A Genomics Approach to Study C. neoformans var. grubii

研究新型隐球菌变种的基因组学方法

• 批准号: 6700223
• 负责人: FRED S DIETRICH
• 金额: $ 36.58万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-02-01 至 2007-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6700223
• 关键词: Cryptococcus neoformans; comparative genomic hybridization; fungal genetics; genetic polymorphism; genetic strain; genotype; high throughput technology; microarray technology; nucleic acid sequence; opportunistic infections; pathologic process; polymerase chain reaction; restriction fragment length polymorphism; serotyping; virulence

DESCRIPTION (provided by applicant): Cryptococcus neoformans is a human pathogen that causes life threatening meningoencephalitis in immunocompromised and immunocompetent hosts. The organism is haploid and has a defined sexual cycle, well developed molecular biology research tools, and robust animal models for virulence studies. The basic structure of the genome is well characterized, being about 20MB distributed over 12 to 14 chromosomes. Currently a genome consortium is sequencing the genome of one representative laboratory strain, JEC21. It is anticipated that the JEC21 sequence will be completed within 12 months. There is considerable diversity among C. neoformans isolates. Isolates have been divided into four serotypes which differ by 10% or more at the DNA sequence level. Debate continues over whether these serotypes (A, B, C, D) should be considered different varieties or species. What is important is that these serotypes differ in not only their polysaccharide capsular antigens, but also in physiological properties and in pathogenicity. The most direct and efficient way to address the underlying nature of variation and its relationship to pathogenicity in C. neoformans is a comparative genomics approach taking advantage of the JEC21 sequence, in comparison with the sequence of a serotype A clinical isolate. JEC21 is a laboratory adapted strain derived from a clinical isolate and an environmental isolate by 12 backcrosses and may be attenuated for virulence. We thus propose to determine and annotate the complete sequence of C. neoformans serotype A strain H99. Greater than 90% of all clinical isolates and 99% of all isolates from AIDS patients are of serotype A, and strain H99 is a well characterized clinical isolate. In collaboration with the Vancouver Genome Center, we have produced the preliminary material and results to establish the feasibility of completing the genome in the manner described in this application. We also propose developing the basic resources to exploit this comparative data, namely a careful analysis of the differences between these two strains and a series of microarrays for genotyping of Cryptococcus strains. The resulting data and material from this study will expand our knowledge of the nature of pathogenicity in this important human fungal pathogen.

描述（由申请方提供）：新型隐球菌是一种人类病原体，可在免疫功能低下和免疫功能正常的宿主中引起危及生命的脑膜脑炎。该生物体为单倍体，具有明确的性周期、发达的分子生物学研究工具和用于毒力研究的稳健动物模型。基因组的基本结构被很好地表征，约20MB分布在12至14条染色体上。目前，一个基因组联盟正在对一种代表性的实验室菌株JEC21的基因组进行测序。预计JEC21序列将在12个月内完成。 C.新形式分离物。分离株被分为四种血清型，在DNA序列水平上相差10%或更多。关于这些血清型（A、B、C、D）是否应被视为不同的品种或物种的争论仍在继续。重要的是，这些血清型不仅在它们的多糖荚膜抗原上不同，而且在生理特性和致病性上也不同。 研究变异的本质及其与致病性的关系，最直接、最有效的方法是建立一个新的致病性基因组。新型流感病毒是一种比较基因组学方法，利用JEC21序列与血清型A临床分离株的序列进行比较。JEC21是通过12次回交从临床分离株和环境分离株衍生的实验室适应菌株，并且可以减毒。因此，我们建议确定和注释C的完整序列。新生儿血清型A株H99。超过90%的所有临床分离株和99%的来自AIDS患者的所有分离株是血清型A，并且菌株H99是充分表征的临床分离株。与温哥华基因组中心合作，我们已经产生了初步材料和结果，以确定以本申请中描述的方式完成基因组的可行性。我们还建议开发基本资源来利用这些比较数据，即仔细分析这两种菌株之间的差异以及一系列用于隐球菌菌株基因分型的微阵列。从这项研究中得到的数据和材料将扩大我们对这种重要的人类真菌病原体的致病性本质的认识。