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Cheng, G.

Publications and source records attributed to Cheng, G..

49 records · Page 3Linked to original sources

UBXN3B Restricts Viral Pathogenesis by Maintaining Hematopoietic Homeostasis

Hematopoiesis is finely regulated to enable timely production of the right numbers and types of mature immune cells to maintain tissue homeostasis. Dysregulated hematopoiesis may compromise antiviral immunity and/or exacerbate immunopathogenesis. Herein, we report an essential role of UBXN3B in maintenance of hematopoietic homeostasis and restriction of immunopathogenesis during respiratory viral infection. Ubxn3b deficient (Ubxn3b-/-) mice are highly vulnerable to SARS-CoV-2 and influenza A infection, characterized by more severe lung immunopathology, lower virus-specific IgG, significantly fewer B cells, but more myeloid cells than Ubxn3b+/+ littermates. This aberrant immune compartmentalization is recapitulated in uninfected Ubxn3b-/- mice. Mechanistically, UBXN3B controls precursor B-I (pre-BI) transition to pre-BII and subsequent proliferation in a cell-intrinsic manner, by maintaining BLNK protein stability and pre-BCR signaling. These results reveal an essential role of UBXN3B for the early stage of B cell development.

immunology↗

Germline DNA replication shapes the recombination landscape in mammals

SummaryGenetic recombination generates novel trait combinations and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots, however megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns, therefore we devised a novel approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis and a distinctive replication pattern in human males underlies the sub-telomeric increase in recombination. We detected a robust correlation between replication and both contemporary and ancestral recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have far-reaching implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.

genomics↗

Dynein/Sunday driver mediate disorders of dynamic profiles of Golgi outposts induced by amyloid precursor protein

Golgi defects including Golgi fragmentation are pathological features of Alzheimer disease (AD). As a pathogenic factor of AD, amyloid precursor protein (APP) induces Golgi fragmentation in soma. However, how APP regulates Golgi outposts (GOs) in dendrites remains unclear. Given that APP resided and affected GOs movements, especially reversed the distribution of multi-compartment GOs (mcGOs), we investigated the regulatory mechanism of mcGOs movements in Drosophila larvae. Knockdown experiments showed the bidirectional mcGOs movements were cooperatively controlled by dynein heavy chain (Dhc) and kinesin heavy chain subunits. Notably, only Dhc mediated APPs regulation on mcGOs movements. Further, by loss-of-function screening, the adaptor protein Sunday driver (Syd) was identified to mediate APP-induced alteration of the direction of mcGOs movements, and dendritic defects. Collectively, by elucidating a model of bidirectional mcGOs movements, we revealed the mechanism of APPs regulation on the direction of mcGOs movements. It provides new insights into AD pathogenesis.

neuroscience↗

Precise Localization and Dynamic Distribution of Japanese Encephalitis Virus in theBrain Nuclei of Infected Mice

