Rapid analysis of genetically modified organisms by in-house developed capillary electrophoresis chip and laser-induced fluorescence system

Optimised LAMP allows single copy detection of 35Sp and NOSt in transgenic maize using Bioluminescent Assay in Real Time (BART)

Loop-mediated amplification (LAMP) has been widely used to amplify and hence detect nucleic acid target sequences from various pathogens, viruses and genetic modifications. Two distinct types of primer are required for LAMP; hairpin-forming LAMP and displacement. High specificity arises from this use of multiple primers, but without optimal conditions for LAMP, sensitivity can be poor. We confirm here the importance of LAMP primer design, concentrations and ratios for efficient LAMP amplification. We further show that displacement primers are non-essential to the LAMP reaction at certain concentrations providing accelerating loop primers are present. We investigate various methods to quantify DNA extracts from GM maize certified reference materials to calculate the target copy numbers of template presented to the LAMP reaction, and show that LAMP can amplify transgenic promoter/terminator sequences in DNA extracted from various maize GM events using primers designed to target the 35S promoter (35Sp) or NOS terminator (NOSt) sequences, detection with both bioluminescence in real-time (BART) and fluorescent methods. With prior denaturation and HPLC grade LAMP primers single copy detection was achieved, showing that optimised LAMP conditions can be combined with BART for single copy targets, with simple and cost efficient light detection electronics over fluorescent alternatives.

Discrimination of transgenic soybean seeds by terahertz spectroscopy

Discrimination of genetically modified organisms is increasingly demanded by legislation and consumers worldwide. The feasibility of a non-destructive discrimination of glyphosate-resistant and conventional soybean seeds and their hybrid descendants was examined by terahertz time-domain spectroscopy system combined with chemometrics. Principal component analysis (PCA), least squares-support vector machines (LS-SVM) and PCA-back propagation neural network (PCA-BPNN) models with the first and second derivative and standard normal variate (SNV) transformation pre-treatments were applied to classify soybean seeds based on genotype. Results demonstrated clear differences among glyphosate-resistant, hybrid descendants and conventional non-transformed soybean seeds could easily be visualized with an excellent classification (accuracy was 88.33% in validation set) using the LS-SVM and the spectra with SNV pre-treatment. The results indicated that THz spectroscopy techniques together with chemometrics would be a promising technique to distinguish transgenic soybean seeds from non-transformed seeds with high efficiency and without any major sample preparation.

A novel reference plasmid for the qualitative detection of genetically modified rice in food and feed

Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice.

Detection of GM soybean by multiplex-touchdown PCR-microchip capillary electrophoresis with response surface methodology optimization

The combination of the molecular technique, the multivariate strategy and microchip capillary electrophoresis (MCE) was applied to rapid and sensitive analysis of genetically modified (GM) soybean in food samples. A multiplex-touchdown polymerase chain reaction (PCR) system was developed for simultaneously amplifying three target sequences in Roundup Ready soybean (RRS). Response surface methodology was introduced to determine the optimal separation condition in MCE with good resolution and short analytical time. The detection of the PCR products of RRS was completed within 4 min under the optimal conditions. The specificity of the method was evaluated by testing non-GM soybean materials and three GM maize varieties (MON810, Bt176 and Bt11). A sensitivity of 0.1% GM organisms content was obtained, which was remarkably lower than the labeling threshold for transgenic food defined as 0.9% in the European regulation. The relative standard deviation of migration time was in the range of 0.17-0.95%. The proposed method was rapid, sensitive and specific and can be used to identify and detect GM soybean in food samples.

Microfabricated polymer chip with integrated U-bend waveguides for evanescent field absorption based detection

A mu-TAS system for evanescent field absorption with integrated polymer waveguides is reported for the first time. A photoresist SU-8 layer is patterned into a microchannel network, with U-bend waveguides and fiber-to-waveguide coupler structures. The aim of this study was to explore the possibility of using evanescent field absorption based sensing in conjunction with capillary electrophoresis for label free detection. We have proposed a novel design to couple the microchannel network with U-bend waveguides in a single step patterning of SU-8. In this novel design, the optical waveguide forms part of the microchannel wall, which aids in the detection process. The suitability of the device for optical applications was proved by absorbance measurement between 450 and 780 nm using Methylene Blue dye. Absorbance measurements were done by passing various concentrations of dye solutions through 200 microm and 500 microm microchannels. The device was also found sensitive to the refractive index (RI) of fluid flowing in the channel. The RI sensitivity was tested by passing sucrose solutions of varying concentrations through the channels and measuring absorbance across the integrated U-bend waveguides. The results indicate that such structures can be used easily for label free detection of molecules either by evanescent wave absorption or by changes associated with RI changes in the microenvironment around a waveguide.

