系统发育信息学及网络资源

系统发育信息学是近年来形成的新的学科方向,是系统学研究领域的一个新兴生长点。系统发育信息学是存贮、管理、注释、开发和加工系统树及其相关生物学信息的交叉学科。它的方法是基于计算机和网络技术,包括大型系统树及其相关生物学数据库的建立,系统树数据库网络的构架,系统树的可视化显示,小系统树的联合与超树的建立、用户查询、搜索和下载等,最终目的是要建立一个囊括地球上所有生物的系统树及其相关信息的数据库,将各种生物在树上精确定位,并进一步通过对系统发育信息的查询、搜索、联合与分析,从中获取生命进化的知识和进行生物学的预测。目前可用的系统发育网络资源主要有CIPRes和系统发育软件(PhylogenyPrograms)网站,已建立的系统发育信息学数据库包括TreeBASE,TreeofLife,Species2000,NCBITaxonomy数据库等。     

互联网上生物学信息资源的检索

本文对因特网上生物学资源的查询途径和利用方法进行了探讨,介绍了一些较为重要的生物学期刊资源站点,讨论了如何通过互联网检索各种生物信息资源,最大限度地利用互联网为生物科学科研服务。     

Comparative Genome Mapping in Brassica

A Brassica nigra genetic linkage map was developed from a highly polymorphic cross analyzed with a set of low copy number Brassica RFLP probes. The Brassica genome is extensively duplicated with eight distinct sets of chromosomal segments, each present in three copies, covering virtually the whole genome. Thus, B. nigra could be descended from a hexaploid ancestor. A comparative analysis of B. nigra, B. oleracea and B. rapa genomes, based on maps developed using a common set of RFLP probes, was also performed. The three genomes have distinct chromosomal structures differentiated by a large number of rearrangements, but collinear regions involving virtually the whole of each the three genomes were identified. The genic contents of B. nigra, B. oleracea and B. rapa were basically equivalent and differences in chromosome number (8, 9 and 10, respectively) are probably the result of chromsome fusions and/or fissions. The strong conservation of overall genic content across the three Brassica genomes mirrors the conservation of genic content observed over a much longer evolutionary span in cereals. However, the rate of chromosomal rearrangement in crucifers is much higher than that observed in cereal genomes.     

Comparative Genome Mapping of Sorghum and Maize

Linkage relationships were determined among 85 maize low copy number nuclear DNA probes and seven isozyme loci in an F2 population derived from a cross of Sorghum bicolor ssp. bicolor x S. bicolor ssp. arundinaceum. Thirteen linkage groups were defined, three more than the 10 chromosomes of sorghum. Use of maize DNA probes to produce the sorghum linkage map allowed us to make several inferences concerning processes involved in the evolutionary divergence of the maize and sorghum genomes. The results show that many linkage groups are conserved between these two genomes and that the amount of recombination in these conserved linkage groups is roughly equivalent in maize and sorghum. Estimates of the proportions of duplicated loci suggest that a larger proportion of the loci are duplicated in the maize genome than in the sorghum genome. This result concurs with a prior estimate that the nuclear DNA content of maize is three to four times greater than that of sorghum. The pattern of conserved linkages between maize and sorghum is such that most sorghum linkage groups are composed of loci that map to two maize chromosomes. This pattern is consistent with the hypothesized ancient polyploid origin of maize and sorghum. There are nine cases in which locus order within shared linkage groups is inverted in sorghum relative to maize. These may have arisen from either inversions or intrachromosomal translocations. We found no evidence for large interchromosomal translocations. Overall, the data suggest that the primary processes involved in divergence of the maize and sorghum genomes were duplications (either by polyploidy or segmental duplication) and inversions or intrachromosomal translocations.     

