Jnimmers week 11

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Biological Databases
Jnimmers
Assignment Table

Week Number Assignment Page Individual Journal Shared Journal
1 Week 1 Assignment Page N/A Week 2 Shared Journal
2 Week 2 Assignment Page Week 2 Individual Journal Week 2 Shared Journal
3 Week 3 Assignment Page CMR2/YOR093C Week 3 Week 3 Shared Journal
4 Week 4 Assignment Page Week 4 Individual Journal Week 4 Shared Journal
5 Week 5 Assignment Page CRISPRlnc Week 5 Week 5 Shared Journal
6 Week 6 Assignment Page Week 6 Individual Journal Week 6 Shared Journal
7 Week 7 Assignment Page Week 7 Individual Journal Week 7 Shared Journal
8 Week 8 Assignment Page Week 8 Individual Journal Week 8 Shared Journal
9 Week 9 Assignment Page Week 9 Individual Journal Week 9 Shared Journal
10 Week 10 Assignment Page Week 10 Individual Journal Week 10 Shared Journal
11 Week 11 Assignment Page Week 11 Individual Journal Sulfiknights Team Page
12/13 Week 12/13 Assignment Page Week 12/13 Individual Journal Sulfiknights Team Page
14 Week 14 Assignment Page Week 14 Individual Journal Week 14 Shared Journal
15 Week 15 Assignment Page Week 15 Individual Journal Week 15 Shared Journal

Individual Journal Assignment

  • Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
  • Invoke your template on your journal entry page so that you:
    • Link from your journal entry page to this Assignment page.
    • Link from your journal entry to your user page.
    • Add the "Journal Entry" category to the end of your wiki page.
  • Because you have invoked your template on your user page, you should also have a:
    • Link from your user page to this Assignment page.
    • Link to your journal entry from your user page.
  • Note that this week, we will add two new categories, "Group Projects" and a category for your team's name. Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.
  • Include both the Acknowledgments and References section as specified by the Week 1 assignment.
  • The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Data/files, Conclusion, Acknowledgments, and References (as specified by the Week 1 assignment).


Presentation Prep: Individual Journal Pages

In preparation for your journal club presentation, you will each individually complete the following assignment on your individual journal page.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
  2. Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
    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.
      • 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?

Journal Club Presentation

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.

  • Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
  • You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
  • You need to present the information in the outline of your journal article listed above, but organized as a presentation. You will need the following:
    • Title slide with the complete reference to the article, team name, team members, date and "BIOL 367".
    • Outline slide (list of key messages for the talk)
    • One or more introduction slides
    • A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
    • A summary/conclusion slide that is a reflection of the outline.
    • Acknowledgments slide
    • References slide
  • Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am on Thursday, November 14
    • You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
  • Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the Presentation Rubric.
  • Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
    1. What is the speaker's take-home message (one short sentence)?
    2. What is the best thing about this presentation?
    3. What needs improvement?
    4. Please comment on the speaking style (language and delivery) of each presenter.
  • Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

Annotated Bibliography

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

Resources

Assignment

  • Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
    • Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
      1. The complete bibliographic reference in the APA style (see this link), with DOI.
      2. The link to the abstract from PubMed.
      3. The link to the full text of the article in PubMedCentral (if not available, write N/A).
      4. The link to the full text of the article (HTML format) from the publisher web site.
      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.
  • 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)?

Annotated Bibliography #1

  1. Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005
  2. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15691908
  3. PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546828/
  4. Publisher Full Text (HTML): https://aem.asm.org/content/71/2/599
  5. Publisher Full Text (PDF): https://aem.asm.org/content/aem/71/2/599.full.pdf
  6. Copyright: Copyright © 2005, American Society for Microbiology. All Rights Reserved.
  7. Article is Open Access
  8. Availability: Online (PubMed,ePub, and PDF)
  9. Publisher: American Society for Microbiology Journals (scientific society), for-profit, not a member of the OAPA
  10. The journal began in 1899
  11. Peer-reviewed articles: Yes
  12. Editorial Board
  13. Impact factor: 5.311
  14. Primary research article
  15. Figures and Data Tab

Annotated Bibliography #2

  1. A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. DOI: 10.1007/s00204-004-0620-x
  2. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/15526190
  3. PubMed Central: Not available
  4. Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-004-0620-x#enumeration
  5. Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-004-0620-x.pdf
  6. Copyright: Springer-Verlag 2004
  7. Article is open access
  8. Availability: in print and online
  9. Publisher: Springer-Verlag (non-scientific society, mass publisher of scientific material,for-profit, not a member of the OAPA
  10. The Springer-Verlag media company was founded in 1842
  11. Peer-reviewed articles: yes
  12. Not Available
  13. Impact factor: 5.98
  14. Primary research article
  15. Data are not available.

