Biology subjects

Zhong, Y.

Publications and source records attributed to Zhong, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Shared and distinct adaptations to early-life exercise training based on inborn fitness

BackgroundLow cardiorespiratory fitness due to genetics increases the risk for cardiometabolic disease. Endurance exercise training promotes cardiorespiratory fitness and improves cardiometabolic risk factors, but with great heterogeneity. Here, we tested the hypothesis that the metabolic phenotype imparted by low parental (inborn) cardiorespiratory fitness would be overcome by early-life exercise training, and that exercise adaptations would be influenced in part by inborn fitness. MethodsAt 26 days of age, male and female rat low-capacity runners (LCR, n=20) and high-capacity runners (HCR, n=20) generated by artificial selection were assigned to either sedentary control (CTRL, n=10) or voluntary wheel running (VWR, n=10) for 6 weeks. Post-intervention, whole-body metabolic phenotyping was performed, and the respiratory function of isolated skeletal muscle and liver mitochondria assayed. Transcriptomics and proteomics were performed on skeletal muscle and liver tissue using RNA-sequencing and mass spectrometry, respectively. ResultsDaily VWR volume was 1.8-fold higher in HCR-VWR compared to LCR-VWR. In LCR, VWR reduced adiposity and enhanced glucose tolerance, coincident with elevated total energy expenditure. While intrinsic skeletal muscle mitochondrial respiratory function was unaffected by VWR, estimated skeletal muscle oxidative capacity increased in VWR groups owing to greater mitochondrial content. In the liver, both maximal oxidative capacity and ATP-linked respiration were higher in HCR-VWR than HCR-CTRL. Transcriptomic and proteomic profiling revealed extensive remodeling of skeletal muscle and liver tissue by VWR, elements of which were both shared and distinct based on inborn fitness. SummaryEarly-life exercise training partially overcomes the metabolic phenotype imparted by low inborn cardiorespiratory fitness. However, molecular adaptations to VWR are partly influenced by inborn fitness, which may have implications for personalized exercise medicine.

physiology↗

bioRxiv2024

Coordinated organic and inorganic nitrogen transformations fuel soil microbial blooms and increase nitrogen retention during snowmelt

Snowmelt in high-elevation watersheds triggers a microbial bloom and crash that affects nitrogen (N) export. Predicting watershed N dynamics as snowpack declines is a challenge because the mechanisms that underlie this microbial bloom and crash are uncertain. Using a multi-omic approach, we show that the dynamic molecular properties of dissolved organic N, plus high gene expression for peptidases that recycle microbial biomass, suggested that microbial turnover provided N for biosynthesis during the microbial bloom. Amino acid fermentation by Bradyrhizobia produced organic acids that also fueled denitrification and dissimilatory nitrate reduction to ammonia (DNRA) during snowmelt. Nitrification in spring was driven by Spring-Adapted Nitrososphaerales, which utilized ammonium derived from osmolyte degradation by Winter-Adapted Solirubrobacteraceae. High DNRA gene expression after snowmelt suggested significant nitrate retention, increasing watershed N retention potential. However, declining snowfall may compromise microbial regulation of soil N retention, with implications for watershed N export.

microbiology↗

bioRxiv2024

OsMORF protein selectively promotes the dual-localized RNA editing factor OsPGL1 binding to its target RNA

Post-transcriptional RNA editing plays a key regulatory role and serves as a genetic information proofreading mechanism. In flowering plants, RNA editing typically involves the removal of amino groups from cytidine to produce uridine in both plastids and mitochondria. In our previous work, we identified OsPGL1 as a rare organelle editing factor that regulates both mitochondrial and chloroplast RNA in rice. This protein mediates RNA editing and is associated with several OsMORFs. We speculated that they may form editing complex to regulate editing events, but we are still unclear about the detailed mechanism between OsMORF proteins and OsPGL1, as well as their roles in target RNA recognition and binding. In this study, we found that three OsMORFs can significantly promote the binding of OsPGL1 to target RNA in vitro. Notably, OsMORF8 can promote OsPGL1 to form a homologous dimer, thereby enhancing RNA binding to a greater extent. The E and DYW motifs do not affect the role of MORF proteins in RNA editing events, ruling out the potential influence of these two special motifs. In addition, we predicted a series of supercomplex structures of OsPGL1, the OsPGL1-RNA ligand complex, the OsPGL1-OsMORF2-OsMORF8-OsMORF9 complex, and the OsPGL1-OsMORF2-OsMORF8-OsMORF9-RNA complex. We determined that the conformational changes and newly added positively charged surface caused by OsMORF on OsPGL1 are the main reasons for MORF to promote the binding of OsPGL1 to RNA. Based on some new discoveries, we have expanded the RNA editing complex model, which greatly enhances our understanding of plant RNA editing complexes. Short summaryPPRs and MORFs are two kinds of RNA editing factors, both can mediate organelle RNA editing, the difference between them is that PPR can directly bind target RNA, MORF does not directly bind RNA, but can independently or assist PPR in performing RNA editing. Function of MORF protein in post-transcriptional processing is not clear, our study verifies the function of MORFs in the process of PPR binding RNA through molecular biology. We also analyzed the interaction network between PPR-MORF-RNA from the perspective of structural biology.

