Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method

We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-μL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.     

新型冠状病毒纳米PCR快速检测方法的建立

新型冠状病毒(SARS-CoV-2)感染可导致致命性肺炎,且极具传染性。自2019年年末在我国出现以来,已在全球蔓延。为了建立一种灵敏、快速检测SARS-CoV-2的分子检测方法,本研究使用金纳米颗粒配合普通PCR检测方法,针对SARS-CoV-2核衣壳蛋白建立了SARS-CoV-2 NanoPCR新型分子检测方法。特异性结果显示,该方法对猪流行性腹泻病毒、牛冠状病毒、犬冠状病毒、水貂冠状病毒、猫传染性腹膜炎病毒均无交叉反应,表明该方法的特异性良好。敏感性结果显示,该方法的最低检测量为3.69×10⁴拷贝/μL,高于普通PCR最低检测量10倍,表明该方法的敏感性良好。使用建立的方法对3份临床样品进行检测,该方法与普通PCR方法结果一致,10倍稀释样品后,NanoPCR相比较普通PCR条带仍然具有较高辨识度。综上,本研究建立的灵敏、特异的NanoPCR方法可以对临床样品进行快速诊断和鉴定。     

香茄环斑病毒HC—RT—PCR—ELISA检测

番茄环斑病毒（ToRSV)是我国对外检疫一类有害生物。目前国内尚无存在的报道。PCR技术是一种快速灵敏的植物病毒检测方法,但核酸内的聚合酶抑制物会导致漏检现象。而只通过凝胶电泳进行结果判定会出现假阳性,这两方面限制了PCR技术在对外检疫中的应用,利用共价结合在PCR管壁上的引物特异性杂交诱捕核酸粗提液中的靶标核酸,洗掉杂质及抑制物质,在同一管内作RT-PCR,凝胶电泳检测液相产物的同时对固相产物进行杂交检测。提高了结果的可靠性及灵敏度。利用所建立的HC-RT-PCR-ELISA成功地从法国进口葡萄苗中检出ToRSV。本方法可用于其他植物病毒及转基因产品的检测。     

A comparison between a PCR method and a conventional culture method for detecting pathogenic Yersinia enterocolitica in food

S. THISTED LAMBERTZ, A. BALLAGI-PORDÁNY, A. NILSSON, P. NORBERG AND M.-L. DANIELSSON-THAM. 1996. The aim of this study was to develop a polymerase chain reaction (PCR) method for the detection of pathogenic Yersinia enterocolitica and to compare it with an official culture method (NMKL-117). Primers were selected for nested PCR directed at the attachment invasion locus, ail , on the bacterial chromosome, as well as at a sequence on the pathogenic marker plasmid, termed virulence factor, virF. The final results obtained by the two methods were similar. However, while the conventional method yielded contradictory data for some steps the PCR method provided unambiguous results. Considerable advantages, i.e. higher sensitivity and specificity of the PCR method, compared with the conventional method for detecting pathogenic Y. enterocolitica , were demonstrated in this study.     

Angiotensin-converting enzyme insertion/deletion polymorphism genotyping error: the cause and a possible solution to the problem

Rigat and colleagues were the first ones to develop a rapid PCR-based assay for identifying the angiotensin converting enzyme insertion/deletion (I/D) polymorphism. Due to a big difference between the length of the wild-type and mute alleles the PCR method is prone to mistyping because of preferential amplification of the D allele causing depicting I/D heterozygotes as D/D homozygotes. The aim of this study was to investigate whether this preferential amplification can be repressed by amplifying a longer DNA fragment in a so called Long PCR protocol. We also aimed to compare the results of genotyping using five different PCR protocols and to estimate the mistyping rate. The study included 200 samples which were genotyped using standard method used in our laboratory, a stepdown PCR, PCR protocol with the inclusion of 4 % DMSO, PCR with the use of insertion specific primers and new Long PCR method. The results of this study have shown that accurate ACE I/D polymorphism genotyping can be accomplished with the standard and the Long PCR method. Also, as of our results, accurate ACE I/D polymorphism genotyping can be accomplished regardless of the method used. Therefore, if the standard method is optimized more cautiously, accurate results can be obtained by this simple, inexpensive and rapid PCR protocol.     

