Team:ETH Zurich/project/infopro

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=== The goal: Emergence of patterns via information processing===
=== The goal: Emergence of patterns via information processing===
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We implement a cellular automaton with bacterial cells containing our logic circuitry. Each bacterial colony serves as a core, computing an XOR gate. First, a sensor device detects the input, ''N''-acyl homoserine lactones (AHL). Check the [http://2014.igem.org/Team:ETH_Zurich/project/background/biotools#Biological_Tools quorum sensing and integrases article] for more information. Then, the cell integrates this signal through a logic gate, performed by serine integrases by sensing on the protein level and acting on the DNA level. A necessary post-processing step allows then the production of a new AHL variant due to activated gene expression through the integrase. Meanwhile, green fluorescent protein (GFP) indicates the state of the colony and serves as a long-lasting visual read out. The produced AHL output-signal then propagates in a directed fashion through a [http://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic] grid to the next bacterial colony. This iterative process faces the challenges of leakiness, cross-talk, protein-level computation and exact diffusion steps. This information pathway is shown in figure 1.
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We implement a cellular automaton with bacterial cells containing our logic circuitry. Each bacterial colony serves as a core, computing an XOR gate. First, a sensor device detects the input, ''N''-acyl homoserine lactones (AHL). Check the [http://2014.igem.org/Team:ETH_Zurich/project/background/biotools#Biological_Tools quorum sensing and integrases article] for more information. Then, the cell integrates this signal through a logic gate, performed by serine integrases by sensing on the protein level and acting on the DNA level. A necessary post-processing step allows then the production of a new AHL variant due to activated gene expression through the integrase. Meanwhile, green fluorescent protein (GFP) indicates the state of the colony and serves as a long-lasting visual read out. The produced AHL output-signal then propagates in a directed fashion through a [http://2014.igem.org/Team:ETH_Zurich/lab/chip millifluidic] grid to the next bacterial colony. This iterative process faces the challenges of [http://2014.igem.org/Team:ETH_Zurich/expresults/rr#Riboregulators leakiness], crosstalk, protein-level computation and exact [http://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel diffusion] steps. This information pathway is shown in figure 1.
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[[File:ETH_Zurich2014_info_processing1.png|center|800px|thumb|'''Figure 1 The information pathway in the project Mosai''coli'' on a colony level.''' Each cell colony is part of a greater memory unit (left-hand side) and gets its input information from the neighboring colonies. The input is given in the form of two different AHLs, here named A and B. This information is then step-wise processed in each of the colonies: sensing - computing - producing - sending. The output molecules serve then as the input for the next colony (middle and left-hand side). This iterative process allows the information processing from the top row of the memory unit to the bottom by chemical wiring via diffusing signals and bio-computations inside of the colonies.]]
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[[File:ETH_Zurich2014_info_processing1.png|center|800px|thumb|'''Figure 1''' The information pathway in the project Mosai''coli'' on a colony level. Each cell colony is part of a greater memory unit (left-hand side) and gets its input information from the neighboring colonies. The input is given in the form of two different AHLs, here named A and B. This information is then step-wise processed in each of the colonies: sensing - computing - producing - sending. The output molecules serve then as the input for the next colony (middle and left-hand side). This iterative process allows the information processing from the top row of the memory unit to the bottom by chemical wiring via diffusing signals and bio-computations inside of the colonies.]]
=== The steps involved: From sensing to sending===
=== The steps involved: From sensing to sending===
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[[File:ETH_Zurich_Information_Processing_chip.png|center|600px|thumb|'''Figure 2 The information pathway in the project Mosai''coli'' on the chip level.''' After initializing the signal in the top row, it propagates through the wells chemically wired by directed diffusion. In each well, a bacterial colony has to be able to proceed in the information pathway: sensing, integrating (computing), producing and sending. These successive iterations leads to possible error propagation and robustness is one major issue of our system.]]
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[[File:ETH_Zurich_Information_Processing_chip.png|center|600px|thumb|'''Figure 2''' The information pathway in the project Mosai''coli'' on the chip level. After initializing the signal in the top row, it propagates through the wells chemically wired by directed diffusion. In each well, a bacterial colony has to be able to proceed in the information pathway: sensing, integrating (computing), producing and sending. These successive iterations leads to possible error propagation and robustness is one major issue of our system.]]
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Latest revision as of 03:38, 18 October 2014

iGEM ETH Zurich 2014