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Volumn 22, Issue 3, 2007, Pages 200-210

Beyond intuitive modeling: Combining biophysical models with innovative experiments to move the circadian clock field forward

Author keywords

Circadian rhythms; Mathematical models; Phosphorylation; Single cell; Tau mutation

Indexed keywords

CRYPTOCHROME; CRYPTOCHROME 1; CRYPTOCHROME 2; PER1 PROTEIN; TAU PROTEIN; TRANSCRIPTION FACTOR CLOCK; UNCLASSIFIED DRUG;

EID: 34249066145     PISSN: 07487304     EISSN: 15524531     Source Type: Journal    
DOI: 10.1177/0748730407301823     Document Type: Conference Paper
Times cited : (17)

References (60)
  • 1
    • 0036178045 scopus 로고    scopus 로고
    • Control of intracellular dynamics of mammalian period proteins by casein kinase I epsilon (CKIepsilon) and CKIdelta in cultured cells
    • Akashi M., Tsuchiya Y., Yoshino T., and Nishida E. (2002) Control of intracellular dynamics of mammalian period proteins by casein kinase I epsilon (CKIepsilon) and CKIdelta in cultured cells. Mol Cell Biol 22: 1693-1703.
    • (2002) Mol Cell Biol , vol.22 , pp. 1693-1703
    • Akashi, M.1    Tsuchiya, Y.2    Yoshino, T.3    Nishida, E.4
  • 2
    • 0034161394 scopus 로고    scopus 로고
    • DCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex
    • Bae K., Lee C., Hardin PE, and Edery I. (2000) dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex. J Neurosci 20: 1746-1753.
    • (2000) J Neurosci , vol.20 , pp. 1746-1753
    • Bae, K.1    Lee, C.2    Hardin, P.E.3    Edery, I.4
  • 3
    • 0034688220 scopus 로고    scopus 로고
    • Circadian clocks limited by noise
    • Barkai N. and Leibler S. (2000) Circadian clocks limited by noise. Nature 403: 267-268.
    • (2000) Nature , vol.403 , pp. 267-268
    • Barkai, N.1    Leibler, S.2
  • 4
    • 12244277104 scopus 로고    scopus 로고
    • Modeling feedback loops of the Mammalian circadian oscillator
    • Becker-Weimann S., Wolf J., Herzel H., and Kramer A. (2004) Modeling feedback loops of the Mammalian circadian oscillator. Biophys J 87: 3023-3034.
    • (2004) Biophys J , vol.87 , pp. 3023-3034
    • Becker-Weimann, S.1    Wolf, J.2    Herzel, H.3    Kramer, A.4
  • 5
    • 34247622366 scopus 로고    scopus 로고
    • Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus
    • Bernard S., Gonze D., Cajavec B., Herzel H., and Kramer A. (2007) Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput Biol. In press.
    • (2007) PLoS Comput Biol
    • Bernard, S.1    Gonze, D.2    Cajavec, B.3    Herzel, H.4    Kramer, A.5
  • 6
    • 0020368354 scopus 로고
    • A two process model of sleep regulation
    • Borbely AA (1982) A two process model of sleep regulation. Hum Neurobiol 1: 195-204.
    • (1982) Hum Neurobiol , vol.1 , pp. 195-204
    • Borbely, A.A.1
  • 7
    • 0017157050 scopus 로고
    • A functional analysis of the circadian pacemaker in nocturnal rodents: V. Pacemaker structure: A clock for all seasons
    • Daan S. and Pittendrigh C. (1976) A functional analysis of the circadian pacemaker in nocturnal rodents: V. Pacemaker structure: a clock for all seasons. J Comp Physiol 106: 333-355.
    • (1976) J Comp Physiol , vol.106 , pp. 333-355
    • Daan, S.1    Pittendrigh, C.2
  • 8
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103.
    • (2002) J Comput Biol , vol.9 , pp. 67-103
    • De Jong, H.1
  • 10
    • 0033593306 scopus 로고    scopus 로고
    • Molecular bases for circadian clocks
    • Dunlap JC (1999) Molecular bases for circadian clocks. Cell 96: 271-290.
