A proximity ligation method to track mobile element hosts

一种追踪移动元件宿主的邻近连接方法

• 批准号: 9907327
• 负责人: Ivan Liachko
• 金额: $ 59.9万
• 依托单位: PHASE GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-01 至 2021-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9907327
• 关键词: Address; Agriculture; Antimicrobial Resistance; Bacteriophages; Benign; Biochemical Pathway; Biological; Biology; Cells; Chromatin; Chromosomes; Client; Communities; Complex; Complex Mixtures; Computer software; DNA; Data; Data Analyses; Data Reporting; Drug resistance; Elements; Evolution; Future; Generations; Genes; Genome; Genomics; Goals; Horizontal Gene Transfer; Hybrids; Individual; Laboratories; Laboratory culture; Lead; Libraries; Ligation; Metagenomics; Methods; Oranges; Organism; Phase; Plasmids; Primer Extension; Proteins; Proto-Oncogene Protein c-kit; Protocols documentation; RNA; Reporting; Research; Sampling; Services; Shotguns; Small Business Innovation Research Grant; Speed; System; Techniques; Technology; Testing; TimeLine; Virulence; Virulent; Virus; Work; base; biochemical evolution; computational platform; cost; cost effective; crosslink; design; experience; extrachromosomal DNA; innovation; interest; member; microbial community; microbiome; microorganism; next generation sequencing; novel; scaffold; software development; technology development; tool; transmission process; transposon/insertion element; user-friendly; web portal

ABSTRACT In this application, we propose to develop Hi-C technology and data analysis software for a user-friendly method to associate antimicrobial resistant (AMR) and virulence gene-containing mobile elements with their associated bacterial strains. Mobile elements are extra-chromosomal DNA or RNA molecules that encode functional elements. These molecules can be transmitted between members of the same species and across disparate species, leading to the rapid evolution of biochemical pathways through the sharing of mobile element-encoded proteins. This has a profound influence on the evolution of microbial communities, with particular impact on the drug resistance and virulence profiles of the members of the communities. To date, there is no cost-effective method for identifying mobile element hosts in a mixed microbial community: A significant fraction of microorganisms are unculturable under laboratory settings and current shotgun genomic methods fail to capture host information. Therefore, a new tool is needed to provide the information critical to understanding mobile element biology. Methods such as chromosome confirmation capture (3C) and Hi-C can be used rapidly and with high accuracy to identify DNA molecules that co-exist within individual cells directly from a mixed culture or biological sample. The goal of this proposal to develop a new class of tools that can be used to identify the hosts and transmission of mobile elements in a complex microbial community. The product proposed in this SBIR Phase II application addresses the need for rapid, culture-free identification of mobile element-host relationships in complex microbial communities. The method is built upon Phase Genomics’ expertise with the use of Hi-C and 3C techniques, which allows to deconvolve complex mixtures of cells within microbial communities, without the need for laboratory culture. In this application, we propose to produce a method that reduces cost, increases speed, and simplifies the analysis of a proximity ligation-based test to associate plasmids with their host. Our approach is based on two discrete work packages: Aim 1 is focused on combining target enrichment and proximity-ligation methods to reduce sequencing costs associated with metagenomic deconvolution. In Aim 2, we will develop and design a customer-facing web portal for upload and analysis of data in which our clients can navigate easily. Upon completion of the proposed project, we will have laid the basis for a first-generation target enrichment Hi- C kit and service that will make our innovative platform commercially available.

抽象的 在此应用程序中，我们建议为用户友好的方法开发HI-C技术和数据分析软件 将抗菌素抗药性（AMR）和含病毒基因移动元件与其相关的 细菌菌株。 移动元件是编码功能元件的染色体外DNA或RNA分子。这些 分子可以在同一物种的成员和各种物种之间传播，导致 通过移动元件编码蛋白的共享生化途径的快速演变。这就是 对微生物群落进化的深远影响，对耐药性和 社区成员的病毒概况。 迄今为止，在混合微生物社区中识别移动元件宿主的成本有效方法： 在实验室环境和当前的shot弹枪基因组下，微生物的很大一部分是无法培养的 方法无法捕获主机信息。因此，需要一个新工具来提供至关重要的信息 了解移动元件生物学。诸如染色体确认捕获（3C）和HI-C等方法 迅速使用并具有高精度以鉴定在单个细胞中共存的DNA分子 直接来自混合培养或生物样品。该提案的目的是开发新的工具类 可以用来识别复杂微生物社区中移动元素的宿主和传播。 SBIR II期应用程序中提出的产品解决了对快速，无文化识别的需求 复杂微生物群落中的移动元素 - 宿主关系。该方法是基于阶段构建的 基因组学专业知识在使用HI-C和3C技术方面的专业知识，该技术允许解析复杂的混合物的复杂混合物 微生物群落中的细胞，无需实验室培养。 在此应用程序中，我们建议产生一种降低成本，提高速度并简化的方法 分析基于连接的基于连接的测试，以将质粒与宿主相关联。我们的方法是基于两个 离散工作包： AIM 1专注于结合目标富集和接近纽带的方法以降低测序成本 与宏基因组解卷积有关。在AIM 2中，我们将开发和设计面向客户的Web门户网站 为了上传和分析我们的客户可以轻松导航的数据。 拟议项目完成后，我们将为第一代目标富集提供基础 C套件和服务将使我们的创新平台在市售。