plant biology↗

bioRxiv2024

IGF2 mediates Hippo signaling to control liver size

The Hippo pathway is a central mechanism in organ size control, but the mediator for its function remains elusive. Here, we show that the expression of insulin-like growth factor II (IGF2) is directly induced by YAP/TAZ transcription cofactors of the Hippo pathway in a developmental stage- and cell type-specific manner. In mouse livers, Igf2 expression is sustained by YAP/TAZ in hepatoblasts and immature hepatocytes at fetal and neonatal stages, coupling with rapid cell proliferation and liver size expansion, whereas turned off in matured hepatocytes following YAP/TAZ inactivation to prevent liver overgrowth. In contrast, YAP/TAZ fails to regulate Igf2 expression in cholangiocytes and diverse liver mesenchymal cells where epigenetic barriers, including DNA and histone methylation, are implanted near Igf2 promoters. Furthermore, IGF2 activates IGF1R signaling and promotes normal and neoplastic liver growth, while the inactivation of IGF2 or IGF1R effectively blocks YAP/TAZ-induced hepatomegaly and hepatoblastoma. In conclusion, our findings reveal that IGF2 is a bona fide mediator of the Hippo pathway, indicating a fundamental role of the Hippo-IGF2-IGF1R signaling axis in organ size regulation and malignancies.

cell biology↗

bioRxiv2024

DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing

Nanopore direct RNA sequencing (DRS) advances RNA biology but is limited by relatively low basecalling accuracy, low throughput, yet high RNA input and costs. Here we introduce a novel DRS toolkit, DEMINERS, which integrates an RNA multiplexing experimental workflow, a machine-learning barcode classifier based on Random Forest and a novel basecaller built on an optimized convolutional neural network providing an additional species-specific training module. With the increased accuracy in barcode classification and basecalling, DEMINERS can demultiplex up to 24 samples and the required RNA input and running time are both substantially reduced. We demonstrated the applications of DEMINERS in clinical metagenomics, cancer transcriptomics and parallel comparison of transcriptomic features in different biological conditions, revealing altered airway microbial diversity in COVID-19 and a potential role of m6A in increasing transcriptomic diversity in glioma and the mature blood-stage of malaria parasites. Overall, DEMINERS is a simple, robust, high-throughput DRS method for accurately estimating transcript levels, poly(A) lengths, and mutation and RNA modification heterogeneity at single-read level, with minimal sequencing biases.

bioinformatics↗

bioRxiv2024

Growth and defence in a unicellular microalga: the coexistence of r and K strategies

r (high reproductivity but stress-sensitive offspring) and K (low reproductivity but high stress-resistant offspring) strategies are two classical life history theories. Contrary to the belief that one species only has a single strategy (i.e., either r or K), we present experimental evidence for the coexistence of both strategies in the isogenic microalga Haematococcus lacustris. Under standard conditions, swimming vegetative cells (SVC) normally grew and divided via binary fission (r strategy) and gradually shifted into non-swimming cysts (NSC) over time. Intriguingly, unlike the prevailing notion that NSC cannot propagate under stress, they were found to reproduce via multiple fission at a barely detectable growth rate, resulting in stress-resistant, non-mobile daughter cells and demonstrating a complete life history (K strategy). Collectively, our findings indicate that H. lacustris adopts both r and K strategies throughout its life history. This research enhances the understanding of the adaptation and survival of microbial populations in changing environments.

ecology↗

bioRxiv2024

Uncovering the mechanistic basis of intracellular Raf inhibitor sensitivity reveals synergistic cotreatment strategies