植物基因组比较作图研究进展

基因组比较作图是基因组研究的重要内容。植物比较作图研究表明,在长期的进化过程中,基因的组成表现出高度的保守性。随着植物遗传图谱和物理图谱的迅速发展,为植物比较作图奠定了重要的基础。现就植物基因组遗传图和物理图以及比较作图的最新研究进展作一介绍。     

Comparative Compositional Mapping of Chicken and Quail Chromosomes

The distribution of various isochore families on mitotic chromosomes of domestic chicken and Japanese quail was studied by the method of fluorescence in situ DNA–DNA hybridization (FISH). DNA of various isochore families was shown to be distributed irregularly and similarly on chromosomes of domestic chicken and Japanese quail. The GC-rich isochore families (H2, H3, and H4) hybridized mainly to microchromosomes and a majority of macrochromosome telomeric regions. In chicken, an intense fluorescence was also in a structural heterochromatin region of the Z chromosome long arm. In some regions of the quail macrochromosome arms, hybridization was also with isochore families H3 and H4. On macrochromosomes of both species, the pattern of hybridization with isochores of the H2 and H3 families resembled R-banding. The light isochores (L1 and L2 families) are mostly detected within macrochromosome internal regions corresponding to G bands, whereas microchromosomes lack light isochores. Although mammalian and avian karyotypes differ significantly in organization, the isochore distribution in genomes of these two lineages of the warm-blooded animals is similar in principle. On macrochromosomes of the two avian species studied, a pattern of isochore distribution resembled that of mammalian chromosomes. The main specific feature of the avian genome, a great number of microchromosomes (about 30% of the genome), determines a compositional specialization of the latter. This suggests the existence of not only structural but also functional compartmentalization of the avian genome.     

Internet上的生物信息资源及获取

Internet正日益成为生命科学研究领域不可或缺的工具。Internet上的生物信息资源内容丰富、信息量大。本文简要介绍了获取这些生物信息资源的几种主要方法。     

Mapping of the Biological Resources of the Continental Shelf

Distribution patterns of the penaeid shrimp and demersal fishspecies are discussed based upon collections totaling in excessof 330,000 shrimp and 2,245,000 fishes. Depth related zonationreveals nearshore, mid-shelf, outer shelf, and trans-shelf assemblages.Estuary related species are particularly prominent on the northwesternGulf shelf, while rock and reef related species are most importantin the fauna of the eastern Gulf shelf. Recognizable elementsin the shelf fauna also include species of tropical affinity;open ocean and upper slope species; inhabitants of seagrassbeds, mangrove swamps, and carbonate rubble and shell hash;burrowers in soft bottoms; and inhabitants of the upper watercolumn. The eastern Gulf shelf is inhabited by twice as manyfish species and eight times as many unique species as the northwesternshelf, reflecting the great diversity of habitat types in theeastern Gulf. A few key species numerically dominate the ichthyofaunaof the northwestern shelf, but dominance is spread through manyspecies in the east. Seasonal shifts in species density primarilyreflect inshore/offshore seasonal migrations of estuary relatedspecies, but seasonal inshore/offshore density shifts are alsoobserved among the true shelf residents. Trophically the shelfsystems are supported by precipitated plankton and organic detritusderived from rivers, bays and estuaries, seagrass beds, andmangrove swamps, although attached algae are also importantproducers in the east. Mollusks, polychaetes, and small crustaceanswhich feed upon this material, in turn, support the demersalfish communities whose species are generally short-lived. Largerlonglived predators are mostly seasonal migrants which appearin the northern Gulf during the warmer months. Bottom-feedinggeneralists are prominent in the northwest, while specialistsare in great evidence in the east. These distributional studieslay the foundation for understanding the shelf ecological systems,and they also provide a basis for informed management decisions.     

