Real-time fluorescent quantitative PCR非特异性扩增的研究进展

Real-time fluorescent quantitative PCR(RT-qPCR)因其高效快速、操作简便、高度敏感等优点获得广泛应用,但因其强大的放大功能而容易出现非特异性扩增的问题,尤其是荧光染料法中更加明显。文章对RT-qPCR的原理、非特异性扩增的发生因素、解决方案及该技术的应用前景进行了综述。

Application of Real-time Fluorescent Quantitative PCR in Plant

Real-time fluorescent quantitative PCR （RQ-PCR） is a detection method by adding fluorescent dye or fluorescent probe into the PCR reaction system, using fluorescent signal accumulation to monitor amplification reactions of PCR reaction process, and finally the unknown template can be quantitatively analyzed through the standard curve. So the detection level of PCR has improved from the qualitative to the quantitative. In order to provide a theoretical reference for further application, the principle, classification, advantages and disadvantages of RQ-PCR were intro- duced, and its application and progress in plants in recent years were reviewed.

Detection of Lactobacillus acidophilus in Fermented Material by Real-time Fluorescent Quantitative PCR

The species distinctive PCR primer of Lactobacillus acidophilus （ L. acidophilus） was designed according to 16S rRNA gene sequences of conunon Lac- tobacillus species in fermented material. Bacterial genome DNA of separated L. acidophilus in fermented sample was taken as template, and L. acidophilus in fer- mented material was conducted the quantitative determination by real-time quantitative PCR （RT-PCR）. Analysis on RT-PCR results shown that contents of L. aci- dophilus in the test sample reached 1.5 billion CFU / g. Test results shown that contents of L. acidophilus in fermented material could be detected accurately by the established RT-PCR method in the test. indicating that the established RT-PCR method could be aookued to the detection of L. acidophilus in fermented material.

Application of Real-time Fluorescent Quantitative PCR in Studies on Plants

Real-Lime fluorescent quantitative PCR is a method for quantitative analysis of gene expression developed in recent years, which has been widely used in various fields such as basic scientific research, clinical diagnosis, disease study, drug research and development since its appearance. It starts relatively late in study on plants, but has already been used for analysis of gene expression in plants and gene identification of exogenous genes. The principles or advantages and dis- advantages of real-time fluorescent quantitative PCR, or its potential problems and condition optimizations in tests were introduced in this study, and then the appli- cation and prospect of real-time fluorescent quantitative PCR in study on plants were also been discussed.

Development of Real-Time Fluorescent PCR for Rapid Detection of Haempohlius parasuis

[ Objective] To develop a real-time fluorescent PCR assay for rapid detection of Haempohlius parasuis （HPS）. [ Method] According to the conservative sequences of 16 S rRNA genes of HPS published in GenBank, a pair of specific primers was designed. The real-time fluorescent PCR was developed by optimizing primer concentration and annealing temperature. And its specificity and reproducibility were evaluated. Ten HPS- suspected samples were detected by the developed method. [ Result] The lowest detection limit of the developed real-time fluorescent PCR was 50 copies/μl. This method had good reproducibility, and its coefficient of variation was lower than 2%. Only HPS rather than Streptococcus suis type 2, Staphylococcus aureus, E. coli DH5 alpha, and swine Salmonella typhi could be detected by the developed real-time fluorescent PCR. The HPS-pesitive samples detected by this method were also positive when they were detected by isolation of bacteria or conventional PCR. [ Conclusion] The developed real-time fluorescent PCR is rapid, sensitive, specific and highly reproducible; thus, it can be used for rapid detection of HPS.

Synchronously Detecting Allergenic Ingredients of Peanut and Sesame in Food by Real-time Fluorescent PCR

Peanut,sesame and other raw materials of food are allergens for special populations.In this study,specific primers and TaqMan probes labeled by different fluorescences were designed targeting Ara h 2 gene of peanut and Ses i 1 gene of sesame.After the optimization of reaction conditions,a real-time fluorescent PCR method was established for simultaneous detection of allergenic ingredients of peanut and sesame in food.Genomic DNA samples of peanut,sesame,rice,wheat,barley,soybean,celery,maize,potato,tomato,walnut,groundnut in shell,cashew nut,sunflower seed,almond,apple,pear and strawberry,pork,beef,mutton and fish were used as templates for PCR amplification with deionized water as negative control template.Results indicated that the established real-time fluorescent PCR method could specifically identify allergenic ingredients of peanut and sesame simultaneously.Sensitivity test showed that the minimum detection limit of this method was 0.01%.Therefore,the established real-time fluorescent PCR method is a specific,sensitive and effective assay for simultaneously detecting allergenic ingredients of peanut and sesame in food.

