Cameron M. Rehmani Seraji Week 10

From OpenWetWare
Revision as of 21:14, 28 March 2017 by Cameron M. Rehmani Seraji (talk | contribs) (→‎Outline: added figure 2)
Jump to navigationJump to search

Electronic Lab Notebook Week 10

Purpose

Part 1

Biological Terms

Part 2

Outline

  • What is the main result presented in this paper????????????????????????????????
    • The overall main result presented in this paper is that S. cerevisiae will have different transcriptional responses to low temperature and low specific growth rate when it is grown in batch cultures and in chemostat cultures.
    • The use of a chemostat cultures helps isolate and study the different physiological phases of S. cerevisiae and its ability to adapt to environmental stress.
  • What is the importance or significance of this work???????????????????????????
    • The importance of this work is
  • Create a flow chart to describe their methods. Answer the following questions if they are relevant to your article.
    • Grow S. cerevisiaein a chemostat --> grown at 12°C or grown at 30°C --> limit glucose or limit ammonia
    • This results in there being four types of growth conditions:
      • 12°C, glucose-limited
      • 12°C, ammonium-limited
      • 30°C, glucose-limited
      • 30°C, ammonium-limited
  • How did they treat the cells (what experiment were they doing?)
    • The goal of the study was to investigate steady-state growth of S. cerevisiae at suboptimal temperatures, with emphasis on genome-wide transcriptional regulation.
  • What strain(s) of yeast did they use? Was the strain haploid or diploid?
    • The strain of yeast they used is prototrophic and haploid. The reference for the strain is S. cerevisiae strain CEN.PK113-7D (MATa)
  • What media did they grow them in? Under what conditions and temperatures?
    • Chemostat
      • They grew the yeast in a 2.0 L chemostat with a working volume of 1.0 L.
      • The dilution rate was set at 0.03 h^-1.
      • The pH was kept at 5.0 by automatic addition of 2 M KOH.
      • The stirrer speed was set at 600 rpm.
    • The yeast was grown at 12°C or 30°C.
    • The yeast was nitrogen-limited or glucose-limited.
    • Biomass dry weight, metabolites, dissolved oxygen, and gas profiles were constant for at least three volume changes before sampling occurred.
  • What controls did they use?
    • The yeast grown at 30°C was used as a control for the yeast grown at 12°C.
    • Glucose-limited and ammonium-limited feed were also used to eliminate the impact of secondary feeds.
  • How many replicates did they perform per condition?
    • It appears that they performed three independent steady-state chemostat cultivations for each of the four different growth conditions.
  • What mathematical/statistical method did they use to analyze the data?????????????????????
  • What transcription factors did they talk about?????????????????????????
  • Table 1:Physiological characteristics of S. cerevisiae grown in ammonium- and glucose-limited anaerobic chemostat cultures
    • Y glu/x is the biomass yield on glucose
    • DW is the dry weight
    • GLU is glucose
    • ETOH is ethanol
    • CO2 is carbon dioxide
    • The biomass yields and fermentation rates were similar at 12°C and 30°C in the glucose-limited and ammonium-limited chemostat cultures. This indicates that growth efficiency was not severely affected by the growth temperature.
  • Figure 1Global transcriptome responses to anaerobic growth at 12°C and 30°C in anaerobic glucose- and ammonium-limited chemostat cultures.
    • There were 202 up regulated genes and 369 down regulated genes in the ammonium-limited media.
    • There were 123 up regulated genes and 136 down regulated genes in the glucose-limited media.
    • There were 96 up regulated genes and 139 down regulated genes in the glucose-limited and ammonium-limited media.
  • Figure 2Heat map representing the transcript level ratio 1065 differently expressed genes in anaerobic glucose-limited and ammonium-limited chemostat cultures grown at 12°C and 30°C.
    • The genes indicated in the figure belong to the enriched GO categories.
    • Nineteen NCR-responsive genes are underlined.
      • Categories include: lipid metabolism, carbohydrate transport, rRNA processing, electron transport, amino acid transport, hexose metabolism, protein synthesis/protein complex assembly, ribosome biogenesis and assembly/RNA processing, nitrogen compound metabolism/amine transport/allantoin metabolism, polysaacharide and trehalose metabolism, M phase of mitotic cell cycle and chromosome segregation, cellular morphogenesis, response to stimulus, nuclear export, ribosome biogenesis and assembly, carbohydrate metabolism, response to stimulus, transport
  • Table 2???????????????????????
  • Table 3???????????????????????
  • Figure 3???????????????????????
  • Figure 4???????????????????????
  • Figure 5???????????????????????
  • Figure 6??????????????????????

Acknowledgments

  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

References

  • Week 10 Assignment Page
  • Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (2007). Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Molecular biology of the cell, 18(12), 5100-5112. doi: 10.1091/mbc.E07-02-0131

Navigation Links

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Cameron_M._Rehmani_Seraji_Week_10&oldid=981162"