Prediction and analysis of phenotypes in the Arabidopsis clock mutant <i>prr7 prr9</i> using the Framework Model v2 (FMv2)

Laurel and Hardy 1 - experimental data (.mat file)

Experimental data, in MATLAB binary file format.

• LH1_data.mat

Laurel and Hardy 1 - Experimental data (excel)

Biomass and metabolite data for Laurel and Hardy 1.

• LH1_experimental_data.xlsx

Laurel and Hardy 1 - simulation data (.mat file)

Model simulation data for Laurel and Hardy 1, in MATLAB binary format.

• plot_LH1_biomass_and_carbon_pools.mat

Laurel and Hardy 1 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions.
Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD;
Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on
...

• Laurel and Hardy 1_DDS.xlsx

TiMet WP1.1a metabolite data, ED-EN in clock mutants

Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab

• Clock mutant ED-EN LC-MS data from AnnaF_stats_2.xlsx

TiMet WP1.1 qRT-PCR LD to LL and DD

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Comments:
Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4
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• ShowExperiment.action?experimentId=2841

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

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
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Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 2013)

A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2".
The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication.
Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the
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• PLM_78.xml
• model.shtml?accession=PLM_78

Modelling circadian regulation of flowering time and hypocotyl elongation, Seaton et al., 2015

Matlab model (could not be represented in SBML) from publication with abstract:
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription.
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• 1031Supplementary%20File%201%20-%20MATLAB%20code.zip
• model.shtml?accession=PLM_1010

Chew_et_al_2014_Framework_Model version 1, Matlab and Simile

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:
1. Arabidopsis leaf carbohydrate model (Rasse and
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• model.shtml?accession=PLM_76
• 134MATLAB%20Framework%20Model.zip
• 1020Framework%20Model%20in%20Simile.zip
• timet-logo-sm.png

Framework Model v2

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model:
Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was
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• frameworkmodel

Linking circadian time to growth rate quantitatively via carbon metabolism

Summary paragraph

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate up time and length scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour, from sleep/wake cycles in mammals to flowering in plants
1–3
. Clock genes are rarely essential but appropriate alleles can confer a competitive advantage
4,5
and have been repeatedly
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TiMet WP1.1 qRT-PCR LD to LL and DD

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Comments:
Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4
...

• ShowExperiment.action?experimentId=2841

P2011.1.2 simulations of clock genes under LD cycles

for Chew, Seaton et al. paper Figure 1

• TiMEt WP1_1 prr79 sims P2011.zip

P2011.1.2 simulations vs. data for WT, normalised for plots

For Chew, Seaton et al. Figure 1

• SBSI plots final.xlsx

P2011.1.2 simulations and data in prr7 prr9 mutant, normalised for plots

For Chew, Seaton et al. Figure 1

• SBSI 79 plots final.xlsx

Arabidopsis clock model P2011.1.2

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1

• PLM_71.xml

P2011.1.2_directupload

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

• PLM_71.xml

Sensitivity analysis results (.mat file)

Model analysis results in binary Matlab format

• sens_analysis_results_WT.mat

Sensitivity analysis results (.mat file)

Model analysis results in binary Matlab format

• sens_analysis_results_WT.mat

Laurel and Hardy 2 - experimental data (.mat file)

Experimental data for Laurel and Hardy 2, in MATLAB binary format.

• LH2_data.mat

Laurel and Hardy 2 - Experimental data (excel)

Mean and SD data for metabolites and biomass, along with metadata used to simulate this experiment.

• Laurel and Hardy 2 - experimental data (excel).xlsx

Laurel and Hardy 2 - complete data

Complete excel spradsheets for Laurel and Hardy 2, including data for the pgm mutant that were not analysed in the Chew et al. 2017 preprint/publication.
Data include fresh and dry biomass, gas exchange, leaf numbers and metabolites in Col0 (WT), prr7prr9, pgm and lsf1 plants.
Metabolite data are from plants after 27 days of growth (end of night) and 28 days (end of day and end of night).

• Laurel and Hardy 2 - complete data.zip

Laurel and Hardy 2 - simulation data (.mat file)

Simulation data for Laurel and Hardy 2, in MATLAB binary format.

