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.

有效的侵入性真菌感染的诊断和治疗是一项重大的未经临床挑战。注释 主要真菌病原体的基因组序列创造了革新医学真菌学的机会 通过应用系统方法。为了最大程度地有用，基因组序列必须耦合 具有全基因组生物资源。全基因组淘汰和标记基因收集的可用性 以及全球遗传相互作用图也有助于催化该模型的研究进度 酿酒酵母的酵母糖酵母。致病真菌中类似资源的产生产生 实验工具实现了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。加密赛车是一种封装的萌芽酵母菌，引起了 真菌性脑膜炎，每年造成约200,000人死亡。 C. Neoformans具有单倍体遗传学，同源 重组和出色的疾病动物模型。在上一个时期，我们使用了生物主义转化和 长长的同源性靶向构造以完成基因淘汰赛，进行了广泛的质量控制 工作，开发了用于筛选池中库的定量方法，并在 小鼠和体外。我们已经通过真菌遗传使菌株无限制地向社区提供了可用的菌株 股票中心（FGSC）。该资源已经在30多个出版物中使用。加速基因组 修改后，我们开发了针对Neoformans的第一个短输血CRISPR-CAS9方法。我们也有 创建了有效的组合本地化和纯化标签。初步工作表明这些 可以大规模部署方法以构建标记的应变收集。此外，我们还有 设计了一种新型方法，可以在C. Neoformans中启用CRISPR-CAS9屏幕。利用这些 技术进步，我们将1）完成加密全基因组标签的收集，包括生产 图像资源和2）构建着针对毒力的第一代遗传相互作用图 决定因素。实现第一个目标将使细胞生物学和/或生化研究 任何蛋白质。第二个目标的完成将通过群集的成员资格去脱磷 具有已知功能的基因，同时定义新模块/途径。此信息将集成到 可搜索和Web可访问的VEUPATHDB数据库。这些新的基因组资源将加速 研究界能够理解和发展疗法的能力 人真菌脑膜炎。