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

Band, Leah R.; Preston, Simon P.

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.

Citation

Band, L. R., & Preston, S. P. (2018). Parameter inference to motivate asymptotic model reduction: an analysis of the gibberellin biosynthesis pathway. Journal of Theoretical Biology, 457, 66-78. https://doi.org/10.1016/j.jtbi.2018.05.028

• Journal Article Type: Article
• Acceptance Date: May 25, 2018
• Online Publication Date: Jul 21, 2018
• Publication Date: Nov 14, 2018
• Deposit Date: Jun 25, 2018
• Publicly Available Date: Jul 22, 2019
• Journal: Journal of Theoretical Biology
• Print ISSN: 0022-5193
• Electronic ISSN: 1095-8541
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 457
• Pages: 66-78
• DOI: https://doi.org/10.1016/j.jtbi.2018.05.028
• Keywords: asymptotic analysis, profile likelihood, plant hormones, hormone biosynthesis
• Public URL: https://nottingham-repository.worktribe.com/output/947258
• Publisher URL: https://www.sciencedirect.com/science/article/pii/S0022519318302753
• Contract Date: Jun 25, 2018