Establishment of a Real-time Fluorescent Quantitative PCR Assay for Detection of Genetically Modified Maize Line MON88017

In order to improve the standardized technical systems of quantitative analyses for genetically modified organisms （GMOs） and products, ensure bio-safety and reduce ecological risk in China, a real-time fluorescent quantitative PCR assay was established for detection of genetically modified maize line MON88017. The established method was evaluated based on the specificity, sensitivity, accuracy and measurement uncertainty. The results showed that the established method had strong specificity in detection of genetically modified maize line MON88017. 1.50% MON88017 sample was detected with 29 replica- tions. The average measured value （ 1. 541% ） was close to the actual value （ 1.50% ） and the relative deviation was 2.70%. The variation coefficient of the measured value was 0.110 g ; the recovery was 100.00% and the measurement uncertainty was 0. 096. The limit of detection for genetically modified maize line MON88017 with the established method was 5 copies at the 97.5% confidence level. Thus, the real-time fluorescent quantitative PCR assay established in this study exhibited high specificity, accuracy and sensitivity, which could provide technical support for the safety supervision of genetically modified organ- isms and products in China.

Effects of Different Temperature and Time Durations of Virus Inactivation on Results of Real-time Fluorescence PCR Testing of COVID-19 Viruses

Summary:The novel coronavirus SARS-CoV-2 caused an outbreak of pneumonia in Wuhan,Hubei province of China in January 2020.This study aims to investigate the effects of different temperature and time durations of virus inactivation on the results of PCR testing for SARS-CoV-2.Twelve patients at the Renmin Hospital of Wuhan University suspected of being infected with SARS-CoV-2 were selected on February 13,2020 and throat swabs were taken.The swabs were stored at room tempcrature(20-25℃),then divided into aliquots and subjected to different temperature for different periods in order to inactivate the viruses(56℃for 30,45,60 min;65,70,80℃for 10,15,20 min).Control aliquots were stored at room temperature for 60 min.Then all aliquots were tested in a real-time fluorescence PCR using primers against SARS-CoV-2.Regardless of inactivation temperature and time,7 of 12 cases(58.3%)tested were positive for SARS-CoV-2 by PCR,and cycle threshold values were similar.These results suggest that virus inactivation parameters exert minimal infuence on PCR test results.Inactivation at 65℃for 10 min may be sufficient to ensure safe,reliable testing.

Detection of Ratoon Stunting Disease in Virus-free Seedcane via Real-time Fluorescence Quantitative PCR

This study was to develop the real-time fluorescence quantitative PCR technique for detecting the ratoon stunting disease （RSD） in virus-free seedcane seedlings. Healthy tissue culture seedlings were obtained from six plants of sugarcane ROC22, which had been confirmed RSD-positive by detecting the sugarcane juice, by employing the sugarcane seedlings production protocol. Real-time fluorescence quantitative PCR was used to detect RSD pathogens in tissue culture sam- pies. The results showed that target fragment of RSD pathogens was not found in all 10 samples in real-time fluorescence quantitative PCR, with the Ct values of 37 - 39. The healthy tissue culture sugarcane seedlings do not carry RSD pathogens, indicating that adopting healthy seedcane seedlings production technique could thoroughly get rid of RSD pathogens.