Japanese encephalitis virus (JEV) is a pathogen that causes severe vector-borne zoonotic diseases, thereby posing a serious threat to human health. Although JEV is potentially neurotropic, its pathogenesis and distribution in the host have not been fully elucidated. In this study, an infected mouse model was established using a highly virulent P3 strain of JEV. Immunohistochemistry and in situ hybridization, combined with anatomical imaging of the mouse brain, were used to dynamically localize the virus and construct three-dimensional (3D) images. Consequently, onset of mild clinical symptoms occurred in some mice at 84h post JEV infection, while most mice displayed typical neurological symptoms at 144h post infection. Moreover, brain pathology revealed typical changes associated with non-suppurative encephalitis, which lasted up to 192h. The earliest detection of viral antigen was achieved at 72h post infection, in the thalamus and medulla oblongata. At 144h post infection, the positive viral antigen signals were mainly distributed in the cerebral cortex, olfactory area, basal ganglia, thalamus, and brainstem regions in mice. At 192h post infection, the antigen signals gradually decreased, and the localization of JEV tended to concentrate in the cerebrum and thalamus, while no viral antigen was detected in the brain at 504h post infection. In this model, the viral antigen was first expressed in the reticular thalamic nucleus (Rt), at a consistent concentration. The expression of the viral antigen in the hippocampal CA2 region, the anterior olfactory nucleus, and the deep mesencephalic nucleus was high and persistent. The 3D images showed that viral signals were mostly concentrated in the parietal cortex, occipital lobe, and hippocampus, near the mid-sagittal plane. In the early stages of infection in mice, a large number of viral antigens were detected in denatured and necrotic neurons, suggesting that JEV directly causes neuronal damage. From the time of its entry, JEV is widely distributed in the central nervous system thereby causing extensive damage.Author summary There are many theories regarding the mechanism of entry of the Japanese encephalitis virus (JEV) into the nervous system. The inflammation cascade effect, resulting from the virus entering the central nervous system (CNS), is a major cause of brain injury in JEV patients. In this study, we found that the earliest point at which viral antigen was detected in the brain tissues following peripheral infection of JEV was at 72h. The virus was located in the nerve nuclei of the thalamus and medulla oblongata and, subsequently, viral antigens were found in the anterior olfactory nucleus. At 96h post infection, the virus was extensively distributed in the brain tissue, and at 144h-192h the viral antigen was widely distributed and highly concentrated. The viral concentration detected in the ventromedial thalamic nucleus (VM), deep mesencephalic nucleus (DpMe), and motor trigeminal nucleus (Mo5) remained high throughout the experiment. The hypertrophic nerve nuclei of JEV include the early anterior olfactory (AO) nucleus and the late hippocampal CA2 region. In the early stages of viral infection (72-144h post infection), the changes in viral antigen concentration and mortality rate were consistent. It was hypothesized that this stage represents the activation of viral proliferation and brain inflammation.View Full Text

pathology↗

Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses

Viruses are the major aetiological agents of acute and chronic severe human diseases that place a tremendous burden on global public health and economy; however, for most viruses, effective prophylactics and therapeutics are lacking, in particular, broad-spectrum antiviral agents. Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). The CbAEs potently blocked viral infection in the extracellular milieu through their lipase activity. Mechanistic studies showed that this lipase activity directly disrupted the viral envelope structure, thus inactivating infectivity. A mutation of CbAE-1 in its lipase motif fully abrogated the virucidal ability. Furthermore, CbAE-2 presented low toxicity in vivo and in vitro, highlighting its potential as a broad-spectrum antiviral drug.

microbiology↗

Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy

Macrophage scavenger receptor 1 (MSR1) mediates the endocytosis of modified low-density lipoproteins and plays an important antiviral role. However, the molecular mechanism underlying MSR1 antiviral actions remains elusive. Herein, we report that MSR1 activates autophagy to restrict infection of Chikungunya virus (CHIKV), an arthritogenic alphavirus that causes acute and chronic crippling arthralgia. Msr1 expression was rapidly upregulated after CHIKV infection in mice. Msr1 knockout mice had elevated viral loads and increased susceptibility to CHIKV arthritis along with a normal type I IFN response. Induction of LC3 lipidation by CHIKV, a marker of autophagy, was reduced in Msr1-/- cells. Mechanistically, MSR1 interacted with ATG12 through its cytoplasmic tail and this interaction was enhanced by CHIKV nsP1 protein. MSR1 repressed CHIKV replication through ATG5-ATG12-ATG16L1 and this was dependent on the FIP200-and-WIPI2-binding domain, but not the WD40 domain of ATG16L1. Our results elucidate an antiviral role for MSR1 involving the autophagic function of ATG5-ATG12-ATG16L1.

