Difference between revisions of "Team:CAU China/Project"

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<p> Overall project summary </p>
 
<p> Overall project summary </p>
  
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<p>In the popular fantasy-comedy film Frozen, produced by Disney early in this year, there is an amazing fairy tale that the princess has the magical ability to make all things frozen,  presenting us a fantastic world related to dreamy snow. Do you believe our cute E.coli has such kind of magical power? Yes, it can be true!</p>
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<p>Our achievement</p>
 
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In our project, we want to move the frozen power from Disney to E.coli, that is, a dynamic  pattern of snowflake emitting red fluorescence, which is actually composed of colons of E.coli expressing RFP, starts to appear and grow up gradually from a single point once we kindle it, showing ideally in figure 1.  
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In our project, we create 4 kinds of transgenic plants. All of them have the resistant to two kinds of herbicides. We use the foot-and-mouth disease virus 2A polyprotein to link to two different resistant genes. In the modeling part, we try to use computer modeling to predict which kind of protein can be linked with 2A and the how the 2A polypeptide affects the protein's function.</p>
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<img src="https://static.igem.org/mediawiki/2014/c/c7/Project_Description_02.jpg" width="500px">
  
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<p>Figure 1. A dynamic pattern of snowflake with E.coli </p>
 
 
<p>How do we realize it?</p>
 
<p>How do we realize it?</p>
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<p>Our design comes from a combination of genetic-engineering modification, belonging to synthetic biology, and Cellular Automaton, an amazing algorithm in math and computing science. </p>
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<p>Firstly, we found that the abuse of herbicide causes a lot of serious problems and the mix use of herbicides can decrease the dose, increase the efficacy, decrease the poison residual and expand the weed control spectrum. Therefore we want to create the transgenic plants which have the resistant to two kinds of herbicides so that when farmers use two kinds of herbicides to kill weeds, the crops will not be affected.  
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<p>We first introduce the concept of Cellular Automaton, CA[1]. There are a lot of classifications of CA and our project applies one of simple bidimensional forms. In our model, the cellular automaton consists of a bidimensional rectangular grid of cells, and every cell is defined as the very basic unit with 2 states, on and off. For a single cell, there are four nearest cells, located in the same distance from the cell, up and down, left and right, which are defined as neighbors. For a CA, its evolution principles play a determining role in altering every cell’s state following the proceeding of time points. To form a pattern of snowflake, the principle is, once a celll’s state is on, it will be always on; if the state of a cell is off, it will turn to be on only when a single neighbor of it is on.</p>
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<p>Then, how can we use E.coli to simulate the CA above?</p>
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<p>To guarantee the mechanism can work out and reach a satisfying effect of view, we do the following design:</p>
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<p>1.A plate for E.coli culture is divided into rectangular grids and every “cell” in the grid is occupied with a single colon of E.coli ;
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2.On-state shows as red fluorescence, coming from the expression of RFP in E.coli, and companies with the production of signal molecular, while off-state shows as nothing illuminating;
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3.Two kinds of E.coli with partly different genetic pathway align alternatively. The two kinds of E.coli interact through two independent quorum sensing systems, LuxI/LuxR/AHL in vibrio fischeri and RpaI/RpaR/pC-HSL in Rhodopseudomonas palustris[2], while neither of them influence themselves.
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4.Based on the work of Ron Weiss(2005)[3], which designs a pathway where receiver cells only respond to signal molecular of medium concentration as figure 2, we design a genetic pathway to fulfill the evolution principles in CA as figure 3.
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<img src="https://static.igem.org/mediawiki/2014/c/c7/Project_Description_02.jpg" width="500px">
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<p>It is conceivable that for a “cell”, any one of its 4 neighbors in grid turns on would cause the produced signal molecular diffuses out of E.coli cells and around, accumulating to a certain concentration and influencing the “cell”. We can deduce that if there are more than one neighbors on, the cell would be immersed in a higher concentration of signal molecular. So, if we modulate related genetic elements in work of Ron Weiss to make the so-called medium concentration of signal molecular as what only one on neighbor produces and accumulates, we can fulfill the principle that an off cell responds and turns on only when one of its neighbors is on.</p>
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<p>Thanks to RFP’s long half-life period, the other evolution principle asking for the maintenance of on state achieves automatically.</p>
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<p>As described in figure 3, the upper kind of cells only respond to blue signal molecular of medium concentration referring to condition of only one on neighbor, expressing RFP and producing green signal molecular. When green signal molecular diffuses to the lower kind of cells and satisfies the same condition, the lower cells respond to green signal molecular, expressing RFP and producing blue signal molecular to influence the upper kind of cells. </p>
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<p>To kindle the whole system, we only need to add correspondent signal molecular to 4 colons of E.coli located in the central of the plate. Then, we would observe a snowflake with red fluorescence starts to grow up from a point automatically just as figure 1.</p>
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<p>We want to do more</p>
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As we know, herbicide is not the only stress to crops in the agriculture industry. There are many other stress, such as pest, freezing and drought stress. So in the future, we want to use the 2A polypeptide to link the resistant genes to these stress environment. Besides, we want to improve the 2A polypeptide so that we can link more genes and the side effect to the proteins will be reduced. </p>
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<li>Project Details</li>
 
<li>Project Details</li>

Revision as of 03:25, 7 September 2015

Team:CAU China/Project - 2014.igem.org

 

Team:CAU China/Project

From 2014.igem.org

  1. Project Details
  2. Materials and Methods
  3. The Experiments
  4. Results
  5. Data analysis
  6. Conclusions

Project Description

Nowadays, as the more and more use of herbicide, lots of problems have come up. Some of these problems are very serious such as the poisonous residue of herbicide and the superweed which have the resistance to the herbicide. What's more,as the students of China Agriculture University, we would like to use what we have learned to make a little improvement in the agriculture industry.

Content

Overall project summary

Our achievement

In our project, we create 4 kinds of transgenic plants. All of them have the resistant to two kinds of herbicides. We use the foot-and-mouth disease virus 2A polyprotein to link to two different resistant genes. In the modeling part, we try to use computer modeling to predict which kind of protein can be linked with 2A and the how the 2A polypeptide affects the protein's function.

How do we realize it?

Firstly, we found that the abuse of herbicide causes a lot of serious problems and the mix use of herbicides can decrease the dose, increase the efficacy, decrease the poison residual and expand the weed control spectrum. Therefore we want to create the transgenic plants which have the resistant to two kinds of herbicides so that when farmers use two kinds of herbicides to kill weeds, the crops will not be affected.

We want to do more

As we know, herbicide is not the only stress to crops in the agriculture industry. There are many other stress, such as pest, freezing and drought stress. So in the future, we want to use the 2A polypeptide to link the resistant genes to these stress environment. Besides, we want to improve the 2A polypeptide so that we can link more genes and the side effect to the proteins will be reduced.

References

1. Cellular automaton: http://en.wikipedia.org/wiki/Cellular_automaton.

2. Genetic pathway of Ron Weiss(2005):Basu S, Gerchman Y, Collins C H, et al. A synthetic multicellular system for programmed pattern formation[J]. Nature, 2005, 434(7037): 1130-1134.

3. quorum sensing system in Rhodopseudomonas palustris:Schaefer A L, Greenberg E P, Oliver C M, et al. A new class of homoserine lactone quorum-sensing signals[J]. Nature, 2008, 454(7204): 595-599.

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