Team:Wageningen UR/Project/ModelingProj1

From 2011.igem.org

(Difference between revisions)
(Modeling synchronized oscillations)
(Modeling synchronized oscillations)
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=== Mathematical model of the construct ===
=== Mathematical model of the construct ===
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Since our bio bricked oscillatory system is based on the design seen above, our first model of the system is a reproduction of the mathematical model in the supplementary information accompanying the publication mentioned. In their simulations, Danino et al. used the following set of delay differential equations, which we used as base for our simulation tool written in matlab. }}
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Since our bio bricked oscillatory system is based on the design seen above, our first model of the system is a reproduction of the mathematical model in the supplementary information accompanying the publication mentioned. In their simulations, Danino et al. used the following set of delay differential equations, which we used for our simulation tool written in matlab. }}
[[File:Equations_hasty_WUR.png|350px|center]]
[[File:Equations_hasty_WUR.png|350px|center]]
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{{:Team:Wageningen_UR/Templates/Style | text= __NOTOC__
{{:Team:Wageningen_UR/Templates/Style | text= __NOTOC__
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The production of AiiA and LuxI depend on the internal AHL concentration in the single cell. The steps from gene to protein (transcription, translation, maturation etc.) are not modeled separately, but taken together in the following Hill function:  }}
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The production of AiiA and LuxI depend on the internal AHL concentration in the single cell. The steps from gene to protein (transcription, translation, maturation etc.) are not modeled separately, but the delay is simulated by the following Hill function:  }}
[[File:Equations2_hasty_WUR.png|150px]]  
[[File:Equations2_hasty_WUR.png|150px]]  
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{{:Team:Wageningen_UR/Templates/Style | text= __NOTOC__
{{:Team:Wageningen_UR/Templates/Style | text= __NOTOC__
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in which tau represents the time step between the relevant internal AHL concentration and the corresponding AiiA and LuxI, so that
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in which tau represents the time step between the relevant internal AHL concentration and the corresponding AiiA and LuxI.
[[File:Equations3_hasty_WUR.png]]
[[File:Equations3_hasty_WUR.png]]
}}
}}

Revision as of 22:03, 11 September 2011

Building a Synchronized Oscillatory System

Modeling synchronized oscillations

Short repetition of the Hasty construct used as base for our system

For a better understanding of the equations which were used for the modeling of the system, figure 1 shows a short repetition of the circuit published by Danino et al. in the paper [http://www.nature.com/nature/journal/v463/n7279/abs/nature08753.html “A synchronized quorum of genetic clocks”], in our team commonly referred to as the "Hasty construct", which was used as a base for our design.


Mainproject01.png

Fig.1: Basic oscillating genetic circuit as published by Danino & Hasty.

The genes luxI and aiiA can be expressed when a AHL-LuxR complex binds to the promoter region. The circuit uses both a positive and negative feedback loop to control the AHL concentration and therefore the expression of the resulting proteins LuxI and AiiA. In the positive loop, LuxI generates more AHL, which, together with LuxR, can form more of the activating AHL-LuxR complex and therefore stimulates even more production of LuxI and consequently AHL. This complex also activates the expression of aiiA. In the negative feedback loop, AiiA degrades the AHL produced. For more detailed information about the circuit read more about the mechanism in the complete project description.


Mathematical model of the construct

Since our bio bricked oscillatory system is based on the design seen above, our first model of the system is a reproduction of the mathematical model in the supplementary information accompanying the publication mentioned. In their simulations, Danino et al. used the following set of delay differential equations, which we used for our simulation tool written in matlab.

Equations hasty WUR.png


Above: Set of delay differential equations derived by Danino et al. to model the oscillatory behaviour of the design using a positive and negative feedback loop.

A:AiiA
I:LuxI
Hi:internal AHL
He:external AHL

The production of AiiA and LuxI depend on the internal AHL concentration in the single cell. The steps from gene to protein (transcription, translation, maturation etc.) are not modeled separately, but the delay is simulated by the following Hill function:

Equations2 hasty WUR.png

in which tau represents the time step between the relevant internal AHL concentration and the corresponding AiiA and LuxI.

Equations3 hasty WUR.png