Project Description

We move the frozen power from Disney to E.coli. We construct E.coli to express RFP to draw a dynamic pattern of snowflake. Once we kindle a spot, the pattern starts and grows up gradually. According to our design, 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, while neither of them influencing themselves. A plate for E.coli culture is divided into rectangular grids and every “cell” in the grid is occupied with a colon of E.coli. On-state shows as red fluorescence while off-state shows as nothing illuminating. To kindle the system, we only need to add correspondent signal molecular to the central 4 colons of E.coli in a plate. Finally, there will be a snowflake with red fluorescence starts to grow up from a point automatically.

Content

Overall project summary

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!

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.

Figure 1. A dynamic pattern of snowflake with E.coli

How do we realize it?

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.

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.

Then, how can we use E.coli to simulate the CA above?

To guarantee the mechanism can work out and reach a satisfying effect of view, we do the following design:

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 ; 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; 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. 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.

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.

Thanks to RFP’s long half-life period, the other evolution principle asking for the maintenance of on state achieves automatically.

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.

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.

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

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.