1
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Singh M, Pal D, Aminedi R, Singh AK. Multiplex Real-Time Loop-Mediated Isothermal Amplification (LAMP) Based on the Annealing Curve Analysis: Toward an On-Site Multiplex Detection of Transgenic Sequences in Seeds and Food Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17658-17665. [PMID: 39044391 DOI: 10.1021/acs.jafc.4c01803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Monitoring of the introduction of unapproved genetically modified (GM) events is required because the approval status of a GM event may differ from country to country. The on-site methods such as loop-mediated isothermal amplification (LAMP) offer a technological answer for the rapid GM detection beyond the laboratories. Real-time LAMP assays detecting one GM target were reported earlier. To increase the efficiency of the assay, a multiplex real-time LAMP simultaneously targeting Figwort Mosaic Virus promoter (P-FMV) that constructs region between the Cauliflower Mosaic Virus 35S promoter and cry1Ac gene (p35S-cry1Ac) and neomycin phosphotransferase II (nptII) marker gene was developed. The assay could detect as low as 0.1% for each GM target within 45 min. To the best of our knowledge, multiplexing in real-time LAMP using the Genie II system with applicability in GM detection has been reported herein for the first time. The developed method provides rapid, on-site, and real-time GM detection in seeds and food products.
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Affiliation(s)
- Monika Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Deepa Pal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Raghavendra Aminedi
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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2
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Nguyen N, Van TV, Nguyen T. The synergy of nucleic acid amplification and miniaturized systems in enhancing liquid biopsy applications. Bioanalysis 2024; 16:499-504. [PMID: 38380670 PMCID: PMC11299790 DOI: 10.4155/bio-2023-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
- Ngoc Nguyen
- School of Biomedical Engineering, International University, Ho Chi Minh 700000, Vietnam & Vietnam National University, Ho Chi Minh City, 700000, Vietnam
| | - Toi Vo Van
- School of Biomedical Engineering, International University, Ho Chi Minh 700000, Vietnam & Vietnam National University, Ho Chi Minh City, 700000, Vietnam
| | - Trieu Nguyen
- Shared Research Facilities, West Virginia University, Morgantown, WV 26506, USA
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3
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Dong M, Kshirsagar A, Politza AJ, Guan W. High Fidelity Machine-Learning-Assisted False Positive Discrimination in Loop-Mediated Isothermal Amplification Using Nanopore-Based Sizing and Counting. ACS NANO 2024; 18:7170-7179. [PMID: 38393338 PMCID: PMC11197460 DOI: 10.1021/acsnano.3c12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, sensitive, and cost-effective method for developing point-of-care nucleic acid testing due to its isothermal nature. Yet, LAMP can suffer from the issue of false positives, which can compromise the specificity of the results. LAMP false positives typically arise due to contamination, nonspecific amplification, and nonspecific signal reporting (intercalating dyes, colorimetric, turbidity, etc.). While dye-labeled primers or probes have been introduced for multiplexed detection and enhanced specificity in LAMP assays, they carry the risk of reaction inhibition. This inhibition can result from the labeled primers with fluorophores or quenchers and probes that do not fully dissociate during reaction. This work demonstrated a nanopore-based system for probe-free LAMP readouts by employing amplicon sizing and counting, analogous to an electronic version of gel electrophoresis. We first developed a model to explore LAMP kinetics and verified distinct patterns between true and false positives via gel electrophoresis. Subsequently, we implemented nanopore sized counting and calibrated the event charge deficit (ECD) values and frequencies to ensure a fair analysis of amplicon profiles. This sized counting method, integrated with machine learning, achieved 91.67% accuracy for false positive discrimination, enhancing LAMP's reliability for nucleic acid detection.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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4
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
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.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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5
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Wu R, Meng B, Corredig M, Griffiths MW. Rapid Detection of Hepatitis A Virus in Foods Using a Bioluminescent Assay in Real-Time (BART) and Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Technology. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:144-157. [PMID: 36640204 PMCID: PMC9839959 DOI: 10.1007/s12560-022-09548-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/30/2022] [Indexed: 06/13/2023]
Abstract
Foodborne hepatitis A infections have been considered as a major threat for public health worldwide. Increased incidences of hepatitis A virus (HAV) infection has been associated with growing global trade of food products. Rapid and sensitive detection of HAV in foods is very essential for investigating the outbreaks. Real-time RT-PCR has been most widely used for the detection of HAV by far. However, the technology relies on fluorescence determination of the amplicon and requires sophisticated, high-cost instruments and trained personnel, limiting its use in low resource settings. In this study, a robust, affordable, and simple assay, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in combination with a bioluminescence-based determination of amplification in real-time (BART), was developed for the detection of HAV in different food matrices, including green onion, strawberry, mussel, and milk. The efficiencies of a one-step RT-LAMP-BART and a two-step RT-LAMP-BART were investigated for the detection of HAV in different food matrices and was compared with that of real-time RT-PCR. The sensitivity of the RT-LAMP-BART assay was significantly affected by Mg2+ concentration (P < 0.05), in addition to primer quality. The optimal Mg2+ concentration was 2 mM for one-step RT-LAMP-BART and 4 mM for two-step RT-LAMP-BART. Compared with cartridge-purified primers, HPLC-purified primers could greatly improve the sensitivity of the RT-LAMP-BART assay (P < 0.05). For detecting HAV in different food matrices, the performance of two-step RT-LAMP-BART was comparable with that of real-time RT-PCR and was better than that of one-step RT-LAMP-BART. The detection limit of the two-step RT-LAMP-BART for HAV in green onion, strawberry, mussel, and milk was 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, 8.3 × 100 PFU/5 g, and 8.3 × 100 PFU/40 mL, respectively. The developed RT-LAMP-BART was an effective, simple, sensitive, and robust method for foodborne HAV detection.
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Affiliation(s)
- Ruiqin Wu
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Milena Corredig
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mansel W Griffiths
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada
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Hardinge P. Molecular Beacons - Loop-Mediated Amplification (MB-LAMP). Methods Mol Biol 2023; 2638:289-299. [PMID: 36781650 DOI: 10.1007/978-1-0716-3024-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
High specificity has been demonstrated in polymerase chain reaction (PCR) with the use of molecular beacons (MBs) to detect amplified sequences containing mutations or single-nucleotide polymorphisms (SNPs). MBs have been adapted for use with the isothermal nucleic acid amplification technology loop-mediated amplification (LAMP) by targeting single-stranded loop sequences under optimized conditions to enable applications such as plant genotyping. LAMP has several benefits over PCR, such as rapid amplification, single-temperature reaction conditions enabling low-cost equipment, and robustness to certain PCR inhibitors. However, and despite the increased number of primers required, the specificity of LAMP is limited, and false positive results can be problematic. In this chapter, design considerations for molecular beacons in LAMP assays are described, as well as a method for MB-LAMP amplification and detection, with an example of gene sequences in genetically modified (GM) maize samples.
