Detection of genetically modified organisms in foods by protein- and DNA-based techniques: bridging the methods

According to European Commission (EC) Regulation 1139/98, foods and food ingredients that are to be delivered to the final consumer in which either protein or DNA resulting from genetic modification is present, shall be subject to additional specific labeling requirements. Since 1994, genetically altered tomatoes, squash, potatoes, canola, cotton, and soy have been on the market. Recently, insect-resistant and herbicide-tolerant maize varieties have been introduced. Soy and maize are 2 of the most important vegetable crops in the world. During the past 4 years, both protein- and DNA-based methods have been developed and applied for detection of transgenic soy and maize, and their derivatives. For protein-based detection, specific monoclonal and polyclonal antibodies have been developed; for immunochemical detection, Western blot analysis and enzyme-linked immunosorbent assays are the most prominent examples. For detection of genetically modified organisms (GMOs) at the level of DNA, polymerase chain reaction-based methods are mainly used. For these reactions, highly specific primer sets are needed. This study compares the principally different methods. Specificity of methods and the possible risks of false-positive or false-negative results are considered in relation to sampling, matrix effects, and food processing procedures. In addition, quantitative aspects of protein- and DNA-based GM detection methods are presented and discussed. This is especially relevant as EC regulation 49/2000, which defines a threshold for an unintentional comingling of 1%, came into force on April 10, 2000.     

Determination of (fluoro)quinolone antibiotic residues in pig kidney using liquid chromatography-tandem mass spectrometry. Part II: intercomparison exercise

A recently in-house validated method for the liquid chromatography-tandem mass spectrometry (LC-MS/MS) determination of eleven (fluoro)quinolone antibiotics (FQs) in pig kidney has been fully validated through an intercomparison exercise. This ring trial involved eight European laboratories and was based on the Commission Decision 2002/657/CE for validation of method and on the IUPAC protocol for method-performances studies. The laboratories data were submitted to a one-way analysis of variance. Satisfactory results were obtained for each FQ with regards to within- and between-laboratory reproducibility and accuracy. The method was validated for the simultaneous qualitative and quantitative determination of the eleven FQs in pig kidney around their maximum residue limit (MRL) as defined in the European Council Regulation 2377/90/EEC.     

A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis

In this paper we compare the effects of three representative PCR inhibitors using quantitative PCR (qPCR) and multiplex STR amplification in order to determine the effect of inhibitor concentration on allele dropout and to develop better ways to interpret forensic DNA data. We have used humic acid, collagen and calcium phosphate at different concentrations to evaluate the profiles of alleles inhibited in these amplifications. These data were correlated with previously obtained results from quantitative PCR including melt curve effects, efficiency changes and cycle threshold (Ct) values. Overall, the data show that there are two competing processes that result from PCR inhibition. The first process is a general loss of larger alleles. This appears to occur with all inhibitors. The second process is more sequence specific and occurs when the inhibitor binds DNA, altering the cycle threshold and the melt curve. This sequence-specific inhibition results in patterns of allele loss that occur in addition to the overall loss of larger alleles. The data demonstrate the applicability of utilizing real-time PCR results to predict the presence of certain types of PCR inhibition in STR analysis.     

The interlaboratory comparison "IMEP-19 trace elements in rice"—a new approach for measurement performance evaluation

The aim of IMEP is to present objectively the quality of chemical measurements. Participants in IMEP compare their reported measurement results with independent external certified reference values with demonstrated traceability and uncertainty, as evaluated according to international guidelines. IMEP-19 focused on measurements of trace elements in rice aiming to support the Commission Regulation (EC) No. 466/2001 on maximum levels for certain contaminants in foodstuff. Measurement results for the elements Cd, Cu, Pb and Zn were reported by 267 field laboratories involved in food analysis from 43 countries. Performance criteria for the evaluation of the reported measurement results in IMEP-19 are suggested. The chosen performance indicators not only take into account the deviation of the reported measurement value from the certified reference value, but also set criteria for maximum and minimum acceptable uncertainty. The IMEP-19 participants' performance is reviewed by means of using new simple graphical tools, called "Naji plots".     