Evaluation of real-time PCR vs automated ELISA and a conventional culture method using a semi-solid medium for detection of Salmonella

AIMS: Evaluation of iQ-Check PCR Salmonella for Salmonella detection in artificially and naturally contaminated food and environmental field samples. METHODS AND RESULTS: Artificially contaminated samples (poultry meat and ground red meat) subjected to cold- and freeze-stress, and 120 naturally contaminated samples (swabs and meat) were tested for Salmonella using the diagnostic semi-solid Salmonella medium (DIASALM) method, the Vidas assay and the iQ-Check PCR assay after 24 h enrichment in buffered peptone water. CONCLUSIONS: Both the iQ-Check PCR and the Vidas assay provide a rapid and user friendly screening method for detection of Salmonella. False negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed. In total 45 of 120 naturally contaminated field samples showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was respectively 92% for the iQ-Check PCR and 95% for the Vidas method. SIGNIFICANCE AND IMPACT OF THE STUDY: False-negative samples were obtained for the inoculated samples using both the iQ-Check PCR assay and the Vidas method when Salmonella cells were severely stressed, e.g. freezing at -18 degrees C for 7 days. Of the 120 naturally contaminated field samples 45 showed Salmonella positive using the DIASALM method. The agreement percentage with the DIASALM method was 92% for the iQ-Check PCR and 95% for the Vidas method respectively.     

High-Resolution Detection of PCR Products from a Microsatellite Marker Using a Nonradioisotopic Technique

We report a safe, rapid, and economical method for polymerase chain reaction (PCR)-based genotype analysis using a microsatellite marker specific for the human chromosome 18 locus, D18S53. This method does not involve radioisotopes and makes use of ethidium bromide fluorescence to detect PCR products. Our method enables direct analysis and easy detection of PCR products on nondenaturing polyacrylamide gels. The genotyping using this method can be scaled up to 100 samples at one time by adding a step of “double loading” of samples in a single sequencing size gel. We could resolve PCR products and DNA fragments, differing in size by only 2 bp, in the range of 150–200 bp by a 7% nondenaturing polyacrylamide gel. This technique can be applied for population-based genomic screening and linkage analysis.     

Development of a highly sensitive nested-PCR procedure using a single closed tube for detection of Erwinia amylovora in asymptomatic plant material

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 microl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity.     

PCR detection of Listeria monocytogenes: a study of multiple factors affecting sensitivity

AIMS: To test, under comparable conditions, several parameters affecting sensitivity of PCR detection in order to establish a PCR procedure suitable for the routine detection of Listeria monocytogenes in food. METHODS AND RESULTS: Beef samples artificially inoculated were used to determine sensitivity of PCR detection under different parameters. As few as 1 CFU g(-1) were detected by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) of 1 ml aliquot and PCR amplification with primers directed to the hlyA gene. This PCR protocol was applied in 60 naturally contaminated foods, comparing two enrichment procedures with the traditional culture method. The highest number of positives was recorded by PCR following a 24-h pre-enrichment step at 30 degrees C and a 24-h enrichment step at 37 degrees C. Afterwards, it was applied in 217 naturally contaminated foods and 56 of them tested positive for L. monocytogenes in which only 17 tested positive using the culture method. CONCLUSIONS: The PCR procedure described has proved to be a rapid and sensitive method suitable for the routine analysis of different types of food. SIGNIFICANCE AND IMPACT OF THE STUDY: The method proposed for the detection of L. monocytogenes, has been validated in naturally contaminated food and is suitable to implement in the food industry.     

应用实时荧光PCR技术检测构巢曲霉的初步研究

目的 根据构巢曲霉（Aspergillus nidulans）3-磷酸甘油醛脱氢酶（Glyceraldehyde-3-phosphate dehydrogenase,GAPDH）基因特异位点设计并合成Taqman探针及引物,建立构巢曲霉实时荧光 PCR检测方法。方法 应用lasergene7.1软件对构巢曲霉与13种常见曲霉主要包括黑曲霉（A.niger）、烟曲霉（A.fumigatus）、杂色曲霉（A.versicolor）、土曲霉（A.terrus）、黄曲霉（A. flavus）、温特曲霉（A.wentii）、寄生曲霉（A. parasiticus）、泡盛曲霉（A.awamori）、米曲霉（A. oryzae ）、棒曲霉（A.cavatus）、赤曲霉（A.ruber ）、亮白曲霉（A.ochraceus）及赭曲霉（A.ochraceus）GAPDH基因序列比对分析,在特异位点设计引物和探针,建立构巢曲霉实时荧光 PCR检测方法,并对该方法进行特异性及敏感性分析。结果 用曲霉属22种41株不同曲霉及其他属的12株病原真菌验证实验表明,所建立的荧光PCR方法特异性强;检测灵敏度可达4.03×10－12μg/ml的模板DNA。 结论 应用实时荧光PCR技术能够有效检测构巢曲霉,该方法具有特异、灵敏、快速等特点,可在实际工作中应用。     

