Model Name: Salazar2009_FloweringPhotoperiod

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Model Format SBML L2 V1
Description

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009.

Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org).

Simulation notes for SBML version of Model3 from Salazar et al., Cell, 2009.

The interlocking-loop circadian clock in this model reaches its entrained limit cycle rather slowly. To ensure that simulations show the stable phase under any light:dark cycle, the model should be run for 720 hours (30 days) before evaluating its behaviour in light:dark cycles. Using the boundary value solver in Matlab, as described in the paper, avoids this issue.

SBML prepared by Dr. Treenut Saithong, based on Matlab by Dr. Domingo Salazar. Model depositor, updates to version 2, Prof. Andrew Millar.

Note comment from Rob Smith on Figure 5.

 
Contact/Model Admin Andrew Millar, University of Edinburgh, andrew.millar@ed.ac.uk
Submitted By Andrew Millar, University of Edinburgh, andrew.millar@ed.ac.uk
Submission Date 2010-05-05 15:16:35.0
Images
Supplementary Data Files
ZIP archive of Matlab model files for the models described in the paper
Figure 1 of the paper, with a cartoon of the model. Model3 is provided as SBML. This is the sum of model 1(b) and model 2(b) shown in the cartoon.
Model Files original file, simplified file (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Journal Cell 
Title Prediction of photoperiodic regulators from quantitative gene circuit models 
Year 2009 
Authors Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ. 
Abstract Photoperiod sensors allow physiological adaptation to the changing seasons. The prevalent hypothesis is that day length perception is mediated through coupling of an endogenous rhythm with an external light signal. Sufficient molecular data are available to test this quantitatively in plants, though not yet in mammals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their light-sensitive proteins are thought to form an external coincidence sensor. Here, we model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, our models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modeling makes this complexity explicit and may thus contribute to crop improvement. 
URL http://www.ncbi.nlm.nih.gov/pubmed/20005809 
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1. Comment by s0921165 on 2011-08-19 12:35:48.0

The FT expression in Figure 5 in Salazar et al. (2009) was simulated using Model 3b. Model 3b is a slight modification of Model 3. Instead of having nTOC1 (nuclear TOC1 protein) replacing CO mRNA directly (as in equation 4 in the Supplementary), Model 3b contains an additional ODE for CO mRNA as follows:

 dCOm/dt = dnTOC1/dt - 0.0004L.vnTOC1.nTOC1

                      

where COm = CO mRNA concentration, L = Light and vnTOC1 = nuclear TOC1 protein degradation rate. The additional term represents CO mRNA degradation rate, which was slightly increased (by 0.04% of its original value) during the light interval. This was done to improve fit for training data set 8.

 

Thus, equation 4 in the Supplementary becomes

 dCOp/dt = vCOm.COm - (1 - L).vCOp.COp/(kCOp + COp)

 

All parameter values remain the same.

2. Comment by s0921165 on 2011-08-19 12:23:46.0

 The FT expression in Figure 5 in Salazar et al. (2009) was simulated using Model 3b. Model 3b is a slight modification of Model 3. Instead of having nTOC1 (nuclear TOC1 protein) replacing CO mRNA directly (as in equation 4 in the Supplementary), Model 3b contains an additional ODE for CO mRNA as follows:

 

 

                        

where COm = CO mRNA concentration, L = Light and vnTOC1 = nuclear TOC1 protein degradation rate. The additional term represents CO mRNA degradation rate, which was slightly increased (by 0.04% of its original value) during the light interval. This was done to improve fit for training data set 8.

 

Thus, equation 4 in the Supplementary becomes

 

 

All parameter values remain the same.