Anthony J. Wavrin Week 11

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**91 genes were up regulated.
**91 genes were up regulated.
====Figure 4====
====Figure 4====
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*only 6 of the 13 overlapping genes between Murata, Sahara, and Schade, and this study were consistently upregulated in all studies.
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*only 6 of the 13 overlapping genes between Murata, Sahara, and Schade, and this study were consistently up-regulated in all studies.
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*only 5 of the 16 overlapping genes between Murata, Sahara, and Schade, and this study were consistently downregulated in all studies.
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*only 5 of the 16 overlapping genes between Murata, Sahara, and Schade, and this study were consistently down-regulated in all studies.
====Figure 5====
====Figure 5====
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*Overall, there is little overlap between genes that were regulated between batch studies and this study with the growth rate studies.
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*This indicates the lack on consistency between data and may suggest other factors affecting the regulation besides solely cold shock.
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====Figure 6====
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*While there is small overlap between the ESR study and the Batch studies, there is consistency between down-regulated genes and up-regulated genes.
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*This is more overlap between the ESR study and this study but, there is a very obvious conflict in which genes that are down-regulated in the ESR study and up-regulated in this study and vice versa.

Revision as of 01:34, 4 April 2013

Contents

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.

Results

Table 1

  • Table 1 shows that the chemostat conditions were either ammonia or glucose limiting by reporting the residual ammonia or glucose, respectively.
  • Growth efficiency between the yeast at 12C and 30C was also relatively constant.
  • Utilization of glucose and production of ethanol and carbon dioxide are not severely different between 12ºC and 30ºC.

Figure 1

  • Figure 1 shows the overlap between significant changes in the transcriptome by gene of the yeast limited by either glucose or ammonia.
  • In total, 1065 genes were significantly "regulated" but, only 235 genes were consistent in both conditions.
  • This is a visual representation of genes that may be nutrient limiting specifically regulated.

Figure 2

  • Genes that were down regulated at 12C in both nutrient limiting conditions are involved with carbohydrate metabolism, response to stimulus, and transportation.
  • Genes that were up regulated at 12C in both nutrient limiting conditions are involved with nuclear export, ribosome biogenesis and assembly, and rRNA processing.

Table 2

  • There were no indications of a build up trehalose or glycogen in the yeast at 12C in either condition.
  • Ammonium limiting yeast had a significant more amount of protein per dry weight at 12C compared to 30C.

Table 3

Table 3A
  • In nitrogen limited yeast, the motif STRE which regulates Msn2/Msn4 and the motif GATAA which codes for Gln3/Gat1/Dal80/Gzf3 is down regulated
    • Msn2/Msn4 is a transcriptional regulator that is activated in stress conditions.
    • Gln3/Gat1/Dal80/Gzf3 are associated with nitrogen catabolism.
  • In nitrogen and glucose limited yeast,the motif PAC is up regulated.
Table 3B
  • In nitrogen and glucose limited yeast, Hsf1p is down regulated.
    • Hsf1p is a trimeric heat shock transcription factor.
  • In the transcription factor changes that were present in both nitrogen and glucose limited yeast, there was only down regulation.

Figure 3

  • Only 139 of the 256 genes that were reported by Murata, Sahara, and Schade were consistent in either up regulation or down regulation.
    • 48 genes were down regulated.
    • 91 genes were up regulated.

Figure 4

  • only 6 of the 13 overlapping genes between Murata, Sahara, and Schade, and this study were consistently up-regulated in all studies.
  • only 5 of the 16 overlapping genes between Murata, Sahara, and Schade, and this study were consistently down-regulated in all studies.

Figure 5

  • Overall, there is little overlap between genes that were regulated between batch studies and this study with the growth rate studies.
  • This indicates the lack on consistency between data and may suggest other factors affecting the regulation besides solely cold shock.

Figure 6

  • While there is small overlap between the ESR study and the Batch studies, there is consistency between down-regulated genes and up-regulated genes.
  • This is more overlap between the ESR study and this study but, there is a very obvious conflict in which genes that are down-regulated in the ESR study and up-regulated in this study and vice versa.
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