Simulating FAS-induced apoptosis by using P systems

In contrast to differential equations, P systems are an unconventional model of computation which takes into consideration the discrete character of the quantity of components and the inherent randomness that exists in biological phenomena. The key feature of P systems is their compartmentalised structure which represents the heterogeneity of the structural organisation of the cells, and where one can take into account the role played by membranes in the functioning of the system, for example signalling at the cell surface, selective uptake of substances from the media, diffusion across different compartments, etc. We show here that P systems can be a reliable tool for Systems Biology and could even outperform in some cases the current simulation techniques based on differential equations. We will also use a strategy based on the well known Gillespie algorithm but running on more than one compartment called Multi-compartmental Gillespie Algorithm.     

Simulating FAS-induced apoptosis by using P systems

In contrast to differential equations, P systems are an unconventional model of computation which takes into consideration the discrete character of the quantity of components and the inherent randomness that exists in biological phenomena. The key feature of P systems is their compartmentalised structure which represents the heterogeneity of the structural organisation of the cells, and where one can take into account the role played by membranes in the functioning of the system, for example signalling at the cell surface, selective uptake of substances from the media, diffusion across different compartments, etc. We show here that P systems can be a reliable tool for Systems Biology and could even outperform in some cases the current simulation techniques based on differential equations. We will also use a strategy based on the well known Gillespie algorithm but running on more than one compartment called Multi-compartmental Gillespie Algorithm.     

模糊膜计算模型与应用研究综述

膜计算是由生物细胞(群)相关机理启发的一类分布式、并行计算模型.膜计算模型已被证明是强大的并且以多项式时间复杂性求解众多的NP(non-deterministic polynomial)问题.膜计算模型与算法是膜计算领域的核心关键问题,特别是面向应用问题的模型和算法.模糊膜计算是近年开发的一种膜计算模型,它能克服先前模型在处理不确定性问题上的限制,得到极为广泛的关注.目前,模糊膜计算模型已在诸如电力系统故障诊断、微网控制中得到应用.首先简要地介绍几种模糊P系统,然后描述它们在工程问题中的应用.     

Modular enzymes

Although modular macromolecular devices are encountered frequently in a variety of biological situations, their occurrence in biocatalysis has not been widely appreciated. Three general classes of modular biocatalysts can be identified: enzymes in which catalysis and substrate specificity are separable, multisubstrate enzymes in which binding sites for individual substrates are modular, and multienzyme systems that can catalyse programmable metabolic pathways. In the postgenomic era, the discovery of such systems can be expected to have a significant impact on the role of enzymes in synthetic and process chemistry.     

生化反应系统的二项矩和属性因子

化学主方程对生化反应系统提供了一个建模框架,但它的分析与模拟一直是计算系统生物学的一个挑战.另一方面,矩封闭方法对化学主方程提供了一种逼近,但普通的矩当其阶趋于无穷时并不趋于0,因此具有局限性.这里,对概率密度函数引进二项矩,它具有2个突出的特点:1)当二项矩的阶充分大时二项矩趋于0; 2)二项矩能够方便地用来重构相应的概率密度函数.基于二项矩,进一步引进反应物种的属性因子,它比普通的统计指标(如噪声强度、Fano因子)具有某些优势.此外,还给出了用二项矩来表示噪声强度和Fano因子的显式公式,并用简单的生物例子来说明二项矩的优势与3种统计指标的特征.     

纯Peer-to-Peer环境下有效的本体匹配方法

目前大多数的Peer-to-Peer(P2P)系统由于欠缺对语义的支持而不能很好地应用于知识共享领域.可能的方法是采用本体(ontology)来描述Peer节点共享资源的语义.针对纯P2P环境下不同节点单独维护局部本体异构的特点,提出了基于历史查询记录的纯P2P环境下的本体匹配方法HOM.首先利用历史查询记录挖掘出概念之间可能存在的映射关系,然后利用向量空间模型VSM(vector space model)方法来识别概念在语言学上可能存在的联系,进而修正概念之间的映射关系,建立不同节点间本体概念的匹配.分析和仿真表明,与现有方法相比,HOM方法考虑了节点的自治特性,并提高了本体匹配的精度.     

