Horstmann Klein Morris Abstract

Mathematical Modeling Reveals Zap1's Role in the Gene Regulatory Network the Controls the Response to Cold Shock in Saccharomyces cerevisiae

Transcription factors are proteins that act together in a gene regulatory network (GRN) by repressing or activating the expression of target genes. The purpose of this study is to determine the GRN for Saccharomyces cerevisiae, budding yeast, that controls the response to cold shock. The Dahlquist Lab has conducted DNA microarray experiments to measure gene expression after 15, 30, and 60 minutes of cold shock treatment to explore the gene expression patterns of both the wild type strain and a mutant strain that had the transcription factor Zap1 deleted. These data were used as input to a MATLAB software package called GRNmap, which uses ordinary differential equations to model the dynamics of a medium-scale gene regulatory network. A modified ANOVA showed that 2559 genes had a log2 fold change significantly different than zero at any timepoints. These significant genes were submitted to the YEASTRACT database to determine the regulatory transcription factors. A network of 34 genes and 98 edges was created and pared down to 15 genes and 27 edges. Parameter values, production rates, regulatory weights, and expression thresholds were compared for each of the GRNs. From the modeling of the network families, we have observed the importance and role of ZAP1 in the gene regulatory network that controls cold shock response in Saccharomyces cerevisiae.

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