Genome biology of Francisella tularensis populations

土拉弗朗西斯菌种群的基因组生物学

• 批准号: 6823974
• 负责人: ANDREW K BENSON
• 金额: $ 19.55万
• 依托单位: UNIVERSITY OF NEBRASKA LINCOLN
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-06-01 至 2006-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6823974
• 关键词: Francisella tularensis; bacteria infection mechanism; bacterial genetics; bioterrorism /chemical warfare; computer program /software; ecology; genetic library; genetic strain; microarray technology; microorganism population study; nucleic acid sequence; phenotype; polymerase chain reaction; southern blotting; virulence

DESCRIPTION (provided by applicant): Francisella tularensis is a highly infectious, risk-group A select bacterial agent that has the potential to be weaponized. It is the cause of tularemia. The applicants' long-term goal is to understand the pathways of genes and gene products that drive unique virulence and transmissibility traits of the four subspecies of F. tularensis. The objective of this R21 application is to identify genes that are responsible for virulence and transmissibility of the most virulent subspecies of this bacterium. The central hypothesis is that increased virulence and transmissibility are attributable to genetic differences. This hypothesis will be tested by pursuing three specific aims: 1) Design and characterize a reference strain collection representing both F. tularensis subsp. tularensis and supsp. holarctica with temporal and spatial representation; 2) Fabricate representative reference microarrays of the tularensis and holarctica subsp. and systematically probe genome diversity of the strain collection using arrays; and 3) Use paired-end sequence mapping to complement data from the microarray-based studies. The principal approaches and methods to be used include alternative strategies and tactics to systematically catalogue subspecies-specific genome segments. This will be accomplished using DNA microarray analyses (arrays derived from shotgun libraries prepared from the representative subsp. tularensis and holarctica) and a novel algorithm for data sorting followed by DNA sequence analyses and confirmation by Southern blotting and PCR. Second, a narrow (10Kb)-size library from a representative holarctica strain will be used to generate paired-end sequence reads, after which the list will be mapped to the subsp. tularensis genome sequence. This will allow length differences that are subspecies-specific to be identified. The outcomes are collectively significant, because they are expected to provide strong preliminary evidence that strain differences in virulence and transmissibility are attributable to genomic differences. Such data are expected to become the foundation for definitive R01-level investigations involving the functional analyses of candidate genes. These studies will significantly increase our understanding of the pathobiology of this organism, provide candidate gene products for vaccine and therapeutics, and provide loci for development of improved diagnostic and forensic markers.

描述（由申请方提供）：土拉热弗朗西丝菌是一种高度传染性、风险组A选择性细菌因子，具有武器化潜力。它是兔热病的病因。申请人的长期目标是了解驱动F.土拉热。该R21申请的目的是鉴定负责该细菌最毒力亚种的毒力和传播性的基因。核心假设是，增加的毒力和传染性是由于遗传差异。这一假设将通过追求三个具体目标来检验：1）设计和表征代表F.土拉热亚种土拉菌和土拉菌亚种2）制作土拉线虫和全北极线虫亚种的代表性参考微阵列;并使用阵列系统地探测菌株集合的基因组多样性;以及3）使用配对末端序列作图来补充来自基于微阵列的研究的数据。所采用的主要办法和方法包括系统地对亚种特异性基因组片段进行编目的替代战略和战术。这将使用DNA微阵列分析（来自鸟枪文库的阵列，所述鸟枪文库是从代表性的亚种制备的）来完成。tularensis和holarctica）和一种新的数据分类算法，然后进行DNA序列分析和Southern印迹和PCR确认。第二，来自代表性的全北极线虫菌株的窄（10 Kb）大小文库将用于产生双端序列读段，之后该列表将被映射到亚种。土拉热菌基因组序列。这将允许识别亚种特异性的长度差异。这些结果具有集体意义，因为它们有望提供强有力的初步证据，证明毒力和传播性的菌株差异可归因于基因组差异。这些数据有望成为确定的R 01级调查的基础，涉及候选基因的功能分析。这些研究将显著增加我们对这种生物体的病理生物学的理解，为疫苗和治疗提供候选基因产物，并为开发改进的诊断和法医标记物提供位点。