Biology subjects

Tong, X.

Publications and source records attributed to Tong, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Non-canonical cytokinesis driven by mechanical uncoupling via nematic flows and adhesion-based invagination

Cleavage - the series of rapid cell divisions that follow fertilization - marks the onset of metazoan development and represents a deeply conserved evolutionary process. Across animals, two principal modes exist: complete (holoblastic) and incomplete (meroblastic) cleavage. While holoblastic cleavage resembles conventional cytokinesis both in vitro and in vivo, the mechanisms underlying meroblastic cleavage have remained poorly understood. Using zebrafish embryos as a model, we show that meroblastic cleavage proceeds through a distinct two-step mechanism. The process begins with the assembly and contraction of a large, arc-shaped actomyosin cable. However, this contractile event alone is insufficient to complete division. A second phase, driven by cadherin-mediated membrane adhesion, is required to invaginate the furrow ridge. Strikingly, this transition depends on mechanical uncoupling of the contractile cable from the surrounding cortex. We demonstrate that such uncoupling arises from an active nematic instability, which both enhances contractility along the cable and generates actin depletion zones that relieve lateral connections. Together, these findings reveal that meroblastic cleavage is governed not by a single actomyosin-based event but by a sequential interplay between cytoskeletal contraction and cadherin-dependent adhesion, highlighting a mechanism fundamentally distinct from canonical cytokinesis.

cell biology↗

bioRxiv2025

Beyond Pollination: Computer Vision Reveals how Flower Visitors, Climate and Agroforestry Management Drive Cocoa Yields in China and Brazil

Cocoa (Theobroma cacao L.) is a multi-billion-dollar crop that is strongly affected by climate change. As a pollination-limited crop, improving little-understood pollination services in agroforestry systems may offer a scalable solution to increase yield sustainably in a changing climate. Here, we use embedded computer vision devices and structural equation models to quantify the interactions of flower visitors and temperature across shade tree-diversity and canopy cover gradients in cocoa systems on fruit set, as a yield precursor. In China and Brazil we show that flower visits are done by nectar and pollen foragers (23.1%), herbivores (6.1%), predators (2.3%), and visitors combining the three functions (63%). Forager visits were driven by increased shade-tree diversity and canopy cover management, with stronger effects in China than in Brazil. Foraging midges in China and multifunctional ants in Brazil enhanced fruit set, showing that diverse pollinators across continents affect cocoa yields. In China, higher canopy cover reduced aphids foraging and feeding on flower tissue, while in Brazil temperature increase reduced flowering. Overall, new technologies can guide implementation of agroforestry management strategies to enhance pollination while reducing pest pressures to ensure sustainable cocoa production under climate change.

ecology↗

bioRxiv2025

Early Brain Functional Connectivity Changes Induced by Antidepressants and Placebo

Major depressive disorder (MDD) is a common and debilitating condition with limited treatment precision. While brain imaging has linked neural features to MDD diagnosis and treatment response, the underlying circuits and their early modulation by treatment remain unclear. To examine changes in functional connectivity within the first two weeks of treatment, we analyzed two independent cohorts of MDD patients receiving antidepressants or placebo. Across patients, a visual-precuneus-thalamus network showed increased functional connectivity regardless of treatment arm or clinical outcome. Placebo response involved attention and striatal systems, while drug-specific effects were localized to the amygdala, mid-cingulate, orbitofrontal cortex, and cerebellum, emerging only in a subset of medicated patients. Notably, the responses of those without drug-specific changes can be predicted with a placebo response prediction model. These early functional connectivity changes reveal common and distinct mechanisms of treatment effects, offering insights that could inform more personalized interventions for MDD.

neuroscience↗

bioRxiv2025

Transcranial magnetic stimulation induced pupil dilations can serve as a cortical excitability measure

The application of non-invasive brain stimulation (NIBS) often relies on proxy estimates of cortical excitability (CE), such as the resting motor threshold (rMT), measured through transcranial magnetic stimulation (TMS). However, estimating the rMT is not always possible, as it requires an intact corticospinal pathway for neural signals to travel from the cortex to the periphery. To broaden the application of NIBS there is a need for additional CE measures. In three experiments combining TMS, transcranial direct current stimulation (tDCS), and eye-tracking, we measured TMS-induced pupil dilations as a potential CE proxy. We present Bayesian evidence (Experiment 1: BF > 9; Experiment 2: BF > 46; Experiment 3: BFs > 6) that TMS-induced pupil dilations serve as an objective CE proxy, with larger pupil size reflecting higher CE. We also show that these effects are not due to auditory, muscle, or sensory confounds. The introduction of this novel measure paves the way for a deeper understanding of CE by enabling objective NIBS measures beyond the motor cortex. Moving away from the reliance on the motor cortex would allow NIBS research and therapy to become more inclusive, allowing access to populations that are affected by damage along the corticospinal pathway.

