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Biology subjects

Zhou, X.

Publications and source records attributed to Zhou, X..

At least 559 records · Page 31Linked to original sources

Development of a mini-replicon-based reverse-genetics system for rice stripe tenuivirus

Negative-stranded RNA (NSR) viruses include both animal- and plant-infecting viruses that often cause serious diseases in human and livestock, and in agronomic crops. Rice stripe tenuivirus (RSV), a plant NSR virus with four negative-stranded/ambisense RNA segments, is one of the most destructive rice pathogens in many Asian countries. Due to the lack of a reliable reverse-genetics technology, molecular studies of RSV gene functions and its interaction with host plants are severely hampered. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV gene functional analysis in Nicotiana benthamiana. We first developed a mini-replicon system expressing RSV genomic RNA3 eGFP reporter (MR3(-)eGFP), a nucleocapsid (NP), and a codon usage optimized RNA-dependent RNA polymerase (RdRpopt), respectively. Using this mini-replicon system we determined that RSV NP and RdRpopt are indispensable for the eGFP expression from MR3(-)eGFP. The expression of eGFP from MR3(-)eGFP can be significantly enhanced in the presence of NSs and P19-HcPro-{gamma}b. In addition, NSvc4, the movement protein of RSV, facilitated eGFP trafficking between cells. We also developed an antigenomic RNA3-based replicon in N. benthamiana. However, we found that the RSV NS3 coding sequence acts as a cis-element to regulate viral RNA expression. Finally, we made mini-replicons representing all four RSV genomic RNAs. This is the first mini-replicon-based reverse-genetics system for monocot-infecting tenuivirus. We believe that this mini-replicon system described here will allow the studies of RSV replication, transcription, cell-to-cell movement and host machinery underpinning RSV infection in plants. IMPORTANCEPlant-infecting segmented negative-stranded RNA (NSR) viruses are grouped into 3 genera: Orthotospovirus, Tenuivirus and Emaravirus. The reverse-genetics systems have been established for members in the genera Orthotospovirus and Emaravirus, respectively. However, there is still no reverse-genetics system available for Tenuivirus. Rice stripe virus (RSV) is a monocot-infecting tenuivirus with four negative-stranded/ambisense RNA segments. It is one of the most destructive rice pathogens and causes significant damages to rice industry in Asian countries. Due to the lack of a reliable reverse-genetics system, molecular characterizations of RSV gene functions and the host machinery underpinning RSV infection in plants are extremely difficult. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV in Nicotiana benthamiana. This is the first mini-replicon-based reverse-genetics system for tenuivirus. We consider that this system will provide researchers a new working platform to elucidate the molecular mechanisms dictating segmented tenuivirus infections in plant.

pathology↗

mTORC2 contributes to murine lupus

The development of many systemic autoimmune diseases, including systemic lupus erythematosus, is associated with overactivation of the type I interferon (IFN) pathway, lymphopenia, and increased follicular helper T (Tfh) cell differentiation. However, the cellular and molecular mechanisms underlying these immunological perturbations remain incompletely understood. Here we show that the mechanistic target of rapamycin complex 2 (mTORC2) promotes Tfh differentiation and disrupts Treg homeostasis. Inactivation of mTORC2 in total T cells, but not in Tregs, greatly ameliorated the immunopathology in a systemic autoimmunity mouse model. This was associated with reduced Tfh differentiation, B cell activation, and reduced T cell glucose metabolism. Finally, we show that type I IFN can synergize with TCR ligation to activate mTORC2 in T cells, which partially contributes to T cell lymphopenia. These data indicate that mTORC2 may act as downstream of type I IFN, TCR, and costimulatory receptor ICOS, to promote glucose metabolism, Tfh differentiation, and T cell lymphopenia, but not to suppress Treg function in systemic autoimmunity. Our results suggest that mTORC2 might be a rational target for systemic autoimmunity treatment.

immunology↗

Autism_genepheno: Text mining of gene-phenotypeassociations reveals new phenotypic profiles ofautism-associated genes

