COBRE: U NEL: CORE A: METABOLOMICS: PROTEOMICS, MICROSCOPY, GENOMICS, CYTOMETRY

COBRE：U NEL：核心 A：代谢组学：蛋白质组学、显微镜检查、基因组学、细胞计数

• 批准号: 8360526
• 负责人: Nandakumar Madayiputhiya
• 金额: $ 28.85万
• 依托单位: UNIVERSITY OF NEBRASKA LINCOLN
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8360526
• 关键词: Animals; Area; Attention; Bioinformatics; Biological; Biological Markers; Biology; Centers of Research Excellence; Cholesterol; Computer software; Consultations; Core Facility; Cytometry; Data; Data Analyses; Dedications; Development; Diagnostic; Dictionary; Disease; Early Diagnosis; Experimental Designs; Faculty; Fractionation; Funding; Genes; Genomics; Glucose; Grant; Guns; Human Genome; Industry; Investigation; Laboratories; Libraries; Lipids; Liquid substance; Malignant neoplasm of lung; Mass Spectrum Analysis; Metabolic Diseases; Metabolism; Microscopy; Molecular Medicine; Mutation; National Center for Research Resources; Nebraska; Organ; Organism; Oxidation-Reduction; Oxidative Stress; Pathogenesis; Peptides; Physiological; Plants; Principal Investigator; Proteins; Proteome; Proteomics; Research; Research Infrastructure; Research Personnel; Resources; Scientist; Services; Source; Stress; Structure; System; Systems Biology; Technology; Testing; Tissues; United States National Institutes of Health; Universities; Validation; base; biological systems; cost; environmental change; human disease; innovation; metabolomics; microorganism; nitrosative stress; product development; programs; protein metabolite; protein profiling; response; small molecule; technology/technique; tool; transcriptomics

