Anthony J. Wavrin Week 11: Difference between revisions
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*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. | *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== | ===Results=== | ||
====Table 1==== | ====Table 1==== | ||
*Table 1 shows that the chemostat conditions were either ammonia or glucose limiting by reporting the residual ammonia or glucose, respectively. | *Table 1 shows that the chemostat conditions were either ammonia or glucose limiting by reporting the residual ammonia or glucose, respectively. | ||
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*This is a visual representation of genes that may be nutrient limiting specifically regulated. | *This is a visual representation of genes that may be nutrient limiting specifically regulated. | ||
====Figure 2==== | ====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. | |||
====Figure 3==== | |||
=====Figure 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. | |||
=====Figure 3B===== |
Revision as of 22:14, 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.
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.
Figure 3
Figure 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.