Understanding host-virus interactions at the single cell level

了解单细胞水平的宿主-病毒相互作用

• 批准号: 9377495
• 负责人: David A VAN VALEN
• 金额: $ 6.48万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-05-04 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9377495
• 关键词: Algorithms; Automobile Driving; Bacteria; Bacterial Physiology; Bacteriophage lambda; Bacteriophages; Benign; Biochemical; Biological Models; Biology; Carbon; Cell Size; Cells; Computer Vision Systems; Consensus; Coupled; Cytolysis; DNA; Data; Data Analyses; Decision Making; Development; Disease; Enzymes; Escherichia coli; Genetic; Genetic Materials; Genome; Goals; Health; Horizontal Gene Transfer; Human; Image; Individual; Infection; Label; Learning; Libraries; Literature; Lysogeny; Lytic; Manuals; Measurement; Measures; Mediating; Modeling; Modern Medicine; Modernization; Molecular; Molecular Target; Outcome; Peptide Hydrolases; Phosphorus; Physiological; Physiology; Plasmids; Play; Probability; Process; Proteins; Regulatory Element; Reporter; Reporting; Resistance; Role; Source; System; Technology; Temperature; Testing; Viral Physiology; Viral Proteins; Viral Regulatory Proteins; Virus; Weight; Work; base; cellular imaging; experimental study; genetic regulatory protein; imaging Segmentation; live cell imaging; microbial; new technology; novel; pathogen; protein function; public health relevance; transcription factor; virus host interaction

 DESCRIPTION (provided by applicant): The microbial world presents one of the largest challenges to modern medicine in the 21st century in the form of novel, untreatable pathogens. Bacteriophages, the viruses that infect bacteria, are a major driver of this challenge. In particular, bacteriophages mediate the exchange of novel genetic materials (a process known as horizontal gene transfer, or HGT) between bacteria, transforming otherwise benign bacteria into human pathogens and driving the rapid emergence of pathogens resistant to existing treatments. Accordingly, there is a critical need to elucidate when, where, and how phage-mediated HGT occurs. One critical aspect of phage-mediated HGT is lysogenization, the process by which phage DNA is integrated into the host bacterium's genome. Which bacterial cells are capable of being lysogenized and how the process of lysogenization is coupled to the physiology of the host bacterial cell are key questions in phage biology that remain unanswered. Recent technological advances in computer vision and single-cell imaging along with our lab's existing expertise in bacterial physiology enable us to interrogate this model system with unprecedented precision and find concrete answers to these long standing questions. We therefore propose to study these questions using E. coli and phage lambda as our initial model system. Our guiding hypothesis is that the physiology of the host bacterial cells plays a critical role in the occurrence of lysogeny. Interrogating this problem of bacteria-phage interactions requires a systems level view of bacterial physiology and detailed dynamic measurements of lysogeny development. The goal of this proposal is to develop a system capable of measuring the activities of viral transcription factors, host proteins, and infection outcomes simultaneously in single cells. The analysis and interpretation of these data will lead to the discovery of novel host-virus interactions underlying lysogenic development and ultimately identify molecular targets that can be exploited to suppress phage-mediated horizontal gene transfer.

 描述（由申请人提供）：微生物世界以新型、无法治疗的病原体的形式对现代医学提出了最大的挑战之一，噬菌体（感染细菌的病毒）是这一挑战的主要驱动力。噬菌体介导细菌之间新型遗传物质的交换（称为水平基因转移或 HGT 的过程），将良性细菌转化为人类病原体，并推动病原体的快速出现因此，迫切需要阐明噬菌体介导的 HGT 发生的时间、地点和方式。溶原化是噬菌体介导的 HGT 发生的过程，即噬菌体 DNA 整合到宿主细菌基因组中的过程。哪些细菌细胞能够被溶原化以及溶原化过程如何与宿主细菌细胞的生理学相结合是噬菌体生物学中仍然存在的关键问题计算机视觉和单细胞成像方面的最新技术进步以及我们实验室在细菌生理学方面的现有专业知识使我们能够以前所未有的精度询问这个模型系统，并找到这些长期存在的问题的具体答案，因此我们建议使用这些方法来研究这些问题。大肠杆菌和 lambda 噬菌体作为我们的初始模型系统，我们的指导假设是宿主细菌细胞的生理学起着至关重要的作用。 研究细菌-噬菌体相互作用的问题需要对细菌生理学进行系统水平的观察，并对溶源发育进行详细的动态测量。该提案的目标是开发一种能够测量病毒转录因子活性的系统。 、宿主蛋白和感染结果同时发生 对这些数据的分析和解释将导致发现溶原性发育的新型宿主-病毒相互作用，并最终确定可用于抑制噬菌体介导的水平基因转移的分子靶标。

项目成果

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.

深度学习可自动对活细胞成像实验中的单个细胞进行定量分析。

• 发表时间: 2016-11
• 影响因子: 4.3
• 作者: Van Valen, David A;Kudo, Takamasa;Lane, Keara M;Macklin, Derek N;Quach, Nicolas T;DeFelice, Mialy M;Maayan, Inbal;Tanouchi, Yu;Ashley, Euan A;Covert, Markus W
• 通讯作者: Covert, Markus W