Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/106734 |
Resumo: | The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942. |
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Triana Dopico, JuliánMontagud Aquino, ArnauSiurana Paula, MariaFuente Herráiz, DavidUrchueguía Fornes, ArantxaGamermann, DanielTorres Gavila, Francisco JavierTena Medialdea, JoséFernández de Córdoba Castellá, Pedro JoséUrchueguía Schölzel, Javier Fermín2014-11-12T02:14:04Z20142218-1989http://hdl.handle.net/10183/106734000933834The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942.application/pdfengMetabolites. Basel. Vol. 4, no. 3 (sept. 2014), p. 680-698Sistemas biológicosGenomaRedesGenome-scale metabolic network reconstructionSystems biologyMetabolic pathwaysFlux balance analysisBiological databasesGeneration and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942Estrangeiroinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSORIGINAL000933834.pdf000933834.pdfTexto completo (inglês)application/pdf914398http://www.lume.ufrgs.br/bitstream/10183/106734/1/000933834.pdf4f5da240cc94e60d9d48f73df0684d24MD51TEXT000933834.pdf.txt000933834.pdf.txtExtracted Texttext/plain52354http://www.lume.ufrgs.br/bitstream/10183/106734/2/000933834.pdf.txt7f787ef4f9ee9aa67330ebf6082c4dd7MD52THUMBNAIL000933834.pdf.jpg000933834.pdf.jpgGenerated Thumbnailimage/jpeg2089http://www.lume.ufrgs.br/bitstream/10183/106734/3/000933834.pdf.jpgebd427e29760b286db770b094fa0669fMD5310183/1067342023-07-15 03:29:05.514167oai:www.lume.ufrgs.br:10183/106734Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-07-15T06:29:05Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
title |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
spellingShingle |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 Triana Dopico, Julián Sistemas biológicos Genoma Redes Genome-scale metabolic network reconstruction Systems biology Metabolic pathways Flux balance analysis Biological databases |
title_short |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
title_full |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
title_fullStr |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
title_full_unstemmed |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
title_sort |
Generation and evaluation of a genome-scale metabolic network model of synechococcus elongatus PCC7942 |
author |
Triana Dopico, Julián |
author_facet |
Triana Dopico, Julián Montagud Aquino, Arnau Siurana Paula, Maria Fuente Herráiz, David Urchueguía Fornes, Arantxa Gamermann, Daniel Torres Gavila, Francisco Javier Tena Medialdea, José Fernández de Córdoba Castellá, Pedro José Urchueguía Schölzel, Javier Fermín |
author_role |
author |
author2 |
Montagud Aquino, Arnau Siurana Paula, Maria Fuente Herráiz, David Urchueguía Fornes, Arantxa Gamermann, Daniel Torres Gavila, Francisco Javier Tena Medialdea, José Fernández de Córdoba Castellá, Pedro José Urchueguía Schölzel, Javier Fermín |
author2_role |
author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Triana Dopico, Julián Montagud Aquino, Arnau Siurana Paula, Maria Fuente Herráiz, David Urchueguía Fornes, Arantxa Gamermann, Daniel Torres Gavila, Francisco Javier Tena Medialdea, José Fernández de Córdoba Castellá, Pedro José Urchueguía Schölzel, Javier Fermín |
dc.subject.por.fl_str_mv |
Sistemas biológicos Genoma Redes |
topic |
Sistemas biológicos Genoma Redes Genome-scale metabolic network reconstruction Systems biology Metabolic pathways Flux balance analysis Biological databases |
dc.subject.eng.fl_str_mv |
Genome-scale metabolic network reconstruction Systems biology Metabolic pathways Flux balance analysis Biological databases |
description |
The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942. |
publishDate |
2014 |
dc.date.accessioned.fl_str_mv |
2014-11-12T02:14:04Z |
dc.date.issued.fl_str_mv |
2014 |
dc.type.driver.fl_str_mv |
Estrangeiro info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10183/106734 |
dc.identifier.issn.pt_BR.fl_str_mv |
2218-1989 |
dc.identifier.nrb.pt_BR.fl_str_mv |
000933834 |
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2218-1989 000933834 |
url |
http://hdl.handle.net/10183/106734 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
Metabolites. Basel. Vol. 4, no. 3 (sept. 2014), p. 680-698 |
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info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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application/pdf |
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