家蝇卵黄蛋白基因的克隆与结构序列分析

家蝇卵黄蛋白基因编码的卵黄蛋白是家蝇胚胎发育的重要营养来源 .根据 3种家蝇卵黄蛋白cDNA保守序列设计引物 ,用PCR技术从家蝇基因组DNA中扩增到大小为 76 8bp的mdYP1基因的部分DNA片段 .经地高辛标记成特异性探针 ,从构建的家蝇基因组文库中筛选出一个阳性克隆 ,并从该克隆中分离到大小为 3991bp的mdYP1基因组基因 .序列分析显示 ,该基因组序列含有约1 6kb的 5′ 上游区和 1 0kb的 3′ 下游区 ,编码区由一个 6 1bp的内含子和大小分别为 2 2 2bp和10 2 8bp的 2个外显子组成 .5′ 上游区含有典型的CAAT TATA盒 .     

Membrane cofactor protein of the complement system. A HindIII restriction fragment length polymorphism that correlates with the expression polymorphism.

An RFLP was found in the DNA of 25 unrelated persons, two families, and five cell lines that correlated with their membrane cofactor protein phenotype. If restricted with HindIII, DNA derived from upper band predominant protein (U) phenotypes had a band at 2 kb, whereas DNA of lower band predominant (L) phenotypes had a 4-kb band. The equal band protein phenotype, in which equal quantities of the two species are expressed, had bands at both 4 and 2 kb. The polymorphic HindIII site was localized to an intron within the membrane cofactor protein gene between exon 1 (codes for 5'UT/signal peptide) and exon 2 (codes for the first short consensus repeat). Using the polymerase chain reaction (PCR), sequences around this site were amplified and a single band of 260 bp was produced. In the U phenotype, the PCR product was restricted with HindIII into 200- and 60-bp fragments. In the L phenotype, there was no change in the size of 260 bp upon restriction with HindIII. For the equal band protein phenotype, the PCR product was partially cleaved. The 260-bp PCR product was subcloned and sequenced. DNA from the U phenotype demonstrated an intact HindIII site (AAGCTT), whereas in the DNA of the L phenotype, this site was altered because a "G" was substituted for a "C" (AAGGTT).     

细胞质雄性不育高粱叶绿体 ndh D 基因的序列变异

片段SAAU－02 700特异地扩增自7种具可育细胞质的高粱材料的总DNA,含有叶绿体psa C(88bp)和ndh D(192bp)基因的部分序列。该片段与Eco Ri HindⅢ酶切的总DNA,线粒体DNA和叶绿体DNA杂交,在总DNA中获得了0.74kb的杂交带,而在叶绿体中获得0.74kb和0．45kb两条杂交带。与线粒体DNA无杂交;与经Hae Ⅲ酶切的总DNA杂交,在不育系中获得4．9kb的杂交带,而保持系的杂交带为4．45kb。参考GenBank中高粱的近缘物种玉米叶绿体基因组的序列,构建了ndh D基因区的酶切位点图谱,借此分析得出高粱不育系的叶绿体ndh D基因序列已发生改变。这种变异与高粱细胞质雄性不育反生的关系正在探讨中。     

肺炎支原体P1蛋白羧基端基因片段在大肠杆菌中克隆的研究

在大肠杆菌中克隆肺炎支原体P1蛋白羧基端基因片段,为P1蛋白基因片段的扩增、表达及探讨羧基端基因片段功能打基础.采用PCR扩增方法获取P1结构基因.扩增产物用SalI和EcoRI酶切消化,回收1kb大小的DNA片段并与pUC19DNA连接,转入大肠杆菌JM109菌株.用X-gal平板及质粒图谱分析方法筛选重组克隆株,再用限制性核酸内切酶酶切图谱分析鉴定.经PCR扩增MPDNA获得1条5.0kbDNA片段.重组质粒限制性内切酶指纹图谱显示出2条带,1条为pUC19载体DNA带,另1条是1kb的插入片段.实验获得肺炎支原体P1蛋白结构基因及含P1蛋白羧基端DNA片段的重组克隆株.     

