A rapid and convenient method for on-site detection of MON863 maize through real-time fluorescence recombinase polymerase amplification

Surface enhanced Raman scattering tag enabled ultrasensitive molecular identification of Hippocampus trimaculatus based on DNA barcoding

Rapid and precise DNA barcode-based identification of biological species holds significant potential for pharmaceutical authentication and biomedical diagnostics. Herein, we present a polymerase chain reaction (PCR)-surface-enhanced Raman scattering (SERS) platform that integrates SERS tags for ultrasensitive and fast authentication of Hippocampus trimaculatus, a high-value traditional Chinese medicine (TCM). The SERS tags are composed of gold nanostars, near-infrared cyanine7 Raman reporters and carboxylated polystyrene shells, which achieve single-particle detection sensitivity under 780 nm irradiation. The tags also show excellent colloidal and SERS stability under physiologically relevant conditions (e.g., phosphate buffer saline, serum, 1 mM NaCl, and pH 1-12), with signal variations less than 5 %. The carboxylated polystyrene shells enable efficient DNA functionalization. Leveraging these advancements, the PCR-SERS assay detects genomic DNA (gDNA) at concentrations as low as 10 copies/μL within 20 thermal cycles, with remarkable specificity for Hippocampus trimaculatus over four common adulterant species. Notably, the method reduces amplification requirements to 5 thermal cycles (detection limit of 106 copies/μL) while completing the entire workflow in less than 30 min (conventional qPCR, 20-30 cycles, 1-2 h). Beyond TCM verification, this PCR-SERS platform holds broad applicability for rapid nucleic acid detection in fields ranging from environmental eDNA monitoring to point-of-care diagnostics.

Spatial double-layer hydrogels enabled visual detection of Cladobotryum mycophilum based on recombinase-aided amplification - CRISPR/Cas12a

Cladobotryum mycophilum, a pathogen responsible for cobweb disease, caused significant and irreversible losses in the mushroom industry. Effective monitoring and early prevention rely on the development of advanced diagnosis methods. This study introduced a novel hydrogel-based C. mycophilum detection method that integrates recombinase-aided amplification (RAA) with the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) system (CRISPR/Cas12a), referred as RCCH. The RAA reaction occurs within cross-linked PEG hydrogel, which is subsequently overlaid with a CRISPR/Cas12a-functionalized hydrogel. The porous network of the PEG hydrogel traps essential enzymes, facilitating spatial co-localization of target DNA and the CRISPR/Cas12a-crRNA complex. Upon activation of Cas12a's trans-cleavage activity, clear and countable fluorescent spots are generated for visual detection. RCCH demonstrates a limit of detection as low as 1 fg/μL, and exceptional selectivity against common fungi Trichoderma viride and T. harzianum and the host mushroom Lentinula edodes. The entire process is completed in under 40 min, indicating RCCH's potential as a rapid, accurate, and practical detection method for monitoring mushroom diseases. This innovative approach offers significant support for enhancing safety in the mushroom industry.

A snapshot on molecular technologies for diagnosing FAdV infections

Fowl adenoviruses (FAdV) are prevalent in chickens worldwide, responsible for several poultry diseases, including inclusion body hepatitis (IBH), hepatitis-hydropericardium syndrome (HHS), and gizzard erosion (GE), which result in significant economic losses in the poultry industry. Consequently, detection and efficient identification of FAdV serotypes are becoming extremely urgent to monitor outbreaks and develop vaccination strategies. Conventional PCR (cPCR) tests, combined with Restriction Fragment Length Polymorphism (RFLP) or sequencing, were developed for FAdV diagnosis. Although these molecular tests have considerably improved the accuracy of FAdV diagnosis compared with conventional methods, certain drawbacks remain unresolved, including lack of sensitivity and post-PCR analysis. Subsequently, advanced molecular technologies such as real-time PCR (qPCR), Loop Isothermal Amplification (LAMP), Cross-Priming Amplification (CPA), Recombinase Polymerase Amplification (RPA), Digital Droplet Polymerase Chain Reaction (ddPCR), Dot Blot Assay Combined with cPCR, Nanoparticle-Assisted PCR (nano-PCR), PCR-Refractory Quantitative Amplification (ARMS-qPCR), CRISPR/Cas13a Technology, and High-Resolution Melting Curve (HRM), have been developed to improve FAdV diagnosis.

