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.

摘要： 基因组和蛋白质组核心（PPG核心B）将提供必要的，尖端的基因组学，蛋白质组学， 生物信息学专业知识，以促进这种高度整合的PPG的翻译影响。核心B将响应- 能够为研究人员提供：（i）对公开可用的DNA和RNA的专家询问 测序数据集和全基因组DNA甲基化数据集，以从这些平台生成可解释的数据， 形式;（ii）测试PPG靶基因DNA变异体与sus之间关联所需的遗传专业知识， （iii）人内皮细胞（EC）系和基因组编辑的细胞系的产生 具有选择的单核苷酸敲入或基于缺失的敲除突变的功能遗传模型 （iv）对免疫沉淀的PPG靶标进行传统的蛋白质组质谱分析 用于蛋白质翻译修饰（PTM）鉴定的蛋白质，包括磷酸化、硝化和ubiq- （v）计算机蛋白质结构建模，以确定功能性非同义词的影响， Mous编码变体对蛋白质结构和功能（蛋白质-蛋白质相互作用，催化活性，后反式- 离子修饰），其中蛋白质-蛋白质相互作用通过表面等离子体共振验证;以及，（vi）实验- 负责监督在PTM或SNP位点发生突变的重组蛋白的生产。作为集中 Core B（位于亚利桑那州图森）将进行所有相关分析 所有四个项目的实验样品，因为每个PPG项目将需要提供服务， 核心B。