Spatial distribution and dose-response relationship for different operation modes in a reaction-diffusion model of the MAPK cascade

The mitogen-activated protein kinase (MAPK) cascade plays a critical role in the control of cell growth. Deregulation of this pathway contributes to the development of many cancers. To better understand its signal transduction, we constructed a reaction-diffusion model for the MAPK pathway. We modeled the three layers of phosphorylation-dephosphorylation reactions and diffusion processes from the cell membrane to the nucleus. Based on different types of feedback in the MAPK cascade, four operation modes are introduced. For each of the four modes, spatial distributions and dose-response curves of active kinases (i.e. ppMAPK) are explored by numerical simulation. The effects of propagation length, diffusion coefficient and feedback strength on the pathway dynamics are investigated. We found that intrinsic bistability in the MAPK cascade can generate a traveling wave of ppMAPK with constant amplitude when the propagation length is short. ppMAPK in this mode of intrinsic bistability decays more slowly than it does in all other modes as the propagation length increases. Moreover, we examined the global and local responses to Ras-GTP of these four modes, and demonstrated how the shapes of these dose-response curves change as the propagation length increases. Also, we found that larger diffusion constant gives a higher response level on the zero-order regime and makes the ppMAPK profiles flatter under strong Ras-GTP stimulus. Furthermore, we observed that spatial responses of ppMAPK are more sensitive to negative feedback than to positive feedback in the broader signal range. Finally, we showed how oscillatory signals pass through the kinase cascade, and found that high frequency signals are damped faster than low frequency ones.     

Gap junctions modulate seizures in a mean-field model of general anesthesia for the cortex

During slow-wave sleep, general anesthesia, and generalized seizures, there is an absence of consciousness. These states are characterized by low-frequency large-amplitude traveling waves in scalp electroencephalogram. Therefore the oscillatory state might be an indication of failure to form coherent neuronal assemblies necessary for consciousness. A generalized seizure event is a pathological brain state that is the clearest manifestation of waves of synchronized neuronal activity. Since gap junctions provide a direct electrical connection between adjoining neurons, thus enhancing synchronous behavior, reducing gap-junction conductance should suppress seizures; however there is no clear experimental evidence for this. Here we report theoretical predictions for a physiologically-based cortical model that describes the general anesthetic phase transition from consciousness to coma, and includes both chemical synaptic and direct electrotonic synapses. The model dynamics exhibits both Hopf (temporal) and Turing (spatial) instabilities; the Hopf instability corresponds to the slow (≲8 Hz) oscillatory states similar to those seen in slow-wave sleep, general anesthesia, and seizures. We argue that a delicately balanced interplay between Hopf and Turing modes provides a canonical mechanism for the default non-cognitive rest state of the brain. We show that the Turing mode, set by gap-junction diffusion, is generally protective against entering oscillatory modes; and that weakening the Turing mode by reducing gap conduction can release an uncontrolled Hopf oscillation and hence an increased propensity for seizure and simultaneously an increased sensitivity to GABAergic anesthesia.     

Emergence of oscillations and spatio-temporal coherence states in a continuum-model of excitatory and inhibitory neurons

A neural field model of the reaction-diffusion type for the emergence of oscillatory phenomena in visual cortices is proposed. To investigate the joint spatio-temporal oscillatory dynamics in a continuous distribution of excitatory and inhibitory neurons, the coupling among oscillators is modelled as a diffusion process, combined with non-linear point interactions. The model exhibits cooperative activation properties in both time and space, by reacting to volleys of activations at multiple cortical sites with ordered spatio-temporal oscillatory states, similar to those found in the physiological experiments on slow-wave field potentials. The possible use of the resulting spatial distributions of coherent states, as a flexible medium to establish feature association, is discussed.     