microbiology↗

Mutations, Recombination and Insertion in the Evolution of 2019-nCoV

BackgroundThe 2019 novel coronavirus (2019-nCoV or SARS-CoV-2) has spread more rapidly than any other betacoronavirus including SARS-CoV and MERS-CoV. However, the mechanisms responsible for infection and molecular evolution of this virus remained unclear. MethodsWe collected and analyzed 120 genomic sequences of 2019-nCoV including 11 novel genomes from patients in China. Through comprehensive analysis of the available genome sequences of 2019-nCoV strains, we have tracked multiple inheritable SNPs and determined the evolution of 2019-nCoV relative to other coronaviruses. ResultsSystematic analysis of 120 genomic sequences of 2019-nCoV revealed co-circulation of two genetic subgroups with distinct SNPs markers, which can be used to trace the 2019-nCoV spreading pathways to different regions and countries. Although 2019-nCoV, human and bat SARS-CoV share high homologous in overall genome structures, they evolved into two distinct groups with different receptor entry specificities through potential recombination in the receptor binding regions. In addition, 2019-nCoV has a unique four amino acid insertion between S1 and S2 domains of the spike protein, which created a potential furin or TMPRSS2 cleavage site. ConclusionsOur studies provided comprehensive insights into the evolution and spread of the 2019-nCoV. Our results provided evidence suggesting that 2019-nCoV may increase its infectivity through the receptor binding domain recombination and a cleavage site insertion. One Sentence SummaryNovel 2019-nCoV sequences revealed the evolution and specificity of betacoronavirus with possible mechanisms of enhanced infectivity.

microbiology↗

Brain activation and connectivity in anorexia nervosa and body dysmorphic disorder when viewing bodies: relationships to clinical symptoms and perception of appearance

Anorexia nervosa (AN) and body dysmorphic disorder (BDD) are characterized by distorted perception of appearance, yet no studies have directly compared the neurobiology associated with body perception. We compared brain activation and connectivity in relevant networks when viewing images of others bodies and tested their relationships with clinical symptoms and subjective appearance evaluations. We acquired fMRI data from 64 unmedicated females (20 weight-restored AN, 23 BDD, 21 controls) during a matching task using photos of others bodies that were unaltered or spatial-frequency filtered. With general linear model and independent components analyses we compared brain activation and connectivity in visual, striatal, and parietal networks and performed univariate and partial least squares multivariate analyses to investigate relationships with clinical symptoms and appearance evaluations. BDD but not AN demonstrated hypoactivity in dorsal visual and parietal networks compared to controls. Yet, AN and BDD showed partially overlapping patterns of hyperconnectivity in the dorsal visual network and hypoconnectivity in parietal network compared with controls. Further, there were significant activity and connectivity differences between AN and BDD in both networks. In both groups, activity and/or connectivity were associated with symptom severity and appearance ratings of others bodies. AN and BDD demonstrate both distinct and partially overlapping aberrant neural phenotypes involved in body processing and visually encoding global features. Nevertheless, in each disorder, aberrant activity and connectivity show relationships to clinically relevant symptoms and subjective perception. Results have implications for understanding distinct and shared pathophysiology underlying perceptual distortions for appearance and may inform future novel treatment strategies.

neuroscience↗

Streamlined low-input transcriptomics through EASY-RNAseq

High-throughput sequencing for transcriptome profiling is an increasingly accessible and important tool for biological research. However, accurate profiling of small cell populations remains challenging due to issues with gene detection sensitivity and experimental complexity. Here we describe a streamlined RNAseq protocol (EASY RNAseq) for sensitive transcriptome assessment starting from low amount of input materials. EASY RNAseq is technically robust enough for sequencing small pools of homogenous and heterogeneous cells, recovering higher numbers of genes and with a more even expression distribution pattern than other commonly used methods. Application of EASY RNAseq to single human embryos at the 8-cell stage was able to achieve detection of 70% protein-coding genes. This workflow may thus serve as a useful tool for sensitive interrogation of rare cell populations.

genomics↗

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

Antibodies are essential for elucidating the roles of genes decoded by genome sequencing. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed the Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 mAbs against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic feature of an antibody. Distinctive combinations of 10,000-20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-target pairs were discovered for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for human membrane proteins and ChIP-seq mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues discovered internalizing tumor antigens for antibody-drug conjugates. By discovering high affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.

systems biology↗

Chiroptical Kirigami Modulators for Terahertz Circular Dichroism Spectroscopy of Biomaterials