Autism is a spectrum disorder with wide variation in type and severity of symptoms. Understanding gene-phenotype associations is vital to unravel the disease mechanisms and advance its diagnosis and treatment. To date, several databases have stored a large portion of gene-phenotype associations which are mainly obtained from genetic experiments. However, a large proportion of gene-phenotype associations are still buried in the autism-related literature and there are limited resources to investigate autism-associated gene-phenotype associations. Given the abundance of the autism-related literature, we were thus motivated to develop Autism_genepheno, a text mining pipeline to identify sentence-level mentions of autism-associated genes and phenotypes in literature through natural language processing methods. We have generated a comprehensive database of gene-phenotype associations in the last five years autism-related literature that can be easily updated as new literature becomes available. We have evaluated our pipeline through several different approaches, and we are able to rank and select top autism-associated genes through their unique and wide spectrum of phenotypic profiles, which could provide a unique resource for the diagnosis and treatment of autism. The data resources and the Autism_genpheno pipeline are available at: https://github.com/maiziezhoulab/Autism_genepheno.

bioinformatics↗

Collagen density defines 3D migration of CTLs and their consequent cytotoxicity against tumor cells

Solid tumors are often characterized by condensed extracellular matrix (ECM). The impact of dense ECM on cytotoxic T lymphocytes (CTL) function is not fully understood. Here, we report that CTL-mediated cytotoxicity is substantially impaired in dense collagen matrices. Although the intrinsic killing machinery including expression of cytotoxic proteins and degranulation was intact, CTL motility was substantially compromised in dense collagen. We found that for 3D CTL migration, persistence and velocity was regulated by collagen stiffness and the porosity, respectively. Interestingly, 3D CTL velocity is strongly correlated with their nuclear deformability/flexibility during migration, which is regulated by the microtubule network. Moreover, CTL migration was completely abolished by inhibition of actin polymerization and or myosin IIA. Remarkably, disruption of the microtubule-networks significantly improves the impaired migration, search efficiency, and cytotoxicity of CTLs in dense collagen. Our work suggests the microtubule network as a promising target to rescue impaired CTL killing capacity in solid tumor related scenarios.

immunology↗

Location, location, location- choice of Voxel-Based Morphometry processing pipeline drives variability in the location of neuroanatomical brain markers

Fundamental and clinical neuroscience has benefited from the development of automated computational analyses of Magnetic Resonance Imaging (MRI) data, such as Voxel-based Morphometry (VBM). VBM determines regional gray matter variations with high spatial resolution and results are commonly interpreted in a regional-specific manner, for instance with respect to which specific brain regions differ in volume between women and men. In excess of 600 papers using VBM are now published every year and a number of different automated VBM processing pipelines are frequently used in analyses although it remains to be fully and systematically assessed whether they come up with the same answers. Here we have therefore examined variability between four commonly used VBM pipelines in two large brain structural datasets. Spatial similarity, reproducibility and reliability of the processed gray matter brain maps was generally low between pipelines. Examination of sex-differences and age-related changes in gray matter volumes revealed considerable differences between the pipelines in terms of the specific regions identified as well as meta-analytic characterization of their function. In contrast, applying machine learning-based multivariate analyses allowed an accurate prediction of sex or age based on the gray matter maps across pipelines, although prediction accuracy differed strongly between them. Together the findings suggest that the choice of pipeline alone leads to considerable variability in brain structural analyses which poses a serious challenge for reproducibility as well as interpretation.

neuroscience↗

A H3K9me2-Binding Protein AGDP3 Limits DNA Methylation and Transcriptional Gene Silencing in Arabidopsis

DNA methylation is critical for tuning gene expression to prevent potentially deleterious gene-silencing. The Arabidopsis DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic loci. However, the mechanism recruiting ROS1 to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor required for ROS1-mediated DNA demethylation, and targets ROS1 to specific loci. We found that AGDP3 could bind to the H3K9me2 mark by its AGD12 cassette. The crystal structure of the AGDP3 AGD12 in complex with an H3K9me2 peptide reveals the molecular basis for the specific recognition, that the dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. Interestingly, a histidine residue located in the methylysine binding aromatic cage enables AGDP3 pH-dependent H3K9me2 binding capacity. Considering the intracellular pH correlates with the histone acetylation status, our results provide the molecular mechanism for the regulation of ROS1 DNA demethylase by the gene silencing H3K9me2 mark and the potential crosstalk with active histone acetylation mark.

