Core B. Genomics and Bioinformatics Core

核心 B. 基因组学和生物信息学核心

• 批准号: 10625575
• 负责人: Frederic D Bushman
• 金额: $ 16.78万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-01 至 2028-02-29
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10625575
• 关键词: Affect; Antigens; Archives; Bacteriophages; Bioinformatics; Canis familiaris; Cattle; Cells; Clinical; Clostridium difficile; Collaborations; Comparative Study; DNA; DNA Modification Process; DNA Sequence Alteration; Data; Gene Expression Profiling; Genes; Genetic Variation; Genome; Genomics; Human; Hybrids; Immune response; Immunodeficient Mouse; Immunology; Infection; Intestines; Investigation; Membrane Proteins; Messenger RNA; Methods; Mus; Outcome; Population; Population Heterogeneity; Protein Analysis; Proteins; RNA vaccine; Reporting; Resources; Sampling; Sequence Analysis; Statistical Data Interpretation; Structure; System; Vaccinated; Vaccines; Variant; Work; archive data; data archive; data management; design; diverse data; fascinate; in vivo; interest; metatranscriptomics; microbiome; microbiome composition; microbiome sequencing; model organism; protein structure; response; statistics; transcription factor; transcriptome sequencing; transposon/insertion element; vaccine candidate; vaccine efficacy

SUMMARY- CORE B (GENOMICS CORE) Core B (Genomics Core) will provide key support to the mVACS team in Clostridioides difficile genome sequence analysis, antigen design, microbiome sequence analysis, routine statistical analysis, and high content data management. Core B will use advanced genomics-based methods to quantify C. difficile genome composition and genetic variation, and associate these with outcomes. Core B will support analysis of protein structure to allow expression of well-folded domains as mRNAs. Core B will characterize DNA inversion systems and other mechanisms of DNA modification and alterations in gene activity that may impact vaccine efficacy. Core B will also carry out transcriptional profiling on C. difficile isolated from the intestine of vaccinated and immunodeficient mice, to assess how C. difficile responds in vivo to effective and ineffective immune responses. The Aims of Core B are: (1) C. difficile genomics to identify optimal targets for modified mRNA vaccines. Long read and short read data will be merged to generate complete assemblies, as in our previous work. Gene content will be enumerated and compared with clinical outcomes. (2) To assess variation in sequence and abundance of C. difficile vaccine targets. C. difficile isolates are known to encode considerable variation in their surface proteins. In addition, DNA inversion systems encode on-off switches affecting surface proteins and transcription factors, resulting in extensive population heterogeneity. This Aim will thus carry out deep assessment of proteins relevant as modified mRNA vaccine targets, and guide antigen design. (3) Transcriptional profiling and microbiome sequencing for mechanistic investigation. Projects 1-3 and the Clinical Core will generate murine and human fecal samples associated with successful or unsuccessful responses to C. difficile infection; Core B will quantify microbiome composition and metatranscriptomic analysis of C. difficile positive samples by RNA-seq. This core will oversee sequence acquisition and analysis is support of these studies. (4) Data management and archiving. Core C will work with Core A for standard statistical analysis and will archive and manage the diverse data types generated by the U19 team.

总结-核心B（基因组学核心） Core B（Genomics Core）将在艰难梭菌基因组测序方面为mVACS团队提供关键支持 分析、抗原设计、微生物组序列分析、常规统计分析和高内容数据 管理核心B将使用先进的基于基因组学的方法来量化C。艰难的基因组组成 和遗传变异，并将这些与结果联系起来。核心B将支持蛋白质结构分析， 允许良好折叠的结构域表达为mRNA。核心B将表征DNA倒位系统和其他 可能影响疫苗效力的DNA修饰和基因活性改变的机制。核心B将 并对C.从接种疫苗和免疫缺陷的肠道分离的艰难梭菌 小鼠，以评估C.艰难梭菌在体内对有效和无效的免疫应答作出反应。的目的 核心B是：（1）C。艰难的基因组学，以确定修饰的mRNA疫苗的最佳靶标。长读和短读 读取的数据将被合并以生成完整的程序集，就像我们以前的工作一样。基因含量将是 并与临床结果进行比较。(2)为了评估C. 艰难疫苗目标。C.已知艰难梭菌分离株在其表面蛋白中编码相当大的变异。 此外，DNA倒位系统编码影响表面蛋白和转录因子的开关， 导致广泛的种群异质性。因此，本目标将对相关蛋白质进行深入评估， 作为修饰的mRNA疫苗靶标，并指导抗原设计。(3)转录谱和微生物组 排序用于机理研究。项目1-3和临床核心将产生小鼠和人类 粪便样本与成功或不成功的反应，以C。艰难梭菌感染;核心B将定量 微生物组组成和C.通过RNA-seq.这一核心 将监督序列采集和分析，以支持这些研究。(4)数据管理和归档。 核心C将与核心A一起进行标准统计分析，并将存档和管理各种数据类型 由U19团队制作。