“电子”cDNA文库筛选指导基因的全长cDNA克隆

“电子”ｃＤＮＡ库筛选主要是指通过采用生物信息学的方法延伸表达序列标签（ＥＳＴ）序列,以获得基因的部分及至全长ｃＤＮＡ序列,避免或部分避免构建与筛选ｃＤＮＡ库等烦琐的实验室工作。该方法具体体现了ＥＳＴ数据库的迅速扩张已导致识别与克隆新基因的策略发生革命性的变化。ＥＳＴ序列ＺＡ７３为本实验室克隆到的可能参与辐射致气管上皮细胞恶性转化过程的基因片段,本研究采用“电子”ｃＤＮＡ库筛选的方法对其可能     

应用大规模测序技术和生物信息学研究造血干/祖细胞的基因表达及新基因的识别和克隆

从新生儿脐血和成人骨髓中分选出造血干／祖细胞（ＨＳＣ／ＨＰＣ）,构建成ｃＤＮＡ文库,对其进行大规模表达序列标签（ＥＳＴ）测序,通过生物信息学等手段分析基因表达谱,并进行新基因的全长ｃＤＮＡ克隆。在所测的１０５１２条可分析ＥＳＴ序列中,有９８６６条来自脐血ＣＤ３４＋细胞,其中４６９７条（４７６％）为已知基因,２６０３条（２６４％）为已知ＥＳＴ,１４１５条（１４３％）代表未知ＥＳＴ。在已知基因中,８２％基因与造血相关,２２７％涉及细胞代谢、结构和迁移,１３０％与细胞分裂和防御相关,２６２％与ＲＮＡ、蛋白质的合成相关,１０６％和细胞信号传递有关。对一些已知和未知的ＥＳＴ,综合测序、生物信息学等方法,进行全长克隆,已获得２３个新基因的全长ｃＤＮＡ。     

产肠毒素大肠杆菌的热敏肠毒素B亚基（LT—B）和耐热肠毒素（ST）基？…

采用基因重组技术构建了表达产肠毒素大肠杆菌（ＥＴＥＣ）的耐热肠毒素（ＳＴ）基因和热敏肠毒素Ｂ亚基（ＬＴ－Ｂ０基因融合抗原的疫苗候选株。将ＳＴ基因的５‘端与ＬＴ－Ｂ基因的３’端连接,并置于同一阅读框。编码ＳＴ的基因是通过ＰＣＲ从ｐＳＬＭ００４质粒中扩增得到的,含有ＳＴ的ｐｒｏ序列,并应用寡核苷酸定点突变技术将编码ＳＴ的第１４位氨基酸残基发生突变,使ＳＴ的第１４位氨基酸残基Ａｌａ突变为Ｌｅｕ。     

GSTs同工酶基因在乳腺癌中的扩增与基因的表达

采用ＤＮＡ和ＲＮＡ的斑点杂交分析方法,对３２例乳腺癌和相应的癌旁正常组织中ＧＳＴ－π、ＧＳＴ－α和ＧＳＴ－μ基因的ＤＮＡ扩增和ＲＮＡ转录表达情况进行研究,发现ＧＳＴ－π在乳腺癌中存在基因扩增和明显的ｍＲＮＡ表达升高,ＧＳＴ－π基因表达调控主要在转录水平进行的;ＧＳＴ－α和ＧＳＴ－μ在乳腺癌中表达水平较低,但仍可见α和μ类ＧＳＴ同工酶ｍＲＮＡ转录在肿瘤和正常组织中发生了较大的变化。结合乳腺癌中雌激素受体（ＥＲ）表达情况还发现ＧＳＴ－π表达水平与ＥＲ的表达存在负相关性。     

果蝇心脏基因一个新人同源基因WNT-10A的研究初报

Ｗｇ基因是控制果蝇心脏前体细胞形成的一个关键基因,根据物种间同源异型基因结构上的保守性与功能上的相似性,我们运用计算机克隆的方法获得了一个新的人同源基因,命名为ＷＮＴ－１０Ａ。该基因有一富集ＧＣ碱基的启动子,ｍＲＮＡ全长约２．４ｋｂ,３′末端包含ＡＴＡＡＡ的加尾信号,编码一段长４１７个氨基酸的蛋白质,与小鼠Ｗｎｔ－１０ａ的编码蛋白高度相似。其心脏ＥＳＴ数目占正常组织ＥＳＴ总数的４５％,表明该基因在心脏组织高度表达,提示其可能与心脏发育有关。该基因与其基因家族成员具有相似的同源框序列,在肿瘤细胞中大量表达（占总ＥＳＴ的３１％）,表明该基因相似于其家族成员,可能与肿瘤的发生有关。     

