Arabidopsis_clock_P2012 - PLM_70, version 2

This model is termed P2012 and derives from the article: <strong>Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs</strong>. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. <a href="http://dx.doi.org10.1186/1752-0509-7-23">Link</a>

The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including:

• TOC1 as a repressor of multiple clock genes, rather than only of LHY/CCA1.
• ABAR transcription modified by TOC1, affecting stomatal aperture.
• TOC1 transcription modified by ABA.

<strong>Notes on the paper
</strong>

In 2018, Daewook Kim made us aware of a likely typo in the printed version of the model equations in the paper, where the term (A_0+c^m_ABAR+g29) in the last equation about c_AR lacks a ^2. 

i.e. Sqrt[ (A_0+c^m_ABAR+g29)-4A_0c^m_ABAR) ] -> Sqrt[ (A_0+c^m_ABAR+g29)^2 -4A_0c^m_ABAR) ].

<strong>SBML curation notes</strong> (please see Comments for each version):

version 1 here is the version published as Supplementary Information and submitted to the Biomodels database.

Copasi and MATLAB versions are attached to version 1.

NB. Use only 'v1' Matlab files. Matlab files named 'v0' have older parameter values for parameters g4, g23, g25, m6, m23, m24, though these differ only slightly. The Copasi version is the same as the published SBML version, and the 'v1' matlab files.

This model has formed the basis for further work by external groups, as described in the following links:

Fogelmark et al. PLoS CB 2014 - <a href="http://dx.doi.org/10.1371/journal.pcbi.1003705">http://dx.doi.org/10.1371/journal.pcbi.1003705</a>

Zhou et al. Nature 2015 - <a href="http://dx.doi.org/10.1038/nature14449">http://dx.doi.org/10.1038/nature14449</a>

Foo et al. PLoS CB 2016 - <a href="http://dx.doi.org/10.3389/fpls.2016.00074">http://dx.doi.org/</a><a href="http://dx.doi.org/10.1371/journal.pcbi.1004748">10.1371/journal.pcbi.1004748 </a>

Calluwe et al. Frontiers 2016 - <a href="http://dx.doi.org/10.3389/fpls.2016.00074">http://dx.doi.org/10.3389/fpls.2016.00074 </a>

Related Publications
Alexandra Pokhilko, Paloma Mas & Andrew J Millar (2013). Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs.. BMC Systems Biology. Retrieved from: http://dx.doi.org/10.1186/1752-0509-7-23

Version Comments

P2012 model with the original light function replaced by an Input Signal Step Function, as described in Adams et al. J. Biol. Rhythms 2012. Initial values were also updated to ZT0 on the 12L:12D limit cycle.