Week 11

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This journal entry is due on Thursday, November 14, at 12:01am PST. (Wednesday night/Thursday morning)

There is an interim deadline for Tuesday, November 12 at 12:01am PST, to decide your team name and select your Project Manager.

The Annotated Bibliography is due Tuesday, November 19 at 12:01am PST.

Overview

  • Everyone will contribute to Creating your team's home page, and in the process, getting yourselves organized for the final project.
  • To find and use scholarly and discipline-specific professional information, understanding the role of journals and publishers in controlling and providing access to scholarly content.
  • To select information that provides relevant evidence on a topic.
  • To differentiate between primary and secondary sources, recognizing how their use and importance vary with each discipline.
  • To evaluate resources for reliability, validity, accuracy, authority, and bias.
  • To prepare and give a journal club presentation, critically evaluating an article from the primary literature.

Grading for this assignment

  • Your individual journal entry with the outline of the journal club paper is worth a total of 10 points.
  • Your individual journal entry with annotated bibliography is worth a total of 10 points.
  • Your team journal entry for this week is also worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.
  • The journal club presentation (delivered on November 14) will be worth a total of 40 points.

Team Membership

The project groups and roles are are:

  1. FunGals: Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
    • Project Manager: Mike
    • Quality Assurance: Iliana
    • Data Analysis: Emma, Kaitlyn
    • Coder: Mike
  2. Sulfiknights: 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
    • Project Manager: Naomi
    • Quality Assurance: Naomi, Joey
    • Data Analysis: Marcus, Ivy
    • Designer: DeLisa
  3. Skinny Genes: Barreto, L., Canadell, D., Valverde‐Saubí, D., Casamayor, A., & Ariño, J. (2012). The short‐term response of yeast to potassium starvation. Environmental microbiology, 14(11), 3026-3042. DOI: 10.1111/j.1462-2920.2012.02887.x
    • Project Manager: Aby
    • Quality Assurance: Christina, Jonar
    • Data Analysis: David, Aby
    • Coder: Mihir

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 (Due Tuesday, November 19, 12:01am PST)

This exercise will be primarily performed in class on Tuesday, November 12. What is not finished in class is due on Tuesday, November 19, 12:01am PST).

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).
    • On your team's page, only include the APA-formatted citations in a list for the 8 or 10 articles; the rest of the information below goes on your individual pages.
    • 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)?

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

  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)

Whole Team Journal Assignment: Creating a Team Wiki Page

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.

  1. Select your team's Project Manager.
  2. Name your team and create your team home page on the wiki.
    • The name of your team home page should simply be the team name.
    • This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
  3. Create a link to your team's page on the course Main page.
  4. Create a template for your team with useful information and links that you will invoke on all pages that you will create for the project.
    • Create a category using your team name and include it on your team's template so that it also gets used on all pages you will create for the project. Also use include the category "Group Projects" in your template.
      • However, please do not add these categories to your own individual templates because we want them to precisely mark pages having to do with the Group Projects and your team, respectively.
  5. Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
  6. Each team member should reflect on the team's progress:
    1. What worked?
    2. What didn't work?
    3. What will I do next to fix what didn't work?
  7. Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.
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