BIOL398-01/S11:Class Journal Week 6

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Contents

Instructions

Formatting

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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?

Read and Reflect

  • 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.

Read and Reflect

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.

Carmen E. Castaneda's Journal Entry

James C. Clements' Journal Entry

Nicholas A. Rohacz's Journal Entry

Alondra Vega's Journal Entry

Reflection on a Quantitative Look on Nitrogen Metabolism

Read and Reflect

  1. ter Schure's first paper was focused on showing that the governing factor in nitrogen metabolism was the concentration of ammonia rather than its flux. In this paper the dilution rate was kept constant at 0.15 h-1. In his later paper he was focused more on the genes that regulated nitrogen in the cell. It was still believed that the concentration of ammonia was the governing factor rather than the flux, but this paper was looking at the genes, GAP1, GLN1,NAD-GDH, NADPH-GDH and the gluatamine synthetase. Also, the dilution rate was no kept constant in this paper, it was changed from 0.05 to 0.29 h-1.
  2. The Microbiology paper helped clarify the sampling of the of the samples. It showed how the steady state came into play and how the samples were specifically collected. Also, it mentioned metabolites and free amino acids and how they dealt with them in their experiment. Their first paper failed to mention any of that information. The labeling of the oligonucleotides is more in detail in the second paper, but I do not think the first paper does a bad job at explaining what is happening when those are added. The enzyme assay section really helped clarify how NADPH-GDH and NAD-GDH were measured under Vmax conditions. We were making that assumption in the model, but now we know for a fact that is what they used.
  3. After reading the second paper, I feel that we have everything we need to run a math model. We have the different dilution rates, the nitrogen level, the glucose level, and we know that two activities were measured under Vmax conditions. I think that with the model we will be able to make a god estimate of the remaining parameters.
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