Imacarae Week 11

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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?
  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. PDF Link: https://sfamjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.12712
  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 has access to it through William H. Hannon Library.
  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
  15. Data available through article?: No.

Modulation of growth, ascorbate-glutathione...

  1. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5
  2. PubMed Abstract Link: https://www.ncbi.nlm.nih.gov/pubmed/?term=Modulation+of+growth%2C+ascorbate-glutathione+cycle+and+thiol+metabolism+in+rice+(Oryza+sativa+L.+cv.+MTU-1010)+seedlings+by+arsenic+and+silicon
  3. PubMedCentral Link: N/A
  4. Link from Publisher: https://link.springer.com/article/10.1007/s10646-018-1994-5
  5. PDF Link: https://link.springer.com/content/pdf/10.1007%2Fs10646-018-1994-5.pdf
  6. Who owns the rights: Springer Science+Business Media, LLC
  7. How is the article available to you?
    • This article NOT open access
    • It is NOT available for free after a certain period of time.
    • LMU pays to access this article.
  8. Print or online: Both
  9. Publisher: Springer US
  10. Operating since: 1832
  11. Peer-reviewd?: Yes
  12. Editorial Board Link: https://www.springer.com/journal/10646/editors
  13. Journal Impact Factor: 2.460 (provided by journal homepage)
  14. Review or primary research article: Primary Research
  15. Data available through article?: No.

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
        • Key words: arsenic, metabolism. Results: 13,712
        • Term combinations: arsenic AND metabolism AND glutathione. It helped most when I searched for these in the title, and I got 219 results.
      • Google Scholar
        • Keywords: arsenic, metabolism, yeast Results: 41,700
        • Term combinations: arsenic AND metabolism AND glutathione [Title]. I got 7,720 results.
      • Web of Science
        • Keywords: arsenic, metabolism Results: 2,796
        • Term combinations: arsenic AND metabolism AND glutathione. I got 510 results.
    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?
          -The advanced search function that was most useful was the ability to make sure that all of the keywords I wanted were in the Title or in the Title/Abstract.
      • Google Scholar
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          -The advanced search option that was most useful was ensuring that the keywords appeared in the title. By doing this, I got 33 results.
      • Web of Science
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          -The advanced search options that were most useful were to include the "TI=" function and to select the "Article" option. This narrowed it down to 10 results.
      • Perform a prospective search on your article in the Web of Science and answer the following:
        • How many articles does this article cite? - 82
        • How many articles cite this article? - 0
  • Reflect:
    1. What impact does the choice of keywords have on your results?
      • The choice of keywords is very important on the results. The words have to be very specific and filtered so that you can get exactly what you want out of your search.
    2. What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?
      • The advantages of Pubmed is that it is a good place to start a search. It has advanced options as well as being able to include keywords in the title or abstracts. The disadvantage is that is very limited to biomedical research and not science as a whole. The advantages to Google Scholar are that it is a quick way to look for something, and it has the APA citations readily available. The disadvantages are that it does not allow for advanced search options, it includes popular sources, and it does not include DOIs within the citations. The advantages of Web of Science is that it includes a broader range of scientific research and it includes a citation network for further research. The disadvantage is that doesn't automatically index all the journals together.

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
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