Parameter inference to motivate asymptotic model reduction: an analysis of the gibberellin biosynthesis pathway

Band, Leah R. and Preston, Simon P. (2018) Parameter inference to motivate asymptotic model reduction: an analysis of the gibberellin biosynthesis pathway. Journal of Theoretical Biology . ISSN 1095-8541

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Abstract

Developing effective strategies to use models in conjunction with experimental data is essential to understand the dynamics of biological regulatory networks. In this study, we demonstrate how combining parameter estimation with asymptotic analysis can reveal the key features of a network and lead to simplified models that capture the observed network dynamics. Our approach involves fitting the model to experimental data and using the Profile Likelihood to identify small parameters and cases where model dynamics are insensitive to changing particular individual parameters. Such parameter diagnostics provide understanding of the dominant features of the model and motivate asymptotic model reductions to derive simpler models in terms of identifiable parameter groupings.

We focus on the particular example of biosynthesis of the plant hormone gibberellin (GA), which controls plant growth and has been mutated in many current crop varieties. This pathway comprises two parallel series of enzyme-substrate reactions, which have previously been modelled using the law of mass action [23]. Considering the GA20ox-mediated steps, we analyse the identifiability of the model parameters using published experimental data; the analysis reveals the ratio between enzyme and GA levels to be small and motivates us to perform a quasi-steady state analysis to derive a reduced model. Fitting the parameters in the reduced model reveals additional features of the pathway and motivates further asymptotic analysis which produces a hierarchy of reduced models. Calculating the Akaike information criterion and parameter confidence intervals enables us to select a parsimonious model with identifiable parameters. As well as demonstrating the benefits of combining parameter estimation and asymptotic analysis, the analysis shows how GA biosynthesis is limited by the final GA20ox-mediated steps in the pathway and generates a simple mathematical description of this part of the GA biosynthesis pathway.

Item Type: Article
RIS ID: https://nottingham-repository.worktribe.com/output/947258
Keywords: asymptotic analysis, profile likelihood, plant hormones, hormone biosynthesis
Schools/Departments: University of Nottingham, UK > Faculty of Science > School of Biosciences
University of Nottingham, UK > Faculty of Science > School of Mathematical Sciences
Identification Number: https://doi.org/10.1016/j.jtbi.2018.05.028
Depositing User: Eprints, Support
Date Deposited: 25 Jun 2018 12:09
Last Modified: 04 May 2020 19:46
URI: http://eprints.nottingham.ac.uk/id/eprint/52588

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