Multi-chromatic and multi-component lateral flow immunoassay for simultaneous detection of CP4 EPSPS, Bt-Cry1Ab, Bt-Cry1Ac, and PAT/bar proteins in genetically modified crops

A multi-chromatic and multi-component lateral flow immunoassay (MCMC-LFIA) was developed for simultaneous detection of CP4 EPSPS, Bt-Cry1Ab, Bt-Cry1Ac, and PAT/bar proteins in genetically modified (GM) crops. Captured antibodies specific to these exogenous proteins were separately immobilized on a nitrocellulose membrane as test zones. Multi-colored microspheres, used as visible multi-probes, were conjugated with corresponding antibodies and sprayed on the conjugate pad. The assay results can be visually interpreted within 10 min by observing the appearance of colored bands. The MCMC-LFIA demonstrated high sensitivity, with detection of limits of 7.8 ng/mL for CP4 EPSPS and 2.5 ng/mL for Bt-Cry1Ab, Bt-Cry1Ac, and PAT/bar proteins, significantly improving the performance of previously reported LFIAs. The MCMC-LFIA exhibited excellent specificity and was validated for practical use in field-based applications. The proposed MCMC-LFIA offers a rapid, sensitive, and user-friendly tool for the on-site large-scale screening of GM materials.

RPA-CRISPR-Cas13a-assisted detection method of transmissible gastroenteritis virus

Background and aim

Transmissible gastroenteritis virus (TGEV) is a highly contagious gastrointestinal virus that causes diarrhea, vomiting, anorexia, dehydration, and weight loss in piglets. In clinical practice, it often occurs in mixed infections with other pathogens, and is therefore difficult to diagnose and prevent. It mainly harms piglets of about 2 weeks old, causing huge losses on farms. The clinical confirmation of TGEV usually requires a laboratory diagnosis, but traditional PCR and immunofluorescence assays have some limitations. Moreover, most farms in China are ill-equipped to accurately diagnose the disease. Therefore, a new detection method with high sensitivity and specificity and less dependence on instrumentation is required.

Methods

We used recombinase polymerase amplification (RPA), combined with the nuclease characteristics of the activated Cas13a protein to establish a visual CRISPR-Cas13a-assisted detection method for TGEV by adding a reporter RNA with fluorescent and quenching moieties to the system.

Result

We selected the optimal RPA primer and best CRISPR RNA (crRNA). The reaction system was optimized and its repeatability, specificity, and sensitivity verified. The TGEV detection system did not cross-react with other common diarrhea viruses, and its detection limit was 101 copies, which is similar with the sensitivity of qPCR. We successfully established an RPA-CRISPR-Cas13a-assisted detection method, and used this detection system to analyze 123 pig blood samples. qPCR was used as the gold standard method. The sensitivity, specificity, positive coincidence rate, and negative coincidence rate of the new method were 100, 98.93, 96.66, and 100%, respectively.

GMOIT: a tool for effective screening of genetically modified crops

BACKGROUND

Advancement in agricultural biotechnology has resulted in increasing numbers of commercial varieties of genetically modified (GM) crops worldwide. Though several databases on GM crops are available, these databases generally focus on collecting and providing information on transgenic crops rather than on screening strategies. To overcome this, we constructed a novel tool named, Genetically Modified Organisms Identification Tool (GMOIT), designed to integrate basic and genetic information on genetic modification events and detection methods.

RESULTS

At present, data for each element from 118 independent genetic modification events in soybean, maize, canola, and rice were included in the database. Particularly, GMOIT allows users to customize assay ranges and thus obtain the corresponding optimized screening strategies using common elements or specific locations as the detection targets with high flexibility. Using the 118 genetic modification events currently included in GMOIT as the range and algorithm selection results, a "6 + 4" protocol (six exogenous elements and four endogenous reference genes as the detection targets) covering 108 events for the four crops was established. Plasmids pGMOIT-1 and pGMOIT-2 were constructed as positive controls or calibrators in qualitative and quantitative transgene detection.

