Title |
A Formalized Design Process for Bacterial Consortia That Perform Logic Computing
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Published in |
PLOS ONE, February 2013
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DOI | 10.1371/journal.pone.0057482 |
Pubmed ID | |
Authors |
Weiyue Ji, Handuo Shi, Haoqian Zhang, Rui Sun, Jingyi Xi, Dingqiao Wen, Jingchen Feng, Yiwei Chen, Xiao Qin, Yanrong Ma, Wenhan Luo, Linna Deng, Hanchi Lin, Ruofan Yu, Qi Ouyang |
Abstract |
The concept of microbial consortia is of great attractiveness in synthetic biology. Despite of all its benefits, however, there are still problems remaining for large-scaled multicellular gene circuits, for example, how to reliably design and distribute the circuits in microbial consortia with limited number of well-behaved genetic modules and wiring quorum-sensing molecules. To manage such problem, here we propose a formalized design process: (i) determine the basic logic units (AND, OR and NOT gates) based on mathematical and biological considerations; (ii) establish rules to search and distribute simplest logic design; (iii) assemble assigned basic logic units in each logic operating cell; and (iv) fine-tune the circuiting interface between logic operators. We in silico analyzed gene circuits with inputs ranging from two to four, comparing our method with the pre-existing ones. Results showed that this formalized design process is more feasible concerning numbers of cells required. Furthermore, as a proof of principle, an Escherichia coli consortium that performs XOR function, a typical complex computing operation, was designed. The construction and characterization of logic operators is independent of "wiring" and provides predictive information for fine-tuning. This formalized design process provides guidance for the design of microbial consortia that perform distributed biological computation. |
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