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.
Bacteriophages mediate horizontal gene transfer (HGT), the exchange of novel genetic materials 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. Our proposal focuses on using novel technologies to answer these questions for bacteriophage lambda and its host, E. coli.
|Van Valen, David A; Kudo, Takamasa; Lane, Keara M et al. (2016) Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. PLoS Comput Biol 12:e1005177|