基因组文库的构建和池化筛选

作为物种保护策略的重要部分,建立濒危畜禽的基因组文库,可有效保存濒危畜禽种质资源。BAC(bacterialartificial chromosome)文库具有高容量、遗传特性稳定和嵌合体少等优点,因而被用于畜禽基因组文库的构建。对BAC文库的构建方法和文库池化筛选系统作一综述。     

新疆细毛羊2倍基因组BAC文库PCR筛选系统的构建与使用

本研究所构建的BAC文库覆盖了8倍新疆细毛羊的基因组,平均插入片段的大小为133kb,同时文库92．5%的克隆插入片段大于100kb,而且有部分克隆甚至大于300kb,假定绵羊的基因组含有3×10~6kb,根据文库的平均插入片段大小为133kb,从文库筛选到目的片段的概率为98．208%。为了验证文库有较好的覆盖率,构建了2倍基因组文库PCR筛选系统,并对位于新疆细毛羊20号染色体MHC基因邻近区段的DMB_EX2、MCMA36、CP73和BM1258 4个分子标记进行了筛选,得到的平均阳性克隆数为1．5个,从筛选结果来看,这与文库插入片段估计的8倍基因组覆盖率相当接近并且没有偏向,这使得本文库成为研究绵羊的功能基因、位置克隆和完善基因组物理图谱的极为有用的资源。     

淀粉酶链霉菌BAC基因组文库的构建及鉴定

提取淀粉酶链霉菌SM33基因组DNA,用Hind III部分酶解后回收40 kb～60 kb大小的高分子量DNA,与质粒载体pIndigoBAC536连接,电击转化EPI300感受态细胞,经蓝白斑筛选共挑取了5 184个白色克隆.从文库中随机挑选10个克隆,酶切检测平均插入片段约为50 kb,覆盖了32.4倍基因组.并且插入片段均具有9～15个Not I酶切位点,符合链霉菌基因组特征.通过对BAC文库的筛选,获得苹果酸脱氢酶基因(mdh)的保守序列,与已知的链霉菌mdh具有很高的相似性.淀粉酶链霉菌BAC基因组文库的建立,对基因克隆、基因组物理图谱、次级代谢途径、新抗生素的发现以及工业用酶的应用等研究均有重要意义.     

PCR介导的cDNA文库矩阵排列筛选方法

描述了一种快速、有效的ｃＤＮＡ库筛选策略。其主要过程是将ｃＤＮＡ库重组子进行矩阵排列,进而用特异引物进行ＰＣＲ逐级筛选以分离目的基因。     

PCR介导的cDNA文库矩阵排列筛选方法

描述了一种快速、有效的ｃＤＮＡ文库筛选策略。其主要过程是将ｃＤＮＡ文库重组子进行矩阵排列,进而用特异引物进行ＰＣＲ逐级筛选以分离目的基因．     

苜蓿核基因组文库的构建及其实验方法的几点改进

目前,基因文库的构建方法虽已逐步普及,但仍有不少实验因最终未能从构建的文库中钓出目的基因而告失败。其主要原因是构建的文库没有达到预期的要求——真实有效.我们对核 DNA 分离和载体左右臂制备等的常用方法进行了改进,构建了苜蓿的核基因组文库,其容量测定、重组子鉴定及初步的杂交筛选都证明该文库真实有效。苜蓿(Medicago sativa L.)DNA 的制备参照 Shure 等(1983)和 Ausubel 等     

优化菌落原位杂交体系筛选野生稻基因组文库

菌落原位杂交仍是当今筛选基因组文库的重要方法之一,但难以保持背景清晰和阳性杂交点明显的稳定的杂交体系.通过对杂交膜不同处理方法的对比,表明利用溶菌酶处理杂交体系进行菌落原位杂交筛选,其杂交结果背景较干净,且能根据杂交信号的强弱很清晰地显色阳性黑点.采用该法筛选野生稻基因组文库,已筛选出22个阳性克隆,并测序分析均为阳性克隆.     

噬菌体cDNA文库筛选方法的改良

cDNA文库的构建和简便、快速的筛选是获得全长基因的重要途径,基于PCR的筛库方法具有快捷、灵敏的特点。研究改进了基于PCR的噬菌体cDNA文库筛选方法,用液体分装的方法,替代了文库筛选的关键步骤——涂板分区,省去了噬菌体文库铺平板、浸染、培养、划块洗脱的操作过程,使筛库的工作量减少,进一步提高了筛选速度和获得阳性克隆的效率。     