Dynamics of Notch Activity in a Model of Interacting Signaling Pathways

Networks of interacting signaling pathways are formulated with systems of reaction-diffusion (RD) equations. We show that weak interactions between signaling pathways have negligible effects on formation of spatial patterns of signaling molecules. In particular, a weak interaction between Retinoic Acid (RA) and Notch signaling pathways does not change dynamics of Notch activity in the spatial domain. Conversely, large interactions of signaling pathways can influence effects of each signaling pathway. When the RD system is largely perturbed by RA-Notch interactions, new spatial patterns of Notch activity are obtained. Moreover, analysis of the perturbed Homogeneous System (HS) indicates that the system admits bifurcating periodic orbits near a Hopf bifurcation point. Starting from a neighborhood of the Hopf bifurcation, oscillatory standing waves of Notch activity are numerically observed. This is of particular interest since recent laboratory experiments confirm oscillatory dynamics of Notch activity.     

A 3D Individual-Based Model to Study Effects of Chemotaxis,Competition and Diffusion on the Motile-Phytoplankton Aggregation

In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells. To quantify the effects of the different processes quoted above on the spatial and temporal distribution of phytoplankton, we used two spatial statistics: the Clark–Evans index and the group belonging percentage. Our simulation study highlights the role of the branching process with a weak-to-medium competition in reinforcing the aggregating structure that forms from attraction mechanisms (under suitable conditions for diffusion and attraction forces), and shows by contrast that aggregations cannot form when competition is high.     

Gas dispersion in volume-cycled tube flow. I. Theory.

A mathematical theory is derived for the dispersion of a contaminant bolus introduced into a fully developed volume-cycled oscillatory pipe flow. The convection-diffusion equation is solved for a tracer gas bolus by expressing the local concentration field as a series expansion of derivatives of the area-averaged concentration. The local, as well as the area-averaged, concentration is determined for a uniform initial slug or Gaussian bolus. The effect of various flow parameters such as Womersley parameter, Schmidt number, and tidal volume is investigated. The overall dispersion is characterized by a time-averaged effective diffusion coefficient, which for long duration coincides with previous dispersion theories based on a constant linear axial concentration profile. The effective diffusion coefficient can be determined from the local time history of concentration, independent of the spatial location or the initial tracer bolus. Furthermore the local peaks of the concentration-time curve follow a decaying curve dictated by the time-averaged effective diffusion coefficient. Thus the theory is directly applicable for dispersion measurements in oscillatory tube flows, a basis for the pulmonary airways application, as shown by Gaver et al. (J. Appl. Physiol. 72: 321-331, 1992).     

Interaction of spatial diffusion and delays in models of genetic control by repression

A class of models based on the Jacob and Monod theory of genetic repression for control of biosynthetic pathways in cells is considered. Both spatial diffusion and time delays are taken into account. A method is developed for representing the effects of spatial diffusion as distributed delay terms. This method is applied to two specific models and the interaction between the diffusion and the delays is treated in detail. The destabilization of the steadystate and the bifurcation of oscillatory solutions are studied as functions of the diffusivities and the delays. The limits of very small and very large diffusivities are analyzed and comparisons with well-mixed compartment models are made.On leave from North Carolina State University     

基于种间竞争模型的毒杂草入侵空间分布模拟研究

以天然草场中毒杂草与可食牧草为研究对象,在种间竞争的生态数学模型的基础上引入入侵扩散因素建立毒杂草入侵扩散模型。采用元胞自动机理论将竞争模型扩展到空间网络进行模拟研究,分析毒杂草属的空间分布类型,为毒杂草的控制提供数据支持。研究表明:(1)在入侵扩散作用下,毒杂草与可食牧草的共存平衡点由一个增加为两个,增加了共存的可能性;(2)入侵扩散作用影响了毒杂草种群的空间分布特征,减少了种群空间分布的聚集程度。     

The geometry and motion of reaction-diffusion waves on closed two-dimensional manifolds

