1. Cellular diversity promotes intercellular Ca[sup]2+ wave propagationMarko Gosak, 2009, izvirni znanstveni članek Opis: Calcium ions are an important second messenger in living cells. Calcium signals in form of waves serve as a means of intercellular communication and thus represent a vibrant subject for experimental and theoretical investigations. Here we study the role of cellular variability on the occurrence of ▫$Ca^{2+}$▫ wave propagation in a net of diffusively coupled cells. Dynamics of individual cells is simulated by a mathematical model for ▫$Ca^{2+}$▫ oscillations. Structural diversity of cells is introduced via variations of the bifurcation parameters, which signify cell sensitivity for external stimulation. Remarkably, for sufficient values of variability ▫$Ca^{2+}$▫ waves emerge, which are mostly ordered for intermediate variability strength. We analyze the spatial profile via the autocorrelation function, which confirms aresonancelike response due to the cellular variability. Thus, the reported phenomenon is a novel observation of diversityinduced spatial coherence resonance in a tissuelike media. Ključne besede: dynamic systems, waves, calcium oscillations, resonance, diversityinduced resonance, cellular variability, coupled cells, intracellular processes Objavljeno: 07.06.2012; Ogledov: 1050; Prenosov: 12 Povezava na celotno besedilo 
2. Establishing the stochastic nature of intracellular calcium oscillations from experimental dataMatjaž Perc, Anne K. Green, C. Jane Dixon, Marko Marhl, 2008, izvirni znanstveni članek Opis: Calcium has been established as a key messenger in both intra and intercellular signaling. Experimentally observed intracellular calcium responses to different agonists show a variety of behaviors from simple spiking to complex oscillatory regimes. Here we study typical experimental traces of calcium oscillations in hepatocytes obtained in response to phenylephrine and ATP. The traces were analyzed with methods of nonlinear time series analysis in order to determine the stochastic/deterministic nature of the intracellular calcium oscillations. Despite the fact that the oscillations appear, visually, to be deterministic yet perturbed by noise, our analyses provide strong evidence that the measured calcium traces in hepatocytes are prevalently of stochastic nature. In particular, bursting calcium oscillations are temporally correlated Gaussian series distorted by a monotonic, instantaneous, timeindependent function, whilst the spiking behavior appears to have a dynamical nonlinear component whereby the overall determinism level is still low. The biological importance of this finding is discussed in relation to the mechanisms incorporated in mathematical models as well as the role of stochasticity and determinism at cellular and tissue levels which resemble typical statistical and thermodynamic effects in physics. Ključne besede: dynamic systems, stochastic processes, cellular signaling, calcium oscillations, time series analyses, noise, temporal correlation Objavljeno: 07.06.2012; Ogledov: 1096; Prenosov: 80 Povezava na celotno besedilo 
3. MLCkinase/phosphatase control of Ca[sup]2+ signal transduction in airway smooth musclesAleš Fajmut, Milan Brumen, 2008, izvirni znanstveni članek Opis: In airway smooth muscles, kinase/phosphatasedependent phosphorylation and dephosphorylation of the myosin light chain (MLC) have been revealed by many authors as important steps in calcium ▫$(Ca^{2+})$▫ signalling pathway from the variation of ▫$Ca^{2+}$▫ concentration in cytosol to the force development. Here, a theoretical analysis of the control action of MLCkinase (MLCK) and MLCphosphatase (MLCP) in ▫$Ca^{2+}$▫ signalling is presented and related to the general control principles of these enzymes, which were previously studied by Reinhart Heinrich and his coworkers. The kinetic scheme of the mathematical model considers interactions among ▫$Ca^{2+}$▫, calmodulin (CaM) and MLCK and the wellknown 4state actomyosin latch bridge model, whereby a link between them is accomplished by the conservation relation of all species of MLCK. The mathematical model predicts the magnitude and velocity of isometric force in smooth muscles upon transient biphasic ▫$Ca^{2+}$▫ signal. The properties of