Synthetic multicellular oscillatory systems: Controlling protein dynamics with genetic circuits

Physica Scripta

Volumn 84, Issue 4, 2011, Pages

  Koseska, Aneta ^a   Volkov, Evgenii ^b   Kurths, Jürgen ^c,d,e  

^a UNIVERSITY OF POTSDAM   (Germany)

^b LEBEDEV PHYSICAL INSTITUTE   (Russian Federation)

^c HUMBOLDT UNIVERSITY   (Germany)

^d POTSDAM INSTITUTE FOR CLIMATE IMPACT RESEARCH   (Germany)

^e UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICAL BEHAVIORS; GENETIC CIRCUITS; INTERCELLULAR COMMUNICATIONS; OSCILLATORY SYSTEM; PROGRAMMABLE MATTER; PROTEIN DYNAMICS; STOCHASTICITY; SYNTHETIC BIOLOGY;

BIOLOGY; DYNAMICS;

PROTEINS;

EID: 80053321531     PISSN: 00318949     EISSN: 14024896     Source Type: Journal    
DOI: 10.1088/0031-8949/84/04/045007     Document Type: Article

References (52)

1. Anderson J, Clarke E, Arkin A and Voigt C 2006 Environmentally controlled invasion of cancer cells by engineered bacteria J. Mol. Biol. 355 619-27 (Pubitemid 41817623)
2. Atay F 2003a Distributed delays facilitate amplitude death of coupled oscillators Physica D 91 094101
3. Atay F 2003b Total and partial amplitude death in networks of diffusively coupled oscillators Physica D 183 1-18
4. Atkinson M, Savageau M, Myers J and Ninfa A 2003 Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli Cell 113 597-607 (Pubitemid 36694185)
5. Bar-Eli K 1985 On the stability of coupled chemical oscillators Physica D 14 242-52
6. Basu S, Mehreja R, Thiberge S, Chen M and Weiss R 2004 Spatiotemporal control of gene expression with pulse-generating network Proc. Natl Acad. Sci. USA 101 6355-60 (Pubitemid 38585978)
7. Crowley M and Epstein I 1989 Experimental and theoretical studies of a coupled chemical oscillator: phase death, multistability and in-phase and out-of-phase entrainment J. Phys. Chem 93 2496-502
8. Danino T, Mondragón-Palomino O, Tsimring L and Hasty J 2010 A synchronized quorum of genetic clocks Nature 463 326-30
9. Dolnik M and Marek M 1988 Extinction of oscillations in forced and coupled reaction cells J. Phys. Chem. 92 2452-5
10. Elowitz M and Leibler S 2000 A synthetic oscillatory network of transcriptional regulators Nature 403 335-8 (Pubitemid 30062393)
11. Elowitz M, Levine A, Siggia E and Swain P 2002 Stochastic gene expression in a single cell Science 297 1183-6 (Pubitemid 36193353)
12. Epstein I and Golubitsky M 1993 Symmetric patterns in linear arrays of coupled cells Chaos 3 1-5
13. Fuqua C and Greenberg P 2002 Listening in on bacteria: acyl-homoserine lactone signalling Nature Rev. Mol. Cell Biol. 3 685-95 (Pubitemid 34987789)
14. García-Ojalvo J, Elowitz M and Strogatz S 2004 Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing Proc. Natl Acad. Sci. USA 101 10955-60 (Pubitemid 38989566)
15. García-Ojalvo J and Sancho J 1999 Noise in Spatially Extended Systems 1st edn (New York: Springer)
16. Gardner T, Cantor C and Collins J 2000 Construction of genetic toggle switch in Escherichia coli Nature 403 339-42
17. Golomb D, Hansel D, Shraiman B and Sompolinsky H 1992 Clustering in globally coupled phase oscillators Phys. Rev. A 45 3516-30
18. Gonze D, Bernard S, Waltermann C, Kramer A and Herzel H 2005 Spontaneous synchronization of coupled circadian oscillators Biophys. J. 89 120-9 (Pubitemid 41098269)
19. Ham T, Lee S, Keasling J and Arkin A 2008 Design and construction of a double inversion recombination switch for heritable sequential genetic memory PLoS ONE 3 e2815
20. Herrero R, Figueras M, Rius J, Pi F and Orriols G 2000 Experimental observation of the amplitude death effect in two coupled nonlinear oscillators Phys. Rev. Lett. 84 5312-5
21. Hooshangi S, Thiberge S and Weiss R 2005 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Proc. Natl Acad. Sci. USA 102 3581-6 (Pubitemid 40354655)
22. Huang G, Mei Y F, Thurmer D J, Coric E and Schmidt O G 2009 Rolled-up transparent microtubes as two-dimensionally confined culture scaffolds of individual yeast cells Lab Chip 9 263-8
23. Klevecz R 1976 Quantized generation time in mammalian cells as an expression of the cellular clock Proc. Natl Acad. Sci. USA 73 4012-6
24. Kobayashi H, Kaern M, Araki M, Chung K, Gardner T, Cantor C and Collins J 2004 Programmable cells: interfacing natural and engineered gene networks Proc. Natl Acad. Sci. USA 101 8414-9 (Pubitemid 38736589)
25. Koseska A and Kurths J 2010 Topological structures enhance the presence of dynamical regimes in synthetic networks Chaos 20 045111
26. Koseska A, Ullner E, Volkov E, Kurths J and García-Ojalvo J 2010 Cooperative differentiation through clustering in multicellular populations J. Theor. Biol. 263 189-202
27. Koseska A, Volkov E and Kurths J 2009 Detuning-dependent dominance of oscillation death in globally coupled synthetic genetic oscillators Europhys. Lett. 85 28002
28. Koseska A, Volkov E, Zaikin A and Kurths J 2007a Inherent multistability in arrays of autoinducer coupled genetic oscillators Phys. Rev. E 75 031916
29. Koseska A, Volkov E, Zaikin A and Kurths J 2007b Quantized cycling time in artificial gene networks induced by noise and intercell communication Phys. Rev. E 76 020901(R)
30. Kramer B E A 2004 An engineered epigenetic transgene switch in mammalian cells Nature Biotech. 22 867-70
31. Kuznetsov A, Kaern M and Kopell N 2004 Synchrony in a population of hysteresis-based genetic oscillators SIAM J. Appl. Math. 65 392-425
32. Lloyd D and Volkov E 1990 Quantized cell cycle times interaction between a relaxation oscillator and ultradian clock pulse BioSystems 23 305-10 (Pubitemid 20074751)
33. Locke J, Millar A and Turner M 2005 Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana J. Theor. Biol. 234 383-93 (Pubitemid 40387462)
34. McMillen D, Kopell N, Hasty J and Collins J 2002 Synchronizing genetic relaxation oscillators by intercell signaling Proc. Natl Acad. Sci. USA 99 679-84 (Pubitemid 34110437)
35. Mirollo R and Strogatz S 1990 Amplitude death in an array of limit-cycle oscillators J. Stat. Phys. 60 245-62
36. Okuda K 1993 Variety and generality of clustering in globally coupled oscillators Physica D 63 424-36
37. Paulsson J and Ehrenberg M 2001 Noise in a minimal regulatory network: plasmid copy number control Q. Rev. Biophys. 34 1-59 (Pubitemid 32510203)
38. Prigogine I and Lefever R 1968 Symmetry breaking instabilities in dissipative systems J. Chem. Phys. 48 1695-701
39. Purnick P and Weiss R 2009 The second wave of synthetic biology: from modules to systems Nature Rev. 10 410-22
40. Rabinovich M, Varona P, Torres J, Huerta R and Abarbanel H 1999 Slow dynamics and regularization phenomena in ensembles of chaotic neurons Physica A 263 405-14 (Pubitemid 129669160)
41. Ramana Reddy D V, Sen A and Johnston G L 1998 Time delay induced death in coupled limit cycle oscillators Phys. Rev. Lett. 80 5109-12 (Pubitemid 128622148)
42. Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R and Benenson Y 2007 A universal RNAi-based logic evaluator that operates in mammalian cells Nature Biotech. 25 795-801 (Pubitemid 47052185)
43. Shpiro A, Curtu R, Rinzel J and Rubin N 2007 Dynamical characteristics common to neuronal competition models J. Neurophysiol. 97 462-73 (Pubitemid 46143370)
44. Stricker J E A 2008 A fast, robust and tunable synthetic genetic oscillator Nature 456 516-9
45. Swain P, Elowitz M and Siggia E 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression Proc. Natl Acad. Sci. USA 99 12795-800
46. Tigges M, Marquez-Lago T, Stelling J and Fussenegger M 2009 A tunable synthetic mammalian oscillator Nature 457 309-12
47. Toiya M, Vanag V and Epstein I 2008 Diffusively coupled chemical oscillators in a microfluidic assembly. Angew. Chem. Int. Edn Engl. 47 7753-5
48. Tsaneva-Atanasova K, Zimliki C, Bertram R and Sherman A 2006 Diffusion of calcium and metabolites in pancreatic islets: killing oscillations with a pitchfork Biophys. J. 90 3434-46
49. Ullner E, Koseska A, Kurths J, Volkov E, Kantz H and García-Ojalvo J 2008 Multistability of synthetic genetic networks with repressive cell-to-cell communication Phys. Rev. E 78 031904
50. Ullner E, Zaikin A, Volkov E and 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
51. Yang L, Dolnik M, Zhabotinsky A and Epstein I 2002 Spatial resonances and superposition patterns in a reaction-diffusion model with interacting Turing modes Phys. Rev. Lett. 88 208303
52. Zhai Y, Kiss I and Hudson J 2004 Amplitude death through a Hopf bifurcation in coupled electrochemical oscillators: experiments and simulations Phys. Rev. E 69 026208