BIOL398-01/S11:Class Journal Week 6

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(Alondra Vega's Journal Entry: saved 2nd part of my entry)
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Read and Reflect
Read and Reflect
#''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<sup>-1</sup>.  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<sup>-1</sup>.  
#''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<sup>-1</sup>.  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<sup>-1</sup>.  
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#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 were measured under V<sub>max</sub> conditions.  We were making that assumption in the model, but now we know for a fact that is what they used.       
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#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 V<sub>max</sub> conditions.  We were making that assumption in the model, but now we know for a fact that is what they used.       
#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 V<sub>max</sub> conditions. I think that with the model we will be able to make a god estimate of the remaining parameters.
#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 V<sub>max</sub> conditions. I think that with the model we will be able to make a god estimate of the remaining parameters.
[[Category:BIOL398-01/S11]]
[[Category:BIOL398-01/S11]]
[[Category: Biomathematical Modeling]]
[[Category: Biomathematical Modeling]]

Revision as of 00:48, 21 February 2011

Contents

Instructions

Formatting

  • 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 "BIOL398-01/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?

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

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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