抗原捕获聚合酶链式反应（AC－PCR）直接分型检测单纯疱疹病毒

用抗单纯疱疹病毒（ＨＳＶ）型共同性ｇＣ和ｇＤ羊克隆抗体（ＭｃＡｂ）,包被即Ｅｐｐｅｎｄｏｒｆ管,捕捉ＨＳＶ,同时加入３个引物：一个是ＨＳＶ─１／ＨＳＶ─２型共同性上游引物,另两个分别是ＨＳＶ─１和ＨＳＶ─２型特异性下游引物。借此建立了能直接分型检测ＨＳＶ的抗原捕获聚合酶链式反应（ＡＣ─ＰＣＲ）。ＨＳＶ─１的扩增产物为４７７ｂｐ,ＨＳＶ─２的为３９９ｂｐ两型病毒经ＡＣ─ＰＣＲ扩增后产生分子量不同的ＤＮＡ片段,致使ＡＣ─ＰＣＲ能直接分型检测ＨＳＶ。ＨＳＶ─１和ＨＳＶ─２扩增产物的克隆和序列分析表明,本方法特异性好。用本法检测Ｂａｌｂ／ｃ幼鼠中枢神经系统ＨＳＶ感染的脑标本,进一步证实本方法不仅敏感、特异,而且分型准确。     

乙型肝炎病毒和丙型肝炎病毒的同步PCR扩增

介绍了一种从人血清中同步扩增和检测ＨＢＶ－ＤＮＡ和ＨＣＶ－ＲＮＡ的方法。ＨＣＶ－ＲＮＡ反转录成ｃＤＮＡ,这种ｃＤＮＡ和从ＨＢＶ中抽提出的ＤＮＡ一起,用根据ＨＢＶ、ＨＣＶ保守区序列设计的特异引物进行同步ＰＣＲ扩增,这种方法对于检测ＨＢＶ和ＨＣＶ重复感染很有用处     

RAPD分析快速鉴定双歧杆菌

本文应用ＲＡＰＤ技术,选用１１种引物,以嗜酸乳杆菌为对照,对６种１３珠双歧杆菌菌株基因组ＤＮＡ进行ＰＣＲ扩增,分析其ＤＮＡ指纹图谱,并计算其相似性指数。结果表明,双歧杆菌和非双歧杆菌之间,其相似性指数有显著差异;选择合适的引物进行扩增,双歧杆菌不同种间和同种不同株间可表现不同的ＤＮＡ指纹图谱。本文还对ＲＡＰＤ技术应用于双歧杆菌分类鉴定的可能性进行讨论。     

杂交水稻及其“三系”线粒体DNA的AP—PCR指纹图谱

为了研究水稻（Ｏｒｙｚａ ｓａｔｉｖａ Ｌ．）细胞质雄性不育（ＣＭＳ）与线粒体基因组的关系,应用ＡＰ－ＰＣＲ 分析,用７ 个任意单引物对６ 种水稻品系线粒体ＤＮＡ 进行了扩增。水稻线粒体ＤＮＡ 的ＡＰ－ＰＣＲ 产物可分为三种类型：（１）所有供试品系均能扩增的片段,它们代表了线粒体ＤＮＡ 在进化上的保守性序列。有４ 个引物检测到这类片段。（２）２ 个以上水稻品系共同出现而在全部供试材料间存在差异的扩增片段,这类片段是检测水稻线粒体ＤＮＡ多态性的主要来源。（３）一种细胞质类型所特有的扩增片段,从引物Ｒ２ 和Ｖ５ 的扩增产物中发现了这类片段,它们可能与ＣＭＳ有关联。另外,ＷＡ型不育系珍汕９７Ａ 与其杂种之间在６ 个引物的扩增图谱上均存在不同程度的差异,说明两者的线粒体ＤＮＡ序列结构可能存在某种差别     