The potential role of pathogens in biological control

It is now well established that pathogens such as viruses, fungi bacteria and protozoans can have profound effects on the dynamics of their invertebrate host populations. Theoretical models of invertebrate host-pathogen interactions which assume uniform structure of the pathogen population may reasonably explain the oscillatory behaviour observed in some systems, but do not adequately describe the existence of more constant populations found in other host-pathogen interactions. An examination of the literature relating to these relatively stable systems suggests that the common thread is the eventual transmission of some of the more protected, longer-lived stages of the pathogen occurring in reservoirs, such as the soil, host cadavers on trees, or the live host itself. In this letter, I propose a new theoretical model which incorporates this population structure and accounts for the range of dynamics observed in natural systems. In particular, I show that host populations may be regulated to low and relatively constant densities if sufficient numbers of pathogens are trans-located from pathogen reservoirs to habitats where transmission can occur. An understanding of pathogen reservoirs may be of value in the design of biological control programmes and may greatly increase the effectiveness of pathogens as biological control agents.     

Multifractality in human heartbeat dynamics.

There is evidence that physiological signals under healthy conditions may have a fractal temporal structure. Here we investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system, the healthy human heartbeat, and show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.     

两种手性Schiff碱镍（Ⅱ）配合物的合成、结构与性质

手性Schiff碱配合物在催化、生物活性、药物合成和功能材料等方面具有重要的应用。本文合成了两对新的手性Schiff碱镍（Ⅱ）配合物,并通过X-单晶衍射、红外光谱对其结构进行了测定,X-单晶衍射分析表明它们都属于P212121手性空间群,并通过圆二色谱对合成化合物的光学对映体性质进行了一步表征。     

P systems with array objects and array rewriting rules

Array P systems were introduced by Paun Gh. which is linking the two areas of membrane computing and picture grammars. Puzzle grammars were introduced by us for generating connected picture arrays in the two-dimensional plane, motivated by the problem of tiling the plane. On the other hand, incorporating into arrays the developmental type of generation used in the well-known biologically motivated L systems, Siromoney and Siromoney proposed a very general rectangular array generating model, called extended controlled tabled L array system (ECTLAS). In this paper we introduce two variations of the array P system, called BPG array P system and parallel array P system. The former has in the regions array objects and basic puzzle grammar rules (BPG), which are a specific kind of puzzle grammar rules. In the latter, the regions have rectangular array objects and tables of context-free rules. We examine these two types of P systems for their array generative power.     

Isolation of two novel candidate hormones using a chemical method for finding naturally occurring polypeptides

Naturally occurring peptides with biological actions have in most cases been detected by observing their biological activities in crude extracts and their isolation has been followed using bioassays. As a complement to the classical biological detection systems, we have proposed a chemical detection system based on fragmentation of peptides in tissue extracts followed by identification of certain of these peptide fragments having distinct chemical features. One such chemical feature is the C-terminal amide structure which is characteristic of many biologically active peptides. We have devised a chemical assay method for peptides having such a structure and have found several previously unknown peptide amides in procine upper small intestinal tissues. We report here the isolation and characterization of two of them, designated PHI and PYY. PHI is related to secretin, vasoactive intestinal polypeptide (VIP, glucagon and gastric inhibitory polypeptide (GIP); PYY is related to the pancreatic polypeptide and to neurotensin. Both peptides exhibit biological activities and appear to be present not only in the intestine but also in brain.     

P systems with array objects and array rewriting rules

Array P systems were introduced by Paun Gh. which is linking the two areas of membrane computing and picture grammars. Puzzle grammars were introduced by us for generating connected picture arrays in the two-dimensional plane, motivated by the problem of tiling the plane. On the other hand, incorporating into arrays the developmental type of generation used in the well-known biologically motivated L systems, Siromoney and Siromoney proposed a very general rectangular array generating model, called extended controlled tabled L array system (ECTLAS). In this paper we introduce two variations of the array P system, called BPG array P system and parallel array P system. The former has in the regions array objects and basic puzzle grammar rules (BPG), which are a specific kind of puzzle grammar rules. In the latter, the regions have rectangular array objects and tables of context-free rules. We examine these two types of P systems for their array generative power.     

水溶性荧光金银纳米簇的生物效应研究进展

荧光金属纳米簇是一种具有独特物理化学特性的新型纳米材料,在生物医学的许多应用中显示出巨大的潜力.阐明它们在复杂的生物环境中的行为对于设计基于金属纳米簇的高效、安全的纳米医药至为关键.在这篇综述中,概述了水溶性的金属纳米簇与生物体系相互作用的最新研究进展,讨论了影响这些生物相互作用过程中的关键参数,并对未来金属纳米簇的生物效应的研究做了展望.     

