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Integrated Host-Pathogen Metabolic Reconstructions

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Metabolic Network Reconstruction and Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

Abstract

The science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious disease is complex due to the multifactorial response of the host to the pathogen. Systems biology approaches and modeling allow one to study, understand, and predict emergent properties of such complex responses. The integration of the host and pathogen metabolic networks and the subsequent merger of their stoichiometric matrices is nontrivial and requires understanding of both pathogen and host metabolism and physiologies. The protocol here describes the detailed process of network and stoichiometric matrix merger using a salmonella-mouse macrophage model. The protocol also discusses the interfacial and objective functions required to actually embark on the analysis of host-pathogen interaction models.

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Acknowledgments

We thank Avinash V. Ghanate for helping us with GEO expression data sets used in the Salmonella-mouse model.

Author information

Authors and Affiliations

  1. Chemical Engineering Division, National Chemical Laboratory, Pune, India

    Anu Raghunathan

  2. Institute of Engineering in Medicine, University of California-San Diego, La Jolla, CA, USA

    Neema Jamshidi

  3. Department of Radiological Sciences, University of California, Los Angeles, CA, USA

    Neema Jamshidi

Authors
  1. Anu Raghunathan
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  2. Neema Jamshidi
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Corresponding author

Correspondence to Anu Raghunathan .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

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Raghunathan, A., Jamshidi, N. (2018). Integrated Host-Pathogen Metabolic Reconstructions. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_9

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

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