多重PCR法检测对皮下和造血器官坏死杆状病毒

根据对虾皮下和造血坏死杆状病毒（ＨＨＮＢＶ）ＨＨＮＢＶ－ＸＩＡ靶基因序列设计了４个多重ＰＣＲ法用引物（Ｐ１、Ｐ２、Ｐ３、Ｐ４）。采用了五种引物组合形式分别对ＨＨＮＢＶ－ＸＩＡ、ＨＨＮＢＶ基因和ＰＲＤＶ－ＪＡＰＡＮ片段进行了物异扩增,建立了多重ＰＣＲ检测ＨＨＮＢＶ方法。通过优化多重ＰＣＲ法检测ＨＨＮＢＶ条件,可从阳性感染的中国对虾ｆｇ级ＤＮＡ中定性检测出皮下和造血器官坏死杆状病毒。     

RAPD在植物育种上的应用及其技术校正

ＲＡＰＤ(ＲａｎｄｏｍＡｍｐｌｉｆｉｅｄＰｏｌｙｍｏｒｐｈｉｃＤＮＡ) ,是在ＰＣＲ的基础上发展起来的一种ＤＮＡ多态性检测技术 ,由Ｗｉｌｌａｍｓ[1] 和Ｗｅｌｓｈ[2 ] 于 1990年建立 ,原理是以一系列不同的 ,少数碱基组成的随机核甘酸序列为引物 ,对样本基因组ＤＮＡ进行ＰＣＲ扩增 ,每个ＲＡＰＤ片段的产生要求在可增范围内存在与引物匹配的反向互补序列。引物结合位点ＤＮＡ序列的改变以及两扩增位点之间碱基的缺失插入或转换都能导致扩增片段的数目和长度的差异 ,经ＰＡＧＥ或琼脂糖凝胶电泳分离和ＥＢ染色来检测ＤＮＡ片段的多态…     

奶山羊β—乳球蛋白cDNA的克隆

从奶山羊乳腺中快速抽提总ＲＮＡ,根据已发表的绵羊β乳球蛋白基因的序列,设计并合成与ｏＢＬＧ基因第一个外显子和最后一个外显子的部分序列相对应并能与特定载体末端互补的一对引物,经反转录－聚合酶链反应（ＲＴ－ＰＣＲ）方法扩增获得了特异性片段。将扩增片段民互性化质粒ｐＤＩＲＥＣＴ退火,获得重组质粒ｐＤＢＬＧ。ＰＣＲ鉴定、限制性分析和分子我均表明已克隆以奶山羊ＢＬＧ的ｃＤＮＡ。     

利用PCR技术行反义寡核苷酸体外抗丁型肝炎病毒基因组RNA中核酶的研究

设计一对ＰＣＲ引物,其中上游引物的５’端除目的基因外,还加Ｔ７ＲＮＡ聚合酶启动子序列,以质粒（ｐＳＶＬＤ３）为模板,通过ＰＣＲ扩增出带有Ｔ７ＲＮＡ聚合酶启动子序列的１３９ｂｐ的ｃＤＮＡ片段,它含有丁型肝炎病毒（ＨＤＶ）基因组ＲＮＡ中核酶（Ｒｉｂｏｚｙｍｅ）区的ｃＤＮＡ该核酶具有自身裂解功能,经测序发现该ｃＤＮＡ有２个碱基变异,以此ＰＣＲ产物为模板,通过Ｔ７ＲＮＡ聚合酶,转录出核酶的前体,并观察到其     

