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Team:Imperial College/Modelling PURdeg
From 2013.igem.org
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<h2>Design</h2> | <h2>Design</h2> | ||
<h3>Objective</h3> | <h3>Objective</h3> | ||
| - | <p | + | <p> Here are some specific objectives for the model to achieve:</p> |
<p>1. The model should contain the gene expression model of the degradation enzymes because the enzyme concentration determines the rate of plastic degradation. In our case for PUR degradation, we used [http://parts.igem.org/Part:BBa_K206000 pBAD strong promoter K206000] for most enzymes</p> | <p>1. The model should contain the gene expression model of the degradation enzymes because the enzyme concentration determines the rate of plastic degradation. In our case for PUR degradation, we used [http://parts.igem.org/Part:BBa_K206000 pBAD strong promoter K206000] for most enzymes</p> | ||
<p>2. The model should show the efficiency of the enzyme secretion to the culture from the cells.It's also improtant in terms of degradation rates. Here we used pelB secretion tag for most enzymes in order to achieve a high efficiency.</p> | <p>2. The model should show the efficiency of the enzyme secretion to the culture from the cells.It's also improtant in terms of degradation rates. Here we used pelB secretion tag for most enzymes in order to achieve a high efficiency.</p> | ||
Revision as of 16:36, 1 October 2013
Contents |
Polyurethane (PUR) Degradation Module
Introduction
We designed a mathematical and deterministic model based on MATLAB extension Simbiology for Polyurethane degradation. The model is quite helpful for the experimental design. As we scaled up the initial concentrations of all substrates to meet the conditions for a bio-reactor, the model can provide preliminary simulations and predictions for our MAPLE system.
Design
Objective
<p> Here are some specific objectives for the model to achieve:1. The model should contain the gene expression model of the degradation enzymes because the enzyme concentration determines the rate of plastic degradation. In our case for PUR degradation, we used [http://parts.igem.org/Part:BBa_K206000 pBAD strong promoter K206000] for most enzymes
2. The model should show the efficiency of the enzyme secretion to the culture from the cells.It's also improtant in terms of degradation rates. Here we used pelB secretion tag for most enzymes in order to achieve a high efficiency.
3.
Polyurethane (PUR) degradation involves 5 different degradation enzymes:</p>
| enzyme | source organism | biobrick | reference |
|---|---|---|---|
| EstCS2 | uncultured unknown bacterium (GU256649.1) | [http://parts.igem.org/Part:BBa_K1149002 BBa_K1149002] | [http://www.microbialcellfactories.com/content/10/1/41 Kang et.al 2011] |
| pueA | Pseudomonas chlororaphis | [http://parts.igem.org/Part:BBa_K1149003 BBa_K1149003] | [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2000.tb09056.x/pdf Stern et al., 2000] |
| pueB | Pseudomonas chlororaphis | [http://parts.igem.org/Part:BBa_K1149004 BBa_K1149004] | [http://www.sciencedirect.com/science/article/pii/S0964830501000427 Howard et al., 2001] |
| pudA | Comamonas acidovorans | [http://parts.igem.org/Part:BBa_K1149005 BBa_K1149005] | [http://www.sciencedirect.com/science/article/pii/S0964830598000663 Allen et al. 1999] |
| pulA | Pseudomonas fluorescens | [http://parts.igem.org/Part:BBa_K1149006 BBa_K1149006] | [http://www.sciencedirect.com/science/article/pii/S0964830598000687 Vega et al., 1999] |