ＥＳＴ在克隆新基因中的应用

随着基因定位（连锁图谱、物理图谱、转录图谱）和ＤＮＡ测序及生物信息技术的迅猛发展,ＥＳＴ已成为人类寻找新的未知基因以及克隆不同时空差异表达基因和疾病相关基因的重要标志物。随着ＥＳＴ数据库的进一步完善,网上克隆和定位候选克隆策略将成为克隆新基因的主要方法,并在虚拟的网上空间将模型生物基因组的研究成果成功地应用于人类基因组的研究中。     

产肠毒素大肠杆菌肠毒素LT,ST融合的研究进展

产肠毒素大肠杆菌（ＥＴＥＣ）肠毒素ＬＴ与ＳＴ融合是ＥＴＥＣ多价疫苗候选株研制的一项重要工作,ＬＴ与ＳＴ的化学偶联研究已证明融合后可使小分子的ＳＴ获得免疫原性成为完全抗原,而基因融合对构建多价疫苗则是更重要的手段。本文着重介绍了近年来对ＬＴ与ＳＴ基因融合的研究,特别是一些影响基因融合效果因素的基础性研究。这些都为候选株的研制提供了研究手段和依据,并对广泛的基因融合研究具有理论意义。     

肿瘤易感基因的克隆策略进展

定位克隆仍是当前克隆肿瘤易感基因的一条主要途径。关联分析方法和检测患ＬＯＨ,纯合性丢失的高发频率区有利于易感基因的定位,削减杂交和脉冲场凝胶电泳的方法有利于目的基因的获取;精细遗传连锁图谱和ＥＳＴ数据库的建立将加速肿瘤易感基因的克隆;从模式生物基因组的研究成果入手来寻找人业肿瘤易感基因是一条可行的途径。     

人肝癌组织中的一个Lis1基因的阅读框移码突变

将ＧＳＴ融合蛋白表达与蛋白质截短检测法（ＰＴＴ）法相结合,检测Ｌｉｓ１基因在肝癌组织中的阅读框移码突变。即从肝癌组织中通过ＲＴ－ＰＣＲ扩增的Ｌｉａ１基因克隆人ＧＳＴ融合蛋白表达载体ｐＧＥＸ０１,并于大肠杆菌ＤＨ５α中进行表达。通过ＳＤＳ－ＰＡＧＥ电泳发现肝癌组织中有截短的ＧＳＴ－Ｌｉｓ１融合蛋白,大小为３３ＫＤ,而全长融合蛋白大小应为７１ＫＤ。经测序验证,发现产生截短蛋白的Ｌｉａ１基因在第１６３位     

小狼毒的新多取代二萜酯和麦角甾醇型三萜新成分

小狼毒的新多取代二萜酯和麦角甾醇型三萜新成分张峻,杨成金,吴大刚（中国科学院昆明植物研究所植物化学开放实验室,昆明６５０２０４）ＡＮＥＷＰＯＬＹＳＵＢＳＴＩＴＵＴＥＤＤＩＴＥＲＰＥＮＥＳＴＥＲＡＮＤＥＲＧＯＳＴＡＮＯＬＴＹＰＥＮＥＷＴＲＩＴＥＲＰＥＮ...     

反硝化反应器喹啉降解相关基因多样性与定量分析

【目的】本文旨在探讨喹啉驯化的反硝化反应器微生物群落中苯甲酰辅酶A还原酶基因(bcrA)和8-羟基-2(1H)喹喏酮基因的加氧酶组分(oxoO)基因的多样性与分布。【方法】根据GenBank数据库oxoO基因序列的保守区设计了oxoO基因专一性引物。扩增采用机械击打与酚-氯仿抽提相结合的方法从反应器生物膜样品中提取微生物总DNA,对oxoO基因和bcrA基因进行基因扩增,并构建oxoO和bcrA基因克隆文库。采用荧光实时定量PCR方法对反应器微生物群落中bcrA和oxoO基因进行定量分析。【结果】定量分析结果表明,在反应器运行过程中,bcrA基因数量逐渐增多,而oxoO基因数量逐渐减少。克隆文库基因序列的系统发育分析表明,bcrA基因克隆文库中部分序列与Thauera等菌株的bcrA基因的相似性为97%以上,其余序列与已知bcrA基因序列的相似性为74%-86%;oxoO基因克隆文库中部分序列与恶臭假单胞菌(Pseudomonas putida)的oxoO基因相似性为99%,而其余序列和已知的oxoO基因的序列相似性较低。【结论】喹啉驯化的反硝化反应器系统中,bcrA和oxoO基因的多样性较丰富,且具有一些新的未知的类型。bcrA和oxoO基因的数量随反应器的运行状况而发生变化,显示出其与反应器中微生物种群构成及功能之间的密切关系。这两个基因可以作为一种潜在的生物分子标记,用于监测含喹啉废水反硝化反应器的运行状态。     