plant biology↗

Geminiviral genomes encode additional proteins with specific subcellular localizations and virulence function

Geminiviruses are plant viruses with limited coding capacity. Geminivirus-encoded proteins were identified applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the reconsideration of this criterion. Here, we show that geminiviral genomes contain additional ORFs. Using tomato yellow leaf curl virus, we demonstrate that some of these novel ORFs are expressed during the infection, and that the encoded proteins display specific subcellular localizations. We prove that the largest of these new ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor. These results imply that the repertoire of geminiviral proteins can be expanded, and that getting a comprehensive overview of the molecular plant-geminivirus interactions will require the detailed study of small ORFs so far neglected.

plant biology↗

Host-derived Reactive Nitrogen Species mediate the Cryptococcus neoformans yeast-to-titan switch via fungal-derived superoxide

In the host lung, the human fungal pathogen Cryptococcus neoformans undergoes a morphological switch from small haploid yeast to large polyploid titan cell, contributing to C. neoformans virulence. Titan cells are less readily phagocytosed and can survive host nitrosative and oxidative stresses. We and others previously showed that titanization is triggered by host-relevant signals including CO2 and lung-resident bacteria, and addition of these factor is sufficient to induce titan cells in vitro. Here we investigate the molecular mechanisms that drive this transition and demonstrate that host-derived immune signals can increase the degree and frequency of titanization. Specifically, host-relevant reactive nitrogen species increase the accumulation of endogenous superoxide within cryptococcal cells, particularly within nuclei, where it can cause genotoxic stress. Consistent with this, we observe the accumulation of Rad51 protein, a marker of the double strand break repair pathway, in titanizing cultures. Blocking superoxide accumulation inhibits titanization, yet titanization also requires superoxide detoxification through Superoxide Dismutase (SOD) activity. Loss of mitochondrial Sod2 activity locks cells in the yeast phase, while Sod1 is required for the production of viable titan daughter cells. We hypothesize that the redox responsive transcription factor Yap1 in part mediates this response by regulating SOD2/SOD1. In addition, we show that Sod1 translocates to the nucleus, where it is likely involved in the detoxification of genotoxic superoxide. Together, these findings reveal a major new regulatory mechanism for the yeast-to-titan transition. Author SummaryDuring fungal infection, host phagocytes produce reactive oxygen and nitrogen species (ROS/RNS), major determinants of infection outcome. Fungal pathogens have developed numerous strategies to neutralize and detoxify ROS, but RNS remain important effectors for infection control. In the lung, the human fungal pathogen Cryptococcus neoformans can undergo a morphological switch from small haploid yeast to large highly polyploid titan cells with increased ROS/RNS stress resistance, and the capacity to produce haploid or aneuploid daughters. Here, we report that RNS are a major signal driving the frequency and degree of titanization and act by increasing endogenous ROS within the fungus. We show that the accumulation of endogenous ROS is required for the yeast-to-titan transition, and is associated with increased genotoxic stress leading to polyploidy. Yet, failure to detoxify this ROS, either in mutants defective in Superoxide Dismutase activity or the oxidative stress response protein Yap1, impairs titan cell budding and reduces progeny viability. Therefore, the interface of exogenous RNS and endogenous ROS regulation during host-pathogen interaction represents an Achilles heel for this major human fungal pathogen.

microbiology↗

Single-cell analysis identifies a key role for Hhip in murine coronal suture development

