Cryptococcus genomic resources

隐球菌基因组资源

• 批准号: 10444326
• 负责人: Hiten D Madhani
• 金额: $ 76.37万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-01 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10444326
• 关键词: AIDS/HIV problem; Accounting; Animal Disease Models; Animals; Biochemical; Biological; C-terminal; CRISPR screen; CRISPR/Cas technology; Cells; Cessation of life; Clinical; Code; Codon Nucleotides; Collection; Communities; Coupled; Cryptococcus; Cryptococcus neoformans; DNA; DNA Sequence; Data; Data Analyses; Databases; Defect; Deposition; Diagnosis; Disease; Encapsulated; Foundations; Fungal Meningitis; Gene Cluster; Gene Deletion; Gene Proteins; Generations; Genes; Genetic; Genome; Genomics; Growth; Haploidy; Human; Image; In Vitro; Investigation; Knock-out; Laboratories; Letters; Libraries; Maps; Medical; Methodology; Methods; Microscopy; Modification; Mus; Mycoses; Oligonucleotides; Online Systems; Open Reading Frames; Pathway interactions; Pharmaceutical Preparations; Positioning Attribute; Production; Proteins; Publications; Quality Control; Research; Resources; Saccharomyces cerevisiae; Saccharomycetales; Site; The science of Mycology; Update; Virulence; Work; Yeast Model System; base; deletion library; design; design and construction; fitness; fungal genetics; gene gun; genome-wide; homologous recombination; knockout gene; machine learning method; member; mutant; next generation sequencing; novel; novel strategies; pathogen; pathogenic fungus; screening; therapy development; tool; web-accessible; web-based informatics; whole genome

Effective diagnosis and treatment of invasive fungal infections is a major unmet clinical challenge. Annotated genomic sequences of the major fungal pathogens create an opportunity to revolutionize medical mycology through the application of systematic approaches. To be maximally useful, genome sequences must be coupled with genome-wide biological resources. The availability of genome-wide knockout and tagged gene collections as well as a global genetic interaction map have been instrumental in catalyzing research progress in the model yeast Saccharomyces cerevisiae. The generation of analogous resources in pathogenic fungi creates experimental tools enabling comprehensive approaches to elucidating the basis of fungal virulence in the mammalian host and to develop drugs. Cryptococcus neoformans is an encapsulated budding yeast that causes fungal meningitis, resulting in ~200,000 fatalities each year. C. neoformans has haploid genetics, homologous recombination, and excellent animal models of disease. In the last period, we used biolistic transformation and long homology targeting constructs to complete a gene knockout collection, performed extensive quality control work, developed quantitative methods for screening the library in pools, and performed pooled screens both in mice and in vitro. We have made the strains available without restriction to the community via the Fungal Genetic Stock Center (FGSC). This resource has already been used in over 30 publications. To accelerate genome modification, we developed the first short-homology CRISPR-Cas9 methods for C. neoformans. We have also created an effective combined localization and purification tag. Preliminary work demonstrates that these methods can be deployed at scale to enable construction of a tagged strain collection. In addition, we have devised a novel method that enables pooled CRISPR-Cas9 screens in C. neoformans. Capitalizing on these technical advances, we will 1) complete the Cryptococcus whole-genome tag collection including production of an image resource, and 2) construct a first-generation genetic interaction map focused on virulence determinants. Accomplishment of the first aim will enable the cell biological and/or biochemical investigations of any protein. Completion of the second aim will deorphanize large fraction genes through membership in clusters of genes with known functions while defining new modules/pathways. This information will be integrated into the searchable and web accessible VEuPathDB database. Together these new genomic resources will accelerate the ability of the research community to understand and develop therapies against the most common cause of human fungal meningitis.

侵袭性真菌感染的有效诊断和治疗是一个主要的未满足的临床挑战。注释 主要真菌病原体的基因组序列为医学真菌学的革命创造了机会 通过采用系统的方法。为了发挥最大的作用，基因组序列必须 全基因组生物资源。全基因组敲除和标记基因集合的可用性 以及全球遗传相互作用图有助于催化该模型的研究进展 酿酒酵母病原真菌中类似资源的产生 实验工具，使全面的方法来阐明真菌毒力的基础， 哺乳动物宿主并开发药物。新型隐球菌是一种封装的芽殖酵母， 真菌性脑膜炎，每年导致约20万人死亡。C. neoformans具有单倍体遗传学，同源 重组，和疾病的优良动物模型。在上一阶段，我们使用了生物射弹转化， 长同源靶向构建体，以完成基因敲除收集，进行了广泛的质量控制 工作，开发了用于筛选库中的库的定量方法，并在两个库中进行了合并筛选。 小鼠和体外。我们已经通过真菌遗传学研究所向社区提供了不受限制的菌株。 库存中心（FGSC）。这一资源已在30多份出版物中使用。为了加速基因组 通过改进，我们开发了第一个用于C.新人类我们还 创建了有效的组合定位和纯化标签。初步研究表明， 可以大规模地使用这些方法以能够构建标记的菌株集合。另外我们有 设计了一种新的方法，可以在C.新人类利用这些 技术进步，我们将1）完成隐球菌全基因组标签收集，包括生产 图像资源，以及2）构建第一代遗传互作图谱，重点关注毒力 决定因素第一个目标的实现将使细胞生物学和/或生物化学研究成为可能， 任何蛋白质。第二个目标的实现将通过聚类中的成员关系来去除大部分基因的冗余 在定义新的模块/途径的同时，这些信息将被整合到 可搜索和网络访问的VEuPathDB数据库。这些新的基因组资源将加速 研究界理解和开发针对最常见的疾病原因的治疗方法的能力 人类真菌性脑膜炎