BIOL398-01/S11:Class Journal Week 6

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(Sarah Carratt's Journal Entry: signed)
Current revision (04:14, 22 February 2011) (view source)
(went back to finish ter Schure part)
 
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=== [[User:Nicholas A. Rohacz|Nicholas A. Rohacz's]] Journal Entry ===
=== [[User:Nicholas A. Rohacz|Nicholas A. Rohacz's]] Journal Entry ===
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#The purpose of this assignment was to practice modeling a chemostat on our own. Picking the state variables and parameters are an important thing to practice in modeling.
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#Reading the paper and understanding what was going on was the easiest part of my assignment to accomplish.
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#However, the most difficult part of this assignment was figuring out what to include in my differential equations, I probably need more practice because I am pretty sure the enzymes play a more major role in the differential equations.
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#I still don't understand exactly what is required in modeling differential equations for a chemostat. I do understand the whole equilibrium aspect of the model, just not what is important inside the chemostat.
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ter Schure
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#In the first paper, they focused more on a changing nitrogen concentration and had a fixed dilution rate, and the goals seemed to focus on the biomass and how changing concentrations affected it. The second paper focused more on a changing dilution rate while keeping the glucose(carbon) and ammonium(nitrogen) concentrations steady, and the goals of the paper focused more all of the reactions happening in the chemostat and how they were affected by a changing dilution rate.
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#The Microbiology paper went over a lot of the experiment in more detail then the bacteriology paper did. Including a more detailed look at the specific activity of the enzymes in the chemostat, as well as a detailed look at how they found all the information in the paper, where the Bacteriology paper was more of a broadened view of the chemostat, and what were the determining factors in biomass concentration.
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#I feel that there is other information that could be discovered in this paper to form a complete model of a Nitrogen based metabolism, such as any fluctuations in the TCA cycle that would lead to a change in a-ketoglutarate concentrations, or if glutamine concentrations were disrupted somehow.
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[[User:Nicholas A. Rohacz|Nicholas A. Rohacz]] 03:00, 22 February 2011 (EST)
=== [[User:Alondra Vega|Alondra Vega's]] Journal Entry ===
=== [[User:Alondra Vega|Alondra Vega's]] Journal Entry ===
Reflection on a Quantitative Look on Nitrogen Metabolism
Reflection on a Quantitative Look on Nitrogen Metabolism
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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.       
#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.
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[[User:Alondra Vega|Alondra Vega]] 02:12, 22 February 2011 (EST)
[[Category:BIOL398-01/S11]]
[[Category:BIOL398-01/S11]]
[[Category: Biomathematical Modeling]]
[[Category: Biomathematical Modeling]]

Current revision

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

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 provided the experimental methods that the Bacteriology paper never discussed. Assumptions are clarified and the authors included much more contextual data. In addition, the organization and detail of the second paper was much more helpful than the rough grouping of information presented in the first. In terms of developing a math model and simulating nitrogen metabolism, I can't think of anything that would be lacking.

Sarah Carratt 01:49, 22 February 2011 (EST)

Carmen E. Castaneda's Journal Entry

Reflection on a Quantitative Look at Nitrogen Metabolism

  1. The purpose for this assignment was to submerge ourselves into the world of mathematical modeling. By this I mean that through this assignment we were given an oppotrunity to develope our own models so that we could test their usefulness.
  2. After revisiting the question with the help of Alondra and Dr. Fitzpatrick, it was easy to declare the state variables and parameters.
  3. It was challenging trying to understand what were asked to do. And once that was understood it was a bit of a challange trying to understand the system in such a way that we could develop a useful model. Which would of been a lot harder if I didn't get help. BUt as i sat down to actually write the system after discussing it, I began to notice I was still not as knowledgeable as i originally had thought. So actually writing the system became a sort of challange.
  4. I think i understand what we are trying to do but I'm not sure if i have the correct approach and if I could of done it without some guidance. Applying and using all the variable, state and parameters, when writing a system is still kind of fuzzy to me. How do I write an equation using all the elements and taking into consideration all the different constants?

Read and Reflect

  1. In the Microbiology paper the authors discussed more thoroughly their approach to examining the activity levels of individual components of the nitrogen regulated genes as exemplified by the S. Cerevisiae. While in the Bacteriology paper, the authors glossed over details as they discussed the affects of different concentrations of Ammonia in the nitrogen metabolism of the S. Cerevisiae.
  2. The Microbiology paper helped me understrand the set up of the experiement more. The detailed organization in this paper made it easier to follow.
  3. I feel that an actual example of the math model they used and how they applied it would be useful. I think given this it will allow to connect the article and its information with mathematical modeling. I feel like a bridge between these two is beginning to form but it's not quite there yet. So a clearer example of how they approached it might help me connect the dots.

Carmen E. Castaneda 01:34, 22 February 2011 (EST)

James C. Clements' Journal Entry

Nicholas A. Rohacz's Journal Entry

  1. The purpose of this assignment was to practice modeling a chemostat on our own. Picking the state variables and parameters are an important thing to practice in modeling.
  2. Reading the paper and understanding what was going on was the easiest part of my assignment to accomplish.
  3. However, the most difficult part of this assignment was figuring out what to include in my differential equations, I probably need more practice because I am pretty sure the enzymes play a more major role in the differential equations.
  4. I still don't understand exactly what is required in modeling differential equations for a chemostat. I do understand the whole equilibrium aspect of the model, just not what is important inside the chemostat.

ter Schure

  1. In the first paper, they focused more on a changing nitrogen concentration and had a fixed dilution rate, and the goals seemed to focus on the biomass and how changing concentrations affected it. The second paper focused more on a changing dilution rate while keeping the glucose(carbon) and ammonium(nitrogen) concentrations steady, and the goals of the paper focused more all of the reactions happening in the chemostat and how they were affected by a changing dilution rate.
  2. The Microbiology paper went over a lot of the experiment in more detail then the bacteriology paper did. Including a more detailed look at the specific activity of the enzymes in the chemostat, as well as a detailed look at how they found all the information in the paper, where the Bacteriology paper was more of a broadened view of the chemostat, and what were the determining factors in biomass concentration.
  3. I feel that there is other information that could be discovered in this paper to form a complete model of a Nitrogen based metabolism, such as any fluctuations in the TCA cycle that would lead to a change in a-ketoglutarate concentrations, or if glutamine concentrations were disrupted somehow.

Nicholas A. Rohacz 03:00, 22 February 2011 (EST)

Alondra Vega's Journal Entry

Reflection on a Quantitative Look on Nitrogen Metabolism

  1. The purpose of this assignment was to attempt to make a model that will simulate what is going on in the sysntem in which we are interested in. This includes parameters and state variables.
  2. The part of the assignment that came most easily to me was reading and differentiating the articles. Finding the state variables and parameters also came easy, assuming that I am on the right path.
  3. The aspect that was the hardest was definitely trying to come up with a model of differential equations to model the system. Also, knowing what to include and what t leave out of the system. For example, I left out GOGAT, but I am pretty sure that it is important in the system. we did not discuss it much during lecture, so I just left it out.
  4. I feel like I understand what the goal of the assignment is, but I do not understand how to make it happen. I tried a system, which seems complicated to solve. I think that i am on the right path, i just need a little more guidance.

Read and Reflect

  1. ter Schure's et al. 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.

Alondra Vega 02:12, 22 February 2011 (EST)

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