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7
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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8
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Mescolini G, Baigent SJ, Catelli E, Nair VK. Rapid, Sensitive, and Species-Specific Detection of Conventional and Recombinant Herpesvirus of Turkeys Vaccines Using Loop-Mediated Isothermal Amplification Coupled With a Lateral Flow Device Readout. Front Vet Sci 2022; 9:873163. [PMID: 35812862 PMCID: PMC9260039 DOI: 10.3389/fvets.2022.873163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/19/2022] [Indexed: 11/23/2022] Open
Abstract
Marek's disease, an economically important disease of chickens caused by virulent serotype 1 strains of the Mardivirus Marek's disease virus (MDV-1), is effectively controlled in the field by live attenuated vaccine viruses including herpesvirus of turkeys (HVT)—both conventional HVT (strain FC126) and, in recent years, recombinant HVT viruses carrying foreign genes from other avian viruses to protect against both Marek's disease and other avian viral diseases. Testing to monitor and confirm successful vaccination is important, but any such test must differentiate HVT from MDV-1 and MDV-2, as vaccination does not prevent infection with these serotypes. End-point and real-time PCR tests are widely used to detect and differentiate HVT, MDV-1 and MDV-2 but require expensive specialist laboratory equipment and trained operators. Here, we developed and validated two tube-based loop-mediated isothermal amplification tests coupled with detection by lateral flow device readout (LAMP-LFD): an HVT-specific test to detect both conventional and recombinant HVT strains, and a second test using novel LAMP primers to specifically detect the Vaxxitek® recombinant HVT. Specificity was confirmed using DNA extracted from virus-infected cultured cells, and limit of detection was determined using plasmid DNA carrying either the HVT or Vaxxitek® genome. The LAMP-LFD tests accurately detected all HVT vaccines, or Vaxxitek® only, in crude DNA as well as purified DNA extracted from field samples of organs, feathers, or poultry house dust that were confirmed positive for HVT by real-time PCR. These LAMP-LFD tests have potential for specific, rapid, simple, and inexpensive detection of HVT vaccines in the field.
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Affiliation(s)
- Giulia Mescolini
- Avian Pathology Service, Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Susan J. Baigent
- Viral Oncogenesis Group, The Pirbright Institute, Woking, United Kingdom
- *Correspondence: Susan J. Baigent
| | - Elena Catelli
- Avian Pathology Service, Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Venugopal K. Nair
- Viral Oncogenesis Group, The Pirbright Institute, Woking, United Kingdom
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9
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Antinori S, Ridolfo AL, Grande R, Galimberti L, Casalini G, Giacomelli A, Milazzo L. Loop-mediated isothermal amplification (LAMP) assay for the diagnosis of imported malaria: a narrative review. LE INFEZIONI IN MEDICINA 2022; 29:355-365. [PMID: 35146340 DOI: 10.53854/liim-2903-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 11/03/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular method to detect malaria recently introduced in the market. LAMP is simple to perform and does not require advanced equipment and training thus satisfying the qualification as a point-of-care diagnostic screening test. In this narrative review, we focus on the role of LAMP for malaria diagnosis in non-endemic settings. We searched PubMed, Embase, Scopus, and Google Scholar, using the following search terms: 'Malaria LAMP' in combination with 'imported malaria' or 'travellers' malaria' or 'non-endemic setting' or 'non-endemic region' or 'malaria screening' or 'malaria diagnosis'. References of each article were also reviewed for possible studies or reports not identified in our search. Overall, 18 studies encompassing 6289 tested samples with 1663 confirmed malaria diagnoses were retrieved. Most of these studies (13/18, 72.2%) were conducted in Europe, and almost half were retrospective. Fourteen studies (77.8%) employed real-time or nested-polymerase chain reaction as the reference method for confirming malaria diagnosis. Sensitivity of LAMP ranged from 93.9 to 100% and specificity from 93.8 to 100% with a negative predictive value of 99.6%-100%. The rate of reported invalid results requiring repeat of the test varied from 0.01% to 5.7%, but they were solved in the majority of cases with a secondary analysis. In non-endemic countries the adoption of LAMP malaria assay as the screening test for malaria diagnosis seems to perform better than conventional methods. However, blood microscopy remains essential to either identify Plasmodium species and quantify parasitaemia and adequately managing malaria cases.
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Affiliation(s)
- Spinello Antinori
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy.,III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Anna Lisa Ridolfo
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Romualdo Grande
- Clinical Microbiology, Virology and Bioemergency, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Laura Galimberti
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Giacomo Casalini
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy
| | - Andrea Giacomelli
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milano, Italy.,III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
| | - Laura Milazzo
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milano, Italy
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Jathoul AP, Branchini BR, Anderson JC, Murray JAH. A higher spectral range of beetle bioluminescence with infraluciferin. Front Bioeng Biotechnol 2022; 10:897272. [PMID: 36091447 PMCID: PMC9459109 DOI: 10.3389/fbioe.2022.897272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Coleopteran bioluminescence is unique in that beetle luciferases emit colors ranging between green (ca.550 nm) and red (ca.600 nm), including intermediate colors such as yellow and orange, allowing up to 3 simultaneous parameters to be resolved in vitro with natural luciferin (D-LH2). Here, we report a more than doubling of the maximum bioluminescence wavelength range using a single synthetic substrate, infraluciferin (iLH2). We report that different luciferases can emit colors ranging from visible green to near-infrared (nIR) with iLH2, including in human cells. iLH2 was designed for dual color far-red to nIR bioluminescence imaging (BLI) in small animals and has been utilized in different mouse models of cancer (including a metastatic hepatic model showing detailed hepatic morphology) and for robust dual parameter imaging in vivo (including in systemic hematological models). Here, we report the properties of different enzymes with iLH2: Lampyrid wild-type (WT) Photinus pyralis (Ppy) firefly luciferase, Ppy-based derivatives previously engineered to be thermostable with D-LH2, and also color-shifted Elaterid-based enzymes: blue-shifted Pyrearinus termitilluminans derivative Eluc (reported D-LH2 λmax = 538 nm) and red-shifted Pyrophorus plagiopthalamus derivative click beetle red (CBR) luciferase (D-LH2 λmax = 618 nm). As purified enzyme, in bacteria or in human cells, Eluc emitted green light (λmax = 536 nm) with DL-iLH2 whereas Ppy Fluc (λmax = 689 nm), x2 Fluc (λmax = 704 nm), x5 Fluc (λmax = 694 nm), x11 Fluc (λmax = 694 nm) and CBR (λmax = 721 nm) produced far-red to nIR peak wavelengths. Therefore, with iLH2, enzyme λmaxes can be separated by ca.185nm, giving almost non-overlapping spectra. This is the first report of single-substrate bioluminescence color emission ranging from visible green to nIR in cells and may help shed light on the color tuning mechanism of beetle luciferases. We also report on the reason for the improvement in activity of x11 Fluc with iLH2 and engineer an improved infraluciferase (iluc) based on this mutant.
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Affiliation(s)
- Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom.,Bioflares Ltd., Trowbridge, Wiltshire, United Kingdom
| | | | - James C Anderson
- Department of Chemistry, University College London, London, United Kingdom
| | - James A H Murray
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom
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11
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Hardinge P. Optimized Loop-Mediated Isothermal Amplification (LAMP) Allows Single Copy Detection Using Bioluminescent Assay in Real Time (BART). Methods Mol Biol 2022; 2524:107-117. [PMID: 35821466 DOI: 10.1007/978-1-0716-2453-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The bioluminescent assay in real time (BART) is a molecular diagnostic tool for the detection of nucleic acid amplification by recording light output. The key component for BART is a thermostable luciferase derived from the firefly Photinus pyralis. Coupling BART detection with the isothermal amplification method loop-mediated isothermal amplification (LAMP) enables rapid molecular diagnostic results using simple equipment. LAMP-BART provides quantitative results from a closed tube and is appropriate to microliter standard tests and nanoliter microfluidic assays. In this chapter, we introduce a protocol to amplify and detect genetic markers using LAMP with BART. Furthermore, we provide advice to optimize LAMP assays for high sensitivity and specificity and to eliminate the incidence of "false positive" results which can occur from the components of the assay. The optimization of genetically modified (GM) maize by targeting the nopaline synthase terminator (NOSt) and 35S promoter (35Sp) sequences is described.
