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: 7010692
• 负责人: FRED S DIETRICH
• 金额: $ 35.72万
• 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 2008-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7010692
• 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; 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（由申请人提供）：加密型新羊角人是一种人类病原体，可在免疫功能低下和免疫能力的宿主中引起生命威胁脑膜脑炎。该生物是单倍体的，具有定义的性周期，发达的分子生物学研究工具以及用于毒力研究的强大动物模型。基因组的基本结构已经很好地表征了，约为20至14个染色体的20MB。目前，一个基因组联盟正在测序一个代表性实验室菌株JEC21的基因组。预计JEC21序列将在12个月内完成。 Neoformans分离株之间存在相当大的多样性。分离株已分为四种血清型，在DNA序列水平上有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，辩论仍在继续。重要的是，这些血清型不仅在它们的多糖囊抗原上有所不同，而且在生理特性和致病性方面也有所不同。 与临床分离株的血清型序列相比，使用JEC21序列的比较基因组学方法是解决变异的潜在性质及其与致病性的最直接方法及其与致病性的关系。 JEC21是一种实验室适应性菌株，该菌株源自临床分离株，并通过12个反向杂交的环境分离株，可能会衰减以造成毒力。因此，我们建议确定和注释Neoformans血清型A菌株H99的完整序列。在所有临床分离株中，超过90％的艾滋病患者中的所有临床分离株和99％的分离株均为血清型A，而H99菌株是一种表征良好的临床分离株。与温哥华基因组中心合作，我们制作了初步材料和结果，以确定以本应用程序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种比较数据，即对这两种菌株之间的差异和一系列用于加密赛车基因分型的微阵列之间的差异进行仔细分析。这项研究的结果数据和材料将扩大我们对这种重要人类真菌病原体中致病性本质的了解。