Measuring synchrony in the mammalian central circadian circuit

Methods in Enzymology

Volumn 552, Issue , 2015, Pages 3-22

  Herzog, Erik D ^a   Kiss, István Z ^b   Mazuski, Cristina ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b Saint Louis University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEUROPEPTIDE;

BIOLUMINESCENCE; CELL COMMUNICATION; CELL MOTION; CELL TRACKING; CIRCADIAN RHYTHM; COMPARATIVE STUDY; COSMIC RADIATION; FOURIER TRANSFORMATION; GENE EXPRESSION; HUMAN; IMAGE PROCESSING; LIMIT OF DETECTION; NEUROTRANSMITTER RELEASE; NONHUMAN; PRIORITY JOURNAL; REVIEW; SUPRACHIASMATIC NUCLEUS; ANIMAL; PHYSIOLOGY; SINGLE CELL ANALYSIS;

MAMMALIA;

ANIMALS; CIRCADIAN RHYTHM; SINGLE-CELL ANALYSIS; SUPRACHIASMATIC NUCLEUS;

EID: 84923292578     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2014.10.042     Document Type: Chapter

References (63)

1. S. An, R.P. Irwin, C.N. Allen, C. Tsai, and E.D. Herzog Vasoactive intestinal polypeptide requires parallel changes in adenylate cyclase and phospholipase C to entrain circadian rhythms to a predictable phase Journal of Neurophysiology 105 5 2011 2289 2296
2. S.J. Aton, C.S. Colwell, A.J. Harmar, J. Waschek, and E.D. Herzog Vasoactive intestinal polypeptide mediates circadian rhythmicity and synchrony in mammalian clock neurons Nature Neuroscience 8 2005 476 483
3. S.J. Aton, J.E. Huettner, M. Straume, and E.D. Herzog GABA and Gi/o differentially control circadian rhythms and synchrony in clock neurons Proceedings of the National academy of Sciences of the United States of America 103 2006 19188 19193
4. E. Batschelet, and E. Batschelet Circular statistics in biology 371 1981 Academic Press London
5. G. Bloch, E.D. Herzog, J.D. Levine, and W.J. Schwartz Socially synchronized circadian oscillators Proceedings of the Royal Society B: Biological Sciences 280 1765 2013 20130035
6. R. Bours, M. Muthuraman, H. Bouwmeester, and A. van der Krol OSCILLATOR: A system for analysis of diurnal leaf growth using infrared photography combined with wavelet transformation Plant Methods 8 1 2012 29
7. M. Brancaccio, E.S. Maywood, J.E. Chesham, A.S. Loudon, and M.H. Hastings A Gq-Ca2 + axis controls circuit-level encoding of circadian time in the suprachiasmatic nucleus Neuron 78 4 2013 714 728
8. F.H. Chan, B.M. Wu, F.K. Lam, P.W. Poon, and A.M. Poon Multiscale characterization of chronobiological signals based on the discrete wavelet transform IEEE Transactions on Biomedical Engineering 47 1 2000 88 95
9. H.Y. Cheng, M. Alvarez-Saavedra, H. Dziema, Y.S. Choi, A. Li, and K. Obrietan Segregation of expression of mPeriod gene homologs in neurons and glia: Possible divergent roles of mPeriod1 and mPeriod2 in the brain Human Molecular Genetics 18 16 2009 3110 3124
10. R.N. Day, and F. Schaufele Fluorescent protein tools for studying protein dynamics in living cells: A review Journal of Biomedial Optics 13 3 2008 031202
11. A. Deckard, R.C. Anafi, J.B. Hogenesch, S.B. Haase, and J. Harer Design and analysis of large-scale biological rhythm studies: A comparison of algorithms for detecting periodic signals in biological data Bioinformatics 29 2013 3174 3180
12. A. Diez-Noguera Methods for serial analysis of long time series in the study of biological rhythms Journal of Circadian Rhythms 11 1 2013 7
13. H.B. Dowse Analyses for physiological and behavioral rhythmicity Methods in Enzymology 454 2009 141 174
14. R. Enoki, S. Kuroda, D. Ono, M.T. Hasan, T. Ueda, and S. Honma Topological specificity and hierarchical network of the circadian calcium rhythm in the suprachiasmatic nucleus Proceedings of the National Academy of Sciences of the United States of America 109 52 2012 21498 21503
15. R. Enoki, D. Ono, M.T. Hasan, S. Honma, and K.I. Honma Single-cell resolution fluorescence imaging of circadian rhythms detected with a Nipkow spinning disk confocal system Journal of Neuroscience Methods 207 1 2012 72 79
16. J.A. Evans, T.L. Leise, O. Castanon-Cervantes, and A.J. Davidson Intrinsic regulation of spatiotemporal organization within the suprachiasmatic nucleus PLoS One 6 1 2011 e15869
