Biology subjects

Xing, Y.

Publications and source records attributed to Xing, Y..

104 records · Page 6Linked to original sources

bioRxiv2019

Polarized Lung Inflammation and Tie2/Angiopoietin-Mediated Endothelial Dysfunction during Severe Orientia tsutsugamushi Infection

Orientia tsutsugamushi infection can cause acute lung injury and high mortality in humans; however, the underlying mechanisms are unclear. Here, we tested a hypothesis that dysregulated pulmonary inflammation and Tie2-mediated endothelial malfunction contribute to lung damage. Using a murine model of lethal O. tsutsugamushi infection, we demonstrated pathological characteristics of vascular activation and tissue damage: 1) a significant increase of ICAM-1, VEGFR2, and angiopoietin-2 (Ang2) proteins in inflamed tissues and lung-derived endothelial cells (EC), 2) a progressive loss of endothelial quiescent and junction proteins (Ang1, VE-cadherin/CD144, occuludin), and 3) a profound impairment of Tie2 receptor at the transcriptional and functional levels. In vitro infection of primary human EC cultures and serum Ang2 proteins in scrub typhus patients support our animal studies, implying endothelial dysfunction in severe scrub typhus. Flow cytometric analyses of lung-recovered cells further revealed that pulmonary macrophages (M{Phi}) were polarized toward an M1-like phenotype (CD80+CD64+CD11b+Ly6G-) during the onset of disease and prior to host death, which correlated with the significant loss of CD31+CD45- ECs and M2-like (CD206+CD64+CD11b+Ly6G-) cells. In vitro studies indicated extensive bacterial replication in M2-type, but not M1-type, M{Phi}s, implying the protective and pathogenic roles of M1-skewed responses. This is the first detailed investigation of lung cellular immune responses during acute O. tsutsugamushi infection. It uncovers specific biomarkers for vascular dysfunction and M1-skewed inflammatory responses, highlighting future therapeutic research for the control of this neglected tropical disease.\n\nAuthor SummaryScrub typhus is a life-threatening disease, infecting an estimated one million people yearly. Acute lung injury is the most common clinical observation; however, its pathogenic biomarkers and mechanisms of progression remain unknown. Here, we used a lethal infection mouse model that parallels certain aspects of severe scrub typhus, primary human endothelial cell cultures, and patient sera to define pathogenic biomarkers following Orientia tsutsugamushi infections. We found a significant increase in the levels of endothelial activation/stress markers (angiopoietins and ICAM-1) in infected mouse lungs and in patient sera, but a progressive loss of endothelium-specific Tie2 receptor and junction proteins (VE-cadherin), at severe stages of disease. These signs of vasculature disruption positively correlated with the timing and magnitude of recruitment/activation of proinflammatory M{Phi} subsets in infected lungs. Bacterial growth in vitro was favored in M2-like, but not in M1-like, M{Phi}s. This study, for the first time, reveals endothelial malfunction and dysregulated inflammatory responses, suggesting potential therapeutic targets to ameliorate tissue damage and pathogenesis.

microbiology↗

bioRxiv2019

PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

Cell-free RNA, including both long RNA and small RNA, has been considered important for its biological functions and potential clinical usage, but the major challenge is to effectively sequence them at the same time. Here we present PolyAdenylation Ligation Mediated-Seq (PALM-Seq), an integrated sequencing method for cell-free long and small RNA. Through terminal modification and addition of 3 polyadenylation and 5 adaptor, we could get mRNA, long non-coding RNA, microRNA, tRNA, piRNA and other RNAs in a single library. With target RNA depletion, all these RNAs could be sequenced with relatively low depth. Using PALM-Seq, we identified pregnant-related mRNAs, long non-coding RNAs and microRNAs in female plasma. We also applied PALM-Seq to sequence RNA from amniotic fluids, leukocytes and placentas, and could find RNA signatures associated with specific sample type. PALM-Seq provides an integrated, cost-effective and simple method to characterize the landscape of cell-free RNA, and can stimulate further progress in cell-free RNA study and usage.