Novel reference gene, High-mobility-group protein I/Y, used in qualitative and real-time quantitative polymerase chain reaction detection of transgenic rapeseed cultivars

With the development of transgenic crops, regulations to label the genetically modified organisms (GMOs) and their derived products have been issued in many countries. Polymerase chain reaction (PCR) methods are thought to be reliable and useful techniques for qualitative and quantitative detection of GMOs. These methods are generally needed to amplify the transgene and compare the amplified results with that of a corresponding reference gene to get the reliable results. Specific primers were developed for the rapeseed (Brassica napus), high-mobility-group protein I/Y(HMG-I/Y) single-copy gene and PCR cycling conditions suitable for the use of this sequence as an endogenous reference gene in both qualitative and quantitative PCR assays. Both methods were assayed with 15 different rapeseed varieties, and identical amplified products were obtained with all of them. No amplification was observed when templates were the DNA samples from the other species of Brassica genus or other species, such as broccoli, stem mustard, cauliflower, Chinese cabbage, cabbage, sprouts, Arabidopsis thaliana, carrot, tobacco, soybean, mung bean, tomato, pepper, eggplant, plum, wheat, maize, barley, rice, lupine, and sunflower. This system was specific for rapeseed. Limits of detection and quantitation in qualitative and quantitative PCR systems were about 13 pg DNA (about 10 haploid genomes) and about 1.3 pg DNA (about 1 haploid genome), respectively. To further test the feasibility of this HMG-I/Y gene as an endogenous reference gene, samples containing transgenic rapeseed GT73 with the inserted glyphosate oxidoreductase (GOX) gene were quantitated. These demonstrated that the endogenous PCR detection systems were applicable to the qualitative and quantitative detection of transgenic rapeseed.     

Dioxin analysis in feed: cell-based assay versus mass spectrometry method

In the determination of contaminants (dioxins, polychlorinated biphenyls, polyaromatic hydrocarbons), cell-based assays are useful methods for screening purposes: they are mainly characterized by high sample throughput and lower costs than the Mass Spectrometry (MS)-based methods. Although cell-based assays can be sensitive enough for the determination of dioxins and related substances in agreement with the presently tolerable limits in food and feed (Regulation No. 2375/2001/EC and Directive 2003/57/EC respectively), their lack of specificity make their use rather questionable in control laboratories. In this paper, we present and compare results obtained from the analysis of a limited number of feed samples by both gas chromatography-high resolution mass spectrometry (GC-HRMS) and cell-based assay (DR-CALUX: dioxin responsive-chemically activated luciferase gene expression) methods. The DR-CALUX screening led to less than 10% false non-compliant and no false compliant results. In addition, there is a good correlation between GC-HRMS and DR-CALUX data. However, these preliminary results have to be confirmed on a larger number of samples to demonstrate that total toxic equivalent (TEQ), including dioxins, furans and dioxin-like polychlorobiphenyls (PCBs) can be monitored in feed and food with a cell-based assay. Presented at AOAC Europe/Eurachem Symposium March 2005, Brussels, Belgium     

Real-time polymerase chain reaction assay for endogenous reference gene for specific detection and quantification of common wheat-derived DNA (Triticum aestivum L.)

A species-specific endogenous reference gene system was developed for polymerase chain reaction (PCR)-based analysis in common wheat (Triticum aestivum L.) by targeting the ALMT1 gene, an aluminium-activated malate transporter. The primers and probe were elaborated for real-time PCR-based qualitative and quantitative assay. The size of amplified product is 95 base pairs. The specificity was assessed on 17 monocot and dicot plant species. The established real-time PCR assay amplified only T. aestivum-derived DNA; no amplification occurred on other phylogenetically related species, including durum wheat (T. durum). The robustness of the system was tested on the DNA of 15 common wheat cultivars using 20 000 genomic copies per PCR the mean cycle threshold (Ct) values of 24.02 +/- 0.251 were obtained. The absolute limits of detection and quantification of the real-time PCR assay were estimated to 2 and 20 haploid genome copies of common wheat, respectively. The linearity was experimentally validated on 2-fold serial dilutions of DNA from 650 to 20 000 haploid genome copies. All these results show that the real-time PCR assay developed on the ALMT1 gene is suitable to be used as an endogenous reference gene for PCR-based specific detection and quantification of T. aestivum-derived DNA in various applications, in particular for the detection and quantification of genetically modified materials in common wheat.     

