BIOL388/S19:Week 14/15

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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, May 09 at midnight PDT (Wednesday night/Thursday morning).

Individual Journal Assignment

  • Store this journal entry as "username Week 15" (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 Ava
  • Fatimah and Edward
  • Austin and Sahil
  • Leanne and Desiree
  • Brianna and Ali

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.

Final Modeling Project

Improving our understanding of the experiment and analysis of our journal club paper, 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, we will use the MATLAB files from the last day of class (zipped package).

Your modeling tasks are as follows:

  1. Use the Arrhenius equation (rate = A*exp(-B/(R*T)) to model the temperature dependence of the chemostat reaction.
    • Figure out the constants A and B from the rate data in the TaiParamsRevised.m file.
    • Simulate the chemostat for T = 15,20, 25 degrees C conditions and graph the time courses of the biomass and nutrients.
  2. Investigate the glucose efficiency/waste constant (that is not really a constant?) for the glucose-limited and ammonium-limited conditions.
    • Note the values of E for glucose-limited and ammonium-limited conditions.
    • For each temperature (12, 30), find a function E(y) that matches the two points of (y,E) data.
    • Modify the chemostat_2nutrient_dynamics.m file to use the functions you've created.
    • Compare the resulting simulation to the previous one.

Your individual journal should detail your efforts, and your 15-minute presentation should cover these topics:

  1. A brief intro to the chemostat problem of Tai et al (2007).
  2. The data we've extracted from the paper and other sources.
  3. Your temperature investigation.
  4. Your efficiency/waste investigation.
  5. Discussion and reflection on your findings.

Your presentation should conform to the presentation guidelines provided for your first research presentation.