molecular biology↗

bioRxiv2019

Exposure to environmental level pesticides stimulates and diversifies evolution in Escherichia coli towards greater antibiotic resistance

Antibiotic resistance is one of the most challenging issues in public health. Antibiotic resistance can be selected by antibiotics at sub-inhibitory concentrations, the concentrations typically occurring in natural and engineered environments. Meanwhile, many other emerging organic contaminants such as pesticides are frequently co-occurring with antibiotics in agriculture-related environments and municipal wastewater treatment plants. To investigate the effects of the co-existing, non-antibiotic pesticides on the development of antibiotic resistance, we conducted long-term exposure experiments using a model Escherichia coli strain. The results revealed that 1) the exposure to a high level (in mg/L) of pesticides alone led to the emergence of mutants with significantly higher resistance to streptomycin; 2) the exposure to an environmental level (in {micro}g/L) of pesticides together with a sub-inhibitory level (in sub mg/L) of ampicillin synergistically stimulated the selection of ampicillin resistance and the cross-selection of resistance to three other antibiotics (i.e., ciprofloxacin, chloramphenicol, and tetracycline). Resistance levels of mutants selected from co-exposure were significantly higher than those of mutants selected from ampicillin exposure only. The comparative genomic and transcriptomic analyses indicate that distinct and diversified genetic mutations in ampicillin- and ciprofloxacin-resistant mutants were selected from co-exposure, which likely caused holistic transcriptional regulation and the increased antibiotic resistance. Together, the findings provide valuable fundamental insights into the development of antibiotic resistance under environmentally relevant conditions, as well as the underlying molecular mechanisms of the elevated antibiotic resistance induced by the exposure to pesticides.\n\nSignificance statementAntibiotic resistance is a major threat to public health globally. Besides clinically relevant environments, the emergence and spread of resistant bacteria in non-clinical environments can also potentially pose risks of therapy failures. This study showed that the long-term, environment-level exposure to pesticides with and without antibiotics significantly stimulated the development of greater antibiotic resistance. The resistant strains selected from the exposure to pesticides are genetically and metabolically distinct from the ones selected by the antibiotic only. Although it is still being debated regarding whether or not a large use of antibiotics in plant agriculture is harmful, our findings provide the first fundamental evidence that greater concerns of antibiotic resistance may result if antibiotics are applied together with non-antibiotic pesticides.

microbiology↗

bioRxiv2019

Assessment of the gene expression profiles of leukocytes from different isolations

BACKGROUNDResearch on peripheral leukocyte gene expression in human health and disease is growing rapidly. However, how to process sample efficiently, simply and stably, and how to reflect human physiological state preferably remains critical issues in large cohort studies.\n\nMETHODSWe used RNA-seq to explore the differences of gene expression profiles among whole blood (WB) and three groups of leukocytes from buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation.\n\nRESULTSThe residual globin mRNA in leukocytes from RBC lysis (1.00% {+/-}1.23%) and PBMC isolation (0.06% {+/-} 0.03%) was much less than that in leukocytes from BC extraction (17.48% {+/-} 6.95%) and WB (24.46% {+/-} 6.43%), resulting in higher transcriptome mapping rates and larger numbers of detected genes. The expression of 616 genes associated with leukocyte function was slightly higher in leukocytes from RBC lysis than that from BC extraction and WB, but barely detected in leukocytes from PBMC isolation.\n\nCONCLUSIONSWe suggest that sample processing based on RBC lysis could allow better applications of gene expression profiling of peripheral leukocytes in large cohort studies.

molecular biology↗

bioRxiv2019

Inherited duplications of PPP2R3B promote naevi and melanoma via a novel C21orf91-driven proliferative phenotype

