Next generation quantitative measurements to validate a model for Saccharomyces cerevisiae

Abstract

Dissertation under the direction of Professor Kenneth A. Debelak The study of dynamical biological systems is currently obstructed by the lack of quantitative methods available for biophysical measurement. The focus of this work is to further develop these methods so the dynamics of genetic circuitry can be studied at the same level of sophistication at which mathematical models have been formulated. The study of biological dynamics provides an interesting research opportunity because these dynamics control the emergent behavior of living organisms and result in the observed robustness of life.

The specific system that provides the focus for this work is an ostensibly simple stress response circuit in baker’s yeast, Saccharomyces cerevisiae, which regulates the organism’s genetic response to nitrogen limitation called Nitrogen Catabolite Repression (NCR). The work presented in this dissertation encompasses many of the aspects of gene expression analysis including cell disruption, cell cycle synchrony, and the amplification and quantitation of genetic signals through Polymerase Chain Reaction (PCR). In each case, a combination of experimental results, engineering intuition, and mathematical analysis is used to further develop current techniques and understanding. Mathematical models are developed for cell disruption, cell cycle synchrony, and endpoint PCR. These models are used to advance the level of quantitation available to each process. When applied, these models provide novel insight to persistent biological problems. For example, cell disruption was found to be a cell cycle dependent process, volume filtration was developed as a theoretical mechanism for extending cell cycle synchrony, and autonomous oscillations within continuous yeast cultures were shown to be a result of pseudo cell cycle synchrony.