烤烟品种南江3号均一化全长cDNA文库构建

目的:为了获得功能基因的信息,构建烤烟品种南江3号的均一化cDNA文库.方法:用RNeasy Plant Mini Kit提取烤烟南江3号叶片和花的RNA,用反转录酶逆转录合成第一链eDNA.以LD-PCR扩增获得的双链cDNA为模板,采用基于双链特异性核酸酶(Duplex-Specific Nuclease,DSN)的均一化cDNA文库技术,构建南江3号盛花期的均一化cDNA文库.结果:构建了南江3号盛花期的均一化cDNA文库,文库重组率大为97.47%,库容量约为1.26×10<'6>,插入片段平均长度大于1.2kb.从文库中随机48个克隆进行PCR检测,挑取20个克隆进行测序,序列通过BLAST比对结果显示文库可能包含大量基因和ESTs序列.结论:该文库为研究南江3号的基因功能和资源提供材料来源.     

青杄均一化cDNA文库构建及EST序列分析

以青杄花粉和针叶为材料,将青杄全长cDNA与Gateway供体载体pDONR222重组,构建了其非剪切型全长cDNA原始文库,利用基因组DNA饱和杂交技术对原始cDNA文库进行均一化处理,构建青杄的均一化全长cDNA文库。文库的总库容量为1.1×106CFU/mL,平均插入片段长度大于1.0 kb,重组率大于95%。定量RT-PCR检测表明,青杄高丰度表达基因EF1-α在均一化cDNA文库中的表达量下降了约41倍。接着对文库中随机的5 144个克隆进行了测序,获得高质量的有效EST(expressedsequence tag)序列为5 144条,经拼接共获得单一基因(unigene)为2 717个,其中包括片段重叠群(contig)628个和单一EST序列(singlet)2 089个。NCBI同源比对分析表明,其中1 887个序列unigenes获得分子功能注释,这些EST涉及细胞生长、信号转导、转录、抗逆、能量代谢等功能。这些数据有助于对青杄的相关功能蛋白及分子机制开展进一步的研究。     

夜香树均一化全长cDNA文库的构建及EST分析

为构建高质量的夜香树(Cestrum nocturnum)均一化全长c DNA文库,以其花朵为材料,采用DSN均一化技术与改进的SMART技术相结合,将连接产物进行脱盐浓缩后电转化进行构建。结果表明,未脱盐连接产物的转化效率为1μL连接产物有7000个菌落,理论重组率为96%;脱盐后,提升为4.1×106个菌落,理论重组率为98%;蓝斑也有插入片段,实际重组率应为100%;插入片段大小平均为1.6 kb。随机挑取500个单克隆(含50个蓝斑)测序,共获得464条EST,单一序列(unigene)为426条,占91.8%,其中片段重叠群26个,单基因400个,冗余率仅为8.1%,表明构建文库的均一化效果较好,可满足后续功能基因的筛选和基因信息的研究。     

早期人胚胎cDNA文库构建及目的基因筛选

收集受精后３、４和５周龄药物流产胚胎,用改良一步法提取总ＲＮＡ,ｏｌｉｇｏ（ｄＴ）纤维素柱纯化ｍＲＮＡ,逆转录合成一链ｃＤＮＡ,完成二链ｃＤＮＡ的合成后,经碱变性电泳检测,合成ｃＤＮＡ的大小为０．４～９．０ｋｂ之间,且主要集中在１．０～２．０ｋｂ。除去多余的接头,收集大于４００ｂｐ的ｃＤＮＡ片段,与载体ｐＳＰＯＲＴ１和和γＺｉｐＬｏｘ连接,分别得到３、４、５周龄人胚胎质粒文加和噬菌体文库。另外,采     

发现新基因的高效方法——cDNA文库的复性式均一化技术

由复性式均一化技术制作的均一化cDNA文库（equalized cDNA library,normalized cDNA library）是近年来发展起来的一种获得EST、发现新基因的高效平台。本文就该技术的原理、方法比较、存在问题和展望进行了阐述。Abstract:The cDNA library normalized by reassociation is a newly-developed,effective platform for EST acquisition and gene discovery.This papper presents the principle,procedure,comparison,deficiencies,application and future of the technique of the normalization.     

盐生杜氏藻(Dunaliella salina)cDNA文库构建及功能基因筛选

采用Qiagen公司的植物总RNA提取技术、Clontech公司的CreatorTM技术平台以及SMARTTM技术进行cDNA文库构建.从杜氏藻中提取出了高质量的总RNA,通过PowerScript反转录酶反转录杜氏藻的总RNA,采用LD-PCR、酶处理等方法对cDNA进行等比例扩增、纯化,同时使用CHROMASPIN-400柱子将cDNA分段化,最后将长片段连入pDNR-LIB质粒,1.5 kV,25 μ F电转化大肠杆菌JM109,得到含1.5×106个克隆子的原始文库,滴度为1.5×106cfuml-1.结合酶切和PCR,对该文库的质量进行了鉴定和统计,文库的平均片段插入长度为1.5kb.采用烯醇酶和UDP葡萄糖脱氢酶的EST作为同源探针,对文库中的功能基因进行筛选,并采用放射性原位杂交法,对扩增文库进行了初筛和复筛,得到了含这两条基因全编码序列的cDNA,烯醇酶为1.8kb,UDP葡萄糖脱氢酶为1.9kb,为今后对该种进行大规模功能基因组学研究奠定基础.     

