Salazar2009_FloweringPhotoperiod - PLM_9, version 2

The model shows how the <em>CONSTANS</em> gene and protein in <em>Arabidopsis thaliana</em> 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 (<a href="http://www.amillar.org">www.amillar.org</a>).	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.<br><br><strong>Related Publications</strong><br>Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ. (2009). Prediction of photoperiodic regulators from quantitative gene circuit models. Cell. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/20005809<br><br><strong>Comments</strong><p>
The <em>FT</em> 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 <em>nTOC1</em> (nuclear TOC1 protein) replacing <em>CO</em> mRNA directly (as in equation 4 in the Supplementary), Model 3b contains an additional ODE for <em>CO</em> mRNA as follows:</p>

 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.

2011-08-19 12:35:48 121 s0921165 s0921165@sms.ed.ac.uk

 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.

2011-08-19 12:23:46 121 s0921165 s0921165@sms.ed.ac.uk

Version Comments

Version 2 of the model does not have the Matlab files attached, these are only on version 1.

Version 2 removes the 'time' variable in the lightFunction, replacing it with 't' for SBML compatibility.

Originally submitted to PLaSMo on 2010-05-05 15:16:35