BIOL398-03/S13:Week 6: Difference between revisions
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== Individual Journal Assignment == | == Individual Journal Assignment == | ||
* Store this journal entry as "''username'' Week | * 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: you can do all of this easily by adding them to your template and then using the template on your pages.) | ** Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.) | ||
*** Link to your journal entry from your user page. | *** Link to your journal entry from your user page. | ||
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# terSchure and coauthors (Microbiology, 1995, 141:1101-1108) considered other conditions, such as changing the dilution rate. Apply our chemostat model to these conditions. | # terSchure and coauthors (Microbiology, 1995, 141:1101-1108) considered other conditions, such as changing the dilution rate. Apply our chemostat model to these conditions. | ||
# The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide. | # The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide. | ||
# The metabolism model we’ve worked out does not directly involve the ammonia feed. Develop and analyze a metabolism model that connects ammonia feed to | # The metabolism model we’ve worked out does not directly involve the ammonia feed. Develop and analyze a metabolism model that connects ammonia feed to alpha-ketogluterate, glutamine, and glutamate levels. Figure 3 tells us that enzyme concentrations depend on feed concentration. That is a good place to start. | ||
# The last line of the terSchure paper is as follows: “If the ammonia concentration is the regulator, this may imply that S. cerevisiae has an ammonia sensor which could be a two-component sensing system for nitrogen, as has been found in gram-negative bacteria (4).” Develop and analyze a model based on this concept. | # The last line of the terSchure paper is as follows: “If the ammonia concentration is the regulator, this may imply that S. cerevisiae has an ammonia sensor which could be a two-component sensing system for nitrogen, as has been found in gram-negative bacteria (4).” Develop and analyze a model based on this concept. | ||
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== Shared Journal Assignment == | == Shared Journal Assignment == | ||
* Store your journal entry in the shared [[BIOL398-03/S13:Class Journal Week | * Store your journal entry in the shared [[BIOL398-03/S13:Class Journal Week 6 | 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 to your journal entry from your user page. | ||
* Link back from the journal entry to your user page. | * Link back from the journal entry to your user page. | ||
Latest revision as of 22:13, 18 February 2013
This journal entry is due on Friday, February 22 at midnight PST (Thursday night/Friday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.
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: you can do all of this easily by adding them to your template and then using the template on your pages.)
- 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 "BIOL398-03/S13" category to the end of your wiki page.
- Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
Project 1 Details
We are focused in this project on Nitrogen metabolism in S. Cerevisiae as discussed in “The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae,” by terSchure et al. We have successfully modeled two curves in Figure 1 A of the paper, namely biomass and residual ammonia. This modeling is at the level of the chemostat. We have also discussed models of metabolic activity within the cell, examining alpha-ketogluterate, glutamine, and glutamate. The following modeling projects are proposed related to these problems.
- terSchure and coauthors (Microbiology, 1995, 141:1101-1108) considered other conditions, such as changing the dilution rate. Apply our chemostat model to these conditions.
- The chemostat model we’ve worked out does not predict the oxygen use and carbon dioxide production of Figure 1 B. Develop and analyze a model of the chemostat that includes oxygen and carbon dioxide.
- The metabolism model we’ve worked out does not directly involve the ammonia feed. Develop and analyze a metabolism model that connects ammonia feed to alpha-ketogluterate, glutamine, and glutamate levels. Figure 3 tells us that enzyme concentrations depend on feed concentration. That is a good place to start.
- The last line of the terSchure paper is as follows: “If the ammonia concentration is the regulator, this may imply that S. cerevisiae has an ammonia sensor which could be a two-component sensing system for nitrogen, as has been found in gram-negative bacteria (4).” Develop and analyze a model based on this concept.
This Week's Assignment
- Select one of these project topics as what you will present next week.
- Find at least one reference beyond the two terSchure et al papers that will be helpful to your modeling effort. Discuss in your journal the relevance of the reference.
- Find a mathematical reference, be it a textbook, a paper, or a website, that is relevant to your project topic. Discuss in your journal the relevance of the reference.
- 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 "BIOL398-03/S13" category to the end of the wiki page (if someone has not already done so).
Reflection
- What was the purpose of this assignment?
- Which project is easiest? Why?
- Which project is hardest? Why?
- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