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12
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Davidson JL, Wang J, Maruthamuthu MK, Dextre A, Pascual-Garrigos A, Mohan S, Putikam SVS, Osman FOI, McChesney D, Seville J, Verma MS. A paper-based colorimetric molecular test for SARS-CoV-2 in saliva. BIOSENSORS & BIOELECTRONICS: X 2021; 9:100076. [PMID: 34423284 PMCID: PMC8364207 DOI: 10.1016/j.biosx.2021.100076] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 04/16/2023]
Abstract
Herein, we describe the development of a paper-based device to detect nucleic acids of pathogens of interest in complex samples using loop-mediated isothermal amplification (LAMP) by producing a colorimetric response visible to the human eye. To demonstrate the utility of this device in emerging public health emergencies, we developed and optimized our device to detect SARS-CoV-2 in human saliva without preprocessing. The resulting device was capable of detecting the virus within 60 min and had an analytical sensitivity of 97% and a specificity of 100% with a limit of detection of 200 genomic copies/μL of patient saliva using image analysis. The device consists of a configurable number of reaction zones constructed of Grade 222 chromatography paper separated by 20 mil polystyrene spacers attached to a Melinex® backing via an ARclean® double-sided adhesive. The resulting device is easily configurable to detect multiple targets and has the potential to detect a variety of pathogens simply by changing the LAMP primer sets.
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Affiliation(s)
- Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Murali Kannan Maruthamuthu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Andres Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Ana Pascual-Garrigos
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Suraj Mohan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Sai Venkata Sravan Putikam
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Fujr Osman Ibrahim Osman
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
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13
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112424. [PMID: 34834787 PMCID: PMC8621059 DOI: 10.3390/plants10112424] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.
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Molecular Detection of Infectious Laryngotracheitis Virus in Chickens with a Microfluidic Chip. Animals (Basel) 2021; 11:ani11113203. [PMID: 34827935 PMCID: PMC8614514 DOI: 10.3390/ani11113203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Infectious laryngotracheitis (ILT) presents a major risk to the chicken industry. Rapid, specific, simple, and point-of-need molecular detection of the virus is crucial to enable chicken farms to take timely action and contain the spread of infection. The current study describes an isothermal amplification assay for infectious laryngotracheitis virus (ILTV) infection and the implementation of this assay in a microfluidic chip suitable for molecular detection and quasi-quantification of ILTV in diagnostic veterinary laboratories with low resources and poultry farms. Our assay performance was compared and favorably agreed with quantitative PCR (qPCR). Clinical tests of our assay and chip with samples from diseased chickens demonstrated good concordance with the gold-standard benchtop qPCR assay. Abstract Infectious laryngotracheitis (ILT) is a viral disease of chickens’ respiratory system that imposes considerable financial burdens on the chicken industry. Rapid, simple, and specific detection of this virus is crucial to enable proper control measures. Polymerase chain reaction (PCR)-based molecular tests require relatively expensive instruments and skilled personnel, confining their application to centralized laboratories. To enable chicken farms to take timely action and contain the spread of infection, we describe a rapid, simple, semi-quantitative benchtop isothermal amplification (LAMP) assay, and a field-deployable microfluidic device for the diagnosis of ILTV infection in chickens. Our assay performance was compared and favorably agreed with quantitative PCR (qPCR). The sensitivity of our real-time LAMP test is 250 genomic copies/reaction. Clinical performance of our microfluidic device using samples from diseased chickens showed 100% specificity and 100% sensitivity in comparison with benchtop LAMP assay and the gold-standard qPCR. Our method facilitates simple, specific, and rapid molecular ILTV detection in low-resource veterinary diagnostic laboratories and can be used for field molecular diagnosis of suspected ILT cases.
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Jamshidi S, Bokharaei-Salim F, Nahand JS, Monavari SH, Moghoofei M, Garshasbi S, Kalantari S, Esghaei M, Mirzaei H. Evaluation of the expression pattern of 4 microRNAs and their correlation with cellular/viral factors in PBMCs of Long Term non-progressors and HIV infected naïve Individuals. Curr HIV Res 2021; 20:42-53. [PMID: 34493187 DOI: 10.2174/1570162x19666210906143136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Long-term non-progressors (LTNPs) are small subsets of HIV-infected subjects that can control HIV-1 replication for several years without receiving ART. The exact mechanism of HIV-1 suppression has not yet been completely elucidated. Although the modulatory role of microRNAs (miRNAs) in HIV-1 replication has been reported, their importance in LTNPs is unclear. OBJECTIVE The aim of this cross-sectional study was to assess the expression pattern of miR-27b, -29, -150, and -221, as well as their relationship with CD4+ T-cell count, HIV-1 viral load, and nef gene expression in peripheral blood mononuclear cells (PBMCs) of untreated viremic patients and in LTNPs. METHODS MiRNAs expression levels were evaluated with real-time PCR assay using RNA isolated from PBMCs of LTNPs, HIV-1 infected naive patients, and healthy people. Moreover, CD4 T-cell count, HIV viral load, and nef gene expression were assessed. RESULTS The expression level of all miRNAs significantly decreased in the HIV-1 patient group compared to the control group, while the expression pattern of miRNAs in the LNTPs group was similar to that in the healthy subject group. In addition, there were significant correlations between some miRNA expression with viral load, CD4+ T-cell count, and nef gene expression. CONCLUSION The significant similarity and difference of the miRNA expression pattern between LNTPs and healthy individuals as well as between elite controllers and HIV-infected patients, respectively, showed that these miRNAs could be used as diagnostic biomarkers. Further, positive and negative correlations between miRNAs expression and viral/cellular factors could justify the role of these miRNAs in HIV-1 disease monitoring.
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Affiliation(s)
- Sogol Jamshidi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Javid Sadri Nahand
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Seyed Hamidreza Monavari
- Departments of Infectious Diseases and Tropical Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah. Iran
| | | | - Saeed Kalantari
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Hamed Mirzaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran. Iran
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Barthet MM. Teaching molecular techniques at home: Molecular biology labs that can be performed anywhere and enable hands-on learning of restriction digestion/ligation and DNA amplification. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:598-604. [PMID: 33900019 DOI: 10.1002/bmb.21517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
COVID 19 has changed about every aspect of life including how we teach in higher education. Laboratory experiments vital for learning hands-on techniques are limited due to social distancing requirements and increased numbers of distance-learning students. The solution to loss of hands-on activities has been to compensate with virtual laboratory modules. Although virtual labs are engaging and offer a simulated hands-on approach to teaching essential molecular techniques, these simulations do not replace hands-on experience. I designed two molecular biology laboratory exercises in response to the current teaching limitations that can be completed 'at-home' and enable low cost hands-on instruction of essential molecular techniques in any distance-learning environment including during the COVID 19 pandemic.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
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Singh M, Pal D, Sood P, Randhawa G. Construct-Specific Loop-Mediated Isothermal Amplification: Rapid Detection of Genetically Modified Crops with Insect Resistance or Herbicide Tolerance. J AOAC Int 2021; 103:1191-1200. [PMID: 33241393 DOI: 10.1093/jaoacint/qsaa043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Insect resistant and herbicide tolerant genetically modified (GM) events have been approved in many countries. Screening methods could facilitate preliminary testing to check the GM status, which may target control elements, transgenes, and marker genes or construct regions. Among these, methods targeting the construct region, i.e., the junction between two genetic elements of a transgenic cassette are more specific. OBJECTIVE Loop-mediated isothermal amplification (LAMP) assays targeting three construct regions were developed; between Cauliflower Mosaic Virus 35S promoter and cry1Ac gene (p35S-cry1Ac), cry2Ab2 gene and nos terminator (cry2Ab2-tnos), and cp4-epsps gene and nos terminator (cp4epsps-tnos). METHOD LAMP assays were performed by incubation at constant temperatures for selected targets. Positive amplification was detected as a change in color from orange to green on addition of SYBR® Green dye in visual LAMP and as real-time amplification curves in real-time LAMP. RESULTS These assays showed acceptable specificity and sensitivity. Visual LAMP was found to be sensitive enough to detect as low as 0.005%, equivalent to two target copies. Real-time LAMP assays were able to detect as low as four copies of the target within 40 min, making them suitable for rapid on-site testing for GM organisms (GMO). Practical utility was also verified using spiked test samples. CONCLUSIONS These assays could be employed to address some of the biosafety or post-release monitoring issues, as well as to check for approved and unapproved GM events in a country. HIGHLIGHTS LAMP assays targeting three construct regions have been developed, enabling screening for approved or unapproved GMO.
