title: Methods for Modeling Brassinosteroid-Mediated Signaling in Plant Development.
abstract: Mathematical modeling of biological processes is a useful tool to draw conclusions that are contained in the data, but not directly reachable, as well as to make predictions and select the most efficient follow-up experiments. Here we outline a method to model systems of a few proteins that interact transcriptionally and/or posttranscriptionally, by representing the system as Ordinary Differential Equations and to study the model dynamics and stationary states. We exemplify this method by focusing on the regulation by the brassinosteroid (BR) signaling component BRASSINOSTEROID INSENSITIVE1 ETHYL METHYL SULFONATE SUPPRESSOR1 (BES1) of BRAVO, a quiescence-regulating transcription factor expressed in the quiescent cells of Arabidopsis thaliana roots. The method to extract the stationary states and the dynamics is provided as a Mathematica code and requires basic knowledge of the Mathematica software to be executed.
authors.affiliation: Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, 08028, Barcelona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Frigola
authors.affiliation: Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut Recerca i Tecnologia Agroalimentaries-Universitat Autonóma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UABUB), 08193, Barcelona, Spain.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Caño-Delgado
authors.affiliation: Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, 08028, Barcelona, Spain. mibanes@ub.edu.
authors.forename: Marta
authors.initials: M
authors.lastname: Ibañes
mesh_terms: D017360:Arabidopsis / Q000187:drug effects* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D060406:Brassinosteroids / Q000494:pharmacology*; D004268:DNA-Binding Proteins; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D008432:Mathematical Computing; D008954:Models, Biological; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D010937:Plant Growth Regulators / Q000494:pharmacology*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D014176:Protein Biosynthesis; D015398:Signal Transduction; D013260:Steroids, Heterocyclic / Q000494:pharmacology*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; C456160:BES1 protein, Arabidopsis; D060406:Brassinosteroids; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D010937:Plant Growth Regulators; D013260:Steroids, Heterocyclic; D014157:Transcription Factors; C023623:brassinolide
keywords: Brassinosteroids; Dynamical systems; Modeling; ODEs; Steady states; Transcriptional circuit