Characterization of monooxygenase gene diversity in benzene‐amended soils

Aim: To understand soil benzene monooxygenase gene diversity by clone library construction and microarray profiling. Methods and Results: A primer set was designed, and benzene monooxygenase gene diversity was characterized in two benzene‐amended soils. The dominant sequence types in the clone libraries were distinct between the two soils, and both sequences were assigned to novel clusters. Monooxygenase gene richness and diversity increased after benzene degradation. Oligonucleotide probes for microarray analysis were designed to detect a number of sequenced clones and reported monooxygenase genes. The microarray detected several genes that were not detected in the clone libraries of the same samples. Six probes were detected in more than one soil. Conclusions: The primer set designed in this study successfully detected diverse benzene monooxygenase genes. The level of diversity may have increased because the degradation of benzene differed from soil to soil. Microarrays have great potential in the comprehensive detection of gene richness as well as the elucidation of key genes for degradation. Significance and Impact of the Study: This study introduces a new primer set that may be used to identify diverse benzene monooxygenase genes in the environment; moreover, it demonstrates the potential of microarray technology in the profiling of environmental samples.     

水稻中一个NBS-LRR抗病同源基因家族的克隆和分析

利用克隆的抗病基因同源序列RS13作为探针,从水稻IR64的BAC文库中筛选到4个阳性克隆,其中一个克隆14E19能够覆盖其余3个克隆。对14E19进行全序列测定和分析,获得了73kb的全长DNA序列,基因预测显示其上有4个编码NBS-LRR结构域的基因(NL),分别命名为NL-A,B,C和D。对具有相同基因组背景的IRBB56同一染色体位置上跨度更大的BAC克隆106P13进行分析,发现其上有10个NL同源拷贝,其中4个同14E19上的NL一样。搜索日本晴、93—11、广陆矮4号的序列,发现三者有类似的同源序列。但与已知的NBS-LRR抗病基因同源性较低,说明NL是一个至少由10个成员(分别命名为NL-A至J)组成的新基因家族。对NL家族进行RT-PCR和cDNA库筛选分析,发现NL-B基因能够在抗白叶枯病品系IRBB4中表达,暗示该基因参与了抗病反应。     

The utility of transposable elements as tools for the isolation of plant genes

Transposable elements are segments of DNA which have the unique capability of being able to excise from one site in the genome and reintegrate into new, different sites elsewhere in the genome. When transposition takes place and integration occurs within a gene locus, mutations are frequently generated producing variegated or recessive phenotypes. This ability of transposable elements to act as mutagenic agents through their association with particular gene sequences has lead to the development of the procedure of transposon tagging or gene tagging in higher plants. Through this technique, transposable elements can be used to clone and isolate genes of interest for which little or nothing is known about the final product (i.e., polypeptide). This offers tremendous potential for the isolation of a variety of agronomically important genes, which are virtually impossible to recover by other currently available gene cloning methodologies. To date, the technique has been used successfully to isolate genes from corn and snapdragon. Using gene transfer technologies, the potential now exists to extend this approach to clone genes from other plant species. Advantages and limitations of transposon tagging for isolating plant genes will be discussed.     

mRNA差异显示技术克隆中国葡萄属野生种核糖体RNA基因

克隆功能基因是研究植物基因结构及功能的重要途径,利用mRNA差异显示技术,筛选获得了中国葡萄属野生种华东葡萄白河-35-1在人工接种白粉菌前后差异表达基因的cDNA片段Vprdrf4。经Northern杂交验证,该片段为正调控片段,Blaset检索表明与真核生物核糖体RNA基因的同源性高达90%以上,GenBank登录号为CD347664。     

Sequence and tissue-specific expression of a putative peroxidase gene from wheat (Triticum aestivum L.)