• plot_LH2_biomass_and_carbon_pools.mat

Laurel and Hardy 2 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on
...

• Laurel and Hardy 2 with malate and fumarate_DDS.xlsx

Laurel and Hardy 3 - experimental data (.mat file)

Experimental data for Laurel and Hardy 3, in MATLAB binary format.

• LH3_data.mat

Laurel and Hardy 3 - Experimental data (excel)

No description specified

• Laurel and Hardy 3 - experimental data (excel).xlsx

Laurel and Hardy 3 - complete data

Excel spreadsheets for biomass, leaf number, gas exchange and metabolites, including pgm and lhycca1.
Key data are for 27-28 day old plants for Col and prr7prr9, analysed for the preprint/publication.
Gas exchange data for lhycca1 showed lower Assimilation per unit area than Col, prr7prr9; A in pgm was higher than Col.
Metabolite data were also collected for Col and lhycca1 at 18 days, before the lhycca1 flowered, but these are marked as unreliable.

• Laurel and Hardy 3 - complete data.zip

Laurel and Hardy 3 - simulation data (.mat file)

Simulation data for Laurel and Hardy 3, in MATLAB binary format.

• plot_LH3_biomass_and_carbon_pools.mat

Laurel and Hardy 3 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on days
...

• Laurel and Hardy 3 with malate and fumarate_DDS.xlsx

All biomass data for study Gibberellins 1

Biomass data for individual plants at day 35, fresh and dry weights, as well as mean and SD, from study Gibberellins 1

• GA_Biomass of full sets_AJM.xlsx

Biomass and metabolite data for study Gibberellins 1

Excel sheet with mean and SD biomass data and charts, individual metabolite replicates, mean, SD and charts
Details on Read.ME worksheet

• GA experiment - biomass + metabolite_AJM.xlsx

Carbon assimilation and partitioning in darkness

14CO2 assimilation in the night-time, in plants of Col, prr7prr9; Ws, lhycca1 genotypes at 18 and 28 days, and partitioning among cellular fractions.

• Labelling data from Gavin George_AJM2.xlsx

Testing thiamine metabolites in Col and prr7prr9

Excel file with data on levels of thiamine and its metabolites TMP and active cofactor TDP, tested in Col and prr7prr9 samples from study Laurel and Hardy 3.
Altered levels of TDP could potentially affect enzymes with TDP cofactors that metabolise malate and fumarate levels, altering their levels in prr7prr9.

• Thiamin Geneva results 10_05_2015_AJM.xlsx

Four-study data compilation with charts

Excel workbook with included Read.Me sheet, including FW and DW biomass data derived from files linked elsewhere;
a compilation of the rosette area and gas exchange data for every plant measured of the Col, lsf1 and prr7prr9 genotypes;
statistical analysis across the experiments;
and charts of the compiled data, some of which are presented as figure panels in the 2022 versions.

• Biomass_FW_DW_gas_exchange_data.xlsx

Flowering time in WT vs prr7prr9 (Nakamichi et al, 2007)

No description specified

• nakamichi2007_WT_vs_prr7prr9_flowering_data.xlsx

Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway

Photoperiodism allows organisms to measure daylength, or external photoperiod, and to anticipate coming seasons. Daylength measurement requires the integration of light signal and temporal information by the circadian clock. In the long-day plant Arabidopsis thaliana, CONSTANS (CO) plays a crucial role in integrating the circadian rhythm and environmental light signals into the photoperiodic flowering pathway. Nevertheless, the molecular mechanism by which the circadian clock modulates the cyclic
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Hypocotyl lengths in WT vs prr7prr9 across photoperiods (Niwa et al, 2009)

No description specified

• niwa2009_WT_vs_prr7prr9_hypocotyl_data.xlsx

The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana

The plant circadian clock generates rhythms with a period close to 24 h, and it controls a wide range of physiological and developmental oscillations in habitats under natural light/dark cycles. Among clock-controlled developmental events, the best characterized is the photoperiodic control of flowering time in Arabidopsis thaliana. Recently, it was also reported that the clock regulates a daily and rhythmic elongation of hypocotyls. Here, we report that the promotion of hypocotyl elongation is
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