云南悬钩子蔷薇NBS LRR类抗病基因同源克隆与分析

为研究云南野生蔷薇属中的NBS类抗病基因,根据已知抗病基因NBS LRR序列中的保守区域设计简并引物,利用RT PCR技术从云南悬钩子蔷薇中进行体外扩增,获得了对应区域的cDNA片段,回收、克隆这些特异片段,测序分析,共得到4个含有NBS LRR保守结构域的抗病基因同源序列(RGAs),分别命名为AC9、AC39、AC50和AC68。它们与已报道的11个NBS类抗病基因相应区段的氨基酸序列相似性为5.4%~79.2%,其中这4个RGAs片段与Mi、RPS2、Pib和RPM1基因聚为一类。表明这4条RGAs序列可进一步用作悬钩子蔷薇抗病候选基因的分子筛选及遗传图谱的构建。     

云南悬钩子蔷薇NBS-LRR类抗病基因同源克隆与分析

为研究云南野生蔷薇属中的NBS类抗病基因,根据已知抗病基因NBSLRR序列中的保守区域设计简并引物,利用RTPCR技术从云南悬钩子蔷薇中进行体外扩增,获得了对应区域的cDNA片段,回收、克隆这些特异片段,测序分析,共得到4个含有NBSLRR保守结构域的抗病基因同源序列（RGAs）,分别命名为AC9、AC39、AC50和AC68。它们与已报道的11个NBS类抗病基因相应区段的氨基酸序列相似性为5.4%~79.2%,其中这4个RGAs片段与Mi、RPS2、Pib和RPM1基因聚为一类。表明这4条RGAs序列可进一步用作悬钩子蔷薇抗病候选基因的分子筛选及遗传图谱的构建。     

草莓G6PDH基因片段的克隆与序列分析

根据不同植物G6PDH同源基因的保守区设计合成简并引物,采用PCR技术从草莓基因组中分离出一个DNA片段并克隆到pMD18-T载体中。序列测定和分析表明,该片段长717 bp,与拟南芥等植物的G6PDH基因的核酸序列具有83%-87%的同源性。结果表明,克隆的片段为草莓G6PDH基因片段。     

基于简并引物同步克隆两个红麻PDIL同源基因cDNA5'-末端序列

探索利用同一套简并引物结合通用引物同步扩增两个红麻PDIL同源基因的cDNA5’-末端序列,以期为同一转录组中两个旁系同源基因cDNA5' RACE的同步扩增提供借鉴.通过红麻HcPDIL5-2a和HcPDIL5-2b cDNA中间片段及3’-末端已知序列的比时,在其完全保守区段设计了一条引物用于两个基因5' RACE的共反转录;在其部分保守区段设计了两条简并引物,并利用其在两个基因的5'RACE扩增时退火温度的差异,结合通用引物巢式PCR同步扩增两个基因的cDNA 5 ’-末端未知序列.在两个基因全长cDNA拼接序列的基础上设计两对特异引物分别扩增它们的cDNA全长序列,测序结果进一步验证了序列拼接和cDNA 5' RACE同步扩增的可靠性.进化分析证实两个基因属于PDIL基因家族成员.     

小麦中雄性不育同源序列的分离、鉴定及表达分析

利用拟南芥中已克隆的雄性核不育基因MS2和水稻中假定雄性不育蛋白的保守区域,设计一对简并引物,并在太谷核不育小麦可育株及不育株花药中进行扩增,得到了一条134bp的片段。以该片段为基础,通过电子延伸得到一个长为1604bp的序列,该序列编码的氨基酸包含一段由200个氨基酸组成的雄性不育保守区。RT-PCR结果表明,该雄性不育同源序列只在小麦可育花药中表达,而在小麦败育花药、叶片和根中不表达,说明该雄性不育同源序列为花药发育特异基因。     

