Tokyo/Works/Formulation

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__NOTOC__
__NOTOC__
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<br>[[Tokyo/Works|Works top]]　　0.[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]　　1.[[Tokyo/Works/Formulation |Formulation]]　　2.[[Tokyo/Works/Assay |Assay1]]　　3.[[Tokyo/Works/Simulation |Simulation]]　　4.[[Tokyo/Works/Assay2 |Assay2]]　　5.[[Tokyo/Works/Future works |Future works]]
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<br>[[Tokyo/Works|Works top]]&nbsp;&nbsp;&nbsp;0.[[Tokyo/Works/Hybrid promoter|Hybrid promoter]]&nbsp;&nbsp;&nbsp;1.[[Tokyo/Works/Formulation |Formulation]]&nbsp;&nbsp;&nbsp;2.[[Tokyo/Works/Assay |Assay1]]&nbsp;&nbsp;&nbsp;3.[[Tokyo/Works/Simulation |Simulation]]&nbsp;&nbsp;&nbsp;4.[[Tokyo/Works/Assay2 |Assay2]]&nbsp;&nbsp;&nbsp;5.[[Tokyo/Works/Future works |Future works]]
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<br>[[Tokyo/Formulation/1.toggle model |Step1]]　　[[Tokyo/Formulation/2.toggle model with hybrid promoter |Step2]]　　[[Tokyo/Formulation/3.AHL-experssing model|Step3]]　　
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<br>[[Tokyo/Formulation/1.toggle model |Step1]]&nbsp;&nbsp;&nbsp;[[Tokyo/Formulation/2.toggle model with hybrid promoter |Step2]]&nbsp;&nbsp;&nbsp;[[Tokyo/Formulation/3.AHL-experssing model|Step3]]　　
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First, the qualitative nature was analyzed by simple dimensionless differential equations for this mutual inhibition system. The results of phase plane analysis for the equations suggested that the values of Hill coefficients were especially important in order that the system had the bistability corresponding to A and B states.
First, the qualitative nature was analyzed by simple dimensionless differential equations for this mutual inhibition system. The results of phase plane analysis for the equations suggested that the values of Hill coefficients were especially important in order that the system had the bistability corresponding to A and B states.
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'''[[Tokyo/Formulation/1.toggle model |　⇒ see more]]'''
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'''[[Tokyo/Formulation/1.toggle model | ==> see more]]'''
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<br>
<br>    [[Image:expression1-2.jpg|200px]]
<br>    [[Image:expression1-2.jpg|200px]]
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Second, the effect of hybrid promoter was introduced into the single cell model. In the case of the model with hybrid promoter, the contribution from the repression of the promoter by LacI and that from the activation by AHL should be considered.; that is, the factor of AHL contribution was added to the differential equations for RB, resulting in the dependence of the phase plane on the AHL concentration. As a result of phase plane analysis for the equations, the system was monostable in the case of lower AHL concentration; whereas it was bistable in the case of higher AHL concentration. The values of Hill coefficients were important for the system bistability even in this case.
Second, the effect of hybrid promoter was introduced into the single cell model. In the case of the model with hybrid promoter, the contribution from the repression of the promoter by LacI and that from the activation by AHL should be considered.; that is, the factor of AHL contribution was added to the differential equations for RB, resulting in the dependence of the phase plane on the AHL concentration. As a result of phase plane analysis for the equations, the system was monostable in the case of lower AHL concentration; whereas it was bistable in the case of higher AHL concentration. The values of Hill coefficients were important for the system bistability even in this case.
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'''[[Tokyo/Formulation/2.toggle model with hybrid promoter |　⇒ see more]]'''
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'''[[Tokyo/Formulation/2.toggle model with hybrid promoter | ==> see more]]'''
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<br>[[Image:expression2-4.jpg|300px|]][[Image:AHLresponse2-2.jpg|300px|]]
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<br>
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<br>[[Image:AHLresponse2-3.jpg|330px|]][[Image:AHLresponse2-4.jpg|300px|]][[Image:AHLresponse2-5.jpg|300px|]]
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<br>[[Image:expression2-4.jpg|280px|]][[Image:AHLresponse2-2.jpg|300px|]]
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<br>[[Image:step2-4.JPG|300px|]][[Image:step2-5.JPG|300px|]][[Image:step2-6.JPG|300px|]]
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== [[Tokyo/Formulation/3.AHL-experssing model|Step3.Single cell model with hybrid promoter and cell-produced AHL]] ==
== [[Tokyo/Formulation/3.AHL-experssing model|Step3.Single cell model with hybrid promoter and cell-produced AHL]] ==
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Third, the system with hybrid promoter was expanded into the system using cell-produced AHL. Here, the new parameter λ was introduced to represent the producing rate of AHL by the promoter A. As a result of phase plane analysis, the values of Hill coefficients were important for the system bistability even in this case. The results of the numerical analysis from Step1 to Step3 suggest the importance of the values of the Hill coefficients in this system.  However, adjustments of Hill coefficients by DNA sequence modification are much more difficult than those of production rate parameters; changes in RBS -35 box, or -10 box allow production efficiency. We thus practically determined the values in the next wet experiments to confirm feasibility of our model.
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Third, the system with hybrid promoter was expanded into the system using cell-produced AHL. Here, the new parameter λ was introduced to represent the producing rate of AHL by the promoter A. As a result of phase plane analysis, the values of Hill coefficients were important for the system bistability even in this case. '''[[Tokyo/Formulation/3.AHL-experssing model| ==> see more]]'''
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'''[[Tokyo/Formulation/3.AHL-experssing model|　⇒ see more]]'''
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<br>The results of the numerical analysis from Step1 to Step3 suggest the importance of the values of the Hill coefficients in this system.  However, adjustments of Hill coefficients by DNA sequence modification are much more difficult than those of the other parameters (α1, α2, and λ); modifications in RBS -35 box, or -10 box allow change of those three parameters. We thus practically determined the values in the next wet experiments to confirm feasibility of our model.
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<br>[[Image:expression3-1.jpg|300px|]]
<br>[[Image:expression3-1.jpg|300px|]]
<br>[[Image:Step3-3.JPG|300px|]][[Image:Step3-4.JPG|300px|]]
<br>[[Image:Step3-3.JPG|300px|]][[Image:Step3-4.JPG|300px|]]
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However, all the individuals behaved in the same way in this deterministic model. To see the bahavior of each individual cell, it is necessary to carry out stocastic simulation.
However, all the individuals behaved in the same way in this deterministic model. To see the bahavior of each individual cell, it is necessary to carry out stocastic simulation.
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'''[[Tokyo/Formulation/4.population model|　⇒ see more]]'''
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'''[[Tokyo/Formulation/4.population model| ==> see more]]'''
<br>[[Image:expression4-1.jpg|400px]]
<br>[[Image:expression4-1.jpg|400px]]

