Multisite phosphorylation and network dynamics of cyclin-dependent kinase signaling in the eukaryotic cell cycle

Multisite phosphorylation of regulatory proteins has been proposed to underlie ultrasensitive responses required to generate nontrivial dynamics in complex biological signaling networks. We used a random search strategy to analyze the role of multisite phosphorylation of key proteins regulating cyclin-dependent kinase (CDK) activity in a model of the eukaryotic cell cycle. We show that multisite phosphorylation of either CDK, CDC25, wee1, or CDK-activating kinase is sufficient to generate dynamical behaviors including bistability and limit cycles. Moreover, combining multiple feedback loops based on multisite phosphorylation do not destabilize the cell cycle network by inducing complex behavior, but rather increase the overall robustness of the network. In this model we find that bistability is the major dynamical behavior of the CDK signaling network, and that negative feedback converts bistability into limit cycle behavior. We also compare the dynamical behavior of several simplified models of CDK regulation to the fully detailed model. In summary, our findings suggest that multisite phosphorylation of proteins is a critical biological mechanism in generating the essential dynamics and ensuring robust behavior of the cell cycle.     

Modelling of predator–prey trophic interactions. Part II: Three trophic levels

A general class of lumped parameter models describing the local dynamics of a tri-trophic chain in a controlled environment is analyzed in detail. The trophic functions characterizing the interactions are defined only by some properties and allow us to treat both prey-dependent and ratio-dependent models in a unified manner. Conditions for existence and stability of extinction and coexistence equilibrium states are determined. Some peculiar aspects of the dynamics of the system depending on the bioecological parameters are presented, with particular attention to bistability situations, limit cycles and chaotic behaviours.     

A comparison of two predator-prey models with Holling's type I functional response

In this paper, we analyze a laissez-faire predator-prey model and a Leslie-type predator-prey model with type I functional responses. We study the stability of the equilibrium where the predator and prey coexist by both performing a linearized stability analysis and by constructing a Lyapunov function. For the Leslie-type model, we use a generalized Jacobian to determine how eigenvalues jump at the corner of the functional response. We show, numerically, that our two models can both possess two limit cycles that surround a stable equilibrium and that these cycles arise through global cyclic-fold bifurcations. The Leslie-type model may also exhibit super-critical and discontinuous Hopf bifurcations. We then present and analyze a new functional response, built around the arctangent, that smoothes the sharp corner in a type I functional response. For this new functional response, both models undergo Hopf, cyclic-fold, and Bautin bifurcations. We use our analyses to characterize predator-prey systems that may exhibit bistability.     

Alternans and 2:1 rhythms in an ionic model of heart cells

ECG alternans is commonly held to be an indicator of electrical instability of the heart, but the development of alternans has not yet been fully understood theoretically. We investigate the onset of alternans and 2:1 rhythms for stimulation at increasing frequencies in the Beeler-Reuter model, a simple ionic model of cardiac tissue. We find hysteresis and bistability at the onset of alternans; well-timed stimuli can switch between the two limit cycles. We determine quantitatively the effect of blocking specific ionic currents. Moreover, we find that calcium buffers generally promote alternans.     

Stochastic Bistability and Bifurcation in a Mesoscopic Signaling System with Autocatalytic Kinase

Bistability is a nonlinear phenomenon widely observed in nature including in biochemical reaction networks. Deterministic chemical kinetics studied in the past has shown that bistability occurs in systems with strong (cubic) nonlinearity. For certain mesoscopic, weakly nonlinear (quadratic) biochemical reaction systems in a small volume, however, stochasticity can induce bistability and bifurcation that have no macroscopic counterpart. We report the simplest yet known reactions involving driven phosphorylation-dephosphorylation cycle kinetics with autocatalytic kinase. We show that the noise-induced phenomenon is correlated with free energy dissipation and thus conforms with the open-chemical system theory. A previous reported noise-induced bistability in futile cycles is found to have originated from the kinase synchronization in a bistable system with slow transitions, as reported here.     

