Elizabeth Polidan Week11

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{{Elizabeth Polidan}}
{{Elizabeth Polidan}}
[[BIOL398-03/S13:Week_12|Week 12 Assignment]]
[[BIOL398-03/S13:Week_12|Week 12 Assignment]]
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'''Slide'''
'''Slide'''
[[Media:PolidanJournalClub2.zip]]
[[Media:PolidanJournalClub2.zip]]

Current revision

alt=My children

Elizabeth Polidan

BIOL 398.03 / MATH 388

  • Loyola Marymount University
  • Los Angeles, CA, USA

Elizabeth Polidan Home

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Week 12 Assignment

Slide Media:PolidanJournalClub2.zip

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.
  9. rRNA


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.
    • Contextual dependency of response to lower temperatures
      • Responses may be due to specific growth rates rather than temperature
      • Responses may be due to specific place in a hierarchical regulation scheme
  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.
    • Figure 2 shows heat map representing the transcription level ratio of the genes that were significantly up or down regulated. The genes are grouped by nutrient limitation and by up vs down.
    • The specific growth rate of 0.03 / h is ~75% of mumax at 12C, as opposed to 10% of mumax at 30C. This results in an increased concentration of the residual nutrients at the lower temperature. An increased concentration of the residual nutrients results in catabolite represession.
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