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Affiliation(s)
- Monika Singh
- ICAR-National Bureau of Plant Genetic Resources, Division of Genomic Resources, New Delhi 110 012, India
| | - Deepa Pal
- ICAR-National Bureau of Plant Genetic Resources, Division of Genomic Resources, New Delhi 110 012, India
| | - Payal Sood
- ICAR-National Bureau of Plant Genetic Resources, Division of Genomic Resources, New Delhi 110 012, India
| | - Gurinderjit Randhawa
- ICAR-National Bureau of Plant Genetic Resources, Division of Genomic Resources, New Delhi 110 012, India
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Fei Z, Wei R, Zhou D, Li N, Xiao P. A novel bioluminescent approach to the loop-mediated isothermal amplification-based detection of Lactobacillus salivarius in feed samples. J Microbiol Methods 2021; 187:106209. [PMID: 33771523 DOI: 10.1016/j.mimet.2021.106209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 11/25/2022]
Abstract
Coupling loop-mediated isothermal amplification (LAMP) with a bioluminescent assay in real-time (LAMP-BART) is a strategy that can be readily leveraged to detect bacteria in particular samples of interest without the need for costly or complicated equipments. However, this approach exhibits poor sensitivity, and it additionally amplifies all target DNA including that derived from non-viable cells. Herein, we sought to overcome these traditional pyrophosphate bioluminescent assay limitations by utilizing 2-deoxyadenosine-5-(α-thio) -triphosphate (dATPαS) in place of dATP when conducting LAMP, thereby markedly reducing and stabilizing overall background signal levels, resulting in a detection limit of 3 CFU/μL. We were additionally able to ouple this LAMP-BART with propidium monoazide (PMAxx™) as a means of eliminating false-positive signals derived from nonviable cells. Herein, we detail the development of this PMAxx™-LAMP-BART assay and its use for the detection of live Lactobacillus salivarius. Our developed approach exhibited 100% specificity, with a 3 CFU/μL limit of detection (LOD) pure culture. In the application of feed, the LOD was 103 CFU per 10 g of spiked dry dog food and 102 CFU per 10 g of spiked chicken feed without enrichment. Traditional culture methods and a MALDI Biotyper were also used to confirm the accuracy of our novel assay system.
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Affiliation(s)
- Zhongjie Fei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Rongbin Wei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Dongrui Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Na Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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El-Tholoth M, Bai H, Mauk MG, Saif L, Bau HH. A portable, 3D printed, microfluidic device for multiplexed, real time, molecular detection of the porcine epidemic diarrhea virus, transmissible gastroenteritis virus, and porcine deltacoronavirus at the point of need. LAB ON A CHIP 2021; 21:1118-1130. [PMID: 33527920 PMCID: PMC7990716 DOI: 10.1039/d0lc01229g] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) are emerging/reemerging coronaviruses (CoVs) of neonatal pigs that cause great economic losses to pig farms and pork processors. Specific, rapid, and simple multiplex detection of these viruses is critical to enable prompt implementation of appropriate control measures. Conventional methods for molecular diagnosis require skilled personnel and relatively sophisticated equipment, restricting their use in centralized laboratories. We developed a low-cost, rapid, semi-quantitative, field deployable, 3D-printed microfluidic device for auto-distribution of samples and self-sealing and real-time and reverse transcription-loop-mediated isothermal amplification (RT-LAMP), enabling the co-detection of PEDV, TGEV and PDCoV within 30 minutes. Our assay's analytical performance is comparable with a benchtop, real-time RT-LAMP assay and the gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay with limits of detection of 10 genomic copies per reaction for PEDV and PDCoV, and 100 genomic copies per reaction for TGEV. Evaluation of clinical specimens from diseased pigs with our microfluidic device revealed excellent concordance with both benchtop RT-LAMP and qRT-PCR. Our portable RT-LAMP microfluidic chip will potentially facilitate simple, specific, rapid multiplexed detection of harmful infections in minimally equipped veterinary diagnostic laboratories and on-site in pigs' farms.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt.
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An innovative and user-friendly smartphone-assisted molecular diagnostic approach for rapid detection of canine vector-borne diseases. Parasitol Res 2021; 120:1799-1809. [PMID: 33649963 PMCID: PMC7920752 DOI: 10.1007/s00436-021-07077-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Present-day diagnostic tools and technologies for canine diseases and other vector-borne parasitic diseases hardly meet the requirements of an efficient and rapid diagnostic tool, which can be suitable for use at the point-of-care in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been always a method of choice in the development and validation of quick, precise, and sensitive diagnostic assays for pathogen detection and to reorganize point-of-care (POC) molecular diagnostics. In this study, we have demonstrated an efficient detection system for parasitic vector-borne pathogens like Ehrlichia canis and Hepatozoon canis by linking the LAMP assay to a smartphone via a simple, inexpensive, and a portable “LAMP box,” All the components of the LAMP box were connected to each other wirelessly. This LAMP box was made up of an isothermal heating pad mounted below an aluminum base which served as a platform for the reaction tubes and LAMP assay. The entire setup could be connected to a smartphone via an inbuilt Wi-Fi that allowed the user to establish the connection to control the LAMP box. A 5 V USB power source was used as a power supply. The sensitivity of the LAMP assay was estimated to be up to 10−6 dilution limit using the amplified, purified, and quantified specific DNA templates. It can also serve as an efficient diagnostic platform for many other veterinary infectious or parasitic diseases of zoonotic origin majorly towards field-based diagnostics.
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Abstract
Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans is critical to facilitate appropriate control measures and treatment. Conventional polymerase chain reaction (PCR)-based molecular diagnostics requires relatively expensive equipment and trained staff, restricting its use to centralized laboratories with significant delays between sample collection and test results. Herein, we report a highly sensitive, rapid, point-of-need, two-stage-molecular test that requires minimal instrumentation and training. Our test, dubbed Penn-RAMP, combines recombinase polymerase amplification (RPA, 38 °C) and loop-mediated isothermal amplification (LAMP, 63 °C) in one tube, enabling nested, two-stage isothermal amplification. We demonstrate Penn-RAMP's efficacy by testing for two common viral respiratory diseases of chickens: infectious laryngotracheitis (ILT) and infectious bronchitis (IB) that impose great economic burden worldwide. Test results of clinical samples with our closed-tube Penn-RAMP assays concord with the gold standard quantitative PCR (qPCR) assay; with 10-fold better limit of detection than LAMP and qPCR. Our closed-tube Penn-RAMP assays have the potential to greatly reduce false negatives while requiring minimal instrumentation and training.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt.
