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Project: Comput-E.coli

Imagine producing a complete, biomaterial structure (say a simple cube or even a complex dodecahedron made of bioplastic) simply by inputing as little as a single signal to a single cell. What about allowing an entire lawn of bacteria to compute, in tandem, a complex mathematical problem? Cellular computation can achieve this and more. Our ultimate aim is to achieve universally computational cells through the exploitation of pattern formation to generate biological cellular automata. To achieve this we envision a ring of N colonies of E. coli, where each colony consists of clones of one of three strains of genetically modified E. coli, realizing three versions of the same circuit. The three strains will implement the same logical functionality but will have different input/output interfaces. Every colony will be connected to its immediate right and left neighbors, only. A colony will process its inputs (two inputs from its neighbors plus its own current state) to decide what its next state will be, after (and only after) the application of a global clock. The colonies will exhibit their collective state by each expressing (or not) an observable gene product (e.g. green fluorescent protein or GFP). To achieve this, we are developing two novel systems. The first will allow for an expedient, reliable means of processing environmental information through the use of Acyl-homoserine lactones (AHLs) and ribozymes. This logic circuit will be fast, reliable and, importantly, highly compact. The second system will allow an entire lawn of cells to autonomously synchronize the expression of their respective circuits through an intercellular communication mechanism used ubiquitously in plants - Ethylene gas synthesis and its perception. This whole construction is, in effect, a synchronous ring of cellular automata implemented as a ring of communicating colonies of three new strains of E. coli. It is an irony that cellular automata, a computational construct originally inspired by living cells, will now be realized in living cells.

The project can be divided into three main components: