Biological computation in yeast

Ongoing efforts within synthetic biology have been directed towards the building of artificial computational devices using engineered biological units as basic building blocks. Such efforts, are limited by the wiring problem: each connection of the basic computational units (logic gates), must be implemented by a different molecule. We propose a non-standard way of implementing logic computations that reduces wiring requirements thanks to a multicellular design with distribution of the output among cells. Practical implementations are presented using a library of engineered yeast cells, in which each genetic construct defines a logic function. This shows the great potential for re-utilization of genetic elements to build distinct cells. The cells are combined in multiple ways to easyly build diferent complex synthetic circuits. In the first manuscript, we proposed a multi-layer design. The engineered cells can perform the IDENTITY, NOT, AND and N-IMPLIES logics and are able to communicate with two different wiring molecules. As a proof of principle, we have implemented many logic gates and more complex circuits such as a 1--bit adder with carry. In the second manuscript, a general architecture to engineer cellular consortia that is independent of the circuit’s complexity is proposed. This design involves cells, performing IDENTITY and NOT logics, organized in two layers. The key aspect of the architecture is the spatial insulation. That design, permits implementation of complex logical functions, such as 4to1—multiplexer only with one wire. ; En el camp de la biologia sintètica els esforços s'han dirigit a construir dispositius computacionals artificials connectant les unitats lògiques bàsiques (portes lògiques). Aquests esforços, estan limitats per l'anomenat “wiring problem”: cada connexió entre les unitats lògiques s'ha d'implementar amb una molècula diferent. En aquesta tesi es mostra una manera no-estàndard d'implementar funcions lògiques que redueix el nombre de cables necessaris gràcies a un disseny ...