The majority of the heredity of melanoma remains unexplained, however inherited copy number changes have not yet been systematically studied. The genetic environment is highly relevant to treatment stratification, and new gene discovery is therefore desirable. Using an unbiased whole genome screening approach for copy number we identify here a novel melanoma predisposing factor, familial duplications of gene PPP2R3B, encoding a regulatory unit of critical phosphatase PP2A. Significant correlation between expression of PPP2R3B in tumour tissue and survival in a large melanoma cohort was confirmed, and associated with a non-immunological expression profile. Mechanistically, construction and extensive characterization of a stable, inducible cellular model for PPP2R3B overexpression revealed induction of pigment cell switching towards proliferation and away from migration. Importantly, this was independent of the known microphthalmia-associated transcription factor (MITF)-controlled pigment cell phenotype switch, and was instead driven by uncharacterised gene C21orf91. Bioinformatic studies point to C21orf91as a novel target of MITF, and therefore a potential hub in the control of phenotype switching in melanoma. This study identifies novel germline copy number variants in PPP2R3B predisposing to melanocytic neoplasia, and uncovers a new potential therapeutic target C21orf91 in the control of pigment cell proliferation.

genomics↗

bioRxiv2019

Leishmania targets the macrophage epigenome and dampens the NF-κB/NLRP3- mediated inflammatory response

Aberrant macrophage activation during intracellular infection generates important immunopathologies that can cause severe human morbidity. A better understanding of microbial immune subversion strategies and macrophage phenotypic and functional responses is a prerequisite for the design of novel, host-directed intervention strategies. Here, we uncover a fine-tuned transcriptional response induced in primary macrophages infected by the human parasite Leishmania amazonensis that prevents NF-{kappa}B and NLRP3 inflammasome activation. This unusual subversion is characterized by respectively suppression and induction of activating and de-activating components of the NF-{kappa}B and NLRP3 pathways. This dichotomic modulation was associated with histone H3 hypoacetylation at promoters of NF-{kappa}B-related, pro-inflammatory genes. Our results reveal a novel Leishmania immune subversion strategy targeting host cell epigenetic regulation to modulate the macrophage phenotype. Modulation of the macrophage epigenetic landscape establishes conditions beneficial for intracellular parasite survival, and opens interesting new venues for host-directed, anti-microbial drug discovery.

cell biology↗

bioRxiv2018

Genetic interactions among Ghd7, Ghd7.1, Ghd8 and Hd1 contribute to large variation in heading date in rice

Several major heading date genes are sensitive to photoperiod and jointly regulate heading date in rice. However, it is not clear how these genes coordinate rice heading. In this study, a near-isogenic F2 population with Ghd7, Ghd7.1, Ghd8 and Hd1 segregating in the Zhenshan 97 (ZS97) background was used to evaluate the genetic interactions among these four genes under natural long-day (NLD) and natural short-day (NSD) conditions, and a series of Ghd7.1-segregating populations in different backgrounds were developed to estimate the genetic effects of Ghd7.1 on heading date under both conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD conditions but was Ghd7 by Ghd7.1 under NSD conditions. Interestingly, Ghd7.1 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and yield was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions. These results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas.

genetics↗

bioRxiv2018

SimulateCNVs: a novel software application for simulating CNVs in WES and WGS data

SummarySimulateCNVs is a fast and novel software application for simulating CNVs in WES and WGS data. Current NGS simulators cannot simulate rearranged genomes and their alignment files for WES data and are not easy to use. SimulateCNVs is the first software application that can simulate CNVs in both WES and WGS data, is easy to install, has many unique features, and can output rearranged genomes, short reads and bam files in a single command.\n\nAvailabilitySimulateCNVs is freely available from https://yjulyxing.github.io/\n\nContactinumia@tamu.edu, ccasola@tamu.edu

