Biology subjects

Luo, Z.

Publications and source records attributed to Luo, Z..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Characterize Oral-to-Blood Microbial DNA Translocation in Individuals with Cocaine Use Disorder

BackgroundCocaine disrupts gut barriers in animal models, potentially enabling microbial translocation and inflammation in the periphery and central nervous system (CNS), but its direct role in inducing inflammation remains controversial. This study aimed to determine if the oral cavity is a source of circulating microbial DNA translocation in individuals with current cocaine use disorder (CUD). ResultsA cross-sectional case-control study was conducted, comparing CUD and demographically matched non-drug controls. Ten CUD (via smoking or vaping) and 24 controls provided paired saliva and blood samples. Microbial 16S rRNA V4 region was sequenced in isolated microbial DNA from saliva and plasma. Single-cell RNA sequencing (scRNAseq) was analyzed in human peripheral blood mononuclear cells. Saliva from CUD, but not plasma, exhibited reduced alpha diversity and altered beta diversity, characterized by enriched Streptococcus and depleted Fusobacterium, Neisseria, and other taxa relative to controls. Controls exhibited low to undetectable microbial translocation in plasma. By contrast, plasma displayed CUD-specific oral enrichment of several Streptococcal species and evidence of translocation into the bloodstream. S. parasanguinis, but not cocaine alone, induced IL-1{beta} and TNF- production in human primary monocytes in vitro. scRNAseq further revealed innate immune activation, impaired T cell function, and heightened susceptibility to infection in CUD. ConclusionsThis pilot study demonstrating that CUD via smoking or snorting exhibited oral microbial dysbiosis and selective oral-to-blood microbial translocation in vivo. These findings suggest that a compromised oral-to-blood barrier, rather than cocaine itself, promotes immune perturbations in CUD.

microbiology↗

bioRxiv2025

Argon inhibits autophagy and improves cerebral ischemia-reperfusion injury via PI3K/Akt/mTOR pathway

It has been reported that argon has neuroprotective effects during cerebral ischemia-reperfusion injury (CIRI). However, the specific mechanism is not fully understood. The aim of this study is to investigate if argon could regulate autophagy to exert a neuroprotective function. A temporary middle cerebral artery ischemia mouse model (tMCAO, ischemia 3h, reperfusion 1h) and the HT22 cell line Oxygen glucose deprivation reperfusion (OGDR) model were used for argon treatment. Transcriptome sequencing and bioinformatics analysis were performed on HT22 OGDR models. Western blot, CCK-8, LDH, transmission electron microscopy, agonists and inhibitors of autophagy and PI3K/Akt/mTOR were used to investigate the specific mechanism. Argon could reduce infarct volume, improve weight recovery, and neurological scores. Enrichment analysis of the KEGG signaling pathway was highly correlated with the PI3K/Akt pathway. Western blot, CCK-8, LDH, and transmission electron microscopy showed that argon could activate the PI3K/Akt/mTOR pathway and inhibit autophagy, promoting a neuroprotective function. After the combined use of autophagy inducer 3, Akt inhibitor MK2206, and mTOR inhibitor rapamycin, respectively, the neuroprotective function of argon was significantly reversed. Our study suggests that argon activating the PI3K/Akt/mTOR pathway and inhibiting autophagy is an important mechanism for its neuroprotective function.

neuroscience↗

bioRxiv2025

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters

Plants produce bioactive compounds as part of their specialized metabolism, with applications in medicine, agriculture, and nutrition. The biosynthesis of a growing number of these specialized metabolites has been found to be encoded in biosynthetic gene clusters (BGCs), creating increasing demand for genome mining tools to automate their detection. plantiSMASH enables the identification of putative plant BGCs through a rule-based approach, available via both command-line and web interfaces. Here, we present plantiSMASH 2.0 (https://plantismash.bioinformatics.nl/), a major update that expands and improves the original framework with revised and additional BGC detection rules (now supporting 12 BGC types), substrate prediction for selected enzyme families, and regulatory analysis through transcription factor binding site detection. The updated plantiSMASH 2.0 database includes 30,423 putative BGCs across 430 genomes. Together, these improvements make plantiSMASH 2.0 a powerful and comprehensive platform for the detection and characterization of plant biosynthetic pathways, supporting and accelerating research in plant specialized metabolism and plant natural product discovery.

