Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2)

  public model
Short description
 cL_m_degr, param m1, modified to ensure light rate > dark rate. Parameter set from PLM_67v2_LDLLLDs_newFFT_1, with modification to m1 (= old_m1 - m2).
Format
SBML (L2V4)
Related Publication
  • Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
  • Flis A, Fern├índez AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ
  • Open biology , 10/ 2015 , Volume 5
  • Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
  • Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.
Contributors
Andrew J Millar

Metadata information

isDerivedFrom
BioModels Database BIOMD0000000412
is
BioModels Database MODEL1510190001
BioModels Database BIOMD0000000598
isDescribedBy
PubMed 26468131
hasTaxon
isVersionOf

Curation status
Curated

Original model(s)
MODEL1510190000

Tags
Name Description Size Actions

Model files

BIOMD0000000598_url.xml SBML L2V4 representation of Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2) 186.73 KB Preview | Download

Additional files

BIOMD0000000598.m Auto-generated Octave file 30.80 KB Preview | Download
BIOMD0000000598-biopax2.owl Auto-generated BioPAX (Level 2) 49.86 KB Preview | Download
BIOMD0000000598.png Auto-generated Reaction graph (PNG) 1.36 MB Preview | Download
BIOMD0000000598.pdf Auto-generated PDF file 495.26 KB Preview | Download
BIOMD0000000598-biopax3.owl Auto-generated BioPAX (Level 3) 79.08 KB Preview | Download
BIOMD0000000598_urn.xml Auto-generated SBML file with URNs 186.65 KB Preview | Download
BIOMD0000000598.xpp Auto-generated XPP file 26.97 KB Preview | Download
BIOMD0000000598.svg Auto-generated Reaction graph (SVG) 0.00 bytes Preview | Download
BIOMD0000000598.vcml Auto-generated VCML file 956.00 bytes Preview | Download
BIOMD0000000598.sci Auto-generated Scilab file 67.00 bytes Preview | Download

  • Model originally submitted by : Andrew J Millar
  • Submitted: Oct 19, 2015 4:14:59 PM
  • Last Modified: Apr 15, 2016 6:00:00 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Apr 15, 2016 6:00:00 PM
    • Submitted by: Andrew J Millar
    • With comment: Current version of Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2)
  • Version: 1 public model Download this version
    • Submitted on: Oct 19, 2015 4:14:59 PM
    • Submitted by: Andrew J Millar
    • With comment: Original import of P2011_PLM_67v6
Curator's comment:
(added: 15 Apr 2016, 17:33:50, updated: 15 Apr 2016, 17:33:50)
Figure 9 (solid lines, that is corresponding to this model P2011.2.1 - PLM_71 ver 2) has been reproduced here.The model was simulated and plots were generated using SimBiology version 5.1 (Matlab R2014b) Note: The SBML model has the kinetic laws in the form of FunctionDefinition, which is not recognized in SimBiology. So, I converted the FunctionDefintion to kinetic law using a tool in libSBML and used SimBiology to simulate the model. The kineticLaw version of the model can be downloaded from below link.