用克隆池PCR法筛选小麦-簇毛麦易位系6VS/6AL基因组TAC文库获得抗病基因候选克隆

用根据抗病基因保守区设计的一对简并性引物,从小麦－簇毛麦易位系6VS／6AL cDNA中PCR扩增获得一个具有抗病基因核苷酸结合位点（Nucleotide binding site,NBS）结构特点的DNA片段克隆N7。从小麦－簇毛麦易位系6VS／6AL基因组TAC（Transformation-competent artificial chromosome,TAC）文库的22块96孔板提取所有2112个克隆池（每个池含约1000个克隆）的质粒,再根据N7的核苷酸序列设计一对特异引物,用克隆池PCR（pooled PCR)法经分级筛选从文库中获得一个阳性克隆。以N7为探针,通过Southern杂交证实了该TAC克隆为真正含有抗病候选基因的克隆。研究结果表明克隆池PCR法对克隆数目巨大的基因组文库的筛选很有效。     

细菌人工染色体基因组文库构建方法的改进

目的:建立一种改进的更简便、易操作的细菌人工染色体(BAC)文库构建方法。方法:在构建猪霍乱沙门氏菌基因组大片段DNA的BAC文库时,对改进的基因组BAC文库构建方法和常规的BAC文库构建方法进行比较。结果:利用改进的方法可简便快速地构建猪霍乱沙门氏菌基因组BAC文库。结论:使用2种方法构建BAC文库,其转化效率,以及在BAC克隆中插入的DNA片段的大小和BAC克隆的稳定性等都相同,从而表明改进的方法更简单、更方便,它能使BAC文库的构建更为高效。     

水稻叶绿体基因文库的构建和精细限制图谱的制作

水稻幼叶在加有高浓度抗坏血酸的缓冲液中匀浆,以获得完整的叶绿体,从中分离到ctDNA得率高达100μg/100g叶,纯度足以用于限制性核酸内切酶分析。ctDNA经Mbo I部分酶解得到的片段克隆到载体pcos 2 EMBL的Bam HI位点,重组DNA经体外包装后感染宿主菌,筛选表型Tc~5Km~R的重组子,通过计数克隆有效率达5×10~4重组菌落/1微克插入DNA。用λ-末端酶对重组环状双链DNA在cos位点切成线性分子,产生两个(ON-L及ON-R)可供标记和杂交的末端,线性Cosmid DNA经限制酶部分消化,凝胶电泳分离,干燥凝胶放射自显影,得到了6种限制性核酸内切酶的限制图谱。水稻ctDNA全长为129.5kb,在ctDNA上Pvu Ⅱ、Sal Ⅰ、Pst Ⅰ、Hind Ⅲ、Eco RI及Bam HI的切点分别为11、12、17、37、67和44个,1R A和B为21.7kb,LSC为73.7kb,SSC为12.4kb。     

堆肥宏基因组柯斯质粒文库的构建和DNA提取技术的改进

堆肥环境中高浓度腐殖酸的存在阻碍了对这个环境中的未培养微生物的宏基因组研究。我们提出了一个确实可行的提取堆肥环境DNA的方法, 这个方法通过使用Sephadex G200＋酸洗PVPP层析柱与电洗脱两步纯化的方法成功地纯化堆肥环境来源的DNA, 用这个DNA成功构建了一个包含约10万个克隆的柯斯质粒文库。从这个文库中筛选到一个新的β-葡萄糖苷酶基因。针对文库低的阳性筛选率问题, 利用分子技术研究了不同的分离速度对提取到的总DNA中真核生物DNA量的影响, 以减少文库中真核生物DNA的污染。     

The 105-kDa protein component of Bacillus cereus non-haemolytic enterotoxin (Nhe) is a metalloprotease with gelatinolytic and collagenolytic activity

The integration site(s) of the IncJ element, R391, was localised to a specific region of the Escherichia coli chromosome, between the uxuA and serB loci (98.0-99.5 min), using classical Hfr mapping techniques. F-prime plasmid hosts, diploid for regions spanning the E. coli chromosome, were used as recipients in R391 and R997 conjugal transfer assays. Analysis of transconjugants revealed the integration of R391 and R997 into specific F-primes that contain the uxuA to serB region, but not F-primes that contain other regions of the chromosome. A comparison of the electrophoretic mobility of the original F-primes with those containing inserts demonstrated the integration of large elements, in excess of 85 kb. Linear integration of the IncJ elements into chromosomal DNA was demonstrated in recombination-deficient (recA) backgrounds in the absence of detectable autonomous stages. These observations account for the inability to isolate plasmid DNA from IncJ hosts, and suggests that the elements exhibit a conjugative transposon-like biology in E. coli.     

Rapid Screening of a Novel Arrayed Medaka (Oryzias latipes) Cosmid Library

Medaka (Oryzias latipes) has many advantages for genetic and developmental studies. With recent advances in the genome analyses of other species, rapid accumulation of resources for medaka genomics is expected. In this study, we generated an arrayed medaka cosmid library from the HNI inbred strain, carrying a 40-kb insert on average. The library consists of approximately 120,000 clones with a 6-fold genomic coverage. Cosmid clones can be screened within 2 days using standard polymerase chain reaction. Considering the advantage of the cosmid insert size and the compact genome size of the medaka, this library provides a powerful tool for future genome analyses.     