bioinformatics↗

bioRxiv2018

Discovery of allele-specific protein-RNA interactions in human transcriptomes

Gene expression is tightly regulated at the post-transcriptional level through splicing, transport, translation, and decay. RNA-binding proteins (RBPs) play key roles in post-transcriptional gene regulation, and genetic variants that alter RBP-RNA interactions can affect gene products and functions. We developed a computational method ASPRIN (Allele-Specific Protein-RNA Interaction), that uses a joint analysis of CLIP-seq (cross-linking and immunoprecipitation followed by high-throughput sequencing) and RNA-seq data to identify genetic variants that alter RBP-RNA interactions by directly observing the allelic preference of RBP from CLIP-seq experiments as compared to RNA-seq. We used ASPRIN to systematically analyze CLIP-seq and RNA-seq data for 166 RBPs in two ENCODE (Encyclopedia of DNA Elements) cell lines. ASPRIN identified genetic variants that alter RBP-RNA interactions by modifying RBP binding motifs within RNA. Moreover, through an integrative ASPRIN analysis with population-scale RNA-seq data, we showed that ASPRIN can help reveal potential causal variants that affect alternative splicing via allele-specific protein-RNA interactions.

bioinformatics↗

bioRxiv2018

Management performance mapping: the value of information for regional prioritization of project interventions

Policymakers and donors often need to identify the locations and settings where technologies are most likely to have important effects, to increase the benefits from agricultural development or extension efforts. Higher quality information may help to target the high-payoff locations. The value of information (VOI) in this context is formalized by evaluating the results of decision making guided by a set of information compared to the results of acting without taking the information into account. We present a framework for management performance mapping that includes evaluating the VOI for decision making about geographic priorities in regional intervention strategies, in case studies of Andean and Kenyan potato seed systems. We illustrate use of Bayesian network models and recursive partitioning to characterize the relationship between seed health and yield responses and environmental and management predictors used in studies of seed degeneration. These analyses address the expected performance of an intervention based on geographic predictor variables. In the Andean example, positive selection of seed from asymptomatic plants was more effective at high altitudes in Ecuador. In the Kenyan example, there was the potential to target locations with higher technology adoption rates and with higher potato cropland connectivity, i.e., a likely more important role in regional epidemics. Targeting training to high performance areas would often provide more benefits than would random selection of target areas. We illustrate how assessing the VOI can help inform targeted development programs and support a culture of continuous improvement for interventions.

ecology↗

bioRxiv2018

Long Noncoding RNA-Maternally Expressed Gene 3 Contributes to Hypoxic Pulmonary Hypertension

The expression and function of long noncoding RNAs (lncRNAs) in the development of hypoxic pulmonary hypertension, especially in the proliferation of pulmonary artery smooth muscle cells (PASMCs) are largely unknown. Here, we characterized the expression of lncRNA-maternally expressed gene 3 (lncRNA-MEG3) was significantly increased and primarily located in the cytoplasm of PASMCs by hypoxia. LncRNA-MEG3 knockdown by lung-specific delivery of small interfering RNAs (siRNAs) significantly prevented the development of hypoxic pulmonary hypertension in vivo. Silencing of lncRNA-MEG3 by siRNAs and gapmers attenuated PASMC responses to hypoxia in vitro. Mechanically, we found that lncRNA-MEG3 acts as a molecular sponge of microRNA-328 (miR-328); upon hypoxia, lncRNA-MEG3 interacts and sequesters miR-328, leading to the upregulation of insulin-like growth factor 1 receptor (IGF1R). Additionally, higher expression of lncRNA-MEG3 and IGF1R, and lower expression of miR-328 were observed in PASMCs of iPAH patients. These data provide insight into the contribution of lncRNA-MEG3 in hypoxia pulmonary hypertension. Upregulation of lncRNA-MEG3 sequesters cytoplasmic miR-328, eventually leading to the expression of IGF1R, revealing a regulatory mechanism by lncRNAs in hypoxia-induced PASMC proliferation.

