Proteome and Genome

蛋白质组和基因组

• 批准号: 9925255
• 负责人: Yves A. Lussier
• 金额: $ 29.65万
• 依托单位: UNIVERSITY OF ARIZONA
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至 2022-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9925255
• 关键词: Adult Respiratory Distress Syndrome; African; Alternative Splicing; Biological Assay; Candidate Disease Gene; Chicago; Code; Computer software; DNA; Data; Data Analyses; Data Storage and Retrieval; Disease; Endothelial Cells; Endothelium; European; Exons; Gel; Gene Expression; Gene Targeting; Genes; Genetic; Genome; Genomics; Genotype; Image; In Vitro; Individual; Infrastructure; Introns; Investigation; Label; Location; Lung; Mass Spectrum Analysis; Mutate; Nitrates; Patients; Phosphorylation; Post-Translational Protein Processing; Predisposition; Proteins; Proteome; Proteomics; RNA; Recombinant Proteins; Regulation; Research; Research Personnel; Resources; Sampling; Secure; Services; Severities; Ships; Single Nucleotide Polymorphism; Software Tools; Structure of parenchyma of lung; Surface Plasmon Resonance; Technology; Testing; Tissue Sample; Tissues; Translational Protein Modification; Ubiquitination; biobank; cost effective; data exchange; data management; delta opioid receptor; delta protein; design; experimental group; experimental study; in silico; in vivo; in vivo Model; laboratory facility; molecular modeling; nitration; novel; protein expression; protein protein interaction; protein structure; protein structure function; screening; tool; transcriptomics; translational impact

ABSTRACT: This Proteome & Genome Core (PPG Core B) will provide essential, cutting edge, proteomic/transcriptomic/genetic expertise to facilitate the translational impact of this highly integrated PPG. This PPG Core will be responsible for providing the research investigators with a well characterized ARDS biobank (i.e. DNA from European descent and African descent subjects), a complete list of tagging single nucleotide polymorphisms (tSNPs) for each PPG candidate gene, mid-throughput genotyping services, and data analysis tools to test for association between PPG-studied SNPs and susceptibility and severity of ARDS. The functional non-synonymous coding SNPs will be screened in silico to identify their impact on protein structure and function (protein-protein interaction, catalytic activity, post-translational modification) by computational protein structure molecular modeling, with protein-protein interaction validated by surface plasmon resonance (SPR) screening. Effects of exon-intron boundary SNPs on alternative splicing of these key genes will be analyzed by in silico prediction and further validated by SNP-containing minigene constructs in individual projects. PPG Core B will provide the service to generate the mutated DNA constructs (with disease-associated SNP) to generate recombinant protein used in SPR, or GRF-labeled protein for cellular location tracking in endothelial cells (to be used in Core D and individual projects). In addition, this PPG Core will further validate the genomic expression data by proteomic approaches (2-D protein gel and mass spectrometry). On top of the protein level characterization, the PPG Core B will define the protein translational modification (PTM) status including phosphorylation, nitration, and ubiquitination via traditional mass spectrometry analysis. PPG Core B will utilize the up-to-date technologies to provide a proteomic-genomic study platform for all three Projects and generate novel information on the genes targeted for investigation in this PPG. This PPG Core will also provide software and hardware infrastructure for (i) federated tissue management (e.g. chain of custody while transferring tissues from any lab to any Core) and (ii) secure data exchange between Cores and Research investigators. Core B will also resource investigators and Cores with TissueMetrix tissue management software that also provides chain of custody management of samples transferred between investigators and Cores and reconciliation between lists of samples send and received. In addition, large files generated by the cores will be transferred to investigators using a secure IPSwitch portal that also manages authentication and keeps logs of accessed files by legitimate users (e.g. genomics, transcriptomic, proteomics, imaging).

摘要：这个蛋白质组和基因组核心（PPG核心B）将提供必要的，尖端的， 蛋白质组学/转录组学/遗传学专业知识，以促进这种高度整合的PPG的翻译影响。 PPG核心将负责为研究者提供充分表征的ARDS 生物库（即来自欧洲血统和非洲血统受试者的DNA），一个完整的标记单 每个PPG候选基因的核苷酸多态性（tSNP），中通量基因分型服务，以及 数据分析工具，以测试PPG研究的SNP与ARDS的易感性和严重性之间的关联。 将通过计算机模拟筛选功能性非同义编码SNP，以确定其对蛋白质的影响 结构和功能（蛋白质-蛋白质相互作用、催化活性、翻译后修饰）， 计算蛋白质结构分子建模，通过表面验证蛋白质-蛋白质相互作用 等离子体共振（SPR）筛选。外显子-内含子边界SNP对这些基因选择性剪接的影响 关键基因将通过计算机预测进行分析，并通过含SNP的微基因构建体进行进一步验证 in individual个别projects项目. PPG核心B将提供服务以产生突变的DNA构建体（具有 疾病相关SNP）以产生用于SPR的重组蛋白，或用于细胞免疫的GRF标记蛋白。 内皮细胞中的位置跟踪（将用于核心D和个别项目）。此外，这款PPG Core 将通过蛋白质组学方法（2-D蛋白质凝胶和质谱）进一步验证基因组表达数据 光谱法）。在蛋白质水平表征之上，PPG核心B将定义蛋白质翻译 修饰（PTM）状态，包括磷酸化，硝化和泛素化，通过传统的质量 光谱分析PPG核心B将利用最新技术提供蛋白质组-基因组 为所有三个项目的研究平台，并产生新的信息的基因为目标的调查， 这个PPG。该PPG核心还将为（i）联合组织提供软件和硬件基础设施 管理（例如，将组织从任何实验室转移到任何中心时的监管链）和（ii）安全数据 Cores和研究人员之间的交流。核心B还将为研究者和核心提供资源， TissueMeetings组织管理软件，还提供样本监管链管理 研究者和Cores之间的转移以及收发样品清单之间的核对。在 此外，核心生成的大型文件将通过安全的IPSwitch门户传送给调查人员 它还管理认证并保存合法用户访问文件的日志（例如Genomics， 转录组学、蛋白质组学、成像）。