Multiscale plant modeling: from genome to phenome and beyond

ML Matthews, A Marshall-Colón - Emerging topics in life …, 2021 - portlandpress.com
Plants are complex organisms that adapt to changes in their environment using an array of
regulatory mechanisms that span across multiple levels of biological organization. Due to …

Leaf energy balance requires mitochondrial respiration and export of chloroplast NADPH in the light

S Shameer, RG Ratcliffe, LJ Sweetlove - Plant Physiology, 2019 - academic.oup.com
Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example,
there is debate about the relative importance of exporting reducing equivalents from …

Green pathways: metabolic network analysis of plant systems

LM Dersch, V Beckers, C Wittmann - Metabolic engineering, 2016 - Elsevier
Metabolic engineering of plants with enhanced crop yield and value-added compositional
traits is particularly challenging as they probably exhibit the highest metabolic network …

A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf

CYM Cheung, RG Ratcliffe, LJ Sweetlove - Plant Physiology, 2015 - academic.oup.com
Flux balance analysis of plant metabolism is an established method for predicting metabolic
flux phenotypes and for exploring the way in which the plant metabolic network delivers …

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

E Cunha, M Silva, I Chaves, H Demirci… - PLoS Computational …, 2023 - journals.plos.org
Over the last decade, genome-scale metabolic models have been increasingly used to study
plant metabolic behaviour at the tissue and multi-tissue level under different environmental …

Stoichiometric analysis of the energetics and metabolic impact of photorespiration in C3 plants

B Huma, S Kundu, MG Poolman, NJ Kruger… - The Plant …, 2018 - Wiley Online Library
Analysis of the impact of photorespiration on plant metabolism is usually based on manual
inspection of small network diagrams. Here we create a structural metabolic model that …

Biochemical characteristics and a genome-scale metabolic model of an indian euryhaline cyanobacterium with high polyglucan content

A Ahmad, R Pathania, S Srivastava - Metabolites, 2020 - mdpi.com
Marine cyanobacteria are promising microbes to capture and convert atmospheric CO2 and
light into biomass and valuable industrial bio-products. Yet, reports on metabolic …

Modeling rice metabolism: from elucidating environmental effects on cellular phenotype to guiding crop improvement

M Lakshmanan, CYM Cheung, B Mohanty… - Frontiers in Plant …, 2016 - frontiersin.org
Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly
needed to understand the underlying mechanisms of environmental stress response and …

Mathematical models of plant metabolism

H Shi, J Schwender - Current Opinion in Biotechnology, 2016 - Elsevier
Highlights•The number of published genome-derived models of plant metabolism is fast
increasing.•However, plant genomes are still considered to be vastly underexplored.• …

Environment-coupled models of leaf metabolism

N Töpfer - Biochemical Society Transactions, 2021 - portlandpress.com
The plant leaf is the main site of photosynthesis. This process converts light energy and
inorganic nutrients into chemical energy and organic building blocks for the biosynthesis …