neuroscience↗

bioRxiv2025

A Universal 6iL/E4 Culture System for Deriving and Maintaining Embryonic Stem Cells Across Mammalian Species

The derivation of authentic embryonic stem cells (ESCs) from diverse mammalian species offers valuable opportunities for advancing regenerative medicine, studying developmental biology, and enabling species conservation. Here, we report the development of a robust, serum-free culture system, termed 6iL/E4 that enables the derivation and long-term self-renewal of ESCs from multiple mammalian species, including mouse, rat, bovine, rabbit, and human. Using systematic signaling pathway analysis, we identified key regulators--including GSK3, STAT3, PDGFR, BRAF, and LATS--critical for ESC maintenance across species. Additionally, inducible expression of KLF2 and NANOG enhances the naive pluripotency and chimeric potential of bovine ESCs. The E4 medium also supports stable ESC growth while minimizing lineage bias. These findings reveal conserved principles underlying ESC self-renewal across divergent mammalian species and provide a universal platform for cross-species stem cell research, disease modeling, and biotechnology applications. In BriefWang et al. developed 6iL/E4, a serum-free system sustaining ESCs from mouse, rat, bovine, rabbit, and human. These findings reveal conserved fundamental mechanisms governing ESC self-renewal across diverse mammalian species. HighlightsO_LIDeveloped 6iL/E4 system for ESC derivation across five mammalian species. C_LIO_LIPDGFR signaling inhibition as critical for ESC derivation across species. C_LIO_LIE4 medium improves ESC maintenance and avoids neural bias of traditional N2B27. C_LIO_LIInducible KLF2/NANOG enhances naive pluripotency and chimera formation in bovine. C_LI

cell biology↗

bioRxiv2025

Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

The intestinal epithelium is often a site of pathology, such as in inflammatory bowel disease (IBD), and its maintenance is highly modulated by interactions with the microenvironment. However, a systematic understanding of how the myriad of niche cues impact distinct epithelial cell types in a diseased context is still lacking. To address this gap, we first benchmarked diverse human colonic organoid injury models against IBD tissue, and established a disease-relevant model of epithelial inflammation using TNF, IFN{gamma}, and IL1{beta}. Using this system, we built a dictionary of epithelial responses to 81 secreted niche factors at single cell resolution via donor-pooled, multiplexed single cell RNA-sequencing (scRNA-seq). The comprehensive nature of our atlas allowed us to map relationships between perturbations, infer the function of less well-characterized ligands, and identify cell type-specific perturbed pathways. Finally, we established the relevance of organoid-derived gene programs by mapping them to single cell and spatial atlases of human IBD tissue. Our resource offers a global view of epithelial responses to microenvironmental cues in a physiologically relevant disease context and generates new hypotheses for signaling factors that may be involved in epithelial homeostasis and repair.

bioengineering↗

bioRxiv2025

Modulation of the GT Family 47 clade B gene affects arabinan deposition in elaters of Marchantia polymorpha