    • (1999) Cell , vol.96 , pp. 271-290
    • Dunlap, J.C.1
  • 12
    • 0034916379 scopus 로고    scopus 로고
    • Casein Kinase I: Another cog in the circadian clockworks
    • Eide EJ and Virshup DM (2001) Casein Kinase I: another cog in the circadian clockworks. Chronobiol Int 18: 389-398.
    • (2001) Chronobiol Int , vol.18 , pp. 389-398
    • Eide, E.J.1    Virshup, D.M.2
  • 13
    • 0036551787 scopus 로고    scopus 로고
    • Reconciling mathematical models of biological clocks by averaging on approximate manifolds
    • Forger DB and Kronauer RE (2002) Reconciling mathematical models of biological clocks by averaging on approximate manifolds. SIAM J Appl Math 62: 1281.
    • (2002) SIAM J Appl Math , vol.62 , pp. 1281
    • Forger, D.B.1    Kronauer, R.E.2
  • 14
    • 0344736694 scopus 로고    scopus 로고
    • A detailed predictive model of the mammalian circadian clock
    • Forger DB and Peskin CS (2003) A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A 100: 14806-14811.
    • (2003) Proc Natl Acad Sci U S a , vol.100 , pp. 14806-14811
    • Forger, D.B.1    Peskin, C.S.2
  • 15
    • 4444289719 scopus 로고    scopus 로고
    • Model based conjectures on mammalian clock controversies
    • Forger DB and Peskin CS (2004) Model based conjectures on mammalian clock controversies. J Theor Biol 230: 533-539.
    • (2004) J Theor Biol , vol.230 , pp. 533-539
    • Forger, D.B.1    Peskin, C.S.2
  • 16
    • 12244269952 scopus 로고    scopus 로고
    • Stochastic simulation of the mammalian circadian clock
    • Forger DB and Peskin CS (2005) Stochastic simulation of the mammalian circadian clock. Proc Natl Acad Sci U S A 102: 321-324.
    • (2005) Proc Natl Acad Sci U S a , vol.102 , pp. 321-324
    • Forger, D.B.1    Peskin, C.S.2
  • 17
    • 33746041826 scopus 로고    scopus 로고
    • An opposite role for tau in circadian rhythms revealed by mathematical modeling
    • Gallego M., Eide EJ, Woolf MF, Virshup Dm, and Forger Db (2006) An opposite role for tau in circadian rhythms revealed by mathematical modeling. Proc Natl Acad Sci USA 103: 10618-10623.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 10618-10623
    • Gallego, M.1    Eide, E.J.2    Woolf, M.F.3    Dm, V.4    Db, F.5
  • 18
    • 33847779219 scopus 로고    scopus 로고
    • Post-translational modifications regulate the ticking of the circadian clock
    • Gallego M. and Virshup DM (2007) Post-translational modifications regulate the ticking of the circadian clock. Nat Rev Mol Cell Biol 8: 139-148.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 139-148
    • Gallego, M.1    Virshup, D.M.2
  • 19
    • 3342965723 scopus 로고    scopus 로고
    • Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing
    • Garcia-Ojalvo J., Elowitz Mb, and Strogatz Sh (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc Natl Acad Sci USA 101: 10955-10960.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 10955-10960
    • Garcia-Ojalvo, J.1    Mb, E.2    Sh, S.3
  • 21
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D. (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.1
  • 22
    • 0029094843 scopus 로고
    • A model for circadian oscillations in the Drosophila period protein (PER)
    • Goldbeter A. (1995) A model for circadian oscillations in the Drosophila period protein (PER). Proc R Soc Lond B 261: 319-324.
    • (1995) Proc R Soc Lond B , vol.261 , pp. 319-324
    • Goldbeter, A.1
  • 23
    • 23244452215 scopus 로고    scopus 로고
    • Spontaneous synchronization of coupled circadian oscillators
    • Gonze D., Bernard S., Waltermann C., Kramer A., and Herzel H. (2005) Spontaneous synchronization of coupled circadian oscillators. Biophys J 89: 120-129.
