NONLINEAR DYNAMICS OF SYNTHETIC GENE REGULATORY CIRCUITS
Cite this article as:
Ivanchenko М. V., Kanakov О. I., Kotelnikov R. А., Krylov I. B. NONLINEAR DYNAMICS OF SYNTHETIC GENE REGULATORY CIRCUITS. Izvestiya VUZ. Applied Nonlinear Dynamics, 2013, vol. 21, iss. 4, pp. 52-134. DOI: https://doi.org/10.18500/0869-6632-2013-21-4-52-134
Built in a cell synthetic gene regulatory elements may function rather independently on the original natural system. Experimental and theoretical studies of small synthetic networks allow for a better understanding of fundamental dynamical mechanisms of gene regulation. This paper gives an introduction to the modern mathematical approaches and methods in this field, primarily in the framework of nonlinear dynamics.
1. Jacob F., Monod J. Genetic regulatory mechanisms in synthesis of proteins // J. Mol. Biol. 1961. Vol. 3. P. 318.
2. Hasty J., McMillen D., Collins J.J. Engineered gene circuits // Nature. 2002. Vol. 420. P. 224.
3. Nandagopal N., Elowitz M.B. Synthetic Biology: Integrated Gene Circuits // Science. 2011. Vol. 333. P. 1244.
4. Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks // Nat. Biotechnol. 2009. Vol. 27. P. 1139.
5. Ro D.K. et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast // Nature. 2006. Vol. 440. P. 940.
6. Lee S.K. et al. Metabolic engineering of microorganisms for biofuels production: From bugs to synthetic biology to fuels // Curr. Opin. Biotechnol. 2008. Vol. 19. P. 556.
7. Sayler G.S., Simpson M.L., Cox C.D. Emerging foundations: Nano-engineering and bio-microelectronics for environmental biotechnology // Curr. Opin. Microbiol. 2004. Vol. 7. P. 267.
8. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli // Nature. 2000. Vol. 403. P. 339.
9. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators // Nature. 2000. Vol. 403. P. 335.
10. Stricker J. et al. A fast, robust and tunable synthetic gene oscillator // Nature. 2008. Vol. 456. P. 516.
11. Friedland A.E. et al. Synthetic gene networks that count // Science. 2009. Vol. 324 P. 1199.
12. O’Brien E.L., van Itallie E., Bennett M.R. Modeling synthetic gene oscillators // Math. Biosciences. 2012. Vol. 236. P. 1.
13. Hill A.V. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves // J. Physiol. 1910. Vol. 40. No. vi-vii.
14. Elowitz M.B. et al. Stochastic gene expression in a single cell // Science. 2002. Vol. 297. P. 1183.
15. Gillespie D.T. Stochastic smulation of chemical kinetics // Annual Review of Physical Chemistry. 2007. Vol. 58. P. 35.
16. Bel G., Munsky M., Nemenman I. The simplicity of completion time distributions for common complex biochemical processes // Phys. Biol. 2010. Vol. 7. P. 016003.
17. Ishiura M. et al. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria // Science. 1998. Vol. 281. P. 1519.
18. Goodwin B.C. Oscillatory behavior in enzymatic control processes // Adv. Enzyme Regul. 1965. Vol. 3. P. 425.
19. Mather W. et al. Delay-induced degrade-and-fire oscillations in small genetic circuits // Phys. Rev. Lett. 2009. Vol. 102, P. 068105.
20. Johnson A.D. et al. Lambda Repressor and cro-components of an efficient molecular switch // Nature. 1981. Vol. 294. P. 217. 21. Nene N., Garcia-Ojalvo J., and Zaikin A. Speed-dependent cellular decision making in nonequilibrium genetic circuits // PLoS ONE. 2012. Vol. 7. P. e40085.
22. Huang S. et al. Bifurcation dynamics in lineage-commitment in bipotent progenitor cells // Dev. Biol. 2007. Vol. 305. P. 695.
23. Cohen M. et al. Dynamic filopodia transmit intermittent delta-notch signaling to drive pattern refinement during lateral inhibition // Dev. Cell. 2010. Vol. 19. P. 78.
24. Widschwendter M. et al. Epigenetic stem cell signature in cancer // Nat. Genet. 2007. Vol. 39. P. 157.
25. Bennett M.R. et al. Transient dynamics of genetic regulatory networks // Biophys. J. 2007. Vol. 92. P. 3501.
26. Buse O., Perez R., Kuznetsov A. Dynamical properties of the repressilator model // Phys. Rev. E. 2010. Vol. 81. P. 066206.
27. Muller S. et al. A generalized model of the repressilator // J. Math. Biol. 2006. Vol. 53. P. 905.
28. Strelkowa N., Barahona M. Transient dynamics around unstable periodic orbits in the generalized repressilator model // Chaos. 2011. Vol. 21. P. 023104.
29. Miller M.B., Bassler B.L. Quorum sensing in bacteria // Annu. Rev. Microbiol. 2001. Vol. 55. P. 165.
30. McMillen et al. Synchronizing genetic relaxation oscillators by intercell signaling // Proc. Natl. Acad. Sci. USA. 2002. Vol. 99. P. 679.
31. Danino T. et al. A synchronized quorum of genetic clocks // Nature. 2010. Vol. 463. P. 326.
32. Mondragon-Palomino O. et al. Entrainment of a population of synthetic genetic oscillators // Science. 2011. Vol. 333. P. 1315.
33. Prindle A. et al. Sensing array of radically coupled genetic biopixels // Nature. 2012. Vol. 481. P. 39.
34. Balagadde F.K. et al. A synthetic Escherichia coli predator-prey ecosystem // Mol. Syst. Biol. 2008. Vol. 4. P. 187.
35. Basu S. et al. A synthetic multicellular system for programmed pattern formation // Nature. 2005. Vol. 434. P. 1130.
36. Tabor J.J. et al. A synthetic genetic edge detection program // Cell. 2009. Vol. 137. P. 1272.
37. Tamsir A., Tabor J.J., Voigt C.A. Robust multicellular computing using genetically encoded NOR gates and chemical ’wires’ // Nature. 2011. Vol. 469. P. 212.
38. Regot S. et al. Distributed biological computation with multicellular engineered networks // Nature. 2011. Vol. 469. P. 207.
39. Balagadde F.K. et al. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat // Science. 2005. Vol. 309. P. 137.
40. Ullner E., Zaikin A. et al. Multistability and clustering in a population of synthetic genetic oscillators via phase-repulsive cell-to-cell communication // Phys. Rev. Lett. 2007. Vol. 99. P. 148103.
41. Koseska A. et al. Cooperative differentiation through clustering in multicellular populations // J. of Theor. Biol. 2010. Vol. 263. P. 189.
42. Potapov I., Volkov E., Kuznetsov A. Dynamics of coupled repressilators: The role of mRNA kinetics and transcription cooperativity // Phys. Rev. E. 2011. Vol. 83. P. 031901.
43. Nene N., Zaikin A. Interplay between path and speed in decision making by high-dimensional stochastic gene regulatory networks // PLoS ONE. 2012. Vol. 7. P. e40085.
BibTeX
author = {М. V. Ivanchenko and О. I. Kanakov and R. А. Kotelnikov and I. B. Krylov},
title = {NONLINEAR DYNAMICS OF SYNTHETIC GENE REGULATORY CIRCUITS},
year = {2013},
journal = {Izvestiya VUZ. Applied Nonlinear Dynamics},
volume = {21},number = {4},
url = {https://old-andjournal.sgu.ru/en/articles/nonlinear-dynamics-of-synthetic-gene-regulatory-circuits},
address = {Саратов},
language = {russian},
doi = {10.18500/0869-6632-2013-21-4-52-134},pages = {52--134},issn = {0869-6632},
keywords = {nonlinear dynamics,Mathematical modeling,gene regulation.},
abstract = {Built in a cell synthetic gene regulatory elements may function rather independently on the original natural system. Experimental and theoretical studies of small synthetic networks allow for a better understanding of fundamental dynamical mechanisms of gene regulation. This paper gives an introduction to the modern mathematical approaches and methods in this field, primarily in the framework of nonlinear dynamics. }}