From bistability to oscillations in a model for the isocitrate dehydrogenase reaction

Considered is a bienzymatic system consisting of isocitrate dehydrogenase (IDH, EC 1.1.1.42), which transforms NADP(+) into NADPH, and of diaphorase (DIA, EC 1.8.1.4), which catalyzes the reverse reaction. Experimental evidence as well as a theoretical model show the possibility of a coexistence between two stable steady states in this reaction system. The phenomenon originates from the regulatory properties of IDH. We extend the analysis of a theoretical model proposed for the IDH-DIA bienzymatic system and investigate the occurrence of different modes of bistability, with or without hysteresis, i.e. in the presence of two or only one limit point bounding the domain of multiple steady states. The analysis indicates that the two types of bistability may sometimes be observed sequentially as a given control parameter is progressively increased. We further obtain conditions in which sustained oscillations develop in the model. These results establish the isocitrate dehydrogenase reaction coupled to diaphorase as a suitable candidate for further experimental and theoretical studies of bistability and oscillations in biochemical systems.     

A food chain ecoepidemic model: Infection at the bottom trophic level

In this paper we consider a three level food web subject to a disease affecting the bottom prey. The resulting dynamics is much richer with respect to the purely demographic model, in that it contains more transcritical bifurcations, gluing together the various equilibria, as well as persistent limit cycles, which are shown to be absent in the classical case. Finally, bistability is discovered among some equilibria, leading to situations in which the computation of their basins of attraction is relevant for the system outcome in terms of its biological implications.     

Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements

Previous studies have suggested that positive feedback loops and ultrasensitivity are prerequisites for bistability in covalent modification cascades. However, it was recently shown that bistability and hysteresis can also arise solely from multisite phosphorylation. Here we analytically demonstrate that double phosphorylation of a protein (or other covalent modification) generates bistability only if: (a) the two phosphorylation (or the two dephosphorylation) reactions are catalyzed by the same enzyme; (b) the kinetics operate at least partly in the zero-order region; and (c) the ratio of the catalytic constants of the phosphorylation and dephosphorylation steps in the first modification cycle is less than this ratio in the second cycle. We also show that multisite phosphorylation enlarges the region of kinetic parameter values in which bistability appears, but does not generate multistability. In addition, we conclude that a cascade of phosphorylation/dephosphorylation cycles generates multiple steady states in the absence of feedback or feedforward loops. Our results show that bistable behavior in covalent modification cascades relies not only on the structure and regulatory pattern of feedback/feedforward loops, but also on the kinetic characteristics of their component proteins.     

Coupling oscillations and switches in genetic networks

Switches (bistability) and oscillations (limit cycle) are omnipresent in biological networks. Synthetic genetic networks producing bistability and oscillations have been designed and constructed experimentally. However, in real biological systems, regulatory circuits are usually interconnected and the dynamics of those complex networks is often richer than the dynamics of simple modules. Here we couple the genetic Toggle switch and the Repressilator, two prototypic systems exhibiting bistability and oscillations, respectively. We study two types of coupling. In the first type, the bistable switch is under the control of the oscillator. Numerical simulation of this system allows us to determine the conditions under which a periodic switch between the two stable steady states of the Toggle switch occurs. In addition we show how birhythmicity characterized by the coexistence of two stable small-amplitude limit cycles, can easily be obtained in the system. In the second type of coupling, the oscillator is placed under the control of the Toggleswitch. Numerical simulation of this system shows that this construction could for example be exploited to generate a permanent transition from a stable steady state to self-sustained oscillations (and vice versa) after a transient external perturbation. Those results thus describe qualitative dynamical behaviors that can be generated through the coupling of two simple network modules. These results differ from the dynamical properties resulting from interlocked feedback loops systems in which a given variable is involved at the same time in both positive and negative feedbacks. Finally the models described here may be of interest in synthetic biology, as they give hints on how the coupling should be designed to get the required properties.     

一类一级饱和反应系统的极限环

本文研究生化反应中一类饱和反应的数学模型：应用微分方程定性理论,完整地解决了该系统极限环的存在性、唯一性和不存在性等问题．     

On evolution under symmetric and asymmetric competitions

This paper considers the coevolution of phenotypic traits in a community comprising two competitive species subject to strong Allee effects. Firstly, we investigate the ecological and evolutionary conditions that allow for continuously stable strategy under symmetric competition. Secondly, we find that evolutionary suicide is impossible when the two species undergo symmetric competition, however, evolutionary suicide can occur in an asymmetric competition model with strong Allee effects. Thirdly, it is found that evolutionary bistability is a likely outcome of the process under both symmetric and asymmetric competitions, which depends on the properties of symmetric and asymmetric competitions. Fourthly, under asymmetric competition, we find that evolutionary cycle is a likely outcome of the process, which depends on the properties of both intraspecific and interspecific competition. When interspecific and intraspecific asymmetries vary continuously, we also find that the evolutionary dynamics may admit a stable equilibrium and two limit cycles or two stable equilibria separated by an unstable limit cycle or a stable equilibrium and a stable limit cycle.     