Raf kinases are crucial effectors in the Ras-Raf-Mek-Erk signaling pathway, making them important targets for the development of cancer therapeutics. This study investigates the variable potency of DFG-out-stabilizing Raf inhibitors in mutant KRas-expressing cell lines. We demonstrate that inhibitor potency correlates with basal Raf activity, with more active Raf being more susceptible to inhibition. We further show that DFG-out-stabilizing inhibitors disrupt high-affinity Raf-Mek interactions, promoting the formation of inhibited Raf dimers. Furthermore, we identify cobimetinib as a Mek inhibitor that uniquely sensitizes Raf to DFG-out inhibitors by disrupting autoinhibited Raf-Mek complexes. Building on this insight, we developed cobimetinib analogs with enhanced sensitization properties. Our findings provide a mechanistic framework for understanding the cellular determinants of DFG-out-stabilizing inhibitor sensitivity and offer strategies for optimizing synergistic Raf-Mek inhibitor combinations.

cell biology↗

bioRxiv2024

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes.

bioinformatics↗

bioRxiv2024

An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish

The larval zebrafish is a vertebrate model for in vivo monitoring and manipulation of whole-brain neuronal activity. Tracing its neural circuits remains challenging. Here, we report an applicable methodology tailored for larval zebrafish to achieve efficient retrograde trans-monosynaptic tracing from genetically defined neurons via EnvA-pseudotyped glycoprotein-deleted rabies viruses. By combinatorially optimizing multiple factors involved, we identified the CVS strain trans-complemented with advanced expression of N2cG at 36 {degrees}C as the optimal combination. It yielded a tracing efficiency of up to 20 inputs per starter cell. Its low cytotoxicity enabled the viable labeling and calcium imaging of infected neurons 10 days post-infection, spanning larval ages commonly used for functional examination. Cre-dependent labeling was further developed to enable cell-type-specific input tracing and circuit reconstruction. We mapped cerebellar circuits and uncovered the ipsilateral preference and subtype specificity of granule cell-to-Purkinje cell connections. Our method offers an efficient way for tracing neural circuits in larval zebrafish.

neuroscience↗

bioRxiv2024

Spatial Transcriptomics Prediction from Histology Images at Single-cell Resolution using RedeHist

Spatial transcriptomics (ST) offers substantial promise in elucidating the tissue architecture of biological systems. However, its utility is frequently hindered by constraints such as high costs, time-intensive procedures, and incomplete gene readout. Here we introduce RedeHist, a novel deep learning approach integrating scRNA-seq data to predict ST from histology images at single-cell resolution. Application of RedeHist to both sequencing-based and imaging-based ST data demonstrated its outperformance in high-resolution and accurate prediction, whole-transcriptome gene imputation, and fine-grained cell annotation compared with the state-of-the-art algorithms.

bioinformatics↗

bioRxiv2024

The comparison of single-cell RNA sequencing platforms based droplets

Single-cell sequencing enables to reveal cellular heterogeneity and discover new cellular subpopulations. In terms of the strategy of single-cell sequencing, the main methods are based with combinatorial index, microwell and microfluidic. Due to the simplicity, methods based droplets are widely used for single-cell sequencing for multi-omics. Therefore, in order to facilitate researchers to choose a suitable platform to meet their application scenarios, we compared several commercial platforms: the Chromium X platform of 10x Genomics, the MobiNova-100 platform of MobiDrop, the SeekOne platform of SeekGene, and the C4 platform of BGI. Based the comprehensive assessment of the data analysis, the Chromium X platform shows a excellent performance, closely followed by MobiNova-100 platform. One-Sentence SummaryAs droplet-based single-cell sequencing platforms, Chromium X and MobiNova-100 have comparable data performance.

cell biology↗

bioRxiv2024

Mitochondrial DNA and 641kb nuclear-mitochondrial DNA in Arabidopsis can be separated by their CpG methylation levels

Methylation on the cytosine in plant mitochondrial DNA has been a controversial issue. Results supporting mitochondrial DNA methylation may have been subject to contamination due to the presence of the nuclear sequence originating from the mitochondrial genome called NUMT (nuclear mitochondrial DNA insertions). Especially in Arabidopsis thaliana Columbia 0, the largest NUMT located on chromosome 2 is nearly twice the size of the entire mitochondrial genome and almost identical. In the presence of such high similarity, it is challenging to eliminate interference in the determination of mitochondrial DNA methylation levels. Here we applied MBD (methyl-CpG binding domain) protein-based affinity assay to separate total DNA, and applied next generation sequencing to the pre- and post-separation DNA samples, and checked their SNP sites. The results revealed successful separation of methylated and non-methylated DNA within the total DNA, with separation achieved between NUMT DNA and mitochondrial DNA. The result suggests that our method can achieve separation based on the differential methylation levels of the whole lengths of NUMT and mitochondrial DNAs, and that mitochondrial DNA barely exhibits CpG methylation, at least in the Columbia 0.

