基于DNA损伤的蛋白调控网络研究

细胞生长的每个阶段都离不开蛋白质相互作用.研究细胞周期的功能、调控机理及参与调控的蛋白质之间的关系对生物工程等领域有重大的应用价值.本文通过研究电离辐射下生物体细胞的DNA损伤后,细胞内以p53为核心的扩展蛋白调控网络的功能、原理及其自修复机理,在现有蛋白网络基础上引入更多蛋白网络调控因子来建立蛋白调控网络,仿真模拟更为全面的细胞周期进程;并且从复杂网络图论和细胞周期调控两个方面分析扩展PMP调控网络的抗扰能力及自修复机理,结果表明:1)蛋白网络在对抗环境中出现的小扰动时具有较强的稳定性.但在面对蓄意攻击时网络的稳定性较差.2)受损的DNA能否被修复取决于p53蛋白的动力学行为,即低损伤与中损伤情况下,p53可诱导细胞周期进程阻滞来完成细胞的自修复;而当高损伤或过损伤时,p53蛋白浓度表现为周期振荡行为并诱导细胞凋亡.     

VPRBP 蛋白与Abl 激酶诱发、抑制前列腺癌的 一种物理机制

在本文基于Hill动力学与Michaelis-Menten方程,建立理论模型研究VPRBP蛋白与Abl激酶诱发、抑制前列腺癌的一种物理机制.研究发现,DNA损伤使得ATM(共济失调毛细血管扩张症突变)很快激活,并激活上调p53蛋白表达,DNA损伤的后续破坏会在很大程度上通过p53表达上调而被抑制. VPRBP通过上调MDM2蛋白的激活水平,使得p53表达水平异常,进而无法正常抑制前列腺癌的发生发展.通过考察Abl在前列腺癌进程中的作用发现,Abl使得AKT的表达水平下调,由于Abl对AKT的抑制作用,致使在AKT信号通路中MDM2表达水平受到抑制,进而稳定p53表达.由此表明了,过少的Abl对AKT的抑制程度减弱,不仅使得细胞代谢出现紊乱,而且还会促使p53正常的周期表达水平异常,对DNA损伤诱发的肿瘤抑制性减弱,进而促进前列腺癌的发生发展.基于本文模型,可以预测VPRBP与Abl作为诱发、抑制前列腺癌的调节剂对现有和潜在的抗癌治疗较为敏感. VPRBP与Abl在诱发、抑制前列腺癌过程中的时滞效应,导致信号通路中p53与PTEN蓄积量增多、AKT蓄积量减少,以及Plk1周期振荡相位转移...     

The role of p53 in the response of tumor cells to sonodynamic therapy in vitro

p53 plays a pivotal role in apoptosis. In addition, p53 is currently extensively investigated as a promising strategy for highly specific anticancer therapy in chemotherapeutics and photodynamic therapy. However, the role of p53 in the response of tumor cells to sonodynamic therapy treatment is still unclear. In this study, we aim to investigate the activation of p53 in sonodynamic therapy. Three murine tumor models with distinct aggressiveness (S180, H-22 and EAC) were treated with 1.75 MHz continuous ultrasound at an acoustic intensity (I_SATA) of 1.4 W for 3 min in the presence of 20 μg/ml hematoporphyrin. The DNA fragment and nuclear damage were observed by TUNEL and single cell gel electrophoresis. Western blotting and RT-PCR were used to analyze the expression of p53, PUMA, Bax and Fas. Then we checked the translocation of p53 by confocal microscopy. DNA sequencing was used to determine the status of p53 gene in three tumor cell lines. Our results indicated that the level of p53 protein and mRNA increased significantly, and p53 activated the expression of its downstream pro-apoptosis gene PUMA, Bax and Fas in the S180 and H-22 cells. Meanwhile, p53 protein translocated onto mitochondria. In the EAC cells, expression and translocation of p53 was not found; the level of PUMA, Bax and Fas remained unaltered. The S180 cells showed most serious DNA fragment and nuclear damage with 77.43% TDNA; H-22 cells in the middle with 58.85% TDNA; whereas EAC cells appeared less nuclear material lost with just 15.82% TDNA. The results of DNA sequencing showed that the sequences of exons 5-8 of the p53 gene of S180, H-22 and EAC cells were the same with the sequences of wild-type p53 provided by NCBI. These results primarily demonstrated that: (1) p53 was activated to promote SDT-induced apoptosis through extrinsic and intrinsic signaling pathways in the S180 and H-22 cells; (2) cellular responses of different cells to SDT were distinct, the aggressive S180 cells were much more sensitive than H-22, whereas EAC cells were relatively less sensitive. The discrepancy among the cell lines may be due to different activation time of p53 protein.     

