BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.mhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1504170000?filename=MODEL1504170000.xppprimaryOK200Mariana Martinez-SanchezNon-curatedlogical modelL3V1https://www.ebi.ac.uk/biomodels/MODEL150417000020920363falseBioModelsSBMLModelsAzpeitia2010 Gene regulatory network to maintain the root stem cell niche (RSCN GRN 2010a)2010MODEL1504170000Non KineticEugenio Azpeitia, Mariana Benítez, Iliusi Vega, Carlos Villarreal, Elena R Alvarez-BuyllaEugenio Azpeitia20920363, <h4>Background</h4>Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner.<h4>Results</h4>We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks.<h4>Conclusions</h4>These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance.. null, 4. Instituto de Ecología & Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México DF, México.mar.esther23@gmail.comUniversidad Nacional Autónoma de México<h4>Background</h4>Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner.<h4>Results</h4>We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks.<h4>Conclusions</h4>These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance.Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche.Azpeitia Eugenio E, Benítez Mariana M, Vega Iliusi I, Villarreal Carlos C, Alvarez-Buylla Elena R ERCell Niches, Materials, PEPI., Genetic, GP88, Microenvironment, Stem, epithelin, aerial root (narrow), Gene, Stem Cell Microenvironments, INSDC_feature:gene, PGRN, PCDGF, root, Niche, GRO:0005338, Cistrons, Cell Microenvironments, all, GrN, Cell Microenvironment, Cell Niche, Stem Cell, Material, Stem Cell Niches, climbing root (narrow), Stem Cell Microenvironment, Genetic Materials, Cistron, GEP, CLN11, Microenvironments, Genetic Material, NichesCell Niches, Materials, A., Pflanze, Non-Governmental Organizations, SCARECROW, sci, GRO:0005338, composed of, Arabis thaliana, Cell Microenvironments, DmelCG6383, viridiplantae, dmTAF[[II]]230, Readability, Tier, Arabidopsis thalianas, A. thalianas, HOW, How, CLN11, l(3)j5D5, 24B, Animalia, Gene Expressions, TFIID TAF250, cel, Mouse-ear Cress, stru, crumb, composition, PGRN, l(3)S053606, CG10293, Mouse-ear, genetic, l(3)j5B5, SHOOT GRAVITROPISM 1, climbing root (narrow), CP-22, Organizations, Arabidopses, auxins, 0904/17, dTAF[[II]]230, organisation, nucleus suprachiasmaticus, CG6383, PEPI, animalia, familial, TAF200, aerial root (narrow), A. thaliana, Niche, TAFII-250, TAF250/230, results, GrN, Cell Microenvironment, TAFII250, Stem Cell, neutropenia, SZ1, Indolylacetic, Arabidopsis thaliana (thale cress), Genetic Materials, Genetic Material, whole organism, Nongovernmental, Stem, content, administrative structure, epithelin, Plant, Maintenances., INSDC_feature:gene, root, CG17603, TAF[[II]], Arabidopsis, Taf250, Material, SR3-5, Stem Cell Microenvironment, Koerper, Cistron, anon-EST:Liang-2.39, inherited genetic, Acids, l(3)S050920, TAF230, V19, Crbs, Auxin, d230, conformation, Microenvironment, P62, Gene, organization and administration, dTAFII250, far, EfW1, Crumbs, dmTAF1, Taf230, thalianas, Indoleacetic, GEP, Non-Governmental, Animal, Niches, TAF250, plantae, Organization, Taf200, CT19912, 0509/20, dTAF[[II]]250, Genetic, l(3)s2612, Cresses, cell, 1384/04, Stem Cell Microenvironments, SGR1, Taf1p, metazoa, Auxins, Maintenances, Expressions, dTAF250, thale-cress, Non-Governmental Organization, Stem Cell Niches, DmelCG10293, CP22, Cress, Expression, Mouse ear, organization, TAF, constitutitional genetic, Indolylacetic Acids, Differentiation, l(3)j1B5, TAF[[II]]250, GP88, Arbisopsis thaliana, organizational structure, clone 2.39, body, Arabidopsis thaliana, l(3)84Ab, whole body, BG:DS00004.13, compositionality, qkr, Cistrons, l(3)S090417, motif, Cell, all, dTAF230, l(3)07207, Cell Niche, p230, KH93F, Metazoa, TAF[[II]]250/230, TFIID, CRB, Crb, background, l(3)S058104, Nongovernmental Organizations, Differentiations, who, thale cress, administrative management, mouse-ear cress, Taf[[II]]250, severe congenital, TAF[[II]]230, thaliana, TAF[II]250, Cell Differentiations, PCDGF, Who/How, Understanding, Mouse-ear Cresses, introduction, Non Governmental Organizations, DmelCG17603, structure, qkr[93F], organizational management, nucleus suprachiasmaticus hypothalami, Severe Chronic Neutropenia, hereditary, Microenvironments, Nongovernmental Organization, suprachiasmatic nucleus (Spiegel-Zwieg), SCN, TAF1Desc, DESCR., Description, Descriptive, Descriptor, description, Product Description/AppearancedTAF[[II]]230, TAF[[II]]250, d230, Cell Niches, GP88, PEPI, Arbisopsis thaliana, Microenvironment, A., Arabidopsis thaliana, TAF200, aerial root (narrow), l(3)84Ab, dTAFII250, A. thaliana, BG:DS00004.13, TAFII-250, Niche, TAF250/230, GRO:0005338, EfW1, Cell, Arabis thaliana, Cell Microenvironments, dTAF230, all, dmTAF[[II]]230, GrN, Stem., Cell Microenvironment, TAFII250, Arabidopsis thalianas, Cell Niche, Stem Cell, dmTAF1, Taf230, p230, A. thalianas, thalianas, TAF[[II]]250/230, TFIID, Arabidopsis thaliana (thale cress), GEP, CLN11, Niches, TAF250, thale cress, Taf[[II]]250, mouse-ear cress, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, Cresses, cell, Stem, Mouse-ear Cress, epithelin, thaliana, Taf1p, Stem Cell Microenvironments, TAF[II]250, PGRN, PCDGF, root, CG17603, Mouse-ear Cresses, TAF[[II]], Mouse-ear, dTAF250, thale-cress, Arabidopsis, DmelCG17603, Taf250, Stem Cell Niches, SR3-5, climbing root (narrow), Stem Cell Microenvironment, Cress, Mouse ear, TAF, Arabidopses, Microenvironments, TAF230, TAF1falseAzpeitia2010 - Gene regulatory network to maintain the root stem cell niche (RSCN_GRN_2010a)No description2016-05-092016-05-092015-04-17MODEL150417000020920363MODEL1504170000