BIOL388/S19:Week 9

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BIOL 388-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Thursday, March 28 at midnight PDT (Wednesday night/Thursday morning).

Individual Journal Assignment

  • Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL388/S19" category to the end of your wiki page.

Homework Partners

Please meet with your partner (either face-to-face or virtually) at least once when preparing this assignment. Even though you may work together to understand the article, your definitions and outline must be done individually. It is not acceptable to do a joint assignment and copy it over to each others' journal page.

  • Angela and Desiree
  • Fatimah and Alison
  • Austin and Ava
  • Leanne and Brianna
  • Sahil and Edward

Electronic Lab Notebook

Because of the nature of the assignment this week, you will have four sections of the electronic notebook:

  1. The purpose: what is the purpose of this assignment?
  2. Answers to the questions posed in the assignment.
  3. The Acknowledgments section.
    • You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
      • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
    • Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist or Dr. Fitzpatrick (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
    • If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
    • If you need to reference content, include the formal citation in your References section (see below).
    • You must also include this statement:
      • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
    • Sign your Acknowledgments section with your wiki signature.
  4. The References section. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising.
    • Do not include citations/references to sources that you did not use.
    • You should include a reference to this week's assignment page.
    • The references should be formatted according to the APA guidelines.

Preparation for Journal Club 2

The paper we will read for Journal Club 2 is:

Tai, S. L., Daran-Lapujade, P., Walsh, M. C., Pronk, J. T., & Daran, J. M. (2007). Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Molecular Biology of the Cell, 18(12), 5100-5112. DOI: 10.1091/mbc.e07-02-0131

For this journal club, the entire class will read and present the same paper referenced above. Each student will create an individual wiki journal page for his or her Week 9 assignment and also contribute to the shared journal page in preparation for the presentation in class on March 28.

  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?
  3. Each pair of students will be assigned a figure from the paper. You will then be responsible for discussing the assigned section and figure. Dr. Dahlquist will prepare the PowerPoint slides this time.
    • Table 1: Angela
    • Figure 1: Fatimah
    • Figure 2: Austin
    • Table 2: Desiree
    • Table 3: Alison
    • Figure 3: Leanne
    • Figure 4: Ava
    • Figure 5: Brianna
    • Figure 6: Sahil and Edward

Online Biological Dictionaries

Shared Journal Assignment

  • Store your shared journal entry in the shared Class Journal Week 9 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL388/S19" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer the following questions on the Class Journal Week 9 page after you have completed the individual assignment.

  1. What aspect of this assignment came most easily to you?
  2. What aspect of this assignment was the most challenging for you?
  3. What (yet) do you not understand?
  4. Compared to the Schade et al. (2004) paper that you read for the first journal club, which paper do you think is stronger and why?
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