    • (2005) Biophys J , vol.89 , pp. 120-129
    • Gonze, D.1    Bernard, S.2    Waltermann, C.3    Kramer, A.4    Herzel, H.5
  • 24
    • 33745725676 scopus 로고    scopus 로고
    • Circadian rhythms and molecular noise
    • Gonze D. and Goldbeter A. (2006) Circadian rhythms and molecular noise. Chaos 16: 026110.
    • (2006) Chaos , vol.16 , pp. 026110
    • Gonze, D.1    Goldbeter, A.2
  • 25
    • 0037154231 scopus 로고    scopus 로고
    • Robustness of circadian rhythms with respect to molecular noise
    • Gonze D., Halloy J., and Goldbeter A. (2002) Robustness of circadian rhythms with respect to molecular noise. Proc Natl Acad Sci U S A 99: 673-678.
    • (2002) Proc Natl Acad Sci U S a , vol.99 , pp. 673-678
    • Gonze, D.1    Halloy, J.2    Goldbeter, A.3
  • 26
    • 4544235175 scopus 로고    scopus 로고
    • Emergence of coherent oscillations in stochastic models for circadian rhythms
    • Gonze D., Halloy J., and Goldbeter A. (2004) Emergence of coherent oscillations in stochastic models for circadian rhythms. Physica A 342: 221-233.
    • (2004) Physica a , vol.342 , pp. 221-233
    • Gonze, D.1    Halloy, J.2    Goldbeter, A.3
  • 27
    • 0012599475 scopus 로고    scopus 로고
    • Stochastic models for circadian rhythms: Effect of molecular noise on periodic and chaotic behaviour
    • Gonze D., Halloy J., Leloup Jc, and Goldbeter A. (2003) Stochastic models for circadian rhythms: effect of molecular noise on periodic and chaotic behaviour. C R Biol 326: 189-203.
    • (2003) C R Biol , vol.326 , pp. 189-203
    • Gonze, D.1    Halloy, J.2    Jc, L.3    Goldbeter, A.4
  • 28
    • 0345826009 scopus 로고    scopus 로고
    • Temporal precision in the mammalian circadian system: A reliable clock from less reliable neurons
    • Herzog ED, Aton SJ, Numano R., Sakaki Y., and Tei H. (2004) Temporal precision in the mammalian circadian system: a reliable clock from less reliable neurons. J Biol Rhythms 19: 35-46.
    • (2004) J Biol Rhythms , vol.19 , pp. 35-46
    • Herzog, E.D.1    Aton, S.J.2    Numano, R.3    Sakaki, Y.4    Tei, H.5
  • 30
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: From theories to phenotypes
    • Kaern M., Elston TC, Blake Wj, and Collins Jj (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Revs 6: 451-464.
    • (2005) Nat Revs , vol.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Wj, B.3    Jj, C.4
  • 31
    • 33749022291 scopus 로고    scopus 로고
    • Functional central rhythmicity and light entrainment, but not liver and muscle rhythmicity, are Clock independent
    • Kennaway DJ, Owens JA, Voultsios A., and Varcoe TJ (2006) Functional central rhythmicity and light entrainment, but not liver and muscle rhythmicity, are Clock independent. Am J Physiol 291: R1172 - R1180.
    • (2006) Am J Physiol , vol.291
    • Kennaway, D.J.1    Owens, J.A.2    Voultsios, A.3    Varcoe, T.J.4
  • 32
    • 0033381569 scopus 로고    scopus 로고
    • Quantifying human circadian pacemaker response to brief, extended, and repeated light stimuli over the phototopic range
    • Kronauer RE, Forger DB, and Jewett ME (1999) Quantifying human circadian pacemaker response to brief, extended, and repeated light stimuli over the phototopic range. J Biol Rhythms 14: 500-515.
    • (1999) J Biol Rhythms , vol.14 , pp. 500-515
    • Kronauer, R.E.1    Forger, D.B.2    Jewett, M.E.3
  • 33
    • 0037795575 scopus 로고    scopus 로고
    • Toward a detailed computational model for the mammalian circadian clock
    • Leloup JC and Goldbeter A. (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100: 7051-7056.