bioinformatics↗

bioRxiv2025

CTDP: Identifying cell types associated with disease phenotypes using scRNA-seq data

Single-cell RNA sequencing enables transcriptome-wide analysis at single-cell resolution, offering unprecedented insights into cellular heterogeneity across biological conditions. However, accurately comparing transcriptomic distributions of cells from distinct biological states, such as healthy versus diseased individuals, remains challenging. To address this, we developed CTDP, a robust and interpretable computational framework that identifies disease phenotype-associated cell types of interest by integrating Lasso-regularized logistic regression with permutation testing. Through comprehensive evaluations on both simulated and real-world datasets, including melanoma immunotherapy, COVID-19 severity, and liver cirrhosis, CTDP consistently outperformed existing methods such as DA-seq, scDist, and PENCIL in both accuracy and robustness. In melanoma, CTDP uncovered immune-responsive clusters and revealed transcriptional regulators like PTPRC, CREM, and JUNB linked to immunotherapy efficacy. In COVID-19, it identified critical severity-associated cell types, such as B cells, NK cells, epithelial cells, and macrophages, which contribute to dysregulated immune responses and inflammation in severe cases. These results highlight CTDPs power in uncovering disease-relevant cell populations and its potential to advance precision medicine through single-cell analysis.

bioinformatics↗

bioRxiv2025

IRP1 deficiency alters mitochondrial metabolism and protects against metabolic syndrome pathologies

Iron regulatory protein 1 (IRP1) is a post-transcriptional regulator of cellular iron metabolism. In mice, loss of IRP1 causes polycythemia through translational de-repression of hypoxia-inducible factor 2 (HIF2) mRNA, which increases renal erythropoietin production. Here we show that Irp1-/- mice develop fasting hypoglycemia and are protected against high-fat diet-induced hyperglycemia and hepatic steatosis. Discovery-based proteomics of Irp1-/- livers revealed a mitochondrial dysfunction signature. Seahorse flux analysis in primary hepatocytes and differentiated skeletal muscle myotubes confirmed impaired respiratory capacity, with a shift from oxidative phosphorylation to glycolytic ATP production. This metabolic rewiring was associated with enhanced insulin sensitivity and increased glucose uptake in skeletal muscle. Under metabolic stress, IRP1 deficiency altered the redox balance of mitochondrial iron, resulting in inefficient energy production and accumulation of amino acids and metabolites in skeletal muscle, rendering them unavailable for hepatic gluconeogenesis. These findings identify IRP1 as a critical regulator of systemic energy homeostasis.

pathology↗

bioRxiv2025

Systemic translocation of S. aureus Drives Anti-CD4 Autoimmunity in Treated HIV Infection

BackgroundIn 2017, our group first demonstrated that autoimmunity contributes to HIV pathogenesis, even without autoimmune disease. This concept is now broadly recognized, exemplified by the role of autoimmunity in severe COVID-19. In people with HIV (PWH) on suppressive ART, anti-CD4 autoantibodies may impair CD4+ T cell recovery, though the mechanisms driving their production remain unclear. Building on evidence from our group and others that Staphylococcus aureus and its peptidoglycan (PGN) promote autoimmunity, we investigated their contribution to anti-CD4 IgG in HIV. MethodsPlasma from 32 ART-naive PWH, 53 ART-treated PWH, and 32 HIV-negative controls was analyzed for IgG autoantibodies and markers of S. aureus translocation using protein array, ELISA, and microarray. EcoHIV mice were injected intraperitoneally with saline, S. aureus PGN, or Bacillus subtilis PGN. PGN structures were compared by mass spectrometry. ResultsAmong 87 autoantibodies, 40% were elevated in ART-naive PWH and largely normalized by ART; however, anti-CD4 IgGs remained elevated in PWH on ART. Anti-CD4 IgG levels inversely correlated with CD4+ T cell counts in ART-treated PWH and positively with S. aureus translocation. In mice, S. aureus PGN induced anti-CD4 IgGs, reduced gut CD4+ T cells, and promoted surface IgG binding and apoptosis in CD4+ T cells. ConclusionS. aureus and its PGN translocation may drive anti-CD4 autoimmunity and hinder immune recovery in PWH on suppressive ART, highlighting S. aureus colonization as a therapeutic target and supporting the development of competitive probiotic interventions such as Bacillus subtilis.