plant biology↗

bioRxiv2024

Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling

The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80s ATPase activity to nucleosome movement. Our investigation reveals that the grappler domain of Arp5 interacts with the acidic pocket of nucleosomes through two distinct mechanisms: an arginine anchor or a hydrophobic/acidic patch. These two modes of binding serve distinct functions within INO80 as shown in vivo by mutations in these regions resulting in varying phenotypes and in vitro by diverse effects on nucleosome mobilization. Our findings suggest that the hydrophobic/acidic patch of Arp5 is likely important for dimer exchange by INO80, while the arginine anchor is crucial for mobilizing nucleosomes.

biochemistry↗

bioRxiv2024

Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability

MotivationUnderstanding single-cell expression variability (scEV) or gene expression noise among cells of the same type and state is crucial for delineating population-level cellular function. While epigenetic mechanisms are widely implicated in gene expression regulation, a definitive link between chromatin accessibility and scEV remains elusive. Advances in single-cell techniques now enable simultaneous measurement of scATAC-seq and scRNA-seq within individual cells, presenting an unprecedented opportunity to address this gap. ResultsThis paper introduces an innovative testing pipeline to investigate the association between chromatin accessibility and scEV. The pipeline hinges on comparing the prediction performance of scATAC-seq data on gene expression levels between highly variable genes (HVGs) and non-highly variable genes (non-HVGs). Applying this pipeline to paired scATAC-seq and scRNA-seq data from human hematopoietic stem and progenitor cells, we observed a significantly superior prediction performance of scATAC-seq data for HVGs compared to non-HVGs. Notably, there was substantial overlap between well-predicted genes and HVGs. The gene pathways enriched from well-predicted genes are highly pertinent to cell type-specific functions. Our findings support the notion that scEV largely stems from cell-to-cell variability in chromatin accessibility, providing compelling evidence for the epigenetic regulation of scEV and offering promising avenues for investigating gene regulation mechanisms at the single-cell level. Availability and implementationThe source code and data used in this paper can be found at https://github.com/SiweiCui/EpigeneticControlOfSingle-CellExpressionVariability.

bioinformatics↗

bioRxiv2024

Mutation of GmDMP genes triggers haploid induction in soybean

The development of homozygous lines is a key step in plant breeding and production. Generally, homozygous lines can be obtained through traditional time-consuming way of several generations selfing or through a way of doubled haploid (DH) technology, which has obvious advantages to accelerate breeding. However, no effective haploid production system so far has been established in soybean. Here we show that mutations of the soybean GmDMP1 and GmDMP2 genes can be used to induce haploid with an average haploid induction rate of 0.61%. We also found that 22.9% of soybean haploids can produce seeds through spontaneous chromosome doubling. Those findings laid a solid foundation for establishing DH technology in soybean, which will accelerate soybean breeding.

genetics↗

bioRxiv2024

Light-gated Integrator for Highlighting Kinase Activity in Living Cells

Protein kinases are key signaling nodes that regulate fundamental biological and disease processes. Illuminating kinase signaling from multiple angles can provide deeper insights into disease mechanisms and improve therapeutic targeting. While fluorescent biosensors are powerful tools for visualizing live-cell kinase activity dynamics in real time, new molecular tools are needed that enable recording of transient signaling activities for post hoc analysis and targeted manipulation. Here, we develop a light-gated kinase activity coupled transcriptional integrator (KINACT) that converts dynamic kinase signals into "permanent" fluorescent marks. KINACT enables robust monitoring of kinase activity across scales, accurately recording subcellular PKA activity, highlighting PKA signaling heterogeneity in 3D cultures, and identifying PKA activators and inhibitors in high-throughput screens. We further leverage the ability of KINACT to drive signaling effector expression to allow feedback manipulation of the balance of GsR201C-induced PKA and ERK activation and dissect the mechanisms of oncogenic G protein signaling.

bioengineering↗

bioRxiv2024

Soil viruses reduce greenhouse gas emissions and promote microbial necromass accrual

