Analysis of components of conserved “backbone sequences”among genomes of Shigella spp. strains

Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora-or strain-specific genes,those floras with closer relationship in the evolution also have conserved “backbone sequences”, which reveal the marks of their origin and evolution, and these “backbone sequences”are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and Sf301 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%-22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common “backbone sequences”.Advanced analysis indicated that the “backbone sequences”are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore,only 20% Sf301-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains.     

基于PVS的UML类图和序列图的一致性检验

针对UML类图和序列图的一致性问题,在充分考虑了类继承关系、关联关系、类方法的可见性以及类方法的前、后置条件等因素对一致性影响的基础上,给出了判定类图和序列图一致性的必要条件和PVS元理论,提出了一种基于定理证明器PVS的一致性检验方法.在检验UML模型一致性时,把一致性检验问题转化为逻辑定理证明问题.实践表明,该方法对于提高UML模型的可信度,减少系统实现阶段的错误起到了一定作用.     

Snake venom thrombin-like enzymes: from reptilase to now

The snake venom thrombin-like enzymes (SVTLEs) comprise a number of serine proteases functionally and structurally related to thrombin. Until recently, only nine complete sequences of this subgroup of the serine protease family were known. Over the past 5 years, the primary structure of several SVTLEs has been characterized, and now this family includes several members. Of particular interest is their possible use in pathologies such as thrombosis. The aim of the present review is to summarize the state of the art concerning the evolutionary, structural and biological features of the SVTLEs.Received 16 August 2003; received after revision 26 September 2003; accepted 1 October 2003     

Association of different mobile elements to generate novel integrative elements

Among the more important problems in modern hospitals is the prevalence of bacterial pathogens expressing resistance to multiple antimicrobial agents. The frequency of multiresistance suggests mechanisms by which bacterial species can concentrate and efficiently exchange a variety of resistance determinants. Mechanisms by which this occurs include insertion of transposons within transposons, coalescence through the activity of insertion sequences and the employment of integrons. In some instances, more than one of these mechanisms is involved in creating large multiresistance genetic elements. The association of the elements with transferable elements or transposons may promote rapid dissemination among clinical strains, and create further opportunities for inclusion of additional resistance determinants.     

平均分排序法合理性分析

依 A rrow提出的选举问题的四条公理为准则 ,利用联合尺度条件 ,阐明目前流行的筛选平均分排序法 (即去掉一个最高分和一个最低分后 ,用余下的各分数的算术平均分作为待评人的最后得分 )是一种看似公正 ,实为错误的排序方法     

Quick trickle permutation based on quick trickle characteristic sequence

0　IntroductionAblockcipherwithoutdataextensionorexpressionisaper mutation .Thesecurityofablockcipherschemeiscorrela tivewiththe permutations.Quicktrickle permutation[1 ] canmakethedatadisorderedwhenactingatthedataandmakeallprobabledistancebetweentwoelementsappear,soithasgoodcryptographicpropertiesandcanbeusedintheblockcipherwhichrequireshighsecurity.Aprivatekeyblockcipherisapermutationinn dimensionvectorspaceoverF2 atthecontrolofakey[2 ,3] .Moreover,manyblockciphersusepermutationstoexecuteso…     

Notable diversity in hemoglobin expression patterns among species of the deep-sea clam, <Emphasis Type="Italic">Calyptogena</Emphasis>

The deep-sea clams Calyptogena nautilei and C. tsubasa, which live in the cold-seep area at a depth of 3570 m in the Nankai Trough, Japan, have abundant hemoglobins (Hbs) in erythrocytes, similar to other Calyptogena species. We determined the cDNA-derived amino acid sequences of Hbs from two Calyptogena species. C. tsubasa was found to contain two dimeric Hbs, Hb I consisting of 145 amino acid residues and Hb II with 137 residues, similar to known Hbs from C. soyoae and C. kaikoi. Sequence identity was over 90% among the orthologous chains of Calyptogena Hbs. On the other hand, surprisingly, C. nautilei contained two monomeric Hbs, Hb III containing 141 residues and Hb IV with 134 residues. In addition, Hbs III and IV showed only 33–42% sequence identity with Hbs I and II from other Calyptogena species. The distal (E7) histidine, one of the functionally important residues of the heme protein, is replaced by glutamine in all Hb chains of Calyptogena species. A phylogenetic analysis indicated that C. nautilei Hb III is closer to Hb I from other Calyptogena species. We suppose that a Hb gene was duplicated at least three times in an immediate ancestor of Calyptogena and, presumably depending on physiological conditions different Hb sets are being expressed: dimeric Hbs I and II in C. soyoae, C. kaikoi and C. tsubasa, and monomeric Hbs III and IV in C. nautilei. Received 13 May 2003; received after revision 5 June 2003; accepted 12 June 2003     

树的拓扑指标Z_1(G)

分子图的拓扑指标Z1(G)是反映分子物理和化学性质的重要拓扑指标,在n个顶点的树中具有最大Z1(G)和最小Z1(G)的树的基础上确定了n个顶点的树中具有次大,第三大及第四大Z1(G)的树.     

相关序列图像复原算法研究

针对气动光学效应降晰过程的复杂性,提出了一种基于图像相关性的两帧序列图像复原算法。该算法利用图像的相关性,结合气动光学效应降晰函数辨识,在大气流场的光学退化模型未知的情况下,采用两帧序列图像降晰函数辨识实现气动光学效应退化图像复原。为了克服降晰函数辨识算法可能带来的误差,在序列图像辨识降晰函数时,提出将辨识得到的两帧序列图像降晰函数结果差的二阶范数作为惩罚项,当该范数不符合要求时,根据序列图像的质心偏移和旋转偏移对图像进行相应的修正。给出了实现该方法的具体步骤,仿真结果证明了算法的有效性。     

Construction of an electronic physical map of Magnaporthe oryzae using genomic position-ready SSR markers

Magnaporthe oryzae is a model for plant pathogenic filamentous fungi. We have assembled a simple sequence repeat (SSR)-based physical map of the species, using in silico sequence data. A set of 120 SSR markers was developed from the genomic sequence of the reference isolate 70-15. These markers were readily amplified from the genomic DNA of other isolates, and high levels of allelic variation characterised the parental isolates of the two crosses tested. All the markers were locatable to one of the seven M. oryzae chromosomes. An SSR-based physical in silico map was constructed, and pre-existing SSR and RFLP loci were integrated into the map, along with 23 Avr (avirulence) genes and two other genes of importance to the plant/pathogen interaction. This map provides a platform for population genetics and functional genomics studies in the model pathogen, and even in other evolu- tionally related pathogens.