signal transduction in the system such as the signalling time, signal duration and signal amplitude, which are reflected in the properties of force developed, are studied by the principles of the metabolic control theory. The analysis of our model predictions confirms as shown by Reinhart Heinrich and his coworkers that MLCK controls the amplitude of signal more than its duration, whereas MLCP controls both. Finally, the simulations of elevated total content of MLCK, a typical feature of bronchial muscles of asthmatic subjects and spontaneously hypertensive rats as well as potentiation of MLCP catalytic activity, are carried out and are discussed in view of an increase in the force magnitude. Ključne besede: cells, calcium, calcium oscillations, myosin light chains, enzyme activities, mathematical models Objavljeno: 07.06.2012; Ogledov: 1238; Prenosov: 10 Povezava na celotno besedilo 
4. Spatiotemporal modelling explains the effect of reduced plasma membrane Ca[sup]2+[/sup] efflux on intracellular Ca[sup]2+[/sup] oscillations in hepatocytesMarko Marhl, Marko Gosak, Matjaž Perc, C. Jane Dixon, Anne K. Green, 2008, izvirni znanstveni članek Opis: In many nonexcitable eukaryotic cells, including hepatocytes, ▫$Ca^{2+}$▫ oscillations play a key role in intra and intercellular signalling, thus regulating many cellular processes from fertilisation to death. Therefore, understanding the mechanisms underlying these oscillations, and consequently understanding how they may be regulated, is of great interest. In this paper, we study the influence of reduced ▫$Ca^{2+}$▫ plasma membrane efflux on ▫$Ca^{2+}$▫ oscillations in hepatocytes. Our previous experiments with carboxyeosin show that a reduced plasma membrane ▫$Ca^{2+}$▫ efflux increases the frequency of ▫$Ca^{2+}$▫ oscillations, but does not affect the duration of individual transients. This phenomenon can be best explained by taking into account not only the temporal,but also the spatial dynamics underlying the generation of ▫$Ca^{2+}$▫ oscillations in the cell. Here we divide the cell into a grid of elements and treat the ▫$Ca^{2+}$▫ dynamics as a spatiotemporal phenomenon. By converting an existing temporal model into a spatiotemporal one, we obtain theoretical predictions that are in much better agreement with the experimental observations. Ključne besede: cellular signalling, calcium oscillations, intracellular oscilations, spatiotemporal dynamics, hepatocytes, stochastic simulations Objavljeno: 07.06.2012; Ogledov: 888; Prenosov: 18 Povezava na celotno besedilo 
5. Role of cascades in converting oscillatory signals into stationary steplike responsesMarko Marhl, Vladimir Grubelnik, 2007, izvirni znanstveni članek Opis: In biological signal transduction pathways intermediates are often oscillatory and need to be converted into smooth output signals at the end. We show by mathematical modelling that protein kinase cascades enable converting oscillatory signals into sharp stationary steplike outputs. The importance of this result is demonstrated for the switchlike protein activation by calcium oscillations, which is of biological importance for regulating different cellular processes. In addition, we found that protein kinase cascades cause memory effects in the protein activation, which might be of a physiological advantage since a smaller amount of calcium transported in the cell is required for an effective activation of cellular processes. Ključne besede: physics, calcium oscillations, mathematical modelling, calcium, calcium oscillations, sygnalling cascade, protein kinase cascades, signal transduction, ultrasensitivity, biochemical switch, cellular dynamics Objavljeno: 07.06.2012; Ogledov: 1180; Prenosov: 41 Povezava na celotno besedilo 
