Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops

Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms

Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.

CRISPR-Cas Detection Coupled with Isothermal Amplification of Bursaphelenchus xylophilus

The pine wood nematode (PWN), Bursaphelenchus xylophilus, causes significant damage to pine trees and, thus, poses a serious threat to pine forests worldwide, particularly in China, Korea, and Japan. A fast, affordable, and ultrasensitive detection of B. xylophilus is urgently needed for disease diagnosis. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have reshaped molecular diagnosis, with high speed, precision, specificity, strength, efficiency, and versatility. Herein, we established two isothermal diagnostics methods based on CRISPR-based platforms (CRISPR/Cas12a and CRISPR/Cas13a) for B. xylophilus-specific detection via fluorescence or lateral-flow strip readout. The guide RNA and CRISPR RNA were designed to target the 5S ribosomal DNA intergenic spacer sequences region of B. xylophilus. Recombinase-aided amplification was used for preamplification whose reaction condition was 37°C for 15 min. The sensitivity of CRISPR/Cas12a could reach 94 copies/µl of plasmid DNA, or 2.37 copies/µl of purified genomic DNA (gDNA) within 45 min at 37°C, while the sensitivity of CRISPR/Cas13a was 1,000 times higher than that of CRISPR/Cas12a of plasmid DNA in 15 min or 100 times higher of purified gDNA at the minimum reaction time of 4 min via fluorescence measurement. The CRISPR/Cas12a assay enabled the detection of 0.01 PWNs per 100 mg of pine wood, 10 times higher than that of the CRISPR/Cas13a assay. This work enriches molecular detection approaches for B. xylophilus and provides huge potential for ultrasensitive and rapid methods to detect B. xylophilus in pine wood, facilitating point-of-sample diagnostic processing for pine wilt disease management.

Paper-Based Simplified Visual Detection of Cry2Ab Insecticide from Transgenic Cottonseed Samples Using Integrated Quantum Dots-IgY Antibodies

In the present study, an easy to use field-deployable methodology was developed for onsite detection of pesticidal crystal protein Cry2Ab from transgenic cotton crops to reduce seed adulteration. Anti Cry2Ab IgG and IgY antibodies were developed against recombinant Cry2Ab protein in New Zealand white rabbits and in white leg horn chickens, respectively. Carboxyl-functionalized CdTe quantum dots (QDs) were used as revealing probes, and nitrocellulose paper was used as an assay matrix. Recombinant Cry2Ab was generated in the lab and used for immunization of chicken and rabbits. After successful immunization and attaining the desired titer values (1:32 000 for IgY and 1:64 000 for IgG), eggs and hyperimmune sera were collected. Anti Cry2Ab IgY was purified as per the standardized protocols, and anti Cry2Ab IgG was purified using protein A affinity chromatography. Sensitivity of the generated antibodies was examined using indirect ELISA methods against recombinant Cr2Ab protein. Specificity evaluation was carried out against other Cry proteins including Cry2Ab, Cry4b, Cry4a, Cry1Ec, and Cry1Ac. Functionalized CdTe QDs were characterized for structure and shape as well as fluorescence properties using standard laboratory techniques. A field-deployable paper-based detection methodology was developed where IgG acted as the capturing antibody and IgY-linked CdTe QDs were used as revealing probes. The limit of detection (LOD) and quantification (LOQ) were found to be 2.91 ng/mL and 9.71 ng/mL, respectively. The effect of matrix interference was assessed on the different plant crude extracts of cottonseed materials.

Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

The objective of the present study was to determine whether the loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and/or isothermal multiple-self-matching-initiated amplification (IMSA) methods can provide rapid detection of the runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 (AML1/ETO) fusion gene in acute myeloid leukemia (AML). According to the sequence of the AML1/ETO fusion gene available in GenBank and the principles of the LAMP, CPA and IMSA methods, specific primers were designed to bind a conserved region of the AML1/ETO gene in each assay. Following optimization of the conditions for the LAMP, CPA and IMSA assays, the specificity and sensitivity of the assays were examined and compared. In addition, 41 clinical samples were assayed using the three methods. It was observed that a ladder-like pattern of DNA products was produced in AML1/ETO-positive samples in all three assays, whereas no DNA product was generated with the controls. The detection limit of the LAMP and CPA assays was 50 copies/tube, and for the IMSA assay was 10 copies/tube. This sensitivity was consistent, and improved in the latter case, compared with that of the reverse transcription-polymerase chain reaction (RT-PCR) assay. Furthermore, the detection rate for bone marrow or peripheral blood samples was 9.76%, and the agreement among the LAMP, CPA, IMSA and RT-PCR methods was 100%. Therefore, the LAMP, CPA and IMSA methods optimized in the present study provided rapid detection of the AML1/ETO fusion gene for an initial clinical diagnosis of AML. In addition, the LAMP, CPA and IMSA assays are straightforward to perform and do not require specialized instruments. Therefore, these three isothermal methods may be used to perform field tests or assays at resource-limited hospitals.

