Team:TU Delft/Modeling/MFA

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For our MFA a Matlab application, Cell Net Analyzer (CNA), was used. CNA already contains a standard simplified ''E. coli'' metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network used for adding [[Team:TU_Delft/Modeling/MFA/additional_pathways|additional pathways]].
For our MFA a Matlab application, Cell Net Analyzer (CNA), was used. CNA already contains a standard simplified ''E. coli'' metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network used for adding [[Team:TU_Delft/Modeling/MFA/additional_pathways|additional pathways]].
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Would you like to more about the details of the implemented pathways? Read the [[Team:TU_Delft/Modeling/MFA/results|Detailed MFA results]] page.
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The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into Omix. Omix is a tool for drawing networks in general, but lends itself espescially 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.
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The detailed results can be found [[Team:TU_Delft/Modeling/MFA/results|here]]
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The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into Omix. Omix is a tool for drawing networks in general, but lends itself espescially 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.
 
==Visualization of pathways==
==Visualization of pathways==
{{:Team:TU_Delft/Modeling/MFA/Pathways}}
{{:Team:TU_Delft/Modeling/MFA/Pathways}}
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===Continue Reading===
===Continue Reading===
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*[[Team:TU_Delft/Modeling/MFA/additional_pathways|Additional Pathways]]
*[[Team:TU_Delft/Modeling/MFA/additional_pathways|Additional Pathways]]
*[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA Results]]
*[[Team:TU_Delft/Modeling/MFA/results|Detailed MFA Results]]
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*[http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html CellNetAnalyzer]
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*[http://www.13cflux.net/omix/ Omix]

Revision as of 13:59, 23 October 2010

Metabolic Flux Analysis

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 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 MFAs? Read more about how a metabolic flux analysis works here.

For our MFA a Matlab application, Cell Net Analyzer (CNA), was used. CNA already contains a standard simplified E. coli metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network used for adding additional pathways.

The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into Omix. Omix is a tool for drawing networks in general, but lends itself espescially 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 detailed results can be found here


Visualization of pathways


Continue Reading

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