Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
Abstract
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.
- Authors:
- Publication Date:
- Research Org.:
- Colorado School of Mines, Golden, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1619683
- Alternate Identifier(s):
- OSTI ID: 1576586; OSTI ID: 1578262
- Report Number(s):
- NREL/JA-5D00-75592
Journal ID: ISSN 2045-2322; 16948; PII: 53188
- Grant/Contract Number:
- SC0019171; AC36-08GO28308
- Resource Type:
- Published Article
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Name: Scientific Reports Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; metabolic flux; agent based modeling; consortia; nitrogen fixation; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; biochemistry; computational models; metabolic engineering; microbial ecology
Citation Formats
Gardner, Joseph J., Hodge, Bri-Mathias S., and Boyle, Nanette R. Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems. United Kingdom: N. p., 2019.
Web. doi:10.1038/s41598-019-53188-0.
Gardner, Joseph J., Hodge, Bri-Mathias S., & Boyle, Nanette R. Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems. United Kingdom. https://doi.org/10.1038/s41598-019-53188-0
Gardner, Joseph J., Hodge, Bri-Mathias S., and Boyle, Nanette R. Mon .
"Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems". United Kingdom. https://doi.org/10.1038/s41598-019-53188-0.
@article{osti_1619683,
title = {Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems},
author = {Gardner, Joseph J. and Hodge, Bri-Mathias S. and Boyle, Nanette R.},
abstractNote = {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.},
doi = {10.1038/s41598-019-53188-0},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United Kingdom},
year = {2019},
month = {11}
}
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