title: Reconstruction of an Immune Dynamic Model to Simulate the Contrasting Role of Auxin and Cytokinin in Plant Immunity.
abstract: In order to increase our understanding of biological dependencies in plant immune signaling pathways, the known interactions involved in plant immune networks are modeled. This allows computational analysis to predict the functions of growth related hormones in plant-pathogen interaction. The SQUAD (Standardized Qualitative Dynamical Systems) algorithm first determines stable system states in the network and then use them to compute continuous dynamical system states. Our reconstructed Boolean model encompassing hormone immune networks of Arabidopsis thaliana (Arabidopsis) and pathogenicity factors injected by model pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) can be exploited to determine the impact of growth hormones in plant immunity. We describe a detailed working protocol how to use the modified SQUAD-package by exemplifying the contrasting effects of auxin and cytokinins in shaping plant-pathogen interaction.
authors.affiliation: Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, 97074, Wuerzburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kaltdorf
authors.affiliation: Deptartment of Bioinformatics, Biocenter University of Würzburg Am Hubland Würzburg Germany, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.affiliation: Deptartment of Bioinformatics, Biocenter University of Würzburg Am Hubland Würzburg Germany, Julius-Maximilians-Universität Würzburg, Würzburg, Germany. muhammad@biozentrum.uni-wuerzburg.de.|Department of Molecular Biology and Genetics, Boğaziçi University, North Campus Kuzey Park Building 310, 34342, Bebek, Istanbul, Turkey. muhammad@biozentrum.uni-wuerzburg.de.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Naseem
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D003583:Cytokinins / Q000378:metabolism*; D007210:Indoleacetic Acids / Q000378:metabolism*; D008954:Models, Biological; D010937:Plant Growth Regulators / Q000378:metabolism; D057865:Plant Immunity; D010944:Plants / Q000235:genetics / Q000276:immunology* / Q000378:metabolism*; D015398:Signal Transduction; D012984:Software
chemical_list: D003583:Cytokinins; D007210:Indoleacetic Acids; D010937:Plant Growth Regulators
keywords: Auxin; Boolean models; Cytokinins; Hormone immune networks; Network simulation; Pathway prediction; Plant immunity; Signaling network