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22
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Wang Q, Shen X, Qiu T, Wu W, Li L, Wang Z, Shou H. Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing. J Zhejiang Univ Sci B 2021; 22:99-111. [PMID: 33615751 DOI: 10.1631/jzus.b2000465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification. In this study, a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin (PVC) sheet. This modified method is named EZ-D, for EASY DNA extraction. Compared with the original cetyl trimethylammonium bromide (CTAB) method, DNA extracted by EZ-D is more efficient in polymerase chain reaction (PCR) amplification due to the more stable performance of the EZ-D stick. The EZ-D method is also faster, easier, and cheaper. PCR analyses showed that DNA extracted from several types of plant tissues by EZ-D was appropriate for specific identification of biological samples. A regular PCR reaction can detect the EZ-D-extracted DNA template at concentration as low as 0.1 ng/μL. Evaluation of the EZ-D showed that DNA extracts could be successfully amplified by PCR reaction for DNA fragments up to 3000 bp in length and up to 80% in GC content. EZ-D was successfully used for DNA extraction from a variety of plant species and plant tissues. Moreover, when EZ-D was combined with the loop-mediated isothermal amplification (LAMP) method, DNA identification of biological samples could be achieved without the need for specialized equipment. As an optimized DNA purification method, EZ-D shows great advantages in application and can be used widely in laboratories where equipment is limited and rapid results are required.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoxia Shen
- Zhejiang Institute of Chinese Medicine, Hangzhou 310023, China
| | - Tian Qiu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei Wu
- Shanghai YouLong Biotech Co., Ltd., Shanghai 200063, China
| | - Lin Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhi'an Wang
- Zhejiang Institute of Chinese Medicine, Hangzhou 310023, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Gao R, Liao X, Zhao X, Liu D, Ding T. The diagnostic tools for viable but nonculturable pathogens in the food industry: Current status and future prospects. Compr Rev Food Sci Food Saf 2021; 20:2146-2175. [PMID: 33484068 DOI: 10.1111/1541-4337.12695] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022]
Abstract
Viable but nonculturable (VBNC) microorganisms have been recognized as pathogenic contaminants in foods and environments. The failure of VBNC cells to form the visible colonies hinders the ability to use conventional media for their detection. Efficient and rapid detection of pathogens in the VBNC state is a prerequisite to ensure the food safety and public health. Despite their nonculturability, VBNC cells have distinct characteristics, such as morphology, metabolism, chemical composition, and gene and protein expression, that have been used as the basis for the development of abundant diagnostic tools. This review covers the current status and advances in various approaches for examining microorganisms in the VBNC state, including but not limited to the methodological aspects, advantages, and drawbacks of each technique. Existing methods, such as direct viable count, SYTO/PI dual staining, and propidium monoazide quantitative polymerase chain reaction (PCR), as well as some techniques with potential to be applied in the future, such as digital PCR, enhanced-surface Raman spectroscopy, and impedance-based techniques, are summarized in depth. Finally, future prospects for the one-step detection of VBNC bacteria are proposed and discussed. We believe that this review can provide more optional methods for researchers and promote the development of rapid, accurate detecting methods, and for inspectors, the diagnostic tools can provide data to undertake risk analysis of VBNC cells.
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Affiliation(s)
- Rui Gao
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyu Liao
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Donghong Liu
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tian Ding
- Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
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A Novel Approach to the Bioluminescent Detection of the SARS-CoV-2 ORF1ab Gene by Coupling Isothermal RNA Reverse Transcription Amplification with a Digital PCR Approach. Int J Mol Sci 2021; 22:ijms22031017. [PMID: 33498408 PMCID: PMC7864175 DOI: 10.3390/ijms22031017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 01/17/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus, which first emerged in December 2019, represents an ongoing global public health emergency. Here, we developed an improved and highly sensitive approach to SARS-CoV-2 detection via coupling bioluminescence in real-time (BART) and reverse-transcriptase loop-mediated amplification (RT-LAMP) protocols (RT-LAMP-BART) and was also compatible with a digital LAMP system (Rainsuit), which did not allow for real-time quantification but did, nonetheless, facilitate absolute quantification with a comparable detection limit of 104 copies/mL. Through improving RNA availability in samples to ensure the target RNA present in reaction, we additionally developed a simulated digital RT-LAMP approach using this same principle to enlarge the overall reaction volume and to achieve real-time detection with a limit of detection of 10 copies/mL, and with further improvements in the overall dynamic range of this assay system being achieved through additional optimization.
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Prasannakumar MK, Parivallal BP, Manjunatha C, Pramesh D, Narayan KS, Venkatesh G, Banakar SN, Mahesh HB, Vemanna RS, Rangaswamy KT. Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay. Mol Biol Rep 2021; 48:467-474. [PMID: 33394228 DOI: 10.1007/s11033-020-06077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/10/2020] [Indexed: 01/15/2023]
Abstract
The use of resistant (R) genes is the most effective strategy to manage bacterial leaf blight (BLB) disease of rice. Several attempts were made to incorporate R genes into susceptible rice cultivars using marker-assisted backcross breeding (MABB). However, MABB relies exclusively on PCR for foreground selection of R genes, which requires expensive equipment for thermo-cycling and visualization of results; hence, it is limited to sophisticated research facilities. Isothermal nucleic acid amplification techniques such as loop-mediated isothermal amplification (LAMP) assay do not require thermo-cycling during the assay. Therefore, it will be the best alternative to PCR-based genotyping. In this study, we have developed a LAMP assay for the specific and sensitive genotyping of seven BLB resistance (R) genes viz., Xa1, Xa3, Xa4, Xa7, Xa10, Xa11, and Xa21 in rice. Gene-specific primers were designed for the LAMP assay. The LAMP assay was optimized for time, temperature, and template DNA concentration. For effective detection, incubation at 60 °C for 30 min was optimum for all seven R genes. A DNA intercalating dye ethidium bromide and a calorimetric dye hydroxynaphthol blue was used for result visualization. Further, sensitivity assay revealed that the LAMP assay could detect R genes at 100 fg of template DNA compared to 1 ng and 10 pg, respectively, in conventional PCR and q-PCR assays. The LAMP assay developed in this study provides a simple, specific, sensitive, robust, and cost-effective method for foreground selection of R genes in the resistance breeding programs of resource-poor laboratory.
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Affiliation(s)
- M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India.
| | - Buela P Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Chennappa Manjunatha
- ICAR-Indian Agricultural Research Institute, Regional Station Wellington, Nilgiris, Tamil Nadu, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, Gangavathi, University of Agricultural Sciences, Raichur, Karnataka, India.
| | - Karthik S Narayan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, India
| | - Gopal Venkatesh
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, India
| | - Sahana N Banakar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - H B Mahesh
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - Ramu S Vemanna
- Department of Biotechnology, Regional Centre for Biotechnology, Gurgaon, Haryana, India
| | - K T Rangaswamy
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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Kim MJ, Shin SW, Kim HB, Kim E, Kim HY. Direct loop-mediated isothermal amplification (LAMP) assay for rapid on-site detection of Bifidobacterium longum subspecies longum, infantis, and suis in probiotic products. Food Chem 2020; 346:128887. [PMID: 33385916 DOI: 10.1016/j.foodchem.2020.128887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
Abstract
As interest in probiotics increases, the need for accurate description of probiotic compositions present in commercial products is also increasing. Since Bifidobacterium longum used as probiotics is labeled at species or subspecies levels, a detection method for distinguishing B. longum subsp. longum, infantis, and suis is needed. Thus, we designed three LAMP primer sets for B. longum subspecies. Each primer set was specific for the target subspecies. The detection level was 0.2 pg for each target DNA (about 102 CFU/mL). To apply these LAMP assays to on-site detection, a direct DNA extraction method was optimized and combined with LAMP assay. Finally, direct LAMP assays were used to monitor the presence of B. longum subspecies in 16 probiotic products. They could specifically and sensitively detect target subspecies within approximately 45 min. These rapid on-site detection methods are useful for identifying B. longum subspecies in probiotic products.
