Difference between revisions of "Team:UT-Tokyo/Model"
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== Introduction == | == Introduction == | ||
We run a simulation about transcription and translation for two reasons. First is to make sure that our gene circuit functions as designed and establishes the loop of gene expression. Although the strain of e-coli used in our experiment, growing environment and sigma factors affect various parameter such as the speed of translation and transcription, and decomposition rate of factors, if there is no parameter sets which we need to establish the loop of gene expression of fluorescent protein, our project is theoretically impossible. In other words, to find the parameter set which establishes the loop means to show that our project is theoretically feasible. In addition, the simulation enables us to improve and redesign our gene circuit with reference to the parameter set. | We run a simulation about transcription and translation for two reasons. First is to make sure that our gene circuit functions as designed and establishes the loop of gene expression. Although the strain of e-coli used in our experiment, growing environment and sigma factors affect various parameter such as the speed of translation and transcription, and decomposition rate of factors, if there is no parameter sets which we need to establish the loop of gene expression of fluorescent protein, our project is theoretically impossible. In other words, to find the parameter set which establishes the loop means to show that our project is theoretically feasible. In addition, the simulation enables us to improve and redesign our gene circuit with reference to the parameter set. | ||
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| + | We run a simulation about transcription and translation for two reasons. First is to make sure that our gene circuit functions as designed and establishes the loop of gene expression. Although the strain of e-coli used in our experiment, growing environment and sigma factors affect various parameter such as the speed of translation and transcription, and decomposition rate of factors, if there is no parameter sets which we need to establish the loop of gene expression of fluorescent protein, our project is theoretically impossible. In other words, to find the parameter set which establishes the loop means to show that our project is theoretically feasible. In addition, the simulation enables us to improve and redesign our gene circuit with reference to the parameter set. | ||
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== Method == | == Method == | ||
Revision as of 16:33, 14 October 2016
Contents
Transcription and Translation
Abstract
We found some parameter sets on which e-coli changes gene expression by a generation. In addition, we also found ones on which circuit establishes the loops stably regardless of small fluctuation (noise in experiment). Therefore, our gene circuit seems likely to work as designed.
Introduction
We run a simulation about transcription and translation for two reasons. First is to make sure that our gene circuit functions as designed and establishes the loop of gene expression. Although the strain of e-coli used in our experiment, growing environment and sigma factors affect various parameter such as the speed of translation and transcription, and decomposition rate of factors, if there is no parameter sets which we need to establish the loop of gene expression of fluorescent protein, our project is theoretically impossible. In other words, to find the parameter set which establishes the loop means to show that our project is theoretically feasible. In addition, the simulation enables us to improve and redesign our gene circuit with reference to the parameter set.
We run a simulation about transcription and translation for two reasons. First is to make sure that our gene circuit functions as designed and establishes the loop of gene expression. Although the strain of e-coli used in our experiment, growing environment and sigma factors affect various parameter such as the speed of translation and transcription, and decomposition rate of factors, if there is no parameter sets which we need to establish the loop of gene expression of fluorescent protein, our project is theoretically impossible. In other words, to find the parameter set which establishes the loop means to show that our project is theoretically feasible. In addition, the simulation enables us to improve and redesign our gene circuit with reference to the parameter set.
Method
| Parameters | character |
| sigma-factor A,B,C | $\sigma_A, \sigma_B, \sigma_C$ |
| anti-sigma factor, A, B, C | $\sigma_{-A}, \sigma_{-B}, \sigma_{-C}$ |
| mRNA of sigma factor A, B, C without toehold switch | $R_A, R_B, R_C$ |
| mRNA of anti-sigma-factor A, B,C without toehold switch | $R_{-A}, R_{-B}, R_{-C}$ |
| mRNA of sigma factor A, B, C with toehold switch | $R_{td, A}, R_{td, B}, R_{td, C}$ |
| taRNA | $[\mathrm(taRNA)]$ |
| IPTG | $[\mathrm(IPTG)]$ |
| immature GFP, RFP, CFP | $[\mathrm(imGFP)], [\mathrm(imRFP)], [\mathrm(imCFP)]$ |
| mature GFP, RFP, CFP | $[\mathrm(GFP)], [\mathrm(RFP)], [\mathrm(CFP)]$ |
| mRNA of GFP, RFP, CFP | $R_{GFP}, R_{RFP}, R_{CFP}$ |
Stability Analysis
Abstract
