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Stochastic Modelling of the Kai-based Circadian Clock

Chris Banks, Allan Clark, Anastasis Georgoulas, Stephen Gilmore, Jane Hillston, Dimitrios Milios, Ian Stark
2013 Electronical Notes in Theoretical Computer Science  
We present two process algebra models of a Kai-protein based circadian clock. Our models are represented in the Bio-PEPA and the continuous pi-calculus process algebras.  ...  We reproduce previous results based on ODE models and then use our models as the basis for stochastic simulation.  ...  We present two process algebra-based models of the Kai-based circadian clock, the first written in Bio-PEPA, the second in the continuous pi-calculus.  ... 
doi:10.1016/j.entcs.2013.07.004 fatcat:r37n2o2fxncstmemrux427mjaa

The cyanobacterial clock and metabolism

Gopal Pattanayak, Michael J Rust
2014 Current Opinion in Microbiology  
Cyanobacteria possess the simplest known circadian clock, which presents a unique opportunity to study how rhythms are generated and how input signals from the environment reset the clock time.  ...  We offer a summary of the current state of knowledge in this system and present a perspective for future lines of investigation.  ...  Thus, the Law of Large Numbers may effectively suppress stochasticity in the clock time [31] .  ... 
doi:10.1016/j.mib.2014.02.010 pmid:24667330 pmcid:PMC4068238 fatcat:vlir6nkxyrbddotzjdirw44joy

2E1424 An explanation of temperature compensation of Kai-protein-based circadian clock(Nonequilibrium state & Biological rhythum,The 48th Annual Meeting of the Biophysical Society of Japan)
2E1424 Kai蛋白質概日時計の温度補償性に関する理論的研究(非平衡・生体リズム,第49回日本生物物理学会年会)

Tetsuhiro Hatakeyama, Kunihiko Kaneko
2011 Seibutsu Butsuri  
Thus, we construct the stochastic kemel using the asyniptotic expansion An explanation of temperature compensation of Kai-proteinbased circadian clock Tetsuhiro Hatakeyama, Kunihiko Kaneko (Linii, of  ...  Furthermore, Kondo and his colleagues recently demonstrated that the period of circadian oscMatien or Kai-proteins indeed is temperature compcnsated, By simulating a rnodel with phosphorationldephospheration  ... 
doi:10.2142/biophys.51.s82_2 fatcat:u6ptpj3l3baotedganohbbraia

Robust circadian clocks from coupled protein-modification and transcription-translation cycles

D. Zwicker, D. K. Lubensky, P. R. ten Wolde
2010 Proceedings of the National Academy of Sciences of the United States of America  
clock ceases to function well when the cell doubling time drops below the 24 hour clock period.  ...  Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.  ...  We thank Tom Shimizu for critically reading the manuscript.  ... 
doi:10.1073/pnas.1007613107 pmid:21149676 pmcid:PMC3012469 fatcat:ljm3wye3xbeutlv65vnn4neody

Robust, coherent and synchronized circadian clock-controlled oscillations along Anabaena filaments

Rinat Arbel-Goren, Valentina Buonfiglio, Francesca Di Patti, Sergio Camargo, Ana Valladares, Enrique Flores, Antonia Herrero, Duccio Fanelli, Joel Stavans
2021 eLife  
The model reproduces the observed spatio-temporal coherence along filaments, and provides a robust description of coupled circadian clocks in a multicellular organism.  ...  A stochastic, one-dimensional toy model of coupled clock cores and their phosphorylation states shows that demographic noise can seed stochastic oscillations outside the region where deterministic limit  ...  Fund; Fondazione Ente Cassa di Risparmio, Florence, Italy (DF, FDP, VB); Project EXPLICS granted by the Italian Ministry of Foreign Affairs and International Cooperation (FDP).  ... 
doi:10.7554/elife.64348 fatcat:2lpczwq5z5f45ia7whyttbez3i

The molecular clockwork of a protein-based circadian oscillator

Joseph S. Markson, Erin K. O'Shea
2009 FEBS Letters  
The molecular clockwork of a protein-based circadian oscillator. FEBS Letters 583 (24) : 3938-3947.  ...  Published Version Abstract The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 is governed by a core oscillator consisting of the proteins KaiA, KaiB, and KaiC.  ...  Acknowledgements We thank Michael Rust for many insightful comments and stimulating discussions about the Kai oscillator, and M.R. and Vikram Vijayan for comments on the manuscript.  ... 
doi:10.1016/j.febslet.2009.11.021 pmid:19913541 pmcid:PMC2810098 fatcat:iwhfxhqahnd3fevuqluochx6zy

Circadian KaiC Phosphorylation: A Multi-Layer Network

Congxin Li, Xiaofang Chen, Pengye Wang, Weichi Wang, Jorg Stelling
2009 PLoS Computational Biology  
Particularly, our model reveals that a single KaiC hexamer is an energy-based, phosphorylation-dependent and self-regulated circadian oscillator modulated by KaiA and KaiB.  ...  Similar results were obtained regardless of the deterministic or stochastic method employed.  ...  Performed the experiments: CL XC PW WW. Wrote the paper: CL WW.  ... 
doi:10.1371/journal.pcbi.1000568 pmid:19936045 pmcid:PMC2773046 fatcat:5kcqsllxgzhs3ppkhcbh4jfkwe

Quantifying the Rhythm of KaiB-C Interaction for In Vitro Cyanobacterial Circadian Clock

