Oscillatory kinetics of gene expression: Protein conversion and slow mRNA transport

The negative feedback between mRNA and regulatory-protein production may result in oscillations in the kinetics of gene expression if the mRNA-protein interplay includes protein conversion. Using a mean-field kinetic model, we show that such oscillations can be amplified due to limitations of the mRNA transport between the nucleus and cytoplasm. This effect may be dramatic for the mRNA population in the nucleus. The article is published in the original.     

Analytical results for a non-Markovian process of gene expression with positive and negative feedbacks

Gene expression is a very complex process and involves many small biochemical reaction steps, resulting in a non-Markovian discrete stochastic process due to molecular memory between individual reactions. At present, this process is successfully investigated by generalized chemical master equation models. However, these models do not consider the role of feedback networks in gene expression. How the interaction between feedbacks and molecular memory affects gene expression still remains not well understood. Here, we establish generalized chemical master equation models of gene expression with positive and negative feedbacks. Assuming that the process of producing proteins follows an Erlang probability distribution, we obtain the analytical expression for this model in a steady state, as well as the measure of the noise of protein numbers. We further find that molecular memory competes with the positive feedback in suppressing the noise of the protein number. For our model with a negative feedback, molecular memory can strengthen the intensity of suppressing this noise. These interesting results imply that molecular memory are as important as the feedbacks to affect gene expression.     

Influence of Cell-Cell Interactions on the Population Growth Rate in a Tumor

The understanding of the macroscopic phenomenological models of the population growth at a microscopic level is important to predict the population behaviors emerged from the interactions between the individuals. In this work, we consider the influence of the population growth rate R on the cell-cell interaction in a tumor system and show that, in most cases especially small proliferative probabilities, the regulative role of the interaction will be strengthened with the decline of the intrinsic proliferative probabilities. For the high replication rates of an individual and the cooperative interactions, the proliferative probability almost has no effect. We compute the dependences of R on the interactions between the cells under the approximation of the nearest neighbor in the rim of an avascular tumor. Our results are helpful to qualitatively understand the influence of the interactions between the individuals on the growth rate in population systems.     

光电负反馈下垂直腔表面发射激光器偏振开关特性研究

基于扩展的自旋反转模型, 对光电负反馈下垂直腔表面发射激光器的偏振开关特性进行了数值仿真和理论分析. 研究结果表明: 对于不同的自旋反转率, 反馈强度和延迟时间对激光器偏振开关特性产生较大影响.在慢自旋反转率下运行时, 随着反馈强度的增加, 开关点电流呈线性增加, 导致X偏振模被压缩, 这与报道的基于各向同性光反馈的情景相反, 产生这一现象的原因是由于光电负反馈提高了X偏振模的阈值; 延迟时间对开关点电流的影响随反馈强度的变化而不同.在快自旋反转率下运行时, 反馈强度对开关点电流的影响与慢自旋反转率时的情形不同, 开关点电流经历先增加后减小的过程, 开关点电流受反馈强度的影响更加敏感; 而延迟时间的影响规律和慢自旋反转率时相似. 此外, 还发现自发辐射噪声对激光器偏振开关特性有较大影响. 关键词： 垂直腔表面发射激光器 偏振开关 光电负反馈 自发辐射噪声     

Immunolocalization of an osteopontin-like protein in dense granules of Toxoplasma gondii tachyzoites and its association with the parasitophorous vacuole

Toxoplasma gondii is an apicomplexan parasite infecting a broad host range, including humans. The parasite invades host cell by active penetration with the participation of its secretory organelles proteins during this process. Until now, only a limited number of secretory proteins have been discovered, and the effectors molecules involved in parasite invasion and survival are not well understood. Osteopontin (OPN) is a multifunctional glycophosphoprotein, secreted by different cell types, which is involved in various physiological and pathological events including cell signaling and survival. For the first time we demonstrated in this work by immunofluorescence and immunoelectron microscopy approaches the localization of an OPN-like protein in dense granules of extracellular T. gondii tachyzoites. Western blotting and RT-PCR confirmed this protein expression by the parasites. Our results also showed, after macrophage invasion, an intense positive labeling for OPN-like protein at the sub-apical portion of tachyzoites, the site of dense granules secretion, and the localization of this protein at the parasitophorous vacuole membrane. These data suggest that dense granules secrete an OPN-like protein, and we speculate that this protein participates during the parasite interaction process with host cells and parasitophorous vacuole formation.     