Stochastic Nature in Cellular Processes

The importance of stochasticity in cellular processes is increasingly recognized in both theoretical and experimental studies. General features of stochasticity in gene regulation and expression are briefly reviewed in this article, which include the main experimental phenomena, classification, quantization and regulation of noises. The correlation and transmission of noise in cascade networks are analyzed further and the stochastic simulation methods that can capture effects of intrinsic and extrinsic noise are described.     

Oscillatory expression and variability in p53 regulatory network

The effect of delay, nonlinearity and noise on oscillatory motion is of permanent interest for theoretical and experimental research. Here we explore a negative feedback loop between p53 and Mdm2 with a time delay, which is a key circuit in the response of cells to damage. This circuit shows noisy sustained oscillations in individual human cells following DNA damage, and damped oscillations at the cell population level. We demonstrate the effect of delay on the oscillation, and the correlation in time course. In a multi-species system, the events at different time points which span a time delay are coupled even when the delay is large compared with the other characteristic times of the system. We also clarify that the dynamics at the single-cell level appears to be coherent resonance, and the origin of the damped oscillation at the macroscopic level out of the sustained ones at the single-cell level can be ascribed to the dephasing process which is induced by the interplay between nonlinearity and noise. The findings are consistent with experimental observations and advance our understanding of the dynamics of the p53 network.     

Mdm2生成速率调控的p53-Mdm2振子的全局动力学和稳定性

肿瘤抑制蛋白p53的动力学在一定程度上可以决定DNA损伤后的细胞命运.p53的动力学行为与p53信号通路中p53-Mdm2振子模块密切相关.然而,p53的负调控子Mdm2的生成速率的增加使其在一些癌细胞中过表达.因此探讨Mdm2生成速率对p53动力学的影响有重要意义.同时,PDCD5作为p53的激活子也调控p53的表达.因此,本文针对PDCD5调控的p53-Mdm2振子模型,通过分岔分析获得了Mdm2生成速率所调控的p53的单稳态、振荡以及单稳态与振荡共存的动力学行为,且稳定性通过能量面进行了分析.此外,噪声强度对p53动力学的稳定性有重要的影响.因此,针对p53的振荡行为,探讨了噪声强度对势垒高度和周期的影响.本文所获得的结果对理解DNA损伤后的p53信号通路调控起到一定的指导作用.     

The birhythmicity increases the diversity of p53 oscillation induced by DNA damage

The tumor suppressor p53 mediates the cellular response to various stresses. It was experimentally shown that the concentration of p53 can show oscillations with short or long periods upon DNA damage. The underlying mechanism for this phenomenon is still not fully understood. Here, we construct a network model comprising the ATM-p53-Wip1 and p53-Mdm2 negative feedback loops and ATM autoactivation. We recapitulate the typical features of p53 oscillations including p53 birhythmicity. We show the dependence of p53 birhythmicity on various factors such as the phosphorylation status of ATM. We also perform stochastic simulation and find the noise-induced transitions between two modes of p53 oscillation,which increases the p53 variability in both the amplitude and period. These results suggest that p53 birhythmicity enhances the responsiveness of p53 network, which may facilitate its tumor suppressive function.     

A mathematical model of a P53 oscillation network triggered by DNA damage

Taking the interaction between a DNA damage repair module, an ATM module, and a P53--MDM2 oscillation module into account, this paper presents a mathematical model of a P53 oscillation network triggered by a DNA damage signal in individual cells. The effects of the DNA damage signal and the delay time of P53-induced MDM2 expression on the behaviours of the P53 oscillation network are studied. In the oscillatory state of the P53--MDM2 oscillator, it is found that the pulse number of P53--P oscillation increases with the increase of the initial DNA damage signal, whereas the amplitude and the period of P53--P oscillation are fixed for different initial DNA damage signals, and the period numbers of P53--P oscillations decrease with the increase of time delay of MDM2 expression induced by P53. These theoretical predictions are consistent with previous experimental results. The combined negative feedback of P53--MDM2 with the time delay of P53-induced MDM2 expression causes oscillation behaviour in the P53 network.     

