6. SYNTHETIC BIOLOGY IN YEAST: RECONSTRUCTING THE GALACTOSE NETWORK TO PROBE THE ROLE OF FEEDBACK INDUCTION IN RESPONSE TO METABOLIC STIMULI

Department: Bioengineering
Faculty Advisor(s): Jeff Hasty

Primary Student
Name: Michael Stephen Ferry
Email: mferry@ucsd.edu
Phone: 858-822-3858
Grad Year: 2009

Abstract
The field of genetics has always attempted to understand how an organism’s genes directed the production of the observable traits, or phenotype of that organism. Increasingly interactions between genes are becoming the focus of modern biology and understanding these relationships is central to all aspects of human health research and molecular genetics. Historically the relationships in complex biological networks have been described in words, cataloguing the qualitative effects perturbations of a genetic system have on an organism’s phenotype. However genome projects have revealed that eukaryotes have on the order of 10^3 to 10^4 genes making a narrative description of the entire genetic system infeasible. Ideally genetic interactions could be described mathematically using basic principles and these ideas could be expanded to cover networks of increasing size. These ideas and strategies have generally come under the field of synthetic biology which is attempting to use a combination of mathematical modeling and genetic experimentation to design new and novel genetic circuits. However, before such concepts can be fully realized the basic principles governing genetic interactions need to be elucidated in a natural genetic circuit. One such natural genetic circuit is the galactose utilization pathway of the bakers yeast Saccharomyces cerevisiae. This pathway is ideal for the modeling of genetic circuits since it is composed of a relatively small number of genes (on the order of 10) is subject to fascinating types of regulation, including positive and negative feedback control and has been qualitatively well characterized by decades of research. My research centers on altering the feedback mechanisms present in the natural genetic circuit and probing the frequency response of the altered networks with respect to metabolic stimuli. This research will lead to a greater understanding of the response characteristics of natural genetic circuits and will lead to an improved version of the galactose network model.

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