Phase tracking and restoration of circadian rhythms by model-based optimal control

IET Systems Biology

Volumn 2, Issue 1, 2008, Pages 16-23

  Shaik, O S ^a   Sager, S ^a   Slaby, O ^a   Lebiedz, Dirk ^b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; OPTIMAL CONTROL SYSTEMS; PHASE SHIFT; PHYSIOLOGY; SYNCHRONIZATION;

CIRCADIAN RHYTHMS; FEEDBACK REGULATION; LIGHT STIMULI; PHASE TRACKING;

GENES;

ALGORITHM; ARTICLE; CHRONOBIOLOGY; CIRCADIAN RHYTHM; DROSOPHILA; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MUTANT; NONHUMAN; OSCILLATOR; PHOTOSTIMULATION; PROTEIN DEGRADATION; PROTEIN SYNTHESIS;

ANIMALS; BIOLOGICAL CLOCKS; CIRCADIAN RHYTHM; COMPUTER SIMULATION; DROSOPHILA; FEEDBACK; MODELS, BIOLOGICAL; OSCILLOMETRY;

EID: 38949095618     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb:20070016     Document Type: Article

References (37)

1. Goldbeter, A.: 'Computational approaches to cellular rhythms', Nature, 2002, 420, p. 238-245 10.1038/nature01259 0028-0836
2. Young, M.W.: 'The molecular control of circadian behavioral rhythms and their entrainment in Drosophila', Annu. Rev. Biochem., 1998, 67, p. 135-152
3. Reppert, S.M., and Weaver, D.R.: 'Coordination of circadian timing in mammals', Nature, 2002, 418, p. 935-941 0028-0836
4. Leloup, J.C., and Goldbeter, A.: 'Modeling the molecular regulatory mechanism of circadian rhythms in Drosophila', BioEssays, 2000, 22, p. 84-93
5. Rajaratnam, S.M., and Arendt, J.: 'Health in a 24-h society', Lancet, 2001, 358, p. 999-1005
6. Dijk, D.J., and Lockley, S.W.: 'Integration of human sleep-wake regulation and circadian rhythmicity', J. Appl. Physiol., 2002, 92, p. 852-62 0161-7567
7. Levi, F.: 'ChroTotherapeutics: the relevance of timing in cancer therapy', Cancer Causes Control, 2006, 17, p. 611-621
8. Goldbeter, A., and Claude, D.: 'Time-patterned drug administration:iNsights from a modeling approach', Chronobiol. Int., 2002, 19, p. 157-175
9. Levi, F.: 'Cancer chronotherapy', Lancet Oncol., 2001, 2, p. 307-315
10. Levi, F., and Mchibler, U.: 'Circadian rhythms: mechanisms and therapeutic implications', Annu. Rev. Pharmacol., 2007, 47, p. 593-628
11. Mormont, M.C., Waterhouse, J., Bleuzen, P., Giachetti, S., Jami, A., Bogdan, A., Lellouch, J., Misset, J.L., Touitou, Y., and Levi, F.: 'Marked 24 h rest/activity rhythms are associated with better quality of life, better response, and longer survival in patients with metastatic colorectal cancer and good performance status', Clin. Cancer Res., 2000, 6, p. 3038-3045
12. Fu, L., and Lee,PC.C.: 'The circadian clock: pacemaker and tumour suppressor', Nature, 2003, 3, p. 350-361 0028-0836
13. Iurisci, I., Filipski, E., Reinhardt, J., Bach, S., Gianella-Borradori, A., Iacobelli, S., Meijer, L., and Levi, F.: 'Improved tumor control through circadian clock induction by seliciclib, a cyclin-dependent kinase inhibitor', Cancer Res., 2006, 66, p. 10720-10728
14. Claude, D., and Clairambault, J.: 'Period shift induction by intermittent stimulation in a Drosophila model of per protein oscillations', Chronobiol. Int., 2000, 17, p. 1-14 10.1081/CBI-100101027
15. Laroche, B., and Claude, D.: 'Flatness-based control of PER protein oscillations in a Drosophila model', IEEE Trans. Autom. Control, 2004, 49, p. 175-183 10.1109/TAC.2003.822859 0018-9286
16. Leloup, J.C., and Goldbeter, A.: 'A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins', J. Biol. Rhythms, 1998, 13, p. 70-87 0748-7304
17. Myers, M.P., Wager-Smith, K., Rothenfluh-Hilfiker, A., and Young, Y.M.: 'Light-induced degradation of TIMELESS and entrainment of the Drosophila circadian clock', Science, 1996, 271, p. 1736-1740 0036-8075
