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Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modelin...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861322/ https://www.ncbi.nlm.nih.gov/pubmed/31740694 http://dx.doi.org/10.1038/s41598-019-53188-0 |
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author | Gardner, Joseph J. Hodge, Bri-Mathias S. Boyle, Nanette R. |
author_facet | Gardner, Joseph J. Hodge, Bri-Mathias S. Boyle, Nanette R. |
author_sort | Gardner, Joseph J. |
collection | PubMed |
description | In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modeling approaches that are currently used assume ideal conditions and that each cell is identical, limiting their application to pure cultures in well-mixed vessels. Here we describe our development of Multiscale Multiobjective Systems Analysis (MiMoSA), a metabolic modeling approach that can track individual cells in both space and time, track the diffusion of nutrients and light and the interaction of cells with each other and the environment. As a proof-of concept study, we used MiMoSA to model the growth of Trichodesmium erythraeum, a filamentous diazotrophic cyanobacterium which has cells with two distinct metabolic modes. The use of MiMoSA significantly improves our ability to predictively model metabolic changes and phenotype in more complex cell cultures. |
format | Online Article Text |
id | pubmed-6861322 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68613222019-11-20 Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems Gardner, Joseph J. Hodge, Bri-Mathias S. Boyle, Nanette R. Sci Rep Article In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their environments. Unfortunately, most of the metabolic modeling approaches that are currently used assume ideal conditions and that each cell is identical, limiting their application to pure cultures in well-mixed vessels. Here we describe our development of Multiscale Multiobjective Systems Analysis (MiMoSA), a metabolic modeling approach that can track individual cells in both space and time, track the diffusion of nutrients and light and the interaction of cells with each other and the environment. As a proof-of concept study, we used MiMoSA to model the growth of Trichodesmium erythraeum, a filamentous diazotrophic cyanobacterium which has cells with two distinct metabolic modes. The use of MiMoSA significantly improves our ability to predictively model metabolic changes and phenotype in more complex cell cultures. Nature Publishing Group UK 2019-11-18 /pmc/articles/PMC6861322/ /pubmed/31740694 http://dx.doi.org/10.1038/s41598-019-53188-0 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Gardner, Joseph J. Hodge, Bri-Mathias S. Boyle, Nanette R. Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title | Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title_full | Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title_fullStr | Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title_full_unstemmed | Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title_short | Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems |
title_sort | multiscale multiobjective systems analysis (mimosa): an advanced metabolic modeling framework for complex systems |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861322/ https://www.ncbi.nlm.nih.gov/pubmed/31740694 http://dx.doi.org/10.1038/s41598-019-53188-0 |
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