A high-throughput multiplex tandem PCR assay for the screening of genetically modified maize

Applicability of a General Analytical Approach for Detection of Genetically Modified Organisms: Collaborative Trial

BACKGROUND

With the commercialization of genetically modified organisms (GMOs) in the market, laboratories have undergone a significantly increased workload. A universal analytical approach was designed to achieve cost-efficient and high-throughput GMOs screening with high specificity and accuracy. The approach provides accurate qualification of authorized and unauthorized GMOs.

OBJECTIVE

This paper describes the assessment of this analytical approach developed to detect majority of commercialized GMOs over the world.

METHODS

Seven elements and three events were detected by qPCR in a single laboratory to detect 59 commercialized GMOs. Certificated reference materials and food/feed samples from Chinese market were also evaluated for the specificity, conformity and robustness of this approach and were challenged in the inter-laboratory study.

RESULTS

The results showed that elements and events selected can best detect GMO presence with good specificity and sensitivity. The results showed a concordance between 97.5% and 99.56% and the variance between 0.65% and 12.88%, which is in line with the minimum requirement of analytical methods of GMO testing.

CONCLUSION

The approach validated here can be used to manipulate GMO presence in food and feed and showed the capacity to manipulate GMOs trace in the trade and domestic agriculture grocery in China.

HIGHLIGHTS

A universal analytical approach used to track GMO presence was evaluated for its specificity, sensitivity and robustness.

Quantitative PCR based detection system for cyanobacterial geosmin/2-methylisoborneol (2-MIB) events in drinking water sources: Current status and challenges

Taste and odor (T&O) are an important issue in drinking water, aquaculture, recreation and a few other associated industries, and cyanobacteria-relevant geosmin and 2-methylisoborneol (2-MIB) are the two most commonly detected T&O compounds worldwide. A rise in the cyanobacterial blooms and associated geosmin/2-MIB episodes due to anthropogenic activities as well as climate change has led to global concerns for drinking water quality. The increasing awareness for the safe drinking, aquaculture or recreational water systems has boost the demand for rapid, robust, on-site early detection and monitoring system for cyanobacterial geosmin/2-MIB events. In past years, research has indicated quantitative PCR (qPCR) as one of the promising tools for detection of geosmin/2-MIB episodes. It offers advantages of detecting the source organism even at very low concentrations, distinction of odor-producing cyanobacterial strains from non-producers and evaluation of odor producing potential of the cyanobacteria at much faster rates compared to conventional techniques.The present review aims at examining the current status of developed qPCR primers and probes in identifying and detecting the cyanobacterial blooms along with geosmin/2-MIB events. Among the more than 100 articles about cyanobacteria associated geosmin/2-MIB in drinking water systems published after 1990, limited reports (approx. 10 each for geosmin and 2-MIB) focused on qPCR detection and its application in the field. Based on the review of literature, a comprehensive open access global cyanobacterial geosmin/2-MIB events database (CyanoGM Explorer) is curated. It acts as a single platform to access updated information related to origin and geographical distribution of geosmin/2-MIB events, cyanobacterial producers, frequency, and techniques associated with the monitoring of the events. Although a total of 132 cyanobacterial strains from 21 genera and 72 cyanobacterial strains from 13 genera have been reported for geosmin and 2-MIB production, respectively, only 58 geosmin and 28 2-MIB synthesis regions have been assembled in the NCBI database. Based on the identity, geosmin sequences were found to be more diverse in the geosmin synthase conserved/primer design region, compared to 2-MIB synthesis region, hindering the design of universal primers/probes. Emerging technologies such as the bioelectronic nose, Surface Enhanced Raman Scattering (SERS), and nanopore sequencing are discussed for future applications in early on-site detection of geosmin/2-MIB and producers. In the end, the paper also highlights various challenges in applying qPCR as a universal system of monitoring and development of response system for geosmin/2-MIB episodes.

Single universal primer recombinase polymerase amplification-based lateral flow biosensor (SUP-RPA-LFB) for multiplex detection of genetically modified maize

In this study, an isothermal paper biosensor, combining single universal primer recombinase polymerase amplification (SUP-RPA) and the lateral flow technique was developed for the multiplex detection of genetically modified maize (GMM). In pre-amplification stage, the event-specific primers contain a universal sequence at the 5' end, with a biotin-labeled deoxycytidine triphosphate (dCTP) deoxynucleotide providing additional amplification, which improves their amplification ability and ensures consistent multiplex amplification efficiency. In the signal recognition strategy, the SUP-RPA products are identified visually using the lateral flow biosensor (LFB) through dual hybridization. The accumulation of gold nanoparticles (AuNPs) produces a characteristic red band. Through this biosensor, a limit of detection of at least 50 copies was achieved, which is sensitive enough to detect MON810, MON863 and MON89034 simultaneously. The entire process of analysis was completed within 30 min and without any large-scale instrumentation. This biosensor, therefore, provides a novel rapid and portable multiple detection method for point-of-care applications, especially genetically modified organism (GMO) event-specific detection.