Direct and rapid electrochemical biosensing of the human interleukin-2 DNA in unpurified polymerase chain reaction (PCR)-amplified real samples

Electrochemical detection of polymerase chain reaction (PCR)-amplified human interleukin-2 (IL-2) coding DNA sample (399bp size) without any purification and pre-treatment is described. To achieve this goal, a sensor was made by immobilization of a 20-mer oligonucleotide (chIL-2) as the probe on the pencil graphite electrode (PGE). This probe is related to the antisense strand of human interleukin-2 gene. The results showed that the electrode could effectively sense the PCR product of human interleukin-2 DNA by anodic differential pulse voltammetry (ADPV) based on guanine oxidation signal. In order to inhibit PCR components interfering effects and improve biosensing performance, various factors were investigated. We found that the desorption of non-specifically adsorbed components of the unpurified PCR samples from PGE surface is easily achieved by washing of the electrode in washing solution for about 300s. The effectiveness of this procedure was confirmed using purified PCR samples. The selectivity of the sensor was assessed with negative control PCR sample and seven different non-complementary PCR products corresponding to 16S rDNA (bigger than 1500bp) of various bacterial genuses. Diagnostic performance of the biosensor is described and the detection limit is found to be 69pM. The reliability of the electrochemical biosensing results was verified by electrophoresis of the PCR products.

Comparative metabolomic study of transgenic versus conventional soybean using capillary electrophoresis-time-of-flight mass spectrometry

In this work, capillary electrophoresis-time-of-flight mass spectrometry (CE-TOF-MS) is proposed to identify and quantify the main metabolites found in transgenic soybean and its corresponding non-transgenic parental line both grown under identical conditions. The procedure includes optimization of metabolites extraction, separation by CE, on-line electrospray-TOF-MS analysis and data evaluation. A large number of extraction procedures and background electrolytes are tested in order to obtain a highly reproducible and sensitive analytical methodology. Using this approach, a large number of metabolites were tentatively identified based on the high mass accuracy provided by TOF-MS analyzer, together with the isotopic pattern and expected electrophoretic mobility of these compounds. In general, the same metabolites and in similar amounts were found in the conventional and transgenic variety. However, significant differences were also observed in some specific cases when the conventional variety was compared with its corresponding transgenic line. The selection of these metabolites as possible biomarkers of transgenic soybean is discussed, although a larger number of samples need to be analyzed in order to validate this point. It is concluded that metabolomic procedures based on CE-MS can open new perspectives in the study of transgenic foods in order to corroborate (or not) the equivalence with their conventional counterparts.

Discrimination of transgenic tomatoes based on visible/near-infrared spectra

VIS-NIR spectroscopy combined with multivariate analysis after the appropriate spectral data pre-treatment has been proved to be a very powerful tool for judgment of the relative pattern of the objects that have very similar properties. In this study, seventy transgenic tomatoes with antisense LeETR2 and 94 of their parents, non-transgenic ones were measured in VIS-NIR diffuse reflectance mode. Principal component analysis (PCA), discriminant analysis (DA) and partial least-squares discriminant analysis (PLSDA) were applied to classify tomatoes with different genes into two groups. Calibrations were developed using PLS regression with the leave-one-out cross-validation technique. The results show that differences between transgenic and non-transgenic tomatoes do exist and excellent classification can be obtained after optimizing spectral pre-treatment. The correct classifications for transgenic and non-transgenic tomatoes were both 100% using PLSDA after derivative spectral pre-treatment. The raw spectra with PLSDA model after the second derivative pre-treatment had the best satisfactory calibration and prediction abilities, with r(c)=0.97964, root mean square error of calibration (RMSEC)=0.099, r(cv)=0.97963, root mean square error of cross-validation (RMSECV)=0.0993 and a factor. The results in the present study show VIS-NIR spectroscopy together with chemometrics techniques could be used to differentiate transgenic tomato, which offers the benefit of avoiding time-consuming, costly and laborious chemical and sensory analysis.

Recent developments in optical detection methods for microchip separations

This paper summarizes the features and performances of optical detection systems currently applied in order to monitor separations on microchip devices. Fluorescence detection, which delivers very high sensitivity and selectivity, is still the most widely applied method of detection. Instruments utilizing laser-induced fluorescence (LIF) and lamp-based fluorescence along with recent applications of light-emitting diodes (LED) as excitation sources are also covered in this paper. Since chemiluminescence detection can be achieved using extremely simple devices which no longer require light sources and optical components for focusing and collimation, interesting approaches based on this technique are presented, too. Although UV/vis absorbance is a detection method that is commonly used in standard desktop electrophoresis and liquid chromatography instruments, it has not yet reached the same level of popularity for microchip applications. Current applications of UV/vis absorbance detection to microchip separations and innovative approaches that increase sensitivity are described. This article, which contains 85 references, focuses on developments and applications published within the last three years, points out exciting new approaches, and provides future perspectives on this field.

