic leverage for ASD-related social impairments.

neuroscience↗

bioRxiv2025

Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity

Tissue acidification is a common feature of hypoxia, inflammation and solid tumor. Acidic pH regulates innate immune response in macrophages by weakening BRD4-containing transcriptional condensates. Yet how disruption of transcriptional condensates leads to gene-specific regulation of immune programs remain unclear. Here, we integrated ATAC-seq, ChIP-seq, and RNA-seq of primary murine macrophages and performed integrative epigenomics analyses to identify transcriptional regulators (TRs) with pH-sensitive regulatory potential and association to BRD4-dependent transcriptional condensates. We determined pH-dependent super-enhancers (SEs) by extended profiles of BRD4 binding and h3K27ac marks. We found RELA, IRF family, and STAT family as candidate TRs enriched at BRD4-associated, pH-sensitive SE regions. RELA and IRF3 preferentially occupied BRD4-associated and pH-sensitive SEs, and displayed markedly reduced binding under acidic conditions, aligning with BRD4 occupancy change. Correspondingly, immune-response genes within BRD4-associated, pH-sensitive SE regions, including Ch25h, Acp2, Gda, and Ifit family, were significantly higher expressed at pH 7.4 than at pH 6.5. Together, these results reveal a set of TRs involved in BRD4-associated, pH-sensitive transcriptional condensates that coordinate macrophage gene activation under physiological conditions, providing mechanistic insight into how acidic stress modulates transcriptional condensates and immune responses.

immunology↗

bioRxiv2025

Web engine for tumor pathology image retrievals on massive scales

Hematoxylin and Eosin staining (H&E) is widely used in clinical practice, but efficient and versatile image retrieval tools are lacking. We developed the H&E Retrieval Engine (HERE, https://hereapp.ccr.cancer.gov) to analyze patient cases based on image similarities to database records. Using H&E image regions as input, HERE searches 21.2 terabytes of whole-slide images from multiple tumor histopathology cohorts through a 12.1-gigabyte memory index, and returns top images containing regions similar to the query. HERE scans high-resolution images in the database using accurate artificial intelligence encoding and ultra-efficient hierarchical skip indexing. HERE demonstrated performance superior to existing image retrieval tools based on blinded pathologist scoring using benchmark queries that represent key image features of human tumors. By pairing spatial transcriptomics with H&E images, HERE also enables retrieving image features from gene transcriptomics input and identifies molecular pathways associated with tumor histologies.

bioinformatics↗

bioRxiv2025

Global Insights into Evolution and Adaptation in KPC and NDM Coproducing Carbapenem-Resistant Klebsiella pneumoniae.

ObjectivesThe worldwide dissemination of carbapenem-resistant Klebsiella pneumoniae co-producing KPC and NDM (KPC-NDM-CRKP) poses a substantial clinical challenge. MethodsThis study characterized 5 KPC-NDM-CRKP isolates from a tertiary hospital in southern China and integrated 460 global isolates genomes to demonstrate the population framework of this epidemic pathogen. Results5 clinical isolates were multidrug resistance, exhibiting high level resistance to first-line drugs including carbapenems and ceftazidime/avibactam. Globally, KPC-2-NDM-1 (50.3%) were the most common and an increasing trend of ST11-KL64 (20%) isolates carrying iucA and rmpA/A2. Resistance and virulence genes were positively associated with specific mobile elements including blaKPC-3 with Tn4401, iucABC with IncHI1B, iroBCDN with IncQ1. The phylogenetic analysis revealed distinct lineage-specific mutations and pan-genome enrichments synergistically promoted adaptive evolution: cluster 1 had membrane transport and secretion but enhanced immune evasion and horizontal gene transfer, cluster 3 adapted metabolically for nutrient-limited niches; cluster 4 reprogrammed metabolism for host adaptation, cluster 6 displayed membrane repair and reduced virulence (e.g., KC187). High-risk iucA/rmpA-positive isolates in cluster 2 acquired enhanced virulence and metabolic adaptive capacity through recombination hotspots (ABC transporters DdpABCD, efflux systems MdtABCD, metabolic enzymes XylB and MtlD, regulators BaeR and OmpR) and pan-genome enrichment (siderophore biosynthesis, toxin-antitoxin VapC and restriction-modification systems). Functionally, these traits correlated with high mucoviscosity, serum resistance, siderophore production and lower survival rates in G. mellonella that contribute to epidemiological success. ConclusionsThese findings demonstrated the discrete mutation, horizontal transfer, and accessory genome plasticity collectively drove the epidemiological success of KPC-NDM-CRKP.

microbiology↗

bioRxiv2025

Loss of miRNA-153 promotes endothelial-to-mesenchymal transition and compromises lung vascular integrity

