Anthony J. Wavrin Week 11: Difference between revisions
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===Materials and Methods=== | ===Materials and Methods=== | ||
*The yeast are grown in four different conditions: | *The yeast are grown in four different conditions: | ||
**12C with glucose as a limiting nutrient | **12C with glucose as a limiting nutrient (experimental) | ||
**30C with glucose as a limiting nutrient | **30C with glucose as a limiting nutrient (control) | ||
**12C with ammonium as a limiting nutrient | **12C with ammonium as a limiting nutrient (experimental) | ||
**30C with ammonium as a limiting nutrient | **30C with ammonium as a limiting nutrient (control) | ||
***Two different limiting nutrients were used to censor the nutrient dependent changes in the transcriptome. | |||
*The chemostat had a 1.0 liter culture of defined synthetic media with either glucose or ammonia as a limiting nutrient. | *The chemostat had a 1.0 liter culture of defined synthetic media with either glucose or ammonia as a limiting nutrient. | ||
*The yeast strain used was CEN.PK113-7D (MATa) and was in a haploid state. | *The yeast strain used was CEN.PK113-7D (MATa) and was in a haploid state. | ||
*The growth rate of the yeast was constant at 0.03 h-1, which is 75% max growth rate at 12C and 10% max growth rate at 30C. | *The growth rate of the yeast was constant at 0.03 h-1, which is 75% max growth rate at 12C and 10% max growth rate at 30C. | ||
*The study used a pair-wise analysis of the DNA microarray data for transcription levels and used Fisher's exact test with a Bonferroni correction for overrepresentation of transcription-factor binding sites. |
Revision as of 21:26, 3 April 2013
Definitions
Outline
Introduction
- Microorganisms are susceptible to temperature changes due to their inability to move, thus they must have physiological means to adapt to these changing environments.
- The temperature situation tested in this study was the effect of cold temperatures, termed cold shock.
- Recent studies have also looked at cold shock in yeast but, used a method of growing them in batch cultures.
- In this study, yeast were grown in chemostats to keep the conditions more constant.
- The yeast's adaptation to cold shock is determined by looking at changes in the transcriptome.
Materials and Methods
- The yeast are grown in four different conditions:
- 12C with glucose as a limiting nutrient (experimental)
- 30C with glucose as a limiting nutrient (control)
- 12C with ammonium as a limiting nutrient (experimental)
- 30C with ammonium as a limiting nutrient (control)
- Two different limiting nutrients were used to censor the nutrient dependent changes in the transcriptome.
- The chemostat had a 1.0 liter culture of defined synthetic media with either glucose or ammonia as a limiting nutrient.
- The yeast strain used was CEN.PK113-7D (MATa) and was in a haploid state.
- The growth rate of the yeast was constant at 0.03 h-1, which is 75% max growth rate at 12C and 10% max growth rate at 30C.
- The study used a pair-wise analysis of the DNA microarray data for transcription levels and used Fisher's exact test with a Bonferroni correction for overrepresentation of transcription-factor binding sites.