CONCLUSIONS

Our study provides a simple, practical tool for selecting, detecting, and screening strategies for a sustainable and efficient application of genetic modification.

Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review

Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.

Two electrochemiluminescence immunosensors for the sensitive and quantitative detection of the CP4-EPSPS protein in genetically modified crops

Two different models of electrochemiluminescence (ECL) immunosensors for the sensitive and quantitative detection of the CP4-EPSPS protein in genetically modified (GM) crops were proposed in this study. One was a signal-reduced ECL immunosensor based on nitrogen-doped graphene, graphitic carbon nitride and polyamide-amine (GN-PAMAM-g-C₃N₄) composites as the electrochemically active substance. The other model was a signal-enhanced ECL immunosensor based on a GN-PAMAM modified electrode for the detection of CdSe/ZnS quantum dots (QDs)-labeled antigens. The ECL signal responses of the reduced and enhanced immunosensors linearly decreased as the increase of the soybean RRS and RRS-QDs content in the range of 0.05% to 1.5% and 0.025% to 1.0%, with the limits of detection of 0.03% and 0.01% (S/N = 3), respectively. Both of the ECL immunosensors showed good specificity, stability, accuracy, and reproducibility in the analysis of real samples. The results indicate that the two immunosensors provide an ultra-sensitive and quantitative approach for the determination of the CP4-EPSPS protein. Due to their outstanding performances, the two ECL immunosensors could be useful tools for achieving the effective regulation of GM crops.

A visual CRISPR/dCas9-mediated enzyme-linked immunosorbent assay for nucleic acid detection with single-base specificity

Specific and economical nucleic acid detection is crucial for molecular diagnoses in resource-limited settings. Various facile readout approaches have been developed for nucleic acid detection, but they have limited specificity. Herein, nuclease-dead Cas9 (dCas9)/sgRNA was used as an excellent DNA recognition probe system to develop a visual clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated enzyme-linked immunosorbent assay (ELISA) for specific and sensitive detection of cauliflwer mosaic virus 35s (CaMV35S) promoter in genetically modified (GM) crops. In this work, the CaMV35S promoter was amplified with biotinylated primers, and then precisely bound with dCas9 in the presence of sgRNA. The formed complex was captured by antibody-coated microplate and bound to a streptavidin-labeled horseradish peroxidase probe for the visual detection. Under the optimal conditions, dCas9-ELISA could detect CaMV35s promoter as low as 12.5 copies μL^-1. Moreover, the proposed method was capable to distinguish the target sequence with single-base specificity. Coupled with one-step extraction and recombinase polymerase amplification, dCas9-ELISA can identify actual GM rice seeds within 1.5 h from sampling to results without expensive equipment and technical expertise. Therefore, the proposed method offers a specific, sensitive, rapid and cost-effective detection platform for molecular diagnoses.

The engineered CRISPR-Mb2Cas12a variant enables sensitive and fast nucleic acid-based pathogens diagnostics in the field

Existing CRISPR/Cas12a-based diagnostic platforms offer accurate and vigorous monitoring of nucleic acid targets, but have the potential to be further optimized for more efficient detection. Here, we profiled 16 Cas12a orthologs, focusing on their trans-cleavage activity and their potential as diagnostic enzymes. We observed the Mb2Cas12a has more robust trans-cleavage activity than other orthologs, especially at lower temperatures. An engineered Mb2Cas12a-RRVRR variant presented robust trans-cleavage activity and looser PAM constraints. Moreover, we found the existing one-pot assay, which simultaneously performed Recombinase Polymerase Amplification (RPA) and Cas12a reaction in one system, resulted in the loss of single-base discrimination during diagnosis. Therefore, we designed a reaction vessel that physically separated the RPA and Cas12a steps while maintaining a closed system. This isolated but closed system made diagnostics more sensitive and specific and effectively prevented contamination. This shelved Mb2Cas12a-RRVRR variant-mediated assay detected various targets in less than 15 min and exhibited equal or greater sensitivity than qPCR when detecting bacterial pathogens, plant RNA viruses and genetically modified crops. Overall, our findings further improved the efficiency of the current CRISPR-based diagnostic system and undoubtedly have great potential for highly sensitive and specific detection of multiple sample types.

