Test of FMv2, study Laurel & Hardy 3
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Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
SEEK ID: https://fairdomhub.org/studies/220
Projects: Millar group, TiMet
Study position: 4
Experimentalists: Yin Hoon Chew, Daniel Seaton, Virginie Mengin, Mark Stitt
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Created: 6th Feb 2017 at 13:18
Last updated: 15th Apr 2022 at 10:35
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Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh
https://orcid.org/0000-0003-1756-3654
SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Programme: SynthSys
Public web page: http://timing-metabolism.eu/
Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated in 2022, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU FP7 TiMet project, https://fairdomhub.org/projects/92.
This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. The updates are not changing the core data or the FMv2 model that has been ...
Submitter: Andrew Millar
Studies: Analysis of Framework Model version 2 (FMv2), Construction of Framework Model version 2 (FMv2), Test of FMv2, follow-on: mechanisms of malate/fumarate accumulation, Test of FMv2, photoperiodic flowering and hypocotyl elongation, Test of FMv2, study Gibberellins 1, Test of FMv2, study Laurel & Hardy 1, Test of FMv2, study Laurel & Hardy 2, Test of FMv2, study Laurel & Hardy 3, Tests of FMv2, compilations and figures
Assays: Assimilation and partitioning of 14CO2 at night, Biomass and metabolites, Biomass and metabolites, Biomass and metabolites, Biomass, leaf area and gas exchange data, Biomass, leaf number and metabolites, Circadian period analysis, Composition of FMv2, FMv2 simulation, FMv2 simulation, FMv2 simulation, Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants, Relationship among FMv2 outputs, Sensitivity analysis of FMv2, Simulating clock gene expression with model P2011.1.2, Thiamine vitamers, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and pgm at days 29 and 35, presented in the preprint/publication, with most data also for Col and lhycca1 at days 21/22/23, not analysed further.
We suggest that the lower carbon assimilation rate measured in lhycca1 (see gas exchange data) might allow a calibirated simulation in the FMv2 model in future to incorporate the indirect effects of nightly carbon starvation in this genotype ...
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
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 ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Experimental data for Laurel and Hardy 3, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Simulation data for Laurel and Hardy 3, in MATLAB binary format.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creator: Daniel Seaton
Submitter: Daniel Seaton
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.
Creators: Yin Hoon Chew, Virginie Mengin, Daniel Seaton
Submitter: Daniel Seaton