Development of a lateral flow test strip for simultaneous detection of BT-Cry1Ab, BT-Cry1Ac and CP4 EPSPS proteins in genetically modified crops

A colloidal gold immunochromatographic strip (ICS) for simultaneous detection of multiple transgenic proteins, including CP4 EPSPS, BT-Cry1Ab and BT-Cry1Ac, was developed in this study. The sensitivity of the strip to the target protein was 5 ng/mL for CP4 EPSPS, 100 ng/mL for BT-Cry1Ab and Cry1Ac, respectively. Parallel analysis for maize, soybean, sugar beet and cotton showed the strip could detect 1% of transgenic content in crops containing BT-Cry1Ab and Cry1Ac, and, at least, 0.1% of content in crops containing CP4 EPSPS. The detection results for seed samples indicated the multicomponent analysis ICS had good accuracy. The analysis could be completed within 10 min and had the advantages of being high-throughput, easy to operate and visual detection. This is the first report of semi-quantitative ICS for detecting three transgenic proteins simultaneously. The developed approach may provide insights into the development of ICS for analyzing simultaneously multiple components in genetically modified crops.

Colorimetric biosensing of nopaline synthase terminator using Fe3O4@Au and hemin-functionalized reduced graphene oxide

In this paper, we present a simple and label-free colorimetric biosensor for detection of the nopaline synthase (NOS) terminator in genetically modified (GM) plants. The "signal on" colorimetric biosensor was developed using a nanocomposite consisted of gold nanoparticles doped magnetic Fe₃O₄ nanoparticles (Fe₃O₄@Au NP), capture probe DNA (cDNA), and hemin-functionalized reduced graphene oxide nanosheets (H-GN). The nanocomposite was successfully prepared by means of Au-S bonds and the strong π interactions between cDNA and H-GN. The sensing approach is based on the excellent peroxidase-mimicking activity of H-GN and its different electrostatic interactions with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In presence of the target NOS, the cDNA in the nanocomposite will hybridize with its complementary sequence, and form dsDNA structure. Due to the weak π interactions between dsDNA and H-GN, a portion of H-GN will be released from the surface of Fe₃O₄@Au NPs and transferred into solution. After magnetic separation was performed, the supernatant was incubated with 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H₂O₂. The released H-GN can catalyze the oxidation reaction of TMB and turn the colorless solution blue. This "signal-on" colorimetric biosensor shows a broad linear range of 0.5-100 nM for the target NOS, with a 0.19 nM detection limit. The application of the biosensor for determination of NOS segments in samples of GM and non-GM tomatoes shows that it can discriminate between GM and non-GM plants. The reliability of the method for samples of NOS-spiked GM tomato suggests satisfactory recoveries in the range of 93.6%-94.2%.

Influence of Heat Processing on DNA Degradation and PCR-Based Detection of Wild-Type and Transgenic Maize

Reliable detection of genetically modified (GM) maize is significant for food authenticity, labelling, quality, and safety assessment. This study aims to evaluate the factors influencing degradation and polymerase chain reaction (PCR) amplification of DNA from the wild type and transgenic maize (events Bt-176 and MON810) during thermal treatment at 100°C and 121°C. A new PCR method was developed targeting the Cry1Ab gene to detect insect-resistant GM plants. The yield of genomic DNAs extracted by the DNeasy plant mini kit dramatically decreased while DNAs obtained by cetyltrimethyl ammonium bromide- (CTAB-) based method did not show any visible changes in the yield by the time of processing. Treatment at 100°C did not significantly affect either genomic DNAs or amplicons. Heating at 121°C induced time-dependent degradation of genomic DNAs and exogenous Cry1Ab gene; however, it did not have any considerable influence on the exogenous 141 bp amplicons or endogenous amplicons in the range of 102 bp to 226 bp with the exception of the event MON810 extracted by the DNeasy plant mini kit. More yield was observed at 226 bp than 140 bp fragment of the invertase gene. The 141 bp fragment of the transgenic CaMV 35S promoter exhibited the highest thermal stability of all the examined amplicons. Analysis of foodstuffs demonstrated 102 bp amplicons specific for the zein gene as the effective marker to detect maize in the processed foods. The obtained results demonstrate that PCR-based detection of the wild type and transgenic maize is dependent on the combination of different parameters of crucial factors such as temperature and duration of exposure, transgenic event, DNA extraction method, DNA marker, and size and location of amplicons.

A high-throughput and ultrasensitive identification methodology for unauthorized GMP component based on suspension array and logical calculator

To solve the problem of the unauthorized GMP components within import and export goods, the LI-US (Logic Identification of unauthorized GMP content by Universal-primer Suspension-array) system, which takes advantage of suspension array and logic calculator, was developed in the present study. Seventeen signal input channels have been optimized and validated in our research to ensure the multiplex practicality of the LI-US system. Three LI-US logic gates, including a YES gate, an OR gate and an AND gate, were designed as different detection strategies for GMP identification. The feasibility and specificity of the LI-US system were validated in the present study. Combining the optimization and evaluation of the signal input procedure, the sensitivity of this LI-US system reached 0.05% of the GMP mass concentration. The practicability evaluation of LI-US demonstrated its application within different substrates and varieties. In conclusion, the LI-US system was developed with extremely high specificity, sensitivity and practicability among different substrates and varieties, which could meet the demands of unauthorized GMP contents for both import and export goods.