| Description |
Title: “Single-cell optogenetic selection and activation of engineered Escherichia coli transcription factors for the characterization and prediction of gene regulatory network dynamics”
Advisory Committee:
John Ngo, PhD – BU BME (Chair)
Mary J. Dunlop, PhD – BU BME (Advisor)
Mo Khalil, PhD – BU BME
Trevor Siggers, PhD – BU Biology
Abstract:
Optogenetics can be used to enact rapid, precise, and reversible changes in gene expression via light inputs. This makes it well-suited for the characterization, perturbation, and control of highly dynamic behavior in cells, whether it is applied to synthetic gene circuits or native gene regulatory networks. In this project, I will use a platform for single-cell optogenetics to induce gene expression with high precision in individual Escherichia coli cells. With this platform, I will develop a method to perform optogenetic selection on individual cells based on their dynamic behavior, expediting the process for designing genetic circuits or engineered proteins. I will employ this method to create engineered chimeric transcription factors that can be rapidly, specifically, and reversibly activated with pulses of blue light to perturb native gene regulatory networks in E. coli. I will activate these engineered transcription factors to observe their effects on downstream gene expression, with an emphasis on characterizing the dynamics of the glutamate decarboxylase (Gad) acid response network. A deep learning model constructed from this data will provide additional insights into patterns behind Gad network regulation and how it affects cell fate in the face of challenges such as antibiotic exposure or low pH, which has implications in the treatment of bacterial infection.
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