Difference between revisions of "Cdomin12 Week 11"

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# Primary research article
 
# Primary research article
 
# Data are not available (dead hyperlink)
 
# Data are not available (dead hyperlink)
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# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast.  ''Molecular Biology of the Cell'', 15, 5492-5502.  doi:  10.1091/mbc.E04-03-0167
 
# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast.  ''Molecular Biology of the Cell'', 15, 5492-5502.  doi:  10.1091/mbc.E04-03-0167

Revision as of 15:22, 12 November 2019

User Page

template: cdomin12

Assignment Page Individual Journal Entries Class Journal
Week 1 cdomin12 Week 1 Class Journal Week 1
Week 2 cdomin12 Week 2 Class Journal Week 2
Week 3 RAD53 / YPL153C Week 3 Class Journal Week 3
Week 4 cdomin12 Week 4 Class Journal Week 4
Week 5 IMG/VR Week 5 Class Journal Week 5
Week 6 cdomin12 Week 6 Class Journal Week 6
Week 7 cdomin12 Week 7 Class Journal Week 7
Week 8 cdomin12 Week 8 Class Journal Week 8
Week 9 cdomin12 Week 9 Class Journal Week 9
Week 10 cdomin12 Week 10 Class Journal Week 10
Week 11 cdomin12 Week 11 Skinny Genes
Week 12/13 Skinny Genes Quality Assurance Skinny Genes
Week 15 Skinny Genes Deliverables Skinny Genes

Contents

1. Ten Biological Terms

2. Outline of Article

1. What is the main result presented in this paper?

2. What is the importance or significance of this work?

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?)

5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?

6. What media did they grow them in? What temperature? What type of incubator? For how long?

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.

Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.

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

    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?

Bibliographic Entries

  1. Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
  2. PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
  3. PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
  4. Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
  5. Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
  6. Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
  7. Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
  8. Availability: in print and online
  9. Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
  10. The journal begain in 1989
  11. Peer-reviewed articles: yest
  12. Editorial board.
  13. Impact factor: 3.512 (2017)
  14. Primary research article
  15. Data are not available (dead hyperlink)


  1. Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
  2. PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
  3. PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
  4. Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
  5. Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
  6. Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article);
  7. Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
  8. Availability: in print and online
  9. Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
  10. The journal begain in 1989
  11. Peer-reviewed articles: yest
  12. Editorial board.
  13. Impact factor: 3.512 (2017)
  14. Primary research article
  15. Data are not available (dead hyperlink)

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)?

  • Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
  • Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
  • Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.

Acknowledgments

1. I worked with User:ymesfin, User:Jcowan4, User:msamdars, and User:dramir36 for this assignment.

2."Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Cdomin12 (talk) 19:53, 11 November 2019 (PST)

References

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