18. Zeng, H., Qian, Z., Myers, M.P., and Rosbash, M.: 'A lightentrainment mechanism for the Drosophila circadian clock', Nature, 1996, 380, p. 129-135 0028-0836
19. Jewett, M.E., Kronauer, R.E., and Czeisler, C.A.: 'Light-induced suppression of endogenous circadian amplitude in humans', Nature, 1991, 350, p. 59-62 10.1038/350059a0 0028-0836
20. Albersmeier, J., and Bock, H.G.: 'Efficient derivative generation in an adaptive BDF method', Proc. HPSC, 2006, Springer Verlag
21. Stelling, J., Gilles, E.D., and Doyle, F.J.: 'Robustness properties of circadian clock architectures', Proc. Natl Acad. Sci. USA, 2004, 101, p. 13210-13215 0027-8424
22. Bagheri, N., Stelling, J., and Doyle, F.J.: 'Quantitative performance metrics for robustness in circadian rhythms', Bioinformatics, 2007, 23, p. 358-364
23. Alper, H., Fischer, C., Nevoigt, E., and Stephanopoulos, G.: 'Tuning genetic control through promoter engineering', Proc. Natl Acad. Sci. USA, 2005, 102, p. 12678-12683 0027-8424
24. de Smit, M.H., and van Duin, J.: 'Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis', Proc. Natl Acad. Sci. USA, 1990, 87, p. 7668-7672 0027-8424
25. Smolke, C.D., Carrier, T.A., and Keasling, J.D.: 'Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures', Appl. Environ. Microbiol., 2000, 66, p. 5399-5405
26. Boulos, Z., Macchi, M.M., Stürchler, M.P., Stewart, K.T., Brainard, G.C., Suhner, A., Wallace, G., and Steffen, R.: 'Light visor treatment for jet lag after westward travel across six time zones', Aviat. Space. Environ. Med., 2002, 73, p. 953-963
27. Slaby, O., Sager, S., Shaik, O., Kummer, U., and Lebiedz, D.: 'Optimal control of self-organized dynamics in cellular signal transduction', Math. Comput. Model. Dyn. syst., 2007, 13, (5), p. 487-502
28. Doedel, E.J.: 'A program for the automatic bifurcation analysis of autonomous systems', Congr. Num., 1981, 30, p. 265-284
29. Leineweber, D.B., Bauer, I., Bock, H.G., and Schloüder, J.P.: 'An efficient multiple shooting based reduced SQP strategy for large-scale dynamic process optimization. Part I: Theoretical aspects', Comput. Chem. Eng., 2003, 27, p. 157-166 10.1016/S0098-1354(02)00158-8 0098-1354
30. Bock, H.G., and Plitt, K.J.: 'A multiple shooting algorithm for direct solution of optimal control problems', Proc. 9th IFAC World Congress, Budapest, 1984, Pergamon p. 243-247
31. Lebiedz, D., and Brandt-Pollmann, U.: 'Manipulation of self-aggregation patterns and waves in a reaction-diffusion system by optimal boundary control strategies', Phys. Rev. Lett., 2003, 91, p. 208-301 0031-9007
32. Lebiedz, D., Sager, S., Bock, H.G., and Lebiedz, P.: 'Annihilation of limit cycle oscillations by identification of critical perturbing stimuli via mixed-integer optimal control', Phys. Rev. Lett., 2005, 95, p. 108-303 0031-9007
33. Sager, S.: 'Numerical methods for mixed-integer optimal control problems', (Der andere Verlag, Toünning, Lübeck, Marburg 2005), Available at http://sager1.de/sebastian/downloads/sager2005.pdf
34. Winfree, A.T.: 'The geometry of biological time', (Springer, New York 2001)
35. Ruoff, P., Vinsjevik, M., Monnerjahn, C., and Rensing, L.: 'The Goodwin model: Simulating the effect of light pulses on the circadian sporulation rhythm of neurospora crassa', J. Theor. Biol., 2001, 209, p. 29-42
36. Ronald, J.K., and Seymonr, B.: 'Clock mutants of Drosophila melanogaster', Proc. Natl Acad. Sci. USA, 1971, 68, p. 2112-2116 0027-8424
37. Leloup, J.C., and Goldbeter, A.: 'Toward a detailed computational model for the mammalian circadian clock', Proc. Natl Acad. Sci. USA, 2003, 100, p. 7051-7056 0027-8424