Team:Tokyo Tech/Genetic toggle switch to implement rewritable function
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!align="center"|[[Team:Tokyo_Tech|Home]] | !align="center"|[[Team:Tokyo_Tech|Home]] | ||
!align="center"|[[Team:Tokyo_Tech/Construction|Construction]] | !align="center"|[[Team:Tokyo_Tech/Construction|Construction]] | ||
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!align="center"|[[Team:Tokyo_Tech/Genetic toggle switch to implement rewritable function|Genetic toggle switch ]] | !align="center"|[[Team:Tokyo_Tech/Genetic toggle switch to implement rewritable function|Genetic toggle switch ]] | ||
!align="center"|[[Team:Tokyo_Tech/Parts|Parts Submitted to the Registry]] | !align="center"|[[Team:Tokyo_Tech/Parts|Parts Submitted to the Registry]] | ||
+ | !align="center"|[[Team:Tokyo_Tech/Result|Result]] | ||
!align="center"|[[Team:Tokyo_Tech/Team|The Team]] | !align="center"|[[Team:Tokyo_Tech/Team|The Team]] | ||
- | !align="center"|[[Team:Tokyo_Tech/ | + | !align="center"|[[Team:Tokyo_Tech/Acknowledgements|Acknowledgements]] |
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= Genetic toggle switch to implement rewritable function= | = Genetic toggle switch to implement rewritable function= | ||
- | We | + | In order to implement rewritable function, we tried to construct Pressure Inducible Genetic Toggle Switch (in short PIGTS). |
+ | We thought two types of model - genetic circuit model and mathematical model - so as to construct PIGTS. | ||
== Genetic circuit model == | == Genetic circuit model == | ||
- | [[Image:Toggle_genetic_circuit_model.png]] | + | [[Image:Toggle_genetic_circuit_model.png|thumb|400px|right|figure 5-1 genetic circuit model]] |
- | + | '''1. Writable function''' | |
+ | * '''Plac''' is induced under 30MPa pressure | ||
- | + | * Express CI and GFP | |
- | + | * CI represses PL and causes low LacI concentration | |
- | + | * Express increasingly CI and GFP('''inserted destruction tags''') ⇒ '''Bright!!''' | |
- | |||
- | + | '''2. Erasable function''' | |
+ | * '''PL''' is induced by heat | ||
- | + | * Express LacI and LacI represses Plac | |
- | + | * Therefore, GFP expression decreases | |
- | + | == Mathematical model == | |
+ | <gallery widths="200px" heights="150px" perrow="1" align="right" caption="Differential equation models"> | ||
+ | Image:Room_pressure_model.png|figure 5-2 Atmospheric pressure model. It is known that n<sub>P<sub>L</sub></sub> = 3.0 from earlier studies | ||
+ | Image:30MPa_pressure_model2.png|figure 5-3 30MPa pressure model | ||
+ | </gallery> | ||
- | + | We used two differential equation models and we call them 'atmospheric pressure model' and '30MPa pressure model'. | |
+ | In order to implement rewritable function, we decided to use the difference of nullclines of each system so as to satisfy the following condition | ||
+ | * Converge to high CI concentration state under 30MPa pressure (writable) | ||
+ | * Bistable under atmospheric pressure (erasable) | ||
- | == | + | |
+ | [[Image:Desirable_condition.png|700px|thumb|left|figure 5-4 Desirable condition<!--. left:under atmospheric pressure (nullclines of figure 5-2), right:under 30MPa pressure (nullclines of figure 5-3).-->]] | ||
+ | |||
+ | {{clear}} | ||
+ | === IPTG assay === | ||
+ | [[Image:Transfer_Function.png|thumb|300px|left|figure 1 Hill function]] | ||
+ | |||
+ | '''Objective''' | ||
+ | |||
+ | By testing how LacI represses the lac promoter, Hill coefficient of lac promoter should be decided. In order to adjust effective concentration of LacI, IPTG was added. | ||
+ | |||
+ | '''Result & Conclusion''' | ||
+ | |||
+ | GFP fluorescence intensity was enhanced in an IPTG-dose dependent manner. It indicates that the LacI repression was getting weak by adding IPTG. Taken together with the graph shown in figure 1 and the formulation of Hill function fitting described above, the characteristics of the lac promoter expressed in Hill function was determined. Finally, we obtained '''n<sub>P<sub>lac</sub></sub> = 2.15'''. | ||
