Lauren M. Magee Week 10

Group 1: Alyssa, Karina, Will, Lauren

• Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (2007). Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Molecular biology of the cell, 18(12), 5100-5112. doi: 10.1091/mbc.E07-02-0131
• Link to PDF version of article

Biological Terms

1. Fluxes: a flow or flowing of a liquid
   • Source: http://www.thefreedictionary.com/fluxes
2. Biogenesis: the principle that living organisms develop only from other living organisms and not from nonliving matter.
   • Source: http://www.thefreedictionary.com/biogenesis
3. Trehalose: a sweet-tasting, crystalline disaccharide, C12H22O11, found in trehala, in the hemolymph of numerous insects, and in many fungi.
   • Source: http://www.thefreedictionary.com/trehalose
4. Suboptimal: being below an optimal level or standard.
   • Source: http://www.thefreedictionary.com/suboptimal
5. Chemostat: an apparatus for growing bacterial cultures at a constant rate by controlling the supply of nutrient medium.
   • Source: http://www.thefreedictionary.com/chemostat
6. Desaturase: an enzyme that removes two hydrogen atoms from a fatty acid, creating a carbon/carbon double bond.
   • Source: http://encyclopedia.thefreedictionary.com/desaturase
7. Prototrophic: having the same metabolic capabilities and nutritional requirements as the wild type parent strain
   • Source: http://www.thefreedictionary.com/Prototrophic
8. Cryostat:a device used to maintain low cryogenic temperatures of samples or devices mounted within the cryostat.
   • Source: http://encyclopedia.thefreedictionary.com/cryostat
9. Immunoprecipitation: the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein.
   • Source: http://encyclopedia.thefreedictionary.com/Immunoprecipitation
10. Catabolism: The metabolic breakdown of complex molecules into simpler ones, often resulting in a release of energy.
    • Source: http://www.thefreedictionary.com/Catabolism

Article Outline

Methods

• The strain of yeast used in this study was Saccharomyces cerevisiae.
• All steady state chemostats grown at a specific growth rate (.03h^(-1)) with a working volume of 1 L.
• Cultures were initially grown in 12C environments and then in 30C environments.
• Carbon or nitrogen limited while all other growth requirements were supplied in excess.
• pH held constant at 5.0 and stirring speed held constant at 600 rpm.
• Before sampling, biomass dry weight, metabolites, dissolved oxygen, and gas profiles had to remain constant for at least 3 volume changes.
• Culture supernatants were obtained with the rapid sampling method.
• Liquid chromatography was used to analyze concentrations of glucose and metabolites.
• Cuvette tests used to examine residual ammonium concentrations.
• Culture dry weights and ethanol evaporation were determined.
• Trehalose measured 3 times and glycogen measured 2 times.
• UV method used to determine the glucose released by glycogen and trehalose.
• Each growth condition was derived independently cultured replicates.
• Average growth coefficients of variation was below .20. Based off of the 3 transcriptome analyses for the four different conditions.
• Microsoft Excel used to analyze microarray add-ins for pairwise comparisons.
• Comparisons of glucose and ammonium limiting anaerobic growth were made using Venn Diagrams. The following data taking into consideration:
  • Database for Annotation
  • Visualization
  • Integrated Discovery
  • Online Genome Sets
• Fischer's exact test was used, employing hypergeometric distribution with a Bonferroni correction.

Guiding Questions

1. What is the main result presented in this paper?
2. What is the importance or significance of this work?
3. How did they treat the cells (what experiment were they doing?)
4. What strain(s) of yeast did they use? Was the strain haploid or diploid?
5. What media did they grow them in? Under what conditions and temperatures?
6. What controls did they use?
7. How many replicates did they perform per condition?
8. What mathematical/statistical method did they use to analyze the data?
9. What transcription factors did they talk about?
10. Briefly state the result shown in each of the figures and tables.