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Introduction 

      Baker’s yeast, or Saccharomyces cerevisiae, is a well known model organism often used to study molecular biology because all of its genome is sequenced and the function of many genes is already known. In fact, Dr. Slekar of James Madison University is currently researching the mutant strains ∆zms1, ∆zms2, and ∆zms1/∆zms2 to better understand pathways involved in dealing with oxidative stress. Both of these mutant strains are known to be susceptible to oxidative stress caused by oxidizing agents that can occur during metabolic processes.

    Wild type ZMS1 and ZMS2 have been found to encode zinc finger regulatory transcription factors. This implies that the mutant strains inability to function correctly in the presence of oxidizing agent could be related to anti-oxidant factors which are regulated by these zinc fingers (Slekar, 2008). Oxidative stress is also known for causing various cancers, cardiovascular disease, and neurodegenerative disease, so by understanding how these stresses are controlled in this model organism one may be able to apply such knowledge to treating, controlling, or preventing such diseases.

      Since not a great amount of detail is known about the regulatory processes involving these genes an exploratory search by aid of microarray technology seemed the most useful course of action. Microarrays are very powerful biological tools with applications in diagnostics, genomics, and general research. By utilizing this tool one can hope to compare expression levels between different strains, such as ∆zms2 and ZMS2, for as many as 6,500 genes at once. In order to accomplish this, we will use the 3DNA Microarray methodology, which is outlined in the Materials and Methods.

    Unfortunately, the complexity of this technique brings about inherent variability which must be addressed in analysis of the data.  For example, an uncontrollable “dye bias” may occur because the scanner may read one color dye used for one strain at a greater intensity than other strains (K.M. Kerr, 2000). In light of this our experiment was designed not only to compare mRNA expression of ∆zms2 and ZMS2 strains, but the dyes used for each strain were reversed so that when compared with other experiments, the magnitude of this dye bias could be evaluated while analyzing gene expression variances between the strains.

      It is our ultimate goal to better understand the pathway of how S. cerevisiae deal with oxidative stress. By knocking out an important transcription factor (∆zms2), we can hope that the difference in expression of mRNA can provide a better understanding of how the oxidative stress pathway works. If it can be completely understood in a model organism, this knowledge may be able to be applied to human diagnostics or therapeutics. By conducting this experiment with dye reversal, we will attempt to accomplish the secondary goal of better understanding the variability caused by factors such as “dye bias”.