Identification of Biological Materials of Unknown Origin

来源不明的生物材料的鉴定

• 批准号: 7559531
• 负责人: Khalid Sayood
• 金额: $ 15.6万
• 依托单位: UNIVERSITY OF NEBRASKA LINCOLN
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-02-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7559531
• 关键词: Address; Algorithms; Antibiotic Resistance; Area; Automation; Award; Bacillus anthracis; Bacteria; Bacterial DNA; Base Sequence; Behavior; Biocompatible Materials; Bioinformatics; Biological; Biological Models; Biological Process; Bioterrorism; Brucella abortus; Burkholderia mallei; Burkholderia pseudomallei; Characteristics; Classification; Cluster Analysis; Commit; Communicable Diseases; Computational Biology; Coxiella; DNA; DNA Sequence; Data; Detection; Development; Discrimination; Doctor of Medicine; Doctor of Philosophy; Escherichia coli; Frequencies; Funding; Genes; Genome; Genomics; Goals; Image; Individual; Institution; Intervention; Investigation; Knowledge; Laboratories; Lead; Mediating; Medical; Mentors; Methods; Microbiology; Modeling; Nebraska; Oligonucleotides; Organism; Outcome; Pathogenicity; Pattern; Phylogenetic Analysis; Play; Polynucleotides; Procedures; Promoter Regions; Public Health; Research; Research Personnel; Research Training; Role; Salmonella enterica; Shigella flexneri; Site; Speech; Staging; Staphylococcus aureus; Stretching; Structure; Study Section; Techniques; Terrorism; Testing; Therapeutic Intervention; Time; Training; Training Activity; Training Programs; Trees; United States National Institutes of Health; Universities; Wood material; Work; base; biosecurity; career; cost; expectation; experience; hazard; information organization; innovation; interest; mathematical model; microbial; organizational structure; programs; tool; virology

The applicant's long term goal is to understand and elucidate structure and organization within DNA sequences and uncover their relationship to biological functions. The objective of this application, which is a step toward the attainment of this long term goal, is to develop techniques for elucidating occult structural features in bacterial DNA which can be used for identification and differentiation of microbial organisms, including organisms whose genome has not been completely sequenced, using short fragments of DNA. A parallel goal is to achieve investigative independence as a computational biologist. The latter goal will be accomplished through coursework and training in the laboratories of Dr. S. Hinrichs, M.D. The urgent need for rapid identification tests for biological materials has intensified because of the threat posed by bio- terrorism. Rapid identification of both the fact and the mode of attack is essential for timely therapeutic intervention. The ability to identify bacteria based on short sequences of incomplete or possibly corrupt sequences allows for hazard detection, automation, and low cost distributed sensing capability. The identification techniques will be developed using three tools; the average mutual information (AMI) profile which reflects statistical relationships between bases along the DNA sequence, a cluster analysis technique developed by the applicant and co-workers which identifies genome specific trinucleotide clustering patterns, and a parsing technique for identification of polynucleotide sequences of interest. Components of the AMI profile which possess discriminatory capabilities will be identified by decomposing the profile and analyzing the coefficients using both supervised and unsupervised classification. The clustering strategy will be refined by correlating parameters in the technique with known biological behavior. Signature trinucleotide and polynucleotide clustering patterns will be identified for organisms of interest. The different classifications will be combined into a tree structured test for a model panel of bacteria of medical interest.

申请人的长期目标是理解和阐明DNA内的结构和组织 序列并发现它们与生物学功能的关系。该应用程序的目的，这是一个 迈向实现这一长期目标的一步是开发阐明神秘结构的技术 细菌DNA的特征，可用于鉴定和分化微生物， 包括使用简短的DNA片段对基因组没有完全测序的生物。一个 并行目标是作为计算生物学家实现研究独立性。后一个目标将是 通过S. Hinrichs博士的实验室进行课程和培训完成的迫切需求 对于生物材料的快速鉴定测试，由于生物构成的威胁，因此加剧 恐怖主义。快速识别事实和攻击方式对于及时治疗至关重要 干涉。基于短序列不完整或可能损坏的细菌识别细菌的能力 序列允许检测危险，自动化和低成本分布式感应能力。这 识别技术将使用三个工具开发；平均相互信息（AMI）概况 这反映了沿DNA序列碱基之间的统计关系，群集分析技术 由申请人和同事开发的，这些申请人识别基因组特异性三核苷酸聚类模式， 以及一种用于鉴定多核苷酸序列的解析技术。 AMI的组件 具有歧视功能的配置文件将通过分解和分析来识别 使用监督和无监督分类的系数。聚类策略将被完善 通过将技术中的参数与已知的生物学行为相关联。签名的三核苷酸和 将确定针对感兴趣的生物的多核苷酸聚类模式。不同的分类将 将其结合成树结构化测试，以进行医学兴趣的细菌模型面板。