BIOL398-05/S17:Week 6

This journal entry is due on Thursday, February 23, at midnight PST. (Wednesday night/Thursday morning). Note that the OpenWetWare server registers time in the Eastern time zone, so it will say 03:00 AM at midnight PST.

Individual Journal Assignment

• Store this journal entry as "username Week 6" (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

Since this class is small, you have already worked with the other members of the class as homework partners on previous assignments. We are not explicitly assigning partners for this week, but you should feel free to consult with the other members of the class in order to complete the assignment. However, unless otherwise stated, each student must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).

Electronic Lab Notebook

Complete your electronic notebook that gives the details of what you did for the assignment this week. Your notebook entry should contain:

1. The purpose: what was the scientific purpose of your investigations?
   • Note that this is different than the learning purpose.
2. Your workflow or methods: what did you actually do? Give a step by step account.
   • There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
   • You may copy protocol instructions to your page and modify them as to what you actually did, as long as you provide appropriate attribution in the acknowledgments and references section.
   • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, etc.
3. Your results: the answers to the questions in the protocol, plus any other results you gathered. Your results will include some or all of the following: images, plots, data, and files.
   • Note that files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the T: drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
   • Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
     • Upload the files to this wiki.
     • Upload the files to Box.
     • Back them up on your personal flash drive.
   • References to data and files should be made within the methods and results section of your notebook, listed above.
   • In addition to these inline links, create a Data and Files section of your notebook to make a list of the files generated in this exercise.
4. A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?
5. The Acknowledgments section, see below.
6. The References section, see below.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge.

1. 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.
2. 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.
3. 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.
4. 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).
5. You must also include this statement unless otherwise noted:
   • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
6. Sign your Acknowledgments section with your wiki signature.

References

1. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
   • methods
   • data
   • facts
   • images
   • documents, including the scientific literature
2. The references in this section should be accompanied by in text citations on your page that refer to these references.
3. Do not include citations/references to sources that you did not use.
4. Generally, you should include a reference to that week's assignment page.
5. The references should be formatted according to the APA guidelines.
6. 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.

This Week's Exercise

This week we will start constructing model(s) of the dynamics of yeast, nitrogen, and carbon. There are at least two problems of interest, each of which involves its own model development.

• Gaining a better understanding of the fermentation/respiration switch.
  • See Albertin, W., Marullo, P., Aigle, M., Dillmann, C., de Vienne, D., Bely, M., & Sicard, D. (2011). Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control. Applied and environmental microbiology, 77(8), 2772-2784. doi: 10.1128/AEM.02547-10 and/or
  • See Van den Brink, J., Canelas, A. B., Van Gulik, W. M., Pronk, J. T., Heijnen, J. J., De Winde, J. H., & Daran-Lapujade, P. (2008). Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism. Applied and environmental microbiology, 74(18), 5710-5723. doi: 10.1128/AEM.01121-08 and/or
  • See Brauer, M. J., Saldanha, A. J., Dolinski, K., & Botstein, D. (2005). Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Molecular biology of the cell, 16(5), 2503-2517. doi: 10.1091/mbc.E04-11-0968
• Diving into the central nitrogen metabolism processes.
  • See Van Riel, N. A. W., Giuseppin, M. L. F., TerSchure, E. G., & Verrips, C. T. (1998). A Structured, Minimal parameter Model of the Central Nitrogen Metabolism inSaccharomyces cerevisiae: the Prediction of the Behaviour of Mutants. Journal of theoretical biology, 191(4), 397-414. doi: 10.1006/jtbi.1997.0600 and/or
  • See Van Riel, N. A. W., Giuseppin, M. L. F., & Verrips, C. T. (2000). Dynamic optimal control of homeostasis: an integrative system approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae. Metabolic engineering, 2(1), 49-68. doi: 10.1006/mben.1999.0137 and/or
  • See ter Schure, E. G., Silljé, H. H., Raeven, L. J., Boonstra, J., Verkleij, A. J., & Verrips, C. T. (1995). Nitrogen-regulated transcription and enzyme activities in continuous cultures of Saccharomyces cerevisiae. Microbiology, 141(5), 1101-1108. doi: 10.1099/13500872-141-8-2019

1. Pick one of the two general projects above.
2. Carefully read the first paper associated with your project.
   • Refer to the Week 3 assignment in reading the paper.
3. Propose a hypothesis about the impact of the ammonium feed rate on a quantity of interest (alcohol, carbon dioxide, glutamate, etc). This quantity may or may not be one quantified in the figures of the Journal Club One paper.
4. Delineate state variables that are necessary to the process.
5. Write a system of differential equations that you think captures the important behaviors.
6. Explain and justify the terms in your differential equation system.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 6 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 "BIOL398-05/S17" category to the end of the wiki page (if someone has not already done so).

Reflection

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?