immunology↗

bioRxiv2025

Microbial Tryptophan Metabolism Activates Host Lysosomal Activity to Facilitate Lipid Breakdown and Ameliorate Hepatic Steatosis

Lysosomes are central to lipid metabolism, yet how gut microbiota-derived metabolites regulate lysosomal function to influence host lipid homeostasis remains unknown. Here, we identify an evolutionarily conserved mechanism in which bacterial tryptophan metabolism activates lysosomal activity to promote lipid breakdown. By developing a lysosomal-responsive lipid reporter in C. elegans to screen for bacterial metabolic states that modulate host lipid storage, we discover that E. coli tryptophan catabolism via tryptophanase TnaA induces lysosomal lipid chaperone LBP-8, driving lipid mobilization. Moreover, tryptophan metabolites enhanced lysosomal acidification and degradation capacity, while genetic disruption of lysosomal regulators reversed these effects. Strikingly, bacterial tryptophan metabolism further promoted mitochondrial {beta}-oxidation through lysosomal lipase activity. This pathway was conserved in mammalian hepatocytes, where E. coli-derived tryptophan metabolites enhance lysosomal function and reduce lipid accumulation. In high-fat diet mice, restoring gut bacterial tryptophan metabolism alleviated hepatic steatosis. Our work uncovers microbiota-regulated lysosomal activation as a critical axis in lipid homeostasis, highlighting its potential as a therapeutic target for metabolic disorders linked to lysosomal dysfunction. SignificanceWe uncover a conserved mechanism by which microbial tryptophan metabolism enhances lysosomal function to maintain host lipid homeostasis. Specifically, we demonstrate that bacterial tryptophan catabolism--via the enzyme TnaA--promotes lysosomal acidification, proteolytic capacity, and structural remodeling in C. elegans, driving lipid breakdown through the lysosomal chaperone LBP-8. This activation boosts mitochondrial {beta}-oxidation and reduces lipid storage. Importantly, the same pathway operates in mammalian hepatocytes and in a high-fat diet mouse model, where restoring bacterial tryptophan metabolism markedly alleviates hepatic steatosis. Our findings bridge microbial metabolism and lysosomal dynamics, offering fresh insights into host-microbe crosstalk and metabolic regulation. HighlightsTnaA-mediated bacterial tryptophan catabolism promotes lipid mobilization via lysosomal chaperone. Bacterial tryptophan metabolites boost lysosomal function, lipid breakdown, and mitochondrial {beta}-oxidation. Conserved microbiota-lysosome-lipid axis from worms to mammalian liver. Restoring gut bacterial tryptophan metabolism alleviates hepatic steatosis in high-fat diet mice.

cell biology↗

bioRxiv2025

Clinical breakthrough: Biomimetic Scaffolds Based on Soluble Collagen for Regenerating Large Volumes of Highly Functional Tissues

Functional tissue regeneration in tissue engineering has long been an aspiration of humanity. However, conventional materials such as metal, ceramic, polymer, and decellularized extracellular matrix (dECM) have not yet yielded the desired outcomes. We have developed a collagen biomimetic material based on soluble collagen. This biomimetic material emulates the composition, structure, and function of native tissue. It possesses high strength, high affinity, high nutrient, and low antigenicity. The biomimetic material had been utilized to fabricate some implants (absorbable surgical suture, artificial tendon, hernia patch) and had demonstrated remarkable functional regeneration in animal experiments. In our previous researches, collagen surgical sutures facilitated wound healing, artificial tendons and artificial muscles (hernia patches) successfully repaired extensive defects of tendons and muscles, respectively. These successful tissue engineering endeavors enabled damaged defect to restore its biological functions and structure. Degradation of these biomimetic implants synchronized with the regeneration of the new tissues. Based on these successful functional regenerations, the present study focuses on regeneration of rabbit sciatic nerve. This collagen biomimetic material was employed to construct an artificial nerve tube (length: 2 cm, inner diameter: 2 mm, outer diameter: 3.5 mm) to repair a 2 cm-long defect in the rabbit sciatic nerve. After 36 weeks, the newly formed functional sciatic nerve successfully bridged the damaged ends, while approximately 92% of the artificial nerve tube has degraded. In this study, we provide an overview of the biomimetic material and its medical applications. We believe that these successful regenerations of tendon, muscle, and nerve all stem from the exceptional characteristics of this biomimetic material. We firmly believe that this collagen biomimetic material exhibits remarkable regenerative capabilities in diverse tissues. It can pave the way for the fabrication of increasingly critical artificial implants, which can be utilized to repair defects in human tissues, including artificial esophagi, tracheae, and small blood vessels. In regenerative medicine of induced pluripotent stem cells (iPS), the biomimetic materials can replace temperature-sensitive materials (PIPAAm) to fabricate cell sheets. This approach expedites the process, enhances cellular vitality, and consequently improves regeneration outcomes. This material technology not only provides a revolutionary solution for clinical treatment but also paves the way for a new development direction in regenerative medicine.

