Team:Tsinghua-A/Model
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Model overview
The system we designed involves many kinds of relationships between populations and individuals. To help us understand these relationships better, we designed models to describe how the amount of E.coli and substance change with time.
Concretely, we designed a fluid model and a solid model, where the solid model takes spatial effects on relationships between populations and individuals into consideration. In fluid model, we use Ordinary Differential Equation (ODE) to describe the behavior of the amount of different characters and molecules. In solid model, however, we use Cellular Automaton (CA) to mimic effects of spatial factors. (See more at Fluid Model and Solid Model)
We use models to do the things listed below:
Concretely, we designed a fluid model and a solid model, where the solid model takes spatial effects on relationships between populations and individuals into consideration. In fluid model, we use Ordinary Differential Equation (ODE) to describe the behavior of the amount of different characters and molecules. In solid model, however, we use Cellular Automaton (CA) to mimic effects of spatial factors. (See more at Fluid Model and Solid Model)
We use models to do the things listed below:
I Design warriors that can be killed only by the warrior from the other group
According to our results from Orthogonality test, we can just determine the circuit of warrior II and what AHL warrior I should secrete. The results are shown as below:
Fig.1 Gene circuit designed from results, the upper one is warrior I while the one below is warrior II
We cannot design a warrior I that can be killed by warrior II but not by itself regardless of whatever receptor-promoter pair we put inside warrior I. (See more at Orthogonality test)
The problem now becomes how to block warrior I’s response to C4HSL secreted by itself. Our model tells us if we design warrior I as below (Fig.2), we can realize that warrior I is only killed by warrior II. It is realized through the regulation of the RBS of TetR to an appropriate intensity. The basic principle here is C4HSL can activate the expression of TetR, which can be used to inhibit the expression of LacI. Therefore, the activating of LacI by C4HSL can be counteracted.
The problem now becomes how to block warrior I’s response to C4HSL secreted by itself. Our model tells us if we design warrior I as below (Fig.2), we can realize that warrior I is only killed by warrior II. It is realized through the regulation of the RBS of TetR to an appropriate intensity. The basic principle here is C4HSL can activate the expression of TetR, which can be used to inhibit the expression of LacI. Therefore, the activating of LacI by C4HSL can be counteracted.
Fig.2 Improved gene circuit, the upper one is warrior I while the one below is warrior II
See more details at Design of characters
See more details at Design of characters
Results are shown below:
II Design an easy way to regulate the killing ability of warriors.
To mimic the situation we investigate in real world, sometimes we need to regulate the killing ability to an appropriate level, like making the two warriors have the same killing ability. What can we do to regulate the killing ability of the warriors? Our model suggests that it is possible to regulate the killing ability of the two warriors by just changing the promoter intensity of some proteins! (Fig.4)
III Design our E.coli War based on our models.
We found that it will be much easier to consider the effects of some factors (Like initial number of each populations and spatial factors) on population interactions if we can visualize it. Therefore, we designed our game---E.coli War ( Game Overview) based on our model to satisfy our needs. What's more, the game can also help us realize educational purpose of our project and make the public know more about synthetic biology! (Exhibition at National Museum and Game Overview)
Our game is made on the structure of html5. The two small videos below are our fluid E.coli War and solid E.coli War.
Our game is made on the structure of html5. The two small videos below are our fluid E.coli War and solid E.coli War.
See more details on Fluid E.coli War and Solid E.coli War.
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