Comparative study of circadian oscillatory network models of Drosophila

Yukino Ogawa, Kazuharu Arakawa, Kazunari Kaizu, Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The circadian clock of Drosophila is a model pathway for research in biological dock mechanisms, both with traditional experimental approaches and with emerging systems biology approaches utilizing mathematical modeling and in silico computer simulation. Dynamic diurnal oscillations are achieved by the complex interaction of components as a system, and mathematical reconstruction his proven to be an invaluable means of understanding such systematic behavior. In this study, we implemented eight published models of the Drosqpbila circadian clock in Systems Biology Markup Language (SBML) for comparative systems biology studies using E-Cell Simulation Environment version 3, to examine the system-level requirements for the clock mechanism to be robust, by calculating the period and amplitude sensitivity coefficients with simulation experiments. While all models were generally robust as determined by the network topology of the oscillatory feedback loop structure, existing models place relatively strong emphasis on transcription regulation, although this is a limitation on robustness. We suggest that more comprehensive modeling including protein phosphorylation, polymerization, and nuclear transport with regard to amplitude sensitivity will be necessary for understanding the light entrainment and temperature compensation of circadian clocks.

Original languageEnglish
Pages (from-to)29-48
Number of pages20
JournalArtificial Life
Volume14
Issue number1
DOIs
Publication statusPublished - 2008 Dec

Fingerprint

Circadian Clocks
Systems Biology
Drosophilidae
Network Model
Drosophila
Comparative Study
Clocks
Computer Simulation
Cell Nucleus Active Transport
Protein Phosphorylation
Temperature Compensation
Sensitivity Coefficient
Markup languages
Polymerization
Phosphorylation
Docks
Entrainment
Feedback Loop
Language
Transcription

Keywords

  • Cell simulation
  • Circadian rhythm
  • Drosophila
  • Mathematical models
  • Systems biology

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Artificial Intelligence
  • Theoretical Computer Science
  • Computational Theory and Mathematics
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Comparative study of circadian oscillatory network models of Drosophila. / Ogawa, Yukino; Arakawa, Kazuharu; Kaizu, Kazunari; Miyoshi, Fumihiko; Nakayama, Yoichi; Tomita, Masaru.

In: Artificial Life, Vol. 14, No. 1, 12.2008, p. 29-48.

Research output: Contribution to journalArticle

Ogawa, Yukino ; Arakawa, Kazuharu ; Kaizu, Kazunari ; Miyoshi, Fumihiko ; Nakayama, Yoichi ; Tomita, Masaru. / Comparative study of circadian oscillatory network models of Drosophila. In: Artificial Life. 2008 ; Vol. 14, No. 1. pp. 29-48.
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