Chemical or biological systems modelled by reaction diffusion (R.D.) equations which support simple one-dimensional travelling waves (oscillatory or otherwise) may be expected to produce intricate two or three-dimensional spatial patterns, either stationary or subject to certain motion. Such structures have been observed experimentally. Asymptotic considerations applied to a general class of such systems lead to fundamental restrictions on the existence and geometrical form of possible structures. As a consequence of the geometrical setting, it is a straightforward matter to consider the propagation of waves on closed two-dimensional manifolds. We derive a fundamental equation for R.D. wave propagation on surfaces and discuss its significance. We consider the existence and propagation of rotationally symmetric and double spiral waves on the sphere and on the torus. On leave of absence from: Department of Mathematics, Glasgow College of Technology, Cowcaddens Road, Glasgow G4 0BA, Scotland, UK     

Experimental evidence and theoretical discussion for long-term oscillations of phosphofructokinase in a compartmentalized system

The activity of rabbit muscle phosphofructokinase (EC 2.7.1.11) has been followed as a function of time under conditions where the enzyme is separated from the bulk solution by an inert membrane. An enzymatic coupling assay allows continuous measurement of the variations in NADH concentration, which is directly related to the enzyme catalytic activity. For given concentrations of substrates (ATP and Fru6P) in the outside reservoir and a given ratio between diffusion coefficients of both substrates, the activity of phosphofructokinase exhibits an oscillatory behavior during a period of about 5 h. The phenomenon is explained in terms of coupling between diffusion of metabolites and non-linear enzyme reaction.     

Effect of diffusion and spatially varying predation risk on the dynamics and equilibrium density of a predator-prey system

Starting from natural planktonic systems, we present a new mechanism involving spatial heterogeneity, and develop a new spatial structure model of planktonic predation systems. Firstly, the effect of diffusion on the dynamics of the system is investigated. We find that diffusion of only prey or both prey and predator between different patches with different predation risk may stabilize the dynamics, depending on the flow rate. Only a medium flow rate can lead to the stability of the system. Too large a rate can cause the system to approach the non-spatial limit case of a well-mixed system. Too large a rate can cause the system to approach the non-spatial limit case as a well-mixed system, which is characterized by its strongly oscillatory dynamics. When only prey diffuse, the smaller the parameter f (the proportion of the patchy volume with larger predation risk to the total volume), the more stable the system. If both populations can diffuse, however, only medium and very small f values may stabilize the system. Also, the response of the spatially averaged equilibrium densities of the system to the increasing of the flow rate is examined. With increasing flow rate, the spatial-averaged equilibrium density of prey decreases, while that of predator depends on which species can diffuse. For the case of prey diffusion only, it first remains unchanged and then slightly decreases, while it increases for the case of combinations as the flow rate increases. Our results are, qualitatively, determined by the spatially heterogeneous mechanism that we propose, and further regulated by top-down forces. Of practical importance, the results reported here indicate that which species diffuse plays a key role in the ways in which diffusion influences the dynamics and the spatial-average equilibrium densities of the system responses to the flow rate's increasing.     

The complex dynamics of a diffusive prey–predator model with an Allee effect in prey

This paper investigates complex dynamics of a predator–prey interaction model that incorporates: (a) an Allee effect in prey; (b) the Michaelis–Menten type functional response between prey and predator; and (c) diffusion in both prey and predator. We provide rigorous mathematical results of the proposed model including: (1) the stability of non-negative constant steady states; (2) sufficient conditions that lead to Hopf/Turing bifurcations; (3) a prior estimates of positive steady states; (4) the non-existence and existence of non-constant positive steady states when the model is under zero-flux boundary condition. We also perform completed analysis of the corresponding ODE model to obtain a better understanding on effects of diffusion on the stability. Our analytical results show that the small values of the ratio of the prey's diffusion rate to the predator's diffusion rate are more likely to destabilize the system, thus generate Hopf-bifurcation and Turing instability that can lead to different spatial patterns. Through numerical simulations, we observe that our model, with or without Allee effect, can exhibit extremely rich pattern formations that include but not limit to strips, spotted patterns, symmetric patterns. In addition, the strength of Allee effects also plays an important role in generating distinct spatial patterns.     

