Hivanson Week 12

Presentation Prep

Purpose

This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

Defining 10 unknown biological terms

1. Thioredoxin system:
2. Glutathione system:
3. Leucine zipper proteins:
4. Lignin:
5. Capillariy electrophoresis:
6. Photodiode Array Detector:
7. Trehalose:
8. MAPK signaling:
9. Regulon:
10. Isoenzymes:
11. Rho zero petites:

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?
   • Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
   • Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
   • Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
10. What mathematical/statistical method did they use to analyze the data?
    • Robust Multichip Average and ANOVA
11. Are the data publicly available for download? From which web site?
    • GEO Database and SGD.
12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
    • Figure 1
      • X represents Concentration in µM; Y represents Time in minutes
      • Quantification by HPLC
      • Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
    • Figure 2
      • X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
      • Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
      • Figure 2 shows a comparison of the control and treatment's expressed gene counts. Notably, at minute 40, the control yeast continued to increase in genes expressed, but the treatment yeast plateaued; this was unexpected, and therefore the researchers considered times greater than or equal to 40 minutes to be unreliable.
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?

Bibliographic Entry

• For your assigned journal article, answer/provide the following on your individual journal entry.
  1. The complete bibliographic reference in the APA style (see this link), with DOI.
  2. The link to the abstract from PubMed (LMU-specific link.
  3. The link to the full text of the article in PubMedCentral (if not available, write N/A).
  4. The link to the full text of the article (HTML format) from the publisher web site.
  5. The link to the full PDF version of the article from the publisher web site.
  6. Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
     • Additionally, is the article available under a Creative Commons license?
  7. How is the article available to you?
     • Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
     • If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
     • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
     • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
  8. Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
  9. What organization is the publisher of the journal?
     • What type of organization is it?
       • Is the publisher for-profit or non-profit?
       • Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
       • Does the publisher belong to the Open Access Publishers Association?
     • What country is the journal published in?
  10. How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
  11. Are the articles in this journal peer-reviewed?
  12. Provide a link to the scientific advisory board/editorial board of the journal.
  13. What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
  14. On what date was the article submitted?
  15. On what date was the article accepted?
  16. Did the article undergo any revisions before acceptance?
  17. When was the article published?
  18. What is the approximate elapsed time between submission and publication?
  19. What are the institutions with which the authors are affiliated?
  20. Have the authors published other articles on this subject? (How will you find this out?) Hint:
      • Google Scholar
      • PubMed (LMU-specific link)
      • Web of Science (LMU pays subscription fee for access)
  21. Is there a conflict of interest for any of the authors?
  22. Are the data associated with this article available? If so, provide a link to the dataset.
      • The data can be accessed through SGD or GEO
  23. Perform a prospective search on your article in the Web of Science and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
      • How many articles does this article cite?
        • 79
      • How many articles cite this article?
        • 26

Presentation

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

References

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