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Team:UPO-Sevilla/Modeling/Signaling
From 2010.igem.org
The signaling circuit
The signaling circuit 3 described in the Circuit Section has been modeled using Matlab Simbiology desktop. The following diagram shows the different parts of the model we have simulated:
For the level of detail considered, the main parts simulated are the following (the number correspond to the equations listed in the table in the next section):
- Generation of L_aspartate induced by AAL
- Diffusion of L_aspartate through the cell wall
- Transcription of the aspA, promoted by FecI_a (active)
- Translation of aspA
- Activation of FecI, induced by the activation of FecR
- Activation of FecR induced by FecA-PrhA
- Plant cell wall lingand, FecA-PrhA binding
Reactions
The reaction equations for the previous parts, and the reactions rates associated, are summarized in the following table:
| # | Reaction | ReactionRate | Active |
|---|---|---|---|
| 1 | ecoli.ammonia + ecoli.fumarate + ecoli.AAL <-> ecoli.L_aspartate + ecoli.AAL | k1*ecoli.ammonia*ecoli.fumarate*ecoli.AAL - k2*ecoli.L_aspartate*ecoli.AAL | true |
| 2 | ecoli.L_aspartate <-> medium.L_aspartate | kWallDiffusion*ecoli.L_aspartate - kWallDiffusionBack*medium.L_aspartate | true |
| 3 | ecoli.DNAaspA + ecoli.FecI_a -> ecoli.ARNm_aspA + ecoli.DNAaspA + ecoli.FecI_a | kTranscript*ecoli.DNAaspA*ecoli.FecI_a | true |
| 4 | ecoli.ARNm_aspA -> ecoli.AAL + ecoli.ARNm_aspA | kTranslation*ecoli.ARNm_aspA | true |
| 5 | ecoli.FecR_a + ecoli.FecI <-> ecoli.FecI_a + ecoli.FecR_a | kFecIActivation*ecoli.FecR_a*ecoli.FecI - kFecIDeactivation*ecoli.FecI_a*ecoli.FecR_a | true |
| 6 | ecoli.FecR + ecoli.[ligand:FecA-PrhA] <-> ecoli.FecR_a + ecoli.[ligand:FecA-PrhA] | kFecRActivation*ecoli.FecR*ecoli.[ligand:FecA-PrhA] - kFecRDeactivation*ecoli.FecR_a*ecoli.[ligand:FecA-PrhA] | true |
| 7 | plant_cell_wall.ligand + ecoli.[FecA-PrhA] <-> ecoli.[ligand:FecA-PrhA] | kCellBinding*plant_cell_wall.ligand*ecoli.[FecA-PrhA] - kCellUnbinding*ecoli.[ligand:FecA-PrhA] | true |
Simulations
The following figure shows the typical evolution of the output of the system (the generated chemoattractant) againts the inputs (the wall cells ligand and the FecA-PrhA components on the outer membrane)
https://static.igem.org/mediawiki/2010/9/9f/UPOSimulation.png
Analysis
Sensibility
Simbiology allows to compute the sensibility of the system against the different parameters.
The following figure shows the sensibility of all state variables (molecules of the different species considered) with respecto to all the parameters.
This analysis is referred to the steady-state of the system. Some parameters do not affect the final steady-state number of molecules, but on the other hand affects the velocity of the system in the transition. This can be seen in the following
Temporal evolution
Sponsors