Instabilities and spatiotemporal patterns behind predator invasions with nonlocal prey competition

We study the influence of nonlocal intraspecies prey competition on the spatiotemporal patterns arising behind predator invasions in two oscillatory reaction–diffusion integro-differential models. We use three common types of integral kernels as well as develop a caricature system, to describe the influence of the standard deviation and kurtosis of the kernel function on the patterns observed. We find that nonlocal competition can destabilize the spatially homogeneous state behind the invasion and lead to the formation of complex spatiotemporal patterns, including stationary spatially periodic patterns, wave trains and irregular spatiotemporal oscillations. In addition, the caricature system illustrates how large standard deviation and low kurtosis facilitate the formation of these spatiotemporal patterns. This suggests that nonlocal competition may be an important mechanism underlying spatial pattern formation, particularly in systems where the competition between individuals varies over space in a platykurtic manner.     

Instabilities and spatiotemporal patterns behind predator invasions with nonlocal prey competition

We study the influence of nonlocal intraspecies prey competition on the spatiotemporal patterns arising behind predator invasions in two oscillatory reaction–diffusion integro-differential models. We use three common types of integral kernels as well as develop a caricature system, to describe the influence of the standard deviation and kurtosis of the kernel function on the patterns observed. We find that nonlocal competition can destabilize the spatially homogeneous state behind the invasion and lead to the formation of complex spatiotemporal patterns, including stationary spatially periodic patterns, wave trains and irregular spatiotemporal oscillations. In addition, the caricature system illustrates how large standard deviation and low kurtosis facilitate the formation of these spatiotemporal patterns. This suggests that nonlocal competition may be an important mechanism underlying spatial pattern formation, particularly in systems where the competition between individuals varies over space in a platykurtic manner.     

Oscillatory Flow Accelerates Autocrine Signaling due to Nonlinear Effect of Convection on Receptor-Related Actions

We study effects of oscillatory convective flow in extracellular space on the velocity of chemical signal propagation having a form of a front wave above a cellular layer. We found that the time-averaged propagation velocity under oscillatory flow for a particular Péclet number amplitude is slower than the velocity under steady laminar flow regime for the same value of the Péclet number, but significantly faster than under no-flow conditions. We derive asymptotic values of the propagation velocity and asymptotic characteristics of the corresponding concentration fronts in high- and low-frequency regimes and show that the reason for the observed velocity increase under the oscillatory flow stems from a nonlinear dependence of the propagation velocity on the Péclet number, particularly from the convex character of the dependence. Our findings suggest that the specific responses of cellular cultures to different flow conditions in the extracellular space (for example, expression of atherosclerosis protective genes under steady laminar flow but not under oscillatory flow) is a consequence of a nonlinear coupling between the extracellular transport and complex intracellular reaction cascades forming a positive feedback loop of the autocrine signaling. This mechanism can operate independently of, or in conjunction with, a direct stress-sensing due to mechanotransduction.     

Gas dispersion in volume-cycled tube flow. II. Tracer bolus experiments.

We present a new method for rapid measurement of local gas dispersion in volume-cycled tube flow. After a small bolus of tracer gas (argon) was injected into the oscillating flow, the time-averaged effective diffusion coefficient (mean value of Deff/D) for axial transport of a tracer gas is evaluated from local argon concentration measurements taken by a mass spectrometer. Two methods are presented for the evaluation of mean value of Deff/D from the concentration measurements: one uses all the sampled data, and the other uses only the local peaks of the concentration. Experiments were conducted in two tubes (radius = 0.85 or 1.0 cm) over a range of frequencies (0.42 less than or equal to f less than or equal to 8.5 Hz) and tidal volumes (7 less than or equal to VT less than or equal to 48 ml). The experimental results show very good agreement with the theoretical predictions of Elad et al. (J. Appl. Physiol. 72: 312-320, 1992). In the absence of oscillations (static fluid), the resulting mean value of Deff/D converges to that of molecular diffusion. We also show that concentration data may be acquired at any radial or axial position, not necessarily at the tracer gas injection point, and the resulting mean value of Deff/D is independent of the spatial position of the sampling catheter. This method is of similar accuracy and is substantially faster than previous methods for measuring gas dispersion in oscillatory flows. The rapidity of these measurements may permit this method to be used for the in vivo assessment of gas transport properties within the pulmonary system.     

