Elizabeth Polidan Week11: Difference between revisions
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'''Outline of Tai et al. (2007)''' | '''Outline of Tai et al. (2007)''' | ||
#Introduction | #Introduction | ||
# | #*A study of differential transcriptional regulation at low temperature was performed using chemostat cultivation rather than batch cultures in order to eliminate any effects associated with differential specific growth rates. | ||
# | #*This contrasts the role of genes in adaptation to rapid transition to cold temperature (cold shock) with their role in longer term acclimation to a low temperature environment. | ||
#Methods | #Methods | ||
## | #*Experimental setup | ||
## | #**Used CEN.PK113-7D (MATa), a strain of S. cerevisiae that has the same nutrient requirements as the wild strain. | ||
## | #**Cultures were grown in 2 liter chemostats at 12oC and 30oC. | ||
## | #**The dilution rate was 0.03 per hour for both temperatures. | ||
## | #**The media was a synthetic media with all required nutrients (save glucose and ammonium) in excess. At each temperature there was a nitrogen limited (glucose in excess) culture and a glucose limited (nitrogen in excess) culture. | ||
#**To avoid issues of temperature-based oxygen solubility differences the system was maintained anaerobically. | |||
#**The pH was maintained at 5.0. | |||
#*Measurements | |||
#**Culture dry weights and whole cell proteins were measured after steady state was reached. | |||
#**Concentrations of glucose and metabolites were measured. | |||
#**Trehalose was measured using three measurements for each chemostat. | |||
#**Glycogen was measured using two measurements for each chemostat. | |||
#**Microarrays were created for each temperature and nutrient combination. | |||
#Analysis | #Analysis | ||
## | #*Analysis of experimental data | ||
#**The MS Excel add-in SAM (significance analysis of microarrays) was used for pair-wise comparisons. | |||
#**Visualizations (Venn diagrams and heat map) were created using Expressionist Analyst. | |||
#**Web-based tools were used for analysis of overrepresentation and sequence analysis. | |||
#*Comparison with batch culture data | |||
#**Batch culture data from three other experiments (from three different teams) was used to compare with the chemostat culture results. | |||
#Discussion | #Discussion | ||
##What transcription factors did they talk about? | ##What transcription factors did they talk about? | ||
Revision as of 22:02, 3 April 2013
Elizabeth Polidan
BIOL 398.03 / MATH 388
- Loyola Marymount University
- Los Angeles, CA, USA
Vocabulary
- trehalose
- A nonreducing disaccharide that acts as a storage carbohydrate and protects cells against various environmental stress conditions.
- Charlemagne-Gilles, H., et al., Role of trehalose in survival of Saccharomyces cerevisiae under osmotic stress, Microbiology (1998), 144, pp. 671-680. (http://mic.sgmjournals.org/content/144/3/671.full.pdf)
- mannoproteins
- Yeast cell wall components composed of proteins with mannose groups attached.
- http://www.biology-online.org/dictionary/Mannoproteins
- prototrophic
- A strain that has the same nutritional requirements as the wild strain from which it is derived.
- http://www.biology-online.org/dictionary/Prototrophic_strains
- fatty-acid desaturase
- Enzymes that put double bonds into the hydrocarbon areas of fatty acids.
- http://www.biology-online.org/dictionary/Desaturase
- cis-regulatory motifs
- A region of DNA or RNA that regulates the expression of genes also located on that same strand of DNA or RNA.
- http://en.wikipedia.org/wiki/Cis-regulatory_element
- HXT5
- Hexose transporter with moderate affinity for glucose.
- http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=HXT5
- HXT6
- High-affinity glucose transporter
- http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=hxt6
- Carbon recovery
- Ratio of amount of recovered carbon to the amount available at the onset of fermentation. It is a measure of efficiency. Usually percentage reflecting # moles produced per 100 moles of substrate used.
- El-Mansi, E.M.T, Bryce, C.F.A., Demain, A.L., and Allman, A.R. editors (2006) Fermentation Microbiology and Biothechnology, 2nd edition, Boca Raton, FL: CRC Press, p. 31.
Outline of Tai et al. (2007)
- Introduction
- A study of differential transcriptional regulation at low temperature was performed using chemostat cultivation rather than batch cultures in order to eliminate any effects associated with differential specific growth rates.
- This contrasts the role of genes in adaptation to rapid transition to cold temperature (cold shock) with their role in longer term acclimation to a low temperature environment.
- Methods
- Experimental setup
- Used CEN.PK113-7D (MATa), a strain of S. cerevisiae that has the same nutrient requirements as the wild strain.
- Cultures were grown in 2 liter chemostats at 12oC and 30oC.
- The dilution rate was 0.03 per hour for both temperatures.
- The media was a synthetic media with all required nutrients (save glucose and ammonium) in excess. At each temperature there was a nitrogen limited (glucose in excess) culture and a glucose limited (nitrogen in excess) culture.
- To avoid issues of temperature-based oxygen solubility differences the system was maintained anaerobically.
- The pH was maintained at 5.0.
- Measurements
- Culture dry weights and whole cell proteins were measured after steady state was reached.
- Concentrations of glucose and metabolites were measured.
- Trehalose was measured using three measurements for each chemostat.
- Glycogen was measured using two measurements for each chemostat.
- Microarrays were created for each temperature and nutrient combination.
- Experimental setup
- Analysis
- Analysis of experimental data
- The MS Excel add-in SAM (significance analysis of microarrays) was used for pair-wise comparisons.
- Visualizations (Venn diagrams and heat map) were created using Expressionist Analyst.
- Web-based tools were used for analysis of overrepresentation and sequence analysis.
- Comparison with batch culture data
- Batch culture data from three other experiments (from three different teams) was used to compare with the chemostat culture results.
- Analysis of experimental data
- Discussion
- What transcription factors did they talk about?
- Briefly state the result shown in each of the figures and tables.
Placeholder for reflection questions.
Critically evaluate the Tai et al. (2007) paper.
- Overall, do you think this paper was clearly written? Why or why not?
- Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
- What else would you like to know about their methods, results, and future directions?
