Quantitative detection of species-specific DNA in feedstuffs and fish meals

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species-derived material in concentrate feed mixtures and fish meals.     

Towards a quantitative application of real-time PCR technique for fish DNA detection in feedstuffs

A real-time PCR method to detect fish DNA in feedstuffs was developed and optimised. A combination of primers and a Taqman-MGB probe was used to selectively amplify the fish mitochondrial 12S ribosomal RNA gene. Qualitative and also quantitative assessments were performed with different protocols: a relative quantification by a standard curve, and a ΔC_T method, by total plant DNA as endogenous controls. Method specificity was evaluated analysing 40 different tissues (mammalians, avian, fish) and flour samples. Sensitivity was evaluated by LOD (limit of detection) estimation. The designed probe–primers set showed an increased sensitivity compared to previously published PCR end point method, reaching a limit of detection of 0.2 pg of fish DNA, and showing to be a robust assay for fish DNA detection. The quantification results, based on ΔC_T method and the relative standard curve, are well reproducible in our experimental condition but, in lacking of separate pure raw materials of a tested feed, they cannot be applied for reliable and precise quantification on field samples but for now as a semi-quantitative PCR method only.     

Standard and Light-Cycler PCR methods for animal DNA species detection in animal feedstuffs

In this work four species-specific primers and probes were designed and evaluated for the detection and quantification of bovine, ovine, swine and chicken mitochondrial DNA in feeds. PCR primers were optimized using conventional and Real Time PCR, to detect short species-specific sequences amplifiable from heat treated material. Both methods confirmed the high specificity of the primers designed. Real time quantitative PCR assay allowed the detection of as few as 0.01 ng and 0.05 ng of ovine and bovine genomic DNA, respectively. The detection limit for swine and chicken genomic DNA was 0.5 ng. Sensitivity levels observed in DNA extracted from meat samples processed according to EU legislation were different compared to those in genomic DNAs previously described. They resulted in swine 5 fg of MBM DNA, in chicken 25 ng, in ovine and bovine 50 ng. We confirmed the efficiency and specificity of primers in RT-PCR to detect 0.5% of bovine, ovine, swine and chicken MBM in contaminated feedstuffs.Industrial relevanceThe variant Creutzfeldt Jakob disease is a rare and fatal human neurodegenerative condition clearly linked with the bovine spongiform encephalopathies (BSE) of cattle. The ban of using animal derived protein in animal feeds has efficiently controlled the development of the BSE epidemic. The work presented by Frezza and collaborators is an application of the real time polymerase chain reaction (a standard procedure used in molecular biology also known as RT‐PCR) to identify specific DNA of four animal species (bovine, ovine, swine and chicken). This method is applied to the analysis of feeds to detect and eventually estimate the amount of animal derived proteins. The difficult aim to detect DNA derived from heat‐treated material was successfully reached using as target short mitochondrial DNA sequences. The method presented could have important application not only in the control of feed production but also in many fields of the food industry as quality and process control.     

SYBR-Green real-time PCR approach for the detection and quantification of pig DNA in feedstuffs

A real-time polymerase chain reaction assay using primers targeting the porcine-specific mitochondrial 12S rRNA gene and universal eukaryotic primers amplifying a conserved fragment of the nuclear 18S rRNA gene has been developed for the detection and quantification of porcine DNA in food and feedstuffs. The 18S rRNA primers were used as endogenous control for the total content of PCR-amplifiable DNA in the sample. The assay was tested on DNA extracted from raw and heat-treated binary mixtures of porcine tissues in a plant matrix, and on DNA extracted from reference feedstuff samples. Analysis of experimental mixtures demonstrated the suitability of the assay for the detection and quantification of porcine DNA in mixtures containing as little as 0.1%.     

实时荧光定量PCR在食品检测领域中应用

实时荧光定量PCR是在定性PCR技术基础上发展起来的核酸定量技术;该技术不仅实现对DNA模板定量,且具有灵敏度高、特异性强、无污染性、及实时性和准确性等特点。该文主要介绍实时荧光定量PCR原理和在食品检测中应用,及其在食品领域发展前景。     

Modelling the limit of detection in real-time quantitative PCR

The limit of detection (LOD) is a critical performance characteristic of an assay that requires careful evaluation during method validation. However, formal calculations for the LOD do not take into account atypical data sets that are generated from real-time PCR techniques, which can be non-normally distributed, truncated, and heteroscedastic. Experimental data sets for the quantification of genetically modified (GM) material were produced using real-time PCR, in order to model the LOD. A bootstrapping computer simulation calculated the probabilities of detecting PCR positive test results from these data sets, and computer modelling defined a function from the resulting probability plots. The LOD was modelled as a function of sample replication level and cycle threshold values. The broad applicability of this bootstrapping and data modelling approach should be of general interest to laboratories conducting trace-level detection.     