Craniofacial development depends on proper formation and maintenance of sutures between adjacent bones of the skull. In sutures, bone growth occurs at the edge of each bone, and suture mesenchyme maintains the separation between them. We performed single-cell RNA-seq analyses of the embryonic, murine coronal suture. Analyzing replicate libraries at E16.5 and E18.5, we identified 14 cell populations. Seven populations at E16.5 and nine at E18.5 comprised the suture mesenchyme, osteogenic cells, and associated populations. Through an integrated analysis with bulk RNA-seq data, we found a distinct coronal suture mesenchyme population compared to other neurocranial sutures, marked by expression of Hhip, an inhibitor of hedgehog signaling. We found that at E18.5, Hhip-/- coronal osteogenic fronts are closely apposed and suture mesenchyme is depleted, demonstrating that Hhip is required for coronal suture development. Our transcriptomic approach provides a rich resource for insight into normal and abnormal development.

developmental biology↗

Differences in gait stability, trunk and foot accelerations between healthy young and older women

Our aim was to evaluate differences in gait acceleration intensity, variability and stability of feet and trunk between older females and young females using inertial sensors. Twenty older females (OF; mean age 68.4, SD 4.1 years) and eighteen young females (YF; mean age 22.3, SD 1.7 years) were asked to walk straight for 100 meters at their preferred speed, while wearing inertial sensors on heels and lower back. We calculated spatiotemporal measures, foot and trunk acceleration characteristics and their variability, as well as trunk stability using the local divergence exponent (LDE). Two-way analysis of variance (including the factors foot and age), Students t-test, and Mann-Whitney U test were used to compare statistical differences of measures between groups. Cohens d effects were calculated for each variable. Foot maximum vertical acceleration and amplitude, trunk-foot vertical acceleration attenuation, as well as their variability were significantly smaller in OF than in YF. In contrast, trunk mediolateral acceleration amplitude, maximum vertical acceleration, and amplitude, as well as their variability were significantly larger in OF than in YF. Moreover, OF showed lower stability (i.e., higher LDE values) in mediolateral acceleration, mediolateral and vertical angular velocity of the trunk. Even though we measured healthy older females, these participants showed lower vertical foot accelerations with higher vertical trunk acceleration, lower trunk-foot vertical acceleration attenuation, less gait stability, and more variability of the trunk, and hence, were more likely to fall. These findings suggest that instrumented gait measurements may help for early detection of changes or impairments in gait performance, even before this can be observed by clinical eye or gait speed.

bioengineering↗

Single-cell sequencing characterizes intratumoral profile of immune cells in old mice

It has long been thought that aging is a major risk factor for cancer incidence. However, accumulating evidence indicates increased resistance of old animals to tumor growth. A systematic understanding of how old individuals defend against tumor invasion is currently lacking. Here we investigated the differences of age-associated alterations in tumor-infiltrating immune cells between young and old mice using single-cell RNA analysis. Our results showed that a higher proportion of cytotoxic CD8+ T cells, nTregs, cDC, and M1-type macrophages, while a higher percentage of exhausted CD8+ T cells, iTregs, pDC, and M2-type macrophages were found in young mice. Importantly, TCR diversity analysis showed top 10 TCR clones consisted primarily of exhausted CD8+ T cells in young mice whereas tip clones were predominantly cytotoxic CD8+ T cells in old mice. Consistently, trajectory inference demonstrated that CD8+ T cells preferentially differentiated into cytotoxic cells in old mice in contrast to exhausted cells in young mice. Meanwhile, we confirmed the main distinctions between young and old mice by flow cytometry. Collectively, our data revealed that a significantly higher proportion of effector immune cells in old mice defend against tumor progression, providing a framework for the immunotherapy of elderly patients with tumors.

immunology↗

Bfimpute: A Bayesian factorization method to recover single-cell RNA sequencing data