We have used a cDNA clone encoding a pathogen-induced putative wheat peroxidase to screen a genomic libary of wheat (Triticum aestivum L. cv. Cheyenne) and isolated one positive clone, lambda POX1. Sequence analysis revealed that this clone contains a gene encoding a putative peroxidase with a calculated pI of 8.1 which exhibits 58% and 83% sequence identity to the amino acid sequence of the turnip (Brassica rapa) peroxidase and a pathogen-induced putative wheat peroxidase, respectively. The two introns in the wheat gene are at the same positions as introns in the peroxidase genes of tomato and horseradish. Results of S1-mapping experiments suggest that this gene is neither pathogen-nor wound-induced in leaves but is constitutively expressed in roots.     

Metagenome microarray for screening of fosmid clones containing specific genes

A critical step in the process of metagenome analysis is to screen for clones that contain specific genes among a large number of clones. To form one of the sequence-based screening tools of a metagenome library, we designed a format of microarray [metagenome microarray (MGA)] that is arrayed with fosmid library clone DNA samples on a glass slide. We evaluated the MGA using random prime labeled fluorescent probes prepared from PCR products of the target gene and found that we could obtain specific hybridization signals only for the fosmid clone that contained the target gene. We found that the detection limit of the MGA was c. 10 ng microL(-1) of fosmid clone DNA, and that the MGA-based hybridization was quantitative within a concentration range of 10-200 ng microL(-1) of fosmid clone DNA. We used the MGA successfully to identify two fosmid clones that contained 16S rRNA genes from a fosmid library from the sediment of the East Sea, Korea. In conclusion, we have demonstrated that the MGA can be used for screening for fosmid clones containing specific genes in a metagenome library, and that this technology has potential application as a high-throughput metagenome screening tool.     

Phylogenetic characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana.

Alvinella pompejana is a polychaetous annelid that inhabits active deep-sea hydrothermal vent sites along the East Pacific Rise, where it colonizes the walls of actively venting high-temperature chimneys. An abundant, morphologically diverse epibiotic microflora is associated with the worm's dorsal integument, with a highly integrated filamentous morphotype clearly dominating the microbial biomass. It has been suggested that this bacterial population participates in either the nutrition of the worm or in detoxification of the worm's immediate environment. The primary goal of this study was to phylogenetically characterize selected epibionts through the analysis of 16S rRNA gene sequences. Nucleic acids were extracted from bacteria collected from the dorsal surface of A. pompejana. 16S rRNA genes were amplified with universal bacterial primers by the PCR. These genes were subsequently cloned, and the resulting clone library was screened by restriction fragment length polymorphism analysis to identify distinct clone types. The restriction fragment length polymorphism analysis identified 32 different clone families in the library. Four of these families were clearly dominant, representing more than 65% of the library. Representatives from the four most abundant clone families were chosen for complete 16S rRNA gene sequencing and phylogenetic analysis. These gene sequences were analyzed by a variety of phylogenetic inference methods and found to be related to the newly established epsilon subdivision of the division Proteobacteria. Secondary structural model comparisons and comparisons of established signature base positions in the 16S rRNA confirmed the placement of the Alvinella clones in the epsilon subdivision of the Proteobacteria.     

两个枣树扩展蛋白基因cDNA全序列的克隆及分析

用定向克隆法构建了枣树(Ziziphus jujubaMill.)快速生长初期结果枝的cDNA文库,经过重组质粒的筛选,克隆获得两个扩展蛋白基因cDNA全序列,分别命名为ZjEXP1(GenBank登录号:FJ449891)和ZjEXP2(GenBank登录号:FJ449892)。ZjEXP1全长1 037 bp,包含编码254个氨基酸的完整开放阅读框;ZjEXP2全长905 bp,包含编码251个氨基酸的完整开放阅读框。两个序列有共同的结构特征,即在N-末端有8个保守的半胱氨酸残基的丰富域,C-末端有4个保守的色氨酸残基的丰富域,中间有一个组氨酸(His-Phe-Asp,HFD)功能域。两者之间的氨基酸同源性为74.0%。从已知的扩展蛋白基因家族的进化分析表明,ZjEXP1和ZjEXP2由一个祖先进化而来,又分别属于两个不同的分支。