Time delay as a key to apoptosis induction in the p53 network

A feedback mechanism that involves the proteins p53 and mdm2, induces cell death as a controlled response to severe DNA damage. A minimal model for this mechanism demonstrates that the response may be dynamic and connected with the time needed to translate the mdm2 protein. The response takes place if the dissociation constant k between p53 and mdm2 varies from its normal value. Although it is widely believed that it is an increase in k that triggers the response, we show that the experimental behaviour is better described by a decrease in the dissociation constant. The response is quite robust upon changes in the parameters of the system, as required by any control mechanism, except for few weak points, which could be connected with the onset of cancer. Received 8 May 2002 / Received in final form 9 July 2002 Published online 17 September 2002     

Stochasticity in many-dimensional nonlinear oscillating systems

Qualitative analytic estimates of the stochasticity limit of one- and many-dimensional nonlinear oscillating systems are derived using the overlapping of first-order resonances as a criterion for stochasticity. Computational results obtained with several very simple transformations are compared with the analytic estimates. Numerical studies significantly below the stochasticity limit of a many-dimensional nonlinear system reveal an example of a very slow instability, the first, to the best of our knowledge.     

Effects of hydroxyapatite nanoparticles on proliferation and apoptosis of human breast cancer cells (MCF-7)

The study aimed to correlate cell proliferation inhibition with oxidative stress and p53 protein expression in cancerous cells. Hydroxyapatite (HAP) (Ca₁₀(PO₄)₆(OH)₂) is the essential component of inorganic composition in human bone. It has been found to have obvious inhibitory function on growth of many kinds of tumor cells and its nanoparticle has stronger anti-cancerous effect than macromolecule microparticles. Human breast cancer cells (MCF-7) were cultured and treated with HAP nanoparticles at various concentrations. Cells viability was detected with MTT colorimetric assay. The morphology of the cancerous cells was performed by transmission electron microscopy and the expression of a cell apoptosis related gene (p53) was determined by ELISA assay and flow cytometry (FCM). The intracellular reactive oxygen species (ROS) level in HAP exposed cells was measured by H₂DCFDA staining. DNA damage was measured by single-cell gel electrophoresis assay. The statistical analysis was done by one way ANOVA. The cellular proliferation inhibition rate was significantly (p < 0.05) increasing in a dose-dependent manner of HAP nanoparticles. Cell apoptotic characters were observed after MCF-7 cells were treated by HAP nanoparticles for 48 h. Moreover, ELISA assay and FCM shows a dose-dependent activation of p53 in MCF-7 cells treated with nanoHAP. These causative factors of the above results may be justified by an overproduction of ROS. In this study, a significant (p < 0.05) increase in the level of intracellular ROS in HAP-treated cells was observed. This study shows that HAP inhibits the growth of human breast cancer MCF-7 cells as well as induces cell apoptosis. This study shows that HAP NPs Induce the production of intracellular reactive oxygen species and activate p53, which may be responsible for DNA damage and cell apoptosis.     

Gaussification and entanglement distillation of continuous-variable systems: a unifying picture

Distillation of entanglement using only Gaussian operations is an important primitive in quantum communication, quantum repeater architectures, and distributed quantum computing. Existing distillation protocols for continuous degrees of freedom are only known to converge to a Gaussian state when measurements yield precisely the vacuum outcome. In sharp contrast, non-Gaussian states can be deterministically converted into Gaussian states while preserving their second moments, albeit by usually reducing their degree of entanglement. In this work-based on a novel instance of a noncommutative central limit theorem-we introduce a picture general enough to encompass the known protocols leading to Gaussian states, and new classes of protocols including multipartite distillation. This gives the experimental option of balancing the merits of success probability against entanglement produced.     