bioengineering↗

bioRxiv2025

High-throughput in vivo screening using barcoded mRNA identifies lipid nanoparticles with extrahepatic tropism for cancer immunotherapy

Interest continues to grow in the use of mRNA vaccines for cancer immunotherapy. While effective for immunization against infectious diseases, current clinical lipid nanoparticle (LNP) formulations used for mRNA delivery suffer from off-target accumulation, poor immune transfection, and reactogenicity, limiting their application to cancer immunotherapy. Development of new mRNA LNPs is severely bottlenecked by the LNP discovery process, which is historically low-throughput due to reliance on low-plexity measurements. Here, we develop a next-generation high-throughput in vivo mRNA LNP screening platform based on barcoded mRNA (b-mRNA). Using this b-mRNA screening platform to simultaneously evaluate 122 LNPs, we identify novel LNP formulations capable of potent hepatic and extrahepatic transfection. We employ novel biochemical characterization techniques to analyze nanoparticle protein corona formation with single-particle resolution and gain insight into the influence of protein adsorption on hepatic and splenic transfection. We evaluate a lead LNP candidate for therapeutic cancer vaccination in a syngeneic mouse model of melanoma and demonstrate a significant reduction in tumor burden and increase in survival compared to a clinical mRNA LNP formulation. Together, our results demonstrate the value of advanced LNP screening and characterization techniques for the development of next-generation mRNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

Breakthrough in Functional Muscle Regeneration: Biomimetic Collagen Scaffold Restores Abdominal Wall Defects in a VML-rabbit Model

Functional regeneration of volumetric muscle loss (VML) remains a significant challenge in the field of regenerative medicine. We have developed a novel biomimetic scaffold (0.4 mm thick hernia patch) derived from soluble collagen. This biomimetic scaffold exhibits exceptional strength, low immunogenicity, and structurally mimics the natural muscle fiber arrangement. The scaffold is utilized to repair a VML rabbit model (30 x 30 mm defect in abdominal wall) using nylon sutures for connection. It was observed that the VML site was gradually covered by regenerated tissue, which consisted of 2-3 mm thick functional muscle. By 32 weeks post-surgery, the newly formed muscle tissue had covered the majority of the VML area, as evidenced by morphological observations and histological evaluations. Approximately 24 weeks after surgery, the scaffold underwent complete degradation. This degradation exhibited a strong correlation with muscle regeneration. Furthermore, it was observed that the nylon sutures gradually migrated towards the VML center as muscle regeneration progressed, and nylon sutures exhibited an adverse impact on muscle regeneration.. The study did not employ exogenous cells or growth factors. However, the collagen scaffold effectively stimulated endogenous muscle regeneration. In contrast to the previous limited partial recovery or fibrotic scar healing, the collagen scaffold successfully induced genuine structural and functional muscle regeneration. The 0.4 mm thick scaffold (hernia patch) exhibits a different structure from the 2-3 mm thick natural abdominal muscle wall. This suggests that a simple scaffold can regenerate functional tissue with a complex structure. This research represents the first successful functional regeneration of VML in clinically relevant animal models through the utilization of artificial materials. This technology possesses transformative potential in the treatment of muscle defects arising from trauma, tumor resection, hernia, or congenital anomalies. Furthermore, it holds substantial medical potentials in addressing neuromuscular diseases, such as Duchenne muscular dystrophy (DMD), amyotrophic lateral sclerosis (ALS), and spinal muscular atrophy (SMA), by collaborating with advanced technologies including CRISPR-Cas9, adeno-associated virus (AAV) gene therapy, and stem cell technology.

