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MODEL1011090001 - Bordbar2010_Macrophage_Metabolism

 

The following model is part of the non-curated branch of BioModels Database. While the syntax of the model has been verified, its semantics remains unchecked. Any annotation present in the models is not a product of BioModels' annotators. We are doing our best to incorporate this model into the curated branch as soon as possible. In the meantime, we display only limited metadata here. For further information about the model, please download the SBML file.


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Reference Publication
Publication ID: 20959820
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N.
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.
Mol. Syst. Biol. 2010 Oct; 6: 422
Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall, La Jolla, CA, USA.  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission Date: 09 Nov 2010 13:26:47 UTC
Last Modification Date: 09 Nov 2010 18:14:57 UTC
Creation Date: 09 Nov 2010 18:14:57 UTC
Non kinetic model: network icon.
Encoders:
bqmodel:isDerivedFrom PubMed 17267599
PubMed 17555602
bqbiol:occursIn Brenda Tissue Ontology alveolar macrophage
bqbiol:hasTaxon Taxonomy Mycobacterium tuberculosis
Taxonomy Homo sapiens
bqbiol:isVersionOf Gene Ontology regulation of growth
Notes

This is the genome scale metabolic reconstruction of the human alveloar macrophage, iAB-AMØ-1410, described in the article:
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Mol Syst Biol. 2010 Oct 19;6:422. PMID: 20959820 , DOI: 10.1038/msb.2010.68

Abstract:
Metabolic coupling of Mycobacterium tuberculosis to its host is foundational to its pathogenesis. Computational genome-scale metabolic models have shown utility in integrating -omic as well as physiologic data for systemic, mechanistic analysis of metabolism. To date, integrative analysis of host-pathogen interactions using in silico mass-balanced, genome-scale models has not been performed. We, therefore, constructed a cell-specific alveolar macrophage model, iAB-AMØ-1410, from the global human metabolic reconstruction, Recon 1. The model successfully predicted experimentally verified ATP and nitric oxide production rates in macrophages. This model was then integrated with an M. tuberculosis H37Rv model, iNJ661, to build an integrated host-pathogen genome-scale reconstruction, iAB-AMØ-1410-Mt-661. The integrated host-pathogen network enables simulation of the metabolic changes during infection. The resulting reaction activity and gene essentiality targets of the integrated model represent an altered infectious state. High-throughput data from infected macrophages were mapped onto the host-pathogen network and were able to describe three distinct pathological states. Integrated host-pathogen reconstructions thus form a foundation upon which understanding the biology and pathophysiology of infections can be developed.

This model was downloaded from the supplementary materials ( link ) to the article. To make this file valid SBML the units of all parameters where changed from mmole per gDW per hour to mmole per hour and the empty reactions with the ids R_EX_retpalm_LPAREN_e_RPAREN_ were removed. The model can be used eg. fpr FBA with the COBRA toolbox , amongst others.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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