Difference between revisions of "Team:UChile OpenBio-CeBiB/Model/Results"

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<img id="graphs1" align=center src="https://static.igem.org/mediawiki/2017/8/83/T--UChile_OpenBio-CeBiB--KmSed7P-R5PCalvin.png">
 
<img id="graphs1" align=center src="https://static.igem.org/mediawiki/2017/8/83/T--UChile_OpenBio-CeBiB--KmSed7P-R5PCalvin.png">
 
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For G6P production from Calvin Cycle, it is possible to highlight 6 Michaelis Menten constants important to consider. This process is most influenced by the F6P-G6P conversion, given it is a reversible reaction. This makes it possible to optimize the cycle in order to determine the best set of parameters to fully achieve maximum carbon uptake, which would then allow us to evaluate the possibility of including new catalysis mechanisms regarding these reactions. Additionally, we have to notice that the majority of the sensitive parameters <b>do not</b> increase the concentration of G6P in steady state given the variation of their values, but instead they actually decrease this amount. Therefore, it may occur that the upper limit of G6P production (which correlates directly to carbon fixation) is already given by the chosen set of parameters. As a summary, the key reaction is the reversible conversion of fructose-6-phosphate to glucose-6-phosphate.</p>
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For G6P production from Calvin Cycle, it is possible to highlight six Michaelis Menten constants important to consider. This process is most influenced by the F6P-G6P conversion, given it is a reversible reaction. This makes it possible to optimize the cycle in order to determine the best set of parameters to fully achieve maximum carbon uptake, which would then allow us to evaluate the possibility of including new catalysis mechanisms regarding these reactions. Additionally, we have to notice that the majority of the sensitive parameters <b>do not</b> increase the concentration of G6P in steady state given the variation of their values, but instead they actually decrease this amount. Therefore, it may occur that the upper limit of G6P production (which correlates directly to carbon fixation) is already given by the chosen set of parameters. As a summary, the key reaction is the reversible conversion of fructose-6-phosphate to glucose-6-phosphate.</p>
  
 
<h4 style="margin-top:30px;">Starch Production from Antisense</h4>
 
<h4 style="margin-top:30px;">Starch Production from Antisense</h4>
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We can observe that the reactions concerning the molecule glucose-6-phosphate are the most sensitive for optimization. Regarding the Michaelis Menten constant of the enzymes, there was no considerable variation. Therefore, it is possible that the enzyme production rate is such that the concentration indicated by the corresponding Michaelis Menten constant is reached.</p>
 
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Revision as of 02:46, 2 November 2017

Document

Results


From the previous procedures, we obtained the following results:



Phase 1: The First Approach

Metabolic Pathway


We observed the production of Glucose 6-phosphate, and an increased of the intermediaries affected by FBP/SBPase. Aditionally, all the compounds reach the steady state with concentrations close to reallity, but the timeline should be reviewed. We considered this model correct for a first approach.

Genetic Pathway

The graphic shows the increase of FBP/SBPasa enzyme, which confirm the expected results. If we expand the timeline, we could observed the steady state.



Metabolic Pathway, B12 Absent

Metabolic Pathway, B12 Present


We observed that in absence of B12, the steady state is reached after than in the case of presence of the vitamin. Besides, in the first graph there is an initial accumulation of UDP-Glucose, which in the second scenario is null due to the full production of starch.

Genetic Pathway, B12 Absent

Genetic Pathway, B12 Present

We observed the same behavior of STA1 and STA6 for both cases, therefore insensitive to B12 vitamin. For GBS2 we observed the expected behavior, having a null production of protein, due to the production of antisense RNA, which is confirmed with the formation of double strand DNA.

Phase 2: Sensitivity Analysis

G6P Production from Calvin Cycle

For G6P production from Calvin Cycle, it is possible to highlight six Michaelis Menten constants important to consider. This process is most influenced by the F6P-G6P conversion, given it is a reversible reaction. This makes it possible to optimize the cycle in order to determine the best set of parameters to fully achieve maximum carbon uptake, which would then allow us to evaluate the possibility of including new catalysis mechanisms regarding these reactions. Additionally, we have to notice that the majority of the sensitive parameters do not increase the concentration of G6P in steady state given the variation of their values, but instead they actually decrease this amount. Therefore, it may occur that the upper limit of G6P production (which correlates directly to carbon fixation) is already given by the chosen set of parameters. As a summary, the key reaction is the reversible conversion of fructose-6-phosphate to glucose-6-phosphate.

Starch Production from Antisense

We can observe that the reactions concerning the molecule glucose-6-phosphate are the most sensitive for optimization. Regarding the Michaelis Menten constant of the enzymes, there was no considerable variation. Therefore, it is possible that the enzyme production rate is such that the concentration indicated by the corresponding Michaelis Menten constant is reached.

G6P Production from Calvin Cycle

Starch Production from Antisense



G6P Production from Calvin Cycle

Starch Production from Antisense



GBS2 effect on Starch Production

STA1 effect on Starch Production

STA6 effect on Starch Production