Detection and Identification of Brenneria nigrifluens, the Causal Agent of the Shallow Bark Canker of Walnut by, PCR Amplification

A 1 kb DNA band from strains of Brenneria nigrifluens, as shown by amplification of their genomic DNA by polymerase chain reaction (PCR) using minisatellite primer designed on the minisatellite sequence of the M13 phage, was isolated, cloned and sequenced. Specific oligonucleotides (F1–C3) were selected into this 1 kb DNA sequence and used in a PCR assay to detect and identify strains of B. nigrifluens . Several strains of B. nigrifluens were assessed with F1–C3 primers producing a specific band of approximately 250 bp pairs in length. This target was successfully amplified from purified genomic DNA, from bacterial culture and directly from infected walnut bark tissue. No amplification was obtained when the PCR assay was performed on other plant-pathogenic species from the following genera Brenneria, Erwinia, Agrobacterium, Pseudomonas, Ralstonia, Pectobacterium, Xanthomonas and from walnut-associated bacteria, indicating the specificity of these primers. The PCR assay with the primers described here provides a rapid, specific and sensitive diagnostic method for B. nigrifluens and a useful tool for epidemiological studies.     

The PCR plateau phase - towards an understanding of its limitations

The DNA polymerases from Thermus aquaticus and Thermus flavus were recently found to bind to short double-stranded DNA fragments without sequence specificity [Kainz et al. (2000) Biotechniques 28, 278-82]. In the present study, it is shown that the accumulation of amplification products during later PCR cycles also exerts an inhibitory effect on several enzymes tested. To simulate later cycle conditions, a 1.7 kb sequence from phage lambda DNA was amplified in the presence of various amounts of a 1 kb double-stranded DNA fragment. A 30-fold molar excess of fragments to polymerase molecules was found to be required for a complete inhibition of Taq, Tfl and Pwo DNA polymerase. This stoichiometric relation remained constant when PCR amplifications were performed using polymerase concentrations of 0.5, 1 or 1.5 U/50 microl reaction volume. The amount of 1 kb DNA fragments required for a complete inhibition was similar to the product yield of the controls (no fragment added), that were run to plateau phase levels. Additionally, PCR mixtures, that were subjected to different numbers of cycles, were compared in their ability to extend 3'-recessed ends by using a hairpin extension assay. The presence of endogenous amplicon DNA accumulated in later PCR cycles was found to inhibit completely the activity of DNA polymerase. PCR mixtures still in quasi-linear phase partially extended the hairpins. In both cases, a further addition of polymerase significantly improved their function. These results indicate that the main factor contributing to the plateau phase in PCR consists of binding of DNA polymerase to its amplification products.     

中国烟草曲叶病毒广西株的初步研究

双生病毒 (Ｇｅｍｉｎｉｖｉｒｕｓ)是一种具有孪生颗粒形态的单链环状ＤＮＡ植物病毒[1] 。根据基因组结构特征及传播介体 ,双生病毒可分为三个亚组[1] :亚组Ⅰ双生病毒全部为叶蝉传播的单组份基因组病毒 ,基因组大小在 2 .6～ 2 .8ｋｂ之间 ,其代表病毒是玉米条纹病毒 (ＭＳＶ) ;亚组Ⅱ双生病毒是单组份基因组病毒 ,基因组大小在 2 .7～ 3.0ｋｂ之间 ;亚组Ⅲ双生病毒全部为粉虱 (Ｂｅｍｉｓｉａｔａｂａｃｉ)传播 ,基因组大小为 2 .5～ 2 .8ｋｂ ,除番茄曲叶病毒ＴＬＣＶ ＡＵＳ[2 ] 等几个病毒为单组份基因组外 ,大多数亚组Ⅲ双生病病毒…     

Nucleotide sequence of BamHI family satellite DNA and its unit length polymorphism in bluegill sunfish Lepomis macrochirus

We have isolated and sequenced a member of tandem repetitive DNA containing BamHI site (BamHI family satellite DNA) from bluegill sunfish Lepomis macrochirus. PCR amplification with specific primers was performed to define the size of unit length repeat of the BamHI family satellite DNA, revealing that there were two distinct size of DNA fragments (0.9 kb and 1.3 kb) in the PCR products. The longer fragment (1.3 kb) consisted of internal sub-duplication of shorter fragment (0.9 kb). We have compared the size of PCR products among four fish populations, and found that both fragments co-existed in one population whereas the longer fragment was dominant in other three populations. The results may reflect ongoing homogenization of satellite DNA type over a short evolutionary time scale.     

In vitro amplification of DNA fragments greater than 10 kb.