Validation of PCR methods for quantitation of genetically modified plants in food.

For enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients, quantitative detection methods such as quantitative competitive (QC-PCR) and real-time PCR are applied by official food control laboratories. The experiences of 3 European food control laboratories in validating such methods were compared to describe realistic performance characteristics of quantitative PCR detection methods. The limit of quantitation (LOQ) of GMO-specific, real-time PCR was experimentally determined to reach 30-50 target molecules, which is close to theoretical prediction. Starting PCR with 200 ng genomic plant DNA, the LOQ depends primarily on the genome size of the target plant and ranges from 0.02% for rice to 0.7% for wheat. The precision of quantitative PCR detection methods, expressed as relative standard deviation (RSD), varied from 10 to 30%. Using Bt176 corn containing test samples and applying Bt176 specific QC-PCR, mean values deviated from true values by -7to 18%, with an average of 2+/-10%. Ruggedness of real-time PCR detection methods was assessed in an interlaboratory study analyzing commercial, homogeneous food samples. Roundup Ready soybean DNA contents were determined in the range of 0.3 to 36%, relative to soybean DNA, with RSDs of about 25%. Taking the precision of quantitative PCR detection methods into account, suitable sample plans and sample sizes for GMO analysis are suggested. Because quantitative GMO detection methods measure GMO contents of samples in relation to reference material (calibrants), high priority must be given to international agreements and standardization on certified reference materials.     

Novel approaches in analysis of Fusarium mycotoxins in cereals employing ultra performance liquid chromatography coupled with high resolution mass spectrometry

Rapid, simple and cost-effective analytical methods with performance characteristics matching regulatory requirements are needed for effective control of occurrence of Fusarium toxins in cereals and cereal-based products to which they might be transferred during processing. Within this study, two alternative approaches enabling retrospective data analysis and identification of unknown signals in sample extracts have been implemented and validated for determination of 11 major Fusarium toxins. In both cases, ultra-high performance liquid chromatography (U-HPLC) coupled with high resolution mass spectrometry (HR MS) was employed. ¹³C isotopically labeled surrogates as well as matrix-matched standards were employed for quantification. As far as time of flight mass analyzer (TOF-MS) was a detection tool, the use of modified QuEChERS (quick easy cheap effective rugged and safe) sample preparation procedure, widely employed in multi-pesticides residue analysis, was shown as an optimal approach to obtain low detection limits. The second challenging alternative, enabling direct analysis of crude extract, was the use of mass analyzer based on Orbitrap technology. In addition to demonstration of full compliance of the new methods with Commission Regulation (EC) No. 401/2006, also their potential to be used for confirmatory purposes according to Commission Decision 2002/657/EC has been critically assessed.     

Development and validation of a solid-phase extraction method coupled to high-performance liquid chromatography with ultraviolet-diode array detection for the determination of sulfonylurea herbicide residues in bovine milk samples