一步法PCR检测大鼠肺支原体核酸的研究

一步法体外扩增结合Ｓｏｕｔｈｅｒｎ杂交检测Ｍ５３鼠肺支原体标准株,设计一对特异寡核苷酸引物及探针,合成、纯化、建立了特异、敏感、快速的检测手段。扩增产物经琼脂糖凝胶电泳鉴定,结果显示鼠肺支原体Ｍ５３株基因组ＤＮＡ７１０ｂｐ特异谱带。对５０只ＳＤ大鼠进行检测,结果ＰＣＲ方法检出率高于分离培养法,扩增产物行Ｓｏｕｔｈｅｒｎｂｌｏｔ杂交验证,采用碱性磷酸酶标记寡核苷酸探针,可与膜上特异靶ＤＮＡ序列杂交,而阴性对照无杂交信号。特异性实验检出１０ｐｇ的ＤＮＡ。充分说明一步法ＰＣＲ,具有高度、特异、灵敏、快速等优势,适应与大、小鼠监测中应用。     

Nested PCR在检测牛白血病病毒前病毒中的应用

用ＮｅｓｔｅｄＰＣＲ检测牛白血病病毒的前病毒形式。从牛白血病病毒基因ｇｐ５１上选择两对引物进行ＮｅｓｔｅｄＰＣＲ体外扩增,产物经２％ａｇａｒｏｓｅ凝胶电泳和用生物素标记的探针鉴定,证实其特异性。结果表明该方法能从两个ＢＡＴ－ＢＬＶ细胞内检测出ＢＬＶ的前病毒ＤＮＡ形式。     

Increased sensitivity of a direct fluorescent antibody test for Legionella pneumophila in bronchoalveolar lavage samples by immunomagnetic separation based on BioMags

In the present study, immunomagnetic separation of Legionella pneumophila from mock bronchoalveolar lavage (BAL) fluid samples, which were artificially spiked with L. pneumophila, and culture positive patient BAL fluid samples, was achieved using BioMags (superparamagnetic particles) loaded with purified rabbit immunoglobulin G specific for L. pneumophila. Bacteria binding onto BioMag-immunomatrix were directly stained with a L. pneumophila species-specific DFA reagent and examined under a fluorescence microscope. BioMag-based immunomagnetic separation (BIMS) followed by DFA staining (BIMS-DFA) could correctly identify all the 20 (100%) BAL samples which were spiked with low numbers (2x10(2) CFU) of L. pneumophila. Cultures could be recovered from 15 (75%) of these 20 spiked BAL samples, 5 (25%) of the samples failed to yield positive cultures. Both culture and BIMS-DFA methods showed 100% positive results when spiked BAL samples containing high bacterial load (10(4) CFU) were tested. The findings with true patient culture positive BAL specimens which were examined retrospectively indicated that BIMS-DFA is significantly more sensitive for detecting L. pneumophila than conventional cytospin method of DFA staining (cytospin-DFA). Out of the 25 culture positive BAL specimens tested, 7 (28%) proved negative by cytospin-DFA whereas BIMS-DFA correctly detected all the 25 (100%) specimens. It is suggested that the BIMS-DFA procedure increases the sensitivity of DFA testing for L. pneumophila in large volume samples such as BAL fluids.     

Evaluation of PCR methods for 5S-rDNA and p30 genes to detect Toxoplasma gondii in blood and other clinical samples

During the last few years the direct diagnosis of Toxoplasma gondii infection has taken advantage of PCR. The present work tested the sensitivity and specificity of PCR for rDNA and p30 genes. Using ascitic fluid from infected mice rDNA PCR detected 0.5 tachyzoite/ml, while nested p30 PCR 1 tachyzoite/ml. The rDNA amplification was positive in all clinical samples from a single immuno compromised patient (blood, urine and bronchoalveolar fluid). In the same patient nested p30 PCR was positive only in urine and bronchoalveolar lavage (BAL) fluid. The rDNA and p30 amplicons were never found in any amniotic fluids tested. These results could prove the usefulness of rDNA amplification to detect T. gondii in blood.     