Development and Preliminary Application of SYBR Green I Real-Time Fluorescence Quantitative PCR Method for Detecting Porcine Parvovirus Virus

According to VP2 gene sequence of the porcine parvovirus virus strain NADL-2 （NC001718） available in GenBank （NC_001718）, a pair of specific primer was designed, and the target fragment of 431 bp was obtained by PCR amplification. The products were ligated with pMD18- T vector and then transformed into bacteria DH5α for recombinant plasmid extraction. After PCR identification and sequencing, recombinant plasmid was used as a standard template to establish the standard curve of SYBR Green I fluorescence quantitative PCR. Sensitivity test, specificity test and repeatability test were also determined. The results indicated that there was a good linear relationship between threshold cycle of the standard curve and template concentration, R2 =0.997 6. Tm ranged from 82.3 to 82.9 ℃, while the sensitivity was 72.1 copies/μl with good specificity and repeatability. The developed SYBR Green I real-time quantitative PCR method to detect PPV VP2 gene laid the basis for further studies on patho- oenesis, early clinical diaonosis of this virus and quantitative analysis of PPV infection.

Development of real-time PCR method for rapid detection and quantification of Heterosigma akashiwo

To rapidly detect the harmful algae H.akashiwo qualitatively and quantitatively, sequences of the 18S rDNA deduced from H.akashiwo were used for designing species-specific primers, and a RFQ-PCR (Real-time Fluorescent Quantitative Polymerase Chain Reaction) method was developed for quantitative detection of H.akashiwo. Primer H.akashiwo and TaqMan probe were designed, and the specificity of primer was checked with PCR. A calibration curve was constructed with cycle threshold value against visual counted cell number. And the value of the curve was tested with other H.akashiwo samples, which were assayed with both the RFQ-PCR method and visual count under microscope.

Primary application of a real-time quantitative polymerase chain reaction for the detection of human breast cancer related novel gene-Metadherin expression

Objective:The aim of this study was to detect the expression level of Metadherin (MTDH) in peripheral blood of the breast cancer patients by real-time fluorescence quantitative polymerase chain reaction (PCR),and to explore the relationship between expression of Metadherin gene in the patients peripheral blood and the clinic-pathological features in breast cancer. Methods:Real-time fluorescence quantitative polymerase chain reaction was employed to determine the expression level of Metadherin gene in 80 peripheral blood samples of breast cancer patients and healthy donors. Results:The expression of Metadherin gene in breast cancer patients peripheral blood were positive,in which 34 breast cancer patients were highly expressed,accounting for 55.7%,while the expression of Metadherin gene in normal females peripheral blood were negative,there was statistical significance (Ratio = 2.02±0.81,P < 0.05); Ratio of the Metadherin expression in breast cancer patients peripheral blood and the glyceraldehyde-3-phosphate dehydrogenase expression was 1.15 ± 0.36. REST software analysis showed that the expression of Metadherin gene was significantly up-regulated in breast cancer. Conclusion:The SYBR Green I quantitative real-time polymerase chain reaction method can successfully detect the expression level of Metadherin gene. Expression level of Metadherin gene in breast cancer patients peripheral blood is closely related to survival,and it maybe involved in the development of breast cancer and used as an indicator of prognosis.

三重荧光PCR技术在食品产气荚膜梭菌毒素基因检测中的应用

目的:建立食品中产气荚膜梭菌常见3种毒素(α、β、ε)的基因cpa、cpb、ext的三重荧光PCR检测方法。方法:设计产气荚膜梭菌的α、β、ε 3种毒素基因的引物和探针,优化退火温度,建立三重荧光PCR方法,探讨其特异性、灵敏度。结果:该方法的特异性较强,仅能检测出产气荚膜梭菌,对其他梭菌与常见食源性致病菌的扩增结果均为阴性;三重荧光PCR体系的检测灵敏度达到0.000 1 ng·μL^(-1)。用建立的方法对实验室样品进行鉴定,发现2份食品样品中有产气荚膜梭菌(均为A型)。结论:本研究建立的三重荧光PCR方法的特异性、灵敏度均较高,且操作简单、检测速度快,适用于食品中产气荚膜梭菌的检测。