    • (2003) Proc Natl Acad Sci U S a , vol.100 , pp. 7051-7056
    • Leloup, J.C.1    Goldbeter, A.2
  • 34
    • 4444301677 scopus 로고    scopus 로고
    • Modeling the mammalian circadian clock: Sensitivity analysis and multiplicity of oscillatory mechanisms
    • Leloup JC and Goldbeter A. (2004) Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms. J Theor Biol 230: 541-562.
    • (2004) J Theor Biol , vol.230 , pp. 541-562
    • Leloup, J.C.1    Goldbeter, A.2
  • 35
    • 0034697620 scopus 로고    scopus 로고
    • Delay model of the circadian pacemaker
    • Lema MA, Golombek DA, and Echave J. (2000) Delay model of the circadian pacemaker. J Theor Biol 204: 565-573.
    • (2000) J Theor Biol , vol.204 , pp. 565-573
    • Ma, L.1    Golombek, D.A.2    Echave, J.3
  • 36
    • 33746071204 scopus 로고    scopus 로고
    • Dynamics of a multistage circadian system
    • Liese T. and Siegelmann H. (2006) Dynamics of a multistage circadian system. J Biol Rhythms 21: 314-323.
    • (2006) J Biol Rhythms , vol.21 , pp. 314-323
    • Liese, T.1    Siegelmann, H.2
  • 39
    • 0034501106 scopus 로고    scopus 로고
    • Genetics of the mammalian circadian system: Photic entrainment, circadian pacemaker mechanisms, and posttranslational regulation
    • Lowrey PL and Takahashi JS (2000) Genetics of the mammalian circadian system: photic entrainment, circadian pacemaker mechanisms, and posttranslational regulation. Annu Rev Genet 34: 533-562.
    • (2000) Annu Rev Genet , vol.34 , pp. 533-562
    • Lowrey, P.L.1    Takahashi, J.S.2
  • 40
    • 0030990993 scopus 로고    scopus 로고
    • Dissection of a circadian oscillation into discrete domains
    • Merrow MW, Garceau NY, and Dunlap JC (1997) Dissection of a circadian oscillation into discrete domains. Proc Natl Acad Sci U S A 94: 3877-3882.
    • (1997) Proc Natl Acad Sci U S a , vol.94 , pp. 3877-3882
    • Merrow, M.W.1    Garceau, N.Y.2    Dunlap, J.C.3
  • 41
    • 8844256589 scopus 로고    scopus 로고
    • Circadian gene expression in individual fibroblasts: Cell-autonomous and self-sustained oscillators pass time to daughter cells
    • Nagoshi E., Saini C., Bauer C., Laroche T., Naef F., and Schibler U. (2004) Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 119: 693-705.
    • (2004) Cell , vol.119 , pp. 693-705
    • Nagoshi, E.1    Saini, C.2    Bauer, C.3    Laroche, T.4    Naef, F.5    Schibler, U.6
  • 42
    • 0036240391 scopus 로고    scopus 로고
    • Clock mutation lengthens the circadian period without damping rhythms in individual SCN neurons
    • Nakamura W., Honma S., Shirakawa T., and Honma K. (2002) Clock mutation lengthens the circadian period without damping rhythms in individual SCN neurons. Nat Neurosci 5: 399-400.
    • (2002) Nat Neurosci , vol.5 , pp. 399-400
    • Nakamura, W.1    Honma, S.2    Shirakawa, T.3    Honma, K.4
  • 43
    • 24944497666 scopus 로고    scopus 로고
    • Tissue-specific disruption of rhythmic expression of Dec1 and Dec2 in clock mutant mice
    • Noshiro M., Furukawa M., Honma S., Kawamoto T., Hamada T., Honma K., and Kato Y. (2005) Tissue-specific disruption of rhythmic expression of Dec1 and Dec2 in clock mutant mice. J Biol Rhythms 20: 404-418.
    • (2005) J Biol Rhythms , vol.20 , pp. 404-418
    • Noshiro, M.1    Furukawa, M.2    Honma, S.3    Kawamoto, T.4    Hamada, T.5    Honma, K.6    Kato, Y.7
  • 44
    • 0346725938 scopus 로고    scopus 로고
    • Drosophila doubletime mutations which either shorten or lengthen the period of circadian rhythms decrease the protein kinase activity of casein kinase I
    • Preuss F., Fan JY, Kalive M., Bao S., Schuenemann E., Bjes ES, and Price JL (2004) Drosophila doubletime mutations which either shorten or lengthen the period of circadian rhythms decrease the protein kinase activity of casein kinase I. Mol Cell Biol 24: 886-898.
