Knguye66 Week 11

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Effects of the Pesticide Thiuram:  Genome-wide Screening of Indicator Genes by Yeast DNA Microarray

Team Information
Project Manager: TBA
Quality Assurance:  Iliana Crespin
Data Analysis: Emma Young, Kaitlyn Nguyen
Coder: Michael Armas

Purpose

The purpose of the Week 11 assignment is to begin the final project by creating an individual journal with an outline of the journal article assigned (to be studied and analyzed), identify and define 10 new terms, create an annotated bibliography, and lastly, a presentation.

10 terms

Outline of your journal article

Journal Article: Effects of the Pesticide Thiuram

  1. What is the main result presented in this paper?
    • According to the DNA microarray experiment, exposure to pesticide thirium led to alterations in gene expression in yeast cells.
      • genes involved in detoxification and stress response were induced
      • induction of genes causes other effects:
      • induction of genes in redox and defense against reaction oxygen: oxidative stress
      • induction of genes in DNA repair: positive toxic chemical
  2. What is the importance or significance of this work?
    • The purpose of this work was to use DNA microarray technology and treat yeast cells to characterize its toxicity on yeast cells and find a biomarker for candidate for the phenom.
      • In the DNA microarray technology, they screened for genes than can detect pesticide thirium
      • While pesticide thiuram has been studied before, one of the most important aspects of this study is that they were able to integrate DNA microarray technology to study and analyze a whole genomic response to it (the first ones that did it!).
  3. What were the limitations in previous studies that led them to perform this work?
    • Previous experiments studied that thirium shows direct mutagenicity (ie. salmonella), oral toxicity in rodents, increased "possible" carcinogenesis in humans and rodents, but were unable to identify if mutagenicity was in yeast Sacchoramyces cerevisiae. Other reports have mentioned that thiuram can be used as an alcohol deterrent to inhibit degradation of acetaldehyde, etc. However, like noted in question #2, while pesticide thirium has been studied before, the significance of this experiment is that all these genomic responses were studied all at once in a comprehensive analysis using DNA microarray technology.
  4. How did they treat the yeast cells (what experiment were they doing?)
  5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    • The strain of yeast used was Saccharomyces cerevisiae S288C (alpha SUC2 mal mel gal2 CUP1), used as an indicator strain for the experiment. The strain was not identified as haploid or diploid in the journal article.
  6. What media did they grow them in? What temperature? What type of incubator? For how long?
    • The yeast cultures were grown in a YPD medium that was diluted and grown overnight, then thirium was added to grow for an extra 15min-2hrs. Following this, a hybridization solution was applied to the yeast DNA microarray, covered, hybridized for 24-48hrs at 65°C. To characterize the toxicity of thirium and find biomarker candidates, the team tried to find conditions that lead to strong growth inhibition. Therefore, the yeast cells were cultured with differing concentrations of thiuram and incubated for 24hrs at 25 °C in a YPD medium.
  7. What controls did they use?
  8. How many replicates did they perform per treatment or timepoint?
  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?
    • 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?

Annotated Bibliography

Conclusion

Acknowledgments

This section is in acknowledgement to partner Michael Armas (User:Marmas), as well as, Iliana Crespin (User:Icrespin), and Emma Young (User:eyoung20). I would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment.

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

User Page

User:knguye66

Template Page

Template:knguye66


Table of all assignments and journal entries for BIO-367-01

Week Individual Journal Entry Shared Journal
Week 1 - Class Journal Week 1
Week 2 knguye66 Week 2 Class Journal Week 2
Week 3 ILT1/YDR090C Week 3 Class Journal Week 3
Week 4 knguye66 Week 4 Class Journal Week 4
Week 5 DrugCentral Week 5 Class Journal Week 5
Week 6 knguye66 Week 6 Class Journal Week 6
Week 7 knguye66 Week 7 Class Journal Week 7
Week 8 knguye66 Week 8 Class Journal Week 8
Week 9 knguye66 Week 9 Class Journal Week 9
Week 10 knguye66 Week 10 Class Journal Week 10
Week 11 knguye66 Week 11 FunGals
Week 12/13 knguye66 Eyoung20 Week 12/13 FunGals
Week 15 knguye66 Eyoung20 Week 15 Class Journal Week 15

References

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