k1*PRODUCT<substrate_i> 2011-01-07T14:21:03Z ceil(sin(PI*tod/12)/2) acc_rate * light(t) acc_rate * acc 2011-01-07T14:58:29Z LD1212(tod) 2011-01-07T17:28:54Z transcription(t) * (ox_toc1(t) + copies_toc1(t) *(L_toc1 + R_toc1_acc * acc) / (1 + L_toc1 + R_toc1_acc * acc + (R_toc1_cca1 * tf_output(rep_CCA1, effcopies_cca1_LHY7, cca1_n))^H_toc1_cca1)) 1+0*t 2011-01-07T14:31:03Z 0*t 2011-01-07T14:30:53Z 1+0*t 2011-01-07T14:30:50Z 1+0*t 2011-01-07T14:31:02Z 0*t 2011-01-07T18:14:42Z 1+0*t 1+0*t 2011-01-07T18:14:40Z translation(t) * T * mrna proteasome(t) * (light(t) * D_l + (1 - light(t)) * D_d) * level (light(t) * Di_l + (1 - light(t)) * Di_d) * level 2011-01-07T14:30:23Z transcription(t) * (ox_cca1(t) + copies_cca1(t) * ((tf_output(rep_TOC1, effcopies_toc1_TOC8, toc1_2) * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1) /(( tf_output(rep_TOC1, effcopies_toc1_TOC8, toc1_2) * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1 + 1) ) 2011-01-07T18:05:12Z rep_pTOC1 * transcription(t) * (L_toc1 + R_toc1_acc * acc) / (1 + L_toc1 + R_toc1_acc * acc + (R_toc1_cca1 * cca1_n)^H_toc1_cca1) 2011-01-07T17:27:48Z rep_TOC1 * transcription(t) * copies_toc1(t) *(L_toc1 + R_toc1_acc * acc) / (1 + L_toc1 + R_toc1_acc * acc + (R_toc1_cca1 * cca1_n)^H_toc1_cca1) 2011-01-07T18:04:25Z rep_pCCA1 * transcription(t) * ((toc1_2 * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1) /((toc1_2 * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1 + 1) 2011-01-07T14:22:48Z rep_CCA1 * transcription(t) * copies_cca1(t) * ((toc1_2 * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1) /((toc1_2 * (light(t) * R_cca1_toc1_2_l + (1-light(t)) * R_cca1_toc1_2_d)) ^ H_cca1_toc1 + 1) 2011-01-07T14:29:56Z 2000-01-01T00:00:00Z (1 + reporter * (effcopies - 1)) * tf 2008-01-01T23:25:42Z carl.troein@ed.ac.uk Carl Troein Institute of Molecular Plant Sciences, University of Edinburgh andrew.millar@ed.ac.uk Millar Andrew J Institute of Molecular Plant Sciences, University of Edinburgh 2009-01-04T17:04:00Z

Two-gene model of the Ostreococcus circadian clock

This is a model of the circadian clock of Ostreococcus tauri, with a negative feedback loop between TOC1 and CCA1 (a.k.a. LHY) and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011).

The model incorporates luciferase reporters, and in this SBML model the four different versions of the model for transcriptional and translational reporter lines (pTOC1::LUC, pCCA1::LUC, TOC1-LUC and CCA1-LUC) are all accessible by setting one of the rep_X parameters to 1 and the others to 0. You can also set all four to 0 to only simulate the non-reporter core of the system.

Input to the system should be provided by modifying the "light" function. An implementation of LD 12:12 is provided as an example, but the model was also used with more complicated light regimes that vary between data sets and are not convenient to express directly in SBML.

The functions "ox_cca1" and "ox_toc1" can be altered to add overexpression of CCA1 and TOC1. Setting either to x gives additional, constitutive transcription at x times the maximal (and typically not realizable) transcription rate of the native gene. The overexpression mutant fits in Figure 7 of Troein et al. (2011) used ox_cca1 = 0.115 and oc_toc1 = 0.0584, respectively.

The functions "copies_toc1" and "copies_cca1" are normally 1 but can be lowered to simulate knockdown experiments. The functions "transcription", "translation" and "proteasome" can be modified to simulate the effects of altering the overall rate of transcription, translation and protein degradation.

The parameters were fitted specifically to data from transgenic reporter lines TOC8, pTOC3, LHY7 and pLHY7 (Corellou et al., Plant Cell 2009). Parameters that begin with "effcopies" describe the effective number of copies of CCA1 or TOC1 in the respective translational fusion lines, with anything above 1 due to the fusion proteins.

For the model fitting, the initial values were fitted to the data in the various time courses. The initial values given here correspond to the limit cycle of the system in LD 12:12. The system converges to the limit cycle in just a few days under most light conditions, so these initial values are biologically meaningful.

The species cca1luc_c and cca1luc_n have been merged into cca1luc (which corresponds to the observable luminescence signal), because Copasi refused to run the system otherwise. For TOC1-LUC, the predicted output signal is the sum of toc1luc_1 and toc1luc_2.

2011-01-07T14:19:06Z 2000-01-01T00:00:00Z 2011-01-07T14:53:26Z 2011-01-07T14:53:13Z 2011-01-07T14:53:15Z 2011-01-07T14:27:49Z 2011-01-07T14:19:16Z 2011-01-07T14:53:05Z 2011-01-07T14:52:33Z 2011-01-07T14:53:15Z 2011-01-07T14:53:19Z 2011-01-07T14:52:52Z 2011-01-07T14:19:25Z 2011-01-07T14:53:12Z 2011-01-07T14:53:08Z 2011-01-07T14:20:14Z 2011-01-07T18:18:41Z 2011-01-07T14:20:31Z 2011-01-07T15:03:45Z 2011-01-07T14:38:01Z 2011-01-07T14:20:18Z 2011-01-07T14:37:50Z 2011-01-07T14:37:55Z 2011-01-07T15:03:35Z 2011-01-07T14:53:48Z 2011-01-07T14:37:48Z 2011-01-07T14:53:49Z 2011-01-07T17:31:40Z 2011-01-07T17:30:20Z 2011-01-07T17:30:19Z 2011-01-07T18:15:26Z 2011-01-07T17:31:29Z 2011-01-07T17:30:10Z 2011-01-07T18:27:53Z 2011-01-07T14:28:08Z 2011-01-07T18:15:53Z 2011-01-07T17:30:16Z 2011-01-07T17:30:12Z 2011-01-07T17:30:57Z 2011-01-07T17:30:52Z 2011-01-07T17:29:17Z 2011-01-07T17:30:36Z 2011-01-07T17:30:42Z 2011-01-07T17:29:21Z 2011-01-07T17:30:31Z 2011-01-07T17:30:15Z 2011-01-07T14:28:14Z 2011-01-07T17:29:50Z 2011-01-07T17:30:04Z 2011-01-07T17:29:39Z 2011-01-07T17:29:26Z 0 30902875945018.46 0 0 0 0 163842821700617.3 0 23225308738435.96 62964889161900.93 0 124370033546632.5 0 1850506308824216 188319532062607.3 0.1828812174632586 1 0.08201322503032867 1.087061268589661 2.078077386923434 0.0001 0.2311070329494072 0.2921304977837297 0.7699701729778862 0.1364905833686477 0.3266194920897148 0.4615505591808016 0.3566139205511183 2.500706288063396 3.275202921038323 1.385639016822662 1.330820809545275 4.904866104286524 10 0.4241778774494377 0.2693801781540909 1.139657555086233 1 1 0 0 0 0 1 Automatically generated report.