Database Searches

  • You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.
  1. PubMed
    • What original keyword(s) did you use? How many results did you get?
      • I searched "arsenic metabolism and got 13,712 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I added the keywords yeast and did a search within 10 years and the search narrowed to 111 results
  2. Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • I searched for "arsenic metabolism and got 285,000 results
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • After including the keyword "yeast" in the search, I got 41,600 results
  3. Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • I originally searched "arsenic toxicity yeast" and got 61 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • After that, I searched "arsenic toxicity yeast" within the 61 results and added the "Highly Cited in Field" filter creating a search of 1 result.
  • Use the advanced search functions for each of these three databases/tools and answer the following:
  1. PubMed
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • The most useful search was after setting the publish date range to 5 years.
  2. Google Scholar
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • Including the search must find a paper betweem 2007 and now because the original paper that my group in analyzing was published in 2007.
  3. Web of Science
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I found the "Highly Cited in Field" filter the most useful to narrow down the search to a singular, highly regarded publishing.
      • 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?

Reflection

  • The primary site used in order to find these articles was Google Scholar by searching the keywords: Arsenic Metabolism, which produced a total of 285,000 results. In order to specify my results, I then searched with the keywords: "Arsenic metabolism yeast"; in order to better find papers that shared greater similarity to the original, assigned paper. This search produced ~41,600results.
  1. The choice of keywords in a search has a major impact in the specificity of the results you get. One word can change the results from being as broad as all phylogenetic domains to something as simple as yeast or any other general species type.
  2. Pubmed is ad

Purpose

  • The purpose of this assignment was to further learn how to read a scientific journal and pull pertinent information from it as well as learning how to analyze complex data from an article in order to present the finding of the data to our peers.

10 definitions of terms

  1. Concomitant
    • At the same time: describing drugs that are administered together or symptoms that occur during the same period.
  2. Promyelocyte,
    • A cell intermediate in development between a myeloblast and a myelocyte.
  3. GSH
    • Reduced glutathione
  4. Proteome
    • The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
  5. Basal
    • At, of, or being the minimum level for maintaining the normal or essential functioning of an organism.
  6. Thiol
    • An organic compound containing the group —SH, i.e. a sulphur-containing analogue of an alcohol.
  7. Antimony/Antimonite (Sb)
    • The chemical element of atomic number 51, a brittle silvery-white metalloid.
  8. Isoenzyme
    • Each of two or more enzymes with identical function but different structure.
  9. Ubiquitinated
    • Of a protein: bound to ubiquitin/A compound found in living cells which plays a role in the degradation of defective and unneeded proteins. It is a single-chain polypeptide.
  10. Motif
    • A distinctive sequence on a protein or DNA, having a three-dimensional structure that allows binding interactions to occur.