    • (2004) Mol Cell Biol , vol.24 , pp. 886-898
    • Preuss, F.1    Fan, J.Y.2    Kalive, M.3    Bao, S.4    Schuenemann, E.5    Bjes, E.S.6    Price, J.L.7
  • 45
    • 0023764577 scopus 로고
    • A mutation of the circadian system in golden hamsters
    • Ralph MR and Menaker M. (1988) A mutation of the circadian system in golden hamsters. Science 241: 1225-1227.
    • (1988) Science , vol.241 , pp. 1225-1227
    • Ralph, M.R.1    Menaker, M.2
  • 46
    • 0033820447 scopus 로고    scopus 로고
    • Comparing clockworks: Mouse versus fly
    • Reppert SM and Weaver DR (2000) Comparing clockworks: mouse versus fly. J Biol Rhythms 15: 357-364.
    • (2000) J Biol Rhythms , vol.15 , pp. 357-364
    • Reppert, S.M.1    Weaver, D.R.2
  • 47
    • 0037194790 scopus 로고    scopus 로고
    • Coordination of circadian timing in mammals
    • Reppert SM and Weaver DR (2002) Coordination of circadian timing in mammals. Nature 418: 935-941.
    • (2002) Nature , vol.418 , pp. 935-941
    • Reppert, S.M.1    Weaver, D.R.2
  • 49
    • 0036840199 scopus 로고    scopus 로고
    • A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator
    • Smolen P., Baxter DA, and Byrne JH (2002) A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophys J 83: 2349-2359.
    • (2002) Biophys J , vol.83 , pp. 2349-2359
    • Smolen, P.1    Baxter, D.A.2    Byrne, J.H.3
  • 50
    • 0034667556 scopus 로고    scopus 로고
    • Two novel doubletime mutants alter circadian properties and eliminate the delay between RNA and protein in Drosophila
    • Suri V., Hall JC, and Rosbash M. (2000) Two novel doubletime mutants alter circadian properties and eliminate the delay between RNA and protein in Drosophila. J Neurosci 20: 7547-7555.
    • (2000) J Neurosci , vol.20 , pp. 7547-7555
    • Suri, V.1    Hall, J.C.2    Rosbash, M.3
  • 51
    • 3543005291 scopus 로고    scopus 로고
    • Identification of mPer1 phosphorylation sites responsible for the nuclear entry
    • Takano A., Isojima Y., and Nagai K. (2004) Identification of mPer1 phosphorylation sites responsible for the nuclear entry. J Biol Chem 279: 32578-32585.
    • (2004) J Biol Chem , vol.279 , pp. 32578-32585
    • Takano, A.1    Isojima, Y.2    Nagai, K.3
  • 53
    • 3042530052 scopus 로고    scopus 로고
    • A precarious balance
    • Tyson JJ (2004) A precarious balance. Curr Biol 14: R262 - R263.
    • (2004) Curr Biol , vol.14
    • Tyson, J.J.1
  • 56
    • 16844383352 scopus 로고    scopus 로고
    • Real-time reporting of circadian-regulated gene expression by luciferase imaging in plants and mammalian cells
    • Welsh DK, Imaizumi T., and Kay SA (2005) Real-time reporting of circadian-regulated gene expression by luciferase imaging in plants and mammalian cells. Method Enzymol 393: 269-288.
    • (2005) Method Enzymol , vol.393 , pp. 269-288
    • Welsh, D.K.1    Imaizumi, T.2    Kay, S.A.3
  • 57
    • 11144311974 scopus 로고    scopus 로고
    • Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression
    • Welsh DK, Yoo SH, Liu AC, Takahashi JS, and Kay SA (2004) Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr Biol 14: 2289-2295.
    • (2004) Curr Biol , vol.14 , pp. 2289-2295
    • Welsh, D.K.1    Sh, Y.2    Liu, A.C.3    Takahashi, J.S.4    Kay, S.A.5


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