心肌细胞团搏动整数倍节律的非线性动力学机制

利用心肌细胞耦合模型研究心肌整数倍节律的动力学机理。确定性模型仿真揭示了心肌细胞团同步搏动加周期分岔的节律变化规律;随机模型仿真发现在加周期分岔序列中分岔点附近会出现整数倍节律,其中,0-1整数倍节律产生于从静息到周期1的Hopf分岔点附近,1-2整数倍节律产生于周期1和周期2极限环间的加周期分岔点附近;对系统相空间轨道的分析进一步揭示出整数倍节律是由系统运动在相邻的两个轨道之间随机跃迁形成的。上述分析结果不仅阐明了心肌整数倍节律的机理,并且揭示了各种整数倍节律与加周期分岔序列中相邻节律的内在联系,为重新认识心律变化的规律开辟了新的途径。     

Periodicity in an epidemic model with a generalized non-linear incidence

We develop and analyze a simple SIV epidemic model including susceptible, infected and perfectly vaccinated classes, with a generalized non-linear incidence rate subject only to a few general conditions. These conditions are satisfied by many models appearing in the literature. The detailed dynamics analysis of the model, using the Poincaré index theory, shows that non-linearity of the incidence rate leads to vital dynamics, such as bistability and periodicity, without seasonal forcing or being cyclic. Furthermore, it is shown that the basic reproductive number is independent of the functional form of the non-linear incidence rate. Under certain, well-defined conditions, the model undergoes a Hopf bifurcation. Using the normal form of the model, the first Lyapunov coefficient is computed to determine the various types of Hopf bifurcation the model undergoes. These general results are applied to two examples: unbounded and saturated contact rates; in both cases, forward or backward Hopf bifurcations occur for two distinct values of the contact parameter. It is also shown that the model may undergo a subcritical Hopf bifurcation leading to the appearance of two concentric limit cycles. The results are illustrated by numerical simulations with realistic model parameters estimated for some infectious diseases of childhood.     

Body-size scaling in an SEI model of wildlife diseases

A number of wildlife pathogens are generalist and can affect different host species characterized by a wide range of body sizes. In this work we analyze the role of allometric scaling of host vital and epidemiological rates in a Susceptible-Exposed-Infected (SEI) model. Our analysis shows that the transmission coefficient threshold for the disease to establish in the population scales allometrically (exponent = 0.45) with host size as well as the threshold at which limit cycles occur. In contrast, the threshold of the basic reproduction number for sustained oscillations to occur is independent of the host size and is always greater than 5. In the case of rabies, we show that the oscillation periods predicted by the model match those observed in the field for a wide range of host sizes.The population dynamics of the SEI model is also analyzed in the case of pathogens affecting multiple coexisting hosts with different body sizes. Our analyses show that the basic reproduction number for limit cycles to occur depends on the ratio between host sizes, that the oscillation period in a multihost community is set by the smaller species dynamics, and that intermediate interspecific disease transmission can stabilize the epidemic occurrence in wildlife communities.     

Infectious disease in consumer populations: dynamic consequences of resource-mediated transmission and infectiousness

Nonhost species can strongly affect the timing and progression of epidemics. One central interaction—between hosts, their resources, and parasites—remains surprisingly underdeveloped from a theoretical perspective. Furthermore, key epidemiological traits that govern disease spread are known to depend on resource density. We tackle both issues here using models that fuse consumer–resource and epidemiological theory. Motivated by recent studies of a phytoplankton–zooplankton–fungus system, we derive and analyze a family of dynamic models for parasite spread among consumers in which transmission depends on consumer (host) and resource densities. These models yield four key insights. First, host–resource cycling can lower mean host density and inhibit parasite invasion. Second, host–resource cycling can create Allee effects (bistability) if parasites increase mean host density by reducing the amplitude of host–resource cycles. Third, parasites can stabilize host–resource cycles; however, host–resource cycling can also cause disease cycling. Fourth, resource dependence of epidemiological traits helps to govern the relative dominance of these different behaviors. However, these resource dependencies largely have quantitative rather than qualitative effects on these three-species dynamics. Given the extent of these results, host–resource–parasite interactions should become more fundamental components of the burgeoning theory for the community ecology of infectious diseases.     