This study proposes a fast, simple and sensitive liquid chromatography diode array detector (LC/UV-DAD)-based method for the simultaneous determination of eight sulfonylurea herbicides (bensulfuron methyl, chlorsulfuron, metsulfuron methyl, primisulfuron methyl, rimsulfuron, thifensulfuron methyl, triasulfuron and tribenuron methyl) in bovine whole milk at concentrations lower than the default limit of 0.01 mg kg(-1) allowed by current legislation (Regulation EC/396/2005 and following Annexes). An effective one-step solid phase extraction (SPE) and clean up procedure was defined with use of Chem Elut cartridges, providing good recoveries for all the analytes tested and with no matrix effects affecting method accuracy. Separation of herbicides was obtained on a C(18) column by acetonitrile- water gradient elution. Method validation has been performed according to European Commission Decision 2002/657/EC criteria, in terms of linearity, recovery, precision, specificity, decision limit (CC(α)) and detection capability (CC(β)). Typical recoveries ranged between 78.4% and 99.7%, at the maximum residue limits (MRLs) levels established by Regulation EC/396/2005, with relative standard deviations (RSD) no larger than 10%.     

气相色谱-质谱法检测涂料中的六溴环十二烷

建立了防火涂料中阻燃剂六溴环十二烷(HBCD)的气相色谱-质谱(GC-MS)分析方法。样品用二氯甲烷进行萃取,萃取液经有机滤膜过滤后,用气相色谱-质谱联用仪进行测定。在选择离子检测模式下以m/z 157、239、319、401为定性离子,m/z 239为定量离子进行结构确证和定量检测。在优化的实验条件下,六溴环十二烷标准溶液在5~100 mg/L的质量浓度范围内线性关系良好,相关系数大于0.999。对市售的空白丙烯酸树脂涂料样品及环氧树脂涂料样品进行加标回收试验,结果表明本方法的平均回收率为92.9%~116.3%, RSD不超过8%。方法的检出限(S/N=3)为30 μg/g,定量限(S/N=10)为100 μg/g。本方法简便、快速、准确性好、精密度高,能够满足检测工作的实际要求。     

Identification of Ensis siliqua samples and establishment of the catch area using a species-specific microsatellite marker

European Council Regulation 104/2000 states that fishery products must be labeled to indicate commercial designation of species, the production method, and the catch area. Therefore, traceability of seafood implies knowledge of the species offered to retail and their origin. Ensis siliqua is a bivalve intensively fished in Europe and sold in fresh and canned forms. Although several published methods clearly differentiate Ensis genus species, none of those assess the origin of the commercial samples. In the present study, a microsatellite marker (Esi-UDC3055F) was developed to establish the catch area of E. siliqua samples. Amplification yielded a fragment of 275 or 302 base pairs, depending on whether they were Iberian or Irish populations. The usefulness of this method was also assessed in commercial samples. The results of this study provide a reliable methodology for the identification of catch area in European E. siliqua commercial samples. The coupling of this methodology with existing techniques for razor clam species identification provides a powerful tool for traceability and labeling enforcement.     

Molecular Cloning,Characterization, and Expression Analysis of Lignin Genes from Sugarcane Genotypes Varying in Lignin Content

Sugarcane (Saccharum spp.) is one of the highest biomass-producing plant and the best lignocellulosic feedstock for ethanol production. To achieve more efficient conversion of biomass to ethanol, a better understanding of the main factors affecting biomass recalcitrance is needed. Therefore, with this objective, here, we report a systematic study on lignin content, deposition, identification, and cloning of genes involved in lignin biosynthesis and their differential expression in five sugarcane clones, EC11003, EC11010, IK 76-91, IK 76-99, and Co 86032. Lignin content among the clones varied from 26.87 to 23.19 % with the highest in the clone EC11010 and the lowest in high sugar Co86032. Lignin deposition studied through phloroglucinol staining of the cell walls implied that the sclerenchyma cells of the energy canes (EC11010 and EC11003) have more lignin deposition followed by the Erianthus (IK 76-91 and IK 76-99) clones whereas Co86032 has the minimum amount of lignin deposition. We cloned partial coding regions of important genes of lignification COMT (650 bp), CCR (332 bp), and PAL (650 bp) from Erianthus, wild relative of sugarcane followed by the expression analysis through real-time PCR. Differential expression analysis showed high level of expression for the three genes in the energy cane EC11010.     

