Elizabeth Polidan Week11

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'''Outline of Tai et al. (2007)'''
'''Outline of Tai et al. (2007)'''
#Introduction
#Introduction
-
##What is the main result presented in this paper?
+
#*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. 
-
##What is the importance or significance of this work?
+
#*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
-
##How did they treat the cells (what experiment were they doing?)
+
#*Experimental setup
-
##What strain(s) of yeast did they use? Was the strain haploid or diploid?
+
#**Used CEN.PK113-7D (MATa), a strain of S. cerevisiae that has the same nutrient requirements as the wild strain.
-
##What media did they grow them in? Under what conditions and temperatures?
+
#**Cultures were grown in 2 liter chemostats at 12oC and 30oC.
-
##What controls did they use?
+
#**The dilution rate was 0.03 per hour for both temperatures.
-
##How many replicates did they perform per condition?
+
#**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
-
##What mathematical/statistical method did they use to analyze the data?
+
#*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 01:02, 4 April 2013

alt=My children

Elizabeth Polidan

BIOL 398.03 / MATH 388

  • Loyola Marymount University
  • Los Angeles, CA, USA

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Vocabulary

  1. 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)
  2. mannoproteins
  3. prototrophic
  4. fatty-acid desaturase
  5. cis-regulatory motifs
  6. HXT5
  7. HXT6
  8. 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)

  1. 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.
  2. 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.
  3. 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.
  4. Discussion
    1. What transcription factors did they talk about?
    2. Briefly state the result shown in each of the figures and tables.

Placeholder for reflection questions.

Critically evaluate the Tai et al. (2007) paper.

  1. Overall, do you think this paper was clearly written? Why or why not?
  2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
  3. What else would you like to know about their methods, results, and future directions?
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