Development of conventional and real-time NASBA for the detection of Legionella species in respiratory specimens

Isothermal nucleic acid sequence-based amplification (NASBA) was applied to detect Legionella 16S rRNA. The assay was originally developed as a Legionella pneumophila conventional NASBA assay with electrochemiluminescence (ECL) detection and was subsequently adapted to a L. pneumophila real-time NASBA format and a Legionella spp. real-time NASBA using molecular beacons. L. pneumophila RNA prepared from a plasmid construct was used to assess the analytical sensitivity of the assay. The sensitivity of the NASBA assay was 10 molecules of in vitro wild type L. pneumophila RNA and 0.1-1 colony-forming units (CFU) of L. pneumophila. In spiked respiratory specimens, the sensitivity of the NASBA assays was 1-10000 CFU of L. pneumophila serotype 1 depending on the background. After dilution of the nucleic acid extract prior to amplification, 1-10 CFU of L. pneumophila serotype 1 could be detected with both detection methods. Finally, 27 respiratory specimens, well characterized by culture and PCR, collected during a L. pneumophila outbreak, were tested by conventional and real-time NASBAs. All 11 PCR positive samples were positive by conventional NASBA, 9/11 and 10/11 were positive by L. pneumophila real-time NASBA and Legionella spp. real-time NASBA, respectively.     

Enhancement of Legionella pneumophila culture isolation from microenvironments by macrophage infectivity potentiator (mip) gene-specific nested polymerase chain reaction

The combination of a Legionella pneumophila culture isolation technique and macrophage infectivity potentiator (mip) gene-specific nested polymerase chain reaction (PCR) is pivotal for effective routine use in an environmental water system laboratory. Detection of Legionella organisms in 169 environmental samples was performed by using modified buffered charcoal yeast extract (MBCYE) agar for conventional culture. Nested PCR specific for L. pneumophila was performed using boiled genomic DNA extracts from filtered and Chelex 100-treated water samples, or by using silica-gel membrane spin column-eluted DNA from concentrated pond, canal and river samples. Overall, the nested PCR was twelvefold more sensitive than the culture method. The target amplicons (471 basepairs) of all 4 biochemically characterized L. pneumophila isolates were sequenced. They had homology at the DNA and protein levels to 3' proximity of the mip-coding gene of L. pneumophila deposited in genome databases. EcoRI- or KpnI-digested PCR fragments with expected sizes were also confirmed in all 52 PCR-positive samples that were isolated from cooling towers and condenser drains. Viable but nonculturable L. pneumophila might have been present in 48 PCR-positive samples. This study demonstrates that detection of the genetically stable mip gene by nested PCR with a modified process of water sample preparation can be rapidly and effectively used to enhance isolation of the L. pneumophila taxon from microenvironments.     

Targeting species-specific low-affinity 16S rRNA binding sites by using peptide nucleic acids for detection of Legionellae in biofilms

Using fluorescence in situ hybridization to detect bacterial groups has several inherent limitations. DNA probes are generally used, targeting sites on the 16S rRNA. However, much of the 16S rRNA is highly conserved, with variable regions often located in inaccessible areas where secondary structures can restrict probe access. Here, we describe the use of peptide nucleic acid (PNA) probes as a superior alternative to DNA probes, especially when used for environmental samples. A complex bacterial genus (Legionella) was studied, and two probes were designed, one to detect all species and one targeted to Legionella pneumophila. These probes were developed from existing sequences and are targeted to low-binding-affinity sites on the 16S rRNA. In total, 47 strains of Legionella were tested. In all cases, the Legionella spp. PNA probe labeled cells strongly but did not bind to any non-Legionella species. Likewise, the specific L. pneumophila PNA probe labeled only strains of L. pneumophila. By contrast, the equivalent DNA probes performed poorly. To assess the applicability of this method for use on environmental samples, drinking-water biofilms were spiked with a known concentration of L. pneumophila bacteria. Quantifications of the L. pneumophila bacteria were compared using PNA hybridization and standard culture methods. The culture method quantified only 10% of the number of L. pneumophila bacteria found by PNA hybridization. This illustrates the value of this method for use on complex environmental samples, especially where cells may be in a viable but noncultivable state.     

