# BIOL398-01/S11:Class Journal Week 6

(Difference between revisions)
 Revision as of 01:48, 21 February 2011 (view source) (→Alondra Vega's Journal Entry)← Previous diff Revision as of 21:45, 21 February 2011 (view source) (→Sarah Carratt's Journal Entry: student response added)Next diff → Line 26: Line 26: === [[User:Sarah Carratt|Sarah Carratt's]] Journal Entry === === [[User:Sarah Carratt|Sarah Carratt's]] Journal Entry === - # + [[User:Sarah Carratt|Sarah Carratt]] 20:45, 21 February 2011 (EST) - # + - # + ==== Reflection on a Quantitative Look at Nitrogen Metabolism ==== - # + - # + # The purpose of this assignment was to get experience setting up a model and understanding/identifying parameters and variables. + # This assignment was much easier for me than many of the previous ones, and the best part for me was just creating the lists of variables and sorting out the problem in my mind. + # The most challenging part of this assignment was thinking of all the variables as one large problem. I still am having trouble knowing how to formulate and propose a system. + # On this assignment, I think I understand each of the parts, but I have all the same concerns as last week with Matlab and models. + + ==== Read and Reflect ==== + + {| border="1" + |+ Comparison of ter Schure papers + ! scope="col" | + ! scope="col" | Microbiology + ! scope="col" | Bacteriology + |- + ! scope="row" | Goals + | Determine what is the regulating factor in nitrogen metabolism. || Study transcription and effect of changing carbon and nitrogen fluxes and dilution rates. + |- + ! scope="row" | Constants + | Dilution Rate at 0.15, Ammonia Flux, Continuous Culture + | Continuous Culture + |- + ! scope="row" | Conclusions + | Ammonia concentration seems to regulate nitrogen metabolism. Expression levels of nitrogen-regulated genes changed under different ammonia concentrations. + | Growth on ammonia alone does not cause repression of GAP1 and GLN1 transcription. Ammonia concentration is not "on/off switch" but rather a gradual regulator. + |} + + The ''Microbiology'' paper....In terms of developing a math model and simulating nitrogen metabolism, I can't think of anything that would be lacking. === [[User:Carmen E. Castaneda|Carmen E. Castaneda's]] Journal Entry === === [[User:Carmen E. Castaneda|Carmen E. Castaneda's]] Journal Entry ===

## Instructions

### Formatting

• Sign your portion of the journal with the standard wiki signature shortcut (`~~~~`).
• Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

### Reflection on a Quantitative Look at Nitrogen Metabolism

1. What was the purpose of this assignment?
2. What aspect of this assignment came most easily to you?
3. What aspect of this assignment was the most challenging for you?
4. What (yet) do you not understand?

• Compare the current ter Schure et al paper (Microbiology, 1995, 141, pp1101-1108) with the previously discussed J. Bacteriology (1995) 177, no. 22, pp6672-6675, paper.
1. In what ways are the goals of the papers different?
2. What things in the Microbiology paper help clarify methods in the Bacteriology paper?
3. Do you feel anything is lacking for the purposes of developing a math model and simulating nitrogen metabolism? If so, what?

## Class Responses

### Sarah Carratt's Journal Entry

Sarah Carratt 20:45, 21 February 2011 (EST)

#### Reflection on a Quantitative Look at Nitrogen Metabolism

1. The purpose of this assignment was to get experience setting up a model and understanding/identifying parameters and variables.
2. This assignment was much easier for me than many of the previous ones, and the best part for me was just creating the lists of variables and sorting out the problem in my mind.
3. The most challenging part of this assignment was thinking of all the variables as one large problem. I still am having trouble knowing how to formulate and propose a system.
4. On this assignment, I think I understand each of the parts, but I have all the same concerns as last week with Matlab and models.

Comparison of ter Schure papers
Microbiology Bacteriology
Goals Determine what is the regulating factor in nitrogen metabolism. Study transcription and effect of changing carbon and nitrogen fluxes and dilution rates.
Constants Dilution Rate at 0.15, Ammonia Flux, Continuous Culture Continuous Culture
Conclusions Ammonia concentration seems to regulate nitrogen metabolism. Expression levels of nitrogen-regulated genes changed under different ammonia concentrations. Growth on ammonia alone does not cause repression of GAP1 and GLN1 transcription. Ammonia concentration is not "on/off switch" but rather a gradual regulator.

The Microbiology paper....In terms of developing a math model and simulating nitrogen metabolism, I can't think of anything that would be lacking.

### Alondra Vega's Journal Entry

Reflection on a Quantitative Look on Nitrogen Metabolism