molecular biology↗

bioRxiv2017

Identification and characterization of m6A circular RNA epitranscriptomes

This study brings together the expanding fields of RNA modifications and circular (circ) RNAs. We find that cells express thousands of m6A methylated circRNAs, with cell-type specificity observed between human embryonic stem cells and HeLa cells. m6A-circRNAs were identified by RNA sequencing of total RNA following ribosome depletion and m6A immunoprecipitation. The presence of m6A-circRNAs is corroborated by the identification of complexes between circRNAs and YTHDF1 and YTHDF2, proteins that \"read\" m6A sites in mRNAs.\n\nFurthermore, m6A modifications on non-linear RNAs depend on METTL3 and METTL14, the known m6A methyltransferase \"writer\" complex components, suggesting that circRNAs are methylated by the same complexes responsible for m6A modification of linear RNAs. Despite sharing m6A readers and writers, m6A-circRNAs are frequently derived from exons not methylated in mRNAs. Nevertheless, m6A-mRNAs that are methylated on the same exons as those composing m6A-circRNAs exhibit less stability than other m6A-mRNA, and this circRNA-mRNA cross-talk is regulated by YTHDF2. Thus, our results expand the m6A regulatory code through identification of the first circRNA epitranscriptome.

bioinformatics↗

bioRxiv2017

Global cropland connectivity: A risk factor for invasion and saturation by emerging pathogens and pests

The geographic pattern of cropland is an important risk factor for invasion and saturation by crop-specific pathogens and arthropods. Understanding cropland networks supports smart pest sampling and mitigation strategies. We evaluate global networks of cropland connectivity for key vegetatively-propagated crops (banana and plantain, cassava, potato, sweetpotato, and yam) important for food security in the tropics. For each crop, potential movement between geographic location pairs was evaluated using a gravity model, with associated uncertainty quantification. The highly-linked hub and bridge locations in cropland connectivity risk maps are likely priorities for surveillance and management, and for tracing intra-region movement of pathogens and pests. Important locations are identified beyond those locations that simply have high crop density. Cropland connectivity risk maps provide a new risk component for integration with other factors - such as climatic suitability, genetic resistance, and trade routes - to inform Pest Risk Assessment and mitigation.

ecology↗

bioRxiv2017

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

SynopsisO_ST_ABSBackgroundC_ST_ABSmcr-1-mediated transmissible colistin resistance in Enterobacteriaceae is concerning, given colistin is frequently used as a treatment of last resort in multidrug-resistant Enterobacteriaceae infections. Reported rates of human mcr-1 gastrointestinal carriage have historically been low.\n\nObjectivesTo identify trends in human gastrointestinal carriage of mcr-1 positive and mcr-1-positive/cefotaxime-resistant Enterobacteriaceae in Guangzhou, China, 2011-2016, and investigate the genetic contexts of mcr-1 in a subset of mcr-1-positive/cefotaxime-resistant strains using whole genome sequencing (WGS).\n\nMethodsOf 8,022 faecal samples collected, 497 (6.2%) were mcr-1- positive, and 182 (2.3%) mcr-1-positive/cefotaxime-resistant. Trends in carriage were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (Illumina), and genetic contexts of mcr-1 were characterised.\n\nResultsWe observed marked increases in mcr-1 (now ~30% prevalence) and more recent (since January 2014) increases in mcr-1-positive/third-generation cephalosporin-resistant Enterobacteriaceae human colonisation (p<0.001). Sub-cultured mcr-1-positive/third-generation cephalosporin-resistant isolates were commonly multi-drug resistant.\n\nWGS of 50 mcr-1/third-generation cephalosporin-resistant isolates (49 Escherichia coli; 1 Klebsiella pneumoniae) demonstrated bacterial strain diversity (39 E. coli sequence types); mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and loss of the mcr-1-associated insertion sequence ISApl1 in some plasmids. Significant sequence similarity with published mcr-1 plasmid sequences was consistent with spread amongst pig, chicken and human reservoirs.\n\nConclusionsThe high positivity rate (~10%) of mcr-1 in multidrug-resistant E. coli colonising humans is a clinical threat; the diverse genetic mechanisms (strains/plasmids/insertion sequences) associated with mcr-1 have likely contributed to its dissemination, and will facilitate its persistence.

microbiology↗