bioengineering↗

bioRxiv2025

Multimodal Validation of the Existence of Transitional Cerebellar Progenitors in the Human Fetal Cerebellum

The developing human cerebellum comprises a series of transient progenitor states that are essential for generating diverse neural subtypes, yet the identity and validation of intermediate cell populations bridging stem-like and lineage-committed neuronal precursors remain limited. In our previous single-cell transcriptomic study, we identified a distinct transitional cerebellar progenitor (TCP) population enriched in specific progenitor zones such as the rhombic lip during human fetal cerebellar development. To address the concerns raised in the Matters Arising regarding the existence of the TCP cells, we provide additional multimodal validations of this population. Rigorous reanalysis of our single-cell transcriptomic data, applying stringent quality control measures, validated the quality of TCP cells and their classification as a transcriptionally distinct population. Multiple orthogonal validations of TCP signature genes (SOX11 and HNRNPH1) using RNAscope in situ hybridization, Xenium-based spatial transcriptomics, and immunohistochemistry on additional fetal cerebellar samples across different stages demonstrated the consistent presence of TCPs in the rhombic lip, transitioning from PRTG+ stem-like zones in the ventricular zone at early developmental stages to the subventricular zone overlapping with EOMES+ unipolar brush cell precursors at later stages. TCP-like populations were also independently identified in two fetal cerebellar single-nucleus transcriptomic atlases, and their gene signature was enriched in a cell population associated with aggressive medulloblastomas. Collectively, these multimodal validations confirm the existence of a transitional progenitor population in the human fetal cerebellum, with implications for cerebellar lineage progression and medulloblastoma origin.

developmental biology↗

bioRxiv2025

Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii

Rust diseases on plants are caused by fungi in the order Pucciniales. Typically, rust fungi have narrow host specificity however the pandemic biotype of Austropuccinia psidii has an unusually broad host range causing disease on over 480 myrtaceous species globally. We assembled and analysed a fully phased chromosome-level genome for the pandemic A. psidii and addressed key outstanding questions of its infection biology. Our research revealed a conserved rust fungal karyotype of 18 haploid chromosomes, in line with fungi for distantly related cereal rusts. We observed chromosomal re-assortment between the two nuclei, with one nucleus carrying 19 and the other 17 chromosomes. The synteny of universal single-copy orthologs is mostly maintained with the distantly related rust fungus Puccinia graminis f. sp. tritici. In contrast, nucleotide composition and methylation profiles of A. psidii are distinct compared to rust fungi with smaller genome sizes that have not undergone massive transposable element expansions. Our analysis of mating type loci supports a tetrapolar mating system for A. psidii with a novel finding of expanded numbers of pheromone peptide precursors. We show that infection dynamics of A. psidii are consistent on four different susceptible host species separated by 65 mya of evolution and that transcriptional regulation during infection reveals two distinct waves of gene expression in early and late infection, including allele-specific expression of candidate effectors. Together, these findings enhance the understanding of the genome biology and pathology of A. psidii, while also providing a valuable resource for future research on this serious rust pathogen.

microbiology↗

bioRxiv2025

Breaking the Tendon Repair Barrier: A Biomimetic Soluble Collagen Scaffold Enables Full Functional Regeneration of Achilles Tendon in Rabbits

