Salazar2009_FloweringPhotoperiod - PLM_9, version 1

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.

Related Publications
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

Comments


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.


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

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

SEEK ID: https://fairdomhub.org/assays/886

Modelling Analysis

BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Salazar2009_FloweringPhotoperiod - PLM_9

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

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Andrew Millar
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Created: 10th Jan 2019 at 17:41

Last updated: 22nd Jan 2019 at 18:21

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