17. J.A. Evans, T.L. Leise, O. Castanon-Cervantes, and A.J. Davidson Dynamic interactions mediated by nonredundant signaling mechanisms couple circadian clock neurons Neuron 80 4 2013 973 983
18. N.C. Foley, T.Y. Tong, D. Foley, J. LeSauter, D.K. Welsh, and R. Silver Characterization of orderly spatiotemporal patterns of clock gene activation in mammalian suprachiasmatic nucleus European Journal of Neuroscience 33 10 2011 1851 1865
19. F. Halberg Frequency spectra and cosinor for evaluating circadian rhythms in rodent data and in man during Gemini and Vostok flights Life Sciences and Space Research 8 1969 188 214
20. R. Harang, G. Bonnet, and L.R. Petzold WAVOS: A MATLAB toolkit for wavelet analysis and visualization of oscillatory systems BMC Research Notes 5 2012 163
21. M.H. Hastings, A.B. Reddy, D.G. McMahon, and E.S. Maywood Analysis of circadian mechanisms in the suprachiasmatic nucleus by transgenesis and biolistic transfection Methods in Enzymology 393 2005 579 592
22. E.D. Herzog Neurons and networks in daily rhythms Nature Reviews Neuroscience 8 10 2007 790 802
23. E.D. Herzog, S.J. Aton, R. Numano, Y. Sakaki, and H. Tei Temporal precision in the mammalian circadian system: A reliable clock from less reliable neurons Journal of Biological Rhythms 19 1 2004 35 46
24. S. Honma, D. Ono, Y. Suzuki, N. Inagaki, T. Yoshikawa, and W. Nakamura Suprachiasmatic nucleus: Cellular clocks and networks Progress in Brain Research 199 2011 129 141
25. M. Ikeda, and M. Ikeda Bmal1 is an essential regulator for circadian cytosolic Ca2 + rhythms in suprachiasmatic nucleus neurons The Journal of Neuroscience 34 36 2014 12029 12038
26. M. Ikeda, T. Sugiyama, C.S. Wallace, H.S. Gompf, T. Yoshioka, and A. Miyawaki Circadian dynamics of cytosolic and nuclear Ca2 + in single suprachiasmatic nucleus neurons Neuron 38 2 2003 253 263
27. R.P. Irwin, and C.N. Allen Simultaneous electrophysiological recording and calcium imaging of suprachiasmatic nucleus neurons Journal of Visual Experiments 82 2013 e50794
28. M.L. Johnson, and S.G. Frasier Nonlinear least squares analysis Methods in Enzymology 117 1985 301 342
29. I.Z. Kiss, M. Quigg, S.-H.C. Chun, H. Kori, and J.L. Hudson Characterization of synchronization in interacting groups of oscillators: Application to seizures Biophysical Journal 94 3 2008 1121 1130
30. B. Kralemann, L. Cimponeriu, M. Rosenblum, A. Pikovsky, and R. Mrowka Phase dynamics of coupled oscillators reconstructed from data Physical Review E 77 6 2008 066205
31. S.J. Kuhlman, J.E. Quintero, and D.G. McMahon GFP fluorescence reports Period 1 circadian gene regulation in the mammalian biological clock Neuroreport 11 7 2000 1479 1482
32. Y. Kuramoto, and D. Battogtokh Coexistence of coherence and incoherence in nonlocally coupled phase oscillators Nonlinear Phenomena in Complex Systems 5 4 2002 380 385
33. T.L. Leise Wavelet analysis of circadian and ultradian behavioral rhythms Journal of Circadian Rhythms 11 1 2013 5
34. T.L. Leise, and M.E. Harrington Wavelet-based time series analysis of circadian rhythms Journal of Biological Rhythms 26 5 2011 454 463
35. T.L. Leise, P. Indic, M.J. Paul, and W.J. Schwartz Wavelet meets actogram Journal of Biological Rhythms 28 1 2013 62 68
36. J.D. Levine, P. Funes, H.B. Dowse, and J.C. Hall Signal analysis of behavioral and molecular cycles BMC Neuroscience 3 2002 1
37. C. Liu, and S.M. Reppert GABA synchronizes clock cells within the suprachiasmatic circadian clock Neuron 25 1 2000 123 128
38. K. Meeker, R. Harang, A.B. Webb, D.K. Welsh, F.J. Doyle 3rd, and G. Bonnet Wavelet measurement suggests cause of period instability in mammalian circadian neurons Journal of Biological Rhythms 26 4 2011 353 362
39. A. Moore, T. Zielinski, and A.J. Millar Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure Methods in Molecular Biology 1158 2014 13 44
40. J. Myung, S. Hong, F. Hatanaka, Y. Nakajima, E. De Schutter, and T. Takumi Period coding of Bmal1 oscillators in the suprachiasmatic nucleus The Journal of Neuroscience 32 26 2012 8900 8918
