Mary Dunlop, Associate Professor
Department of Biomedical Engineering
Boston University

Optogenetic Feedback Control of Gene Expression in Single Cells

Abstract:
In this talk I will discuss a novel approach for controlling gene expression dynamics in single cells that can be used to precisely drive expression in thousands of cells in parallel. Using recent advances in the fields of machine learning and control theory, we train a deep neural network to accurately predict the response of an optogenetic system in E. coli cells. We then use the network in a deep model predictive control framework to impose arbitrary and cell-specific gene expression dynamics on thousands of single cells in real time, applying the framework to generate complex time-varying patterns. We also showcase the framework’s ability to link expression patterns to dynamic functional outcomes by controlling expression of an antibiotic resistance gene. These approaches offer powerful methods that can be used to quantify and control cell-to-cell heterogeneity in antibiotic resistance, providing a detailed view into strategies bacteria can use to evade drug treatment.

Biography:
Mary Dunlop is an Associate Professor of Biomedical Engineering at Boston University with additional appointments in Bioinformatics and in the Molecular Biology, Cell Biology & Biochemistry program. She graduated from Princeton University with a B.S.E. in Mechanical and Aerospace Engineering and a minor in Computer Science. She then received her Ph.D. from the California Institute of Technology, where she studied synthetic biology with a focus on dynamics and feedback in gene regulation. Her lab engineers novel synthetic feedback control systems and also studies naturally occurring examples of feedback in gene regulation. Her work has focused on understanding the role of cell-to-cell heterogeneity in bacterial systems.  In recognition of her outstanding research and service contributions, she has received many honors including election as an AIMBE Fellow which honors the top 2% of medical and biological engineers, the NSF Transitions Award, ACS Synthetic Biology Young Investigator Award, DOE Early Career Award, and NSF CAREER Award. She is also the recipient of several teaching awards, including Boston University’s Biomedical Engineering Professor of the Year Award and the College of Engineering Teaching Excellence Award.