The synthesis of a 10.9-kb DNA fragment from a bacteriophage lambda template was used in the search for conditions to extend the range for the polymerase chain reaction (PCR). Using the same primer sequences and conditions (denaturation at 94 degrees C, 1 min; annealing at 57 degrees C, 1 min; polymerization at 70 degrees C, 20 to 30 min) as published by W. Rychlik, W. J. Spencer, and R. E. Rhoads [(1990) Nucleic Acids Res. 18, 6409-6412], unsatisfactory results were obtained with AmpliTaq and native Taq polymerase (poor reproducibility, low product yield, nonspecific products), whereas Tub polymerase completely failed to amplify this fragment. Only after changes in the following parameters were reliable results obtained but only with Tub polymerase: A two-step PCR procedure with primer annealing and extension at 65 degrees C followed by DNA denaturation at 94 degrees C for 1.5 min was performed. The DNA fragment desired was specifically amplified when the enzyme concentration was reduced to 0.4 U/50 microliters and extension times as low as 4 to 12 min with an optimum at 8 min were used. A prolongation to 20 min or more resulted in an accumulation of unspecific products with a concomitant reduction in the yield of the fragment. Under the conditions described above it was also possible to amplify a DNA fragment even significantly longer (15.6 kb).     

马立克氏病血清I型致瘤株病毒感染的早期检测

马立克氏病 (MD)是养禽业最重要的疫病之一 ,一直缺少有效的早期诊断方法。根据血清I型马立克氏病毒(MDV1)meq基因的核酸序列设计了一对寡苷酸核引物 ,分别对MDV1致瘤株 (京 - 1株 )、非致瘤株 (MD11/ 75C株、CV1988株 )、MDV2 (SB 1株 )、HVT(Fc 12 6株 )的核酸进行扩增。结果表明 :京 - 1株扩增到约 1 15kb核酸片段 ,MD11/ 75C株和CVI988株扩增到约 1 0kb核酸片段 ,而SB 1株、Fc 12 6株没得到任何扩增产物。PCR产物Dotblot结果显示 ,京 - 1株、MD11/ 75C株和CVI988株的扩增产物都与Digoxigenin标记的meq基因探针杂交 ,说明都是特异性的扩增产物。对MSB1细胞DNA及MDV感染鸡的血液及肝、肾肿瘤等DNA扩增都得到 1 15kb条带。将京 - 1株和CVI988株感染的细胞DNA混合再扩增 ,同时得到 1 15kb和 1 0kb的核酸条带 ,所以根据扩增产物大小可以区别致瘤株京 - 1株及非致瘤株CV1988株 ,这表示可从CVI988株病毒免疫鸡体内检测到MDV强毒 ,适于早期确诊强毒感染。     

Methacarn fixation for genomic DNA analysis in microdissected, paraffin-embedded tissue specimens.

We recently found methacarn to be a versatile fixative for analysis of RNA and protein applicable for microdissected specimens from paraffin-embedded tissue (PET). In this study we investigated the performance of methacarn for genomic DNA analysis using microdissected rat tissues. We found that extensive portions of DNA up to 2.8 kb could be amplified by nested PCR using DNA templates extracted by a simple and rapid extraction procedure from a 1 x 1-mm area of cerebral cortex of a 10-microm-thick section. By nested PCR, a 522-bp fragment from a single cell could be amplified in 20% of cresyl violet-stained Purkinje cells, and the minimal number of cells required, as estimated using hippocampal neurons, was on the order of 10-20. Although tissue staining with hematoxylin and eosin affected the PCR, amplification of a 522-bp fragment was successful, with 150-270 cells by 35 cycles of single-step PCR. Immunostaining resulted in a substantial decrease of yield and degradation of extracted DNA. However, even after immunostaining, a 184-bp DNA fragment could be amplified with 150-270 cells by 35 cycles of PCR. The results thus demonstrate the superior performance of methacarn to that reported with formalin in genomic DNA analysis using microdissected PET specimens.     

Selection of RAPD marker for growth of seedlings at low temperature in rice.