41. J. Nawrath, M.C. Romano, M. Thiel, I.Z. Kiss, M. Wickramasinghe, and J. Timmer Distinguishing direct from indirect interactions in oscillatory networks with multiple time scales Physical Review Letters 104 3 2010 038701
42. J.S. O'Neill, E.S. Maywood, J.E. Chesham, J.S. Takahashi, and M.H. Hastings cAMP-dependent signaling as a core component of the mammalian circadian pacemaker Science 320 5878 2008 949 953
43. G. Parati Assessing circadian blood pressure and heart rate changes: Advantages and limitations of different methods of mathematical modelling Journal of Hypertension 22 11 2004 2061 2064
44. S. Pauls, N. Foley, D. Foley, J. LeSauter, M. Hastings, and E. Maywood Differential contributions of intra-cellular and inter-cellular mechanisms to the spatial and temporal architecture of the suprachiasmatic nucleus circadian circuitry in wild-type, cryptochrome-null and vasoactive intestinal peptide receptor 2-null mutant mice European Journal of Neuroscience 40 2014 2528 2540
45. A. Pikovsky, M. Rosenblum, and J. Kurths Synchronization: A universal concept in nonlinear sciences 2003 Cambridge University Press Cambridge, UK
46. T.S. Price, J.E. Baggs, A.M. Curtis, G.A. Fitzgerald, and J.B. Hogenesch WAVECLOCK: Wavelet analysis of circadian oscillation Bioinformatics 24 23 2008 2794 2795
47. W.S. Rasband ImageJ 1997-2014 U.S. National Institutes of Health Bethesda, Maryland, USA http://imagej.nih.gov/ij/
48. R. Refinetti Laboratory instrumentation and computing: Comparison of six methods for the determination of the period of circadian rhythms Physiology & Behavior 54 5 1993 869 875
49. R. Refinetti Non-stationary time series and the robustness of circadian rhythms Journal of Theoretical Biology 227 4 2004 571 581
50. R. Refinetti, G.C. Lissen, and F. Halberg Procedures for numerical analysis of circadian rhythms Biological Rhythm Research 38 4 2007 275 325
51. M. Shono, H. Shono, Y. Ito, M. Muro, Y. Maeda, and H. Sugimori A new periodogram using one-way analysis of variance for circadian rhythms Psychiatry and Clinical Neurosciences 54 3 2000 307 308
52. P.G. Sokolove, and W.N. Bushell The chi square periodogram: Its utility for analysis of circadian rhythms Journal of Theoretical Biology 72 1 1978 131 160
53. M. Straume, S.G. Frasier-Cadoret, and M.L. Johnson Least-squares analysis of fluorescence data Topics in fluorescence spectroscopy 2002 Springer USA 177 240
54. S. Strogatz Sync: The emerging science of spontaneous order 2003 Penguin Books Ltd. London, England
55. M. Thiel, M.C. Romano, J. Kurths, M. Rolfs, and R. Kliegl Twin surrogates to test for complex synchronisation EPL (Europhysics Letters) 75 4 2006 535
56. A.B. Webb, S.R. Taylor, K.A. Thoroughman, F.J. Doyle III, and E.D. Herzog Weakly circadian cells improve resynchrony PLoS Computational Biology 8 11 2012 e1002787
57. D.K. Welsh, T. Imaizumi, and S.A. Kay Real-time reporting of circadian-regulated gene expression by luciferase imaging in plants and mammalian cells Methods in Enzymology 393 2005 269 288
58. D.K. Welsh, and S.A. Kay Bioluminescence imaging in living organisms Current Opinion in Biotechnology 16 1 2005 73 78
59. D.K. Welsh, and T. Noguchi Cellular bioluminescence imaging Cold Spring Harbor Protocols 8 2012 pii: pdb.top070607
60. S. Yamaguchi, H. Isejima, T. Matsuo, R. Okura, K. Yagita, and M. Kobayashi Synchronization of cellular clocks in the suprachiasmatic nucleus Science 302 5649 2003 1408 1412
61. S. Yamazaki, R. Numano, M. Abe, A. Hida, R.I. Takahashi, and M. Ueda Resetting central and peripheral circadian oscillators in transgenic rats Science 288 5466 2000 682 685
62. S.H. Yoo, S. Yamazaki, P.L. Lowrey, K. Shimomura, C.H. Ko, and E.D. Buhr PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues Proceedings of the National Academy of Sciences of the United States of America 101 15 2004 5339 5346
63. T. Zielinski, A.M. Moore, E. Troup, K.J. Halliday, and A.J. Millar Strengths and limitations of period estimation methods for circadian data PLoS One 9 5 2014 e96462