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：这款蛋白质组和基因组核心（PPG Core B）将提供必要的、前沿的