The effects of reversibility and noise on stochastic phosphorylation cycles and cascades

The phosphorylation-dephosphorylation cycle is a common motif in cellular signaling networks. Previous work has revealed that, when driven by a noisy input signal, these cycles may exhibit bistable behavior. Here, a recently introduced theorem on network bistability is applied to prove that the existence of bistability is dependent on the stochastic nature of the system. Furthermore, the thermodynamics of simple cycles and cascades is investigated in the stochastic setting. Because these cycles are driven by the ATP hydrolysis potential, they may operate far from equilibrium. It is shown that sufficient high ATP hydrolysis potential is necessary for the existence of a bistable steady state. For the single-cycle system, the ensemble average behavior follows the ultrasensitive response expected from analysis of the corresponding deterministic system, but with significant fluctuations. For the two-cycle cascade, the average behavior begins to deviate from the expected response of the deterministic system. Examination of a two-cycle cascade reveals that the bistable steady state may be either propagated or abolished along a cascade, depending on the parameters chosen. Likewise, the variance in the response can be maximized or minimized by tuning the number of enzymes in the second cycle.     

Qualitative analysis of a predator-prey system with limit cycles

Fairly regular multiannual microtine rodent cycles are observed in boreal Fennoscandia. In the southern parts of Fennoscandia these multiannual cycles are not observed. It has been proposed that these cycles may be stabilized by generalist predation in the south.We show that if the half-saturation of the generalist predators is high compared to the number of small rodents the cycles are likely to be stabilized by generalist predation as observed. We give examples showing that if the half-saturation of the generalist predators is low compared to the number of small rodents, then multiple equilibria and multiple limit cycles may occur as the generalist predator density increases.     

Immigration can destabilize tri-trophic interactions: implications for conservation of top predators

Top predators often have large home ranges and thus are especially vulnerable to habitat loss and fragmentation. Increasing connectance among habitat patches is therefore a common conservation strategy, based in part on models showing that increased migration between subpopulations can reduce vulnerability arising from population isolation. Although three-dimensional models are appropriate for exploring consequences to top predators, the effects of immigration on tri-trophic interactions have rarely been considered. To explore the effects of immigration on the equilibrium abundances of top predators, we studied the effects of immigration in the three-dimensional Rosenzweig-MacArthur model. To investigate the stability of the top predator equilibrium, we used MATCONT to perform a bifurcation analysis. For some combinations of model parameters with low rates of top predator immigration, population trajectories spiral towards a stable focus. Holding other parameters constant, as immigration rate is increased, a supercritical Hopf bifurcation results in a stable limit cycle and thus top predator populations that cycle between high and low abundances. Furthermore, bistability arises as immigration of the intermediate predator is increased. In this case, top predators may exist at relatively low abundances while prey become extinct, or for other initial conditions, the relatively higher top predator abundance controls intermediate predators allowing for non-zero prey population abundance and increased diversity. Thus, our results reveal one of two outcomes when immigration is added to the model. First, over some range of top predator immigration rates, population abundance cycles between high and low values, making extinction from the trough of such cycles more likely than otherwise. Second, for relatively higher intermediate predator migration rates, top predators may exist at low values in a truncated system with impoverished diversity, again with extinction more likely.     

The effect of delayed host self-regulation on host-pathogen population cycles in forest insects

Delayed host self-regulation using a Beverton-Holt function and delayed logistic self-regulation are included in a host-pathogen model with free-living infective stages (Anderson and May's model G) with the purpose of investigating whether adding the relatively complex self-regulations decrease the likelihood of population cycles. The main results indicate that adding delayed self-regulation to the baseline model increases the likelihood of population cycles. The dynamics display some of the key features seen in the field, such as cycle peak density exceeding the carrying capacity and a locally stable equilibrium coexisting with a stable cycle (bistability). Numerical studies show that the model with more complex forms of self-regulation can generate cycles which match most aspects of the cycles observed in nature.