利用混合样本池法对鸡显性白羽基因PMEL17突变位点的检测

显性白羽基因座是影响鸡羽色形成的重要基因座位之一, 该基因座上的显性等位基因I 会抑制黑色素合成, 从而使携带该基因的个体全身羽毛呈现白色。目前已确认鸡显性白羽基因座编码PMEL17蛋白: 是一种黑素细胞特异性蛋白, 在黑素细胞的分化与成熟中起到重要作用, 并证明PMEL17基因的突变与显性白羽的形成有关。文章利用混合样本池建立了一种低成本、高效率, 并能在大规模群体中检测PMEL17基因突变的方法, 称为PCR产物混合样本池法。该方法的基本步骤如下: 首先, 提取个体基因组DNA, 并设计相关引物对每一个体单独进行PCR扩增; 其次, 将PCR产物等比例混合, 10个样品混在一个池中; 然后, 将PCR产物混合池样品于非变性聚丙烯酰胺凝胶上进行电泳; 最后, 待电泳结束后进行银染, 根据凝胶上所显条带判定是否存在突变体。此外, 文章还将这种方法与传统基因组DNA混合样本池法进行了比较试验, 并利用该方法对试验鸡群显性白羽基因PMEL17突变进行检测, 证实该方法具有较高准确度。     

食用菌SSR序列开发策略研究进展

SSR序列开发策略主要有3大类:传统的基因文库筛选法、GenBank筛选法和富集文库筛选法。文中在对传统的基因文库筛选法、GenBank筛选法的优缺点及在食用菌SSR分子标记的开发应用进行综述的基础上,重点综述了富集文库筛选法,即基于RAPD技术的SSR开发策略、SSR兼并引物法、序列标签法构建SSR富集文库、vectorette PCR染色体步移法分离SSR位点、Suppression PCR染色体步移法分离SSR位点、引物延伸法构建SSR富集文库以及SSR杂交捕获法构建SSR富集文库的具体设计原理和步骤,并提出食用菌中SSR分子标识的开发现状和展望。     

Calibration-curve-free quantitative PCR: a quantitative method for specific nucleic acid sequences without using calibration curves

We have developed a simple quantitative method for specific nucleic acid sequences without using calibration curves. This method is based on the combined use of competitive polymerase chain reaction (PCR) and fluorescence quenching. We amplified a gene of interest (target) from DNA samples and an internal standard (competitor) with a sequence-specific fluorescent probe using PCR and measured the fluorescence intensities before and after PCR. The fluorescence of the probe is quenched on hybridization with the target by guanine bases, whereas the fluorescence is not quenched on hybridization with the competitor. Therefore, quench rate (i.e., fluorescence intensity after PCR divided by fluorescence intensity before PCR) is always proportional to the ratio of the target to the competitor. Consequently, we can calculate the ratio from quench rate without using a calibration curve and then calculate the initial copy number of the target from the ratio and the initial copy number of the competitor. We successfully quantified the copy number of a recombinant DNA of genetically modified (GM) soybean and estimated the GM soybean contents. This method will be particularly useful for rapid field tests of the specific gene contamination in samples.     

Development of a Highly Sensitive Nested-PCR Procedure Using a Single Closed Tube for Detection of Erwinia amylovora in Asymptomatic Plant Material

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 μl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity.     

Development of a PCR assay combined with a short enrichment culture for detection of Campylobacter jejuni in estuarine surface waters

Abstract Two extraction procedures were examined, and it was found that DNA recovered from Campylobacter jejuni lysed by the cetyltrimethylammonium bromide (CTAB) method was more suitable for use as a PCR template than DNA released by the boiling method. The region targeted for PCR amplification was a 1.73-kb portion of the flagellin A gene of C. jejuni . The detection limit was lower than 30 cells per 100 ml in artificially contaminated waters. PCR assay and conventional culturing method had the same sensitivity, but results of the PCR technique were available within 48 h and so shortened the time necessary for detection by 48 h.     