The plant cell wall polymer -1,5-linked arabinan is associated with important functions in plant physiology, such as cell wall flexibility and desiccation tolerance in angiosperms. However, its biosynthetic mechanism remains obscure. A putative arabinan arabinosyltransferase (AraT) is the Arabidopsis ARABINAN-DEFICIENT1 in GT family 47 clade B (GT47B), but its role is inferred by its mutant cell wall phenotypes, and not through in vitro assays. With seven other genes in the clade, investigating the function of the members in GT47B is hampered by the high genetic redundancy in Arabidopsis. Instead, we probe the function of the only two genes in GT47B in the liverwort model organism Marchantia polymorpha, named MpARAD-Like 1 (MpARADL1) and MpARADL2. Mparadl1 and Mparadl2 loss-of-function mutants and overexpression lines were generated, and their cell wall composition was probed using Comprehensive Microarray Polymer Profiling (CoMPP), glycosyl linkage analysis and immunolabelling. Interestingly, Mparadl2 mutants have much less of the 1,5--L-arabinan epitope in elaters since LM6 antibody recognition showed a notable reduction. However, 5-linked Araf levels in the Marchantia thallus tested with glycosyl linkage analysis are comparable between mutants and wild type, suggesting that there is another enzyme forming 5-Araf linkages in Marchantia. Our attempts to obtain the biochemical activity of these enzymes through the expression and purification of AtARAD1, MpARADL1 and MpARADL2 proteins in the HEK293 cell heterologous expression system were unsuccessful. Therefore, we suspect that an evolutionarily conserved, and clade-specific mechanism is required to confer solubility for purification and subsequent activity characterisation of GT47B proteins. Previous studies have shown that co-expression of protein interaction partners can enhance protein solubility in the HEK293 cell system, but co-expression of MpARADL2 with AtARAD1 and MpARADL1 did not yield soluble proteins, prompting further investigation into the protein-protein interactors of GT47B proteins.

plant biology↗

bioRxiv2025

The Building Blocks of Early Land Plants: Glycosyltransferases and Cell Wall Architecture in the model liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha has emerged as an important plant model for developmental studies and may become central to elucidate the complex process of cell wall polysaccharide biosynthesis. This study comprehensively analyses the composition and structure of cell wall glycans across eight different M. polymorpha tissue types. We show that while the cell walls largely mirror known land plant cell wall composition, they also exhibit some unique characteristics. For example, -(1,5)-arabinan was prominently present in the sporophyte tissue, which may indicate a specialised role in this life stage. Furthermore, M. polymorpha cell walls displayed a remarkably low overall pectin content, yet the abundance of pectic arabinan in sporophytes hint at its putative role in the evolution and complexity of spermatophyte cell walls. Through comparative analyses of glycosyltransferase (GT) families across plant species, we found that M. polymorpha has a diversified GT repertoire compared for example, to the model plant Arabidopsis thaliana, indicating uniqueness in its cell wall biosynthesis pathways. To support research underpinning cell wall biosynthesis, we developed a Gateway compatible compendium of 93 M. polymorpha GTs, providing a valuable resource for genetic and functional studies. Our study thus works as a foundation to drive new insights into cell wall evolution, structure and function across the plant kingdom.

plant biology↗

bioRxiv2025

How The Transition of Aphid Life Cycles Affect Endosymbiotic Bacteria

How symbiotic bacteria coordinate and respond to their hosts during complex life cycle transitions is a fascinating and unresolved topic, particularly for organisms that exist solely in natural environments, where their intricate life cycles make laboratory cultivation extremely challenging. Complex life cycles are often associated with host alternation in aphids, especially in eriosomatine gall-forming aphids, which exhibit seven distinct morphs throughout their life cycle while shifting their host plants seasonally. Despite these dramatic changes, these aphids maintain the obligate symbiotic bacterium, Buchnera aphidicola, to enhance their nutritional status. The bacterial communities in our wild-derived samples were dominated by aphid symbionts, including Buchnera, Regiella inseticola, Wolbachia, Arsenophonus, and Serratia symbiotica. Buchnera and Regiella prevailed in Tetraneura akinire and Tetraneura sorini, while Buchnera and Arsenophonus were more abundant in Eriosoma harunire. Our study, utilizing 16S rRNA metagenomic sequencing on the aphid Tetraneura akinire, demonstrates that Buchnera plays significant roles during most life cycle stages but is absent during the sexual male stage, where it is replaced by Regiella. Moreover, Buchnera densities exhibit significant variability across the aphids life cycles and are notably lower in gall generations. This result contradicts the previous hypothesis that galls provide superior nutrition compared to aphids in grassroot-feeding generations. In this study, we reveal the dynamics of symbiotic bacteria across the complex life cycles of three eriosomatine aphid species that form galls on the same Japanese elm tree, Ulmus davidiana var. japonica. Within the framework of tripartite symbiosis, the seemingly passive symbiotic bacteria adjust the hosts specific life stages and influence the changing host ecology in a cascading manner.

evolutionary biology↗

bioRxiv2025

Autocrine CXCL1-CXCR2 Signaling Mediates Leptomeningeal Resistance to Radiation Therapy

