Difference between revisions of "Team:Humboldt Berlin/Model"

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                         <h3 class="headline3">PET degradation by <i>Chlamydomonas reinhardtii</i></h3>
 
                         <h3 class="headline3">PET degradation by <i>Chlamydomonas reinhardtii</i></h3>
 
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                             A C. reinhardtii which expresses and secretes the enzymes PETase and MHETase could pose as a solution for the problem of micro-plastic polluted water. Nevertheless, the viability of PET-degradation by C. reinhardtii at a larger scale is yet unknown.  To assess the efficiency of PET-degradation by C. reinhardtii, a model of the expression, secretion and kinetics of the enzymes PETase and MHETase in C. reinhardtii was designed. The goal of the model is to simulate the degradation of PET while taking into account the parameters of enzyme kinetics, expression rate, secretion rate and cultivation density. By varying the parameters, an approximation on PET degradation under various conditions can be made to examine what the appropriate parameters are for an optimal PET-degradation. To achieve this, the kinetics of MHETase and the optimized PETase (I179F) were taken from literature (Palm et al., 2019) (Ma et al., 2019).  
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                             A C. reinhardtii which expresses and secretes the enzymes PETase and MHETase could pose as a solution for the problem of micro-plastic polluted water. Nevertheless, the viability of PET-degradation by C. reinhardtii at a larger scale is yet unknown.  Models of biological systems allow us to design experiments in silico that are difficult to reproduce in vivo and give us special insights into the role that parameters might play in the given biological system. Therefore, to assess the efficiency of PET-degradation by C. reinhardtii, a model of PET degradation was designed.  
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<p class="block-text medium-sized">
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The overall goal of the model is to determine the time needed to degrade 1 mg of PET. The expression rate, secretion rate and kinetics of the enzymes, such as also the cultivation density, influence the degradation rate of PET. Based on this assumption, the model was designed to take these factors into account. The model was programmed in Tellurium (Choi et al., 2018) and encompasses six reactions. The reactions are as follows, as can be seen on Fig. 1:
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R1: Expression of PETase <b>
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R2: Expression of MHETase <b>
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R3: Secretion of PETase <b>
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R4: Secretion of MHETase <b>
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R5: Degradation of PET to MHET <b>
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R6: Degradation of MHET to TPA and EG <b>
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                         </p>
 
                         </p>

Revision as of 14:32, 8 October 2019

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Modeling

Why Modeling?

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ideonella grafic
Fig. 1. - Hello

PET degradation by Chlamydomonas reinhardtii

A C. reinhardtii which expresses and secretes the enzymes PETase and MHETase could pose as a solution for the problem of micro-plastic polluted water. Nevertheless, the viability of PET-degradation by C. reinhardtii at a larger scale is yet unknown. Models of biological systems allow us to design experiments in silico that are difficult to reproduce in vivo and give us special insights into the role that parameters might play in the given biological system. Therefore, to assess the efficiency of PET-degradation by C. reinhardtii, a model of PET degradation was designed.

The overall goal of the model is to determine the time needed to degrade 1 mg of PET. The expression rate, secretion rate and kinetics of the enzymes, such as also the cultivation density, influence the degradation rate of PET. Based on this assumption, the model was designed to take these factors into account. The model was programmed in Tellurium (Choi et al., 2018) and encompasses six reactions. The reactions are as follows, as can be seen on Fig. 1:

R1: Expression of PETase R2: Expression of MHETase R3: Secretion of PETase R4: Secretion of MHETase R5: Degradation of PET to MHET R6: Degradation of MHET to TPA and EG

1 mg of PET is degraded after 22.2 hours

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Pverview of the hierarchical and modular cloning system

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