实时荧光定量PCR技术在食用油脂检测中的应用

荧光定量PCR检测技术具有快速、准确的优点,在转基因食品检测等领域得到了广泛的应用。采用荧光定量PCR技术进行油脂转基因、掺假检测也成为研究热点。利用不同油料作物所含有的独特核酸序列,采用荧光定量PCR技术可简单、高效、快速地检测出油脂中所含的特定核酸成分,从而判定油脂原料的构成,为打击食用油脂掺假造假提供判定依据。植物油的加工过程中都经过多个步骤的处理,其中的核酸降解严重,含量极低,所以从植物油中提取出较高质量的DNA是对油脂进行荧光定量PCR检测鉴定的关键。本文主要对油脂DNA提取方法及存在的难点、引物设计特点和结果分析进行了论述,以期为今后荧光定量PCR检测技术进一步推广与应用提供思路。     

实时荧光定量技术在食品微生物检测和研究中的应用

实时荧光定量PCR技术是通过检测PCR产物中荧光讯号强度来达到定量的目的,不仅实现了对核酸信息量的分析比较,而且与常规PCR相比,它具有特异性更强、能有效解决PCR污染问题、自动化程度高等特点。文章概述了实时荧光定量PCR技术的原理、优缺点及其在食品微生物检测中的应用与研究进展,并探讨了它的技术发展和应用前景。     

实时荧光定量PCR在食品致病菌及转基因成分检测中应用

与传统定性PCR技术相比,实时荧光定量PCR有更多的优点,其速度快,特异性更强、灵敏度更高、无污染性、自动化水平高等,且能对DNA模板进行定量。本文综述了实时荧光定量PCR技术原理、分类及其应用,并对其存在的问题和发展前景进行了展望。     

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79?bp fragment of the mitochondrial (mt) 12?S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18?S rRNA gene system, yielding a 77?bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.     

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79?bp fragment of the mitochondrial (mt) 12?S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18?S rRNA gene system, yielding a 77?bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.     

实时荧光定量PCR技术快速检测志贺氏菌

目的 建立实时荧光定量PCR法快速检测志贺氏菌。方法 提取志贺氏菌基因组为模板扩增virA基因片段, 将目的片段连接至pMD19-T载体得到重组质粒, 转化大肠杆菌DH5α感受态细胞, 验证所得到的重组质粒, 以紫外分光光度计测量重组质粒吸光度值A260, 并换算为质粒拷贝数后作梯度稀释得到不同浓度的质粒标准品; 进行荧光定量PCR分析并通过特异性、灵敏性实验以验证该方法的可行性。结果 重组质粒标准品浓度在103~108 copies/μL范围内线性关系良好(r2>0.99), 实时荧光定量PCR检测志贺氏菌时出现良好的扩增曲线, 鼠伤寒沙门氏菌、金黄色葡萄球菌和大肠杆菌均未出现扩增曲线。志贺氏菌的检出限为100 CFU/mL。 结论 本方法便捷、高效、可靠, 可用于志贺氏菌的快速定性定量检测。     

Two quantitative hexaplex real-time PCR systems for the detection and quantification of DNA from twelve allergens in food

According to the EU and Swiss legislation, allergens in food have to be labelled. Consumers, exhibiting allergic reaction, must be able to avoid such food and its products. In order to provide efficient and reliable methods, two novel hexaplex quantitative real-time polymerase chain reaction systems were developed and validated. The first system simultaneously determines DNA contents from cashew, peanut, hazelnut, celery, soy, mustard, whereas the second system determines DNA contents from milk (beef), egg (chicken), almonds, sesame, pistachio and walnut. The two tests exhibited a good specificity and a detection limit of at least 0.1?% for all analytes. This was additionally verified using samples from proficiency tests. Application on samples from the market revealed realistic and useful information about allergen contents. Quantitative results according to weight are not possible yet.     

实时荧光定量PCR技术在粮油转基因成分检测中的应用

随着转基因技术在谷物育种中的广泛应用,以及转基因粮油及其制品消费的不断增加,加强粮油转基因成分的检测技术的研究极为必要.阐述了实时荧光定量PCR技术在粮油转基因成分检测中的应用,主要从实时荧光定量PCR技术,实验室条件,实验步骤以及应用范围等方面进行了阐述.     