Leptomeningeal metastasis (LM) is a fatal neurological complication of cancer. Proton craniospinal irradiation (pCSI) has emerged as a promising life-prolonging intervention for LM patients, but the response to this treatment varies. Here, we aimed to characterize the molecular basis of pCSI resistance and response. Proteomic analysis of CSF collected from LM patients at baseline (before pCSI), and at multiple time points post-treatment, identified the CXC-motif chemokine, CXCL1, as associated with LM growth. Higher CXCL1 levels in the CSF prior to pCSI correlated with worse response to this treatment. To define the role of CXCL1 in LM, we established syngeneic mouse models of LM-CSI. We found that both metastatic cancer and host cells generate CXCL1. Genetic interruption of Cxcl1 expression in metastatic cancer, but not host cells, impaired cancer cell growth within the leptomeninges. Moreover, a subset of LM cancer cells expressed Cxcr2, the primary receptor for Cxcl1, and this population was enriched over time in the leptomeninges. Transcriptomic profiling of this rare population revealed an enrichment in pathways implicated in cell cycle progression. Finally, interruption of Cxcl1-Cxcr2 signaling with intrathecally-delivered Cxcr2 antagonist hampered LM growth and sensitized the cells to CSI. Our results demonstrate that the Cxcl1-Cxcr2 signaling axis mediates LM growth, and identifies a potential actionable intervention to improve response to pCSI and halt LM progression. One Sentence SummaryCXCL1-CXCR2 axis is a potential actionable therapeutic target to halt leptomeningeal metastasis progression and enhance response to craniospinal irradiation.

cancer biology↗

bioRxiv2025

Myelin transcription factors 1 and 3 have overlapping but distinct roles in insulin secretion and survival of human β cells

Aims/hypothesisGenetic and environmental factors work together to cause islet beta-cell failure, leading to type 2 diabetes (T2D). How these factors are integrated to regulate beta cells remains largely unclear. Based on our previous findings that the family of Myelin transcription factors (MYT1, MYT1L, and ST18) prevents mouse beta-cell failure by repressing the overactivation of stress response, their regulation by obesity-related nutrition signals in human beta cells, and their association with T2D, we postulate that these factors prevent human beta-cell failure under normal physiology and obesity-related stress. MethodsMYT1 or ST18 were knocked down in primary human beta cells using shRNA. Beta-cell survival, secretory function, and gene expression were examined after islet cells were cultured in vitro or xenotransplanted into mice under normal or obesity-related stress. ResultsIn culture, MYT1-knockdown (KD) caused beta-cell death, while ST18-KD compromised glucose-stimulated insulin secretion. Under obesity-induced stress as xenotransplants, ST18-KD also caused beta-cell death. Accordingly, MYT1-KD deregulated several genes and genesets in cell death and cellular stress response, while ST18-KD deregulated those regulating stress response, mitochondria, and ion channels. Corresponding to these gene expression changes, ST18-KD reduces glucose-stimulated Ca2+ influx in beta cells. In addition, the MYT1- and ST18-regulated genes are enriched for T2D-associated loci, with an enrichment of 2.05-fold relative to random distribution. Conclusions/interpretationThe MYT TFs complement each other to integrate genetic and environmental factors to prevent beta-cell failure and T2D, with their major effects exerted on beta-cell viability and/or Ca2+ influx. Graphical AbstractNutrient-responsive transcription factors MYT1 and ST18 regulate human beta-cell survival and secretory functions. Under low metabolic stress, MYT1 regulates cell survival while ST18 regulates insulin secretion. Under high metabolic stress, ST18 also regulates beta-cell survival. MYT1, at least partly, regulates cell survival through stress-related apoptotic processes, while ST18 regulates insulin secretion via Ca2+ influx. Research in context summaryO_ST_ABSBackgroundC_ST_ABSO_LIThe myelin transcription factors (MYT TFs, including MYT1, MYT1l, and ST18) prevent mouse beta-cell failure by depressing the overactivation of stress-response genes. C_LIO_LISNPs in all three MYT loci are associated with human type 2 diabetes. C_LIO_LIThe expression and nuclear localization of MYT1 and ST18 were increased in primary human beta cells under acute metabolic stress but downregulated in type 2 diabetes. C_LIO_LIThe co-knockdown of MYT1, MYT1L, and ST18 in a human beta-cell line resulted in apoptosis. C_LI Key questionO_LIHow does MYT1 or ST18 regulate human beta-cell function and survival? C_LI New findingsO_LIMYT1 prevents human beta-cell death under normal and metabolic stress conditions, corresponding to deregulation of a few genes involved in cell death under cellular stress. C_LIO_LIST18 promotes insulin secretion under normal physiological conditions by regulating Ca2+ influx and prevents beta-cell death under metabolic stress. C_LIO_LIThe MYT1- and ST18-regulated genes are enriched for type 2 diabetes-risk loci. C_LI Clinical impactO_LIRegulators of the MYT-TF activities could be explored to delay/prevent beta-cell failure and the development of type 2 diabetes. C_LI

