Lydia M. Contreras

Lydia M. Contreras
Dept. of Chemical Engineering
University of Texas at Austin

Abstract: Using synthetic biology and machine learning tools to characterize and engineer RNAs
Regulatory RNAs enable bacteria to dynamically respond to stresses caused by changes in environmental conditions. Specifically, bacterial small RNAs, a class of RNA regulators, exert dynamic control on complex networks by regulating gene expression. Understanding their functions is a goal in both medicine and biotechnology given their relevance to pathogenesis and their potential to manage global regulatory networks that affect biological production of industrially-relevant compounds. Given the importance of molecular structure to RNA functioning, fundamental sRNA characterization and applied engineering efforts  depend heavily on the understanding and design of their specific shapes. Specifically, knowledge of the RNA structural landscape supports identification of interfaces relevant to regulation. In this talk, we will describe the development and application of tools that allow in vivo characterization of thousands of potential interacting interfaces in RNA molecules, as determined based on their molecular accessibility. We will describe how insights obtained from these synthetic probing approaches can be used in the functional characterization of newly discovered RNAs and in the rational design of bacterial sRNAs to achieve a tunable gradient of global control for metabolic engineering applications.

Biography: 
Dr. Lydia M. Contreras is an Associate Professor (and Jim and Barbara Miller Faculty Fellow) of Chemical Engineering at the University of Texas-Austin; she is also a member of the Institute of Cell and Molecular Biology. She teaches Introduction to Chemical Engineering Computing, 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 in 2003, where she graduated Cum Laude.  She completed her PhD in Chemical Engineering from Cornell University in 2008, 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) with Dr. Marlene Belfort, 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: Biotechnology and Bioengineering Daniel I.C. Wang Award, 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, Society of Hispanic Professional Engineers (SHPE) Young Investigator Award, and an Innovative Early-Career Frontiers of Engineering Educator. She lives in Austin, Tx with her husband Chris and is a proud mom to toddler twins.