麦类粮食3种检疫性病原真菌三重荧光PCR检测方法的建立

麦类壳多胞斑点病菌(Parastagonospora pseudonodorum)、小麦基腐病菌(Oculimacula yallundae)、小麦全蚀病菌(Gaeumannomyces graminis var.tritici)是麦类作物上的重要检疫性病原真菌。建立一种可以同时检测上述3种植物病原真菌的三重荧光PCR方法,可以实现进境麦类粮食中这3种病原真菌的快速准确检疫鉴定。在对麦类壳多胞斑点病菌TUB2基因、小麦基腐病菌ITS1基因、小麦全蚀病菌EF1-α基因单重荧光PCR扩增引物与探针浓度优化的基础上,对三重荧光PCR扩增的引物与探针浓度进行优化,据此进一步对三重荧光PCR扩增程序的退火温度进行优化,建立了可同时检测上述3种植物病原真菌的三重荧光PCR方法,并对该方法的特异性和灵敏度分别进行了验证。结果表明:三重荧光PCR扩增时,TUB2基因、ITS1基因、EF1-α基因的引物与探针最优添加量分别为0.5、0.6和0.6μL,最优退火温度为60℃。特异性验证结果显示,3种靶标菌株均出现了显著扩增;而10株非靶标菌株均未出现扩增,结果为阴性。灵敏度验证结果显示,3种靶标病菌的检测灵敏度分别为41、39、45 fg/μL。本研究建立的三重实时荧光PCR检测方法特异性强、灵敏度高,能够同时快速准确鉴定麦类壳多胞斑点病菌、小麦基腐病菌、小麦全蚀病菌,适用于口岸进境粮食这3种病原真菌的快速准确鉴定。

三重实时荧光PCR检测纯培养物和环境水体中霍乱弧菌方法的建立及应用

本研究建立了检测O1群、O139群、非O1和非O139群霍乱弧菌(Vibrio cholerae)的三重实时荧光PCR方法,并进行纯培养物和环境水体标本的检测评价。根据O1群和O139群霍乱弧菌O抗原编码基因rfb序列和霍乱弧菌种特异的溶血素编码基因hlyA序列设计引物和探针,利用荧光标记物,建立同时检测霍乱弧菌O1群、O139群、非O1和非O139群的三重实时荧光PCR方法,对所建立的方法分别进行了灵敏度和特异性评价,同时与传统培养法进行了比较。研究建立的方法能特异扩增出O1群、O139群、非O1和非O139群霍乱弧菌;而对其它8种弧菌没有扩增;实时荧光PCR检测252份环境水体标本的增菌液,与常规分离方法相比显示了较高灵敏度,所有常规分离方法阳性标本其荧光PCR检测亦为阳性。本研究可用于环境水体样本中霍乱弧菌常规分离前的快速筛查和纯培养物的确认。

基于全自动核酸提取的荧光定量PCR鉴别羊肉制品真伪

目的建立一种基于自动化的快速核酸提取方法,联合三重实时荧光定量PCR技术,鉴别羊肉制品的真伪。方法分别采用全自动核酸提取法、磁珠手提法与柱提法对不同状态羊肉制品进行核酸提取,比较不同方法的提取时间差异,通过三重实时荧光定量PCR扩增结果评估不同方法的提取效果。以GB/T38164—2019《常见畜禽动物源性成分检测方法实时荧光PCR法》为对照,对市售的羊肉制品进行平行检测,评估本方法的检测性能。结果与磁珠手提法、柱提法相比,全自动核酸提取法的提取时间缩短了15~30 min,且提取的核酸扩增效果更好。全自动核酸提取法在羊猪混合样品中羊源核酸检出限为0.010mg/g。全自动核酸提取法在生鲜肉、生肉及熟肉制品等多种类型产品中提取的羊源核酸PCR检测结果的变异系数(coefficient of variation,CV)均小于3.000%。分别采用三重实时荧光定量PCR法与GB/T38164—2019对全自动提取的21份市售的涵盖不同类型的羊肉制品核酸进行平行检测,符合率为100.00%。结论本研究方法可为羊肉制品掺假的快速真伪鉴别提供操作简便、稳定灵敏、快速准确的整套解决方案。