实时荧光定量PCR技术在肉及肉制品中的应用

实时荧光定量PCR技术作为一种DNA定量检测的工具,可应用于肉制品种类鉴别和定量分析中。相比于传统感官和理化的鉴别方法,该技术具有灵敏性高、特异性强、操作简便、省时省力等特点。使用Taq Man荧光探针和荧光染料可以直接测定PCR循环后产物的总量,确定扩增DNA片段的种类及数量,从而确定肉品种类及添加量。因此,可以将该技术应用到肉制品成分及安全的检测中。本文介绍了实时荧光定量PCR技术的基本原理,主要综述了该技术在肉品种类鉴定方面的应用,简述其在肉制品细菌污染检测的应用,并对该技术在肉类研究中的应用进行展望。      

Targets and methods for the detection of processed animal proteins in animal feedstuffs

Bovine spongiform encephalopathy (BSE), or ‘mad cow disease’, is one of several transmissable spongiform encephalopathies (TSEs) known to affect certain mammals and is spread through the ingestion of infected animal tissue. It is believed that the inadvertent contamination of meat and bone meal (MBM) with infected animal tissue and the subsequent use of this material as a feed supplement contributed to the spread of the disease in cattle. As a result, the use of processed animal proteins (PAPs) in animal feeds is regulated in many parts of the world. Although feed testing is the only definitive means to certify compliance, regulatory compliance often relies solely on paper certification. Recently, rapid methods have become available that can be used by regulators to determine compliance during routine inspections. We describe a rapid, immunochromatographic strip test that can detect 0.1% MBM in animal feed. The test takes 15 min to perform and large numbers of samples can be screened for PAPs simultaneously.     

Rapid detection and identification of Streptococcus macedonicus by species-specific PCR and DNA hybridisation

The aim of this study was to develop a simple and specific method for the rapid detection and identification of Streptococcus macedonicus. The method was based on polymerase chain reaction (PCR) using species-specific primers derived from the 16S rRNA gene. Specific identification was proven on seven S. macedonicus strains, while 16 strains belonging to different lactic acid bacteria species were tested negative. The PCR assay was capable of detecting 100 pg of S. macedonicus DNA, and it was also efficient on single colonies of the bacterium. Furthermore, the same bacterial strains were used for the specificity evaluation of a S. macedonicus species-specific probe. Neither species-specific PCR nor DNA hybridisation experiments could differentiate Streptococcus waius from S. macedonicus, due to the identity of the 16S rRNA gene of the two species, indicating high phylogenetical relatedness. This was further confirmed by the comparative sequence analysis of the 16S-23S rRNA intergenic regions. It was thus clearly demonstrated that S. waius, recently described as a novel Streptococcus species, is phylogenetically identical to S. macedonicus.     

实时荧光PCR定性定量检测混合食用油脂中的花生油成分

为鉴别鉴定花生油在食用油脂中的存在与否及其含量,研究了定性定量检测花生特异性基因片段的分子生物学检测方法。结果表明,生花生需加热处理后再提取DNA才能作为PCR扩增的模板,食用油脂中可提取出用于定性定量PCR的DNA,花生的Arah1基因是具有花生种属特异性的基因,采用实时荧光PCR方法检测Arah1基因片段可定性定量检测混合食用油脂中的花生油成分。     

A papaya-specific gene, papain, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic papayas

Genetically modified (GM) papaya lines have been approved for commercialization and are widely cultivated in many countries. As a step towards the development of reliable qualitative and quantitative PCR methods for detecting GM papayas, one papaya (Fructus Caricae Carica papaya L.) species specific gene, papain, was selected and validated as suitable for using as an endogenous reference gene in transgenic papaya PCR detection. In this article, both qualitative and quantitative PCR assays for the papain gene were assayed with 11 different papaya varieties and identical amplification products were obtained with all of them. No amplified fragments could be detected when DNA samples from 18 kinds of other species were used as templates, which demonstrated that this system was specific for papaya. In real-time quantitative PCR analysis, the detection limit was as low as 10 pg of DNA. Southern blot analysis confirmed that the papain gene was two copies in the tested papaya varieties and no allelic variation was testified among these tested papaya varieties. In addition, the common used exogenous genes of the coat protein (CP) and the replicase (RP) were also assayed in qualitative and real-time quantitative PCR. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Wentao Xu and Weibin Bai contributed equally to this work.     

实时荧光PCR方法在食品真伪辨别中的应用

实时荧光PCR技术以其特异性、灵敏性、简便、快速的优点,广泛应用于食品鉴伪检测。本文阐述了实时荧光PCR的原理以及其在肉制品、高价值食品、乳制品、果汁、水产品和油脂鉴伪检测方面的应用情况。