INBRE-2 GENOMICS OF ALASKAN SOIL TO MONITOR PATHOGENIC FUNGI

用于监测致病真菌的阿拉斯加土壤 INBRE-2 基因组学

• 批准号: 8167418
• 负责人: Donald L Taylor
• 金额: $ 7.09万
• 依托单位: UNIVERSITY OF ALASKA FAIRBANKS
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-03-01 至 2011-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8167418
• 关键词: Alaska; Alaska Native; Candida; Clinical; Computer Retrieval of Information on Scientific Projects Database; Cryptococcus; Databases; Development; Disease Outbreaks; Funding; Genbank; Genomics; Goals; Grant; Health; Human; Immune; Individual; Institution; Knowledge; Libraries; Lung diseases; Medical; Meningitis; Molecular; Monitor; Phylogenetic Analysis; Pilot Projects; Research; Research Personnel; Resources; Soil; Source; Surveys; Systemic infection; The science of Mycology; United States National Institutes of Health; Work; base; fungus; human disease; interest; pathogen; soil sampling

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Soil is the major environmental reservoir of fungi that cause human diseases. Surveys of medically important fungi have been carried out using selective isolation approaches, but, to our knowledge, comprehensive molecular surveys of fungal diversity in soil have yet to be applied to surveillance in medical mycology. The Taylor lab has spearheaded extensive soil sampling combined with in-depth sequencing of PCR clone libraries in order to characterize fungal diversity in Interior Alaska. To date, we have generated roughly 100,000 fungal ITS clone sequences, a number surpassing the total number of fungal ITS sequences in GenBank. Here, we propose a pilot study to investigate the diversity of fungi of concern to human health recovered from these soil PCR libraries. We will carry out comprehensive phylogenetic analyses of all fungi of medical interest in our massive sequence database. As exemplars, we present here phylogenetic analyses of the genus Cryptococcus, a leading causative agent of respiratory diseases and meningitis in immune-compromised individuals, and the genus Candida, species of which belong to the normal human flora, but which occasionally cause dangerous systemic infections. Sequences recovered from Alaskan soils in both fungal groups are diverse, and include putative new species with no prior known sequences. We also propose to amplify and sequence additional loci in cases where the relationship of Alaskan entities to known clinical strains is uncertain based solely on ITS sequences. Our ultimate goal is to obtain additional external funding to expand this surveillance work through application of an Affymetrix microarray that is under development and through sampling of soils in additional regions of Alaska, particularly the southeast where monitoring for the outbreak pathogen Cryptococcus gattii would seem warranted.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 土壤是引起人类疾病的真菌的主要环境库。 已经使用选择性隔离方法对医学上重要的真菌进行了调查，但是据我们所知，土壤中真菌多样性的全面分子调查尚未应用于医学真菌学的监测。 泰勒实验室（Taylor Lab）已将广泛的土壤采样与PCR克隆文库的深入测序相结合，以表征阿拉斯加内部的真菌多样性。 迄今为止，我们已经生成了大约100,000个真菌的克隆序列，这一数字超过了其在GenBank中的真菌总数。 在这里，我们提出了一项试点研究，以研究从这些土壤PCR图书馆中回收的人类健康所关注的真菌多样性。我们将对大量序列数据库中所有医学兴趣的真菌进行全面的系统发育分析。作为示例，我们在这里提出了对免疫功能低下个体中呼吸道疾病和脑膜炎的主要病因的系统发育分析，而念珠菌属的念珠菌（属于正常的人类植物群），但偶尔会引起危险的全身感染。 从两个真菌组中从阿拉斯加土壤中回收的序列都是多种多样的，其中包括未知序列的假定新物种。 我们还建议在阿拉斯加实体与已知临床菌株的关系的情况下，放大和序列其他基因座，仅基于其序列不确定。 我们的最终目标是获得额外的外部资金，通过应用正在开发的Affymetrix微阵列以及在阿拉斯加其他地区的泥土进行采样，尤其是东南部，在那里监视疫情病原体Gattioi gattii似乎是有必要的。