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
- Fluxes: a flow or flowing of a liquid
- Biogenesis: the principle that living organisms develop only from other living organisms and not from nonliving matter.
- Trehalose: a sweet-tasting, crystalline disaccharide, C12H22O11, found in trehala, in the hemolymph of numerous insects, and in many fungi.
- Suboptimal: being below an optimal level or standard.
- Chemostat: an apparatus for growing bacterial cultures at a constant rate by controlling the supply of nutrient medium.
- Desaturase: an enzyme that removes two hydrogen atoms from a fatty acid, creating a carbon/carbon double bond.
- Prototrophic: having the same metabolic capabilities and nutritional requirements as the wild type parent strain
- Cryostat:a device used to maintain low cryogenic temperatures of samples or devices mounted within the cryostat.
- Immunoprecipitation: the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein.
- Catabolism: The metabolic breakdown of complex molecules into simpler ones, often resulting in a release of energy.
- 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
- Integrated Discovery
- Online Genome Sets
- Fischer's exact test was used, employing hypergeometric distribution with a Bonferroni correction.
- What is the main result presented in this paper?
- What is the importance or significance of this work?
- How did they treat the cells (what experiment were they doing?)
- What strain(s) of yeast did they use? Was the strain haploid or diploid?
- What media did they grow them in? Under what conditions and temperatures?
- What controls did they use?
- How many replicates did they perform per condition?
- What mathematical/statistical method did they use to analyze the data?
- What transcription factors did they talk about?
- Briefly state the result shown in each of the figures and tables.