Lan Ma, Rama Ranganathan, Zhi Xie
2012 PLoS ONE  
Here, we first propose a mathematical model of cyanobacterial circadian clock that explains the recently observed dynamics of the four phospho-states of KaiC as well as the interactions among the three  ...  An oscillator consisting of KaiA, KaiB, and KaiC proteins comprises the core of cyanobacterial circadian clock.  ...  Acknowledgments We thank S Helms, F Poelwijk and W Russ for comments, S Leibler for the plasmids of GST-KaiB and GST-KaiA, and E Ross for the constructs of Cerulean and Venus.  ... 
doi:10.1371/journal.pone.0042581 pmid:22900029 pmcid:PMC3416856 fatcat:wffbptczovbadnvgss2ho3arjm

Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure

Maria L. Guerriero, Ozgur E. Akman, Gerben van Ooijen
2014 Frontiers in Plant Science  
Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more  ...  Stochastic models have proven useful for understanding the effect of regular variations.  ...  Most published models of the circadian clock in Arabidopsis are continuous deterministic models based on ordinary differential equations (ODEs).  ... 
doi:10.3389/fpls.2014.00564 pmid:25374576 pmcid:PMC4204444 fatcat:ie4i5wbz6badfpqjsmjr2u4t4q

A Cyanobacterial Circadian Clock Based on the Kai Oscillator

T. Kondo
2007 Cold Spring Harbor Symposia on Quantitative Biology  
How do the three Kai proteins interact to produce a pre- A Cyanobacterial Circadian Clock Based on the Kai Oscillator T.  ...  On the basis of classical observation of circadian rhythm, we have two models for the entrainment of the circadian clock.  ...  ACKNOWLEDGMENTS I thank the current and former lab members who contributed to our studies of the cyanobacterial circadian clock.  ... 
doi:10.1101/sqb.2007.72.029 pmid:18419262 fatcat:seq5vlradrdqzfmd34blqotc4i

Bacterial Circadian Programs

C. H. Johnson
2007 Cold Spring Harbor Symposia on Quantitative Biology  
Since that time, however, the cyanobacterial circadian system has progressed from a curiosity to a major model system for analyzing clock phenomena.  ...  A biochemical oscillator can be reconstituted in vitro with these three purified Kai proteins and displays the key properties of temperature-compensated rhythmicity.  ...  Kondo's sabbatical in my laboratory with the help of Dr. Susan Golden, and later Dr. Masahiro Ishiura. The labs of these four scientists (Kondo, Golden, Ishiura, and Johnson)  ... 
doi:10.1101/sqb.2007.72.027 pmid:18419297 fatcat:qoamgv6y2vb3lbfy3hfnt2vb2u

Hourglass Model for a Protein-Based Circadian Oscillator

Eldon Emberly, Ned S. Wingreen
2006 Physical Review Letters  
We propose that stability of the Kai-protein oscillator relies on active synchronization by (i) monomer exchange between KaiC hexamers during the day, and (ii) formation of clusters of KaiC hexamers at  ...  Our results highlight the importance of collective assembly or disassembly of proteins in biochemical networks, and may help guide design of novel protein-based oscillators.  ...  If each KaiC hexamer is following its own stochastic cycle of phosphorylation and dephosphorylation, how are these cycles synchronized to form a coherent clock?  ... 
doi:10.1103/physrevlett.96.038303 pmid:16486780 pmcid:PMC1995810 fatcat:cihkdz3ivbcplch2llnazafv6i

The Cyanobacterial Circadian System: From Biophysics to Bioevolution

Carl Hirschie Johnson, Phoebe L. Stewart, Martin Egli
2011 Annual Review of Biophysics  
Models of the complete in vivo system have important implications for our understanding of circadian clocks in higher organisms, including mammals.  ...  Recent studies have unveiled the molecular machinery responsible for the biological clock in cyanobacteria and found that it exerts pervasive control over cellular processes including global gene expression  ...  O'Shea, and their laboratory members, whose seminal contributions continue to make the study of cyanobacterial clocks fascinating.  ... 
doi:10.1146/annurev-biophys-042910-155317 pmid:21332358 pmcid:PMC3093959 fatcat:a43i7airw5g63onljgv4xhgrqa

A Cyanobacterial Circadian Clockwork

Carl Hirschie Johnson, Tetsuya Mori, Yao Xu
2008 Current Biology  
Cyanobacteria have become a major model system for analyzing circadian rhythms.  ...  The timing of cell division is gated by a circadian checkpoint, but the circadian pacemaker is not influenced by the status of the cell division cycle.  ...  We also thank Takao Kondo, Susan Golden, Masahiro Ishiura, and their laboratory members; these labs together with ours initiated the study of circadian clocks in S. elongatus and continue to make seminal  ... 
doi:10.1016/j.cub.2008.07.012 pmid:18786387 pmcid:PMC2585598 fatcat:y52hi5i4and4zottxbsynkoulm

Circadian period-heterogeneity is governed by clonal inheritance of variable gene expression [article]

K L Nikhil, Sandra Korge, Achim Kramer
2019 bioRxiv   pre-print
While the presence of inter-oscillator coupling is hypothesized to counterbalance such heterogeneity in circadian clock networks, our knowledge of mechanisms governing network heterogeneity remains elusive  ...  A ubiquitous feature of circadian clock across life forms is its organization as a network of coupled oscillators.  ...  Barbara Koller for the technical help with NanoString experiments.  ... 
doi:10.1101/731075 fatcat:p4tr7eafmzfpdjv5zf2vnngxji
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