Dataset Information

WormJam-GEM

ABSTRACT: Whole-genome metabolic reconstructions for the model organism Caenorhabditis elegans.

SUBMITTER: Nicolas Rodriguez

PROVIDER: MODEL1807230002 | BioModels | 2018-12-10

REPOSITORIES: BioModels

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	MODEL1807230002?filename=WormJam-GEM.xml	Xml

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Publications

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism <i>Caenorhabditis elegans</i>.

Witting Michael M Hastings Janna J Rodriguez Nicolas N Joshi Chintan J CJ Hattwell Jake P N JPN Ebert Paul R PR van Weeghel Michel M Gao Arwen W AW Wakelam Michael J O MJO Houtkooper Riekelt H RH Mains Abraham A Le Novère Nicolas N Sadykoff Sean S Schroeder Frank F Lewis Nathan E NE Schirra Horst-Joachim HJ Kaleta Christoph C Casanueva Olivia O

Frontiers in molecular biosciences 20181114

Metabolism is one of the attributes of life and supplies energy and building blocks to organisms. Therefore, understanding metabolism is crucial for the understanding of complex biological phenomena. Despite having been in the focus of research for centuries, our picture of metabolism is still incomplete. Metabolomics, the systematic analysis of all small molecules in a biological system, aims to close this gap. In order to facilitate such investigations a blueprint of the metabolic network is r ...[more]

PMID: 30488036

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Project description:Gebauer2016 - Genome-scale model of Caenorhabditis elegans metabolism (without bacteria) This model is one of the two versions of ElegCyc presented in the paper. It describes the metabolism of a worm raised in a medium without bacteria. This model is described in the article: A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism. Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C. Cell Syst 2016 May; 2(5): 312-322 Abstract: We present a genome-scale model of Caenorhabditis elegans metabolism along with the public database ElegCyc (http://elegcyc.bioinf.uni-jena.de:1100), which represents a reference for metabolic pathways in the worm and allows for the visualization as well as analysis of omics datasets. Our model reflects the metabolic peculiarities of C. elegans that make it distinct from other higher eukaryotes and mammals, including mice and humans. We experimentally verify one of these peculiarities by showing that the lifespan-extending effect of L-tryptophan supplementation is dose dependent (hormetic). Finally, we show the utility of our model for analyzing omics datasets through predicting changes in amino acid concentrations after genetic perturbations and analyzing metabolic changes during normal aging as well as during two distinct, reactive oxygen species (ROS)-related lifespan-extending treatments. Our analyses reveal a notable similarity in metabolic adaptation between distinct lifespan-extending interventions and point to key pathways affecting lifespan in nematodes. This model is hosted on BioModels Database and identified by: MODEL1704200000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:Gebauer2016 - Genome-scale model of Caenorhabditis elegans metabolism (with bacteria) This model is one of the two versions of ElegCyc presented in the paper. It describes the metabolism of a worm raised in a medium with bacteria This model is described in the article: A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism. Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C. Cell Syst 2016 May; 2(5): 312-322 Abstract: We present a genome-scale model of Caenorhabditis elegans metabolism along with the public database ElegCyc (http://elegcyc.bioinf.uni-jena.de:1100), which represents a reference for metabolic pathways in the worm and allows for the visualization as well as analysis of omics datasets. Our model reflects the metabolic peculiarities of C. elegans that make it distinct from other higher eukaryotes and mammals, including mice and humans. We experimentally verify one of these peculiarities by showing that the lifespan-extending effect of L-tryptophan supplementation is dose dependent (hormetic). Finally, we show the utility of our model for analyzing omics datasets through predicting changes in amino acid concentrations after genetic perturbations and analyzing metabolic changes during normal aging as well as during two distinct, reactive oxygen species (ROS)-related lifespan-extending treatments. Our analyses reveal a notable similarity in metabolic adaptation between distinct lifespan-extending interventions and point to key pathways affecting lifespan in nematodes. This model is hosted on BioModels Database and identified by: MODEL1704200001. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.