Team:Tsinghua-A/Project
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Project
I Why we design this project?
The relationships between populations and individuals are very complex. For gregarious animals like ants, there exists an ant society, in which a clear division of labor can be seen. Despite of it, how the society is organized is still a mystery. For animals so simple as ants, the interactions between individuals still involve lots of genes. Similarly, for us human, how our society works is also a very complicated problem. Though difficult to study, the knowledge of the organization of societies is really precious as it directs our further research into behaviors and more importantly, gives us more angles to view history and instructs us to make the present society better.
As all of these systems are too complicated and uncontrollable, it is hard for us to study these systems directly to understand the nature of these relationships. To achieve this goal, this year we decided to use our knowledge of synthetic biology to construct a simple system which can be used to simulate many kinds of relationships between individuals and populations. Through this system, we can simplify the complex natural system so we can get a better understanding of these relationships.
What's more, we found that it will be much easier to consider effects of some factors (Like the 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) to satisfy our needs.
Despite of the research values of our system, we found that as it is very simple and even kind of fun, it can be easily understood by the public. Therefore, we use our game to make more kids learn more about synthetic biology in an enjoyable way. To our surprise, when they were playing these games, they found many interesting results which can even promote our understanding of this system. (Exhibition at National Museum and Game Discovery) Furthermore, this can also be helpful for our further research design.
As all of these systems are too complicated and uncontrollable, it is hard for us to study these systems directly to understand the nature of these relationships. To achieve this goal, this year we decided to use our knowledge of synthetic biology to construct a simple system which can be used to simulate many kinds of relationships between individuals and populations. Through this system, we can simplify the complex natural system so we can get a better understanding of these relationships.
What's more, we found that it will be much easier to consider effects of some factors (Like the 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) to satisfy our needs.
Despite of the research values of our system, we found that as it is very simple and even kind of fun, it can be easily understood by the public. Therefore, we use our game to make more kids learn more about synthetic biology in an enjoyable way. To our surprise, when they were playing these games, they found many interesting results which can even promote our understanding of this system. (Exhibition at National Museum and Game Discovery) Furthermore, this can also be helpful for our further research design.
II Gene circuit
In our system, E.coli is divided into two groups, with each group having three characters. Warriors attack the enemies, farmers provide nutrients for everybody, while beggars sit there doing nothing.
Concretely, the gene circuit of each character is displayed below.
Concretely, the gene circuit of each character is displayed below.
III Invertase assay
In our system, we hope farmers can produce invertase and secrete it outside the cell to help other E.coli survive. To test if invertase can work as we expected, we transformed invertase and its transport system to E.coli and co-cultured it with cells that can express RFP. We found that E.coli that can produce invertase can truly support the survival of other E.coli. (Fig.2)
More details can be seen at Invertase assay
IV Orthogonality test
Because of the similarities between AHLs and between their receptors, warriors may be not only killed by the AHL secreted by the warriors from the other side, but also by itself, if the circuits are not well designed. This is a serious problem we faced when choosing the AHL-receptor-promoter pairs. This problem has been discussed by many groups in iGEM, like ETH_Zurich 2014. However, all previous results are obtained by adding AHL artificially to test the respond of specific receptor-promoter combination. In our project, we let E.coli to secrete AHL itself, so different concentrations of AHL in our system may make the previous studies unsuitable for our system here.
Therefore, we did Orthogonality test to fit our own needs to help us design gene circuits of warriors. Results are shown below.
Therefore, we did Orthogonality test to fit our own needs to help us design gene circuits of warriors. Results are shown below.
However, we failed to choose an orthogonal gene circuit from our results. We can just determine the circuit of warrior II and what AHL warrior I should secrete, as is shown below:
We cannot design a warrior I that can be killed by warrior II but not killed by itself regardless of whatever receptor-promoter we put inside warrior I.
(More details can be seen at Orthogonality test)
V Killing test
Because we use RFP to indicate the level of LacI inside the cell during Orthogonality test, we are not sure if the results will be the same when we use a complete circuit. Therefore, we designed two warriors and beggars as below to verify results got from Orthogonality test.