PCR筛选BAC文库和直接BAC末端测序方法的建立

建立了一种用PCR方法筛选富含高度重复序列的大麦BAC DNA 文库和直接对 BAC DNA进行末端测序的方法.用PCR技术进行大麦BAC DNA 文库(含816个平板,每个平板含384个克隆)的筛选分4步进行.在实验中,建立了两个水平的BAC DNA池(一级池和二级池).一个二级池由一个平板(含有384个克隆)的DNA 组成,一个一级池由连续10个稀释100倍的二级池的DNA混合而成(如1～10,11～20等),共82个一级池.BAC DNA 文库筛选的第一步是对82个一级池的筛选.得到阳性一级池后(如2号一级池),对其所含的10个二级池(从11～20)进行第二步筛选.得到阳性二级池后,培养相应的阳性平板的所有克隆(384个),从头开始(左上侧),每相邻的4个克隆为一组,在96孔板上(4 X 96=384) 进行第三轮PCR反应;之后对筛选结果为阳性的4个克隆分别进行菌落 PCR(第四轮)得到单一阳性克隆.根据BAC DNA Hind III 酶切指纹图谱,对同一引物筛选的BACs进行重叠群作图(Contig).对代表contig 的两端的BAC DNA直接进行末端测序并对测序结果Blast,以检测其在大麦中是否属于单拷贝序列.根据测序和Blast结果设计引物,用中国春附加系(附加大麦染色体)对来自BAC克隆的引物进行染色体定位并用分离群体进行遗传学作图,以确定是否可以用作下一步的染色体步行.     

The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae

Ca(2+)-dependent cyclic lipodepsipeptides are an emerging class of antibiotics for the treatment of infections caused by Gram-positive pathogens. These compounds are synthesized by nonribosomal peptide synthetase (NRPS) complexes encoded by large gene clusters. The gene cluster encoding biosynthetic pathway enzymes for the Streptomyces fradiae A54145 NRP was cloned from a cosmid library and characterized. Four NRPS-encoding genes, responsible for subunits of the synthetase, as well as genes for accessory functions such as acylation, methylation and hydroxylation, were identified by sequence analysis in a 127 kb region of DNA that appears to be located subterminally in the bacterial chromosome. Deduced epimerase domain-encoding sequences within the NRPS genes indicated a D: -stereochemistry for Glu, Lys and Asn residues, as observed for positionally analogous residues in two related compounds, daptomycin, and the calcium-dependent antibiotic (CDA) produced by Streptomyces roseosporus and Streptomyces coelicolor, respectively. A comparison of the structure and the biosynthetic gene cluster of A54145 with those of the related peptides showed many similarities. This information may contribute to the design of experiments to address both fundamental and applied questions in lipopeptide biosynthesis, engineering and drug development.     

不吸水链霉菌基因文库的构建及初步筛选

采用碱裂解法从不吸水链霉菌提取染色体DNA,用Sau3AI对染色体DNA进行部分水解,利用透析袋法回收3.5～9kb之间的DNA片段。以pUC18为载体,用BamHI对其进行酶切,再用热敏磷酸酶去磷酸化,酶切产物与外源DNA按一定比例混合后,加入T4DNA连接酶进行连接。连接产物用受体菌E.coliDH5α进行转化,根据α-互补性质产生的颜色反应,挑选白色菌落,构建了相应的不吸水链霉菌基因文库。分别利用特异性探针2-1-1及1-2-1对不吸水链霉菌基因文库进行筛选,利用DIG-Ⅱ-dUTP对特异性探针进行标记,与基因文库中的阳性转化子进行Southern杂交,通过显色反应对杂交结果进行检测,由于时间关系,暂未筛选出阳性克隆,但这些工作对以后的相关实验研究具有很好的借鉴作用。     

Conservation and variation in the large scale organisation of the globin gene domains of duck and chicken

Summary The genomic DNA of cloned recombinants containing the duck globin genes was compared to that of the analogous domains of the chicken. A 36 kb insert including the three alpha-type globin genes was isolated from a newly prepared duck genomic library in the cosmid PJB8; another recombinant contained a 45 kb insert with the four beta globin genes. In the alpha globin gene domain, the relative positions of genes, of repetitive sequences, and of the A+T-rich segments (AT-rich linkers, ATRLs) which frame the gene cluster (Moreau et al. 1982), were found to be closely maintained between duck and chicken. Although ATRLs and repetitive sequences also frame the gene cluster in the beta globin domains of duck and chicken, there is more genetic drift in their relative positions than in the alpha domain. It is of interest that several repetitive DNA segments were detected in the chicken beta globin domain which do not exist in corresponding positions in the duck. In view of the strict conservation in both species of genes and their relative positions in the cluster, this observation seems to exclude a simple function of repetitive sequences in the control of individual genes. The data are discussed with regard to the possible significance of repetitive and AT-rich DNA segments in genome organisation and function.