RPA-CRISPR/Cas12a Combined with Rolling Circle Amplification-Enriched DNAzyme: A Homogeneous Photothermal Sensing Strategy for Plant Pathogens

Alternaria is an endemic fungus associated with brown spot disease, which is one of the most serious citrus diseases. In addition, the mycotoxins metabolized by Alternaria threaten human health seriously. Herein, a novel homogeneous and portable qualitative photothermal method based on recombinase polymerase amplification (RPA), CRISPR/Cas12a, and rolling circle amplification (RCA) for the detection of Alternaria is described. Using RCA primers as substrates for CRISPR/Cas12a trans-cleavage, the two systems, RPA-CRISPR/Cas12a and RCA-enriched G-quadruplex/hemin DNAzyme, are intelligently combined. Target DNA at fg/μL levels can be detected with high specificity. Additionally, the practicability of the proposed method is demonstrated by analyzing cultured Alternaria from different fruit and vegetable samples, as well as citrus fruit samples collected in the field. Furthermore, the implementation of this method does not require any sophisticated equipment and complicated washing steps. Therefore, it has great potential to screen Alternaria in poor laboratories.

An integrated nucleic acid detection method based on a microfluidic chip for collection and culture of rice false smut spores

Rice false smut spores (RFSS), which are airborne spores caused by Ustilaginoidea virens (U. virens), not only cause severe yield loss and grain quality reduction, but also produce toxins that are harmful to humans and animals. Nucleic acid detection has become the main method for RFSS monitoring due to its high specificity and sensitivity. However, nucleic acid detection requires multiple steps of spore collection, DNA extraction, nucleic acid amplification and detection, which has a high demand for personnel and is hard to link with other intelligent equipment to achieve automation. Microfluidic chip has become an important approach for integrated detection of pathogens owning to miniaturization and integration in recent years. Yet there is a lack of portable methods that integrate the collection of airborne fungal spores and nucleic acid detection. Because RFSS have thick cell walls and require liquid nitrogen grinding to extract DNA, breaking the walls on-chip is difficult. Therefore, the realization of RFSS wall breaking on-chip is a major difficulty and also a very meaningful study. This study uses RFSS as the research object and provides a novel method of culturing RFSS on-chip to solve the problem of hard wall breaking, realizing the integrated detection of RFSS. The mycelium grown by RFSS germination could be easily broken to release DNA for on-chip detection, which eliminates the need for manual DNA extraction and resolves the issue of difficult wall breaking. This chip can collect RFSS based on the aerodynamic theory and achieve gas-liquid coupling through a simple microvalve structure. A micromixer is constructed to mix the liquid, and then accomplish detection quickly by recombinase polymerase amplification and lateral flow dipsticks (RPA-LFD). The detection sensitivity of this method is 1 × 10²-1 × 10⁵ CFU ml^-1. It can realize the "sample in and answer out" detection of RFSS due to its simple operation, independence from precision instruments, high sensitivity and specificity. The result shows that it can be used for the early detection of RFSS, has great application prospects and is expected to promote the development of on-site instant detection equipment.

Recent advances in recombinase polymerase amplification: Principle, advantages, disadvantages and applications

After the outbreak of SARS-CoV-2, nucleic acid testing quickly entered people's lives. In addition to the polymerase chain reaction (PCR) which was commonly used in nucleic acid testing, isothermal amplification methods were also important nucleic acid testing methods. Among several common isothermal amplification methods like displaced amplification, rolling circle amplification, and so on, recombinase polymerase amplification (RPA) was recently paid more attention to. It had the advantages like a simple operation, fast amplification speed, and reaction at 37-42°C, et al. So it was very suitable for field detection. However, there were still some disadvantages to RPA. Herein, our review mainly summarized the principle, advantages, and disadvantages of RPA. The specific applications of RPA in bacterial detection, fungi detection, virus detection, parasite detection, drug resistance gene detection, genetically modified food detection, and SARS-CoV-2 detection were also described. It was hoped that the latest research progress on RPA could be better delivered to the readers who were interested in RPA.