This groundbreaking research employs biomimetic artificial tendons for the first time globally to successfully regenerate a 2 cm defect in the rabbit Achilles tendon. The artificial tendon, woven by collagen threads derived from soluble collagen, is a biomimetic tendon with a composition, structure and function akin to natural tendons. The biomimetic tendon exhibits exceptional tensile strength of (43.4 MPa), surpassing that of the natural Achilles tendon (39.1MPa). The remarkable mechanical properties, coupled with its favorable biocompatibility and low immunogenicity, underscore the substantial clinical application potential of this biomimetic material. A biomimetic tendon was implanted to repair a rabbit model of a 2 cm tendon defect without employing exogenous cells or growth factors. Twenty weeks after transplantation, the mechanical properties of the regenerated tendon were restored to approximately 80.1% of those of the natural Achilles tendon. This biomimetic tendon not only provides mechanical support during the initial phase of cell recruitment but also sustains strength to facilitate functional tendon reconstruction until material degradation and complete tendon regeneration. The regenerated tendon tissue exhibited regularly arranged dense collagen fibers along the longitudinal axis of the natural tendons, demonstrating high mechanical strength and seamless integration. Histological analysis further revealed a progressive enhancement in collagen fiber diameter, density, and structural integrity within regenerated tendons over time, closely resembling the characteristics of natural Achilles tendons eventually. Notably, there were no apparent immune reactions or inflammatory responses during the experimental cycle. These findings unequivocally demonstrate the remarkable efficacy of biomimetic tendons in facilitating functional tissue regeneration, underscoring their significant medical and scientific value. This study not only presents a novel treatment approach for tendon injury repair but also establishes the foundation for future clinical tendon and ligament regeneration and repair, with extensive clinical application prospects.

bioengineering↗

bioRxiv2025

Genetic architecture of the S-locus supergene revealed in a tetraploid distylous species

SummaryO_LIHeterostyly is a polymorphic floral adaptation controlled by supergenes and maintained in populations by disassortative mating. The molecular basis of distyly has been investigated in several unrelated families. Previous studies have been limited to diploid species and have not included Rubiaceae, which has the highest number of heterostylous species. C_LIO_LIHere, we investigate the genetic architecture of tetraploid Schizomussaenda henryi (Rubiaceae) to identify candidate style-length genes, evidence for hemizygosity and the potential role of gene duplication in the evolution of the S-locus. Chromosome-level genome assemblies and transcriptomic approaches identified the S-locus region comprised of four hemizygous genes. C_LIO_LIThe candidate gene SchzAUX22 may regulate style length and filament growth by acting in the auxin signaling pathway. Comparative studies of the two sub-genomes of S. henryi indicated strong similarities and no significant sub-genome dominance, as expected from autotetraploidy. Evidence from haplotype-resolved assemblies of a short-styled plant indicated that it possessed the ssSS genotype, consistent with autotetraploidy, which was estimated to have originated [~]3.6 Mya. Analysis of Ks values between S-locus genes and their paralogs indicated that the S-locus likely originated through stepwise duplication. C_LIO_LIOur study provides comprehensive genomic analysis of distyly in a polyploid and demonstrates that despite whole genome doubling the S-locus supergene remains intact and functional as an outbreeding mechanism. Our results contrast with many other heterostylous lineages where polyploidy is associated with breakdown of the polymorphism and transitions to self-fertilization. C_LI

plant biology↗

bioRxiv2025

Phage-Nanoparticle Cocktails as a Novel Antibacterial Approach: Synergistic Effects of Bacteriophages and Green-Synthesized Silver Nanoparticles

Bacteriophages have emerged as promising natural antibacterial agents, offering a targeted approach to combating bacterial infections. While phage-antibiotic cocktails are widely explored to enhance antibacterial efficacy and prevent resistance, research on phage-nanoparticle combinations remains limited. However, antibiotic resistance continues to rise, necessitating alternative strategies. Combining bacteriophages with nanoparticles presents a novel approach that could enhance antibacterial potency while reducing the risk of resistance, yet studies in this area are still scarce. We explore the synergy between green tea extract-capped silver nanoparticles (G-TeaNPs) and bacteriophages in combating pathogenic bacteria (Staphylococcus aureus, Salmonella enterica). G-TeaNPs show no antiphage activity, ensuring compatibility in phage-NP formulations. These combinations significantly reduce bacterial counts in a short time (only 3 hours), e.g., S. aureus survival is around 30% after incubations with just 0.001 mg/mL of G-TeaNPs, with G-TeaNPs and phages alone result in around 80% and 70% survival, respectively. Cytotoxicity tests against eukaryotic 3T3 NIH fibroblast cells confirmed biocompatibility at effective concentrations. Additionally, we examine G-TeaNPs impact on the free-living protist Acanthamoeba castellanii. Both green tea extract and G-TeaNPs can reduce A. castellanii cell counts by 80%, but only at concentrations larger than 10 mg/mL. Microscopy revealed nanoparticle uptake by amoebae, causing intracellular accumulation and vacuolization, while green tea extract induced similar changes without uptake. Our findings highlight G-TeaNPs as safe, effective agents in phage-nanoparticle antibacterial formulations with dual antimicrobial and amoebicidal properties for therapeutic and environmental applications.

