副溶血性弧菌全基因组DNA芯片的研制和芯片质量的评价

摘要 目的 研制副溶血性弧菌全基因组芯片,建立芯片杂交方法,并对芯片质量进行评价。方法 利用副溶血性弧菌全基因组序列,挑选出4770条基因,PCR扩增各基因并将PCR产物纯化,点样制备芯片;设计了两个质控杂交组合,采用双色荧光杂交策略,对芯片质量进行评价;PCR方法验证部分芯片结果。结果 芯片杂交与理论预期结果以及PCR验证结果完全一致。结论 成功的研制了一批质量良好的副溶血性弧菌全基因组DNA芯片,并建立了基于DNA芯片的副溶血性弧菌比较基因组学技术平台,建立了一套系统的芯片数据分析的标准方法。     

功能基因组学研究概述

21世纪是生物时代和信息时代,基因组学的研究已从结构基因组学转向功能基因组学,功能基因组学时代对于基因功能的研究也由单一基因转向大规模、批量分析。对功能基因组学及相关学科的概念作了概述,综述了功能基因组学的研究内容与方法,主要包括应用差异显示反转录PCR、基因表达序列分析（SAGE）、微点阵、蛋白质组学和生物信息学等方法来研究基因组表达概况、基因组多样性和模式生物学等。     

Genomics of the filamentous fungi - moving from the shadow of the bakers yeast

Fungi have now well and truly entered the genomic age. We currently know the complete DNA sequence for 18 fungal species and many more fungal genome sequencing projects are in progress. Whilst yeasts dominated the early genomic years, recently there has been a dramatic increase in filamentous fungal genome projects. The implications of this wealth of genetic information for mycologists worldwide is immense. In this review we summarise the background to fungal genome projects with an emphasis on the filamentous fungi. We discuss efforts to determine gene function and to compare genomes from different species. Since this is such a fast-moving field, useful web sites are listed that will enable the reader to keep up to date with developments.     

从结构基因组学到功能基因组学

基因组学研究随着模式生物基因组全序列测定的完成由结构基因组学阶段发展到功能基因组学阶段,基因组学成为当今最为活跃、最有影响的前沿学科.以结构基因组学的研究成果为基础,功能基因组学中各学科因其原理不同及其关键技术的特点和优势,具有各自的应用范畴和发展趋势.功能基因组学不断渗透入现代科学的各领域,促成了适用于不同研究目的新兴学科的诞生.     

植物抗性基因研究新趋势

多种生物基因组的大规模测序结果表明,抗性基因在基因组上成簇存在,从结构基因组、比较基因组、功能基因组与生物信息学等方面论述了植物抗性基因研究的新趋势。     

Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.     

乳酸菌基因组学研究进展

乳酸菌广泛应用于食品发酵工业中,其中有些菌种是重要的益生菌。目前,对乳酸菌的研究已从最初的形态学研究进入到了分子水平的研究。乳酸菌全基因组测序研究已在全球展开。乳酸菌基因组研究有助于揭示乳酸菌的遗传和代谢机制,加速重要益生功能基因的挖掘,同时为乳酸菌的应用提供众多可能性。本文就乳酸菌基因组研究的概况、重要乳酸菌基因组、乳酸菌的功能基因组以及比较基因组进行了综述。     

小麦的比较基因组学和功能基因组学

小麦是异源多倍体植物,具有大的染色体组,并且基因组中重复序列所占比例较高,这些特征限制了小麦基因组研究的进展。比较基因组学方法为运用模式植物进行小麦基因组学研究提供了一个操作平台。功能基因组学的研究集中于基因组中转录表达的部分,基因功能的确定是功能基因组学研究的主要内容。对比较基因组学在小麦基因组研究中的应用和小麦功能基因组学的研究内容和方法进行了综述。     

基因组时代的昆虫学研究

昆虫种类繁多,它与生态系统中的生物多样性,以及人类的日常生活和生产密切相关。自2000年黑腹果蝇Drosophila melanogaster全基因组测序完成以来,至今已先后开展了88种昆虫全基因组测序工作,这标志着昆虫学研究进入了基因组时代。本文综述了近年来昆虫基因组测序进展,以及基于基因组的昆虫学研究方法及应用等两方面的研究成果。同时,着重介绍了昆虫全基因组测序进程,昆虫基因组在个体生物学、多物种间及种群,及系统生物学研究中的应用等方面的内容。最后,还探讨了基因组时代昆虫学研究所面临的挑战。     

A less laborious approach to the high-throughput production of recombinant proteins in Escherichia coli using 2-liter plastic bottles

Contemporary approaches to biology often call for the high-throughput production of large amounts of numerous proteins for structural or functional studies. Even with the highly efficient protein expression systems developed in Escherichia coli, production of these proteins is laborious and time-consuming. We have simplified established protocols by the use of disposable culture vessels: common 2-liter polyethylene terephthalate beverage bottles. The bottles are inexpensive, fit conveniently in commonly available flask holders, and, because they are notched, provide sufficient aeration to support the growth of high-density cultures. The use of antibiotics and freshly prepared media alleviates the need for sterilization of media and significantly reduces the labor involved. Uninoculated controls exhibited no growth during the time required for protein expression in experimental cultures. The yield, solubility, activity, and pattern of crystallization of proteins expressed in bottles were comparable to those obtained under conventional culture conditions. After use, the bottles are discarded, reducing the risk of cross-contamination of subsequent cultures. The approach appears to be suitable for high-throughput production of proteins for structural or functional studies.     