Inter-laboratory validation of visual loop-mediated isothermal amplification assays for GM contents screening

Loop-mediated isothermal amplification (LAMP) has been widely used in many fields of molecular diagnostics, including detection of genetically modified organisms (GMOs). Herein, we report a collaborative ring trial validation of three established visual LAMP assays targeting three common GM elements, namely CaMV35S promoter, FMV35S promoter and NOS terminator, respectively. The high specificity of each assay was confirmed in different GM events analyses, and the sensitivity of each was determined to be 10, 10, and 50 haploid genome equivalents (HGEs) for CaMV35S promoter, FMV35S promoter, and NOS terminator, respectively. The probability of detection was also determined based on specificity and sensitivity data from 10 participating laboratories that returned correct results for the practical sample tests. These results demonstrate that the three visual LAMP assays are sensitive and time-saving, with high application potential for on-spot testing and routine screening of GMOs.

A Comparative Study of Three Detection Techniques for Leifsonia xyli Subsp. xyli, the Causal Pathogen of Sugarcane Ratoon Stunting Disease

The ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli (Lxx), is one of the most economically devastating diseases impacting sugarcane. RSD causes significant yield losses and variety degradation. Diagnosis of RSD is challenging because it does not exhibit any discernible internal and external symptoms. Moreover, the Lxx bacteria are very small and difficult to isolate, cultivate, and detect. In this study, conventional polymerase chain reaction (PCR), real-time quantitative PCR (RT-qPCR), and Lxx-loop-mediated isothermal amplification (Lxx-LAMP) were utilized to specifically detect the presence of Lxx pathogens in the juice from Lxx-infected sugarcane stalks and an Lxx-pMD18-T recombinant plasmid. The results showed that Lxx was a highly specific causal pathogen for RSD. All three techniques provided great reproducibility, while Lxx-LAMP had the highest sensitivity. When the DNA extract from Lxx-infected sugarcane juice was used as a template, Lxx-LAMP was 10 and 100 times more sensitive than RT-qPCR and conventional PCR, respectively. When the Lxx-pMD18-T recombinant plasmid was used as a template, Lxx-LAMP was as sensitive as RT-qPCR but was 10 times more sensitive than conventional PCR. Based on the Lxx-LAMP detection system established, adding 0.4 μM loop primers (LF/LP) can accelerate the reaction and reduce the total time required. In addition, the optimal amount of Bst DNA polymerase for Lxx-LAMP reactions was determined to be 6.0 U. The results provide technical support for the detection of RSD Lxx pathogen that will help manage sugarcane RSD.

Rapid sex identification method of spinach (Spinacia oleracea L.) in the vegetative stage using loop-mediated isothermal amplification

A LAMP-mediated, simple and rapid method for sex identification in spinach was developed. Nutrient compositional analysis showed a higher iron content in male than female plants. Spinach (Spinacia oleracea L.) is a dioecious plant with its sex determined by the XY system. Male and female floral organs differ morphologically, but plants do not differ in the vegetative stage before flowering. PCR with Y chromosome markers has been used to determine the sex of dioecious plants before flowering. In this study, we developed a genotype-specific loop-mediated isothermal amplification (LAMP) for sex identification of individual vegetative-stage spinach plants, using primers designed for the genomic region flanked by male-specific markers. LAMP could specifically detect spinach males. The method was further modified to omit DNA purification and use just an aliquot of crude leaf extract homogenized in water. We compared the nutrient composition of males and females, finding higher amounts of iron in the males. Our method could therefore be used for rapidly discriminating male plants in the field, which is useful for efficient hybrid breeding.

Current and new approaches in GMO detection: challenges and solutions

In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.

A portable automatic endpoint detection system for amplicons of loop mediated isothermal amplification on microfluidic compact disk platform

In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10⁻³ ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment.