НЕЛИНЕЙНАЯ ДИНАМИКА СИНТЕТИЧЕСКИХ СЕТЕЙ ГЕННОЙ РЕГУЛЯЦИИ

Синтетические регуляторные элементы, встроенные в клетку, могут функционировать в известной степени независимо от основной, природной системы. Экспериментальные и теоретические исследования малых синтетических сетей позволяют лучше понять динамические механизмы генной регуляции в целом. Цель данной статьи – дать представление о современных математических подходах и методах в этой области, в первую очередь, в рамках нелинейной динамики.

Литература

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.

 

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