{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/multiscale-metabolic-modeling-of-c4-plants","title":"Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves","arxiv_id":"1502.07969","date":"2015-02-27","proceeding":null,"authors":[],"abstract":"C4 plants, such as maize, concentrate carbon dioxide in a specialized\ncompartment surrounding the veins of their leaves to improve the efficiency of\ncarbon dioxide assimilation. Nonlinear relationships between carbon dioxide and\noxygen levels and reaction rates are key to their physiology but cannot be\nhandled with standard techniques of constraint-based metabolic modeling. We\ndemonstrate that incorporating these relationships as constraints on reaction\nrates and solving the resulting nonlinear optimization problem yields realistic\npredictions of the response of C4 systems to environmental and biochemical\nperturbations. Using a new genome-scale reconstruction of maize metabolism, we\nbuild an 18000-reaction, nonlinearly constrained model describing mesophyll and\nbundle sheath cells in 15 segments of the developing maize leaf, interacting\nvia metabolite exchange, and use RNA-seq and enzyme activity measurements to\npredict spatial variation in metabolic state by a novel method that optimizes\ncorrelation between fluxes and expression data. Though such correlations are\nknown to be weak in general, here the predicted fluxes achieve high correlation\nwith the data, successfully capture the experimentally observed base-to-tip\ntransition between carbon-importing tissue and carbon-exporting tissue, and\ninclude a nonzero growth rate, in contrast to prior results from similar\nmethods in other systems. We suggest that developmental gradients may be\nparticularly suited to the inference of metabolic fluxes from expression data.","url_abs":"http://arxiv.org/abs/1502.07969v1","url_pdf":"http://arxiv.org/pdf/1502.07969v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"multiscale-metabolic-modeling-of-c4-plants","repo_url":"https://github.com/ebogart/multiscale_c4_source","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}