Electronic Implementation of a Repressilator with Quorum Sensing Feedback

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Hellen, Edward H ^a   Dana, Syamal K ^b   Zhurov, Boris ^c   Volkov, Evgeny ^c  

^a UNIVERSITY OF NORTH CAROLINA AT GREENSBORO   (United States)

^b INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^c LEBEDEV PHYSICAL INSTITUTE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEIN A; PROTEIN C;

ARTICLE; COMPETITION; OSCILLATION; PROTEIN SYNTHESIS; QUORUM SENSING; SIMULATION; STEADY STATE;

BIOMIMETICS; ELECTRICAL EQUIPMENT AND SUPPLIES; FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; QUORUM SENSING;

EID: 84877024634     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062997     Document Type: Article

References (31)

1. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapaman &Hall/CRC, UK.
2. Hasty J, McMillen D, Collins JJ, (2002) Engineered Gene Circuits. Nature 420: 224.
3. Elowitz M, Lim WA, (2010) Build life to understand it. Nature 468: 889-890.
4. Elowitz MB, Leibler S, (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335.
5. Kobayashi Y, Shibata T, Kuramoto Y, Mikhailov AS, (2010) Evolutionary design of oscillatory genetic networks. Eur. Phys. J. B 76: 167-178.
6. Kobayashi Y, Shibata T, Kuramoto Y, Mikhailov AS, (2011) Robust network clocks: Design of genetic oscillators as a complex combinatorial optimization problem. Phys. Rev. E 83: 060901 (R).
7. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, et al. (2012) A sensing array of radically coupled genetic'biopixels'. Nature 481: 39-44.
8. Wagemakers A, Buldú JM, García-Ojalvo J, Sanjuán MAF, (2006) Synchronization of electronic genetic networks. Chaos 16: 013127.
9. Smith H, (1987) Oscillations and multiple steady states in a cyclic gene model with repression. J. Math. Biol. 25: 169-190.
10. Müller S, Hofbauer J, Endler L, Flamm C, Widder S, et al. (2006) A generalized model of the repressilator. J. Math. Biol. 53: 905-937.
11. Tuttle LM, Salis H, Tomshine J, Kaznesis YN, (2005) Model-Driven designs of an oscillatory gene network. Biophys. J. 89: 3873.
12. Bennet MR, Volfson D, Tsimring L, Hasty J, (2007) Transient dynamics of genetic regulatory networks. Biophys. J. 92: 3501.
13. Strelkowa N, Barahona M, (2010) Switchable genetic oscillator operating in quasi-stable mode. J. Royal Soc. Interface 7: 1071.
14. Buse O, Perez R, Kuznetsov A, (2010) Dynamical properties of the repressilator model. Phys. Rev. E 81: 066206.
15. Ullner E, Zaikin A, Volkov EI, García-Ojalvo J, (2007) Multistability and Clustering in a Population of Synthetic Genetic Oscillators via Phase-Repulsive Cell-to-Cell Communication. Phys. Rev. Lett. 99: 148103.
16. Koseska A, Ullner E, Volkov E, Kurths J, García-Ojalvo J, (2010) Cooperative differentiation through clustering in multicellular populations. J. Theor. Biol. 263: 189-202.
17. Potapov I, Volkov E, Kuznetsov A, (2011) Dynamics of coupled repressilators: the role of mRNA kinetics and transcription cooperativity. Phys. Rev. E 83: 031901.
18. Lerat E, Moran NA, (2004) Evolutionary history of quorum-sensing systems in bacteria. Molecular Biology and Evolution 21: 903.
19. Goryachev AB, (2011) Understanding Bacterial Cell-Cell Communication with Computational Modeling. Chem. Rev. 111: 238-250.
20. You L, Cox RS, Weiss R, Arnold FH, (2004) Programmed population control by cell-cell communication and regulated killing. Nature 428: 868-871.
21. Liu C, Fu X, Liu L, Ren X, Chau CKL, et al. (2011) Sequential establishment of stripe patterns in an expanding cell population. Science 334: 238-241.
22. McMillen D, Kopell N, Hasty J, Collins JJ, (2002) Synchronizing genetic relaxation oscillators by intercell signaling. PNAS U.S.A. 99: 679.
23. García-Ojalvo J, Elowitz M, Strogatz SH, (2004) Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. PNAS U.S.A. 101: 10955.
24. Kuznetsov A, Kaern M, Kopell N, (2004) Synchrony in a population of hysteresis-based genetic oscillators. SIAM, J. Appl. Math. 65: 392-425.
25. Danino T, Mondragón-Palomino O, Tsimring L, Hasty J, (2010) A synchronized quorum of genetic clocks. Nature 463: 326-330.
26. Potapov I, Zhurov B, Volkov E, (2012) "Quorum sensing" generated multistability and chaos in a synthetic genetic oscillator. Chaos 22: 023117.
27. Ermentrout B (2002) Simulating, analyzing and animating dynamical systems: a guide to XPPAUTO for researchers and students. SIAM Books, Philadelphia, PA.
28. Hellen EH, Volkov E, Kurths J, Dana SK, (2011) An electronic analog of synthetic genetic networks. PLoS ONE 6(8): e23286.
29. Hellen EH, Dana SK, Kurths J, Sinha S (2012) Noise-aided Logic in an Electronic Analog of Synthetic Genetic Networks. arXiv: 1212.4470.
30. Wiesenfeld K, McNamara B, (1986) Small-signal amplification in bifurcating dynamical systems. Phys. Rev. A 33: 629.
31. Tyson JJ, Novák B, (2010) Functional Motifs in Biochemical Reaction Networks. Annu. Rev. Phys. Chem. 61: 219-240.