Quantitative PCR with 16S rRNA-Gene-Targeted Species-Specific Primers for Analysis of Human Intestinal Bifidobacteria

A highly sensitive quantitative PCR detection method has been developed and applied to the distribution analysis of human intestinal bifidobacteria by combining real-time PCR with Bifidobacterium genus- and species-specific primers. Real-time PCR detection of serially diluted DNA extracted from cultured bifidobacteria was linear for cell counts ranging from 10⁶ to 10 cells per PCR assay. It was also found that the method was applicable to the detection of Bifidobacterium in feces when it was present at concentrations of >10⁶ cells per g of feces. Concerning the distribution of Bifidobacterium species in intestinal flora, the Bifidobacterium adolescentis group, the Bifidobacterium catenulatum group, and Bifidobacterium longum were found to be the three predominant species by examination of DNA extracted from the feces of 46 healthy adults. We also examined changes in the population and composition of Bifidobacterium species in human intestinal flora of six healthy adults over an 8-month period. The results showed that the composition of bifidobacterial flora was basically stable throughout the test period.     

Quantitative Competitive RNA PCR for Quantitation of Virion-Associated HIV-1 RNA

Quantitative competitive PCR is a highly sensitive technique that allows accurate quantitation of small amounts of RNA. We have modified the original method to include the use of an internal standard at all stages of sample analysis. In this way, the method can accommodate for variations in the recovery of viral particles and in the isolation of genomic RNA as well as provide a suitable competitive substrate during quantitative RNA PCR. We have used this method to characterize changes in virus load in plasma of HIV-1-seropositive individuals following their vaccination against opportunistic infections.     

Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR

Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. Primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe. The detection limit was 10(2) to 10(3) gene copies, which was lowered to 10(0) to 10(1) gene copies by hybridization. Using the dioxygenase-specific primers, an increase in catechol 2, 3-dioxygenase genes was detected in petroleum-amended soils. The dioxygenase genes were enumerated by competitive quantitative PCR with a 163-bp competitor that was amplified using the same primers. Target and competitor sequences had identical amplification kinetics. Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration. Therefore, this technique can be used to accurately and reproducibly quantify catechol 2, 3-dioxygenase genes in complex environments such as petroleum-contaminated soil. Direct, non-cultivation-based molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.     

Development of Primers to O-Antigen Biosynthesis Genes for Specific Detection of Escherichia coli O157 by PCR

The chemical composition of each O-antigen subunit in gram-negative bacteria is a reflection of the unique DNA sequences within each rfb operon. By characterizing DNA sequences contained with each rfb operon, a diagnostic serotype-specific probe to Escherichia coli O serotypes that are commonly associated with bacterial infections can be generated. Recently, from an E. coli O157:H7 cosmid library, O-antigen-positive cosmids were identified with O157-specific antisera. By using the cosmid DNAs as probes, several DNA fragments which were unique to E. coli O157 serotypes were identified by Southern analysis. Several of these DNA fragments were subcloned from O157-antigen-positive cosmids and served as DNA probes in Southern analysis. One DNA fragment within plasmid pDS306 which was specific for E. coli O157 serotypes was identified by Southern analysis. The DNA sequence for this plasmid revealed homology to two rfb genes, the first of which encodes a GDP-mannose dehydratase. These rfb genes were similar to O-antigen biosynthesis genes in Vibrio cholerae and Yersinia enterocolitica serotype O:8. An oligonucleotide primer pair was designed to amplify a 420-bp DNA fragment from E. coli O157 serotypes. The PCR test was specific for E. coli O157 serotypes. PCR detected as few as 10 cells with the O157-specific rfb oligonucleotide primers. Coupled with current enrichment protocols, O157 serotyping by PCR will provide a rapid, specific, and sensitive method for identifying E. coli O157.     

Oligonucleotide Primers for PCR Amplification of Coelomate Introns

Abstract Seven novel oligonucleotide primer pairs for polymerase chain reaction amplification of introns from nuclear genes in coelomates were designed and tested. Each pair bound to adjacent exons that are separated by a single intron in most coelomate species. The primer sets amplified introns in species as widely separated by the course of evolution as oysters (Mollusca: Protostoma) and salmon (Chordata: Deuterostoma). Each primer set was tested on a further 6 coelomate species and found to amplify introns in most cases. These primer sets may therefore be useful tools for developing nuclear DNA markers in diverse coelomate species for studies of population genetics, phylogenetics, or genome mapping.     

