Cell CollectiveModelsTomas Helikarhttps://cellcollective.org/#2404/budding-yeast-cell-cycle8.8410000000000011SBML1Cell Collectivehttps://cellcollective.org/#2404:1/budding-yeast-cell-cycleIt has been suggested that irreducible sets of states in Probabilistic Boolean Networks correspond to cellular phenotype. In this study, we identify such sets of states for each phase of the budding yeast cell cycle. We find that these "ergodic sets" underly the cyclin activity levels during each phase of the cell cycle. Our results compare to the observations made in several laboratory experiments as well as the results of differential equation models. Dynamical studies of this model: (i) indicate that under stochastic external signals the continuous oscillating waves of cyclin activity and the opposing waves of CKIs emerge from the logic of a Boolean-based regulatory network without the need for specific biochemical/kinetic parameters; (ii) suggest that the yeast cell cycle network is robust to the varying behavior of cell size (e.g., cell division under nitrogen deprived conditions); (iii) suggest the irreversibility of the Start signal is a function of logic of the G1 regulon, and changing the structure of the regulatory network can render start reversible.Ergodic sets as cell phenotype of budding yeast cell cycle.Todd Robert G RG, Helikar Tomáš Tcyclin, GH05739, Size, cyclin-dependent protein kinase regulator activity, Activity, Logics, Laboratory, Processes, Cell Volume, Phases, baker's yeast, Saccharomyces italicus, Divisions, Endomycetale, III, GH14582, Cycle, yeast, G1/S-specific cyclin, 2, 3, Volume, lager beer yeast, cyclin-dependent protein kinase, DmelCG2043, Cell Division Cycles, Cycles, study, M Phases, lcp3, Cell Division Phase, M, N, Cell Division Cycle, LCP-3, cell-division cycle, Saccharomyes cerevisiae, Cell Division, Saccharomyces uvarum var. melibiosus, Division, Division Phase, Budding Yeast, Candida robusta, CP3, Endomycopses, Saccharomyces capensis, Cell Cycles, CG7776, brewer's yeast, CYC2BAT, Behaviors, Cell Volumes, Budding, single-organism behavior, size of cell, Budding Yeasts, Saccharomycetale, CYCA2, LcpIII, Process, e(Pc), Volumes, function, Cell Divisions, L[[3]]CP3, Cell, results, Saccaromyces cerevisiae, Division Cycles, CYCLIN, Acceptance Processes, CYCLIN A2, Sccharomyces cerevisiae, Acceptance Process, Stickstoff, Sizes, laboratory, LCP3, M Phase, Saccharomyces oviformis, Yeasts, Acceptance, Yeast, PCNA, Phase, DmelCG7776, Cyclin, DMLCP3, Division Cycle, l(2)28-28-12, conformation., mitotic-like cyclin 3B from Arabidopsis, anon-35Fa, Regulons, azote, intrinsic regulator activity, G2/M-specific cyclin, nitrogeno, DmelCG5861, Phenotypes, Cell Sizes, nitrogen, anon-35Fc, Endomycopsis, DmelLcp3, E(PC), BG:DS02740.11, anon-48Ac, CG2043, 7N, General activity, EndomycetalesBudding Yeasts, Saccharomycetale, Yeasts, Cell Division Cycles, Cycles, Endomycetale, Yeast, Budding Yeast, Endomycopses, Division Cycle, Endomycopsis, Cycle, Cell Division Cycle, cell-division cycle, Cell Division, Cell Cycles., Endomycetales, Budding, Cell, Division CyclesBudding Yeasts, Saccharomycetale, Yeasts, Cell Division Cycles, Cycles, Endomycetale, Yeast, Budding Yeast, Endomycopses, Division Cycle, Endomycopsis, Cycle, Cell Division Cycle, cell-division cycle, Cell Division, Cell Cycles., Endomycetales, Budding, Cell, Division Cyclescyclin, GH05739, Size, cyclin-dependent protein kinase regulator activity, Activity, Logics, Laboratory, Processes, Cell Volume, Phases, baker's yeast, Saccharomyces italicus, Divisions, Endomycetale, III, GH14582, Cycle, yeast, G1/S-specific cyclin, 2, 3, Volume, lager beer yeast, cyclin-dependent protein kinase, DmelCG2043, Cell Division Cycles, Cycles, study, M Phases, lcp3, Cell Division Phase, M, N, Cell Division Cycle, LCP-3, cell-division cycle, Saccharomyes cerevisiae, Cell Division, Saccharomyces uvarum var. melibiosus, Division, Division Phase, Budding Yeast, Candida robusta, CP3, Endomycopses, Saccharomyces capensis, Cell Cycles, CG7776, brewer's yeast, CYC2BAT, Behaviors, Cell Volumes, Budding, single-organism behavior, size of cell, Budding Yeasts, Saccharomycetale, CYCA2, LcpIII, Process, e(Pc), Volumes, function, Cell Divisions, L[[3]]CP3, Cell, results, Saccaromyces cerevisiae, Division Cycles, CYCLIN, Acceptance Processes, CYCLIN A2, Sccharomyces cerevisiae, Acceptance Process, Stickstoff, Sizes, laboratory, LCP3, M Phase, Saccharomyces oviformis, Yeasts, Acceptance, Yeast, PCNA, Phase, DmelCG7776, Cyclin, DMLCP3, Division Cycle, l(2)28-28-12, conformation., mitotic-like cyclin 3B from Arabidopsis, anon-35Fa, Regulons, azote, intrinsic regulator activity, G2/M-specific cyclin, nitrogeno, DmelCG5861, Phenotypes, Cell Sizes, nitrogen, anon-35Fc, Endomycopsis, DmelLcp3, E(PC), BG:DS02740.11, anon-48Ac, CG2043, 7N, General activity, EndomycetalesfalseBudding Yeast Cell CycleIt has been suggested that irreducible sets of states in Probabilistic Boolean Networks correspond to cellular phenotype. In this study, we identify such sets of states for each phase of the budding yeast cell cycle. We find that these ergodic sets underly the cyclin activity levels during each phase of the cell cycle. Our results compare to the observations made in several laboratory experiments as well as the results of differential equation models. Dynamical studies of this model: (i) indicate that under stochastic external signals the continuous oscillating waves of cyclin activity and the opposing waves of CKIs emerge from the logic of a Boolean-based regulatory network without the need for specific biochemical/kinetic parameters; (ii) suggest that the yeast cell cycle network is robust to the varying behavior of cell size (e.g., cell division under nitrogen deprived conditions); (iii) suggest the irreversibility of the Start signal is a function of logic of the G1 regulon, and changing the structure of the regulatory network can render start reversible.2014-05-302016-01-222016-01-22240423049686