Recent advances in the application of capillary electromigration methods for food analysis

This article reviews the latest developments in the application of capillary electromigration methods for the analysis of foods and food components. Nowadays, methods based on CE techniques are becoming widely used in food analytical and research laboratories. This review covers the application of CE to analyze amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions, chiral compounds, and other compounds in foods, as well as to investigate food interactions and food processing. The use of microchips as well as other foreseen trends in CE analysis of foods is discussed. Papers that were published during the period June 2002-June 2005 are included following the previous review by Frazier and Papadopoulou (Electrophoresis 2003, 24, 4095-4105).

Technophiles seek genomic imperfections with the Greek gods at Atlantis

The 8th International Symposium on Mutations in the Genome covered a broad range of technological developments and their applications to detecting genomic sequence variation.

Microchip capillary gel electrophoresis using programmed field strength gradients for the ultra-fast analysis of genetically modified organisms in soybeans

We have developed a novel method for the ultra-fast analysis of genetically modified organisms (GMOs) in soybeans by microchip capillary gel electrophoresis (MCGE) using programmed field strength gradients (PFSG) in a conventional glass double-T microchip. Under the programmed electric field strength and 0.3% poly(ethylene oxide) sieving matrix, the GMO in soybeans was analyzed within only 11 s of the microchip. The MCGE-PFSG method was a program that changes the electric field strength during GMO analysis, and was also applied to the ultra-fast analysis of PCR products. Compared to MCGE using a conventional and constantly applied electric field, the MCGE-PFSG analysis generated faster results without the loss of resolving power and reproducibility for specific DNA fragments (100- and 250-bp DNA) of GM-soybeans. The MCGE-PFSG technique may prove to be a new tool in the GMO analysis due to its speed, simplicity, and high efficiency.

Nanoparticle-based DNA biosensor for visual detection of genetically modified organisms

Although screening of raw ingredients and food products for genetically modified organisms (GMO) may be accomplished by detecting either the exogenous DNA or the novel protein, DNA is the preferred analyte because of its superior stability during food processing. The development of DNA biosensors is of increasing importance due to the growing demand for rapid and reliable methods for GMO detection. We report the first DNA biosensor in a dry-reagent dipstick configuration for visual detection and confirmation of GMO-related sequences by hybridization within minutes. The sensor is disposable and does not require special instrumentation. It detects the 35S promoter and nopaline synthase (NOS) terminator sequences that are present in the majority of transgenic plants. The target sequences are amplified by the polymerase chain reaction (PCR) and hybridized (7min) with probes bearing oligo(dA) tail. The biotinylated product is applied to the sensor followed by immersion in the appropriate buffer. Migration of the buffer rehydrates gold nanoparticles conjugated to oligo(dT), which hybridize with the oligo(dA) tails. The hybrids are captured by immobilized streptavidin at the test zone of the sensor giving a characteristic red line due to the accumulation of the nanoparticles. The excess of nanoparticle conjugates are captured at the control zone by immobilized oligo(dA) strands. Amplified 35S or NOS DNA is detectable at 0.16nM. Soybean powder certified reference material with 0.1% GMO content is clearly detectable after 35 and 40 amplification cycles for 35S and NOS sequence, respectively. The sensor was also applied to real samples from various sources.

Capillary electrophoresis in food authenticity

Food authenticity is a term which simply refers to whether the food purchased by the consumer matches its description. False description can occur in many forms, from the undeclared addition of water or other cheaper materials, or the wrong declaration of the amount of a particular ingredient in the product, to making false statements about the source of ingredients i.e., their geographic, plant, or animal origin. The aim of this review is to summarize applications of capillary electrophoresis in food authentication.

Fast electrophoresis in conventional capillaries by employing a rapid injection device and contactless conductivity detection

A purpose-made set-up featuring an automated fast injector allowed the easy optimization of the injected amount and the adjustment of the separation length of conventional capillaries from a minimum of 5 cm upward. It was found that a compromise in capillary length for separation efficiency and analysis time also has to take into account the injected amount, which in turn affects the sensitivity and hence the detection limit. The versatility of the system was demonstrated by the analysis of the major cations and anions in natural water samples in less than 1 min, the concurrent determination of a mixture of amino acids and carbohydrates in 160 s, and of three active ingredients in a pharmaceutical preparation in 40 s. Plate numbers were typically around 50,000 and detection limits down to 1 muM could be achieved.