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Title: 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:
 [1];  [2];  [1]
  1. Colorado School of Mines, Golden, CO (United States). Dept. of Chemical & Biological Engineering
  2. Colorado School of Mines, Golden, CO (United States). Dept. of Chemical & Biological Engineering ; National Renewable Energy Lab. (NREL), Golden, CO (United States); Univ. of Colorado, Boulder, CO (United States). Dept of Electrical, Computer and Energy Engineering
Publication Date:
Research Org.:
Colorado School of Mines, Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1576586
Grant/Contract Number:  
SC0019171
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; metabolic flux; agent based modeling; consortia; nitrogen fixation

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 States: 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 States. doi: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 States. doi:10.1038/s41598-019-53188-0. https://www.osti.gov/servlets/purl/1576586.
@article{osti_1576586,
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 States},
year = {2019},
month = {11}
}

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