Team:TU Delft/Modeling/MFA

From 2010.igem.org

(Difference between revisions)

Latest revision as of 14:38, 27 October 2010

Metabolic Flux Analysis

This model is an extension of the alkane degradation sub-project

A metabolic flux analysis (MFA) is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. Several product pathways were introduced to the metabolic network of E. coli along with the hydrocarbon degradation from our BioBricks to see what the maximal theoretical yields on alkanes are compared to glucose.

Are you not familiar with a metabolic flux analysis? Read more about how a metabolic flux analysis works.

For our MFA a Matlab application, [http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html CellNetAnalyzer] (CNA), was used. CNA already contains a simplified E. coli metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network is the construct as it was intended in our project. To investigate the potential of this system to make something useful of the alkanes several product pathways were added the E. coli metabolic network in silico. We also describe how the network was generated.

The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into [http://www.13cflux.net/omix/ Omix]. Omix is a tool for drawing networks in general, but lends itself especially well for biochemical pathways. From the networks that were drawn with Omix we made a tool in which you yourself can select different substrates and products and see what pathways are used in an ideal situation. The tool is below this text. The selectable substrates are glucose, dodecane (C₁₂-alkane) and tridecane (C₁₃-alkane). The selectable outputs are, biomass growth, NO₃ electron acceptor, PHB, isoprene and hydrogen. With biomass growth and NO₃ as electron acceptor the fluxes are optimized towards biomass production. Biomass is produced using the 12 key metabolites as precursors. The key metabolites have a red color. The substances with a yellow color are extracellular. For the three other outputs, PHB, isoprene and hydrogen, the fluxes are optimized towards production of these substances. The numbers next to some of the reactions in the tool are the EC numbers of the corresponding enzymes.

Do you want to know more? Read the detailed results of the metabolic flux analysis

Visualization of pathways

Continue Reading

Used tools

[http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html CellNetAnalyzer]
[http://www.13cflux.net/omix/ Omix]

@@ Line 1: / Line 1: @@
-= Metabolic Flux Analysis =
+{{Team:TU_Delft/frame_check}}
+__NOTOC__
+==Metabolic Flux Analysis==
-A metabolic flux analysis is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. With this analysis it is also possible to find whether a system is not viable because of a co-factor imbalance. Lastly, several product pathways were introduced to ''E. coli'' with hydrocarbon degradation to see what maximal theoretical yields on hydrocarbons are.
+This model is an extension of the [https://2010.igem.org/Team:TU_Delft#page=Project/alkane-degradation alkane degradation sub-project]
-How a metabolic flux analysis works, is explained [[Team:TU_Delft/Modeling/MFA/explanation|here.]]
+A metabolic flux analysis (MFA) is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. Several product pathways were introduced to the metabolic network of ''E. coli'' along with the hydrocarbon degradation from our BioBricks to see what the maximal theoretical yields on alkanes are compared to glucose.
-For our MFA a Matlab application, Cell Net Analyzer, was used. CNA already contains a standard simplified ''E. coli'' metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. ''(link to pages with assumptions)'' The resulting network is the standard network used for adding additional pathways.
+Are you not familiar with a metabolic flux analysis? Read more about [[Team:TU_Delft/Modeling/MFA/explanation|how a metabolic flux analysis works]].
-*implement interactive tool with metabolic network for different pathways here
+For our MFA a Matlab application, [http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html CellNetAnalyzer] (CNA), was used. CNA already contains a simplified ''E. coli'' metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network is the construct as it was intended in our project. To investigate the potential of this system to make something useful of the alkanes several product pathways were added the ''E. coli'' metabolic network in silico. We also describe [[Team:TU_Delft/Modeling/MFA/additional_pathways|how the network was generated]].
+The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into [http://www.13cflux.net/omix/ Omix]. Omix is a tool for drawing networks in general, but lends itself especially well for biochemical pathways. From the networks that were drawn with Omix we made a tool in which you yourself can select different substrates and products and see what pathways are used in an ideal situation. The tool is below this text. The selectable substrates are glucose, dodecane (C<sub>12</sub>-alkane) and tridecane (C<sub>13</sub>-alkane). The selectable outputs are, biomass growth, NO<sub>3</sub> electron acceptor, PHB, isoprene and hydrogen. With biomass growth and NO<sub>3</sub> as electron acceptor the fluxes are optimized towards biomass production. Biomass is produced using the 12 key metabolites as precursors. The key metabolites have a red color. The substances with a yellow color are extracellular. For the three other outputs, PHB, isoprene and hydrogen, the fluxes are optimized towards production of these substances. The numbers next to some of the reactions in the tool are the EC numbers of the corresponding enzymes.
+Do you want to know more? Read the [[Team:TU_Delft/Modeling/MFA/results| detailed results of the metabolic flux analysis]]
+==Visualization of pathways==
+{{:Team:TU_Delft/Modeling/MFA/Pathways}}
+===Continue Reading===
+*[[Team:TU_Delft/Modeling/MFA/explanation|MFA explanation]]
+*[[Team:TU_Delft/Modeling/MFA/additional_pathways|Pathway constructs]]
+*[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA Results]]
-*Implemented pathways
+===Used tools===
+*[http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html CellNetAnalyzer]
+*[http://www.13cflux.net/omix/ Omix]
-refer to detailed results page here
-[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA results]]
-Go back to previous page here
-[[Team:TU_Delft/Modeling|Click here if you don't like MFA]]