三重荧光PCR检测沙门氏菌、金黄色葡萄球菌和大肠埃希氏菌O157:H7

目的建立一种检验沙门氏菌、金黄色葡萄球菌、大肠埃希氏菌O157:H7的TaqMan探针三重荧光PCR方法。方法针对沙门氏菌属特异性invA基因、金黄色葡萄球菌rpoB基因、大肠埃希氏菌O157:H7的rfbE基因设计引物与探针,建立三重荧光PCR体系,对引物与探针浓度及退火温度优化,并进行特异性和敏感性研究。结果引物与探针的最优添加量为:invA 0.2μL、ropB 0.4μL、rfbE 0.5μL;最优退火温度为60℃。特异性试验显示16株非目标菌株扩增结果为阴性;目标菌株均出现显著扩增。敏感性试验显示,3种微生物对应的最低菌体数量检出量依次为:230、38、670 CFU。结论该方法特异性好、灵敏度高,能够快速检测沙门氏菌、金黄色葡萄球菌、大肠埃希氏菌O157:H7。

基于P72、MGF和CD2v基因的非洲猪瘟三重荧光定量PCR检测方法的建立

非洲猪瘟在临床上出现多种毒株,主要分为野毒株和基因变异毒株。因其在临床上造成不同程度的危害,有必要建立一种方法进行正确诊断和健康监测。为实现野毒株和基因变异毒株的鉴别诊断,研究根据GenBank中的ASFV中国流行株(登录号:MK333180.1)的P72、CD2v、MGF基因保守序列设计引物,建立一种可以同时检测上述三种基因的三重荧光定量PCR方法。三重荧光定量PCR方法对猪细小病毒(PPV)、猪伪狂犬病病毒2型(PRV)和猪圆环病毒(PCV2)检测均无交叉反应,表现出较强的特异性。敏感性检测显示针对P72、CD2v和MGF重组质粒标准品的最低检测下限为103~102 copies/mL。在重复性试验中,大部分组间变异系数均小于2%或接近2%,具有较好的重复性。试验表明,三重荧光定量PCR方法可用来鉴别野毒株和基因变异毒株。

诺如病毒和轮状病毒三重荧光定量PCR检测方法的建立

为了建立一种能同时检测GI型诺如病毒(GI-NV)、GII型诺如病毒(GII-NV)和A群轮状病毒(A-RV)的三重荧光定量PCR检测方法,本试验根据GI-NV和GII-NV的开放阅读框1(Orf1)与开放阅读框2(Orf2)基因之间保守序列、A-RV的非结构蛋白3(Nsp3)基因保守序列,分别设计合成3对特异性引物和3个TaqMan探针,人工合成含有目标序列的基因,制备重组质粒标准品,绘制标准曲线,并对该检测方法的特异性、灵敏度、重复性进行评估。同时通过检测收集的109份动物源食品样品,对建立的方法与商品化试剂盒进行检测比对。结果显示:该方法可以特异性地区分GI-NV、GII-NV和A-RV,而与其他病原无交叉反应;该方法的最低检出限均为1×102 copies/μL的质粒标准品,具有较高的敏感性;组内和组间重复性试验结果显示,变异系数均小于5%,重复性较好;该方法与商品化的试剂盒检测结果符合率为100%。结果表明,本试验建立的检测方法能够快速、准确区分GI-NV、GII-NV和A-RV。

布鲁氏菌、弓形虫及巴尔通体多重TaqMan荧光PCR检测方法的建立及应用

为建立一种应用于宠物布鲁氏菌、弓形虫及巴尔通体的高通量、高灵敏、高特异的检测方法,根据各自保守序列合成了特异性引物及TaqMan探针,通过优化反应体系,建立了多重TaqMan荧光PCR检测方法,并利用该方法对2021年厦门市抽检的304份犬猫全血样品进行了检测。结果显示:该方法特异性好,可特异性扩增布鲁氏菌、弓形虫和巴尔通体阳性核酸,其他对照菌株核酸均无扩增信号;抗干扰性强,检测混合模板时,不同成分间无交叉干扰反应;灵敏度高,最低检出限均为3×10^(0)copies/μL;重复性好,批内及批间重复试验变异系数均小于2%。应用该方法在4 h内即可完成304份临床样品的快速检测,此次临床抽检样品中未检出布鲁氏菌、弓形虫及巴尔通体阳性核酸。该方法大大提高了检测效率,为多种动物布鲁氏菌、弓形虫及巴尔通体感染的早期诊断及筛查提供了技术支持。