Single-cell RNA-seq (scRNA-seq) offers opportunities to study gene expression of tens of thousands of single cells simultaneously, to investigate cell-to-cell variation, and to reconstruct cell-type-specific gene regulatory networks. Recovering dropout events in a sparse gene expression matrix for scRNA-seq data is a long-standing matrix completion problem. We introduce Bfimpute, a Bayesian factorization imputation algorithm that reconstructs two latent gene and cell matrices to impute final gene expression matrix within each cell group, with or without the aid of cell type labels or bulk data. Bfimpute achieves better accuracy than other six publicly notable scRNA-seq imputation methods on simulated and real scRNA-seq data, as measured by several different evaluation metrics. Bfimpute can also flexibly integrate any gene or cell related information that users provide to increase the performance. Availability: Bfimpute is implemented in R and is freely available at https://github.com/maiziezhoulab/Bfimpute.

bioinformatics↗

DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing is used to capture cell-specific gene expression, thus allowing reconstruction of gene regulatory networks. The existing algorithms struggle to deal with dropouts and cellular heterogeneity, and commonly require pseudotime-ordered cells. Here, we describe DeepDRIM a supervised deep neural network that represents gene pair joint expression as images and considers the neighborhood context to eliminate the transitive interactions. Deep-DRIM yields significantly better performance than the other nine algorithms used on the eight cell lines tested, and can be used to successfully discriminate key functional modules between patients with mild and severe symptoms of coronavirus disease 2019 (COVID-19).

bioinformatics↗

MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction

MotivationThe mathematically optimal solution in computational protein folding simulations does not always correspond to the native structure, due to the imperfection of the energy force fields. There is therefore a need to search for more diverse suboptimal solutions in order to identify the states close to the native. We propose a novel multimodal optimization protocol to improve the conformation sampling efficiency and modeling accuracy of de novo protein structure folding simulations. ResultsA distance-assisted multimodal optimization sampling algorithm, MMpred, is proposed for de novo protein structure prediction. The protocol consists of three stages: The first is a modal exploration stage, in which a structural similarity evaluation model DMscore is designed to control the diversity of conformations, generating a population of diverse structures in different low-energy basins. The second is a modal maintaining stage, where an adaptive clustering algorithm MNDcluster is proposed to divide the populations and merge the modal by adjusting the annealing temperature to locate the promising basins. In the last stage of modal exploitation, a greedy search strategy is used to accelerate the convergence of the modal. Distance constraint information is used to construct the conformation scoring model to guide sampling. MMpred is tested on a large set of 320 non-redundant proteins, where MMpred obtains models with TM-score[≥]0.5 on 268 cases, which is 20.3% higher than that of Rosetta guided with the same set of distance constraints. The results showed that MMpred can help significantly improve the model accuracy of protein assembly simulations through the sampling of multiple promising energy basins with enhanced structural diversity. AvailabilityThe source code and executable versions are freely available at https://github.com/iobio-zjut/MMpred. Contactzgj@zjut.edu.cn or zhng@umich.edu or sujz@wmu.edu.cn

bioinformatics↗

scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species

MotivationIn single cell analyses, cell types are conventionally identified based on known marker gene expressions. Such approaches are time-consuming and irreproducible. Therefore, many new supervised methods have been developed to identify cell types for target datasets using the rapid accumulation of public datasets. However, these approaches are sensitive to batch effects or biological variations since the data distributions are different in cross-platforms or species predictions. ResultsWe developed scAdapt, a virtual adversarial domain adaptation network to transfer cell labels between datasets with batch effects. scAdapt used both the labeled source and unlabeled target data to train an enhanced classifier, and aligned the labeled source centroid and pseudo-labeled target centroid to generate a joint embedding. We demonstrate that scAdapt outperforms existing methods for classification in simulated, cross-platforms, cross-species, and spatial transcriptomic datasets. Further quantitative evaluations and visualizations for the aligned embeddings confirm the superiority in cell mixing and preserving discriminative cluster structure present in the original datasets. Availabilityhttps://github.com/zhoux85/scAdapt. Contactangyd25@mail.sysu.edu.cn or luojinx5@mail.sysu.edu.cn

