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?
   • Limitations included the ways the assays were conducted as well as research regarding As(III).
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., 2000.
   • Yeast cells were prepared by metal sensitivities assays.
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 (haploid), 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?
   • They used untreated S. cerevisiae cell RNA as the control.
   • It is unclear of how much out of the total 20micrograms of RNA was untreated or exposed.
8. How many replicates did they perform per treatment or timepoint?
   • There is no mention of replicates for each treatment.
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?
    • To determine whether or not genes with the consensus motif were present in the S. cerevisiae promoter, the generalized additive model (GAM) was used.

      -GAM was used to prevent errors that considered unequal promoter lengths between the regulated genes and the rest of the genome.

      -A normal statistical analysis test could lead to biased P-values.

11. Are the data publicly available for download? From which web site?
    • The data is publicly available from https://www.physiology.org/doi/full/10.1152/physiolgenomics.00236.2006 at the very end of the page under "Supplemental Data."
12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
    • Figure 1:

      -Axes: Straight axes not present. Flow chart show sulfate assimilation.

      -How measurements were made: Components were made with the help of references of previous research.

      -Trends and conclusions: Sulfate assimilation pathway and the making of GSH are interconnected

    • Figure 2:

      -Axes: X axis shows time in hours. Y axis shows kinetic activity.

      -How measurements were made: Measurements were made through cell aliquots.

      -Trends and conclusions: Exposure to sulfate will increase or decrease the production or metabolites over a period of time.

    • Figure 3:

      -Axes: X axis shows the cells affected by a certain concentration of As(III). Y axis shows the amount of sulfur proteins and GSH present within the cells.

      -How measurements were made: After an hour of exposure, cells were labeled with sulfate for four hours and measured.

      -Trends and conclusions: The amount of sulfate incorporated into proteins and GSH are inversely related with varying concentrations of As(III)

    • Figure 4:

      -Axes: X axis (A) shows exposure to a certain concentration of As(III) at different time points and (B) the time at which mutants show after electrophoresis. Y axis (A) shows mutant strains.

      -How measurements were made: Measurements of up and downregulation of the transcription of that gene.

      -Trends and conclusions: Wild type genes are upregulated while yap1 and met4 are downregulated with an increase in As(III)

    • Figure 5:

      -Axes: X axis shows the metaloid concentrations that affected each strain. Y axis shows each of the deletion mutants tested.

      -How measurements were made: Measurements were made by growth tests

      -Trends and conclusions: Dilutions show the response to different toxins

13. How does this work compare with previous studies?
    • This work is supplementary to the collection of studies that observe the response of yeast genes to environmental stresses, in this case, As(III).
14. What are the important implications of this work?
    • The cell's defense against As(III) is determined by deletion mutations.
15. What future directions should the authors take?
    • The authors should explore how the yeast cells respond to other toxins such as lead and mercury.
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?
    • The authors heavily supported their conclusions with the various components of the data.

Annotated Bibliography

Cadmium and arsenic responses in the ectomycorrhizal....

1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal(loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712
2. PubMed abstract: https://www.ncbi.nlm.nih.gov/pubmed/30411517
3. PubMedCentral link: N/A
4. Full text article from publisher: https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.12712
5. The link to the full PDF version of the article from the publisher web site.
6. Rights belong to: Society for Applied Microbiology and John Wiley & Sons Ltd.
7. How is the article available to you?
   • The article is NOT open access.
   • The article is NOT free after a certain period of time.
   • LMU did NOT buy a subscription or pay a fee for my access.
   • The article is behind a paywall.
8. Print or Online: Both
9. Publisher: Society for Applied Microbiology and John Wiley & Sons Ltd
   • For-profit or non-profit: Non-profit
   • It is a scientific society.
   • Member of the Open Access Publishers Association?: No
   • Publication Country: USA
10. Operation duration: Since 1938
11. Peer-reviewing: None.
12. Editorial board link: https://sfamjournals.onlinelibrary.wiley.com/hub/journal/13652672/homepage/editorialboard.html
13. Journal Impact Factor: 140 (not provided on homepage)
14. Review or primary research article: Primary research

Metabolome Modulation During Arsenic Stress...

1. Tripathi, R. D., Tripathi, P., Dwivedi, S., Dubey, S., & Chakrabarty, D. (2012). Arsenomics: omics of arsenic metabolism in plants. Frontiers in physiology, 3, 275. https://doi.org/10.3389/fphys.2012.00275
2. PubMed Abstract Link: https://www.ncbi.nlm.nih.gov/pubmed/22934029
3. PubMedCentral Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429049/
4. Link from Publisher: https://www.frontiersin.org/articles/10.3389/fphys.2012.00275/full
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.
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. Who is the publisher of the journal?
   • 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.)
14. Is the article a review or primary research article?
15. Are the data associated with this article available? If so, provide a link to the dataset.

References Questions

• You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
  1. Use a keyword search for the first three databases/tools and answer the following:
     • PubMed
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Google Scholar
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Web of Science
       • What original keyword(s) did you use? How many results did you get?
       • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
  2. Use the advanced search functions for each of these three databases/tools and answer the following:
     • PubMed
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Google Scholar
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Web of Science
       • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • Perform a prospective search on your article in the Web of Science and answer the following:
       • How many articles does this article cite?
       • How many articles cite this article?
• Reflect:
  1. What impact does the choice of keywords have on your results?
  2. What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

Data/files

Journal Club Presentation

Conclusion

This week I was able to read and critically analyze our article research. I learned that toxic compounds are dangerous to yeast cells, and these yeast cells are able to upregulate or downregulate the transcription of specific genes to protect the cell. I was able to understand the relationship of sulfur and GSH metabolism in regard to arsenic exposure. The results of this research has importance within molecular biology and human health.

Acknowledgments

• To my Sulfiknight members, DeLisa, Naomi, Joey, and Marcus. We worked during and outside of class to help each other understand our article as well as the assignment.
• Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Imacarae (talk) 22:16, 13 November 2019 (PST)

References

• Biology-Online Dictionary: Biology-Online Dictionary. Biology Online, 12 May 2014, [www.biology-online.org/dictionary/Main_Page www.biology-online.org/dictionary/Main_Page]
• NCI Dictionary of Cancer Terms. National Cancer Institute, [www.cancer.gov/publications/dictionaries/cancer-terms www.cancer.gov/publications/dictionaries/cancer-term].
• 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