According to results of Orthogonality test, the warrior I will be killed by itself when it is cultivated without warrior II. Furthermore, warrior II doesn’t kill itself but can kill E.coli from the other side successfully. All results we got here are consistent with our Orthogonality test! They greatly enhance the reliability of our previous data. (Fig.6)
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More details can be found at Killing test
VI Improved orthogonal gene circuit
The problem now becomes how to block warrior I’s response to C4HSL secreted by himself. Our model tells us if we design the warrior I as below (Fig.7), we can make it only be killed by warrior II by just regulating the RBS of TetR to an appropriate intensity.
See more details at Design of characters
Results are shown below:
See more information at Improved gene circuit
VII Regulation of killing ability
Sometimes, to mimic the situation we investigate in real world, it may be necessary to regulate killing ability to an appropriate level, like making two warriors have the same killing ability. What can we do to regulate the killing ability of 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.9)
See more details at Regulation of killing ability
VIII Fluid and Solid model
Because of our limited time, we have not constructed all characters and used it to investigate some interesting questions, but our model can help us study the behaviors of this system.
Concretely, we designed a fluid model and a solid model, where the solid model has taken spatial effects on relationships between populations and individuals into consideration. In the fluid model, we use Ordinary Differential Equation (ODE) to describe the behavior of the amount of different characters and molecules. In the solid model, however, we use Cellular Automaton (CA) to mimic effects of spatial factors. (See more at Fluid Model and Solid Model)
As is shown above, fluid model helped us a lot on experimental design. Besides, they can also be used to help us design our game---E.coli War! The game can be used to help us consider effects of some factors on population interactions. Besides, it can even help us realize the educational purpose of our project and make the public know more about synthetic biology!
Concretely, we designed a fluid model and a solid model, where the solid model has taken spatial effects on relationships between populations and individuals into consideration. In the fluid model, we use Ordinary Differential Equation (ODE) to describe the behavior of the amount of different characters and molecules. In the solid model, however, we use Cellular Automaton (CA) to mimic effects of spatial factors. (See more at Fluid Model and Solid Model)
As is shown above, fluid model helped us a lot on experimental design. Besides, they can also be used to help us design our game---E.coli War! The game can be used to help us consider effects of some factors on population interactions. Besides, it can even help us realize the educational purpose of our project and make the public know more about synthetic biology!
IX E.coli War
Our games are made on structure of html5.The videos below are two short videos of our Fluid E.coli War and Solid E.coli War.
See more details on Fluid E.coli War and Solid E.coli War
After we designed our game preliminarily, we visited Beijing Perfect World Network Technology Co., Ltd (Perfect World), one of the largest game company in China, to learn more about the design of a game. The useful advice from the experts help us a lot in improving our E.coli War, making it more fun and easier for kids to play.
See more details at Visiting Perfect World
Afterwards, when children played this game during our exhibition in China Science and Technology Museum (CSTM), they found many interesting results which can even promote our understanding of this system. (Fig.10) (See more details at Exhibition at National Museum and Game Discovery) Furthermore, this can also be helpful for our further research design.
After we designed our game preliminarily, we visited Beijing Perfect World Network Technology Co., Ltd (Perfect World), one of the largest game company in China, to learn more about the design of a game. The useful advice from the experts help us a lot in improving our E.coli War, making it more fun and easier for kids to play.
See more details at Visiting Perfect World
Afterwards, when children played this game during our exhibition in China Science and Technology Museum (CSTM), they found many interesting results which can even promote our understanding of this system. (Fig.10) (See more details at Exhibition at National Museum and Game Discovery) Furthermore, this can also be helpful for our further research design.
X Summary
In conclusion, we designed a very general system to study many complex relationships and also a useful model to describe this system. In the future, it will be convenient to investigate some interesting questions with regard to relationships between populations and individuals by using this system.
What’s more, we designed two interesting games--- Fluid E.coli War and Solid E.coli War to make the public more interested in synthetic biology. Conversely, their finding of many interesting results and disciplines in the games could also be of great help to our research. By this way, we combine our project to the world perfectly. Through the promotion of our games, our project can influence our world and vice versa!
What’s more, we designed two interesting games--- Fluid E.coli War and Solid E.coli War to make the public more interested in synthetic biology. Conversely, their finding of many interesting results and disciplines in the games could also be of great help to our research. By this way, we combine our project to the world perfectly. Through the promotion of our games, our project can influence our world and vice versa!
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