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Affiliation(s)
- Mi-Ju Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - So Won Shin
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeon-Be Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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Bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells. Sci Rep 2020; 10:21886. [PMID: 33318599 PMCID: PMC7736893 DOI: 10.1038/s41598-020-78996-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/02/2020] [Indexed: 12/02/2022] Open
Abstract
Microfluidic droplet generation affords precise, low volume, high throughput opportunities for molecular diagnostics. Isothermal DNA amplification with bioluminescent detection is a fast, low-cost, highly specific molecular diagnostic technique that is triggerable by temperature. Combining loop-mediated isothermal nucleic acid amplification (LAMP) and bioluminescent assay in real time (BART), with droplet microfluidics, should enable high-throughput, low copy, sequence-specific DNA detection by simple light emission. Stable, uniform LAMP–BART droplets are generated with low cost equipment. The composition and scale of these droplets are controllable and the bioluminescent output during DNA amplification can be imaged and quantified. Furthermore these droplets are readily incorporated into encapsulated droplet interface bilayers (eDIBs), or artificial cells, and the bioluminescence tracked in real time for accurate quantification off chip. Microfluidic LAMP–BART droplets with high stability and uniformity of scale coupled with high throughput and low cost generation are suited to digital DNA quantification at low template concentrations and volumes, where multiple measurement partitions are required. The triggerable reaction in the core of eDIBs can be used to study the interrelationship of the droplets with the environment and also used for more complex chemical processing via a self-contained network of droplets, paving the way for smart soft-matter diagnostics.
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El-Tholoth M, Mauk MG, Anis E, Bau HH. A closed-tube, single-step, real time, reverse transcription-loop-mediated isothermal amplification assay for infectious bronchitis virus detection in chickens. J Virol Methods 2020; 284:113940. [PMID: 32687868 PMCID: PMC7367007 DOI: 10.1016/j.jviromet.2020.113940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/24/2022]
Abstract
A closed tube, single-step-real-time-RT-LAMP assay was developed for detection and semi-quantification of IBV in closed tube. The least limit of detection of our assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens using our assay shows a very good concordance with RT-qPCR assay.
Infectious bronchitis (IB) is a viral infection of the chicken respiratory tract that causes substantial economic burden on the industry. Simple, specific and rapid diagnosis of this disease is critical for the initiation of appropriate control measures. Conventional molecular diagnostic methods require a relatively sophisticated equipment and skilled staff. Here we describe a rapid, simple, semi-quantative, closed-tube, single-step, real-time- reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for IB and compare our assay with quantative, reverse transcription- polymerase chain reaction (RT-qPCR). The limit of detection (LOD) of our RT-LAMP assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens with our RT-LAMP showed a very good concordance with RT-qPCR. Our assay enables simple, specific, rapid molecular detection and semi-quantification of the infectious bronchitis virus (IBV) in veterinary diagnostic laboratories. Furthermore, our RT-LAMP detection is carried out in a sealed tube, eliminating the risk of false-positive results in subsequent tests because of any contamination of the work area as in the case of lateral flow strip or gel electrophoresis-based amplicon detection.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 19348, United States
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
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Fei Z, Zhou D, Dai W, Xiao P. Rapid and highly sensitive detection of Escherichia coli O157:H7 in food with loop-mediated isothermal amplification coupled to a new bioluminescent assay. Electrophoresis 2020; 41:1793-1803. [PMID: 32335921 DOI: 10.1002/elps.202000046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/07/2020] [Accepted: 04/17/2020] [Indexed: 02/05/2023]
Abstract
Testing for bioluminescent pyrophosphate is a convenient method of DNA detection without complex equipments, but it is insufficiently sensitive and offers no particular time advantage over other rapid detection methods. The shortcomings of the traditional bioluminescent pyrophosphate method have been addressed by using 2-deoxyadenosine-5-(α-thio)-triphosphate (dATPαS) instead of dATP for LAMP, thus reducing the high background signal and generating a constant background value. In this study, LAMP coupled to a novel bioluminescent pyrophosphate assay was developed to detect E. coli O157:H7. The new method has a limit of detection of <10 copies/μL or 5 CFU/mL; its sensitivity is higher than that of the conventional LAMP assay. Moreover, a food-borne pathogen can be detected when a single DNA template is included in the LAMP assay, making it 100 times more sensitive than the traditional LAMP method. Three hundred food samples were tested with this assay and the accuracy of detection was verified with a culture method and MALDI Biotyper. The assay only took 90-120 min and detected <10 copies of the pathogen. This method had the advantages of rapidity, sensitivity, and simplicity, so it is very competitive for the rapid and highly sensitive detection of food-borne pathogens.
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Affiliation(s)
- Zhongjie Fei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Dongrui Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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Ding G, Jin Z, Zhang Y, Han Y, Li G, Jing Y, Li W. Detection of Genetically Modified Rice by Loop-Mediated Isothermal Amplification Assays on a Self-Priming Compartmentalization Chip. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01766-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Rapid visual detection of Vibrio parahaemolyticus in seafood samples by loop-mediated isothermal amplification with hydroxynaphthol blue dye. World J Microbiol Biotechnol 2020; 36:76. [PMID: 32390085 DOI: 10.1007/s11274-020-02851-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
The detection and monitoring of Vibrio parahaemolyticus pathogen in aquatic foods have become essential for preventing outbreaks. In this study, loop-mediated isothermal amplification (LAMP) assay with the azo dye, hydroxynaphthol blue (HNB) was developed targeting species-specific tlh gene. The assay was carried out on 62 seafood samples that included clam and shrimp and compared with conventional LAMP assay performed with the commonly used fluorescent dye, conventional PCR, and real-time PCR (RT-PCR). Of 62 samples studied for tlh gene, 32 (51.61%) gave positive by HNB-LAMP, which comprised 22 (70.96%) clam samples and 10 (32.25%) shrimp samples. The HNB-LAMP assay was found to be highly sensitive, specific, and superior to conventional PCR (p > 0.05). RT-PCR presented higher sensitivity than HNB-LAMP; however, it has the limitation of being cost-intensive and requiring technical expertise to perform. HNB-LAMP is affordable, rapid, simple, and easy to perform, allowing naked eye visualization.
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Hardinge P, Murray JAH. Full Dynamic Range Quantification using Loop-mediated Amplification (LAMP) by Combining Analysis of Amplification Timing and Variance between Replicates at Low Copy Number. Sci Rep 2020; 10:916. [PMID: 31969573 PMCID: PMC6976701 DOI: 10.1038/s41598-020-57473-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022] Open
Abstract
Quantification of nucleic acid targets at low copy number is problematic with the limit of detection at 95 percent confidence predicted to be 3 molecules or higher for quantitative PCR. Conversely the accuracy of digital PCR is diminished at higher concentrations of template approaching 100 percent positive partitions, with the Poisson distribution showing that an average of only 3 molecules per partition represents an amplification frequency of greater than 95 percent. Therefore a full range of template concentrations cannot be quantified accurately with these methods alone without dilution. Here we report the development of quantification metrics for use with loop-mediated amplification (LAMP) as a bridge between concentrated and dilute template concentrations. The basis for this is that real-time monitoring of LAMP reactions either by bioluminescent reporting (BART) or by fluorescent dye binding shows increasing variation in timings between replicates at low copy number due to the LAMP amplification mechanism. This effect increases with decreasing copy number, closely associated with the amplification frequency. The use of an artificial template showed that the increasing variation is not linked to the use of displacement primers during the initiation of amplification and is therefore a fundamental feature of the LAMP initiation event. Quantification between 1 and 10 copies of a template was successfully achieved with a number of methods with a low number of replicates with the strongest correlation to timing variance. These ultra-quantification methods for LAMP amplification either singularly or in combination have potential in a full dynamic range quantification strategy based on LAMP, in a closed tube, undiluted sample molecular diagnostic.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff, CF10 3AX, UK
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Baldi P, La Porta N. Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry. FRONTIERS IN PLANT SCIENCE 2020; 11:570862. [PMID: 33193502 PMCID: PMC7655913 DOI: 10.3389/fpls.2020.570862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 05/14/2023]
Abstract
Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.
