Robust multicellular computing using genetically encoded NOR gates and chemical 'wiresg'

Nature

Volumn 469, Issue 7329, 2011, Pages 212-215

  Tamsir, Alvin ^a   Tabor, Jeffrey J ^b   Voigt, Christopher A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR; YELLOW FLUORESCENT PROTEIN;

BIOFILM; CELL ORGANELLE; COLIFORM BACTERIUM; COMPUTER SIMULATION; GENETIC ANALYSIS; GENETICALLY MODIFIED ORGANISM; MOLECULAR ANALYSIS; SPATIAL ANALYSIS;

ARTICLE; BACTERIUM CULTURE; CELL; CELL COMMUNICATION; COMPUTER PROGRAM; CULTURE MEDIUM; DEVICE; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE; LOGIC; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; QUORUM SENSING;

BIOENGINEERING; CELL COMPARTMENTATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; LOGIC; PROMOTER REGIONS, GENETIC; QUORUM SENSING; SYSTEMS BIOLOGY;

ESCHERICHIA COLI;

EID: 78651397316     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09565     Document Type: Article

References (30)

1. Neumann, J. V. The Generaland Logical Theory of Automata(Wiley, 1951).
2. Turing, A. M. Thechemical basisofmorphogenesis. 1953. Bull. Math. Biol. 52, 119-152 (discussion), 153-197 (1990).
3. Wolfram, S. A New Kind of Science 23-113(Wolfram Media, 2002).
4. Brenner, K., Karig, D. K., Weiss, R. & Arnold, F. H. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. Proc. Natl Acad. Sci. USA 104, 17300-17304 (2007).
5. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellularsystemforprogrammed patternformation. Nature434, 1130-1134 (2005).
6. Li, F., Long, T., Lu, Y., Ouyang, Q. & Tang, C. Theyeastcell- cyclenetwork is robustly designed. Proc. NatlAcad. Sci. USA 101, 4781-4786 (2004).
7. Niklas, K. J. The bio-logicand machineryof plant morphogenesis. Am. J. Bot. 90, 515-525 (2003).
8. Morris, M. K., Saez-Rodriguez, J., Sorger, P. K. & Lauffenburger, D. A. Logic-based models for the analysis of cell signaling networks. Biochemistry 49, 3216-3224 (2010).
9. Mayo, A. E., Setty, Y., Shavit, S., Zaslaver, A. & Alon, U. Plasticityofthecis-regulatory nput function of a gene. PLoS Biol. 4, e45 (2006).
10. Anderson, J. C., Voigt, C. A. & Arkin, A. P. Environmental signal integration bya modular AND gate. Mol. Syst. Biol. 3, 133 (2007).
11. Guet, C. C., Elowitz, M. B., Hsing, W. & Leibler, S. Combinatorialsynthesisofgenetic networks. Science 296, 1466-1470 (2002).
12. Rinaudo, K. et al. A universal RNAi-based logicevaluatorthatoperates in mammalian cells. Nature Biotechnol. 25, 795-801 (2007).
13. Weber, W. et al. Asynthetic mammalian genecircuit revealsantituberculosis compounds. Proc. NatlAcad. Sci. USA 105, 9994-9998 (2008).
14. Ellis, T., Wang, X. & Collins, J. J. Diversity-based, model-guidedconstruction of syntheticgenenetworkswith predictedfunctions. Nature Biotechnol. 27, 465-471 (2009).
15. Lou, C. et al. Synthesizinga novelgeneticsequential logiccircuit:a push-on push-off switch. Mol. Syst Biol. 6, 350 (2010).
16. Tabor, J. J. et al. Asyntheticgeneticedgedetection program. Cell137, 1272-1281 (2009).
17. Friedland, A. E. et al. Syntheticgenenetworksthatcount. Science324, 1199-1202 (2009).
18. Tan, C., Marguet, P. & You, L Emergentbistabilitybyagrowth- modulatingpositive feedback circuit. Nature Chem. Biol. 5, 842-848 (2009).
19. Scharle, T. W. Axiomatization of propositional calculuswith Shefferfunctors. Notre Dame J. Formal Logic 6, 209-217 (1965).
20. Yokobayashi, Y., Weiss, R. & Arnold, F. H. Directed evolution of ageneticcircuit Proc. NatlAcad. Sci. USA99, 16587-16591 (2002).
21. Sneppen, K. et al. A mathematical model fortranscriptional interference by RNA polymerase traffic in Escherichia coli. J. Mol. Biol. 346, 399-409 (2005).
22. Pesci, E. C., Pearson, J. P., Seed, P. C. & Iglewski, B. H. Regulation of lasand rh quorum sensing in Pseudomonasaeruginosa. J. Bacteriol. 179, 3127-3132 (1997).
23. Karig, D. & Weiss, R. Signal- amplifyinggeneticcircuitenablesinvivoobservationof weak promoter activation in the Rhl quorum sensing system. Biotechnol. Bioeng. 89, 709-718 (2005).
24. Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B. Gene regulation at the single-cell level. Science 307, 1962-1965 (2005).
25. Pedraza, J. M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965-1969 (2005).
26. Katz, R. H. & Borriello, G. ContemporaryLogicDesign 141-146 (Prentice Hall, 1994).
27. Danino, T., Mondragon-Palomino, O., Tsimring, L & Hasty, J. Asynchronized quorum ofgeneticclocks. Nature 463, 326-330(2010).
28. Clancy, K. & Voigt, C. A. Programmingcells: towardsan automated 'genetic compiler'. Curr. Opin. Biotechnol. 21, 572-581 (2010).
29. Ilachinski, A. Cellular Automata: A Discrete Universe 1-18(World Scientific, 2001).
30. Raju, B. S. & Mullick, S. K. Programmablecellulararrays. Int. J. Control14, 1041-1061 (1971).