Difference between revisions of "Dbashour Week 12"
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Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021. | Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021. | ||
| − | + | =List of 10 Unknown Words and Their Definitions= | |
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# | # | ||
| Line 14: | Line 14: | ||
# | # | ||
| − | + | =Outline of Article= | |
| − | + | == Background Information on Purpose of Experiment == | |
* Low temperatures are known to have several effects on biochemical and physiological properties in various cells | * Low temperatures are known to have several effects on biochemical and physiological properties in various cells | ||
* Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment | * Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment | ||
| Line 21: | Line 21: | ||
*low temperature-dependent gene expression and low temperature response are still unclear | *low temperature-dependent gene expression and low temperature response are still unclear | ||
* '''The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells''' | * '''The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells''' | ||
| − | + | == Cold shock and microarray procedures of yeast samples == | |
* S. cerevisiae YPH500 was used for all the analyses | * S. cerevisiae YPH500 was used for all the analyses | ||
* Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm | * Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm | ||
| Line 33: | Line 33: | ||
* Cy3-dUTP and Cy5-dUTP were used as cDNA probes | * Cy3-dUTP and Cy5-dUTP were used as cDNA probes | ||
* Labeled with fluorophore in order to carry out microarray hybridization | * Labeled with fluorophore in order to carry out microarray hybridization | ||
| − | *Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray | + | * Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray |
* Microarrays were scanned by laser microscope | * Microarrays were scanned by laser microscope | ||
* Process repeated twice | * Process repeated twice | ||
| Line 41: | Line 41: | ||
* Fluorescence intensities were normalized | * Fluorescence intensities were normalized | ||
* Data was clustered and referred to the Munich Information Center for Protein Sequences functional database | * Data was clustered and referred to the Munich Information Center for Protein Sequences functional database | ||
| − | * | + | * Functional relationships among the genes in each cluster was determined |
| − | + | == Results and Discussion == | |
| − | * | + | === Global Expression Analysis of Low Temperature Response in Yeast Cells Using a cDNA Microarray === |
| − | * | + | * Changes in expression of genes in yeast after cold shock was analyzed using cDNA of 5,803 genes in a yeast genome |
| − | * | + | * Ratio of fluorescent intensities was 2 fold for a mainly all the cDNA spots on the data |
| + | * Roughly 25% of yeast genes' expression levels were affected by cold shock | ||
| + | * Increase in number of genes up-regulated | ||
| + | * Increase in number of genes down-regulated | ||
| + | * Significantly up or down-regulated genes were classified according to the MIPS functional database | ||
| + | * Up-regulated and down-regulated genes increased in almost all categories when exposed to low temperatures | ||
| + | ** Suggests that changes in gene expression are due to the introduction of low temperatures in order to adapt to their environment | ||
| + | ** Other cells have demonstrated this ^^ when exposed to other environmental stresses | ||
| + | === Clustering Analysis of Global Expression Data === | ||
IV. Conclusion | IV. Conclusion | ||
* | * | ||
Revision as of 09:48, 21 November 2017
Contents
Article
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
List of 10 Unknown Words and Their Definitions
Outline of Article
Background Information on Purpose of Experiment
- Low temperatures are known to have several effects on biochemical and physiological properties in various cells
- Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment
- In yeast, the NSR1, TIP1, and OLE1 genes have been identified as important cold-inducible genes through past research
- low temperature-dependent gene expression and low temperature response are still unclear
- The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells
Cold shock and microarray procedures of yeast samples
- S. cerevisiae YPH500 was used for all the analyses
- Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm
- 50 ml of the culture were collected for a reference time of 0
- Cells flash-frozen in liquid nitrogen
- Stored at -80°C in preparation for RNA
- The remaining cells were cold shocked at 10°C then cultured at the same temperature
- Cells collected at 0.25, 0.5, 2, 4, and 8 hours after the cold shock
- Cells flash-frozen in liquid nitrogen
- Stored at -80°C in preparation for RNA
- Cy3-dUTP and Cy5-dUTP were used as cDNA probes
- Labeled with fluorophore in order to carry out microarray hybridization
- Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray
- Microarrays were scanned by laser microscope
- Process repeated twice
- Averaged the expression ratios of the separate experiments for final data
- Images analyzed by computer program
- Data analyzed by analysis software
- Fluorescence intensities were normalized
- Data was clustered and referred to the Munich Information Center for Protein Sequences functional database
- Functional relationships among the genes in each cluster was determined
Results and Discussion
Global Expression Analysis of Low Temperature Response in Yeast Cells Using a cDNA Microarray
- Changes in expression of genes in yeast after cold shock was analyzed using cDNA of 5,803 genes in a yeast genome
- Ratio of fluorescent intensities was 2 fold for a mainly all the cDNA spots on the data
- Roughly 25% of yeast genes' expression levels were affected by cold shock
- Increase in number of genes up-regulated
- Increase in number of genes down-regulated
- Significantly up or down-regulated genes were classified according to the MIPS functional database
- Up-regulated and down-regulated genes increased in almost all categories when exposed to low temperatures
- Suggests that changes in gene expression are due to the introduction of low temperatures in order to adapt to their environment
- Other cells have demonstrated this ^^ when exposed to other environmental stresses
Clustering Analysis of Global Expression Data
IV. Conclusion
V. Further Implications
Deliverable
Journal Club Week 12 Presentation
