BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013.cpshttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013-octave.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=curation_image.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000893?filename=GonzalezMiranda2013.odeprimary200OKJohannes MeyerManually curatedordinary differential equation modelL2V4https://www.ebi.ac.uk/biomodels/BIOMD000000089323820037falseBioModelsSBMLModelsGonzalezMiranda2013 The effect of circadian oscillations on biochemical cell signaling by NF κB2013MODEL1912160002J M González-MirandaJ M González-Miranda23820037, We report the results of a numerical investigation of a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation. The main result is that a circadian rhythm, even when it represents a weak perturbation, enhances the signaling capabilities of NF-κB oscillations. This is done by turning rest states into periodic oscillations, and periodic oscillations into quasiperiodic oscillations. Strong perturbations result in complex periodic oscillations and even in chaos. Circadian rhythms would then result in a NF-κB dynamics that is more complex than the simple oscillations and rest states, initially reported for this model. This renders it more amenable for information coding.. null, 335. Departamento de Física Fundamental, Universidad de Barcelona, Av. Diagonal 647, 08028 Barcelona, Spain. jmgonzalezm@ub.edujohannes.p.meyer@gmail.comEMBL-EBIBIOMD0000000893The NF-kappaB signaling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-kappaB transcription factor [Hoffmann, A., et al. (2002) Science 298, ; Nelson, D. E., et al. (2004) Science 306, .] How the cell uses the oscillations to differentiate input conditions and send specific signals to downstream genes is an open problem. We shed light on this issue by examining the small core network driving the oscillations, which we show is designed to produce periodic spikes in nuclear NF-kappaB concentration. The presence of oscillations is extremely robust to variation of parameters, depending mainly on the saturation of the active degradation rate of IkappaB, an inhibitor of NF-kappaB. The oscillations can be used to regulate downstream genes in a variety of ways. In particular, we show that genes to whose operator sites NF-kappaB binds and dissociates fast can respond very sensitively to changes in the input signal, with effective Hill coefficients of >20.We report the results of a numerical investigation of a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation. The main result is that a circadian rhythm, even when it represents a weak perturbation, enhances the signaling capabilities of NF-κB oscillations. This is done by turning rest states into periodic oscillations, and periodic oscillations into quasiperiodic oscillations. Strong perturbations result in complex periodic oscillations and even in chaos. Circadian rhythms would then result in a NF-κB dynamics that is more complex than the simple oscillations and rest states, initially reported for this model. This renders it more amenable for information coding.Minimal model of spiky oscillations in NF-kappaB signaling.On the effect of circadian oscillations on biochemical cell signaling by NF-κB.González-Miranda J M JMKrishna Sandeep S, Jensen Mogens H MH, Sneppen Kim KfalseGonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB This is a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation. 2024-08-222024-09-022019-12-16BIOMD0000000893SBO:0000180SBO:0000177SBO:0000183SBO:0000179SBO:00001842382003716829571C17132NCIT:C16348C17380NCIT:C104199BIOMD0000000893MODEL1912160002CL:0000000EFO:0004354