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Affiliation(s)
- Paolo Baldi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Paolo Baldi,
| | - Nicola La Porta
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), San Michele a/Adige, Trento, Italy
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35
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Pearson MD, Nguyen L, Zhao Y, McKenna WL, Morin TJ, Dunbar WB. Fast and accurate quantification of insertion-site specific transgene levels from raw seed samples using solid-state nanopore technology. PLoS One 2019; 14:e0226719. [PMID: 31881056 PMCID: PMC6934305 DOI: 10.1371/journal.pone.0226719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/02/2019] [Indexed: 11/19/2022] Open
Abstract
Many modern crop varieties contain patented biotechnology traits, and an increasing number of these crops have multiple (stacked) traits. Fast and accurate determination of transgene levels is advantageous for a variety of use cases across the food, feed and fuel value chain. With the growing number of new transgenic crops, any technology used to quantify them should have robust assays that are simple to design and optimize, thereby facilitating the addition of new traits to an assay. Here we describe a PCR-based method that is simple to design, starts from whole seeds, and can be run to end-point in less than 5 minutes. Subsequent relative quantification (trait vs. non-trait) using capillary electrophoresis performed in 5% increments across the 0-100% range showed a mean absolute error of 1.9% (s.d. = 1.1%). We also show that the PCR assay can be coupled to non-optical solid-state nanopore sensors to give seed-to-trait quantification results with a mean absolute error of 2.3% (s.d. = 1.6%). In concert, the fast PCR and nanopore sensing stages demonstrated here can be fully integrated to produce seed-to-trait quantification results in less than 10 minutes, with high accuracy across the full dynamic range.
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Affiliation(s)
| | - Leslee Nguyen
- Ontera, Inc., Santa Cruz, California, United States of America
| | - Yanan Zhao
- Ontera, Inc., Santa Cruz, California, United States of America
| | | | - Trevor J. Morin
- Ontera, Inc., Santa Cruz, California, United States of America
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Singh M, Pal D, Sood P, Randhawa G. Loop-mediated isothermal amplification assays: Rapid and efficient diagnostics for genetically modified crops. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.106759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Yan H, Zhang J, Ma D, Yin J. qPCR and loop mediated isothermal amplification for rapid detection of Ustilago tritici. PeerJ 2019; 7:e7766. [PMID: 31592112 PMCID: PMC6776072 DOI: 10.7717/peerj.7766] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/26/2019] [Indexed: 01/15/2023] Open
Abstract
Loose smut of wheat caused by the basidiomycete fungus Ustilago tritici, a seed-borne disease, is difficult to control because of the expanse of wheat planting area and difficulty in pathogen detection. In this study, real-time fluorescence quantitative PCR (qPCR) and loop-mediated isothermal amplification (LAMP) assays are used to rapidly amplify the DNA of U. tritici. Five pairs of primers for qPCR and two series primers for LAMP were designed. Primarily, the specificity of the primer was assessed by using genomic DNA of U. tritici, Fusarium graminearum, Blumeria graminis, Rhizoctonia cerealis, Puccinia striiformis, Bipolaris sorokiniana, and Alternaria solani as templates. Further, the amplification systems were optimized. Finally, the sensitivity of qPCR and LAMP assays were evaluated. The results showed that the primer Y-430 F/R, Y-307 F/R, Y-755 F/R, and Y-139 F/R for qPCR and primers L-139 and L-988 for LAMP could be used for U. tritici detection. In the sensitivity test, the detection limit of qPCR assay was identified as 10 pg μL−1 of genomic DNA, the detection limit for LAMP assay was 100 fg μL−1. We successfully performed qPCR and LAMP assays on wheat loose smut wheat samples. This paper establishes two methods for U. tritici detection, which can be used for diagnosis of wheat loose smut in the laboratory and in the field.
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Affiliation(s)
- Hanwen Yan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Collaborative Innovation Center for Grain Industry, College of Agricultural, Yangtze University, Jingzhou, Hubei, China
| | - Jian Zhang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Collaborative Innovation Center for Grain Industry, College of Agricultural, Yangtze University, Jingzhou, Hubei, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Collaborative Innovation Center for Grain Industry, College of Agricultural, Yangtze University, Jingzhou, Hubei, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Collaborative Innovation Center for Grain Industry, College of Agricultural, Yangtze University, Jingzhou, Hubei, China
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Hardinge P, Murray JAH. Lack of specificity associated with using molecular beacons in loop mediated amplification assays. BMC Biotechnol 2019; 19:55. [PMID: 31370820 PMCID: PMC6676609 DOI: 10.1186/s12896-019-0549-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background Loop mediated isothermal amplification of nucleic acid templates is a rapid, sensitive and specific method suitable for molecular diagnostics. However the complexity of primer design and the number of primers involved can lead to false positives from non-specific primer interactions. Standard methods of LAMP detection utilise the increasing concentrations of DNA or inorganic pyrophosphate and therefore lack specificity for identifying the desired LAMP amplification. Molecular beacons used in PCR reactions are target specific and may enhance specificity with LAMP. Results We present a potential molecular beacon approach to LAMP detection targeting the single stranded region between loops, and test this for LAMP molecular beacons targeting the 35S promoter and NOS terminator sequences commonly used in GM crops. From these studies we show that molecular beacons used in LAMP, despite providing a change in fluorescent intensity with amplification, appear not to anneal to specific target sequences and therefore target specificity is not a benefit of this method. However, molecular beacons demonstrate a change in fluorescence which is indicative of LAMP amplification products. We identify the LAMP loop structure as likely to be responsible for this change in signal. Conclusions Molecular beacons can be used to detect LAMP amplification but do not provide sequence specificity. The method can be used to determine effectively LAMP amplification from other primer-driven events, but does not discriminate between different LAMP amplicons. It is therefore unsuitable for multiplex LAMP reactions due to non-specific detection of LAMP amplification. Electronic supplementary material The online version of this article (10.1186/s12896-019-0549-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Hardinge
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - James A H Murray
- Cardiff School of Biosciences, Cardiff, Museum Avenue, Cardiff, CF10 3AX, UK
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F. Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13. CRISPR J 2019; 2:165-171. [PMID: 31225754 PMCID: PMC7001462 DOI: 10.1089/crispr.2019.0011] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nucleic acid detection is vital for agricultural applications including trait detection during breeding, pest surveillance, and pathogen identification. Here, we use a modified version of the CRISPR-based nucleic acid detection platform SHERLOCK to quantify levels of a glyphosate resistance gene in a mixture of soybeans and to detect multiple plant genes in a single reaction. SHERLOCK is rapid (∼15 min), quantitative, and portable, and can process crude soybean extracts as input material for minimal nucleic acid sample preparation. This field-ready SHERLOCK platform with color-based lateral flow readout can be applied for detection and quantitation of genes in a range of agricultural applications.
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Affiliation(s)
- Omar O. Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Jonathan S. Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Max J. Kellner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
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41
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Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers. Sci Rep 2019; 9:7400. [PMID: 31089184 PMCID: PMC6517417 DOI: 10.1038/s41598-019-43817-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 11/08/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as an alternative to PCR based methods. There are numerous reported techniques to detect the LAMP amplification including turbidity, bioluminescence and intercalating fluorescent dyes. In this report we show that quenched fluorescent labels on various LAMP primers can be used to quantify and detect target DNA molecules down to single copy numbers. By selecting different fluorophores, this method can be simply multiplexed. Moreover this highly specific LAMP detection technique can reduce the incidence of false positives originating from mispriming events. Attribution of these events to particular primers will help inform and improve LAMP primer design.
