BIOL398-05/S17:Week 10

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BIOL398-05: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Thursday, March 30 at midnight PDT (Wednesday night/Thursday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 10" (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 "BIOL398-05/S17" 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.

  • Lauren, Cameron
  • Nika, Conor
  • Maggie

Electronic Lab Notebook

Because of the nature of the assignment this week, you need only complete the following sections of the electronic notebook:

  1. The purpose: what is the purpose of this assignment?
  2. 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 (such as the methods of a protocol) also acknowledge it here and include a 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.
  3. The References section. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising.
    • In the case of the definitions, you will provide a citation for each definition (see below).
    • For the outline itself, state at the beginning that is is an outline of the ter Schure (1995) paper and provide the complete reference in your References section.
    • 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.
    • For more detailed instructions on how to cite journal articles, books, or web pages, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Read

The class will be divided up into three groups to make a 20 minute Journal Club Presentation on one of the following three articles which each represent major aspects of the final project for this class:

  1. Group 1: Lauren, Cameron
    • 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
  2. Group 2: Nika, Conor
    • Vu, T. T., & Vohradsky, J. (2007). Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic acids research, 35(1), 279-287. doi: 10.1093/nar/gkl1001
    • Link to PDF version of article: Use for reading/printing and for capturing tables for your PowerPoint slide.
    • Link to full text in HTML: Use for inserting figures/images into your PowerPoint slide.
  3. Group 3: Maggie
    • Ahnert, S. E., & Fink, T. M. A. (2016). Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space. Journal of The Royal Society Interface, 13(120), 20160179. doi: 10.1098/rsif.2016.0179

Background Reading on Cold Stress

Review articles on cold stress that may be helpful:

Preparation for Journal Club 2

  1. Individually, 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.
  2. Individually, 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.
    • What is the main result presented in this paper?
    • What is the importance or significance of this work?
    • Create a flow chart to describe their methods. Answer the following questions if they are relevant to your article.
      • How did they treat the cells (what experiment were they doing?)
      • What strain(s) of yeast did they use? Was the strain haploid or diploid?
      • What media did they grow them in? Under what conditions and temperatures?
      • What controls did they use?
      • How many replicates did they perform per condition?
      • What mathematical/statistical method did they use to analyze the data?
    • What transcription factors did they talk about?
    • Briefly state the result shown in each of the figures and tables.
  3. As a group, prepare a 20 minute PowerPoint presentation to give to the class on Thursday, March 30.
    • A 20-minute presentation should include about 20 slides (one per minute). Include the following slides:
      • Title slide with the full citation of the journal article in APA style: authors, year, title, journal name, volume, page numbers, the names of the group members, the date, and the class number and title.
      • Outline slide
      • Introduction to your paper that includes the importance of significance of the work and the background information needed to understand the article.
      • A slide for every figure and table in the paper with an explanatory title that is a phrase or sentence that explains the main point of the figure/table.
      • One or more slides based on the Discussion and summarizing the paper (your outline slide can become your summary if reworded properly.
    • Upload your slides to the OpenWetware wiki by the Week 10 journal assignment deadline. Each member of your group should have a link to the same PowerPoint file. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The journal club presentation is worth 50 points. The same presentation grade will be given to the entire group.

Additional Tips for Your PowerPoint Slides

  • When putting the figures into your PowerPoint slide, do the following:
    1. First download the image as a file to your computer's hard drive from the HTML version of the article. (Right-clicking the image in most web browsers will open a menu with "Save image as" as one of the options.
    2. Then in PowerPoint, select "Insert image from file" and browse to your file. If you just copy/paste the image, this could lead to problems when showing a PowerPoint presentation made on a Mac on a Windows PC.
    3. When enlarging images, be careful to not change the aspect ratio of the image.
    4. You may choose to crop large figures into smaller pieces to facilitate your presentation; in this case it would be acceptable to create two or even three slides from the same figure. Each slide needs to have a descriptive title and summary information on the slide.
  • When putting the tables into your PowerPoint slide, do the following:
    1. Capture the image from the PDF version of the article. In the full version of Adobe Acrobat (available on most LMU lab computers) use the "camera" icon to draw a marquee around the table. This will capture the table to your computers's clipboard. You can then paste this into the PowerPoint slide.
    2. When enlarging or reducing the table to fit the slide, be careful to not change the aspect ratio.
    3. You may choose to crop large tables into smaller pieces to facilitate your presentation; in this case it would be acceptable to create two or even three slides from the same table. Each slide needs to have a descriptive title and summary information on the slide.

Online Biological Dictionaries

Shared Journal Assignment

  • Store your shared journal entry in the shared Class Journal Week 10 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 "BIOL398-04/S15" category to the end of the wiki page (if someone has not already done so).

Reflection

Critically evaluate the paper you were assigned.

  1. Overall, do you think this paper was clearly written? Why or why not?
  2. Based on what is written in the methods section, do you think you could reproduce their experiments/models and data analysis?
  3. What else would you like to know about their methods, results, and future directions?
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