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<p>Our team designed three separate models were created to monitor behaviors of the genetics system, enzyme kinetics, and metabolism. Then they were fused into one mechanism predicting P.E.B.B.L.E’s growth.</p> | <p>Our team designed three separate models were created to monitor behaviors of the genetics system, enzyme kinetics, and metabolism. Then they were fused into one mechanism predicting P.E.B.B.L.E’s growth.</p> | ||
<h3>Kinetics Model </h3> | <h3>Kinetics Model </h3> | ||
− | <p>The enzyme kinetics model describes the biochemical pathway that our bacteria have to degrade and assimilate PET plastic. Kinetics models in general use differential equations to describe the interactions between the enzymes in the metabolites, chemicals used in metabolism, and they describe the rate of change in the concentration of these metabolites. Click on the biochemical pathway in the picture to see the equations and assumptions used to describe the main metabolites in the PET degradation pathway. | + | <p>The enzyme kinetics model describes the biochemical pathway that our bacteria have to degrade and assimilate PET plastic. Kinetics models in general use differential equations to describe the interactions between the enzymes in the metabolites, chemicals used in metabolism, and they describe the rate of change in the concentration of these metabolites. Click on the biochemical pathway in the picture to see the equations and assumptions used to describe the main metabolites in the PET degradation pathway. <br /> |
+ | <br /> | ||
Example of the Kinetics | Example of the Kinetics | ||
</p> | </p> | ||
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<h3>Metabolism Model </h3> | <h3>Metabolism Model </h3> | ||
<p><p>The last modeled portion of the project used the Flux Balance Analysis tool to predict the growth rate of the E. coli cells on the sole carbon source of PET. The original matrix and parameters where downloaded from the CoBRA toolbox iJO1366 model [ ]. The model was then expanded to include this new pathway and genes and then the system was optimized for biomass growth and the objective value was proportional to the growth rate of the bacteria. | <p><p>The last modeled portion of the project used the Flux Balance Analysis tool to predict the growth rate of the E. coli cells on the sole carbon source of PET. The original matrix and parameters where downloaded from the CoBRA toolbox iJO1366 model [ ]. The model was then expanded to include this new pathway and genes and then the system was optimized for biomass growth and the objective value was proportional to the growth rate of the bacteria. | ||
− | FBA uses a stochastic matrix of the all the metabolisms’ chemical reactions and optimizes these various equations to produce a unit of biomass, which is inferred as another metabolite of the system. The general form of the model is: | + | FBA uses a stochastic matrix of the all the metabolisms’ chemical reactions and optimizes these various equations to produce a unit of biomass, which is inferred as another metabolite of the system. The general form of the model is:<br/ > |
− | max { v_g: S v=O} | + | <center> |
− | s.t. L≤v≤U and v≠0 | + | max { v_g: S v=O} <br /> |
− | The variable column V are fluxes, which are bounded by the upper and lower bounds of U and L. The S matrix is a matrix of stoichiometric coefficients for the metabolites in the reactions. A flux is best described as the number of times the reaction must run forwards or backwards for the entire system to meet the homogenous assumption that the rates of the metabolites changing are zero. The dimensions of the matrix is MxN, where M is number of metabolites and N is number of reactions in the metabolism. The maximized flux, vg, is the flux for the biomass growth equation. | + | s.t. L≤v≤U and v≠0 <br /> |
+ | </center> | ||
+ | <p>The variable column V are fluxes, which are bounded by the upper and lower bounds of U and L. The S matrix is a matrix of stoichiometric coefficients for the metabolites in the reactions. A flux is best described as the number of times the reaction must run forwards or backwards for the entire system to meet the homogenous assumption that the rates of the metabolites changing are zero. The dimensions of the matrix is MxN, where M is number of metabolites and N is number of reactions in the metabolism. The maximized flux, vg, is the flux for the biomass growth equation. | ||
</p> </p> | </p> </p> | ||
<div class="column third_size"> | <div class="column third_size"> | ||
+ | <img src="https://static.igem.org/mediawiki/2018/6/68/T--RHIT--FluxModel.png" class="image"> | ||
+ | </div> | ||
+ | <div class="column two_thirds_size"> | ||
+ | <p>For the fake chemical reaction: 2 [A] ↔ [B] + 3 [C] | ||
+ | The reaction is input into the matrix so that metabolite A loses 2 units, while metabolites B and C gain 1 and 3 units respectively. | ||
+ | The dotted column shows the biomass growth reaction with it producing 1 unit of biomass. All the reactions have some bounds on the flux values so that the system will return a real number. <br /><br /><br /><br /> | ||
+ | </p> | ||
</div> | </div> | ||
+ | |||
<div class="column third_size"> | <div class="column third_size"> |
Revision as of 17:55, 22 June 2018