Composition of Framework Model FMv1.5

Model files for FMv1.5. The model is based on FMv1 of Chew et al. PNAS 2014, which is also in FAIRDOMHub and linked to the Model record as an 'Attribution'. FMv1 was extended in this work by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.

Submitter: Andrew Millar

Biological problem addressed: Model Analysis Type

Investigation: Temperature effects on Arabidopsis floral induc...

Study: Construction of the Framework Model v1.5

Data images of Arabidopsis Fei-0 and Ler plants, as .JPG files in .ZIP archive

Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale. Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat. Areas are then measured in image processing.

Creator: Yin Hoon Chew

Submitter: Andrew Millar

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Leaf number in Col-0 and 35S:miR156 Arabidopsis rosettes

Data for Fig. Supp 7B in Chew et al. PNAS 2014 Leaf number of the growing rosettes, from 5 to 37 days after sowing. Data and also results of three FMv1 model simulations, with default, fitted and linear (i.e. no juvenile-adult transition in phyllochron)

Creator: Yin Hoon Chew

Submitter: Andrew Millar

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Data images of Arabidopsis Col-0 and 35S:miR156 plants, as .JPG files in .ZIP archive

Experiment conducted in early April 2014 Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale. Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat.

Areas are then measured in image processing.

Creator: Yin Hoon Chew

Submitter: Andrew Millar

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framework model v1_5

Model associated with the following:

Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006

Creator: Hannah Kinmonth-Schultz

Submitter: Hannah Kinmonth-Schultz

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The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

Abstract (Expand)

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that … control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits. This work updates the first biorXiv version, February 2017,with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.

Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar

Date Published: 6th Feb 2017

Publication Type: Tech report

Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT

Abstract

BioRxiv preprint:

Authors: Hannah A Kinmonth-Schultz, Melissa J MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim

Date Published: No date defined

Publication Type: Not specified

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