| The chemostat, a continuous culture system, may provide a better controlled environment for detailed studies using highly sensitive, genome-wide techniques than the widely used batch culture. However, the relation and relevance of the chemostat to batch culture has not been fully characterized. In the first chapter of this thesis I use genome-wide transcriptional profiling to compare batch timepoints and a steady-state chemostat culture under phosphate, sulfate, leucine and uracil limitation. The profiles, together with physiological data, show that phosphate and sulfate limited batch cultures maintain homeostasis as the limiting nutrient is depleted, and are comparable to the chemostat near the point when the limiting nutrient is exhausted. Importantly, there is not a stress response in the chemostat. Leucine and uracil limited chemostat cultures also appear to lack a stress response, but the existence of a comparable point is more difficult to ascertain. Comparison of changes across the timecourses revealed induction of genes involved in the metabolism of the limiting nutrient for most nutrients, but there was no relevant response found for uracil limitation. Several other clusters specific to particular limitations provide insight into the response to those limitations. In the second chapter, I present the design and implementation of Java Treeview, a general, cross platform, open source visualization program for genome-wide microarray data. |