Spatio-temporal analysis of DNA damage repair using the X-ray microbeam

Cellular response to radiation damage is made by a complex network of pathways and feedback loops whose spatiotemporal organization is still unclear despite its decisive role in determining the fate of the damaged cell. The single-cell approach and the high spatial resolution offered by microbeams provide the perfect tool to study and quantify the dynamic processes associated with the induction and repair of DNA damage. The soft X-ray microbeam has been used to follow the development of radiation induced foci in live cells by monitoring their size and intensity as a function of dose and time using yellow fluorescent protein (YFP) tagging techniques. Preliminary data indicate a delayed and linear rising of the intensity signal indicating a slow kinetic for the accumulation of DNA repair protein 53BP1. A slow and limited foci diffusion has also been observed. Further investigations are required to assess whatever such diffusion is consistent with a random walk pattern or if it is the result of a more structured lesion processing phenomenon. In conclusion, our data indicates that the use of microbeams coupled to live cell microscopy represent a sophisticated approach for visualizing and quantifying the dynamics changes of DNA proteins at the damaged sites.     

DNA损伤致p53-Mdm2相互作用的动力学模型

最新实验结果表明，在受到各种辐射而引起DNA损伤后，在单体细胞和群体细胞情况下，细胞中的p53蛋白浓度表现为非衰减振荡和衰减振荡两种不同的动力学行为.通过研究p53-Mdm2负反馈回路的非线性动力学行为，分析了各种(特别是DNA损伤、p53和 Mdm2蛋白浓度三者之间)动力学关系，提出了一个能同时描述这两种不同动力学行为的非线性模型. 关键词： p53-Mdm2负反馈回路 非衰减振荡和衰减振荡 非线性动力学模型     

Hes1调控 AKT-MDM2-p53-PTEN通路的一种物理机制

基于Hill动力学与Michaelis-Menten方程,建立理论模型研究发状分裂相关增强子1(hairy and enhancer of split 1,Hes1)调控蛋白激酶B (Protein Kinase B,AKT)-鼠双微体2 (Murine Double Minute2,MDM2)-抗癌基因p53(p53)-第10号染色体缺失的磷酸酶及张力蛋白同源的基因(Phosphatase and tensin homolog deleted on chromosome ten,PTEN)通路的一种物理机制.研究发现,Hes1通过与PTEN结合抑制PTEN表达,并调控AKT信号.表明了Hes1蛋白的合成,以及Hes1与PTEN相互作用调控AKTMDM2-p53-PTEN通路信号,将会有效地控制细胞结果 . Hes1作为AKT-MDM2-p53-PTEN信号通路中上游调节的重要因素,还可以在一定程度上通过影响p53蛋白功能,改变p53对肿瘤的抑制性.理论结果可用于预测Notch通路信号异常诱导的致癌性,并进一步揭示了Notch信号通路影响细胞AKT-MDM2-p53-PTEN通路的激活...     

Time-Resolved Fluorescence Anisotropy Study of the Interaction Between DNA and a Peptide Truncated from the p53 Protein Core Domain

Time-resolved fluorescence anisotropy spectroscopy was applied to study the interaction between a peptide truncated from the binding site of tumor suppressor p53 protein and the DNAs covalently labeled with 6-carboxyfluorescein (FAM) dye. Fluorescence intensity quenching and changes of anisotropy decay lifetime were monitored when FAM labeled DNA formed complex with the peptide. The results demonstrated that the sequence of DNA could not define the binding specificity between the peptide and DNA. But the anisotropy decay of FAM can be used to examine the binding affinity of the peptide to DNA. The fluorescent dynamics of FAM can also be used to represent the rigidity of the complex formed between the peptide and DNA.     

统计物理的微观动力学基础

统计的基本出发点是研究系统具有的随机性,不同系统在不同情形下的宏观热力学性质起源于系统内部随机性的差异,通过对宏观热力学系统的微观非线性动力学进行研究探索，我们可以进一步更为深入地理解物态方程、相变等诸多的宏观热力学现象。本文通过哈密顿系统的非线性动力学研究，以及遍历性理论的动力学随机性研究对此问题进行了分析，研究表明，动力学系统的全局性混沌是系统统计成立的根本要素，系统的无限大自由度（热力学极限）已不是决定性的因素，人们可以在此基础上建立少自由度系统的统计力学及热力学。