弱光反馈下正交时变光注入VCSEL的双稳特性研究

基于垂直腔面发射激光器(VCSEL)的自旋反转模型(SFM),研究了弱光反馈下正交时变光注入VCSEL的双稳特性。研究结果表明,当副激光器(S-VCSEL)受到主激光器(M-VCSEL)正交时变光注入时,弱光反馈的引入不改变正交时变光注入VCSEL的双稳宽度随光注入扫描速率增大而增大的性质;对于确定的光注入扫描速率,随着反馈强度的增大,双稳宽度将变窄;当M-VCSEL与S-VCSEL之间存在频率失谐Δν(等于νm-νs,νm、νs分别为主、副激光器自由运行时的频率)时,随着Δν从负值逐渐增加到正值,双稳宽度总体呈现先减小后增大的趋势,无反馈时在负频区域双稳环宽度呈现的较大波动在引入光反馈后可得到一定程度的抑制。     

Multiple-pattern stability in a photorefractive feedback system

We report on the observation of a multiple-pattern stability region in a photorefractive single-feedback system. Whereas hexagonal patterns are predominant for feedback with positive diffraction length we show that a variety of stable non-hexagonal patterns are generated for certain negative diffraction lengths. For the same values of the control parameters square, rectangular, or squeezed hexagonal patterns are found alternating in time. Besides these pure states, we found a number of different mixed-pattern states. We review the linear stability analysis for this system and show that the special shape of the threshold curves in the investigated parameter region gives a first explanation for the occurrence of a multiple-pattern region. Received: 22 June 1999 / Revised version: 30 August 1999 / Published online: 3 November 1999     

Struggle for space: viral extinction through competition for cells

The design of protocols to suppress the propagation of viral infections is an enduring enterprise, especially hindered by limited knowledge of the mechanisms leading to viral extinction. Here we report on infection extinction due to intraspecific competition to infect susceptible hosts. Beneficial mutations increase the production of viral progeny, while the host cell may develop defenses against infection. For an unlimited number of host cells, a feedback runaway coevolution between host resistance and progeny production occurs. However, physical space limits the advantage that the virus obtains from increasing offspring numbers; thus, infection clearance may result from an increase in host defenses beyond a finite threshold. Our results might be relevant to devise improved control strategies in environments with mobility constraints or different geometrical properties.     

光电负反馈下单向耦合注入垂直腔表面发射激光器的混沌同步特性研究

基于自旋反转模型（SFM）,对光电负反馈下单向耦合注入垂直腔表面发射激光器（VCSEL）的混沌同步特性进行了数值仿真和理论分析.研究结果表明：随着反馈强度的增加,激光器输出功率呈现两个不同的混沌区域.在单一偏振模区域,能实现很好的同步性,但接近两模共存时,同步质量急剧下降;在两模共存区域,偏振模的连续性差,同步质量不理想.两模共存时的同步质量比单一偏振模差的这一特性,与已报道的基于光反馈的情景相反.产生这一特殊现象的原因是光电负反馈诱发了偏振模竞争效应.此外,还发现内部参数的变化对两个混沌区域的选取有较大 关键词： 线性偏振模 光电负反馈 垂直腔表面发射激光器（VCSEL） 混沌同步     

Cascade replication of soliton solutions in the one-dimensional complex cubic-quintic Ginzburg-Landau equation

In the framework of the one-dimensional cubic-quintic complex Ginzburg-Landau equation, we demonstrate two methods to achieve cascade replication of dissipative solitons from a single one by using external forces whose positions and magnitudes are being precisely controlled. The first method combines high amplitude positive currents and negative currents to increase the efficiency of the process significantly and to make the process repeatable. By using two repulsive forces whose locations are time dependent, the second method enables one to obtain multiple dissipative solitons in only one cascade replication process.     