bioinformatics↗

Dependency of LKB1-inactivated lung cancer on aberrant CRTC-CREB activation

Lung cancer with loss-of-function of the LKB1 tumor suppressor is a common aggressive subgroup with no effective therapies. LKB1-deficiency induces constitutive activation of cAMP/CREB-mediated transcription by a family of three CREB-regulated transcription coactivators (CRTC1-3). However, the significance and mechanism of CRTC activation in promoting the aggressive phenotype of LKB1-null cancer remain poorly characterized. Here we observed overlapping CRTC expression patterns and mild growth phenotypes of individual CRTC-knockouts in lung cancer, suggesting functional redundancy of CRTC1-3. We consequently designed a dominant-negative mutant (dnCRTC) to block all three CRTCs to bind and co-activate CREB. Expression of dnCRTC efficiently inhibited the aberrantly activated cAMP/CREB-mediated oncogenic transcriptional program induced by LKB1-deficiency, and specifically blocked the growth of LKB1-inactivated lung cancer. Collectively, this study provides direct proof for an essential role of the CRTC-CREB activation in promoting the malignant phenotypes of LKB1-null lung cancer and proposes the CRTC-CREB interaction interface as a novel therapeutic target.

cancer biology↗

ATAC-seq reveals megabase-scale domains of a bacterial nucleoid

Here we adapted ATAC-seq to probe chromosome accessibility of bacterial cells. We found that the chromosome of Caulobacter crescentus is composed of eight differentially compacted regions we name Chromosomal Accessibility Domains (CADs). This domain structure is depended on the cell cycle stage, DNA gyrase activity, and the nucleoid-associated protein (NAP) GapR, but not on the function of SMC. We show the chromosome is punctuated by four highly transposase-inaccessible transcribed regions (HINTs). The HINTs include Caulobacters ribosomal RNA clusters and its largest ribosomal protein gene cluster. Further, we show that HINTs are also formed by rDNA in E. coli and provide evidence that their high levels of transcription do not strictly govern their formation. Overall, this work argues that physical forces, including those created by the activities of DNA gyrase and specific NAPs, significantly contribute to bacterial nucleoid structure at the megabase scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/426053v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@2b9812org.highwire.dtl.DTLVardef@cd430org.highwire.dtl.DTLVardef@3ed5cforg.highwire.dtl.DTLVardef@1471dad_HPS_FORMAT_FIGEXP M_FIG C_FIG SignificanceIn bacteria, chromosomal DNA is highly compacted and organized. Many forces contribute to bacterial DNA compaction, including the transcription, DNA replication, and the activities of topoisomerases and nucleoid-associated proteins. At the megabase scale, the resulting chromosome structure is important for coordinating cell cycle events; for example, in E. coli the improper structuring of a Mb-scale nucleoid domain leads to errors in the fidelity of chromosome segregation. It was previously unknown whether Mb-scale regions of a bacterial chromosome could be differentially compacted, and which factors might contribute to this spatial variation in compaction. Our work provides a novel method for measuring global chromosome compaction in bacteria. By applying this method in the bacterium Caulobacter crescentus, we show that the Caulobacter nucleoids compaction varies between megabase-scale domains. We also show that DNA gyrase and the nucleoid-associated protein GapR are key players in shaping the uneven compaction of the chromosome.

microbiology↗

T cell stiffness is enhanced upon formation of immunological synapse

T cells are activated by cognate target cells via an intimate contact, termed immunological synapse (IS). Cellular mechanical properties, especially stiffness, are essential to regulate cell functions, T cell stiffness at a subcellular level at the IS still remains largely elusive. In this work, we established an atomic force microscopy (AFM)-based elasticity mapping method on whole T cells to obtain an overview of the stiffness with a resolution of ~ 60 nm. Using Jurkat T-cells and primary human CD4+ T cells, we show that in the T cells in contact with functionalized surfaces, the lamellipodia are stiffer than the cell body. Upon IS formation, T cell stiffness is substantially enhanced both at the lamellipodia and in cell body. Chelation of intracellular Ca2+ abolishes IS-induced stiffening at the lamellipodia but has no influence on cell body-stiffening, suggesting different regulatory mechanism of IS-induced stiffening between the lamellipodia and the cell body.

biophysics↗