6. Noiseinduced spatial dynamics in the presence of memory lossMatjaž Perc, Marko Marhl, 2007, izvirni znanstveni članek Opis: We study the spatial dynamics of noiseinduced waves in twodimensional excitable media in dependence on the duration of the artificially imposed refractory time that is introduced to each constitutive system unit after an excitation. Due to the introduction of refractory times, a randomly induced spatial wave is temporarily unable to transmit information to the opposite site of its propagation direction. Thus, once the wave leaves the absorbing boundaries of the spatial grid the system has little or no recollection, depending on the duration of the refractory time, of its existence. We show that even in the presence of such memory loss, selforganization of excitatory events leads to noiseinduced spatial periodicity in the media. We present a simple analytical treatment of a twounit system to capture and explain the essence of the observed phenomenon. Since refractory times are widespread in biological systems, our results provide interesting insights into functioning of reallife organisms at the cellular as well as tissue level. Ključne besede: noise, spatiotemporal noise, intensity, pattern formation, refractory time, calcium oscillations Objavljeno: 07.06.2012; Ogledov: 1195; Prenosov: 64 Povezava na celotno besedilo 
7. Selective regulation of protein activity by complex Ca[sup]2+ oscillations : a theoretical studyBeate Knoke, Marko Marhl, Stefan Schuster, 2007, samostojni znanstveni sestavek ali poglavje v monografski publikaciji Opis: Calcium oscillations play an important role in intracellular signal transduction. As a second messenger, ▫$Ca^{2+}$▫ represents a link between several input signals and several target processes in the cell. Whereas the frequency of simple ▫$Ca^{2+}$▫ oscillations enables a selective activation of a specific protein and herewith a particular process, the question arises of how at the same time two or more classes of proteins can be specifically regulated. The question is general and concerns the problem of how one second messenger can transmit more than one signal simultaneously (bowtie structure of signalling). To investigate whether a complex ▫$Ca^{2+}$▫ signal like bursting, a succession of lowpeak and highpeak oscillatory phases, could selectively activate different proteins, several bursting patterns with simplified square pulses were applied in a theoretical model. The results indicate that bursting ▫$Ca^{2+}$▫ oscillations allow a differential regulation of two different calciumbinding proteins, and hence, perform the desired function. Ključne besede: biophysics, calcium oscillations, cellular dynamics, mathematical models, signalling, bowtie structures, bursting, decoding Objavljeno: 07.06.2012; Ogledov: 1073; Prenosov: 11 Povezava na celotno besedilo 
8. Theoretical and experimental investigation of calciumcontraction coupling in airway smooth musclePrisca Mbikou, Aleš Fajmut, Milan Brumen, Etienne Roux, 2006, izvirni znanstveni članek Opis: We investigated theoretically and experimentally the ▫$Ca^{2+}$▫contraction couplingin rat tracheal smooth muscle. ▫$[Ca^{2+}]_i$▫, isometric contraction and myosin light chain (MLC) phosphorylation were measured in response to 1 mM carbachol. Theoretical modeling consisted in coupling a model of ▫$Ca^{2+}dependent$▫ MLC kinase (MLCK) activation with a fourstate model of smooth muscle contractile apparatus. Stimulation resulted in a shorttime contraction obtained within 1 min, followed by a longtime contraction up to the maximal force obtained in 30 min. ML7 and Wortmannin (MLCK inhibitors) abolished the contraction. Chelerythrine (PKC inhibitor) did not change the shorttime, but reduced the longtime contraction. ▫$[Ca^{2+}]_i$▫ responses of isolated myocytes recorded during the first 90 s consisted in a fast peak, followed by a plateau phase and, in 28 % of the cells, superimposed ▫$Ca^{2+}$▫ oscillations. MLC phosphorylation was maximal at 5 s and then decreased, whereas isometric contraction followed a Hillshaped curve. The model properlypredicts the time course of MLC phosphorylation and force of the shorttime response. With oscillating ▫$Ca^{2+}$▫ signal, the predicted force does not oscillate. According to the model, the amplitude of the plateau and the frequency of oscillations encode for the amplitude of force, whereas the peak encodes for force velocity. The longtime phase of the contraction, associated with a second increase in MLC phosphorylation, may be explained, at least partially, by MLC phosphatase (MLCP) inhibition, possibly via PKC inhibition. Ključne besede: biophysics, mathematical modelling, modelling, calcium oscillations, contractions, force development, muscle cells, smooth muscles, myosin kinase Objavljeno: 07.06.2012; Ogledov: 1021; Prenosov: 59 Povezava na celotno besedilo 
