Team:Calgary/Project/OurSensor/Modelling/QuantitativeModelling
From 2013.igem.org
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- | <p> | + | <p>In the beginning of the project we were looking for a reporter system. The wet lab team has made a list of possible reporters that can be used <i>in vitro</i>. We wanted to ensure that the reporter system gave us a rapid output, was stable and did not require cellular machinery to work. We wanted to test this <i>in silico </i> before we tested it in the wetlab. We wanted to ensure there was concrete evidence to support our choice of one reporter enzyme over another. Given that it is much easier to do simulations using models than to do experiments in the lab, we simulated horseradish peroxidase (HRP) and beta-galactosidase which are one of the most rapid reporters known in the literature. We programmed differential equations modelling enzyme kinetics in Mathematica to produce a interactive plot of output over time, with parameters such as initial enzyme concentration and initial substrate concentration being the parameters that can be adjusted. </p> |
- | <p>After careful examination of the models under various parameters, | + | <p>After careful examination of the models under various parameters, we decided to use HRP because it is fast and give accurate response, evident from the kinetic models. However it turns out that we couldn't produce HRP in <i>E. coli</i>. After some more literature search we found a substitue of horseradish peroxidase, <a href=" https://2013.igem.org/Team:Calgary/Project/OurSensor/Reporter/PrussianBlueFerritin><span class= 'Green'><b>ferritin</b></a>, which is known to has fast kinetics and accurate response just like horseradish peroxidase.</p> |
Revision as of 03:32, 28 September 2013
Quantitative Modelling
Quantitative Modelling
Enzyme kinetics for potential reporter proteins
In the beginning of the project we were looking for a reporter system. The wet lab team has made a list of possible reporters that can be used in vitro. We wanted to ensure that the reporter system gave us a rapid output, was stable and did not require cellular machinery to work. We wanted to test this in silico before we tested it in the wetlab. We wanted to ensure there was concrete evidence to support our choice of one reporter enzyme over another. Given that it is much easier to do simulations using models than to do experiments in the lab, we simulated horseradish peroxidase (HRP) and beta-galactosidase which are one of the most rapid reporters known in the literature. We programmed differential equations modelling enzyme kinetics in Mathematica to produce a interactive plot of output over time, with parameters such as initial enzyme concentration and initial substrate concentration being the parameters that can be adjusted.