简并PCR技术及其在基因克隆中的应用

本文简要介绍简并PCR技术,包括什么是简并引物,如何设计简并引物,进行简并PCR的反应条件,应用简并PCR获得全长基因的方法和简并PCR技术的应用范围,并对简并PCR技术的局限性及其新进展进行讨论。在此基础上,简述基因的克隆策略以及简并PCR技术在基因克隆中的应用。简并PCR技术是寻找和发现“新”基因或蛋白质家族新成员的一种非常有用的工具。 Abstract:Degenerate PCR is introduced in this paper,including what is degenerate PCR,how to design degenerate primers,how to optimize degenerate PCR parameters,how to applying degenerate PCR to obtain full-length gene and which fields can apply degenerate PCR.The limits and recent advances of degenerate PCR are also discussed.Based on this introduction,strategies of gene cloning and applications of degenerate PCR in gene cloning are summarized in brief.Degenerate PCR is a very useful tool for searching and discovering new genes and new members of a protein family.     

甜瓜STK类R基因同源序列的克隆与分析

以植物丝氨酸/苏氨酸蛋白激酶类( serine-threonine kinase,STK)抗病基因产物催化结构域I和Ⅸ的保守氨基酸序列( FGK/V/L/SVYK/RG,DY/IYSF/YGV/I/M)设计简并引物,对甜瓜(Cucumis melo L.)基因组DNA进行PCR扩增,得到大约500 bp的目的条带,通过重组质粒克隆并经PCR检测后得到12条不同的DNA序列,命名为tg1～tg12,其中tg2、tg5、tg9和tg12(Genbank登录号为JN646853 ～JN646856)可以编码完整的氨基酸序列.Blast分析结果显示:4条序列均具有ATP结合部位、底物结合部位和激酶结构域的活化环(A-loop)等,属于典型的蛋白激酶基因家族,可能是STK类R基因的同源序列片段;4条序列与蓖麻(Ricinus communisL.)的STK同源性均较高.氨基酸序列比对结果显示tg2、tg5、tg9和tg12均具有R基因的9个保守结构域,为STK类候选抗病基因类序列.分子系统树显示tg2、tg5、tg9和tg12与已知的R基因(Pto、Lr10和Lectin)在氨基酸水平上的相似性仅为33.5％ ～53.4％,且4个甜瓜同源序列的氨基酸相似性也较低,表明甜瓜RGAs标记可能具有较高的特异性.     

红霉素合成蛋白基因的克隆和高表达

文献报道红霉素合成蛋白DEBS2 (6-脱氧红霉内酯B合酶)(374 kD)基因在大肠杆菌(Escherichia coli)中异源表达量比较低,难以开展后续蛋白纯化和结构等研究.为获得该大蛋白基因的异源高表达,本研究通过PCR的方法,对编码红霉素合成蛋白DEBS2的基因起始5'端设计了起始密码子之后的十一个简并密码子序列,随机筛选获得在表达宿主BL21(DE3)中高表达的简并序列质粒,质粒命名为DEBS2-17.结果 表明:mRNA的起始二级结构影响200 kD以上的蛋白质表达水平.本研究为开展红霉素合成蛋白的结构及生化研究提供理论基础,同时对表达分子量200 kD以上蛋白具有一定借鉴意义.     

云南元江普通野生稻中Pi-ta和Pib同源基因的克隆和分析

用高保真PCR技术从云南元江普通野生稻中克隆了抗稻瘟病Pi-ta同源基因的编码区及Pib基因的部分同源序列。Pi-ta同源基因的编码区序列与报道的栽培稻有99.7%的同源性。根据前人的结果,从元江普通野生稻的Pi-ta基因推导的氨基酸序列中918位点为丝氨酸,属于Pi-ta~-等位基因,不能对含有AVRPita基因的稻瘟病菌产生抗性。与Pi-ta基因相比,元江普通野生稻中的Pib同源基因第一外显子与栽培稻的相应序列间存在较大差异,其中有一段87 bp的DNA序列缺失,而且不能按正常的Pib基因序列的阅读框进行翻译。因此认为,元江普通野生稻不具有基于Pi-ta和Pib基因的抗稻瘟病遗传基础。     