洋葱伯克霍尔德氏菌产邻苯二酚2,3-双加氧酶的研究

对洋葱伯克霍尔德氏菌L 68生长及产邻苯二酚2,3 双加氧酶(C23D)的条件进行了研究,其最适产酶pH7.2;最适生长温度30～35℃;最适培养时间48h;苯酚浓度0.09%最有利于菌体产酶.对菌株L 68产生的C23D酶进行了纯化,超声波破碎后的细胞提取液经硫酸铵分级沉淀、DEAESepharoseFastFlow层析、Hydroxyapatite层析、SephadexG 150层析后,收率为20%,酶比活力提高了230倍.SDS PAGE检测得到了分子量为(34±1)kDa的蛋白.     

PCR扩增Sry基因进行鲸类动物性别的鉴定

哺乳动物Y染色体短臂上的Sry 基因决定雄性发育方向。本研究参照哺乳动物Sry 基因保守区序列设计引物, 以非性别特异性的线粒体DNA 细胞色素b 基因作为阳性对照, 用PCR 扩增江豚、长喙真海豚等鲸类动物的Sry 基因片断并对其进行凝胶电泳分析来鉴定鲸类动物的性别。通过此方法对87 个已知性别鲸类动物标本的检验, 结果完全正确, 并进一步应用此方法成功地完成了另外33 个未知性别鲸类标本的性别鉴定。由此建立了一套简单、快速、可靠的鲸类动物的性别鉴定方法。     

Specific Oligonucleotide Primers for Detection of Lecithinase-Positive Bacillus spp. by PCR

Volume 61, no. 1, p. 100, Table 3: in columns 7 and 8, row 3, "-" should read "+." [This corrects the article on p. 98 in vol. 61.].     

猕猴桃6个LOX基因家族成员实时定量PCR引物特异性的检测与应用

从基因家族成员的视角开展基因表达研究是阐明基因功能的重要组成内容,实时定量PCR（QPCR）技术是分析基因表达的有效手段.以猕猴桃脂氧合酶（LOX）基因家族6个成员为对象,分析了引物特异性的检测方法.该方法整合了熔点曲线分析、琼脂糖电泳、交叉PCR扩增和PCR产物测序等分析手段,有效消除其他成员的交叉扩增干扰,为利用QPCR检测基因家族成员表达提供了特异、准确与可行的途径.     

竞争PCR定量检测免疫小鼠细胞因子表达水平

目的：利用竞争PCR技术定量检测各种细胞因子的表达水平。方法：在机体免疫应答过程中,细胞因子作为免疫调节分子在免疫网络系统中发挥重要的调节功能,T细胞能够通过产生并分泌各种细胞因子来调节机体的免疫反应。本研究采用竞争PCR技术,通过提取的小鼠脾脏组织总RNA,经反转录得到cDNA,利用一种修饰的竞争模板pQRS进行竞争PCR扩增,然后利用琼脂糖凝胶电泳分析并与竞争模板产物比较而定量。结论：结果表明竞争PCR能够初步定量免疫前后小鼠脾脏组织表达的IL-2、IL-4、IL-10、IL-12和IFN-γ的表达量。为深入研究免疫前后小鼠体内各种细胞因子的动态水平和分析细胞免疫水平奠定了基础。     

Development of a Quantitative Competitive PCR Assay for Detection and Quantification of Escherichia coli O157:H7 Cells

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify Escherichia coli O157:H7 cells. From 10³ to 10⁸ CFU of E. coli O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (r² = 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.     

Catechol 2,3-Dioxygenase-catalyzed Synthesis of Picolinic Acids from Catechols

Various picolinic acid derivatives were synthesized from ammonia and hydroxymuconic semialdehyde derivatives that were oxidatively prepared from various catechols by the action of Pseudomonas catechol 2,3-dioxygenase (C23O, metapyrocatechase).     