The use of melting curves as a novel approach for validation of real-time PCR instruments

Validation of PCR thermal cycler performance is crucial in order to obtain reliable results. In this study, high resolution melting curve (HRM) analysis is presented as a novel validation method for real-time PCR instruments. By applying HRM analysis using a defined PCR amplicon and EvaGreen dye, information about the temperature accuracy and thermal homogeneity of the heating block was obtained. This pilot study shows the potential of our technique for temperature validation of real-time quantitative PCR thermal cyclers. Our data correlated well with the temperature accuracy data obtained from the Mobile Temperature Acquisition System (MTAS; r2 = 0.93), which conforms to the National Institute of Standards and Technology criteria, and our method was reproducible in independent runs (r2 = 0.95). The advantages of this HRM-based method include: (i) temperature measurement under real world conditions in the reaction liquid in closed reaction tubes; (ii) temperature measurement of all wells; and (iii) applicability to all real-time PCR instruments capable of HRM analysis.     

Rapid detection and identification of Streptococcus ratti by a species-specific PCR method

To establish a rapid and species-specific detection and identification method of Streptococcus ratti by polymerase chain reaction, two PCR primer pairs specific to S. ratti were designed on the basis of the nucleotide sequence of the dextranase gene (dex) of S. ratti ATCC19645(T). The primer pairs specifically detected S. ratti, but none of the other mutans streptococci (16 strains of 6 species). The PCR procedure was capable of detecting 1 pg of genomic DNA purified from S. ratti ATCC19645. We developed the Streptococcus mutans-, Streptococcus sobrinus-, Streptococcus downei- and Streptococcus salivarius-specific PCR methods (the dex PCR methods) with the primer pairs specific for a portion of the dex gene of each species. The mixture of these primer pairs including S. ratti (this study) successfully differentiated the five species of mutans streptococci by species-specific amplicons of different lengths. These results suggest that the present PCR method is suitable for the specific detection and identification of S. ratti, and that the mixture of primer pairs for the dex PCR methods is useful for species-specific detection and rapid discrimination of each species in mutans streptococci.     

Accurate and efficient data processing for quantitative real-time PCR using a tripartite plant virus as a model

Real-time PCR is becoming a preferred method for quantification of minute amounts of nucleic acids. To achieve the full potential of this technique, accurate and convenient models for post-PCR data analysis are required. In this study, three different models were chosen to quantify the definitive copy numbers of Cucumber mosaic virus (CMV) genomic RNAs using raw fluorescence data of real-time PCR, and equations were proposed to compare their expression levels in virions or in planta. The results, as confirmed by standard curve and Northern blotting methods, show that the expression levels of different genes can be compared more accurately and more efficiently by these equations, especially using theoretical fluorescence (F0) and calibration factors (CF), determined by linear regression PCR (LinRegPCR). Thus, these equations, combined with data analysis by the LinRegPCR method, can greatly enhance the high-throughput quantification ability of real-time PCR, and permit accurate, reliable, and facile investigation of the changes in CMV RNAs accumulation.     

Detection of Shigella spp. in food with a nested PCR method – sensitivity and performance compared with a conventional culture method

A nested PCR method was developed and its performance evaluated by detection of Shigella flexneri in food. The nested PCR amplifies sequences within an invasion-associated locus (ial) on the invasion plasmid specific for Shigella and enteroinvasive Eschrichia coli (EIEC). The nested PCR detected Sh. flexneri in lettuce inoculated with 2, 20 and 200 cfu g-1 after 1, 7 and 18 d of storage, respectively. In comparison, a culture method (NMKL no. 151) detected 10(5) cfu g-1 after 1 but not after 7 d of storage. The presence of inhibitors in blue cheese and shrimps reduced the sensitivity of the PCR assay. To overcome this inhibition, a sample preparation step based on buoyant density centrifugation was developed. This treatment resulted in a successful recovery of Sh. flexneri in lettuce, milk, shrimp and blue cheese inoculated with 10 cfu g-1. The proposed method, which includes a combination of enrichment, buoyant density centrifugation and a nested PCR, can be completed in less than two working days.