Endothelial-to-mesenchymal transition (EndMT) is a biological process through which lung vascular endothelial cells (ECs) transdifferentiate into mesenchymal-like cells. EndMT has recently been implicated in the development and progression of pulmonary vascular remodeling in pulmonary hypertension (PH); however, its underlying regulatory mechanisms remain incompletely understood. MicroRNAs (miRNAs) are key post-transcriptional regulators of EC gene expression and cellular responses to various stimuli. Notably, microRNA-153 (miR-153) has been shown to directly target SNAI1 to modulate epithelial-to-mesenchymal transition (EMT), a process closely related to EndMT and extensively studied in cancer. Whether miR-153 also participates in EndMT regulation, however, remains unknown. In this study, we demonstrate that 72-hour hypoxic exposure induces SNAI1-mediated EndMT in human lung vascular ECs. Hypoxia also increased cell proliferation and disrupted intercellular junctions, leading to enhanced endothelial permeability. Reduced miR-153 expression was observed in both hypoxia- and TGF-{beta}1-induced EndMT, as well as in ECs isolated from PH patients exhibiting an EndMT phenotype. Similar to hypoxia, TGF-{beta}1 promoted EC permeability. Loss of miR-153 enhanced SNAI1-mediated EndMT, endothelial survival, and permeability under normoxic conditions, whereas miR-153 overexpression attenuated EndMT induced by hypoxia or TGF-{beta}1. However, miR-153 restoration did not completely recover endothelial barrier integrity disrupted by these stimuli. In conclusion, miR-153 serves as a critical regulator of EndMT, maintaining endothelial identity and barrier function. Therapeutic delivery of miR-153 may therefore represent a novel strategy to inhibit EndMT and attenuate pulmonary vascular remodeling in PH.

physiology↗

bioRxiv2025

Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use

Certain bacterial infections, such as those involving prosthetics, can require antimicrobial therapy over months to years, potentially increasing the burden of antimicrobial resistance. Here we longitudinally track the antimicrobial resistome in mice during continuous antibiotic dosing over 21 months. The burden of antibiotic resistance genes (ARGs) initially increases, but, surprisingly, declines in later months, approaching levels observed in untreated animals. ARG burden is regulated by taxonomy and declines as ARG-harboring taxa that initially bloom are replaced by commensals. Furthermore, we find that the dynamics of antibiotic-induced ARG burden are influenced by age-related differences in microbial taxonomy and can be removed by fecal microbiota transplantation. We show that commensals may regulate the resistome by limiting the growth of ARG-harboring taxa, thereby providing antimicrobial expansion resistance.

microbiology↗

bioRxiv2025

Structural Impact of Alzheimer's Disease Mutations on Transmembrane TREM2-DAP12 Interactions: An Atomistic Perspective

Triggering receptor expressed on myeloid cells 2 (TREM2) is an immunomodulatory receptor that plays a critical role in microglial activation through its association with the adaptor protein DNAX-activation protein 12 (DAP12). Genetic studies have identified rare TREM2 variants as key risk factors for Alzheimers disease (AD), with mutations affecting both the extracellular and transmembrane domains. While the TREM2-DAP12 complex is essential for microglial activation and is implicated in Alzheimers disease pathology, the structural and mechanistic effects of transmembrane domain mutations, particularly within different TREM2 isoforms, remain unclear. In this study, we employ multi-scale molecular dynamics simulations to investigate the impact of six TREM2 mutations (four in isoform 1, two in isoform 2) and one wild-type control (isoform 2) on complex stability. By integrating coarse-grain and all-atom simulations with unsupervised machine learning techniques, we reveal distinct conformational states and residue-level interactions that govern complex formation. Our findings demonstrate how mutations such as W191X in TREM2 isoform 2 disrupt critical interactions, leading to destabilisation of the complex and potential impairments in neuroimmune signalling. These results provide new insights into the structural mechanisms linking TREM2 mutations to AD and offer a foundation for developing targeted therapeutic strategies.

biophysics↗

bioRxiv2025

Vitamin D attenuates TNF-α-mediated neurotoxicity and improves functional recovery in experimental intracerebral haemorrhage

While the neuroprotective effects of vitamin D (Vit-D) have been demonstrated pre-clinically in a wide range of neurologic conditions, its potential use in the treatment of spontaneous intracerebral hemorrhage (ICH) has not been fully explored. We previously reported that Vit-D could expedite hematoma clearance in experimental ICH by inducing the conversion of M1 to M2 macrophage to enhance erythrophagocytosis1,2. Here, we provide new evidence on the dose-dependent effects of Vit-D on neuronal survival and functional recovery, lending further support for the clinical testing of Vit-D in the management of ICH.

neuroscience↗