CBE Seminar - Lydia Contreras

Finding a Needle in a Haystack: Parsing Large-Scale Data to Define Regulatory Networks for Strain Engineering

Lydia Contreras

Chevron Centennial Teaching Fellow in Chemical Engineering
Assistant Professor
McKetta Department of Chemical Engineering

Finding a Needle in a Haystack: Parsing Large-Scale Data to Define Regulatory Networks for Strain Engineering

 

Abstract

Two important questions in strain engineering are: how to search the genome for targets that regulate a phenotype of interest? and, (ii) how to achieve controllable and even predictable coordination between endogenous and stress-inducing heterologous pathways? Although a large number of “omics” approaches are being attempted to address these questions, it is unclear how to interpret this massive amount of data in the context of biological pathways and utilize it to uncover underlying biological mechanisms for strain engineering. This seminar will address characterization tools that we are developing to automate the identification of global regulators that could be exploited in strain engineering.  Specifically, we will present a general pipeline for engineering desirable complex phenotypes based on a rational and predictive systems analysis of global regulation and on the intracellular assaying of relevant targets. Our approach has combined bioinformatics, biophysical models and synthetic biology tools for prediction of pathways of interest in microbial organisms with extremophilic traits.

Bio

Dr. Lydia M. Contreras is an Assistant Professor of Chemical Engineering and a member of the Institute of Cell and Molecular Biology at the University of Texas-Austin. She teaches Thermodynamics, Introduction to Chemical Engineering Analysis, and Fundamental and Applications of Cellular Regulation. Dr. Contreras obtained a B.S.E. in Chemical Engineering from Princeton University, where she graduated Cum Laude.  She completed her PhD in Chemical Engineering from Cornell University, focusing on engineering bacterial cells for improved production of therapeutic proteins. As a postdoctoral associate at the Wadsworth Center (New York State Department of Health), she focused on understanding mechanisms of infection in pathogenic bacteria. She began her career at the University of Texas-Austin in 2011, where she leads a research team focused on RNA biochemistry to study gene regulation mechanisms associated with stress-responses for applications in health and biotechnology.  She has received several academic, teaching and service awards including: Department of Thrust Reduction Agency (DTRA) Young Investigator, Airforce Office of Scientific Research Young Investigator, NSF CAREER, Health and Environmental Institute (HEI) Walter E. Rosenblith New Investigator, Norman Hackerman Advanced Research Program (NHARP) Early Career, and an Innovative Early-Career Frontiers of Engineering Educator. She resides in Austin, Texas with her husband Chris Vinson.