microbiology↗

bioRxiv2025

Discovery of Chirally-dependent Protein O-2-Hydroxyglutarylation by D2HG and L2HG

Mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 are common in multiple types of human cancer, leading to the accumulation of D-2-hydroxyglutarate (D2HG) and the promotion of tumorigenesis1. Here we discovered a novel O-2- hydroxyglutarylation by D2HG using chemical proteomics and further revealed distinct chiral preferences for D/L2HG modifications. Notably, we identified two kinases, MRCKA and SLK, modified by D2HG and L2HG respectively, and detected reduced phosphorylation of their substrates, suggesting an inhibitory effect of D/L 2HG modifications on the kinases activity.

biochemistry↗

bioRxiv2025

VZV gE Promotes STING Degradation via Midnolin-Proteasome Pathway to Inhibit cGAS-STING Signaling

Varicella-zoster virus (VZV) infects 85 million individuals annually and it is known for its intricate interplay with host cellular mechanisms, significantly impacting antiviral immune responses. Previous studies have highlighted the critical role of VZV glycoprotein E (gE) in virus-host interactions, but the precise mechanisms remain to be elucidated. Our results demonstrate that VZV gE interacts with STING, specifically through the gE (350-480aa) and STING (151-160aa) regions. This interaction predominantly involves incompletely glycosylated gE. Functional assays revealed that gE inhibits the cGAS-STING signaling pathway. gE enhances VZV proliferation and promotes STING degradation via the proteasome pathway, without affecting STING ubiquitination. We identified Midnolin as a mediator in this degradation process, with gE facilitating the interaction between STING and Midnolin. In vivo, gE expression in mice led to diminished antiviral responses upon HSV-1 infection, highlighting gEs role in modulating immune signaling. Our findings provide significant insights into VZVs evasion of host immune responses. By promoting STING degradation through an unconventional Midnolin-proteasome pathway, VZV gE effectively suppresses antiviral signaling, facilitating enhanced viral proliferation. The findings contribute significantly to the understanding of VZV pathogenesis and provide new therapeutic strategies against VZV.

microbiology↗

bioRxiv2024

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Phased telomere to telomere (T2T) genome assemblies are revolutionising our understanding of long hidden genome biology "dark matter" such as centromeres, rDNA repeats, inter-haplotype variation, and allele specific expression (ASE). Yet insights into dikaryotic fungi that separate their haploid genomes into distinct nuclei is limited. Here we explore the impact of dikaryotism on the genome biology of a long-term asexual clone of the wheat pathogenic fungus Puccinia striiformis f. sp. tritici. We use Oxford Nanopore (ONT) duplex sequencing combined with Hi-C to generate a T2T nuclear-phased assembly with >99.999% consensus accuracy. We show that this fungus has large regional centromeres enriched in LTR retrotransposons, with a single centromeric dip in methylation that suggests one kinetochore attachment site per chromosomes. The centromeres of chromosomes pairs are most often highly diverse in sequence and kinetochore attachment sites are not always positionally conserved. Each nucleus carries a unique array of rDNAs with >200 copies that harbour nucleus-specific sequence variations. The inter-haplotype diversity between the two nuclear genomes is caused by large-scale structural variations linked to transposable elements. Nanopore long-read cDNA analysis across distinct infection conditions revealed pervasive allele specific expression for nearly 20% of all heterozygous gene pairs. Genes involved in plant infection were significantly enriched in ASE genes which appears to be mediated by elevated CpG gene body methylation of the lower expressed pair. This suggests that epigenetically regulated ASE is likely a previously overlooked mechanism facilitating plant infection. Overall, our study reveals how dikaryotism uniquely shapes key eukaryotic genome features.

genomics↗