Development and evaluation of a Taqman duplex real-time PCR quantification method for reliable enumeration of Legionella pneumophila in water samples

This study describes the development and evaluation of a specific Legionella pneumophila Taqman duplex real-time PCR (qPCR) for fast and reliable quantification of this human pathogen in suspected man-made water systems. The qPCR assay was 100% specific for all L. pneumophila serogroups 1-15 with a sensitivity of 60 genome units/l and an amplification efficiency of 98%. Amplification inhibitors were detected via an exogenous internal positive control, which was amplified simultaneously with L. pneumophila DNA using its own primer and probe set. Mean recovery rates of the qPCR assay for tap water and cooling circuit water, spiked with a known number L. pneumophila bacteria, were 93.0% and 56.3%, respectively. Additionally, by using the Ultraclean Soil DNA isolation kit, we were able to remove amplification inhibitors ubiquitously present in cooling water. The practical value of our qPCR assay was evaluated through analysis of 30 water samples from showers, taps, eyewash stations, fire sprinklers and recirculation loops with qPCR and traditional culture. In conclusion, the described L. pneumophila Taqman duplex real-time assay proved to be specific, sensitive and reproducible. This makes it a promising method complementing the current time-consuming culture standard method.     

Internally controlled real-time PCR method for quantitative species-specific detection and vapA genotyping of Rhodococcus equi

We developed a novel quantitative real-time PCR (Q-PCR) method for the soil actinomycete Rhodococcus equi, an important horse pathogen and emerging human pathogen. Species-specific quantification was achieved by targeting the chromosomal monocopy gene choE, universally conserved in R. equi. The choE Q-PCR included an internal amplification control (IAC) for identification of false negatives. A second Q-PCR targeted the virulence plasmid gene vapA, carried by most horse isolates but infrequently found in isolates from other sources. The choE-IAC and vapA assays were 100% sensitive and specific as determined using 178 R. equi isolates, 77 nontarget bacteria, and a panel of 60 R. equi isolates with known vapA+ and vapA-negative (including vapB+) plasmid genotypes. The vapA+ frequency among isolate types was as follows: horse, 85%; human, 20%; bovine and pig, 0%; others, 27%. The choE-IAC Q-PCR could detect up to one genome equivalent using R. equi DNA or 100 bacteria/ml using DNA extracted from artificially contaminated horse bronchoalveolar lavage (BAL) fluid. Quantification was linear over a 6-log dynamic range down to approximately 10 target molecules (or 1,000 CFU/ml BAL fluid) with PCR efficiency E of >0.94. The vapA assay had similar performance but appeared unsuitable for accurate (vapA+) R. equi quantification due to variability in target gene or plasmid copy number (1 to 9). The dual-reaction Q-PCR system here reported offers a useful tool to both medical and veterinary diagnostic laboratories for the quantitative detection of R. equi and (optional) vapA+ "horse-pathogenic" genotype determination.     

TNF receptor 1 and 2 contribute in different ways to resistance to Legionella pneumophila-induced mortality in mice

