Difference between revisions of "Anthony J. Wavrin Week 11"

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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 20:26, 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.