{"id":339,"date":"2016-01-22T11:50:15","date_gmt":"2016-01-22T19:50:15","guid":{"rendered":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/?page_id=339"},"modified":"2018-07-09T13:07:26","modified_gmt":"2018-07-09T20:07:26","slug":"computational-models","status":"publish","type":"page","link":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/computational-models\/","title":{"rendered":"Computational models"},"content":{"rendered":"<h5><strong>This page is dedicated to different models which are and will be built\u00a0in our lab. We will upload\u00a0all developed\u00a0models.<\/strong><\/h5>\n<p>&nbsp;<\/p>\n<ol>\n<li>\n<h6><span style=\"text-decoration: underline;\"><a href=\"http:\/\/dx.doi.org\/10.1186\/s12934-015-0377-3\" target=\"_blank\" rel=\"noopener noreferrer\">The\u00a0flux balance model of <em class=\"EmphasisTypeItalic\">Methylomicrobium buryatense<\/em> strain 5G(B1)<\/a>\u00a0and <i>Methylomicrobium<\/i> <i>alcaliphilum<\/i> 20ZR:<\/span><\/h6>\n<\/li>\n<\/ol>\n<p style=\"text-align: justify;\">The model was constructed and used for evaluating metabolic engineering strategies for biofuels and chemical production with a methanotrophic bacterium as the catalytic platform. The initial metabolic reconstruction was based on whole-genome predictions. Each metabolic step was manually verified, gapfilled, and modified in accordance with genome-wide expression data.\u00a0 The flux balance simulations suggest that only the transfer of electrons from methanol oxidation to methane oxidation steps can support measured growth and methane\/oxygen consumption parameters, while the scenario employing NADH as a possible source of electrons for particulate methane monooxygenase cannot. COBRA version of the model in <strong><span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2016\/04\/Cobra_model_5gb1.xls\">xls<\/a><\/span><\/strong> and <strong><span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2016\/04\/i5GB1_update.zip\">SBML<\/a><\/span><\/strong> formats (<a href=\"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/01\/iIA407_20Z_COBRA.xls\"><span style=\"color: #ff0000;\"><strong>xls<\/strong><\/span><\/a>\u00a0for <em>M. <\/em><i>alcaliphilum<\/i> 20ZR as well as an <strong><span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-content\/uploads\/2018\/07\/iIA407_20Z_COBRA_ext.xls\">extended model<\/a><\/span><\/strong> for <em>M. <\/em><i>alcaliphilum<\/i> 20ZR\u00a0 including MXALa reaction ).<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This page is dedicated to different models which are and will be built\u00a0in our lab. We will upload\u00a0all developed\u00a0models. &nbsp; The\u00a0flux balance model of Methylomicrobium buryatense strain 5G(B1)\u00a0and Methylomicrobium alcaliphilum 20ZR: The model was constructed and used for evaluating metabolic engineering strategies for biofuels and chemical production with a methanotrophic bacterium as the catalytic platform. [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-339","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/339","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/comments?post=339"}],"version-history":[{"count":20,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/339\/revisions"}],"predecessor-version":[{"id":823,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/339\/revisions\/823"}],"wp:attachment":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/media?parent=339"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}