Mapping the Pathways to Staphylococcal Pathogenesis by Comparative Secretomics

The gram-positive bacterium Staphylococcus aureus is a frequent component of the human microbial flora that can turn into a dangerous pathogen. As such, this organism is capable of infecting almost every tissue and organ system in the human body. It does so by actively exporting a variety of virulence factors to the cell surface and extracellular milieu. Upon reaching their respective destinations, these virulence factors have pivotal roles in the colonization and subversion of the human host. It is therefore of major importance to obtain a clear understanding of the protein transport pathways that are active in S. aureus. The present review aims to provide a state-of-the-art roadmap of staphylococcal secretomes, which include both protein transport pathways and the extracytoplasmic proteins of these organisms. Specifically, an overview is presented of the exported virulence factors, pathways for protein transport, signals for cellular protein retention or secretion, and the exoproteomes of different S. aureus isolates. The focus is on S. aureus, but comparisons with Staphylococcus epidermidis and other gram-positive bacteria, such as Bacillus subtilis, are included where appropriate. Importantly, the results of genomic and proteomic studies on S. aureus secretomes are integrated through a comparative “secretomics” approach, resulting in the first definition of the core and variant secretomes of this bacterium. While the core secretome seems to be largely employed for general housekeeping functions which are necessary to thrive in particular niches provided by the human host, the variant secretome seems to contain the “gadgets” that S. aureus needs to conquer these well-protected niches.     

Internet Resources for Gene Expression Analysis in Arabidopsis thaliana

The number of online databases and web-tools for gene expression analysis in Arabidopsis thaliana has increased tremendously during the last years. These resources permit the database-assisted identification of putative cis-regulatory DNA sequences, their binding proteins, and the determination of common cis-regulatory motifs in coregulated genes. DNA binding proteins may be predicted by the type of cis-regulatory motif. Further questions of combinatorial control based on the interaction of DNA binding proteins and the colocalization of cis-regulatory motifs can be addressed. The database-assisted spatial and temporal expression analysis of DNA binding proteins and their target genes may help to further refine experimental approaches. Signal transduction pathways upstream of regulated genes are not yet fully accessible in databases mainly because they need to be manually annotated. This review focuses on the use of the AthaMap and PathoPlant^® databases for gene expression regulation analysis and discusses similar and complementary online databases and web-tools. Online databases are helpful for the development of working hypothesis and for designing subsequent experiments.     

如何查找Internet网上的基因突变信息资源

Ｉｎｔｅｒｎｅｔ网上蕴藏着极其丰富的基因突变信息资源 ,为了更有效地获取和利用这些信息资源为我国的人类基因组计划和突变研究服务。本文结合自己的实践,介绍Ｉｎｔｅｒｎｅｔ上基因突变信息资源及其查找方法 ,希望能对从事人类基因计划和突变研究以及基因突变信息处理等方面的科研人员有所帮助和启迪。１基因突变数据库随着人类基因组计划和突变研究的深入开展 ,产生了大量的基因突变以及多态性数据 ,借助传统的科学期刊系统发表这些数据已属不可能 ,必须建立相应的突变数据库来加速这些信息资源的处理和利用。为此建立了大量的基因突…     

Intrnet上的分子生物学免费软件资源

Internet的迅猛发展使得大量的分子生物学数据库和软件与之连接[1],为分子生物学的研究带来了极大的便利,为生命科学的研究带来了机遇和挑战.生命科学网络资源的利用应当成为我国生命科学工作者的必备素质之一.本文简单介绍常用的基于Macintosh和Windows的分子生物学免费软件资源.     

Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F₂ lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species.     

微生物学网络资源在多媒体教学中的应用

提供了一些重要的微生物学教学资源网站,并对网络微生物教学资源的查找与下载方法以及在多媒体教学应中注意的问题进行了探讨。     

Internet上的分子生物学免费软件资源

Ｉｎｔｅｒｎｅｔ的迅猛发展使得大量的分子生物学数据库和软件与之连接［１］,为分子生物学的研究带来了极大的便利,为生命科学的研究带来了机遇和挑战。生命科学网络资源的利用应当成为我国生命科学工作者的必备素质之一。本文简单介绍常用的基于Ｍａｃｉｎ－ｔｏｓｈ...