Date(s) - 05/02/2017
4:00 pm - 5:00 pm
416 Dougherty Engineering Building
Department of Chemical & Biomolecular Engineering
University of Tennessee, Knoxville
Advisor: Dr. Steven Abel, Assistant Professor
4:00 p.m. Tuesday, May 2, 2017
416 Dougerty Engineering Building
“Characterizing Signal Transduction Networks Using Computer Simulations and Machine Learning”
Signal transduction networks are biochemical reaction networks that allow cells to sense and respond to their local environment. It is of both fundamental and practical importance to understand the relationship between a signaling network’s underlying network of interactions and its responses to stimuli. For example, a central goal of synthetic biology is to engineer signal transduction networks to respond to environmental conditions in a desired manner. We combine computational modeling of signal transduction networks with machine learning methods to characterize and redesign signaling responses. We first consider ethylene signaling in the plant A. thaliana, and the relationship between network topology and plant growth rates. We demonstrate the importance of feedforward and feedback loops for the network to generate nontrivial growth patterns observed experimentally in response to ethylene. We then focus on a network design question: To what degree can a network topology give rise to varied responses by varying the underlying kinetic parameters? Using machine learning methods, we generate large libraries of parameters sets giving a desired behavior, which are then mined to discover design criteria for generating a particular response. For the specific examples of an oscillating circuit and the T cell receptor signaling network, we show that the network topologies exhibit significant flexibility in generating alternative responses, with distinct patterns of kinetic rates emerging for different targeted responses.
Aaron Prescott completed his BS in Biochemistry at Washington State University in 2010. Prior to this, he worked as a laboratory technician in the US Navy charged with monitoring and maintaining radiological and chemical conditions for the nuclear propulsion plants aboard aircraft carriers. After acquiring his BS, he spent two years working for the US Department of Agriculture as a lab technician. While at this position, he utilized molecular and microbiology methods to study soil-borne pathogens affecting cereal grains in no-till cropping systems. He came to the University of Tennessee in 2013 and has been conducting research as a PhD student under the guidance of Steven Abel, Assistant Professor of Chemical and Biomolecular Engineering. His research uses computational methods to understand emergent biological phenomena.