多肽的表面展示与结构库

表面展示是一种新的基因操作技术,它使表达的多肽以融合蛋白形式展现在噬菌体或细胞表面,保持相对独立的空间结构和生物活性。该技术可用于研究多肽(蛋白质)的性质、相互识别和作用,并据此从巨大展示库中选择特定靶功能的多肽结构。常用丝状噬菌体、T₄噬菌体、λ噬菌体以及细胞构建表面展示系统。表面展示库包括重组噬菌体抗体库、随机短肽库、多肽构象库、cDNA展示库和基因突变体展示库。表面展示技术可用于人工抗体和疫苗的制备、抗原决定簇的定位、蛋白质相互作用位点的确定、特异调节分子的分离、细胞表面工程的研究、多肽药物的研制,以及生物分子实验定向进化等研究。     

基于CUDA并行平台实现核膜系统求解可满足性问题的研究

膜系统能以空间换时间的方式在多项式时间内求解NP难问题,作为膜系统中的一个新类型,核膜系统不仅包含了不同类型膜系统的特征,而且能提供一种统一性的描述．因此基于核膜系统构建系统模型,并以此求解一个典型的NP难问题：可满足性问题．为了加速对核膜系统的仿真过程,程序将在CUDA并行方式下仿真实现,通过与传统的串行方式比较,使用CUDA能减少95％的仿真时间,这也表明使用CUDA并行方式非常适合仿真核膜系统．     

A hemispherical electronic eye camera based on compressible silicon optoelectronics

The human eye is a remarkable imaging device, with many attractive design features. Prominent among these is a hemispherical detector geometry, similar to that found in many other biological systems, that enables a wide field of view and low aberrations with simple, few-component imaging optics. This type of configuration is extremely difficult to achieve using established optoelectronics technologies, owing to the intrinsically planar nature of the patterning, deposition, etching, materials growth and doping methods that exist for fabricating such systems. Here we report strategies that avoid these limitations, and implement them to yield high-performance, hemispherical electronic eye cameras based on single-crystalline silicon. The approach uses wafer-scale optoelectronics formed in unusual, two-dimensionally compressible configurations and elastomeric transfer elements capable of transforming the planar layouts in which the systems are initially fabricated into hemispherical geometries for their final implementation. In a general sense, these methods, taken together with our theoretical analyses of their associated mechanics, provide practical routes for integrating well-developed planar device technologies onto the surfaces of complex curvilinear objects, suitable for diverse applications that cannot be addressed by conventional means.     

珠江三角洲地区初中体育教师队伍现状研究

采用问卷调查法对珠江三角洲地区9个地市的36所初级中学体育教师的数量、性别、年龄、学历、职称、地缘结构以及知识结构等方面进行了调查.结果显示:体育教师的数量已经满足了教学的需要;女性体育教师偏少;教师队伍呈年轻化趋势;学历达标率较高;职称结构较为合理;地缘结构呈现出多元化;知识结构欠合理,表现在体育人文科学知识和体育生物科学知识较为缺乏.为此,应加强在职体育教师的培训;改进和完善初中学校体育教育人力资源的聘用机制;建立竞争使用机制,实行真正意义上的聘任制.     

癌症的系统生物学模型研究进展

系统生物学研究采用的是系统性的研究方法,即获取并整合目标系统不同层次的生物学信息,构建适用于该生物系统的数学模型,对该系统的特征性行为进行系统性研究.癌症是一种复杂的生物系统,已成为系统生物学研究的热点领域.癌症的系统生物学模型是对传统的癌症动物模型的补充,主要包括:统计推断模型、生化网络模型、以及组织水平模型等.本文综述了这些系统模型方法在癌症研究中的应用情况及其取得的重要研究成果.     

Applications of membrane systems in distributed systems

Based on the biological model of cell-to-cell communication proposed by A. Rustom et al. (Science, 2004, 303: 1007—1010), we investigate the possibilities to apply P systems with dynamic channels transporting membrane vesicles for describing processes in distributed systems.     

Applications of membrane systems in distributed systems

Based on the biological model of cell-to-cell communication proposed by A. Rustom et al. (Science, 2004, 303: 1007-1010), we investigate the possibilities to apply P systems with dynamic channels transporting membrane vesicles for describing processes in distributed systems.