Robust Min‐system oscillation in the presence of internal photosynthetic membranes in cyanobacteria

The oscillatory Min system of Escherichia coli defines the cell division plane by regulating the site of FtsZ‐ring formation and represents one of the best‐understood examples of emergent protein self‐organization in nature. The oscillatory patterns of the Min‐system proteins MinC, MinD and MinE (MinCDE) are strongly dependent on the geometry of membranes they bind. Complex internal membranes within cyanobacteria could disrupt this self‐organization by sterically occluding or sequestering MinCDE from the plasma membrane. Here, it was shown that the Min system in the cyanobacterium Synechococcus elongatus PCC 7942 oscillates from pole‐to‐pole despite the potential spatial constraints imposed by their extensive thylakoid network. Moreover, reaction‐diffusion simulations predict robust oscillations in modeled cyanobacterial cells provided that thylakoid network permeability is maintained to facilitate diffusion, and suggest that Min proteins require preferential affinity for the plasma membrane over thylakoids to correctly position the FtsZ ring. Interestingly, in addition to oscillating, MinC exhibits a midcell localization dependent on MinD and the DivIVA‐like protein Cdv3, indicating that two distinct pools of MinC are coordinated in S. elongatus. Our results provide the first direct evidence for Min oscillation outside of E. coli and have broader implications for Min‐system function in bacteria and organelles with internal membrane systems.     

Oscillatory Flow Accelerates Autocrine Signaling due to Nonlinear Effect of Convection on Receptor-Related Actions

We study effects of oscillatory convective flow in extracellular space on the velocity of chemical signal propagation having a form of a front wave above a cellular layer. We found that the time-averaged propagation velocity under oscillatory flow for a particular Péclet number amplitude is slower than the velocity under steady laminar flow regime for the same value of the Péclet number, but significantly faster than under no-flow conditions. We derive asymptotic values of the propagation velocity and asymptotic characteristics of the corresponding concentration fronts in high- and low-frequency regimes and show that the reason for the observed velocity increase under the oscillatory flow stems from a nonlinear dependence of the propagation velocity on the Péclet number, particularly from the convex character of the dependence. Our findings suggest that the specific responses of cellular cultures to different flow conditions in the extracellular space (for example, expression of atherosclerosis protective genes under steady laminar flow but not under oscillatory flow) is a consequence of a nonlinear coupling between the extracellular transport and complex intracellular reaction cascades forming a positive feedback loop of the autocrine signaling. This mechanism can operate independently of, or in conjunction with, a direct stress-sensing due to mechanotransduction.     

Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators

Models of the hexagonally arrayed spatial activity pattern of grid cell firing in the literature generally fall into two main categories: continuous attractor models or oscillatory interference models. Burak and Fiete (2009, PLoS Comput Biol) recently examined noise in two continuous attractor models, but did not consider oscillatory interference models in detail. Here we analyze an oscillatory interference model to examine the effects of noise on its stability and spatial firing properties. We show analytically that the square of the drift in encoded position due to noise is proportional to time and inversely proportional to the number of oscillators. We also show there is a relatively fixed breakdown point, independent of many parameters of the model, past which noise overwhelms the spatial signal. Based on this result, we show that a pair of oscillators are expected to maintain a stable grid for approximately t = 5µ ³ /(4πσ) ² seconds where µ is the mean period of an oscillator in seconds and σ² its variance in seconds². We apply this criterion to recordings of individual persistent spiking neurons in postsubiculum (dorsal presubiculum) and layers III and V of entorhinal cortex, to subthreshold membrane potential oscillation recordings in layer II stellate cells of medial entorhinal cortex and to values from the literature regarding medial septum theta bursting cells. All oscillators examined have expected stability times far below those seen in experimental recordings of grid cells, suggesting the examined biological oscillators are unfit as a substrate for current implementations of oscillatory interference models. However, oscillatory interference models can tolerate small amounts of noise, suggesting the utility of circuit level effects which might reduce oscillator variability. Further implications for grid cell models are discussed.