We have developed a polymerase chain reaction (PCR)-based assay that could effectively reduce the time period required to screen and select the cold tolerance gene of rice seedlings under field conditions. The two specific random amplified polymorphic DNA (RAPD) fragments for the assay were identified on the basis of quantitative trait loci (QTL) analysis which were found to be tightly linked to cold sensitivity. The two RAPD fragments, OPT8(600) in the cold sensitivity rice cultivar 'Dular (indica)' and OPU20(1200) in the resistance rice cultivar 'Toyohatamochi (japonica)', were identified after screening 11 RAPD fragments using 2 random primers on the genomic DNAs of 'Dular' and 'Toyohatamochi'. These primers, when used in a multiplexed PCR, specifically amplified a 0.6 kb and a 1.2 kb fragment in the sensitive and resistant rice cultivars, respectively. When this assay was performed on the genomic DNAs of 16 japonica, 3 Tongil (indica/ japonica), and 2 indica rice cultivars, the primers amplified a 0.6 kb fragment in all of the cold sensitivity rice cultivars or 1.2 kb fragment in all of the resistance ones. These markers can be of potential use in the marker-assisted selection (MAS) for cold tolerance in rice seedling. As screening for resistance can now be conducted independent of the availability of low temperature, the breeding of cold tolerance cultivars can be hastened.     

年轻与衰老2BS细胞中差异表达基因片段的筛选及特征分析

为探索人衰老机制 ,采用差异显示法分别从年轻和衰老 2BS细胞中筛选出特异的cDNA片段 .衰老相关细胞cDNA片段长 2 86bp ,命名为orc ,GenBank登录号为AI35 30 6 5 ;年轻相关的cDNA片段长 2 35bp ,命名为yrc ,GenBank登录号为AI35 30 6 4.Southernblot分析表明 ,yrc在衰老和年轻2BS细胞、BGC 82 3细胞中的BamHⅠ酶切图谱均出现约 3 0kb杂交带 .Northern印迹分析显示 ,yrc在年轻和衰老 2BS细胞中均有 1 0kb和 0 5kb杂交带 ,其中 1 0kb带在两种细胞间差异不大 ,而0 5kb带则在年轻细胞中明显高于衰老细胞 .在胎儿心、肺、肝中也可见 0 5kb和 1 0kb两条杂交带 ;而在胎盘及胎儿肌肉、肾、脑、皮肤中 ,则只可见 0 5kb杂交带 ,无 1 0kb带 .orc基因转录本长约 2 0kb ,在衰老 2BS细胞中的表达高于年轻细胞 .结果表明 ,orc和yrc分别与细胞衰老和年轻相关 ,yrc 0 5kb转录本在维持细胞年轻状态及胎儿组织发育过程中可能具有调节作用     

用富集文库克隆人胰岛素基因组基因

通过构建可富集人胰岛素基因的λ噬菌体文库,克隆了人胰岛素基因组基因．首先从中国人血液白细胞中提取到人基因组ＤＮＡ,用ＥｃｏＲⅠ和ＢｇｌⅡ对基因组ＤＮＡ进行全酶切,经０．４％琼脂糖凝胶电泳,特异回收９．５ｋｂ左右的ＤＮＡ片段．将该片段与λＥＭＢＬ３／ＢａｍＨⅠ臂连接,构建成一个特殊的人基因组λ噬菌体文库（富集文库）,效价为２×１０４．同时采用ＰＣＲ方法及用引物Ⅰ：５′ＧＧＡＣＡＧＧＣＴＡＣＡＴＣＡＧＧＡＡＧＡＧＧ３′,引物Ⅱ：５′ＣＴＧＣＧＴＣＴＡＡＴＴＧＣＡＧＴＡＧＴＴＣ３′,从人基因组ＤＮＡ中扩增出一段含胰岛素基因的１．３６ｋｂＤＮＡ片段,做为放射性标记探针,对文库进行了噬菌斑原位杂交筛选,从１×１０４个噬菌斑中筛选到一个含人胰岛素基因组基因的阳性克隆,并进一步完成了亚克隆和该基因１７３２ｂｐＤＮＡ序列的测定．结果该基因的１７３２ｂｐＤＮＡ序列包括部分５′端和３′端与国外发表的人胰岛素α型等位基因的序列相同     

Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides

The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.     

Cloning and sequencing of an Aspergillus niger gene coding for β-fructofuranosidase

A 1.7 kb DNA fragment encoding b-D-fructofuranosidase in a strain of Aspergillus niger was amplified by PCR, inserted into a 4.4 kb cloning vector and sequenced. Comparison of this sequence with suc1 (GenBank) showed that this invertase gene had suffered a single base deletion followed by a single base insertion 49bp further down-stream with the result that 16 amino acids are coded by a different reading frame.     