cell biology↗

bioRxiv2024

Optogenetic Central Amygdala Stimulation is Highly Reinforcing and Strongly Outcompetes Fentanyl Self-Administration in Male, but not Female, Rats

The central nucleus of the amygdala plays a key role in many aspects of substance use disorders, in particular biasing behaviors toward one drug or natural reward over another, yet the role of this region in opioid self-administration remains unclear. Here, we report that pharmacological inactivation of the central amygdala reduces fentanyl self-administration, while intra-central amygdala opioid receptor antagonism dose-dependently increases fentanyl self-administration. We tested whether optogenetic activation of the central amygdala would increase motivation for fentanyl in rats with a long fentanyl self-administration history. While pairing fentanyl delivery with optogenetic central amygdala activation increased fentanyl self-administration, optoactivation itself was highly reinforcing and, in choice settings, was pursued over fentanyl despite mounting effort requirements, delays, and sporadic reward availability. Of note, under free response conditions, these effects were limited to male rats; while female rats avidly responded for optogenetic activation of the central amygdala, this activation was less effective in enhancing fentanyl intake, and it was not preferred over fentanyl. In contrast, under discrete trial choice which precluded independent regulation of intake of the two options, both females and males preferred optoactivation to fentanyl. These results demonstrate that optogenetic stimulation of neural activity within the anterior central amygdala does not appear to potentiate the reinforcing effects of fentanyl, but is itself highly reinforcing regardless of sex, and, in male rats can robustly outcompete fentanyl. In contrast, in females, fentanyl intake is relatively insensitive to competing opportunities for optoactivation, except when opportunities to obtain drug or optoactivation are sparse.

neuroscience↗

bioRxiv2024

Retinoid X Receptor Signaling Mediates Cancer Cell Lipid Metabolism in the Leptomeninges

Cancer cells metastatic to the leptomeninges encounter a metabolically-challenging extreme microenvironment. To understand adaptations to this space, we subjected leptomeningeal-metastatic (LeptoM) mouse breast and lung cancers isolated from either the leptomeninges or orthotopic primary sites to ATAC-and RNA-sequencing. When inhabiting the leptomeninges, the LeptoM cells demonstrated transcription downstream of retinoid-X-receptors (RXRs). We found evidence of local retinoic acid (RA) generation in both human leptomeningeal metastasis and mouse models in the form of elevated spinal fluid retinol and expression of RA-generating dehydrogenases within the leptomeningeal microenvironment. Stimulating LeptoM cells with RA induced expression of transcripts encoding de novo fatty acid synthesis pathway enzymes in vitro. In vivo, while deletion of Stra6 did not alter cancer cell leptomeningeal growth, knockout of Rxra/b/g interrupted cancer cell lipid biosynthesis and arrested cancer growth. These observations illustrate a mechanism whereby metastatic cancer cells awake locally-generated developmental cues for metabolically reprograming, suggesting novel therapeutic approaches.

cancer biology↗

bioRxiv2024

Contrastive functional connectivity defines neurophysiology-informed symptom dimensions in major depression

