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Investigating Host–Pathogen Behavior and Their Interaction Using Genome-Scale Metabolic Network Models

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Book cover Immunoinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1184))

Abstract

Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype–phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host–pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.

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Authors and Affiliations

  1. Chemical Engineering Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India

    Priyanka P. Sadhukhan & Anu Raghunathan

Authors
  1. Priyanka P. Sadhukhan
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  2. Anu Raghunathan
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Correspondence to Anu Raghunathan .

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Editors and Affiliations

  1. Indian Statistical Institute, Kolkata, West Bengal, India

    Rajat K. De

  2. Indian Statistical Institute, Kolkata, West Bengal, India

    Namrata Tomar

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Sadhukhan, P.P., Raghunathan, A. (2014). Investigating Host–Pathogen Behavior and Their Interaction Using Genome-Scale Metabolic Network Models. In: De, R., Tomar, N. (eds) Immunoinformatics. Methods in Molecular Biology, vol 1184. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1115-8_29

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  • DOI: https://doi.org/10.1007/978-1-4939-1115-8_29

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1114-1

  • Online ISBN: 978-1-4939-1115-8

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