{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Pdf":["https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.pdf"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000-biopax2.owl","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000-biopax3.owl"],"Svg":["https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.svg"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000_url.xml","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000_urn.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.vcml","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.m","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.xpp","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.sci","https://www.ebi.ac.uk/biomodels/model/download/MODEL0911120000?filename=MODEL0911120000.png"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Oxana Sorokina"],"curationStatus":["Non-curated"],"modellingApproach":["ordinary differential equation model"],"levelVersion":["L2V4"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL0911120000"],"publication_pubmed":["19761615"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Sorokina2009 PhyA FHL ON OFF 9h"],"publication_year":["2009"],"submissionId":["MODEL0911120000"],"publication_authors":["Oxana Sorokina, Anita Kapus, Kata Terecskei, Laura E Dixon, László Kozma-Bognár, Ferenc Nagy, Andrew J Millar"],"first_author":["Oxana Sorokina"],"publication":["19761615,\n Background
Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media.Results
The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation.Conclusion
Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic.. null, 3.\n Institute of Molecular Plant Sciences, The University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JH, UK."],"submitter_mail":["o.sorokina@sms.ed.ac.uk"],"submitter_affiliation":["The Univerity of Edinburgh"],"pubmed_abstract":["Background
Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media.Results
The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation.Conclusion
Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic."],"pubmed_title":["A switchable light-input, light-output system modelled and constructed in yeast."],"pubmed_authors":["Sorokina Oxana O, Kapus Anita A, Terecskei Kata K, Dixon Laura E LE, Kozma-Bognar Laszlo L, Nagy Ferenc F, Millar Andrew J AJ"],"additional_accession":[]},"is_claimable":false,"name":"Sorokina2009_PhyA_FHL_ON_OFF_9h","description":"\n \n Final version obtained by merging of the PhyA_FHL model with On_OFF 9h long experiment 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. \n 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\n for more information. \n In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. \n \n 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.\n\n\n","dates":{"last_modification":"2011-07-27","publication":"2005-01-01","submission":"2009-11-15"},"accession":"MODEL0911120000","cross_references":{"pubmed":["19761615"],"biomodels__db":["MODEL0911120000"],"go":["GO:0010017"],"taxonomy":["4932"]}}