BackgroundMajor depressive disorder (MDD) is a prevalent psychiatric disorder characterized by substantial clinical and neurobiological heterogeneity. Conventional studies that solely focus on clinical symptoms or neuroimaging metrics often fail to capture the intricate relationship between these modalities, limiting their ability to disentangle the complexity in MDD. Moreover, patient neuroimaging data typically contains normal sources of variance shared with healthy controls, which can obscure disorder-specific variance and complicate the delineation of disease heterogeneity. MethodsWe employed contrastive principal component analysis to extract disorder-specific variations in fMRI-based resting-state functional connectivity (RSFC) by contrasting MDD patients (N=233) with age-matched healthy controls (N=285). We then applied sparse canonical correlation analysis to identify latent dimensions in the disorder variations by linking the extracted contrastive connectivity features to clinical symptoms in MDD patients. ResultsTwo significant and generalizable dimensions linking distinct brain circuits and clinical profiles were discovered. The first dimension, associated with an apparent "internalizing-externalizing" symptom dimension, was characterized by self-connections within the visual network and also associated with choice reaction times of cognitive tasks. The second dimension, associated with personality facets such as extraversion and conscientiousness typically inversely associated with depression symptoms, is primarily driven by self-connections within the dorsal attention network. This "depression-protective personality" dimension is also associated with multiple cognitive task performances related to psychomotor slowing and cognitive control. ConclusionsOur contrastive RSFC-based dimensional approach offers a new avenue to dissect clinical heterogeneity underlying MDD. By identifying two stable, neurophysiology-informed symptom dimensions in MDD patients, our findings may enhance disease mechanism insights and facilitate precision phenotyping, thus advancing the development of targeted therapeutics for precision mental health. Trial RegistrationEstablishing Moderators and Biosignatures of Antidepressant Response for Clinical Care for Depression (EMBARC), NCT#01407094

neuroscience↗

bioRxiv2024

Monovalent XBB.1.5 mRNA Vaccine Recalls a More Durable and Coordinated Antibody Response to SARS-CoV-2 Spike than the Bivalent WT/BA.5 mRNA Vaccine

In the fall of 2023, the monovalent XBB.1.5 mRNA vaccine for COVID-19 became available. However, the comparative magnitude, durability, and functionality of antibody responses induced by the XBB.1.5 vaccine compared with the 2022-2023 bivalent wildtype (WT) + Omicron BA.5 vaccine remains to be fully determined. In this study, we compared antibody profiles generated by these two vaccines in healthcare workers. We show that the monovalent XBB.1.5 vaccine induced higher magnitude binding, neutralizing, and Fc-gamma receptor (Fc{gamma}R) binding antibodies to the XBB.1.5 spike compared with the bivalent vaccine against the WT and BA.5 spikes, both at both peak immunogenicity and at 6 months post-vaccination. Moreover, antibody interaction architectures and correlations remained more robust at 6 months post-vaccination with the XBB.1.5 vaccine, whereas these correlations were largely lost at 6 months with the bivalent vaccine. Our results suggest that the XBB.1.5 vaccine led to a more durable and functionally coordinated antibody response compared to the bivalent vaccine.

immunology↗

bioRxiv2024

A causative SNP in the promoter of myogenin is essential for myogenic differentiation

Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.

genetics↗

bioRxiv2024

Unraveling the impact of host genetics and factors on the urinary microbiome in a young population

The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp PDC80 and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (AUC=0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to 8 host loci (p < 5x10-8). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

microbiology↗

bioRxiv2024

Circular DNA vcDNA-S7 derived from segmented-dsRNA virus BmCPV attenuated viral infection through RNase H1

Viral circDNA derived from insect positive-sense single-stranded RNA viruses plays a crucial role in regulating viral infections depending on the RNAi pathway. Our previous research has revealed that Bombyx mori cypovirus (BmCPV), a segmented-dsRNA virus, can generate viral circDNA vcDNA-S7, which can be transcribed to form RNA and further processed into small RNAs to defend against the virus through RNAi. However, whether vcDNA-S7 employs other mechanisms to resist the viruses. Presently, vcDNA-S7 has been found to resist BmCPV infection via a novel mechanism that depends on ribonuclease RNase H1 activity. It was found that the expression level of RNase H1 increased upon BmCPV infection (RNA virus) but not upon B. mori nucleopolyhedrovirus (BmNPV) (DNA virus) infection. RNase H1 has been shown to negatively regulate BmCPV infections. In addition, vcDNA-S7 was found to form a heteroduplex with the viral RNA and subsequently recruit RNase H1 to degrade the viral RNA within the heteroduplex, ultimately leading to the suppression of viral replication. Furthermore, the resistance of vcDNA-S7 to viruses was significantly reduced when cellular RNase H1 gene was silenced. These findings not only reveal a new antiviral mechanism involving circular DNA formed by reovirus but also offer intriguing insights into the antiviral function of RNase H1 in cells.

immunology↗