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Computational modeling of the cell-autonomous mammalian circadian oscillator

Olga A. Podkolodnaya, Natalya N. Tverdokhleb, Nikolay L. Podkolodnyy
2017 BMC Systems Biology  
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock.  ...  This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating systems.  ...  Acknowledgements The authors thank editors of the special issue for their support during the work on the article.  ... 
doi:10.1186/s12918-016-0379-8 pmid:28466791 fatcat:gfjmzpsnnfeghhxzkpfcmwrklm

A tunable synthetic mammalian oscillator

Marcel Tigges, Tatiana T. Marquez-Lago, Jörg Stelling, Martin Fussenegger
2009 Nature  
The mammalian circadian clock consists of a central pacemaker in the suprachiasmatic nuclei of mammalian brains 9 , with subsidiary oscillators in most peripheral cell types 4, 5, 10 .  ...  Autonomous and self-sustained oscillator circuits mediating the periodic induction of specific target genes are minimal genetic time-keeping devices found in the central and peripheral circadian clocks  ...  Weber for conceptual input and/or critical comments on the manuscript. This work was supported by the Swiss National Science Foundation and the EC Framework 6 (COBIOS).  ... 
doi:10.1038/nature07616 pmid:19148099 fatcat:xuvqnwbawzhhdfvhfw3p2w5dlm

Robust synchronization of the cell cycle and the circadian clock through bidirectional coupling

Jie Yan, Albert Goldbeter
2019 Journal of the Royal Society Interface  
By merging detailed models for the two networks in mammalian cells, we previously showed that unidirectional coupling to the circadian clock can entrain the cell cycle to 24 or 48 h, depending on the cell  ...  cycle autonomous period, while complex oscillations occur when entrainment fails.  ...  Ling Yang for discussions and continuous support, Dr Claude Gérard for his contribution to the initial development of the coupled cell cycle-circadian clock model, and Drs G. T. J. van der Horst, I.  ... 
doi:10.1098/rsif.2019.0376 pmid:31506042 pmcid:PMC6769306 fatcat:siog7t7eyzfbpbkepezpvezuwu

Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms

Claude Gérard, Albert Goldbeter, Edmund J. Crampin
2012 PLoS Computational Biology  
Citation: Gérard C, Goldbeter A (2012) Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms. PLoS Comput Biol 8(5): e1002516.  ...  Using detailed computational models for the two networks we investigate the conditions in which the mammalian cell cycle can be entrained by the circadian clock.  ...  Acknowledgments We acknowledge fruitful discussions with Professor David Rand and the other members of the consortium C5Sys, ''Circadian and Cell Cycle Clock Systems in Cancer.''  ... 
doi:10.1371/journal.pcbi.1002516 pmid:22693436 pmcid:PMC3364934 fatcat:3dbw5dvvhbamtm3xjqmlhnb6sa

For whom the bells toll: Networked circadian clocks

G. Mark FREEMAN, Alexis B. WEBB, Sungwon AN, Erik D. HERZOG
2008 Sleep and Biological Rhythms  
We focus on how populations of circadian oscillators synchronize in a variety of biological systems and describe recent efforts to model mathematically coupling and synchrony in the mammalian suprachiasmatic  ...  This review highlights the mechanisms and benefits of coupling circadian oscillators.  ...  ACKNOWLEDGMENTS The authors declare no conflict of interest. This work was supported by National Institutes of Health Grants MH63104 and MH78993.  ... 
doi:10.1111/j.1479-8425.2008.00344.x fatcat:wdi75z3pzbcxjivy63ow7ybv5m

A systems theoretic approach to analysis and control of mammalian circadian dynamics

John H. Abel, Francis J. Doyle
2016 Chemical engineering research & design  
We provide an overview of the routes by which the circadian system can be systemically manipulated, and present in silico proof of concept results for phase resetting of the clock via model predictive  ...  The mammalian circadian clock is a complex multi-scale, multivariable biological control system.  ...  We especially thank Ankush Chakrabarty for a critical reading of the manuscript, and Peter C. St. John for open-source code and data. We also thank Steve A. Kay, Erik D. Herzog, and Linda R.  ... 
doi:10.1016/j.cherd.2016.09.033 pmid:28496287 pmcid:PMC5421650 fatcat:5hwo5yn5e5cx3dogpuvhamgp2e

Multi-rhythmicity generated by coupling two cellular rhythms

Jie Yan, Albert Goldbeter
2019 Journal of the Royal Society Interface  
Analysis of a detailed model for these coupled cellular rhythms previously showed that the cell cycle can be entrained at the circadian period of 24 h, or at a period of 48 h, depending on the autonomous  ...  The cell cycle and the circadian clock represent two major cellular rhythms, which are coupled because the circadian clock governs the synthesis of several proteins of the network that drives the mammalian  ...  Ling Yang for discussions and continuous support, and Dr Claude Gérard for his contribution to the initial development of the coupled cell cycle-circadian clock model.  ... 
doi:10.1098/rsif.2018.0835 pmid:30836895 pmcid:PMC6451392 fatcat:xsyycktzdrgrbnmygnfcizqgjq

Supporting Information from Multi-synchronization and other patterns of multi-rhythmicity in oscillatory biological systems

Albert Goldbeter, Jie Yan
2022 figshare.com  
In the second part, we focus on the coupling of the cell cycle and the circadian clock and show how an additional source of multi-rhythmicity arises from the bidirectional coupling of these two cellular  ...  (multi-rhythmicity), which has been predicted by a variety of models for biological oscillators.  ...  on the model for the coupled circadian clock and cell cycle oscillators in mammalian cells, see(Yan and Goldbeter, 2019c).  ... 
doi:10.6084/m9.figshare.19367098.v2 fatcat:2rd6kuurgnh6rehkzupya5bkru