Yeast genomic databases and the challenge of the post-genomic era

Since the completion of the yeast genome sequence in 1996, three genomic databases, the Saccharomyces Genome Database, the Yeast Proteome Database, and MIPS (produced by the Munich Information Center for Protein Sequences), have organized published knowledge of yeast genes and proteins onto the framework of the genome. Now, post-genomic technologies are producing large-scale datasets of many types, and these pose new challenges for knowledge integration. This review first examines the structure and content of the three genomic databases, and then draws from them and other resources to examine the ways knowledge from the literature, genome, and post-genomic experiments is stored, integrated, and disseminated. To better understand the impact of post-genomic technologies, 20 collections of post-genomic data were analyzed relative to a set of 243 previously uncharacterized genes. The results indicate that post-genomic technologies are providing rich new information for nearly all yeast genes, but data from these experiments is scattered across many Web sites and the results from these experiments are poorly integrated with other forms of yeast knowledge. Goals for the next generation of databases are set forth which could lead to better access to yeast knowledge for yeast researchers and the entire scientific community. Electronic Publication     

Incorporating Genomics into the Toolkit of Nematology

The study of nematode genomes over the last three decades has relied heavily on the model organism Caenorhabditis elegans, which remains the best-assembled and annotated metazoan genome. This is now changing as a rapidly expanding number of nematodes of medical and economic importance have been sequenced in recent years. The advent of sequencing technologies to achieve the equivalent of the $1000 human genome promises that every nematode genome of interest will eventually be sequenced at a reasonable cost. As the sequencing of species spanning the nematode phylum becomes a routine part of characterizing nematodes, the comparative approach and the increasing use of ecological context will help us to further understand the evolution and functional specializations of any given species by comparing its genome to that of other closely and more distantly related nematodes. We review the current state of nematode genomics and discuss some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies.     

副溶血性弧菌全基因组DNA芯片的研制和质量评价

【目的】研制副溶血性弧菌全基因组芯片,建立芯片杂交方法,并对芯片质量进行评价。【方法】利用副溶血性弧菌全基因组序列,挑选出4770条基因,PCR扩增各基因并将PCR产物纯化,点样制备芯片;设计了两个质控杂交组合,采用双色荧光杂交策略,对芯片质量进行评价;PCR方法验证部分芯片结果。【结果】芯片杂交与理论预期结果以及PCR验证结果完全一致。【结论】成功的研制了一批质量良好的副溶血性弧菌全基因组DNA芯片,并建立了基于DNA芯片的副溶血性弧菌比较基因组学技术平台,建立了一套系统的芯片数据分析的标准方法。     

Proteome-Scale Analysis of Biochemical Activity

ABSTRACT

During the last 10 years, there has been a large increase in the number of genome sequences available for study, altering the way that the biology of organisms is studied. In particular, scientific attention has increasingly focused on the proteome, and specifically on the role of all the proteins encoded by the genome. We focus here on several aspects of this problem. We describe several technologies in widespread use to clone genes on a genome-wide scale, and to express and purify the proteins encoded by these genes. We also describe a number of methods that have been developed to analyze various biochemical properties of the proteins, with attention to the methodology and the limitations of the approaches, followed by a look at possible developments in the next decade.     

Genome sequencing of the important oilseed crop Sesamum indicum L

The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described.     

Analysis of phenetic trees based on metabolic capabilites across the three domains of life

Here, we used data of complete genomes to study comparatively the metabolism of different species. We built phenetic trees based on the enzymatic functions present in different parts of metabolism. Seven broad metabolic classes, comprising a total of 69 metabolic pathways, were comparatively analyzed for 27 fully sequenced organisms of the domains Eukarya, Bacteria and Archaea. Phylogenetic profiles based on the presence/absence of enzymatic functions for each metabolic class were determined and distance matrices for all the organisms were then derived from the profiles. Unrooted phenetic trees based upon the matrices revealed the distribution of the organisms according to their metabolic capabilities, reflecting the ecological pressures and adaptations that those species underwent during their evolution. We found that organisms that are closely related in phylogenetic terms could be distantly related metabolically and that the opposite is also true. For example, obligate bacterial pathogens were usually grouped together in our metabolic trees, demonstrating that obligate pathogens share common metabolic features regardless of their diverse phylogenetic origins. The branching order of proteobacteria often did not match their classical phylogenetic classification and Gram-positive bacteria showed diverse metabolic affinities. Archaea were found to be metabolically as distant from free-living bacteria as from eukaryotes, and sometimes were placed close to the metabolically highly specialized group of obligate bacterial pathogens. Metabolic trees represent an integrative approach for the comparison of the evolution of the metabolism and its correlation with the evolution of the genome, helping to find new relationships in the tree of life.     

cDNA微阵列技术在植物功能基因组学研究中的应用

cDNA微阵列 (cDNAMicroarrays)技术是近年发展起来的分子生物学研究新型工具 ,以分子杂交为基本原理 ,在检测植物基因表达水平、研究基因表达图谱、特异基因检测以及发现新基因和分离差异表达基因等方面有着独特的优势 ,已成为植物功能基因组学研究的重要手段。     

Opening sequence: computational genomics in the era of high-throughput sequencing

A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011.