Difference between revisions of "Dmadere Week 11"

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(→‎Definitions: added definitions)
(→‎Article Outline: uploaded half of the answers)
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#What is the main result presented in this paper?
 
#What is the main result presented in this paper?
 +
#*The main result presented in this paper was that the yeast was able to undergo this environmental stress from arsenite with the transcription factors Met4p and Yap1p from the incorporation of sulfur in the glutathione biosynthesis when there is an increased amount of arsenite present.
 
#What is the importance or significance of this work?
 
#What is the importance or significance of this work?
 +
#*The significance of this work was to see if other transcription factors in addition to the ones mentioned in the introduction were able to also undergo arsenic stress and to study how that process works.
 
#What were the limitations in previous studies that led them to perform this work?
 
#What were the limitations in previous studies that led them to perform this work?
 +
#*The limitation in the previous study that led the researchers perform this work was whether protein glutathionylation occurs in response to metals. With this limitation, they knew that Met4p controls GSH biosynthesis pathways and has known to be essential in controlling the sulfur assimilation expression genes and biosynthesis genes. From this limitation, they wanted to test yeast’s response to arsenite and see if the transcriptional regulators Yap1p and Met4p guide the sulfate assimilation pathway into the glutathione pathway.
 
#How did they treat the yeast cells (what experiment were they doing?)
 
#How did they treat the yeast cells (what experiment were they doing?)
 +
#*The yeast cells after incubation were cleaned, combined, vacuum-dried, and resuspended in hybridization buffer to then be incubated at 100 Celsius for 2 min and 37 Celsius for 30 min to be analyzed in a microarray. The yeast cells were also exposed to 0.2  and 1.2 mM of sodium arsenite for further testing of their responses to the metal.
 
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
 
#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
 +
#*The yeast strains that they used were W303-1A, RW124, CC849-1B, RW104, and YPDahl166. The paper did not specify whether these strains were haploid or diploid.
 
#What media did they grow them in? What temperature? What type of incubator? For how long?
 
#What media did they grow them in? What temperature? What type of incubator? For how long?
 +
#*The media that the yeast strains were grown in was YNB media (0.67% yeast nitrogen base) with 2% glucose or in SC medium (YNB containing 2% glucose) at a temperature of 30 Celsius.
 
#What controls did they use?
 
#What controls did they use?
 +
#*The controls that they used included the untreated yeast cells known as the wildtype cells.
 
#How many replicates did they perform per treatment or timepoint?
 
#How many replicates did they perform per treatment or timepoint?
 +
#*There are no replicates mentioned in the data that was provided.
 
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
 
#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
 +
#*To prepare the RNA, they isolated it from growing yeast cells that were both treated with and without sodium arsenite, and primed 20 micrograms of the total with 3 micrograms of hexamer and 3 micrograms of primer. It was then labeled in a reverse transcription reaction in a volume of 30 microliters with Cy3-dUTP or Cy5-dUTP. The cDNA was then cleaned, combined, vacuum-dried, and resuspended in hybridization buffer to be incubated.
 
#What mathematical/statistical method did they use to analyze the data?
 
#What mathematical/statistical method did they use to analyze the data?
 
#Are the data publicly available for download? From which web site?
 
#Are the data publicly available for download? From which web site?

Revision as of 10:57, 14 November 2019

Definitions

  1. Hematological Cancer
  2. Aquaglyceroporin
  3. Hexamer
  4. Proteolytic activity
  5. Chelation
  6. Flux
  7. Promyelocytic leukemia
  8. Metabolite
  9. Biosynthesis
  10. Isoenzyme
  11. Assimilation

Article Outline

  1. What is the main result presented in this paper?
    • The main result presented in this paper was that the yeast was able to undergo this environmental stress from arsenite with the transcription factors Met4p and Yap1p from the incorporation of sulfur in the glutathione biosynthesis when there is an increased amount of arsenite present.
  2. What is the importance or significance of this work?
    • The significance of this work was to see if other transcription factors in addition to the ones mentioned in the introduction were able to also undergo arsenic stress and to study how that process works.
  3. What were the limitations in previous studies that led them to perform this work?
    • The limitation in the previous study that led the researchers perform this work was whether protein glutathionylation occurs in response to metals. With this limitation, they knew that Met4p controls GSH biosynthesis pathways and has known to be essential in controlling the sulfur assimilation expression genes and biosynthesis genes. From this limitation, they wanted to test yeast’s response to arsenite and see if the transcriptional regulators Yap1p and Met4p guide the sulfate assimilation pathway into the glutathione pathway.
  4. How did they treat the yeast cells (what experiment were they doing?)
    • The yeast cells after incubation were cleaned, combined, vacuum-dried, and resuspended in hybridization buffer to then be incubated at 100 Celsius for 2 min and 37 Celsius for 30 min to be analyzed in a microarray. The yeast cells were also exposed to 0.2 and 1.2 mM of sodium arsenite for further testing of their responses to the metal.
  5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    • The yeast strains that they used were W303-1A, RW124, CC849-1B, RW104, and YPDahl166. The paper did not specify whether these strains were haploid or diploid.
  6. What media did they grow them in? What temperature? What type of incubator? For how long?
    • The media that the yeast strains were grown in was YNB media (0.67% yeast nitrogen base) with 2% glucose or in SC medium (YNB containing 2% glucose) at a temperature of 30 Celsius.
  7. What controls did they use?
    • The controls that they used included the untreated yeast cells known as the wildtype cells.
  8. How many replicates did they perform per treatment or timepoint?
    • There are no replicates mentioned in the data that was provided.
  9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
    • To prepare the RNA, they isolated it from growing yeast cells that were both treated with and without sodium arsenite, and primed 20 micrograms of the total with 3 micrograms of hexamer and 3 micrograms of primer. It was then labeled in a reverse transcription reaction in a volume of 30 microliters with Cy3-dUTP or Cy5-dUTP. The cDNA was then cleaned, combined, vacuum-dried, and resuspended in hybridization buffer to be incubated.
  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?

Data & Files

DM_Yeast_Undergoes_Arsenic_Stress.pdf

Annotated Bibliography

Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. doi: 10.1242/bio.20148938

  1. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Global+analysis+of+protein+aggregation+in+yeast+during+physiological+conditions+and+arsenite+stress
  2. PubMed Central Full Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197440/
  3. Publisher Full Text (HTML): https://bio.biologists.org/content/3/10/913.short
  4. Publisher Full Text (PDF): https://bio.biologists.org/content/biolopen/3/10/913.full.pdf
  5. Copyright:2014. Published by The Company of Biologists Ltd (information found on PDF version of article)
  6. Article is Open Access.
  7. Article is available only online. The journal website allows for a subscription, but only for access to online content.
  8. Publisher: The Company of Biologists Ltd (not a scientific society), non-profit, OAPA member, United Kingdom
  9. The journal began in 2012.
  10. The articles in the journal are peer-reviewed.
  11. Editors and Board: https://bio.biologists.org/content/edboard
  12. Journal Impact Factor: 1.962
  13. The article is a primary research article.
  14. Data from article: https://bio.biologists.org/content/3/10/913.supplemental

Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: 10.1002/j.1460-2075.1992.tb05295.x

  1. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/1600951
  2. PubMed Central Full Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC556703/
  3. Publisher Full Text: https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1992.tb05295.x
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