Introducing an Optimization- and explicit Runge-Kutta- based Approach to Perform Dynamic Flux Balance Analysis.

Scientific Reports
Wheaton L Schroeder, Rajib Saha

Abstract

In this work we introduce the generalized Optimization- and explicit Runge-Kutta-based Approach (ORKA) to perform dynamic Flux Balance Analysis (dFBA), which is numerically more accurate and computationally tractable than existing approaches. ORKA is applied to a four-tissue (leaf, root, seed, and stem) model of Arabidopsis thaliana, p-ath773, uniquely capturing the core-metabolism of several stages of growth from seedling to senescence at hourly intervals. Model p-ath773 has been designed to show broad agreement with published plant-scale properties such as mass, maintenance, and senescence, yet leaving reaction-level behavior unconstrainted. Hence, it serves as a framework to study the reaction-level behavior necessary for observed plant-scale behavior. Two such case studies of reaction-level behavior include the lifecycle progression of sulfur metabolism and the diurnal flow of water throughout the plant. Specifically, p-ath773 shows how transpiration drives water flow through the plant and how water produced by leaf tissue metabolism may contribute significantly to transpired water. Investigation of sulfur metabolism elucidates frequent cross-compartment exchange of a standing pool of amino acids which is used to regulate t...Continue Reading

References

Apr 19, 2002·Current Opinion in Plant Biology·Tony H H Chen, Norio Murata
Aug 31, 2002·Biophysical Journal·Radhakrishnan MahadevanFrancis J Doyle
Mar 26, 2003·Tree Physiology·J. H. M. Thornley, M. G. R. Cannell
Apr 6, 2006·The Plant Cell·C Robertson McClung
Jan 9, 2008·PLoS Computational Biology·Clinton H HansenNed S Wingreen
Apr 11, 2009·Trends in Plant Science·Silvia GonzaliPierdomenico Perata
Sep 17, 2009·Plant Physiology·Mark G PoolmanDavid A Fell
Nov 6, 2009·Molecular Systems Biology·Matthew A OberhardtJason A Papin
Jan 2, 2010·Plant Physiology·Cristiana Gomes de Oliveira Dal'MolinLars Keld Nielsen
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Marco TerzerJörg Stelling
Oct 27, 2010·Plant Physiology·Cristiana Gomes de Oliveira Dal'MolinLars Keld Nielsen
Dec 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Shira Mintz-OronTomer Shlomi
Feb 10, 2012·PLoS Computational Biology·Ali R Zomorrodi, Costas D Maranas
May 4, 2013·Plant Physiology·Mark G PoolmanDavid A Fell
Aug 9, 2013·Plant Physiology·Eva Grafahrend-BelauBjörn H Junker
Apr 2, 2014·Nature Reviews. Microbiology·Chris J Paddon, Jay D Keasling
May 28, 2014·Journal of Experimental Botany·Margaret SimonsBertrand Hirel
Mar 27, 2016·Plant Physiology·James P Santiago, Mechthild Tegeder
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Jul 22, 2017·Plant, Cell & Environment·Rachael J Oakenfull, Seth J Davis
Dec 27, 2017·Current Opinion in Plant Biology·Mechthild Tegeder, Ulrich Z Hammes

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Citations

Jan 29, 2021·PLoS Computational Biology·Adil AlsiyabiRajib Saha
Oct 27, 2021·The Plant Journal : for Cell and Molecular Biology·Sanu ShameerLee J Sweetlove

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Software Mentioned

GAMS
OKRA
ORKA Variability Analysis ( FVA
SOA
Perl
lux B alance A nalysis ( FBA )
ORKA
Windows
dFBA
GitHub

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