Phylum- and Class-Specific PCR Primers for General Microbial Community Analysis

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, and Planctomycetes and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of Basidiomycota were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy.     

荧光定量PCR测定端粒长度

目的应用实时荧光定量聚合酶链式反应（Q—PCR）方法测定端粒长度。方法选取9种人类细胞株,提取基因组DNA,采用Q—PCR方法测定相对T／S比率,DNA印迹法测定末端限制性片段（TRF）长度,进行二者之间的相关性分析。结果定量PCR测定端粒长度相对T／S比率为0．68±0．57,DNA印迹法测量平均TRF值为8．57±2．34,两种方法测定结果的相关性分析R2=0．7807（P〈0．01）。结论采用荧光定量PCR方法测量端粒长度具有重复性好、省时、简便、可靠的特点,可高通量处理大量样品。     

人乳铁蛋白基因在昆虫细胞中的表达

将人乳铁蛋白ｃＤＮＡ（ｈＬＦｃ）克隆在质粒ｐＢａｃＰＡＫ８的ＢａｍＨＩ和ＳａｃＩ位点,构建成转移质粒８ｈＬＦｃ。该质粒ＤＮＡ与ＡｃＮＰＶ ＢａｃＰＡＫ６病毒株基因组ＤＮＡ经共转染草地夜峨培养细胞Ｓｆ２１,在培养的贴壁细胞中挑出空斑,经过３轮纯化,结合斑点杂交筛选,获得重组病毒。用蛋白质免疫印迹法检测到在重组病毒感染的Ｓｆ－２１细胞中存在乳铁蛋白基因的表达产物。酶联免疫检测结果表明：重组人乳铁蛋白在     

邻苯二酚2,3—双加氧酶在大肠杆菌的表达与定域

本文在大肠杆菌/枮草芽孢杆菌间的穿梭质粒pTG 402的基础上构建了几个新的带有显色标志基闲xylE的表达质粒,摸索了该基因所编码的邻苯二酚2,3-双加氧酶(CatO_2ase)的表达条件,分析了该酶一级结构与二级结构的亲水性和疏水性,测定了它在大肠杆菌中的产量与分布。结果表明,CatO_2ase与各质粒的表达量不等,表达量高低与培养时间、宿主菌及诱导与否等影响因素有关;表达后有部分酶可在胞外测出,但大部分仍定域于膜内,亲、疏水性分析示该酶不具分泌性蛋白的显著特点。因该酶易于检测和定量,可作为一种选择性标记和监测指示系统在基因工程中推广应用,同时亦为用基因工程菌消除芳烃类化合物的污染提供了理论依据。     

Suicide Inactivation of Catechol 2,3-Dioxygenase from Pseudomonas putida mt-2 by 3-Halocatechols

The inactivation of catechol 2,3-dioxygenase from Pseudomonas putida mt-2 by 3-chloro- and 3-fluorocatechol and the iron-chelating agent Tiron (catechol-3,5-disulfonate) was studied. Whereas inactivation by Tiron is an oxygen-independent and mostly reversible process, inactivation by the 3-halocatechols was only observed in the presence of oxygen and was largely irreversible. The rate constants for inactivation (K₂) were 1.62 × 10⁻³ sec⁻¹ for 3-chlorocatechol and 2.38 × 10⁻³ sec⁻¹ for 3-fluorocatechol. The inhibitor constants (K_i) were 23 μM for 3-chlorocatechol and 17 μM for 3-fluorocatechol. The kinetic data for 3-fluorocatechol could only be obtained in the presence of 2-mercaptoethanol. Besides inactivated enzyme, some 2-hydroxyhexa-2,4-diendioic acid was formed from 3-chlorocatechol, suggesting 5-chloroformyl-2-hydroxypenta-2,4-dienoic acid as the actual suicide product of meta-cleavage. A side product of 3-fluorocatechol cleavage is a yellow compound with the spectral characteristics of a 2-hydroxy-6-oxohexa-2,4-dienoic acid indicating 1,6-cleavage. Rates of inactivation by 3-fluorocatechol were reduced in the presence of superoxide dismutase, catalase, formate, and mannitol, which implies that superoxide anion, hydrogen peroxide, and hydroxyl radical exhibit additional inactivation.