Probing the mechanism of hypoxia selectivity of copper bis(thiosemicarbazonato) complexes: DFT calculation of redox potentials and absolute acidities in solution

Density functional theory (DFT) calculations have been performed using the uB3LYP/6-31++G(d,p) model to calculate the solution phase one-electron reduction potentials (E(calc)) and absolute pKa values of a series of copper bis(thiosemicarbazonato) complexes. The effects of solvation in water and dimethylsulfoxide (DMSO) are incorporated as a self-consistent reaction field (SCRF) using the integral equation formalism polarisable continuum model (IEFPCM) and are found to be essential for quantitative agreement with an average error in E(calc) of -0.02 V compared to experiment. The bonding and spin densities are examined through the use of Natural Bond Order analysis and the results used to rationalise the calculated and observed reduction potentials. Calculated estimates of pKa values of several copper(II) species are presented and their implications for the mechanisms of transport and trapping within hypoxic cells are considered. Reduction is found to be a prerequisite for protonation of the complexes which suggests their transport in the blood stream as neutral species, and the mechanistic sequence is identified as a sequential electrochemical-chemical (EC) process. The complex equilibria of protonation, reoxidation and dissociation are discussed and the copper(I) diprotonated, cationic complex of diacetyl bis(4-methyl-3-thiosemicarbazonato)copper(II), Cu(I)ATSMH2(+), is identified as a possible candidate for the initial species trapped in hypoxic cells.     

Effects of Induced Exosomes from Endometrial Cancer Cells on Tumor Activity in the Presence of Aurea helianthus Extract

Endometrial cancer (EC) cells metastasize to various regions, including the ovaries, fallopian tubes, cervix, blood, liver, bone, and brain. Various carcinogens are known to cause EC. Exosomes are released from several types of cells and contain various cellular components. In this study, flow cytometry and quantitative PCR were used to evaluate marker levels, cell migration, cell invasion, and mitochondrial membrane potential, and cellular senescence tests were used to estimate cancer activity. The microRNAs were profiled using next-generation sequencing. Although tocopherol-α and rutin content in Aurea helianthus is high, A. helianthus extract was more useful in modulating tumor activity compared to the two aforementioned substances. Notably, we established that the extract induced bioactive exosomes in EC cells, and profiling of miRNAs in the extract-inducing exosomes (EIE) indicated their potency to be developed as a biological drug. The extract and EIE contributed to the following five biological process categories for EC cells: (1) cell migration and invasion suppression, (2) cellular senescence activation by attenuating mitochondrial membrane potential and enhancing autophagy, (3) reproductive cancer activity attenuation, (4) drug susceptibility activation, and (5) EIE containing miRNAs associated with decreasing inflammation.     

Evaluation of a polymerase chain reaction-based heteroduplex assay for detecting the adulteration of processed orange juice with mandarin juice

A polymerase chain reaction (PCR)-based heteroduplex assay was evaluated for the detection of mandarin juice in processed orange juice. PCR amplification of a fragment of the chloroplast trnT-trnL intergenic spacer derived from mixtures of DNA extracted from orange and mandarin juice resulted in heteroduplex formation. The heteroduplex resulted from the co-amplification of a fragment containing an 8 base-pair indel that distinguished mixtures of orange and mandarin juice from orange juice and mandarin juice alone. The heteroduplex assay was evaluated against authentic juices obtained from different citrus species and confirmed that the marker was homogeneous within Citrus. The data obtained demonstrated maternal inheritance of chloroplast type in Citrus sp. and allowed the identification and confirmation of the maternal parentage of unknown and known citrus hybrids. Analysis of the quantitative potential of the PCR and polyacrylamide gel electrophoresis (PAGE) analysis demonstrated good repeatability with a coefficient of variation of 7.5%. Greatest sources of variance in experimental results were attributable to species and varietal differences in the levels of the PCR target. Mandarin juice contained approximately 18% (w/v) less PCR target sequence than did orange juice. The assay was tested in a blind trial using processed juices and correctly identified 20/22 samples with no false-positive results.     

