BIOL398-01/S11:Class Journal Week 6 - Revision history

Nicholas A. Rohacz: /went back to finish ter Schure part/

2011-02-22T08:14:03Z

went back to finish ter Schure part

←Older revision		Revision as of 08:14, 22 February 2011
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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.		#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.
	#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.		#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
		+	#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.
		+	#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.
		+	#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.

	[[User:Nicholas A. Rohacz\|Nicholas A. Rohacz]] 03:00, 22 February 2011 (EST)		[[User:Nicholas A. Rohacz\|Nicholas A. Rohacz]] 03:00, 22 February 2011 (EST)

Nicholas A. Rohacz: /need to save by midnight, have not completed read and reflect yet, will be late but completed./

2011-02-22T08:00:34Z

need to save by midnight, have not completed read and reflect yet, will be late but completed.

←Older revision		Revision as of 08:00, 22 February 2011
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	=== [[User:Nicholas A. Rohacz\|Nicholas A. Rohacz's]] Journal Entry ===		=== [[User:Nicholas A. Rohacz\|Nicholas A. Rohacz's]] Journal Entry ===

-	#	+	#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.
-	#	+	#Reading the paper and understanding what was going on was the easiest part of my assignment to accomplish.
-	#	+	#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.
-	#	+	#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.
-	#	+

		+	[[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

Alondra Vega: /* Alondra Vega's Journal Entry */ added my signature forgot to put it earlier

2011-02-22T07:12:25Z

Alondra Vega's Journal Entry: added my signature forgot to put it earlier

←Older revision		Revision as of 07:12, 22 February 2011
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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.
		+	[[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]]

Sarah Carratt: /* Sarah Carratt's Journal Entry */ signed

2011-02-22T06:49:29Z

Sarah Carratt's Journal Entry: signed

←Older revision		Revision as of 06:49, 22 February 2011
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	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.		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.
		+
		+	[[User:Sarah Carratt\|Sarah Carratt]] 01:49, 22 February 2011 (EST)

	=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===		=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===

Sarah Carratt: /* Sarah Carratt's Journal Entry */ updated

2011-02-22T06:49:01Z

Sarah Carratt's Journal Entry: updated

←Older revision		Revision as of 06:49, 22 February 2011
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	=== [[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 ====		==== Reflection on a Quantitative Look at Nitrogen Metabolism ====
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	\|}		\|}

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

	=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===		=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===

Carmen E. Castaneda: /* Carmen E. Castaneda's Journal Entry */ added and refined entry

2011-02-22T06:34:21Z

Carmen E. Castaneda's Journal Entry: added and refined entry

←Older revision		Revision as of 06:34, 22 February 2011
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	#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.		#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.
	#After revisiting the question with the help of Alondra and Dr. Fitzpatrick, it was easy to declare the state variables and parameters.		#After revisiting the question with the help of Alondra and Dr. Fitzpatrick, it was easy to declare the state variables and parameters.
-	#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.	+	#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.
-	#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.	+	#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 '''		'''Read and Reflect '''

-	#	+	#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.
-	#	+	# The ''Microbiology'' paper helped me understrand the set up of the experiement more. The detailed organization in this paper made it easier to follow.
-	#	+	# 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.
		+	[[User:Carmen E. Castaneda\|Carmen E. Castaneda]] 01:34, 22 February 2011 (EST)
		+
	=== [[User:James C. Clements\|James C. Clements']] Journal Entry ===		=== [[User:James C. Clements\|James C. Clements']] Journal Entry ===

Alondra Vega: /* Alondra Vega's Journal Entry */ added the first part of my journal entry

2011-02-22T05:26:37Z

Alondra Vega's Journal Entry: added the first part of my journal entry

←Older revision		Revision as of 05:26, 22 February 2011
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	=== [[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
-	#	+	#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.
-	#	+	#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.
-	#	+	#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.
-	#	+	#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		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 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<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>.
	#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.

Carmen E. Castaneda: added my reflection to the first part of the assignment

2011-02-22T02:23:04Z

added my reflection to the first part of the assignment

←Older revision		Revision as of 02:23, 22 February 2011
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	=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===		=== [[User:Carmen E. Castaneda\|Carmen E. Castaneda's]] Journal Entry ===
		+
		+	'''Reflection on a Quantitative Look at Nitrogen Metabolism'''
		+
		+	#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.
		+	#After revisiting the question with the help of Alondra and Dr. Fitzpatrick, it was easy to declare the state variables and parameters.
		+	#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.
		+	#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.
		+
		+	'''Read and Reflect '''

	#		#
	#		#
	#		#
-	#
-	#
-
	=== [[User:James C. Clements\|James C. Clements']] Journal Entry ===		=== [[User:James C. Clements\|James C. Clements']] Journal Entry ===

Sarah Carratt: /* Sarah Carratt's Journal Entry */ student response added

2011-02-22T01:45:15Z

Sarah Carratt's Journal Entry: student response added

←Older revision		Revision as of 01:45, 22 February 2011
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	=== [[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 ===

Alondra Vega: /* Alondra Vega's Journal Entry */

2011-02-21T05:48:22Z

Alondra Vega's Journal Entry

←Older revision		Revision as of 05:48, 21 February 2011
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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>.
-	#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.	+	#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]]