ABSTRACTSTerahertz circular dichroism (TCD) offers spectroscopic capabilities for understanding mesoscale chiral architecture and low-energy vibrations of macromolecules in (bio)materials1-5. However, the lack of dynamic polarization modulators comparable to polarization optics for other parts of electromagnetic spectrum impedes proliferation of TCD spectroscopy6-10. Here we show that tunable optical elements fabricated from patterned plasmonic sheets with periodic kirigami cuts make possible polarization modulation of THz radiation under application of mechanical strain. A herringbone pattern of microscale metal stripes enables dynamic range of polarization rotation modulation exceeding 80{degrees} over thousands of cycles. Upon out-of-plane buckling, the plasmonic stripes function as reconfigurable semi-helices of variable pitch aligned along the THz propagation direction. Several biomaterials, exemplified by elytrons of Chrysina gloriosa beetles, revealed distinct TCD fingerprints associated with the helical substructure in the biocomposite. Analogous kirigami modulators will also enable other applications in THz optics, such as polarization-based terahertz imaging and phase-encrypted telecommunication.

biophysics↗

Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis

Meiosis is the specialized cell division during which parental genomes recombine to create genotypically unique gametes. Despite its importance, mammalian meiosis cannot be studied in vitro, greatly limiting mechanistic studies. In vivo, meiocytes progress asynchronously through meiosis and therefore the study of specific stages of meiosis is a challenge. Here, we describe a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic sub-stages. Interrogating the H3K4me3 landscape revealed dynamic chromatin transitions between sub-stages of meiotic prophase I, both at sites of genetic recombination and at gene promoters. We also leveraged this method to perform the first comprehensive, genome-wide survey of histone marks in meiotic prophase, revealing a heretofore unappreciated complexity of the epigenetic landscape at meiotic recombination hotspots. Ultimately, this study presents a straightforward, scalable framework for interrogating the complexities of mammalian meiosis.

genomics↗

BGDMdocker: an workflow base on Docker for analysis and visualization pan-genome and biosynthetic gene clusters of Bacterial

MotivationAt present Docker technology has received increasing level of attention throughout the bioinformatics community. However, its implementation details have not yet been mastered by most biologists and applied widely in biological researches. In order to popularizing this technology in the bioinformatics and sufficiently use plenty of public resources of bioinformatics tools (Dockerfile and image of scommunity, officially and privately) in Docker Hub Registry and other Docker sources based on Docker, we introduced full and accurate instance of a bioinformatics workflow based on Docker to analyse and visualize pan-genome and biosynthetic gene clusters of a bacteria in this article, provided the solutions for mining bioinformatics big data from various public biology databases. You could be guided step-by-step through the workflow process from docker file to build up your own images and run an container fast creating an workflow.\n\nResultsWe presented a BGDMdocker (bacterial genome data mining docker-based) workflow based on docker. The workflow consists of three integrated toolkits, Prokka v1.11, panX, and antiSMASH3.0. The dependencies were all written in Dockerfile, to build docker image and run container for analysing pan-genome of total 44 Bacillus amyloliquefaciens strains, which were retrieved from public? database. The pan-genome totally includes 172,432 gene, 2,306 Core gene cluster. The visualized pan-genomic data such as alignment, phylogenetic trees, maps mutations within that cluster to the branches of the tree, infers loss and gain of genes on the core-genome phylogeny for each gene cluster were presented. Besides, 997 known (MIBiG database) and 553 unknown (antiSMASH-predicted clusters and Pfam database) genes of biosynthesis gene clusters types and orthologous groups were mined in all strains. This workflow could also be used for other species pan-genome analysis and visualization. The display of visual data can completely duplicated as well as done in this paper. All result data and relevant tools and files can be downloaded from our website with no need to register. The pan-genome and biosynthetic gene clusters analysis and visualization can be fully reusable immediately in different computing platforms (Linux, Windows, Mac and deployed in the cloud), achieved cross platform deployment flexibility, rapid development integrated software package.\n\nAvailability and implementationBGDMdocker is available at http://42.96.173.25/bapgd/ and the source code under GPL license is available at https://github.com/cgwyx/debian_prokka_panx_antismash_biodocker.\n\nContactchenggongwyx@foxmail.com\n\nSupplementary informationSupplementary data are available at biorxiv online.

bioinformatics↗