Towards a portable microchip system with integrated thermal control and polymer waveguides for real-time PCR

A novel real-time PCR microchip platform with integrated thermal system and polymer waveguides has been developed. The integrated polymer optical system for real-time monitoring of PCR was fabricated in the same SU-8 layer as the PCR chamber, without additional masking steps. Two suitable DNA binding dyes, SYTOX Orange and TO-PRO-3, were selected and tested for the real-time PCR processes. As a model, cadF gene of Campylobacter jejuni has been amplified on the microchip. Using the integrated optical system of the real-time PCR microchip, the measured cycle threshold values of the real-time PCR performed with a dilution series of C. jejuni DNA template (2 to 200 pg/microL) could be quantitatively detected and compared with a conventional post-PCR analysis (DNA gel electrophoresis). The presented approach provided reliable real-time quantitative information of the PCR amplification of the targeted gene. With the integrated optical system, the reaction dynamics at any location inside the micro reaction chamber can easily be monitored.     

Chemical analysis as a specific class of measurements

 Specific features of the procedures involved in chemical analysis (sampling, sample preparation, matrix and impurities identification, quantitative analysis) are considered, and their effect on the uncertainty of the result of a quantitative determination of the component of interest is discussed. Received: 19 August 1998 / Accepted: 4 September 1998     

Application of dispersive liquid-liquid microextraction for the determination of aflatoxins B1, B2, G1 and G2 in cereal products

The application of dispersive liquid-liquid microextraction (DLLME) technique for the rapid analysis of aflatoxins B(1), B(2), G(1) and G(2) in maize, rice and wheat products has been evaluated. After extraction of aflatoxins from cereal matrices with a mixture of methanol/water 8:2 (v/v), the analytes were rapidly transferred from the extract to another small volume of organic solvent, chloroform, by DLLME. Aflatoxins were determined using high performance liquid chromatography with florescence detection and photochemical post-column derivatization. Parameters affecting both extraction and DLLME procedures, such as extraction solvent, type and volume of DLLME extractant, volume of water and salt effect, were systematically investigated and optimized to achieve the best extraction efficiency. Under the optimal experimental conditions, the whole analytical method provides enrichment factors around 2.5 times and detection limits (0.01-0.17 μg kg(-1)) below the maximum levels imposed by current regulation for aflatoxins in cereals and cereal products intended for direct human consumption. Recoveries (67-92%) and repeatability (RSD<10, n=3), tested in three different cereal matrices, meet the performance criteria required by EC Regulation No. 401/2006 for the determination of the levels of mycotoxins in foodstuffs. The proposed method was successfully applied to the analysis of retail cereal products with quantitative results comparable to the immunoaffinity chromatography (IAC). The main advantages of developed method are the simplicity of operation, the rapidity to achieve a very high sample throughput and low cost.     

Development and validation of a liquid chromatography-tandem mass spectrometry method for the simultaneous determination of nine corticosteroid residues in bovine liver samples

A liquid chromatography tandem mass spectrometry (LC-MS/MS) confirmatory method for the simultaneous determination of nine corticosteroids in liver, including the four MRL compounds listed in Council Regulation 37/2010, was developed. After an enzymatic deconjugation and a solvent extraction of the liver tissue, the resulting solution was cleaned up through an SPE Oasis HLB cartridge. The analytes were then detected by liquid chromatography-negative-ion electrospray tandem mass spectrometry, using deuterium-labelled internal standards. The procedure was validated as a quantitative confirmatory method according to the Commission Decision 2002/657/EC criteria. The results showed that the method was suitable for statutory residue testing regarding the following performance characteristics: instrumental linearity, specificity, precision (repeatability and intra-laboratory reproducibility), recovery, decision limit (CCα), detection capability (CCβ) and ruggedness. All the corticosteroids can be detected at a concentration around 1 μg kg(-1); the recoveries were above 62% for all the analytes. Repeatability and reproducibility (within-laboratory reproducibility) for all the analytes were below 7.65% and 15.5%, respectively.