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Metabolomics is the study of the repertoire of non-proteinaceous, endogenously-synthesized small molecules present in any organism. Small molecules present in the metabolome are ultimately the product of cellular metabolism. These molecules are varied from peptide, glucose, cholesterol, ATP and lipids etc. The change in levels of these metabolites in consequence of certain metabolic process or disease state and can be used as biomarkers. The power of metabolomic investigations versus transcriptomic and proteomic ones is that the metabolite dictionary is believed to be an order of magnitude smaller than the repertoire of expressed genes in an organism. In addition, metabolite profiles provide direct versus inferred readouts on the functional consequences of genetic and environmental changes. Furthermore, small metabolites structure is independent of the species under investigation and can be easily relate to different species. Recent developments at the University of Nebraska have led to the advent of genomics, bioinformatics and proteomics supported by dedication of faculty lines and creation of related core facilities at both UNL and UNMC. Therefore, we have developed a new capacity in the complementary area of metabolomics, which is at the cutting edge of functional biology research and is important for the programs of a number of investigators in the Redox Biology Center as well as for the other related research labs at UNL. Mass spectrometry based high-throughput proteomics and metabolomics, a part of system biology, is foundational for a full understanding of a biological system including a metabolic process or disease state, and has received considerable attention since the sequencing of the human genome. Oxidative/nitrosative damage by reactive radical species appears to be central to the pathogenesis of many human diseases and is central to a broad range of biotic and abiotic stress and physiological responses in microorganisms, plants and other animals. Specific modified proteins or metabolites are generated following stressing insults and accumulate in different degenerated tissues and fluids, determining altered organ functionalities. System biology based technologies have been propitious to the development of molecular medicine, especially in the discovery of diagnostic biomarkers of oxidative and nitrosative stress enabling early detection of diseases, such as lung cancer, from these biological fluids. The Laboratory for Proteomics and Metabolomics analysis at the Redox Biology Center (RBC) supports scientists within the RBC and the University of Nebraska. The Core provides all the tools of modern functional proteomics and metabolomics. Equipped with cutting edge mass spectrometry based state-of-the-art technologies for proteomics and metabolomics; protein and metabolite profiling, protein identification, protein and peptide fractionation and quantitation, differential expression analysis, shot gun proteomics, personalized experimental design consultation and comprehensive individualized bioinformatics support. The past year was very productive for the core. We were able to implement the only discovery proteomic differential expression analysis platform (mudPIT) in the state of Nebraska and were able to provide service to 27 users in 2010 and 35 in 2011. We implemented a state of the art proteomic bioinformatic platform for extensive data analysis. In addition, a new SRM/MRM targeted proteome analytical platform was developed and used for service at UNL and UNMC researchers. At present this is the only platform we have to achieve the targeted proteome analysis and validation. Late last year we procured a UPLC system and set up a routine metabolite profiling platform. Since there is no centralized metabolite library available to search and identify we developed new Bioinformatic software called METLIBUNL. Using this software one can add many new metabolite to the library and search the data. This unit is available for all users. We also procured other innovative software such as the LIPDVIEW for lipid profiling. The utilization of the unique technology and techniques available at the Laboratory for Proteomics and Metabolomics provided data that supported many investigators with the submission of several external grants including RO1 at NIH. This unit also attracted two industries including BioRad for a product development and testing.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 代谢组学是研究存在于任何生物体中的非蛋白质的、内源性合成的小分子的所有组成部分的学科。 存在于代谢组中的小分子最终是细胞代谢的产物。 这些分子包括肽、葡萄糖、胆固醇、ATP和脂质等。这些代谢产物的水平变化是某些代谢过程或疾病状态的结果，可以用作生物标志物。 代谢组学研究相对于转录组学和蛋白质组学研究的力量在于，代谢物字典被认为比生物体中表达基因的库小一个数量级。此外，代谢物谱提供了遗传和环境变化的功能后果的直接与推断的读数。此外，小分子代谢物的结构与所研究的种属无关，并且可以很容易地与不同种属相关。内布拉斯加大学的最新发展导致了基因组学，生物信息学和蛋白质组学的出现，这些都得到了UNL和UNMC教师队伍的奉献和相关核心设施的创建的支持。因此，我们在代谢组学的补充领域开发了一种新的能力，这是功能生物学研究的前沿，对氧化还原生物学中心的一些研究人员的计划以及UNL的其他相关研究实验室非常重要。 基于质谱的高通量蛋白质组学和代谢组学是系统生物学的一部分，是全面了解包括代谢过程或疾病状态的生物系统的基础，并且自从人类基因组测序以来已经受到相当大的关注。 由活性自由基物种引起的氧化/亚硝化损伤似乎是许多人类疾病的发病机制的核心，并且是微生物、植物和其他动物中广泛的生物和非生物胁迫和生理反应的核心。特定的修饰蛋白质或代谢物在应激损伤后产生，并在不同的变性组织和体液中积累，决定器官功能的改变。基于系统生物学的技术已经有利于分子医学的发展，特别是在氧化和亚硝化应激的诊断生物标志物的发现中，使得能够从这些生物流体中早期检测疾病，例如肺癌。 氧化还原生物学中心（RBC）的蛋白质组学和代谢组学分析实验室为RBC和内布拉斯加大学的科学家提供支持。 核心提供现代功能蛋白质组学和代谢组学的所有工具。配备了最先进的基于质谱的蛋白质组学和代谢组学技术;蛋白质和代谢物分析，蛋白质鉴定，蛋白质和肽分级和定量，差异表达分析，鸟枪蛋白质组学，个性化实验设计咨询和全面的个性化生物信息学支持。 过去的一年对核心来说是非常富有成效的。我们能够在内布拉斯加州实施唯一的发现蛋白质组差异表达分析平台（mudPIT），并在2010年和2011年分别为27名和35名用户提供服务。我们实现了一个最先进的蛋白质组生物信息学平台，用于广泛的数据分析。此外，还开发了一个新的SRM/MRM靶向蛋白质组分析平台，并用于UNL和UNMC研究人员的服务。这是目前我们唯一能够实现靶向蛋白质组分析和验证的平台。去年年底，我们采购了一个UPLC系统，并建立了一个常规代谢物分析平台。由于没有集中的代谢物库可用于搜索和识别，我们开发了新的生物信息学软件METLIBUNL。使用该软件可以添加许多新的代谢物到库中并搜索数据。该设备适用于所有用户。我们还采购了其他创新软件，如用于脂质分析的LIPDVIEW。 利用蛋白质组学和代谢组学实验室提供的独特技术和方法提供了支持许多研究人员提交的数据，包括NIH的RO 1。 该单位还吸引了包括BioRad在内的两个行业进行产品开发和测试。