Elizabeth Polidan Week11

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#**Batch culture data from three other experiments (from three different teams) was used to compare with the chemostat culture results.
#**Batch culture data from three other experiments (from three different teams) was used to compare with the chemostat culture results.
#Discussion
#Discussion
 +
#*A comparison of the gene expression 12oC vs 30oC (figure 1)
 +
#**In the nitrogen limited system 571 genes showed significant up or down regulation. 
 +
#**In the carbon limited system 259 genes showed significant up or down regulation.
 +
#**There were 235 genes that showed significant differences in gene expression in both the nitrogen and carbon limited systems. 
 +
##What transcription factors did they talk about?
##What transcription factors did they talk about?
##Briefly state the result shown in each of the figures and tables.  
##Briefly state the result shown in each of the figures and tables.  

Revision as of 01:37, 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
    • A comparison of the gene expression 12oC vs 30oC (figure 1)
      • In the nitrogen limited system 571 genes showed significant up or down regulation.
      • In the carbon limited system 259 genes showed significant up or down regulation.
      • There were 235 genes that showed significant differences in gene expression in both the nitrogen and carbon limited systems.
    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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