细胞信号网络功能鲁棒的简并性拓扑特征

细胞信号网络对于外界环境的干扰表现出优良的鲁棒性,但是其维持功能鲁棒的内在机制尚未明确,本文研究了细胞信号网络功能鲁棒性的拓扑特征。选择布尔网络模型模拟细胞网络的动态行为,利用网络节点状态的扰动模拟外界环境干扰。基于演化策略探寻不同网络拓扑的功能并分析其在干扰环境下的鲁棒性,采用埃德尔曼提出的基于信息论的计算方法评估网络拓扑的简并度、冗余度和复杂度等拓扑属性,对比分析它们与功能鲁棒度的相关性及作用机理。结果显示,在网络模型的演化过程中,其拓扑简并度与功能鲁棒度显著正相关,相关性水平高于拓扑冗余度与鲁棒度的相关性。并且,随着鲁棒度的提升,网络的节点数和复杂度也随之升高,同样简并度与网络的节点数和复杂度的相关性高于拓扑冗余度与网络的节点数和复杂度的相关性。这说明增加的网络节点以简并的方式同时提高了网络拓扑的鲁棒度和复杂度。因此,细胞网络功能鲁棒性的拓扑特征是简并而不是冗余,简并为解决生物系统的复杂问题提供了有效手段,为人工系统的可靠性设计提供有益的借鉴。     

氨基酸的分子结构与遗传密码简并及二维集合分类

根据氨基酸遗传密码子的简并程度,可将64个遗传密码子分为高简并度类（3,4,6度简并组）和低简并度类（1,2度简并组）两大类。高简并度类有9个氨基酸,其分子量比较小,等电点的分布比较集中。低简并度类有11个氨基酸,其分子结构比较复杂,参考Taylor对氨基酸特性的分类图,本文提出以分子量（M）及等电点（P）作为氨基酸的化学特性坐标,作出其二维集合MP分类图,MP分类图可以反映出氨基酸的各种属性,如分子量的大小,简并度的高低,极性与非极性、带电荷或不带电荷,疏水性与亲水性,以及氨基酸残基的种类等。根据氨基酸的分类分析,可以认为：高简并度氨基酸多数是脂烃类和羟脂烃类的氨基酸,分子量比较小,分子结构比较简单,大部分为疏子性,主要组成跨膜结构或蛋白质的结构域,可能是出现较早的氨基酸;而低简并度的氨基酸,分子结构比较复杂,分子量比较大,多数是和蛋白质功能有密切联系的基团,可能是进化出现较晚的结构。     

Evolutionary processes and evolutionary noise at the molecular level

Summary The distinction between molecular sites that mainly carry out general functions and sites committed to specific functions is analyzed, notably in terms of different evolutionary variabilities. Functional density is defined as the proportion of sites involved in specific functions. Weighted functional density, by representing the relative variability at specific-function sites is to some extent a measure of the specificity of molecular interactions. The relationship between general- and specific-function sites on the one hand and the covarions of Fitch on the other is discussed. The functional –degeneracy– of amino acids is described as increasing the interdependence of general functions. It is predicted that proteins that do not possess general-function sites besides their specific-function sites tend to –freeze– their primary structure, according to an evolutionary process that is an autocatalytic function of the decrease in site variability. This limits the use of weighted functional density as an indicator of the overall degree of interaction specificity of a protein to values that are not close to unity.Directeur de Recherche at Centre National de la Recherche Scientifique, Paris.     

DPPrimer – A Degenerate PCR Primer Design Tool

Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design. Embedded features such as search for functional domains, similarity score selection and phylogebetic tree further enhance the user friendliness of DPPrimer tool. Performance of DPPrimer tool was evaluated by successful PCR amplification of ADP-glucose phosphorylase genes from wheat, barley and rice.

Availability

DPPrimer is freely accessible at http://202.141.12.147/DGEN_tool/index.html     

线粒体遗传密码及基因组遗传密码的对称分析

病毒、细菌和真核生物的氨基酸编码都使用相同的遗传密码,表明它们可能有共同的来源。但人和牛的线粒体的遗传密码和基因组的遗传密码相比,出现以下不同;（1）ATA编码甲硫氮酸M而不是异亮氨酸I。（2）TGA不再是终止密码子X而编码色氨酸W。（3）AGA和AGG不再是精氨酸R的密码子而变为终止密码子X。应用高维空间拓扑分析的方法,对线粒体遗传密码和基因组遗传密码的6维编码空间进行对称性分析,得到如下结果：（1）线粒体遗传密码的起始密码子是2个而不是1个。（2）线粒体遗传密码的终止密码子是4个而不是3个。（3）线粒体遗传密码空间只有2、4、6三种偶数简并度而没1、3两种奇数简并度,表明其对称度较高。（4）线粒体遗传密码空间除丝氨酸S分成两个平行的子空间之外,终止密码子X亦分成两个平行的子空间,表明其连通度较低。（5）线粒体遗传密码一基因组遗传密码相比,共有3个简并平面出现变异,即：1001λλ（M和I）,011λ1λ（W和X）,以及1011λλ（S和X或S和R）。（6）基因组遗传密码的1、3两种奇数简并度可能来源于线粒体遗传密码的1001λλ平面和011λ1λ平面的对称性破缺。对线粒体遗传密码变异的生物学意义及遗传密码的起源进行了分析和讨论。     

Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2

We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L. Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the nucleotide motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP. To date, we have identified five such SCRs in human and chimpanzee CR1, one in human and chimpanzee CR1L, but none in either rat or mouse Crry in keeping with the number of internal duplications of the long homologous repeat (LHR) found in CR1 and CR1L. In fact, at the genomic level, the ancestral LHR must have contained eight SCRs rather than seven as previously thought. Since g-like SCRs are found immediately downstream of d SCRs, we suggest that there must have been a functional dg set which has been retained by CR2 and MCP but which is degenerate in CR1 or CR1L. Interestingly, dg is also present in the CR2 component of mouse CR1. The degeneration of the g SCR must have occurred prior to the formation of primate CR1L and prior to the duplication events which resulted in primate CR1. In this context, the apparent conservation of g-like SCRs may be surprising and may suggest the existence of mechanisms unrelated to protein coding. These results provide examples of the many processes which have contributed to the evolution of the extensive repertoire of CCPs.     

An evolutionary system using development and artificial Genetic Regulatory Networks for electronic circuit design

Biology presents incomparable, but desirable, characteristics compared to engineered systems. Inspired by biological development, we have devised a multi-layered design architecture that attempts to capture the favourable characteristics of biological mechanisms for application to design problems. We have identified and implemented essential features of Genetic Regulatory Networks (GRNs) and cell signalling which lead to self-organization and cell differentiation. We have applied this to electronic circuit design.