1. BIO 398-01: Bioinformatics Lab
Analyzing Acclimation Response of Saccharomyces Cerevisiae to Low Temperature
BIO : Bioinformatics Lab
April 27, 2010
Alex George
Bobak Seddighzadeh

2. Outline Background of Yeast Tai et al. Paper Data Analysis
Experimental Design
Data significance
Data Analysis
Hypothesis
Materials / Methods
Results
Discussion

3. Saccharomyces cerevisiae
Unicellular eukaryotic organism
Model organism
Response to cold-shock has been comprehensively studied
Optimal temperature for growth between 25-35°C
Below 10°C cell growth stops
Ideally, transcriptional response of yeast can be applied to human biology

4. Chemostat culture of Tai et al
Chemostat culture of Tai et al. allowed for new analysis of cold temperature response
Controlled specific growth rate by using a chemostat culture because of its previous implications on genome-wide transcription
Used two nutrient-limiting batches grown aerobically to limit variables
Reduced content dependency of transcriptional responses

5. Results identify a ‘core’ set of regulated genes in response to prolonged exposure to cold temperature
Analyzing common group of regulated genes between nutrient-limited cultures establishes a ‘core’ set of context-independent, regulated genes
This ‘core’ set of genes was analyzed and compared to previous studies to provide further data for cold temperature response of S. cerevisiae

6. Down-regulation of metabolism was most significant in Nitrogen-limited cultures
Out of the top 15 down-regulated GO terms, over half were associated with metabolism
Down-regulation of sugar metabolism indicates acclimation of yeast to cold temperature
In addition, the metabolism of amino acids and allantois were down-regulated showing the importance of keeping proteins in the cell
Finally, the down-regulation of iron (Fe) transporters is probably a result of anaerobic growth conditions because of its function in aerobic respiration

7. Table ##: Fourteen most significant up-regulated GO terms of Nitrogen-limited cultures

8. Table ##: Fifteen most significant down-regulated GO terms of Nitrogen-limited cultures

9. Protein production is main result of cold temperature transcriptional regulation in Nitrogen-limited cultures
GMP and IMP (key players in nucleic acid synthesis) indicates mRNA production
Up-regulation of both ribosomal subunits shows the necessity for protein production
Also, cold temperatures slow down initiation of translation
One-third of the top 15 GO terms are related to methylation, indicating the presence of newly transcribed mRNA and tRNA needed for protein synthesis
Biotin production and subsequent metabolism is a result of anaerobic growth due to its function in - oxidation