Cameron M. Rehmani Seraji Week 10
From OpenWetWare
Electronic Lab Notebook Week 10
Purpose
Part 1
Biological Terms
- Trehalose:A nonreducing disaccharide, also known as mushroom sugar or mycose, that acts as a reserve carbohydrate in certain fungi (especially yeasts), algae, and lichens.
- Mannoproteins:Yeast cell wall components that are proteins with large numbers of mannose groups attached; highly antigenic.
- Desaturase:Any of several enzymes that putdouble bonds into the hydrocarbon areas of fatty acids.
- Transcriptome:the entire set of mRNAs transcribed from a cell's genome.
- In vivo:Occurring or made to occur within a living organism; literally it means ‘in life’.
- Orthologues:a gene, protein, or biopolymeric sequence that is evolutionarily related to another by descent from a common ancestor, having diverged as a result of a speciation event.
- Exogenous:Developed or originating outside the organism, as exogenous disease.
- Motif:The smallest group of atoms in a polymer that, when under the influence of a rotation-translation operator, will assemble the rest of the atoms in the chain.
- Diurnal:Refers to the condition of being active during the day as observed in the behavior of certain plants and animals.
- Prototrophic Strains:Strain's that have the same nutritional requirements as the wild-type strain.
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.
- Chemostat
- 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
- Figure 1???????????????????????
- Figure 2??????????????????????
- 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
- Cameron M. Rehmani Seraji
- Weekly Journal Entries
- Cameron M. Rehmani Seraji Week 2
- Cameron M. Rehmani Seraji Week 3
- Cameron M. Rehmani Seraji Week 4
- Cameron M. Rehmani Seraji Week 5
- Cameron M. Rehmani Seraji Week 6
- Cameron M. Rehmani Seraji Week 7
- Cameron M. Rehmani Seraji Week 7 Redo
- Cameron M. Rehmani Seraji Week 9
- Cameron M. Rehmani Seraji Week 10
- Cameron M. Rehmani Seraji Week 11
- Cameron M. Rehmani Seraji Week 12
- Cameron M. Rehmani Seraji Week 14/15
- Weekly Assignment Pages
- Shared Journal Pages
- Template:Cameron M. Rehmani Seraji