James P. McDonald Week 11

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Biological Terms

  1. Trehalose: "A crystalline disaccharide that is found in various organisms, is about half as sweet as sucrose, and is sometimes used as a sweetener in commercially prepared foods." [[1]]
  2. Batch Culture: "A large-scale closed system culture in which cells are grown in a fixed volume of nutrient culture medium under specific environmental conditions." [[2]]
  3. Transcriptome: "The complete set of RNA transcripts produced by the genome at any one time." [[3]]
  4. Ergosterol: "Crystalline steroid alcohol that occurs especially in yeast, molds, and ergot and is converted by ultraviolet irradiation ultimately into vitamin D2" [[4]]
  5. Cryostat: "An apparatus for maintaining a constant low temperature especially below 0°C" [[5]]
  6. Cuvette: "A transparent or translucent box-shaped container with precisely-measured dimensions for holding liquid samples to be put into a spectrophotometer." [[6]]
  7. Desaterase: "Any of several enzymes that putdouble bonds into the hydrocarbon areasof fatty acids." [[7]]
  8. Mannoproteins: "Yeast cell wall components that are proteins with large numbers of mannose groups attached; highly antigenic." [[8]]
  9. Prototrophic: "Strain's that have the same nutritional requirements as the wild-type strain." [[9]]
  10. Supernatant: "The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids." [[10]]



  • Transcriptional regulation was studied in Saccharomyces cerevisiae in response to low temperatures.
    • This study focused on long-term low-temperature acclimation rather than rapid transitions to low temperature or "cold shock."
    • This experiment was performed in a chemostat, in contrast to most literature, which used batch cultures.
    • Transcription levels of various genes were measured at low temperatures.
  • The main result of the study revealed that there are large differences in transcription levels in many of the genes between the literature data, that looked at for rapid transitions to cold temperatures, and this study, that looked at long-term low-temperature acclimation.


  • The effect of cold temperatures on transcription in yeast has been studied greatly.
    • The studies has always been done in batch cultures.
    • This study uses a steady-state chemostat model to eliminate the effects of specific growth rates.
  • Other studies focused on a rapid transition to low temperatures, a cold shock.
    • This study focuses looks at the effects on yeast transcription with a slow transition to low-temperatures.
    • This allowed the yeast to acclimate rather than quickly adapt.
  • These different measures were taken in this experiment so that they could compare their results with the literature data.
    • The results showed big differences between this study and the literature data.

Materials and Methods

  • The yeast used was phototropic, haploid, S. cerevisiae strain: CEN.PK113-7D (MATa)
  • The yeast was grown in steady-state chemostats in anaerobic conditions.
    • Chemostats allowed for the control of the specific growth rates.
    • The chemostats were 2.0 l with a working volume of 1.0 l.
    • The dilution rate was 0.03h-1.
    • The pH was kept constant at 5.0.
    • The stirrer speed was set constant at 600 rpm.
    • The yeast were grown at temperatures of 12oC and 30oC.
    • The growth medium was a defined synthetic medium, limited by carbon or by nitrogen. All other growth requirements were present in excess.
    • For each chemostat, triplicate trehalose measurements and duplicate glycogen measurements were made.
  • The yeast were grown in four different conditions:
    • 12oC, glucose limiting.
    • 30oC, glucose limiting.
    • 12oC, ammonia limiting.
    • 30oC, ammonia limiting.
  • There were three independently cultured replicates for each of the four conditions.
  • The data was analyzed using microarray analysis and statistical assessment.
    • RNA quality was determined using the microarray analysis.
    • Microsoft Excel was used for significance analysis.
    • Data was visualized using venn diagrams and heat maps on specific software.
    • Web-based software was used for the promoter analysis.
    • Statistical assessment was done for overrepresentation of GO biological processes and overrepresentation of transcription-factor binding sites.
  • The data results from this study were compared with datasets from other studies.
  • Transcription factors: Mbp1p, Hap2-Hap1, Hap3-Hap1, Fhl1p, Sfp1p, Gln3p, Gln3-Dal82, Hap2-Dal82, Aft2p, Hsf1p, Nrg1p, Phd1p, Rcs1p, Rox1p, Sok2p, Nrg1-Aft2, Phd1-Nrg1, Rox1-Phd1, Sok2-Nrg1


Table 1

  • Table displaying the physiological characteristics of the yeast grown in all four conditions.
    • Shows that the biomass yields and fermentation rates were similar at 12oC and 30oC, proving that the growth efficiency of the yeast was not greatly affected by the temperature.

Figure 1

  • Venn Diagram showing the number of genes that had significantly different transcript levels at the two temperatures, 12oC and 30oC.
    • 494 genes had significant changes in glucose limitation, while 806 had significant changes in nitrogen limitation.

Figure 2

Table 2

Table 3

Figure 3

Figure 4

Figure 5

Figure 6


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