The Mammalian Circadian Timing System and the Suprachiasmatic Nucleus as Its Pacemaker

Michael H. Hastings, Elizabeth S. Maywood, Marco Brancaccio
2019 Biology  
Finally, it will consider new directions in analysing the cell-autonomous and circuit-level SCN clockwork and will highlight the surprising discovery of a central role for SCN astrocytes as well as SCN  ...  This review will consider, briefly, comparative circadian clock biology and will then focus on the mammalian circadian system, considering its molecular genetic basis, the properties of the suprachiasmatic  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology8010013 pmid:30862123 pmcid:PMC6466121 fatcat:plsn2gn575gafkcilnpmiz3zu4

Unveiling "Musica Universalis" of the Cell: A Brief History of Biological 12-Hour Rhythms

Bokai Zhu, Clifford C Dacso, Bert W O'Malley
2018 Journal of the Endocrine Society  
These oscillations often cycle at different harmonics of the circadian rhythm, and among these, the~12-hour oscillation is most prevalent.  ...  Finally, we posit that biological rhythms are also musica universalis: whereas the circadian rhythm is synchronized to the 24-hour light/dark cycle coinciding with the Earth's rotation, the mammalian 12  ...  Oren Levy and Yisrael Schnytzer from Bar-Ilan University for sharing the processed transcriptome data of C. rota. We apologize for omission of relevant works and citations due to space constraints.  ... 
doi:10.1210/js.2018-00113 pmid:29978151 pmcid:PMC6025213 fatcat:lsacma44uvayhihzv7jh4pxl3m

A Cell-Autonomous Mammalian 12 hr Clock Coordinates Metabolic and Stress Rhythms

Bokai Zhu, Qiang Zhang, Yinghong Pan, Emily M. Mace, Brian York, Athanasios C. Antoulas, Clifford C. Dacso, Bert W. O'Malley
2017 Cell Metabolism  
The mammalian 12h rhythm is cell-autonomous, driven by a dedicated 12h pacemaker distinct from the circadian clock and can be entrained in vitro by metabolic and ER stress cues.  ...  Besides circadian rhythms, oscillations cycling with a 12h period exist. However, the prevalence, origin, regulation and function of mammalian 12h rhythms remain elusive.  ...  In addition, this research also was supported by grants from the Center for Advancement of Science in Space, Peter J. Fluor Family Fund, Philip J. Carroll, Jr.  ... 
doi:10.1016/j.cmet.2017.05.004 pmid:28591634 pmcid:PMC5526350 fatcat:edwzj3adrbbw7l3g7lwak3ip3y

The rhythms of life

Jürgen A Ripperger
2007 Genome Biology  
This year's symposium not only provided insights into the latest research of circadian rhythms in cyanobacteria, Neurospora, Drosophila, Arabidopsis and mammals, but also on metabolic cycles in yeast,  ...  I will focus here only on some aspects of the meeting.  ...  Taken together, the results point strongly to a model in which a cell-autonomous oscillator rhythmically modulates a morphogenic gradient.  ... 
doi:10.1186/gb-2007-8-8-313 pmid:17764590 pmcid:PMC2374983 fatcat:kdcemmwqrnh6xibqnrxye57uky

Page 577 of Biological Reviews Vol. 68, Issue 4 [page]

1993 Biological Reviews  
Oscillations and control features in glycolysis in numerical analysis of a comprehensive model. Proceedings of the National Academy of Sciences, U.S.A. 78, 2952-2956. Turetzky, D. (ed.) (1990).  ...  . & BENNINK, C. (1990). the binary logic of antigen processing and presentation of T cells. Cell 62, 203-209.  ... 

EFFICIENT MULTISCALE SIMULATION OF CIRCADIAN RHYTHMS USING AUTOMATED PHASE MACROMODELLING TECHNIQUES

SHATAM AGARWAL, JAIJEET ROYCHOWDHURY
2007 Biocomputing 2008  
We present the application of efficient, numerically wellconditioned algorithms for abstracting (potentially large) systems of differential equation models of circadian oscillators into compact, accurate  ...  Further, we apply the macromodels to simulate a system of 400 coupled circadian oscillators, achieving speedups of 240× and accurately reproducing synchronization and locking phenomena amongst the oscillators  ...  Models of Drosophila and mammal circadian rhythms Computational models are available for circadian rhythms in Drosophila, Neurospora, cyanobacteria and mammalian systems. 1,2 These models, useful for computing  ... 
doi:10.1142/9789812776136_0039 fatcat:p3yi4dzdtfb2vjxxphutciziyi

Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics

Mohammad Mofatteh, Fabio Echegaray-Iturra, Andrew Alamban, Francesco Dalla Ricca, Anand Bakshi, Mustafa G Aydogan
2021 eLife  
division oscillator and the circadian clock.  ...  In this review, we provide an overview of the recent evidence supporting an emerging concept of 'autonomous clocks,' which under normal conditions can be entrained by the cell cycle and/or the circadian  ...  Acknowledgements Care was taken to cite appropriate references; we apologize to the authors of numerous other outstanding papers that contributed to the study of biological time control, but could not  ... 
doi:10.7554/elife.72104 pmid:34586070 fatcat:xjugtw2wnzh2fowg2znrm3t6eq
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