+ | {{clear}} | ||
+ | == Calculate the domain of appropriate parameters == | ||
+ | [[Image:Desirable_condition_94.png|400px|thumb|right|figure 5-5 The domain of appropriate parameters if α<sub>Plac</sub> = 3.0]] | ||
+ | |||
+ | It is known that Plac activity under 30MPa pressure is '''94.0''' times stronger than Plac activity under atmospheric pressure, so, '''β<sub>30P<sub>lac</sub></sub>''' = 94.0. | ||
+ | If 30MPa additional activity rate of PL ('''β<sub>30P<sub>L</sub></sub>''') or the ratio of Plac - RBS strength ('''α<sub>P<sub>lac</sub></sub>''') and PL-RBS strength('''α<sub>P<sub>L</sub></sub>''') are not appropriate value, we can't construct PIGTS. | ||
+ | So we calculated the domain of appropriate β<sub>30P<sub>L</sub></sub> and the ratio of α<sub>P<sub>lac</sub></sub> and α<sub>P<sub>L</sub></sub>. | ||
+ | |||
+ | [[Image:PL_pressure_response.png|200px|none|thumb|left|figure 5-6 Pressure-response ability of PL]] | ||
+ | We identified '''β<sub>30P<sub>L</sub></sub> = 1.42''' by our experiment under 30MPa pressure(figure 5-6). Therefore, we can implement rewritable function if we choose '''P<sub>L</sub> - RBS strength range from 2.4 to 7.4'''. |
Latest revision as of 14:22, 26 October 2008
Home | Construction | Acrylic container | Development of promoter | Genetic toggle switch | Parts Submitted to the Registry | Result | The Team | Acknowledgements |
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Contents |
Genetic toggle switch to implement rewritable function
In order to implement rewritable function, we tried to construct Pressure Inducible Genetic Toggle Switch (in short PIGTS). We thought two types of model - genetic circuit model and mathematical model - so as to construct PIGTS.
Genetic circuit model
1. Writable function
- Plac is induced under 30MPa pressure
- Express CI and GFP
- CI represses PL and causes low LacI concentration
- Express increasingly CI and GFP(inserted destruction tags) ⇒ Bright!!
2. Erasable function
- PL is induced by heat
- Express LacI and LacI represses Plac
- Therefore, GFP expression decreases
Mathematical model
We used two differential equation models and we call them 'atmospheric pressure model' and '30MPa pressure model'. In order to implement rewritable function, we decided to use the difference of nullclines of each system so as to satisfy the following condition
- Converge to high CI concentration state under 30MPa pressure (writable)
- Bistable under atmospheric pressure (erasable)
IPTG assay
Objective
By testing how LacI represses the lac promoter, Hill coefficient of lac promoter should be decided. In order to adjust effective concentration of LacI, IPTG was added.
Result & Conclusion
GFP fluorescence intensity was enhanced in an IPTG-dose dependent manner. It indicates that the LacI repression was getting weak by adding IPTG. Taken together with the graph shown in figure 1 and the formulation of Hill function fitting described above, the characteristics of the lac promoter expressed in Hill function was determined. Finally, we obtained nPlac = 2.15.
Calculate the domain of appropriate parameters
It is known that Plac activity under 30MPa pressure is 94.0 times stronger than Plac activity under atmospheric pressure, so, β30Plac = 94.0. If 30MPa additional activity rate of PL (β30PL) or the ratio of Plac - RBS strength (αPlac) and PL-RBS strength(αPL) are not appropriate value, we can't construct PIGTS. So we calculated the domain of appropriate β30PL and the ratio of αPlac and αPL.
We identified β30PL = 1.42 by our experiment under 30MPa pressure(figure 5-6). Therefore, we can implement rewritable function if we choose PL - RBS strength range from 2.4 to 7.4.