Hivanson Week 12

Presentation Prep

Questions about your article

1. What is the main result presented in this paper?
   • CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
     • Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
2. What is the importance or significance of this work?
   • This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
   • The researchers found that Yap3, 5, and 7 are involved in the yeast OSR, and that their functions were not previously known.
3. What were the limitations in previous studies that led them to perform this work?
   • Some similar studies did not have biological replicates, nor control groups.
   • This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
4. How did they treat the yeast cells (what experiment were they doing?)
   • CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
   • Diploid strain BY4743 was used.
6. What media did they grow them in? What temperature? What type of incubator? For how long?
   • 2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
   • 30ºC
   • New Brunswick BioFlo fermentors
   • Grown until OD600 of 1.5
7. What controls did they use?
   • The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
8. How many replicates did they perform per treatment or timepoint?
   • 3
9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
10. What mathematical/statistical method did they use to analyze the data?
11. Are the data publicly available for download? From which web site?
12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
    • What do the X and Y axes represent (if applicable)?
    • How were the measurements made?
    • What trends are shown by the plots and what conclusions can you draw from the data?
13. How does this work compare with previous studies?
14. What are the important implications of this work?
15. What future directions should the authors take?
16. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

Presentation

Ivanson, Kaplan, Miller on Sha et al., 2013