Team:Aachen/Project/Model
From 2014.igem.org
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To determine if this idea was actually feasible, we decided to model the system using the CAD tool TinkerCell (Chandran, Bergmann and Sauro, 2009). | To determine if this idea was actually feasible, we decided to model the system using the CAD tool TinkerCell (Chandran, Bergmann and Sauro, 2009). | ||
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To compare the response time of the fluorescence signal between our theoretical system and a traditional biosensor, we included a direct expression of GFP in the same plot (below). In the results show above, the strength of the promotor used for the direct GFP expression (traditional approach) is even twice as high as the strength of the promotor upstream of the TEV coding sequence in our new approach. Despite the weaker promotor, a '''higher GFP concentration is generated in the model of the novel biosensor''', predicting a quicker responde time of our system. | To compare the response time of the fluorescence signal between our theoretical system and a traditional biosensor, we included a direct expression of GFP in the same plot (below). In the results show above, the strength of the promotor used for the direct GFP expression (traditional approach) is even twice as high as the strength of the promotor upstream of the TEV coding sequence in our new approach. Despite the weaker promotor, a '''higher GFP concentration is generated in the model of the novel biosensor''', predicting a quicker responde time of our system. | ||
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- | The model was fitted to the data gathered from the characterization experiment conducted in shake flasks. Additionally, the data from the characterization experiment of the double plasmid construct K1319014 + K1319008 in the chip system was included in the plot. The data was derived from the plate reader output of the four central spots of the chip. The development of the fluorescence is presented [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter#reachachievementschip here]. It is shown that the fluorescent response occurs later than in the characterization experiment in shake flasks. This is explainable as the solid agar chip poses a greater diffusion barrier than liquid medium as used in the shake flasks. Further, the rate of fluorescence increase over time is smaller than in the characterization experiments in shake flasks. The reason | + | The model was fitted to the data gathered from the characterization experiment conducted in shake flasks. Additionally, the data from the characterization experiment of the double plasmid construct K1319014 + K1319008 in the chip system was included in the plot. The data was derived from the plate reader output of the four central spots of the chip. The background from the uninduced chip was substracted from the fluorescent response to correct the data and avoid effects from cell growth leading to wrong signal strengths. The development of the fluorescence is presented [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter#reachachievementschip here]. |
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+ | It is shown that the fluorescent response in chips occurs later than in the characterization experiment in shake flasks. This is explainable as the solid agar chip poses a greater diffusion barrier than liquid medium as used in the shake flasks. Further, the rate of fluorescence increase over time is smaller than in the characterization experiments in shake flasks. The reason is that the sensor cells need oxygen to produce GFP. However, they are embedded in solid agar in which the amount of available oxygen is lower compared to a shaking liquid system. | ||
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+ | The right prediction of the outcome of the characteization experiments by the model shows that our molecular approach is valid. A faster and stronger fluorescent signal could be proven both theoretically and empirically. | ||
{{Team:Aachen/BlockSeparator}} | {{Team:Aachen/BlockSeparator}} |
Revision as of 23:02, 17 October 2014
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