A Synthetic Multicellular Memory Device

ACS Synthetic Biology

Volumn 5, Issue 8, 2016, Pages 862-873

  Urrios, Arturo ^a   Macia, Javier ^a   Manzoni, Romilde ^a   Conde, Núria ^a   Bonforti, Adriano ^a,c   De Nadal, Eulàlia ^a   Posas, Francesc ^a   Solé, Ricard ^a,b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b SANTA FE INSTITUTE   (United States)

^c Centre per A la Innovació de la Diabetis Infantil Sant Joan de Déu CIDI   (Spain)

Author keywords

biological computation; logic circuits; memory devices; multicellular consortia; synthetic biology

Indexed keywords

PHEROMONE; BIOMIMETIC MATERIAL;

ARTICLE; BIOENGINEERING; COCULTURE; DEVICES; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY; SYNTHETIC MULTICELLULAR MEMORY DEVICE; YEAST CELL; MEMORY; METABOLISM; PHYSIOLOGY; PROCEDURES; YEAST;

BIOMIMETIC MATERIALS; EQUIPMENT AND SUPPLIES; MEMORY; PHEROMONES; SYNTHETIC BIOLOGY; YEASTS;

EID: 84983319518     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00252     Document Type: Article

References (39)

1. Jablonka, E. and Lamb, M. J. (2006) The evolution of information in the major transitions J. Theor. Biol. 239, 236-246 10.1016/j.jtbi.2005.08.038
2. Burrill, D. R. and Silver, P. A. (2010) Making cellular memories Cell 140, 13-18 10.1016/j.cell.2009.12.034
3. Ajo-Franklin, C. M., Drubin, D. A., Eskin, J. A., Gee, E. P. S., Landgraf, D., Phillips, I., and Silver, P. A. (2007) Rational design of memory in eukaryotic cells Genes Dev. 21, 2271-2276 10.1101/gad.1586107
4. Rodrigo, G. and Jaramillo, A. (2007) Computational design of digital and memory biological devices Syst. Synth. Biol. 1, 183-195 10.1007/s11693-008-9017-0
5. Purnick, P. E. M. and Weiss, R. (2009) The second wave of synthetic biology: from modules to systems Nat. Rev. Mol. Cell Biol. 10, 410-422 10.1038/nrm2698
6. Siuti, P., Yazbek, J., and Lu, T. K. (2013) Synthetic circuits integrating logic and memory in living cells Nat. Biotechnol. 31, 448-453 10.1038/nbt.2510
7. Xiong, W. and Ferrell, J. E. (2003) A positive-feedback-based bistable 'memory module' that governs a cell fate decision Nature 426, 460-465 10.1038/nature02089
8. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339-342 10.1038/35002131
9. Fernando, C. T., Liekens, A. M., Bingle, L. E., Beck, C., Lenser, T., Stekel, D. J., and Rowe, J. E. (2009) Molecular circuits for associative learning in single-celled organisms J. R. Soc., Interface 6, 463-469 10.1098/rsif.2008.0344
10. Sorek, M., Balaban, N. Q., and Loewenstein, Y. (2013) Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks PLoS Comput. Biol. 9, e1003179 10.1371/journal.pcbi.1003179
11. Shah, N. J. and Sarkar, C. A. (2011) Robust networks technologies for generating switch-like cellular responses PLoS Comput. Biol. 7, e1002085 10.1371/journal.pcbi.1002085
12. Kwok, R. (2010) Five hard truths for synthetic biology Nature 463, 288-290 10.1038/463288a
13. Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellén, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., and Solé, R. (2011) Distributed biological computation with multicellular engineered networks Nature 469, 207-211 10.1038/nature09679
14. Macia, J., Posas, F., and Solé, R. (2012) Distributed computation: the new wave of synthetic biology devices Trends Biotechnol. 30, 342-349 10.1016/j.tibtech.2012.03.006
15. Solé, R. and Macia, J. (2013) Expanding the landscape of biological computation with synthetic multicellular consortia Nat. Comput. 12, 485-497 10.1007/s11047-013-9380-y
16. Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical wires Nature 469, 212-215 10.1038/nature09565
17. Sardanyes, J., Bonforti, A., Conde, N., Solé, R., and Macía, J. (2015) Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia Front. Physiol. 6, 281 10.3389/fphys.2015.00281
18. Hoffman-Sommer, M., Supady, A., and Klipp, E. (2012) Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates Front. Physiol. 3, 287 10.3389/fphys.2012.00287
19. Ingalls, B. P. (2013) Mathematical Modelling in Systems Biology, MIT Press, Cambridge, MA.
20. Yi, T. M., Kitano, H., and Simon, M. I. (2003) A quantitative characterization of the yeast heterotrimeric G protein cycle Proc. Natl. Acad. Sci. U. S. A. 100, 10764-10769 10.1073/pnas.1834247100
21. Strogatz, S. (1994) Nonlinear Dynamics and Chaos, Addison Wesley, New York.
22. Bashor, C. L., Horwitz, A. A., Peisajovich, S. G., and Lim, W. A. (2010) Rewiring Cells: Synthetic biology as a tool to interrogate the organizational principles of living systems Annu. Rev. Biophys. 39, 515-537 10.1146/annurev.biophys.050708.133652
23. Weber, W. and Fussenegger, M. (2012) Emerging biomedical applications of synthetic biology Nat. Rev. Genet. 13, 21-35 10.1038/nrg3094
24. Ruder, W. C., Lu, T., and Collins, J. J. (2011) Synthetic Biology Moving into the Clinic Science 333, 1248-1252 10.1126/science.1206843
25. Solé, R. V., Munteanu, A., Rodriguez-Caso, C., and Macia, J. (2007) Synthetic protocell biology. From reproduction to computation Philos. Trans. R. Soc., B 362, 1727-1739 10.1098/rstb.2007.2065
26. Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T. S., Cantor, C. R., and Collins, J. J. (2004) Programmable cells: Interfacing natural and engineered gene networks Proc. Natl. Acad. Sci. U. S. A. 101, 8414-8419 10.1073/pnas.0402940101
27. Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells Biotechnol. Bioeng. 87, 478-484 10.1002/bit.20142
28. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression Nature 429, 423-429 10.1038/nature02551
29. Tan, C. M., Song, H., Niemi, J., and You, L. C. (2007) A synthetic biology challenge: making cells compute Mol. BioSyst. 3, 343-353 10.1039/b618473c
30. Benenson, Y. (2009) Biocomputers: from test tubes to live cells Mol. BioSyst. 5, 675-685 10.1039/b902484k
31. Goni-Moreno, A., Amos, M., and de la Cruz, F. (2013) Multicellular Computing Using Conjugation for Wiring PLoS One 8, e65986 10.1371/journal.pone.0065986
32. Bernstein, H. C. and Carlson, R. P. (2012) Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems Comput. Struct. Biotechnol. J. 3, 1-8 10.5936/csbj.201210017
33. Macia, J., Manzoni, R., Conde, N., Urrios, A., de Nadal, E., Solé, R., and Posas, F. (2016) Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia PLoS Comput. Biol. 12, e1004685 10.1371/journal.pcbi.1004685
34. Ruder, W. C., Lu, T., and Collins, J. J. (2011) Synthetic biology moving into the clinic Science 333, 1248-1252 10.1126/science.1206843
35. Pepper, J. W. and Rosenfeld, S. (2012) The emerging medical ecology of the human gut micro biome Trends Ecol. Evol. 27, 381-384 10.1016/j.tree.2012.03.002
36. Solé, R., Montañez, R., and Duran-Nebreda, S. (2015) Synthetic circuit designs for earth terraformation Biol. Direct 10, 37 10.1186/s13062-015-0064-7
37. Solé, R. (2007) Scaling laws in the drier Nature 449, 151-153 10.1038/449151a
38. Solé, R. (2015) Bioengineering the biosphere? Ecol Complex. 22, 40-49 10.1016/j.ecocom.2015.01.005
39. Solé, R. (2016) Synthetic transitions: towards a new synthesis Philos. Trans. R. Soc., B 371, 20150438 10.1098/rstb.2015.0438