Imacarae Week 11

Imacarae's User Page

Assignment	Shared Entries	Individual Entries
Week 1	Class Journal Week 1	----
Week 2	Class Journal Week 2	Imacarae Week 2
Week 3	Class Journal Week 3	HSF1/YGL073W Week 3
Week 4	Class Journal Week 4	Imacarae Week 4
Week 5	Class Journal Week 5	CancerSEA Week 5
Week 6	Class Journal Week 6	Imacarae Week 6
Week 7	Class Journal Week 7	Imacarae Week 7
Week 8	Class Journal Week 8	Imacarae Week 8
Week 9	Class Journal Week 9	Imacarae Week 9
Week 10	Class Journal Week 10	Imacarae Week 10
Week 11	Sulfiknights	Imacarae Week 11
Week 12/13	Sulfiknights	Sulfiknights DA Week 12/13
----	Sulfiknights	Sulfiknights DA Week 14

Purpose

• To create our team's home page and to get ourselves organized for the final project.
• To learn how to search the primary literature.
• To prepare and give a journal club presentation.

10 definitions

Research article Quantitative transciptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenitecan be found here

1. Metabolite: A substance that is a product of metabolic action or that is involved in a metabolic process [1]
2. Glutathione: Tripeptide: glutamylcysteinylglycine. It is an important cofactor for the enzyme glutathione peroxidase in the uptake of amino acids and participates in leucotriene synthesis [2]
3. Promyelocytic leukemia: A nuclear structure (promyelocytic leukaemia body, Kremer body) containing multimers of promyelocytic leukaemia (PML) protein and a range of other nucleoproteins which assists in repair of double-strand breaks in DNA. PML protein is a RING finger motif protein that acts as a tumour suppressor and is implicated in the pathogenesis of a variety of tumours [3]
4. Chelation: the combination of a metal ion with a chemical compound, forming a ring [4]
5. Northern blot analysis: used to separate and identify RNA fragments; transfers RNA from an agarose gel to a nitrocellulose filter followed by probe detection [5]
6. Ortholog/orthologous:genes or proteins found in different species that are so similar in their amino acid sequences that they are assumed to have originated from a single ancestral gene [6]
7. Permease: a membrane-bound protein in bacteria that is responsible for transport of a specific substance in or out of the cell [7]
8. Ubiquitination: the post-translational modification of one or more ubiquitin monomers (regulatory proteins) by covalent attachment [8]
9. Homocysteine: a sulphur-containing amino acid that is an intermediate in the synthesis of cysteine [9]
10. Hybridize: The process of forming a double stranded nucleic acid from joining two complementary strands of DNA [10]

Journal Outline

1. What is the main result presented in this paper?
   • Toxins, such as arsenic, will change the transcription of important genes in Saccharomyces cerevisiae cells and lead to an increase of sulfur metabolites and glutathoine levels.
   • These important genes encode for survival metabolic pathways such as protein synthesis, stress defense, or redox maintenance.
   • Yap1p and Met4p are essential to controlling the cells' response to arsenic exposure.
2. What is the importance or significance of this work?
   • Yeast cells' response to arsenic is reflective of what happens with human cells in response to toxins. By understanding how exactly the cells are affected, such as through the alteration of transcription, we can know how our cells can be altered to combat toxicity.
3. What were the limitations in previous studies that led them to perform this work?
4. How did they treat the yeast cells (what experiment were they doing?)
   • RNA was isolated through a process described by Dormer, U. H et al. These cells were already exposed to sodium arsenite.
5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
   • The strains of Saccharomyces cerevisiae used were W303-1A (diploid), RW124, CC849-1B, RW104, and YPDahl166.
6. What media did they grow them in? What temperature? What type of incubator? For how long?
   • Media: YNB medium (0.67% yeast nitrogen base) with 2% glucose as a carbon source
   • Temperature: 30°C
   • Incubation and timing: 100°C for the first 30 min and 37°C for the next 5 min.
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?
   • 20 micrograms of RNA was primed with 3micrograms of Invitrogen and 3micrograms of ABgene.
   • Hybridization happened at 42°C for 12–18 hours.
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.
13. What do the X and Y axes represent?
14. How were the measurements made?
15. What trends are shown by the plots and what conclusions can you draw from the data?
16. How does this work compare with previous studies?
17. What are the important implications of this work?
18. What future directions should the authors take?
19. 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

• Will be done next Tuesday.

References

• Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
• Dormer, U. H., Westwater, J., McLaren, N. F., Kent, N. A., Mellor, J., & Jamieson, D. J. (2000). Cadmium-inducible expression of the yeast GSH1 gene requires a functional sulfur-amino acid regulatory network. Journal of Biological Chemistry, 275(42), 32611-32616. doi: 10.1111/j.1432-1033.1996.00633.x