Latest revision as of 05:09, 27 October 2007



Works top   0.Hybrid promoter   1.Formulation   2.Assay1   3.Simulation   4.Assay2   5.Future works


Step1   Step2   Step3　　


Numerical analysis for single cell

Step1. Single cell model:mutual inhibition

First, the qualitative nature was analyzed by simple dimensionless differential equations for this mutual inhibition system. The results of phase plane analysis for the equations suggested that the values of Hill coefficients were especially important in order that the system had the bistability corresponding to A and B states. ==> see more

Expression1-2.jpg


Step2. Single cell model with hybrid promoter

Second, the effect of hybrid promoter was introduced into the single cell model. In the case of the model with hybrid promoter, the contribution from the repression of the promoter by LacI and that from the activation by AHL should be considered.; that is, the factor of AHL contribution was added to the differential equations for RB, resulting in the dependence of the phase plane on the AHL concentration. As a result of phase plane analysis for the equations, the system was monostable in the case of lower AHL concentration; whereas it was bistable in the case of higher AHL concentration. The values of Hill coefficients were important for the system bistability even in this case. ==> see more


Expression2-4.jpgAHLresponse2-2.jpg


Step2-4.JPGStep2-5.JPGStep2-6.JPG



Step3.Single cell model with hybrid promoter and cell-produced AHL

Third, the system with hybrid promoter was expanded into the system using cell-produced AHL. Here, the new parameter λ was introduced to represent the producing rate of AHL by the promoter A. As a result of phase plane analysis, the values of Hill coefficients were important for the system bistability even in this case. ==> see more
The results of the numerical analysis from Step1 to Step3 suggest the importance of the values of the Hill coefficients in this system. However, adjustments of Hill coefficients by DNA sequence modification are much more difficult than those of the other parameters (α1, α2, and λ); modifications in RBS -35 box, or -10 box allow change of those three parameters. We thus practically determined the values in the next wet experiments to confirm feasibility of our model.


Expression3-1.jpg
Step3-3.JPGStep3-4.JPG




　


　Before(Hybrid promoter)　<<　Formulation >>　Formulation Step.1　>>>>　Next(Assay1)

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