Team:ETH Zurich/Project

From 2013.igem.org

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<h1>Information processing</h1>
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<p align="justify">Each minesweeper square in the computer game corresponds to a bacterial colony on the agar mine-field. We have two bacterial strains: 1. the mine strain with the sender cells and 2. the non-mine strain with the receiver cells. The cells communicate through diffusion of OHHL and change color to give the player information in order to logically carry out the next move in the game. The colonies remain white as seen on the agar plate until any substrate is added. The left and the right click of the mouse is simulated with the addition of the multi-substrate mix and the single substrate.</p>[[File:infoproc14.png|800px|center|thumb|<b>Figure 1: Signal transduction from secreted signaling molecule to colorimetric response.</b>]]
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<p align="justify">The biology is explained here. The sender colony secretes the quorum sensing molecule 3-oxo-N-hexanoyl-L-homoserine lactone
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([https://2013.igem.org/Team:ETH_Zurich/Experiments_2 OHHL]) that diffuses through the agar to the surrounding cells. The receiver cells passively take up the OHHL by diffusion where the signaling molecule forms a complex with the inactive LuxR to activate it. The information is translated via mutated pLuxR promoters of different OHHL affinities which leads to the secretion of different hydrolases. Within minutes after the addition of substrate a change in color indicates the identity of the played colony and number of surrounding  mine colonies.
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If we located bacterial colonies in the place of squares like in the traditional game, the colonies placed in the corners would be further away compared to the colonies along the edges. We decided on a hexagonal honeycomb-like pattern, where colonies are placed at all edges of the hexagon except from the center. In this set-up the number of mine colonies restricted is to only one, two or three that can surround a non-mine colony. This also facilitates the selection of suitable reporter enzymes. To plate the field, liquid cultures of mine and non-mine cells are grown to an OD<sub>600</sub> of 0.5, then, using a pipette, 1.5μl of liquid culture are placed according to the grid.
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<h1><b>How to play minesweeper using E.Coli</b></h1>
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<h1>How is Colisweeper played ?</h1>
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<div style="position:relative;left:-105px;top:10px">[[Image:Igem_wallpaper.png|700px]]</div>
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[[File:Project description10.png|300px|left|thumb|<b>Figure 2: Project description</b>]]
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<div style="position:relative;top:-445px;left:620px;width:50%;height:auto;font-family:Comic Sans MS;font-size:20px;color:white">As you certainly know a classic minesweeper has 4 options. Non mine cells opening without any event, fields next to a mine indicating how many mines they are close to (1,2,3,4...), mine cells itself ending the game until one is revealed and last but not least the flagging option to mark fields as mine fields.<br><br>The goal of the game is to reveal all non mine as fast as possible.<br><br>Actually to simulate the "click" we decided to add a substrate starting a reaction or expressing a reporter.To play this with E.coli we need first of all non mine cells expressing a neutral reporter. We also choose to use quorum sensing for the bacteria close to a mine cell to know about how many mines are close to our cell. For the mine cell we will use a second colony expressing a different reporter obviously. The non mine cells and mine neighbouring cells are the same colony an the expression of the different reporters will be regulated by a band-pass filter for quorum sensing<br>To play in a comfortable way the substrates will be mixed in one solution.<br>Finally for the flagging option a constitutive expressed reporter is used with a separate substrate.<br><br> Now you're ready to sweep baby !<br>But let's have a closer look...</div>
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<p align="justify">Inspired by the computer game Minesweeper, we aspire to incorporate all the same features and rules in the biological version. To replicate the "mouse click"  in the computer game, you can add a substrate to the colony of your choice which leads to a colorful enzyme-susbtrate reaction. The agar mine field consists of colonies which can be one of the following:
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<br><br><b>a non-mine colony</b>, which will display the "safe colour" when played
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<br><b>a non-mine colony located close to one or more mines</b>, which on addition of a multi-substrate reveals the number of mines in the vicinity of this colony  
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<br><b>a mine colony</b>, which when played reveals the mine color and the game is over
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<br><br>You also have the option to flag a mine - if you are certain that a colony is a mine, you can flag it using a second substrate.</p>
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<div style="position:relative;top:align;padding:10px"><h1><b>The set up</b></h1></div>
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<div style="position:relative;top:-400px;padding:10px;width:auto;height:auto;font-size:18px;color:white">Set up description</div>
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<div style="position:relative;top:align;padding:10px"><h1><b>Mine cells / Sender cells</b></h1></div>
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<div style="position:relative;top:align;padding:10px"><h1><b>Non mine cells neighbouring mine cells</b></h1></div>
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<div style="position:relative;right:-800px;padding:10px">[[Image:Lowmineconc.png|400px]]</div>
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<div style="position:relative;top:-260px;padding:10px;width:auto;height:auto;font-size:18px;color:white">Description of receiver cell response to low AHL concentration</div>
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<div style="position:relative;right:-700px;padding:15px">[[Image:highmineconc.png|500px]]</div>
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<div style="position:relative;top:-260px;padding:15px;width:auto;height:auto;font-size:18px;color:white">Description of receiver cell response to high AHL concentration</div>
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<div style="position:relative;top:align;padding:10px"><h1><b>Non mine cells</b></h1></div>
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<h1><b>Experiments</b></h1>
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<h1><b>Results</b></h1>
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Latest revision as of 10:05, 3 October 2013

Header2.png
80px-Eth igem logo.png

Information processing

Each minesweeper square in the computer game corresponds to a bacterial colony on the agar mine-field. We have two bacterial strains: 1. the mine strain with the sender cells and 2. the non-mine strain with the receiver cells. The cells communicate through diffusion of OHHL and change color to give the player information in order to logically carry out the next move in the game. The colonies remain white as seen on the agar plate until any substrate is added. The left and the right click of the mouse is simulated with the addition of the multi-substrate mix and the single substrate.

Figure 1: Signal transduction from secreted signaling molecule to colorimetric response.


The biology is explained here. The sender colony secretes the quorum sensing molecule 3-oxo-N-hexanoyl-L-homoserine lactone (OHHL) that diffuses through the agar to the surrounding cells. The receiver cells passively take up the OHHL by diffusion where the signaling molecule forms a complex with the inactive LuxR to activate it. The information is translated via mutated pLuxR promoters of different OHHL affinities which leads to the secretion of different hydrolases. Within minutes after the addition of substrate a change in color indicates the identity of the played colony and number of surrounding mine colonies.

If we located bacterial colonies in the place of squares like in the traditional game, the colonies placed in the corners would be further away compared to the colonies along the edges. We decided on a hexagonal honeycomb-like pattern, where colonies are placed at all edges of the hexagon except from the center. In this set-up the number of mine colonies restricted is to only one, two or three that can surround a non-mine colony. This also facilitates the selection of suitable reporter enzymes. To plate the field, liquid cultures of mine and non-mine cells are grown to an OD600 of 0.5, then, using a pipette, 1.5μl of liquid culture are placed according to the grid.


How is Colisweeper played ?

Figure 2: Project description

Inspired by the computer game Minesweeper, we aspire to incorporate all the same features and rules in the biological version. To replicate the "mouse click" in the computer game, you can add a substrate to the colony of your choice which leads to a colorful enzyme-susbtrate reaction. The agar mine field consists of colonies which can be one of the following:

a non-mine colony, which will display the "safe colour" when played
a non-mine colony located close to one or more mines, which on addition of a multi-substrate reveals the number of mines in the vicinity of this colony
a mine colony, which when played reveals the mine color and the game is over

You also have the option to flag a mine - if you are certain that a colony is a mine, you can flag it using a second substrate.