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Zhang H, Xu Y, Fohlerova Z, Chang H, Iliescu C, Neuzil P. LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification. Trends Analyt Chem 2019; 113:44-53. [PMID: 32287531 PMCID: PMC7112807 DOI: 10.1016/j.trac.2019.01.015] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. Introduction of loop mediated isothermal amplification (LAMP) and its principle. Classical microfluidics-based LAMP for DNA/RNA detection. Paper-based LAMP. Microfluidic-based digital LAMP. Future of microfluidic LAMP development.
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Affiliation(s)
- Haoqing Zhang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ying Xu
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerova
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic.,Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600 Brno, Czech Republic
| | - Honglong Chang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ciprian Iliescu
- Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore, MD6, 14 Medical Drive #14-01, 117599, Singapore
| | - Pavel Neuzil
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China.,Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
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Anupama KP, Chakraborty A, Karunasagar I, Karunasagar I, Maiti B. Loop-mediated isothermal amplification assay as a point-of-care diagnostic tool for Vibrio parahaemolyticus: recent developments and improvements. Expert Rev Mol Diagn 2019; 19:229-239. [PMID: 30657706 DOI: 10.1080/14737159.2019.1571913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION A number of DNA-based diagnostic tools have been developed for the detection of Vibrio parahaemolyticus in seafood. However, the loop-mediated isothermal amplification (LAMP) has distinct advantages with regards to its simplicity, speed and the ease of performing without any need for sophisticated equipment. Over the last decade, LAMP has emerged as a potential tool for the detection of V. parahaemolyticus. Area covered: The literature search was restricted to LAMP assay and its variants for the detection of V. parahaemolyticus. The focus in this review is to enlist the various techniques that have been developed using the principle of the LAMP towards improved simplicity, sensitivity and specificity of the assay. Expert commentary: LAMP assay and its variants are significantly faster and require minimum accessories compared to other DNA based molecular techniques such as PCR and their types. Despite the availability of several versions, LAMP-based diagnostics is not the first choice for the detection of V. parahaemolyticus in the seafood sector. Our recommendation would be to explore the possibilities of developing cost-effective LAMP kits and implementing these kits as point-of-care diagnostic tools for rapid and sensitive detection of pathogenic V. parahaemolyticus.
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Affiliation(s)
- Karanth Padyana Anupama
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Anirban Chakraborty
- b Division of Molecular Genetics and Cancer , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Iddya Karunasagar
- c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Indrani Karunasagar
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India.,c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Biswajit Maiti
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
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Shang Y, Sun J, Ye Y, Zhang J, Zhang Y, Sun X. Loop-mediated isothermal amplification-based microfluidic chip for pathogen detection. Crit Rev Food Sci Nutr 2018; 60:201-224. [DOI: 10.1080/10408398.2018.1518897] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuting Shang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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Optimised LAMP allows single copy detection of 35Sp and NOSt in transgenic maize using Bioluminescent Assay in Real Time (BART). Sci Rep 2018; 8:17590. [PMID: 30514874 PMCID: PMC6279926 DOI: 10.1038/s41598-018-36207-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/09/2018] [Indexed: 11/23/2022] Open
Abstract
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.
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Dobnik D, Gruden K, Žel J, Bertheau Y, Holst-Jensen A, Bohanec M. Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1194-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Takabatake R, Kagiya Y, Minegishi Y, Yeasmin S, Futo S, Noguchi A, Kondo K, Mano J, Kitta K. Development and evaluation of rapid screening detection methods for genetically modified crops using loop-mediated isothermal amplification. Food Chem 2018; 252:390-396. [PMID: 29478558 DOI: 10.1016/j.foodchem.2017.12.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 09/20/2017] [Accepted: 12/10/2017] [Indexed: 12/30/2022]
Abstract
We developed new loop-mediated isothermal amplification (LAMP)-based detection methods for the screening of genetically modified (GM) maize and soybean events. The LAMP methods developed targeted seven sequences: cauliflower mosaic virus 35S promoter; 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens strain CP4 (cp4epsps); phosphinothricin acetyltransferase (pat) gene; mannose-6-phosphate isomerase gene; Pisum sativum ribulose 1, 5-bisphosphate carboxylase terminator; a common sequence between Cry1Ab and Cry1Ac genes; and a GA21 construct-specific sequence. We designed new specific primer sets for each target, and the limit of detection (LOD) was evaluated using authorized GM maize and soybean events. LODs for each target were ≤ 0.5%. To make the DNA extraction process simple and rapid, we also developed a direct LAMP detection scheme using crude cell lysates. The entire process, including pretreatments and detection, could be completed within 1 h.
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Affiliation(s)
- Reona Takabatake
- Analytical Science Division, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yukari Kagiya
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | | | | | - Satoshi Futo
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Akio Noguchi
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Kazunari Kondo
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Junichi Mano
- Analytical Science Division, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Kazumi Kitta
- Analytical Science Division, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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Shin DS, Heo GI, Son SH, Oh CS, Lee YK, Cha JS. Development of an Improved Loop-Mediated Isothermal Amplification Assay for On-Site Diagnosis of Fire Blight in Apple and Pear. THE PLANT PATHOLOGY JOURNAL 2018; 34:191-198. [PMID: 29887775 PMCID: PMC5985645 DOI: 10.5423/ppj.ft.03.2018.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 05/25/2023]
Abstract
Fast and accurate diagnosis is needed to eradicate and manage economically important and invasive diseases like fire blight. Loop-mediated isothermal amplification (LAMP) is known as the best on-site diagnostic, because it is fast, highly specific to a target, and less sensitive to inhibitors in samples. In this study, LAMP assay that gives more consistent results for on-site diagnosis of fire blight than the previous developed LAMP assays was developed. Primers for new LAMP assay (named as DS-LAMP) were designed from a histidine-tRNA ligase gene (EAMY_RS32025) of E. amylovora CFBP1430 genome. The DS-LAMP amplified DNA (positive detection) only from genomic DNA of E. amylovora strains, not from either E. pyrifoliae (causing black shoot blight) or from Pseudomonas syringae pv. syringae (causing shoot blight on apple trees). The detection limit of DS-LAMP was 10 cells per LAMP reaction, equivalent to 104 cells per ml of the sample extract. DS-LAMP successfully diagnosed the pathogens on four fire-blight infected apple and pear orchards. In addition, it could distinguish black shoot blight from fire blight. The Bühlmann-LAMP, developed previously for on-site diagnosis of fire blight, did not give consistent results for specificity to E. amylovora and on-site diagnosis; it gave positive reactions to three strains of E. pyrifoliae and two strains of P. syringae pv. syringae. It also, gave positive reactions to some healthy sample extracts. DS-LAMP, developed in this study, would give more accurate on-site diagnosis of fire blight, especially in the Republic of Korea, where fire blight and black shoot blight coexist.
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Affiliation(s)
- Doo-San Shin
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Gwang-Il Heo
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Soo-Hyeong Son
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Young-Kee Lee
- Department of Agro-food Safety and Crop Protection, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Jae-Soon Cha
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
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Qi H, Yue S, Bi S, Ding C, Song W. Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors. Biosens Bioelectron 2018; 110:207-217. [PMID: 29625328 DOI: 10.1016/j.bios.2018.03.065] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022]
Abstract
As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.
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Affiliation(s)
- Hongjie Qi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Shuzhen Yue
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Sai Bi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China.
| | - Caifeng Ding
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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International collaborative ring trial of four gene-specific loop-mediated isothermal amplification assays in GMO analysis. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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