This year is the first year the University of Groningen is joining the iGEM competition. Our team – The Groningen Transformers – will focus on cell-cell signal systems, cellular automata and the Conway’s Game of Life!

Overall project

One of the patterns created by the Game of Life

Since we have a multidisciplinairy team we choose a project where labwork and modelling have to work together, for example by measuring parameters and optimizing our model every day. In our brainstorm sessions we all agreed that it would be fun to create a system in Escherichia coli which could repeat itself after one initial pulse. A cellular automata is a system in which rules are applied to cells and their neighbours in a two dimensional grid. We would like to create patterns and behaviors with simple rules. It is very important that complex behavior can be produced by simple rules [Mitchell, 2002] because… A very interesting example of a cellular automata is the Game of Life, invented by the mathematician John Conway in 1970. In this game grid cells can be live or dead. The most common rules are: with 2 or 3 neighbors a grid cell stays alive, with more or less it dies and with 3 neighbors a grid cell becomes alive. See figure x.

It will be a great challenge to make this game with a biological system. We already thought of a combination of biobricks (link floor met parts voor ons systeem) and the necessary parts we have to add ourselves. Because this project is quite ambitious we will first try to make the subparts for the system.

In the game of life cells have two states, in our case GFP expression or no GFP expression. Therefore we need a double threshold switch. We make this with a HSL/cI hybrid promotor that can be activated by a low HSL concentration; producing GFP and a promotor which will be switched on at higher HSL concentration; producing cI to block the first promotor, see figure x. This quorum sensing system was first discovered in Vibrio fischeri [Greenberg, 1999). The cells have to send HSL molecules to other cells. This double threshold switch makes the cells either ‘dead’; no GFP expression or ‘alive’; GFP expression and thereby forming our pattern on a two dimensional grid.

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The value of this game for biology is that we can synchronize cells better. Nowadays synchronisation can be done by nitrogen starvation for example, and in nature cells can synchronize via quorum sensing.

Project Details

To make a system where a cell or colony would react like a 'cell' in the Conway's game of life, a couple of things are needed:

• An interval device - Here cells need to know from its neighbours if they are 'dead' or 'alive', and when alive if its not overcrowded.
• A sender device - Cells need to let others known in what state they are: 'dead' or 'alive'.
• A receiver device - Cells need to obtain and process information from their neighbours.
• A reset function - After it gets overcrowded around one cell, it needs to reset, become 'dead'.

The Registry of Standard Parts a lot of biobricks are involved in the AHL quorum sensing system of Vibrio fischeri. For our system this was really helpful, since we did not want to use a cell-cell signal system witch would interfere with E. coli's own quorum sensing system. We could use these bricks to create a system where cells will communicate with eachother and sense it at the same time. Moreover quite some other repressors and activators are present in the Registry. We chose to use the parts from the Registry as basic elements in the system. For some specific features we need to make and add them ourselves.

The grid can be made ourselves by putting colonies on an agar plate. HSL can diffuse trough agar plates, via this the cells can communicate with eachother, and turn 'on' (alive) or 'off' (dead). The exact distance and layout still needs to be determined.

The Experiments

Part 3

Results