9. Modeling of molecular and cellular mechanisms involved in [Ca sup 2+] signal encoding in airway myocytesMarko Marhl, Denis Noble, Etienne Roux, 2006, pregledni znanstveni članek Opis: In airway myocytes signal transduction via cytosolic calcium plays an important role. In relation with experimental results we review models of basic molecular and cellular mechanisms involved in the signal transduction from the myocyte stimulation to the activation of the contractile apparatus. We concentrate on mechanisms for encoding of input signals into Ca2+ signals and the mechanisms for their decoding. The mechanisms are arranged into a general scheme of cellular signaling, the socalled bowtie architecture of signaling, in which calcium plays the role of a common media for cellular signals and links the encoding and decoding part. The encoding of calcium signals in airway myocytes is better known and is presented in more detail. Inparticular, we focus on three recent models taking into account the intracellular calcium handling and ion fluxes through the plasma membrane. Themodel of membrane conductances was originally proposed for predicting membrane depolarization and voltagedependent Ca2+ influx triggered by initialcytosolic Ca2+ increase as observed on cholinergic stimulation. Cellular models of intracellular Ca2+ handling were developed to investigate the role of a mixed population of InsP3 receptor isoforms and the cellular environment in the occurrence of Ca2+ oscillations, and the respective role ofthe sarcoplasmic reticulum, mitochondria, and cytosolic Ca2+binding proteins in cytosolic Ca2+ clearance. Modeling the mechanisms responsible for the decoding of calcium signals is developed in a lesser extent; however, the most recent theoretical studies are briefly presented in relation with the known experimental results. Ključne besede: biophysics, mathematical modelling, modelling, calcium oscillations, contractions, airway smooth muscle cells, muscle cells, smooth muscles, encoding, decoding, bowtie structures Objavljeno: 07.06.2012; Ogledov: 1119; Prenosov: 15 Povezava na celotno besedilo 
10. Critical and supercritical spatiotemporal calcium dynamics in beta cellsMarko Gosak, Andraž Stožer, Rene Markovič, Jurij Dolenšek, Matjaž Perc, Marjan Rupnik, Marko Marhl, 2017, izvirni znanstveni članek Opis: A coordinated functioning of beta cells within pancreatic islets is mediated by oscillatory membrane depolarization and subsequent changes in cytoplasmic calcium concentration. While gap junctions allow for intraislet information exchange, beta cells within islets form complex syncytia that are intrinsically nonlinear and highly heterogeneous. To study spatiotemporal calcium dynamics within these syncytia, we make use of computational modeling and confocal highspeed functional multicellular imaging. We show that model predictions are in good agreement with experimental data, especially if a high degree of heterogeneity in the intercellular coupling term is assumed. In particular, during the first few minutes after stimulation, the probability distribution of calcium wave sizes is characterized by a power law, thus indicating critical behavior. After this period, the dynamics changes qualitatively such that the number of global intercellular calcium events increases to the point where the behavior becomes supercritical. To better mimic normal in vivo conditions, we compare the described behavior during supraphysiological nonoscillatory stimulation with the behavior during exposure to a slightly lower and oscillatory glucose challenge. In the case of this protocol, we observe only critical behavior in both experiment and model. Our results indicate that the loss of oscillatory changes, along with the rise in plasma glucose observed in diabetes, could be associated with a switch to supercritical calcium dynamics and loss of beta cell functionality. Ključne besede: beta cells, islets of Langerhans, selforganized criticality, intercellular dynamics, calcium waves, glucose oscillations, computational model, confocal calcium imaging Objavljeno: 23.01.2018; Ogledov: 538; Prenosov: 234 Celotno besedilo (3,43 MB) Gradivo ima več datotek! Več...