Outline of your journal article

  1. Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11-inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
  2. What is the main result presented in this paper?
    • This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
  3. What is the importance or significance of this work?
    • Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
  4. What were the limitations of previous studies that led them to perform this work?
    • This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
  5. How did they treat the yeast cells (what experiment were they doing?)
    • Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
  6. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    • The researchers used characteristic strains of Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, in this experiment, the strains used were haploid. These strains include
  7. What media did they grow them in? What temperature? What type of incubator? For how long?
    • The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose as a carbon source) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
  8. What controls did they use?
    • In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
  9. How many replicates did they perform per treatment or timepoint?
    • Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
  10. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
    • The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
  11. What mathematical/statistical method did they use to analyze the data?
    • The microarray data were analyzed using the linear models for microarray data (LIMMA) package in the statistical language R. T-statistics we also used in order to rank the genes being studied based on the results from the linear model analysis.
  12. Are the data publicly available for download? From which web site?
    • The data is publicly available for download here doi: 10.1152
  13. 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?
    • Figure 1 depicts a flow chart to show sulfur assimilation. Straight axes not present. Components were made with the help of references of previous research.
    • Figure 2 depicts intracellular concentrations of metabolites in response to the presence of arsenic. The X axis represents hours after exposure to the arsenite, and the Y axis represents metabolite concentrations, given in μM. The measurements were made by analyzing cell aliquots that were collected at different time points after As(III) treatment. The figure depicts multiple different metabolite concentrations, however, the general trends of the plots show a general increase of sulfur metabolite concentrations as the exposure to As(III) increases in time.
    • Figure 3 depicts the balance of sulfate utilization in As(III)-exposed cells. The X axis shows the amount of Sulfur in proteins and Glutathione(GSH) in 10^5 cpm, the Y axis shows the concentration of As(III) that the proteins are exposed to (0 mM control, 0.1 mM, and 0.2 mM. The measurements were made by aliquots analysis of the three concentrated cultures by taking the reported amount of radioactivity produced by the As(III)-exposed cells. As a general trend, the greater the concentration of the exposed As(III), the greater amount of sulfur found within the Glutathione instead of the proteins.
    • Figure 4A shows the results of the microarray data given the expression changes of genes in the sulfur assimilation and GSH biosynthesis in response to As(III) presence at 15, 30, and 60 min and 18 h. The X axis of the microarray data shows an assortment of genes being tested for their expression response to As(III) presence. The Y axis shows time that passed since the immediate exposure of the As(III) at varying concentrations. As a general trend, as the concentration of the As(III) increased, so did the expression of the different genes being analyzed by the microarray over time.
    • Figure 4B shows the expression of genes in RNA extracted from wildtype, met4Δ, and yap1Δ cells at certain time points after being exposed to 0.2 mM As(III). The X axis showed the time points at which the genes were analyzed for expression and the Y axis shows three MET genes being analyzed with 18s rRNA being the loading control. The measurements were made using 32P-labeled genes and a common trend of the Figure was that wild-type cells show high expression of their genes after exposure to As(III) than mutant met4Δ and yap1Δ cells.
    • Figure 5 depicts serial dilutions of wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ cultures spotted on SC-agar plate supplemented with the metal indicated on the figure. Growth was monitored after 2–3 days at 30°C. The X-axis shows which metal is being supplemented onto each plate at varying concentrations and the y-axis shows the condition of the cell cultures being plated (wildtype, met4Δ, acr3Δ, and acr3Δ met4Δ). The general trend of the figure showed that wild type cells grew the best regardless of the concentration and metal supplemented, however in the 10 cadmium microM supplemented plate, no strain of yeast (wild or mutant) grew well.
  14. How does this work compare with previous studies?
    • This work's results agreed with the results of previous studies, however, the assimilation of sulfur and its role in assisting in GSH biosynthesis were newly discovered findings made by the researchers.
  15. What are the important implications of this work?
    • This work provides insight on how yeast has evolved in order to combat dangerous/toxic materials such as arsenic as well as the functional importance of sulfur and glutathione in combating toxic compounds.
  16. What future directions should the authors take?
    • Using human cells, the authors should proceed in finding if humans possess genes that have the ability to create products that could actively combat arsenic poisoning. If so, finding a way to create a medicine that could activate those genes and halt the spread of arsenic in the body and get rid of it
  17. 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?
    • Besides the fact that their materials and methods section lacked some small details of the equipment used as well as the confusion surrounding the mathematical model they used, I believe that the authors supported their conclusion very well using the data that they acquired, however, a better/simpler explanation of the research and methods could make this such a more exciting read for a reader.

Conclusion

  • I found the connection between toxic compounds and the reactions of yeast cells in order to combat the toxicity of said compound.

Data and Files

Acknowledgments

  • I would like to acknowledge Dr. Kam D. Dahlquist
  • Thank you to my group: the Sulfiknights | Ivy Macaraeg, DeLisa Madere, Naomi Tesfaiohannes & Marcus Avila. We met in lab and spoke over the phone, coordinating roles, responsibilities, and dividing work between the 5 of us.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Jnimmers (talk) 23:09, 13 November 2019 (PST)

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
  • (2006). Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J. (Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 13 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170.