穴蚁蛉幼虫全长均一化cDNA文库的构建

通过构建穴蚁蛉幼虫(俗称蚁狮)全长均一化cDNA文库,以期了解蚁狮的抗菌肽、毒素蛋白以及其它药用蛋白种类,为日后筛选、克隆表达和分离纯化这些药用蛋白奠定基础.用针刺诱导蚁狮产生抗茵物质后,分离纯化总RNA,结合SMART全长文库与DSN(duplex-specific nuclease)均一化技术,构建全长均一化cDNA文库,并通过平板计数和菌落PCR方法鉴定文库.随机挑选192个单克隆进行5′端测序,并与NCBI数据库进行比对分析.结果显示,构建出的文库平均插入片段长度为1 200bp,原始文库的滴度达到7.5×105 CFU/mL,而扩增文库则为1.95×1011CFU/mL.在所挑选的单克隆中,共获得190条有效序列,平均读长1 340 bp,文库重组率达到98.96%.与NCBI数据库比对后发现,这些序列可能是一些编码蚁狮免疫、消化及毒性蛋白的基因.     

Rapid identification of potential drought tolerance genes from Solanum tuberosum by using a yeast functional screening method

Identification of major stress tolerance genes of a crop plant is important for the rapid development of its stress-tolerant cultivar. Here, we used a yeast functional screen method to identify potential drought-tolerance genes from a potato plant. A cDNA expression library was constructed from hyperosmotic stressed potato plants. The yeast transformants expressing different cDNAs were selected for their ability to survive in hyperosmotic stress conditions. The relative tolerances of the selected yeast transformants to multiple abiotic stresses were also studied. Specific potato cDNAs expressed in the tolerant yeast transformants were identified. Sixty-nine genes were found capable of enhancing hyperosmotic stress tolerance of yeast. Based on the relative tolerance data generated, 12 genes were selected, which could be most effective in imparting higher drought tolerance to potato with better survival in salt and high-temperature stresses. Orthologues of few genes identified here are previously known to increase osmotic stress tolerance of yeast and plants; however, specific studies are needed to confirm their role in the osmotic stress tolerance of potato.     

An Expression Profile of Active Genes in Human Colonic Mucosa

An expression profile of genes active in the human colonic mucosawas obtained by collecting 959 partial sequences from a 3'-directedcDNA library. Seven genes were found to produce mRNA each ofwhich comprized more than 1% of total mRNA. Four of these genesare novel, and are likely to be uniquely expressed in the colonicmucosa, and the other three have been identified as genes forfatty acid binding protein, immunoglobulin lambda chain, andcarcinoma-associated antigen GA733-2. In the remaining 952 clones,310 were composed of 118 species occurred recurrently but lessthan 1%, and 533 clones appeared only once. Because the 3'-directedcDNA library faithfully represents the mRNA population in thesource tissue, these numbers represent the relative activitiesof the gene expression. Altogether 156 gene species were identified in GenBank, anda significant portion of these genes encode proteins found inGolgi apparatus and lysosomes, chromosome-encoded mitochondrialproteins, cell surface proteins, and components in the proteinsynthesis machinery. The types and proportions of genes identifiedis consistent with the known major activities of the colonicmucosa such as mucous protein production, energy-dependent waterabsorption, and rapid cell proliferation and turnover.     

A method for the preparation of normalized cDNA libraries enriched with full-length sequences

We developed a new method for the preparation of normalized cDNA libraries enriched with full-length sequences. It is based on the properties of the recently characterized duplex-specific nuclease from the hepatopancreas of the Kamchatka crab. The duplex-specific nuclease is thermostable, effectively cleaves double-stranded DNA, and is inactive toward single-stranded DNA (Shagin et al., Genome Res., 2002, vol. 12, pp. 1935–1942). Our method enables the normalization of cDNA samples enriched with full-length sequences without use of laborious and ineffective stages of physical separation. The efficiency of the method was demonstrated in model experiments using cDNA samples from several human tissues.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 186–194.Original Russian Text Copyright © 2005 by Zhulidov, Bogdanova, Shcheglov, Shagina, Wagner, Khazpekov, Kozhemyako, Lukyanov, Shagin.     

Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.

Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed prior to any data analysis. To remove these biases, many normalization methods are used by researchers. However, not all biases are eliminated from the microarray data because not all types of errors from experimental protocols are known. In this paper, we report an effective way of removing various types of biases by treating each microarray dataset independently to detect biases present in the dataset. After the biases contained in each dataset were identified, a combination of normalization methods specifically made for each dataset was applied to remove biases one at a time.     

High Efficiency Selection of Full-length cDNA by Improved Biotinylated Cap Trapper

We report here an improved protocol for the preparation of full-lengthcDNA libraries that improves the previously reported method(Carninci, P., Kvam, K., Kitamura, A. et al. 1996, Genomics,137, 327–336), that allows long cDNAs to be cloned moreefficiently. One potential disadvantage of the original biotinylatedCAP trapper protocol is the exposure of mRNA to chemical andenzymatic attacks during the biotinylation of the cap structure,before the first-strand cDNA synthesis (and selection of full-lengthcDNA by biotinylated cap). Here, we show that the biotinylationof the cap structure is very specific and effective even ifbiotinylation is performed on the mRNA/cDNA hybrid producedby the first-strand cDNA synthesis reaction. Consequently, mRNAremains protected from chemical and enzymatic degradation duringthe overnight biotinylation step, thus making it possible toselect full-length cDNAs of longer average size. We herein reportthe efficiency and specificity of the new version of the protocolfor cap structure biotinylation and capture of full-length cDNA.