Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model

Alexandra Pokhilko; Karen Halliday; Andrew Millar

Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model

Alexandra Pokhilko, Karen Halliday, Andrew Millar

School of Biological Sciences

Research output: Other contribution

Abstract / Description of output

[from the record in PlaSMo] This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, published 6 March 2012. Link

The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including:

the Evening Complex genes (ELF4, ELF3, LUX),
light-regulated degradation of ELF3 by COP1,
TOC1 as a repressor rather than an activator of LHY/CCA1.

These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).

Compared to the model version submitted to the Biomodels database, this version slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. This will facilitate the use of a generic SBML StepFunction to better describe the light-dark cycle, in a subsequent version of this model.

Original language	English
Type	Pokhilko2011_A.thal.Clock_Model
Media of output	SBML model
Publication status	Published - 2012

Keywords / Materials (for Non-textual outputs)

Biological Clocks
Circadian Rhythms
mathematical modeling
MODEL SIMULATION
Systems Biology

Access to Document

5 Finished

TiMet: Linking the clock to metabolism
Millar, A.
EU government bodies
1/03/10 → 28/02/15
Project: Research
A modelling portal for the UK plant systems biology community
Millar, A., Tindal, C., Muetzelfeldt, R. & Ougham, H.
BBSRC
16/09/08 → 15/09/10
Project: Research
Regulation of biological signalling by temperature (ROBUST)
Halliday, K., Gilmore, S. & Millar, A.
BBSRC
14/04/08 → 13/10/13
Project: Research

2 Article
1 Other contribution

Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock
Keily, J., MacGregor, D. R., Smith, R. W., Millar, A. J., Halliday, K. J. & Penfield, S., 31 Oct 2013, In: The Plant Journal. 76, 2, p. 247-57 11 p.
Research output: Contribution to journal › Article › peer-review

Open Access
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
Pokhilko, A., Fernández, A. P., Edwards, K. D., Southern, M. M., Halliday, K. J. & Millar, A. J., 2012, In: Molecular Systems Biology. 8, 574.
Research output: Contribution to journal › Article › peer-review

Open Access
File
The Biodare Data Repository
Zielinski, T., Moore, A., Troup, E., Beaton, M., Adams, R., Halliday, K. & Millar, A., 2011
Research output: Other contribution

Plant Systems Modelling database
Millar, A. (Creator), University of Edinburgh, 2009
https://fairdomhub.org/projects/129 and one more link, http://www.plasmo.ed.ac.uk (show fewer)
Dataset

1 Participation in conference

International Symposium on Plant Photobiology
Karen Halliday (Organiser)
3 Jun 2013 → 6 Jun 2013
Activity: Participating in or organising an event types › Participation in conference

Cite this

@misc{0f3c97c7546c4e0b94376ed67a935ad0,

title = "Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model",

abstract = "[from the record in PlaSMo] This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Pi{\~n}as Fern{\'a}ndez, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, published 6 March 2012. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including: the Evening Complex genes (ELF4, ELF3, LUX), light-regulated degradation of ELF3 by COP1, TOC1 as a repressor rather than an activator of LHY/CCA1.These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).Compared to the model version submitted to the Biomodels database, this version slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. This will facilitate the use of a generic SBML StepFunction to better describe the light-dark cycle, in a subsequent version of this model.",

keywords = "Biological Clocks, Circadian Rhythms, mathematical modeling, MODEL SIMULATION, Systems Biology",

author = "Alexandra Pokhilko and Karen Halliday and Andrew Millar",

year = "2012",

language = "English",

type = "Other",

}

TY - GEN

T1 - Mathematical model of the Arabidopsis circadian clock

T2 - Pokhilko 2011 model

AU - Pokhilko, Alexandra

AU - Halliday, Karen

AU - Millar, Andrew

PY - 2012

Y1 - 2012

N2 - [from the record in PlaSMo] This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, published 6 March 2012. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including: the Evening Complex genes (ELF4, ELF3, LUX), light-regulated degradation of ELF3 by COP1, TOC1 as a repressor rather than an activator of LHY/CCA1.These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).Compared to the model version submitted to the Biomodels database, this version slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. This will facilitate the use of a generic SBML StepFunction to better describe the light-dark cycle, in a subsequent version of this model.

AB - [from the record in PlaSMo] This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, published 6 March 2012. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including: the Evening Complex genes (ELF4, ELF3, LUX), light-regulated degradation of ELF3 by COP1, TOC1 as a repressor rather than an activator of LHY/CCA1.These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).Compared to the model version submitted to the Biomodels database, this version slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. This will facilitate the use of a generic SBML StepFunction to better describe the light-dark cycle, in a subsequent version of this model.

KW - Biological Clocks

KW - Circadian Rhythms

KW - mathematical modeling

KW - MODEL SIMULATION

KW - Systems Biology

M3 - Other contribution

ER -

Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Research output

Datasets

Activities

Cite this