水稻NBS-LRR类R基因同源序列

根据多数抗病基因(R)编码蛋白质的核苷酸结合区(nucleotide binding site, NBS)和富含亮氨酸重复(leucine-rich repeat,LRR)保守区域特点,设计PCR特异扩增引物,从水稻中克隆了大小约为520 bpDNA片段23个.通过序列同源比较分析发现, 它们编码的蛋白质氨基酸序列包括有NBS-LRR类基因所具有的kinase-1a,kinase-2a, kinase-3a和保守的domain 2区域,它们属于R基因同源序列(R gene homologous sequence, 简称RS).聚类结果发现它们分为4类.遗传定位结果表明它们分布在1,3,4,7~11染色体上,其中10个RS位于已知R基因所在的染色体区间.用水稻抗白叶枯病基因Xa4的近等基因系和基因累加系对克隆的NBS-LRR同源序列进行RFLP分析,发现序列RS13可能来自Xa4基因家族.     

赤子爱胜蚓5个Dmrt基因的序列分析

本文采用简并PCR技术,扩增了赤子爱胜蚓Dmrt基因的DM结构域,经序列分析,获得了Dmrt基因家族的5个成员EfDmrt2、EfDmrt3、EfDmrt4a、EfDmrt4b、EfDmrt4c.与其他动物相关的Dmrt基因进行聚类分析,结果表明,不同进化地位动物的Dmrt基因DM域编码序列存在高度的同源性,显示Dmrt基因在系统进化上高度保守,序列上的相似性可能暗示它们在功能上的保守性.     

山地麻蜥7个Dmrt基因成员的克隆及序列分析

Dm rt基因家族是一个与性别决定相关的基因家族。该家族成员都含有一个具有DNA结合能力的保守基序———DM结构域,在性别决定和分化发育的调控中担负着重要的功能。本文采用简并PCR技术,扩增和克隆了山地麻蜥(Erem ias breuchleyi)基因组中的DM结构域,通过SSCP技术筛选和测序得到了7个具有不同DM序列的克隆。结果显示,在山地麻蜥基因组中存在着Dm rt基因家族的多个成员,与其他动物相关的Dm rt基因进行聚类分析,显示该基因家族在动物系统进化上具有高度的保守性。     

作物数量遗传学基础 二、遗传力及其估算

两栖类染色体的研究,过去多使用以生殖 细胞和端蚌尾部上皮细胞为材料的水低渗压片 法^[6]。然而,生殖细胞和峪蚌组织受季节的限 制颇大,所得的中期分裂相亦不甚多。随着 低等脊稚动物组织培养技术^[1,2]与血液培养技 术^[3]的发展,近年来已更多的使用离体培养的 细胞来进行研究。     

Degenerate PCR method for identification of an antiapoptotic gene in BHV-1

To investigate on the hypothetical presence of an antiapoptotic gene, we utilized the CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) strategy amplifying unknown sequences from a background of genomic (bovine herpesvirus type-1) BHV-1 DNA. An alignment of carboxyl-terminal domains belonging to three proteins encoded by gamma34.5, MyD116 and GADD34 genes, was carried out to design degenerate PCR primers in highly conserved regions. This allowed the amplification of a 110 bp fragment. This fragment was subjected to automatic sequencing and DNA sequence analysis revealed that its position resided between the nt 14363 and the nt 14438 in bovine herpesvirus type-1 (BHV-1) Cooper strain sharing an identity of 86% (UL14). Transient transfections showed that UL14 protein is efficient in protecting MDBK and K562 cells from sorbitol induced apoptosis. The protein's anti-apoptotic function may derive from its heat shock protein-like properties.     

