Genomic/Genetic and Proteome

基因组/遗传学和蛋白质组

• 批准号: 10871778
• 负责人: Nathan A. Ellis
• 金额: $ 23.03万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-20 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10871778
• 关键词: Acute Respiratory Distress Syndrome; Bioinformatics; Biological Assay; Blood Vessels; Cell Line; Cellular Structures; Code; Computer Models; Cytoskeleton; DNA; DNA Methylation; DNA sequencing; Data; Data Set; Disease; EMS1 gene; Endothelial Cells; Endothelium; Focal Adhesions; Gene Proteins; Generations; Genes; Genetic; Genome; Genomics; Human; ITGB4 gene; Immunoprecipitation; Incidence; Inflammatory; Integrin beta4; Knock-in; Knock-out; Lung; Mass Spectrum Analysis; Methylation; Modeling; Mutation; Myosin Light Chain Kinase; Nucleotides; P-Selectin; Peripheral; Phosphorylation; Post-Translational Protein Processing; Predisposition; Production; Proteins; Proteome; Proteomics; Recombinant Proteins; Regulation; Research; Research Personnel; Role; Sampling; Services; Severities; Signal Transduction; Single Nucleotide Polymorphism; Site; Sphingosine-1-Phosphate Receptor; Structural Models; Structure; Surface Plasmon Resonance; TLR4 gene; Testing; Translational Protein Modification; Ubiquitination; Variant; Vascular Permeabilities; experimental analysis; genetic analysis; genome editing; genome-wide; in silico; methylome; nitration; non-muscle myosin; promoter; protein function; protein protein interaction; protein structure; restoration; transcriptome sequencing; translational impact

ABSTRACT: The Genome and Proteome Core (PPG Core B) will provide essential, cutting-edge genomics, proteomics, and bioinformatics expertise to facilitate the translational impact of this highly integrated PPG. Core B will be respon- sible for providing the research investigators with: (i) expert interrogation of publicly available DNA and RNA sequencing datasets and genome-wide DNA methylome datasets to generate interpretable data from these plat- forms; (ii) genetic expertise needed to test for associations between PPG target gene DNA variants and sus- ceptibility and severity of ARDS; (iii) generation of human endothelial cell (EC) lines and genome-edited cell line models with selected single nucleotide knock in or deletion-based knock out mutations for functional genetic analyses; (iv) execution of traditional proteomic mass spectrometry analysis of immunoprecipitated PPG target proteins for protein translational modification (PTM) identification, including phosphorylation, nitration, and ubiq- uitination; (v) in silico computational protein-structure modeling to identify the impact of functional non-synony- mous coding variants on protein structure and function (protein-protein interaction, catalytic activity, post-trans- lational modification), with protein-protein interactions validated by surface plasmon resonance; and, (vi) exper- tise to oversee production of recombinant proteins with mutations at sites of PTMs or SNPs. As a centralized core for all genome and proteome analyses, Core B (located in Tucson AZ) will perform all relevant analysis of experimental samples for all four projects as each PPG Project will require the services provided by Core B.

抽象的： 基因组和蛋白质组核心（PPG核B）将提供必不可少的，尖端的基因组学，蛋白质组学和 生物信息学专业知识，以促进这种高度综合的PPG的翻译影响。核心将是响应 可为研究调查人员提供以下方面的信息：（i）对公开DNA和RNA的专家询问 测序数据集和全基因组DNA甲基甲基数据集，以从这些平台中生成可解释的数据 形式； （ii）测试PPG靶基因DNA变异和SUS所需的遗传学知识 ARDS的可疑性和严重性； （iii）人类内皮细胞（EC）线和基因组编辑的细胞系的产生 具有选定的单核苷酸敲击或基于缺失的敲除突变的模型用于功能遗传 分析； （iv）执行免疫沉淀PPG目标的传统蛋白质组学质谱分析 蛋白质转化修饰（PTM）鉴定的蛋白质，包括磷酸化，硝化和Ubiq- 插（v）在计算机计算蛋白结构建模中，以确定功能性非合伙的影响 关于蛋白质结构和功能的摩尔编码变体（蛋白质 - 蛋白质相互作用，催化活性，转交后 - litation修饰），通过表面等离子体共振验证蛋白质 - 蛋白质相互作用；和（vi）实验 可以在PTM或SNP的位点监督具有突变的重组蛋白的产生。作为集中式 所有基因组和蛋白质组分析的核心，核心B（位于图森AZ）将执行所有相关分析 所有四个项目的实验样本，因为每个PPG项目都需要由 核心B。