Viral-induced microbial mortality has been proposed as a major contributor in shaping microbial community structure and function, soil carbon (C) accrual and mobilization of plant available nutrients. Yet, how soil viruses influence soil organic C (SOC) turnover and sequestration remains unknown. Here, we performed microcosm experiments with two distinct soils from grassland (GL) and agricultural (AG) sites and interrogated the roles of soil viruses in driving microbial community succession, SOC transformation and sequestration. The results show that soil viruses affected microbial C use efficiency and reduced respiration in microbial communities obtained from both GL and AG soils. Soil viruses affected microbial successional trajectories (via predation of dominant populations) and functional gene profiles triggering a significant decrease in CO2 and N2O emissions. The impact of soil viruses on microbial community composition in GL microcosms was much less pronounced compared with that in AG microcosms, suggesting contrasting virus-host interaction patterns under different environmental settings. Viral infection significantly enhanced microbial necromass accumulation thereby increasing SOC and total nitrogen (TN) content. The results implicate viral-mediated microbial mortality as a key factor influencing the distribution of C between mineralization and soil C storage pathways. We proposed "viral loop" to explain the crucial function of soil viruses in SOC turnover and sequestration.

ecology↗

bioRxiv2024

Protocatechuic acid induces endogenous oxidative stress in CR-hvKP by regulating the EMP-PPP pathway

BackgroundKlebsiella pneumoniae is an important opportunistic pathogen and zoonotic pathogen. The widespread use of antibiotics has led to the emergence of a large number of multidrug-resistant Klebsiella pneumoniae in clinical animal husbandry, posing a serious threat to global health security. Protocatechuic acid (PCA) is a phenolic acid substance naturally present in many vegetables and fruits. It is a safe and highly developed new type of antibacterial synergist. PurposeThis study explored the antibacterial and synergistic mechanisms of PCA against Carbapenem-resistant hypervirulent Klebsiella pneumoniae. Study designMetabolomic analysis using PCA to investigate the metabolic effects of CR-hvKP and further explore the antibacterial mechanisms resulting from this metabolic regulation. MethodsThe MIC of PCA was measured by microdilution, and its bactericidal effect was observed by DAPI staining. Resistance and hemolysis tests were performed to ensure safety. The synergy of PCA and meropenem was tested by checkerboard assay. The biofilm inhibition was assessed by crystal violet and EPS assays. The membrane morphology, permeability, and potential were examined by SEM, PI, NPN, and DiSC3(5). The metabolic changes were evaluated by AlamarBlue, metabolomics, enzyme activity, ELISA, molecular docking, and qRT-PCR. The oxidative stress and metabolic disorders were verified by NADP(H), ROS, MDA, and ATP assays. ResultsThe results showed that PCA can synergize with antibiotics and inhibit the biofilm and membrane functions of CR-hvKP at low concentrations. Metabolomics revealed that PCA affects the EMP and PPP pathways of CR-hvKP, causing oxidative stress. This involves the binding of PGAM and the downregulation of BPGM, leading to the accumulation of glycerate-3P. This results in the inhibition of G6PDH and the imbalance of NADPH/NADP+, disrupting the energy metabolism and increasing the oxidative stress, which impair the biofilm and membrane functions and enhance the antibiotic efficacy. ConclusionThe results demonstrate that PCA regulates the EMP-linked PPP pathway of CR-hvKP, inhibits biofilm and membrane functions, and synergizes with antibiotics to kill bacteria, providing new insights and candidates for natural antibacterial enhancers. Author SummaryKlebsiella pneumoniae is a common pathogenic bacterium that can infect both humans and animals, causing serious diseases such as pneumonia, meningitis, and sepsis. Due to the overuse of antibiotics, this bacterium has developed resistance to many drugs, posing a significant threat to global health security. Through our research, we have discovered a natural substance called protocatechuic acid (PCA) that can enhance the effectiveness of antibiotics against this bacterium. PCA is found in many vegetables and fruits and is a safe and non-toxic antibacterial adjuvant. Our analysis of the metabolomics of PCA on Klebsiella pneumoniae has revealed its antibacterial and synergistic mechanisms. The study found that PCA can affect the bacteriums sugar metabolism pathway, leading to the generation of endogenous oxidative stress. This disrupts their energy metabolism, damages their cell membranes and biofilms, making them more susceptible to being killed by antibiotics. Through this mechanism, PCA can synergize with common antibiotics such as meropenem, enhancing their bactericidal ability. Our research has demonstrated that PCA is an effective antibacterial adjuvant, providing new candidates and insights for the development of natural antibacterial agents. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/583678v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@2e2963org.highwire.dtl.DTLVardef@9f3c51org.highwire.dtl.DTLVardef@3125a8org.highwire.dtl.DTLVardef@9f39b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