Ketosynthase Domain Probes Identify Two Subclasses of Fungal Polyketide Synthase Genes

Analysis of fungal polyketide synthase gene sequences suggested that these might be divided into two subclasses, designated WA-type and MSAS-type. Two pairs of degenerate PCR primers (LC1 and LC2c, LC3 and LC5c) were designed for the amplification of ketosynthase domain fragments from fungal PKS genes in each of these subclasses. Both primer pairs were shown to amplify one or more PCR products from the genomes of a range of ascomycetous Deuteromycetes and Southern blot analysis confirmed that the products obtained with each pair of primers emanated from distinct genomic loci. PCR products obtained from Penicillium patulum and Aspergillus parasiticus with the LC1/2c primer pair and from Phoma sp. C2932 with both primer pairs were cloned and sequenced; the deduced protein sequences were highly homologous to the ketosynthase domains of other fungal PKS genes. Genes from which LC1/2c fragments were amplified (WA-type) were shown by a phylogenetic analysis to be closely related to fungal PKS genes involved in pigment and aflatoxin biosynthetic pathways, whereas the gene from which the LC3/5c fragment was amplified (MSAS-type) was shown to be closely related to genes encoding 6-methylsalicylic acid synthase (MSAS). The phylogenetic tree strongly supported the division of fungal PKS genes into two subclasses. The LC-series primers may be useful molecular tools to facilitate the cloning of novel fungal polyketide synthase genes.     

Primers for the amplification of nuclear introns in Heliconius butterflies

I described the development of degenerate polymerase chain reaction (PCR) primers for intron‐containing regions of nine candidate wing patterning and pigmentation genes in Heliconius butterflies. Primers were developed by comparing sequence data from Drosophila melanogaster, Precis coenia, and a variety of other insects so they are likely to be applicable widely among the butterfly family Nymphalidae and perhaps Lepidoptera in general. The amplified regions are highly variable and should be useful for inferring relationships among closely related species and estimating the phylogeographical and population genetic structure of individual species.     

梅花类黄酮3'-羟化酶基因片段基于基因组DNA的简并PCR法克隆

用本研究设计的"预先去杂-SDS法"从梅花嫩叶提取到高质量的基因组DNA.根据11条已公开发表的并提交到GenBank的类黄酮3'-羟化酶基因cDNA的假定氨基酸序列的保守区设计2个正向简并引物和3个反向简并引物组成6对引物,仅有1对引物能以PCR法同时从梅花'南京红须'、'南京红'和'粉皮宫粉'的基因组DNA扩增到一个469 bp的核苷酸片段,这3个片段在总体上有99.72%的一致性,与11条类黄酮3'-羟化酶基因cDNA的相应区域有65.57%的一致性.同时,"GGEK"并非类黄酮3'-羟化酶的特征性模体.这是首次从木本植物的基因组DNA克隆到类黄酮3'-羟化酶基因片段.本研究结果可为梅花类黄酮3'-羟化酶基因全长的克隆奠定基础.     

Properties of short double-stranded RNAs carrying randomized base pairs: toward better controls for RNAi experiments

Short interfering RNAs (siRNAs) are mediators of RNA interference (RNAi), a commonly used technique for selective down-regulation of target gene expression. Using an equimolar mixture of A, G, C, and U phosphoramidites during solid-phase synthesis, we introduced degenerate positions into RNA guide and passenger strands so that, when annealed, a large pool of distinct siRNA duplexes with randomized base pairs at defined sites was created. We assessed the randomization efficiency by deep sequencing one of the RNAs. All possible individual sequences were present in the pool with generally an excellent distribution of bases. Melting temperature analyses suggested that pools of randomized guide and passenger strands RNAs with up to eight degenerate positions annealed so that mismatched base-pairing was minimized. Transfections of randomized siRNAs (rnd-siRNAs) into cells led to inhibition of luciferase reporters by a miRNA-like mechanism when the seed regions of rnd-siRNA guide strands were devoid of degenerate positions. Furthermore, the mRNA levels of a select set of genes associated with siRNA off-target effects were measured and indicated that rnd-siRNAs with degenerate positions in the seed likely show typical non-sequence-specific effects, but not miRNA-like off-target effects. In the wake of recent reports showing the preponderance of miRNA-like off-target effects of siRNAs, our findings are of value for the design of a novel class of easily prepared and universally applicable negative siRNA controls.