Use of the polymerase chain reaction to identify mosquito species of the Anopheles gambiae complex

A nonradiometric method has been developed for distinguishing between the sibling species Anopheles gambiae Giles and An. arabiensis Patton, two important Afrotropical vectors of malaria. DNA fragments of species diagnostic length are amplified by polymerase chain reaction (PCR) from a small amount of unknown DNA and three different PCR primers. All three PCR primers are based on ribosomal DNA (rDNA) sequences. A universal plus-strand primer (A0) is derived from a conserved region at the 3' end of the 28S rDNA coding region. Two species-specific minus-strand primers (Aa0.5 and Ag1.3) are derived from sequences in the intergenic spacers. The Ag1.3 sequence is approximately 1.3 kb downstream of A0; the Aa0.5 sequence is about 0.5 kb downstream of A0. When mosquito DNA is amplified in the presence of all three primers, a 1.3 kb fragment is produced if An. gambiae DNA is used as template, and a 0.5 kb fragment is produced if An. arabiensis DNA is used. Amplification of DNA from An.gambiae/An. arabiensis hybrids produces both the 1.3 kb and the 0.5 kb fragments. Neither diagnostic fragment is produced when DNA from other species in the An. gambiae complex is used as template.     

Detection of Staphylococcus hyicus exfoliative toxin genes by dot blot hybridization and multiplex polymerase chain reaction

We designed a novel DNA probe and novel PCR primer sets for detecting the genes coding for Staphylococcus hyicus (S. hyicus) exfoliative toxin (ET). In dot blot hybridization, the novel DNA probe hybridized with chromosomal DNA of ExhA-, ExhB-, ExhC-, ExhD-, and SHETA-producing strains. This probe also hybridized with the plasmid DNA of a SHETB-producing strain. In Southern blot hybridization, the probe hybridized with a 1.5 kb HindIII fragment of chromosomal DNA from a SHETA-producing strain. The above fragment was cloned into E. coli and the nucleotide sequence of the SHETA gene determined, this gene proved to have almost the same homology (99.6%) as the ExhB gene. It was therefore thought that SHETA is a subtype of ExhB. In multiplex PCR using five primer sets, each gene gave a band distinguishable from the others. This multiplex PCR system has high specificity among the well-known S. hyicus ET genes. Of the 69 known ET-producing S. hyicus strains, 38, 19, 10, 2 and 1 strains have exhB, exhD exhA, shetb and exhC genes, respectively.     

Genetics of subpeptin JM4-A and subpeptin JM4-B production by Bacillus subtilis JM4

Subpeptin JM4-A and subpeptin JM4-B are two novel antimicrobial peptides produced by Bacillus subtilis JM4. To identify putative genes involved in their production, degenerate PCR primers targeted to conserved motifs of nonribosomal peptide synthetases (NRPSs) were used. A resulting 1.2 kb PCR product had high sequence similarity to genes of NRPSs, and then a 2.8 kb DNA fragment flanking it was cloned subsequently. Gene disruption of the resulting 4 kb DNA fragment produced subpeptin-deficient mutant, suggesting that subpeptin JM4-A and subpeptin JM4-B were biosynthesized by NRPSs. Based on this result, a 48 kb gene cluster was cloned, which consisted of nine coding sequences (CDSs) involved in antimicrobial peptide biosynthesis, regulation, and resistance. Disruption of two relatively large CDSs subA and subC led to subpeptin-deficient mutants, which supported the involvement of the cloned gene cluster in subpeptin biosynthesis.     

PCR产物的RFLP分析在黄芪亚族（豆科）系统学研究中的应用初探

用聚合酶链式反应（ＰＣＲ）将豆科黄芪亚族７属９种及甘草亚族１属１种植物叶绿体基因组中ｎｄｈＦ和ｐｓｂＡ基因中一段约３．１ｋｂ的ＤＮＡ扩增出来,并摸索出一最佳的ＰＣＲ条件,使得此条带得以特异性扩增,可直接用于限制性内切酶水解。通过对此扩增片段的限制性片段长度多态性（ＲＦＬＰ）的初步分析,认为利用ＰＣＲ扩增出的ＤＮＡ进行ＲＦＬＰ分析来探讨植物的系统进化问题在中国现行条件下大有潜力,其方法简单易行,结果