Emergent bistability: Effects of additive and multiplicative noise

Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been proposed which involves only positive feedback and no cooperativity in the regulation. An additional positive feedback loop is effectively generated due to the inhibition of cellular growth by the synthesized proteins. The mechanism, demonstrated for a synthetic circuit, may be prevalent in natural systems also as some recent experimental results appear to suggest. In this paper, we study the effects of additive and multiplicative noise on the dynamics governing emergent bistability. The calculational scheme employed is based on the Langevin and Fokker-Planck formalisms. The steady state probability distributions of protein levels and the mean first passage times are computed for different noise strengths and system parameters. In the region of bistability, the bimodal probability distribution is shown to be a linear combination of a lognormal and a Gaussian distribution. The variances of the individual distributions and the relative weights of the distributions are further calculated for varying noise strengths and system parameters. The experimental relevance of the model results is also pointed out.     

光注入和光电反馈联合作用下垂直腔表面 发射激光器的动力学特性研究

基于自旋反转模型, 研究了垂直腔表面发射激光器(VCSEL) 在光注入和光电反馈共同作用下的动力学特性. 研究结果表明: 一个受到主VCSEL光注入的副VCSEL, 在同时存在光电正反馈时, 其输出的两个线偏振模式(X和Y偏振模) 可呈现周期、 倍周期、 多周期、 混沌等丰富的动力学状态, 且两偏振模动力学态的演化路径存在差异. 各动力学状态在由反馈强度f与注入强度η 所构成的参数空间的分布区域随着主、 副VCSEL 的频率失谐Δν(Δν=ν_m-ν_s, ν_m, ν_s 分别为主、 副VCSEL自由运行时的振荡频率) 的变化而发生改变. 当Δν为正失谐时, 呈现混沌的区域相比零失谐和负失谐时有明显的扩展, 即副VCSEL能在更大的参数范围内实现混沌输出. 对于特定的频率失谐, 分析了光电正反馈强度f和光注入强度η对混沌输出带宽的影响. 通过合理选择反馈强度以及注入强度, 可使副VCSEL混沌输出带宽显著增加.     

Elastic band structures of two-dimensional solid phononic crystal with negative Poisson's ratios

In this paper, the elastic band structures of two-dimensional solid phononic crystals (PCs) with both negative and positive Poisson's ratios are investigated based on the finite difference domain method. Systems with different combinations of mass density ratio and shear modulus ratio, filling fractions and lattices are considered. The numerical results show that for the PCs with both large mass density ratio and shear modulus ratio, the first bandgap becomes narrower with its upper edge becoming lower as Poisson's ratio of the scatterers decreases from −0.1 to −0.9. Generally, introducing the material with a negative Poisson's ratio for scatterers will make this bandgap lower and narrower. For the PCs with large mass density ratio and small shear modulus ratio, the first bandgap becomes wider with Poisson's ratio of the scatterers decreasing and that of the host increasing. It is easy to obtain a wide low-frequency bandgap by embedding scatterers with a negative Poisson's ratio into the host with a positive Poisson's ratio. The PCs with large filling fractions are more sensitive to the variations of Poisson's ratios. Use of negative Poisson's ratio provides us a way of tuning bandgaps.     

How to control chaotic behaviour and population size with proportional feedback

We study the control of chaos in one-dimensional discrete maps as they often occur in modelling population dynamics. For managing the population, we seek to suppress any possible chaotic behavior, leading the system to a stable equilibrium. In this Letter, we make a rigorous analysis of the proportional feedback method under certain conditions fulfilled by a wide family of maps. We show that it is possible to stabilize the chaotic dynamics towards a globally stable positive equilibrium, that can be chosen among a broad range of possible values. In particular, the size of the population can be enhanced by control in form of population reduction. This paradoxical phenomenon is known as the hydra effect, and it has important implications in the design of strategies in such areas as fishing, pest management, and conservation biology.     

Coherence and stochastic resonance in a delayed bistable system

Both coherence resonance (CR) and stochastic resonance (SR) in a delayed bistable system driven by additive and multiplicative white noises and a weak harmonic excitation are studied by using the theory of two-state model. For the weak noise intensity and delayed feedback, the analytic expressions of power-spectrum and linear-spectrum amplification are derived to quantify the CR and the SR, respectively. The study shows that the peak in the power spectrum at the frequency corresponding to the time delay attains the maximum for an appropriate amount of additive noise intensity and the CR manifests. The feedback gain plays an important role in the SR. For example, the positive feedback gain enhances the SR, but the negative feedback gain suppresses the system output and makes the SR disappear. Moreover, the system also exhibits the frequency SR.