An on-site adaptable test for rapid and sensitive detection of Potato mop-top virus, a soil-borne virus of potato (Solanum tuberosum)

Potato mop-top virus (PMTV) is considered an emerging threat to potato production in the United States. PMTV is transmitted by a soil-borne protist, Spongospora subterranean. Rapid, accurate, and sensitive detection of PMTV in leaves and tubers is an essential component in PMTV management program. A rapid test that can be adapted to in-field, on-site testing with minimal sample manipulation could help in ensuring the sanitary status of the produce in situations such as certification programs and shipping point inspections. Toward that goal, a rapid and highly sensitive recombinase polymerase amplification (RPA)-based test was developed for PMTV detection in potato tubers. The test combines the convenience of RPA assay with a simple sample extraction procedure, making it amenable to rapid on-site diagnosis of PMTV. Furthermore, the assay was duplexed with a plant internal control to monitor sample extraction and RPA reaction performance. The method described could detect as little as 10 fg of PMTV RNA transcript in various potato tissues, the diagnostic limit of detection (LOQ) similar to that of traditional molecular methods.

Establishment and evaluation of qPCR and real-time recombinase-aided amplification assays for detection of largemouth bass ranavirus

Largemouth bass ranavirus disease (LMBVD) caused by largemouth bass ranavirus (LMBV) has resulted in severe economic losses in the largemouth bass (Micropterus salmoides) farming industry in China. Early and accurate diagnosis is the key measure for the prevention and control of LMBVD. In this study, a quantitative polymerase chain reaction (qPCR) and a real-time recombinase-aided amplification (real-time RAA) assay were established for the detection of LMBV. The sensitivity and specificity of these two methods, and the efficacy for detection of LMBV from clinical samples were also evaluated. Results showed that the real-time RAA reaction was completed in <30 min at 39℃ with a detection limit of 58.3 copies, while qPCR reaction required 60 min with a detection limit of 5.8 copies. Both methods were specific for LMBV, where no cross-reactions observed with the other tested fish pathogens. Comparing the amplification results of both assays to the results obtained by virus isolation using 53 clinical tissue samples, results showed that the clinical sensitivity of real-time RAA and qPCR were 93.75% and 100% respectively, and the clinical specificity of both were 100%. Our results showed that qPCR is more suitable for quantitative analysis and accurate detection of LMBV in the laboratory, while real-time RAA is more suitable as a point-of-care diagnostic tool for on-site detection and screening of LMBV under farm conditions and in poorly equipped laboratories.

A nanomaterial-free and thionine labeling-based lateral flow immunoassay for rapid and visual detection of the transgenic CP4-EPSPS protein

Nanomaterial-based lateral flow immunoassays (LFIAs) have been widely used for the on-site detection of genetically modified components. However, the practical applications are often limited by the complex matrix, such as in red samples. In this study, a thionine (Thi) labeling-based LFIA was developed for the first time to detect CP4-EPSPS protein. The optimal labeling concentration of Thi was 0.5 mg/mL, and the antibody could be rapidly coupled to Thi in 10 min. The visual limit of detection (vLOD) levels for transgenic soybean, sugar beet, and cotton containing the CP4-EPSPS protein reached 0.05%, 0.1%, and 0.1%, respectively, and had no interference from other proteins. After storage at 4 °C for three months, the LFIA sensitivity remained unchanged and showed good stability. This method could be used to screen and detect a variety of transgenic crops containing the CP4-EPSPS protein, and the results were consistent with the current standard assay. This study pioneered the development of an immunochromatographic method using Thi as a marker and applied it to the detection of the CP4-EPSPS protein in herbicide-tolerant transgenic crops. This provides a new method for the rapid immunoassay of Thi as a dye and has good prospects for practical application.