Legionella pneumophila is one of the most important pathogens which cause community-acquired pneumonia. Although TNF-alpha is considered to play an important role in response to bacteria, the role of the TNF-alpha receptor on L. pneumophila infection remains to be elucidated. To investigate this, we infected TNF receptor deficient mice with L. pneumophila. L. pneumophila was inoculated intranasally into TNF receptor (TNFR)-1-knock-out mice or TNFR2-knock-out mice. The mortality rate, histology of the lung, bacterial growth in the lung, and bronchoalveolar lavage (BAL) fluids were investigated. The bacterial growth of L. pneumophila in the macrophages was also studied. Almost all the mice survived after an intranasal inoculation of 1x10(6)CFU/head of L. pneumophila, but more than 90% mice were killed after inoculation of 1x10(8)CFU/head of L. pneumophila. In the case of TNFR1-knock-out mice and TNFR2-knock-out mice, a high mortality rate was observed after inoculation of 1x10(7)CFU/head of L. pneumophila in comparison to wild-type mice. The lung histology from both the TNFR1-knock-out mice documented severe lung injury at day 3 after inoculation. The clearance of L. pneumophila in the lung of the TNFR1-knock-out mice was slower than those from both the TNFR2-knock-out mice and the wild-type mice. Moreover, L. pneumophila growth in the peritoneal macrophages from the TNFR1-knock-out mice was observed. Interestingly, a lack of neutrophils accumulation in the BAL fluids and a dysregulation of cytokines (IFN-gamma, interleukin-12, and TNF-alpha) were observed in the TNFR1-knock-out mice. On the contrary, large accumulation of neutrophils in BAL fluids was observed in TNFR2-knock-out mice. These data suggested that a TNFR1 deficiency led to a compromise of the innate immunity against L. pneumophila, while a TNFR2 deficiency induced an excessive inflammatory response and resulted in death. The present study confirmed that TNFR1 and TNFR2 play a crucial, but different role in the control of L. pneumophila-induced mortality.     

Development and use of the assay for Legionella pneumophila detection based on fluorescent real-time/endpoint polymerase-chain reaction

The aim of the work was to develop a PCR-based assay for detection of L. pneumophila and L. micdadei in environmental samples as well as in clinical samples from low respiratory tract and to assess its analytic characteristics. The assay was used during investigation of the outbreak developed in July 2007 in town Verkhnyaya Pyshma (Sverdlovsk region). Polymerase-chain reaction (PCR)with fluorescent detection,sequencing and cloning of DNA fragments were used. Developed assay based on the PCR with fluorescent real-time/ endpointdetection is able to detect L. pneumophila in clinical and environmental samples and to quantify amount of bacterial DNA in water. Specificity of analysis (100%) was assessed using the panel of bacterial strains and samples from healthy individuals. Analytic sensitivity of assay and quantitation limit was 1000 GU in 1 ml. Sensitivity of the assay of artificially contaminated biological samples was 1000 bacteria in 1 ml. During outbreak investigation L. pneumophila DNAwas detected in 4 lung samples from 4 fatal cases, from 1 of 2 sputum samples, 1 of 2 bronchoalveolar lavage samples with X-ray confirmed pneumonia. Legionella's DNA was found in samples from cooling towers, central hot water supply as well as from showerheads in apartments of 3 patients. Fountain and drinking water samples were PCR-negative. Specificity of PCR-positive results was confirmed by sequencing. Use of the assay during outbreak in- vestigation allowed to confirm the diagnosis in fatal cases and quickly identify the possible source of infection.     

Quantitative TaqMan PCR for detection of Pneumocystis jiroveci

We developed a quantitative real-time PCR assay for detection and quantification of Pneumocystis jiroveci in bronchoalveolar lavage (BAL) specimens based on primers and probe targeting the gene encoding beta-tubulin. The assay was able to detect 50 DNA copies per ml of a standard plasmid containing the target sequence. The intra- and interassay coefficients of variation were 0.46%-4.27% and 0.05-2.00% over 5 log(10) values. Fifty-seven controls of human, viruses, bacteria and fungi DNA samples were amplified and found negative. Fifty-three BAL samples sent to the laboratory for diagnosis of pneumocystosis were prospectively investigated by real-time PCR and direct microscopic examinations (DME) using Giemsa stain and direct immunofluorescence. All PCR negative samples were negative by microscopy. Among the 24 (45%) BAL found PCR positive, 8 were positive by microscopy (35%). The copy numbers of the target gene were between 4.4 x 10(3) and 2.8 x 10(6) per ml for the microscopically positive samples and between 8 and 9.2 x 10(3) per ml for the microscopically negative samples. In conclusion, we developed a rapid, sensitive and specific real time PCR for the diagnosis and quantification of Pneumocystis jiroveci in BAL samples.