1
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El-Tholoth M, Bau HH. Molecular Detection of Respiratory Tract Viruses in Chickens at the Point of Need by Loop-Mediated Isothermal Amplification (LAMP). Viruses 2024; 16:1248. [PMID: 39205222 PMCID: PMC11359210 DOI: 10.3390/v16081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Accurate and timely molecular diagnosis of respiratory diseases in chickens is essential for implementing effective control measures, preventing the spread of diseases within poultry flocks, minimizing economic loss, and guarding food security. Traditional molecular diagnostic methods like polymerase chain reaction (PCR) require expensive equipment and trained personnel, limiting their use to centralized labs with a significant delay between sample collection and results. Loop-mediated isothermal amplification (LAMP) of nucleic acids offers an attractive alternative for detecting respiratory viruses in broiler chickens with sensitivity comparable to that of PCR. LAMP's main advantages over PCR are its constant incubation temperature (∼65 °C), high amplification efficiency, and contaminant tolerance, which reduce equipment complexity, cost, and power consumption and enable instrument-free tests. This review highlights effective LAMP methods and variants that have been developed for detecting respiratory viruses in chickens at the point of need.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Veterinary Sciences Program, Health Sciences Division, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
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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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Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
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4
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Moehling TJ, Browne ER, Meagher RJ. Effects of single and multiple nucleotide mutations on loop-mediated isothermal amplification. Analyst 2024; 149:1701-1708. [PMID: 38426313 DOI: 10.1039/d3an01927f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Testing is pivotal for early identification of disease and subsequent infection control. Pathogens' nucleic acid sequence can change due to naturally-occurring genetic drift or intentional modification. Because of the reliance on molecular assays for human, animal, and plant disease diagnosis, we must understand how nucleotide mutations affect test accuracy. Primers designed against original lineages of a pathogen may be less efficient at detecting variants with genetic changes in priming regions. Here, we made single- and multi-point mutations in priming regions of a model SARS-CoV-2 template that was used as input for a loop-mediated isothermal amplification (LAMP) assay. We found that many of the modifications impacted assay sensitivity, amplification speed, or both. Further research exploring mutations at every position in each of the eight priming regions should be conducted to evaluate trends and determine generalizability.
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Affiliation(s)
- Taylor J Moehling
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
| | - Erica R Browne
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
| | - Robert J Meagher
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
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5
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de Stigter Y, van der Veer HJ, Rosier BJHM, Merkx M. Bioluminescent Intercalating Dyes for Ratiometric Nucleic Acid Detection. ACS Chem Biol 2024; 19:575-583. [PMID: 38315567 PMCID: PMC10877566 DOI: 10.1021/acschembio.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Rapid and sensitive DNA detection methods that can be conducted at the point of need may aid in disease diagnosis and monitoring. However, translation of current assays has proven challenging, as they typically require specialized equipment or probe-specific modifications for every new target DNA. Here, we present Luminescent Multivalent Intercalating Dye (LUMID), off-the-shelf bioluminescent sensors consisting of intercalating dyes conjugated to a NanoLuc luciferase, which allow for nonspecific detection of double-stranded DNA through a blue-to-green color change. Through the incorporation of multiple, tandem-arranged dyes separated by positively charged linkers, DNA-binding affinities were improved by over 2 orders of magnitude, detecting nanomolar DNA concentrations with an 8-fold change in green/blue ratio. We show that LUMID is easily combined with loop-mediated isothermal amplification (LAMP), enabling sequence-specific detection of viral DNA with attomolar sensitivity and a smartphone-based readout. With LUMID, we have thus developed a tool for simple and sensitive DNA detection that is particularly attractive for point-of-need applications.
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Affiliation(s)
- Yosta de Stigter
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Harmen J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J. H. M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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6
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Pauly MD, Ganova-Raeva L. Point-of-Care Testing for Hepatitis Viruses: A Growing Need. Life (Basel) 2023; 13:2271. [PMID: 38137872 PMCID: PMC10744957 DOI: 10.3390/life13122271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Viral hepatitis, caused by hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), or hepatitis E virus (HEV), is a major global public health problem. These viruses cause millions of infections each year, and chronic infections with HBV, HCV, or HDV can lead to severe liver complications; however, they are underdiagnosed. Achieving the World Health Organization's viral hepatitis elimination goals by 2030 will require access to simpler, faster, and less expensive diagnostics. The development and implementation of point-of-care (POC) testing methods that can be performed outside of a laboratory for the diagnosis of viral hepatitis infections is a promising approach to facilitate and expedite WHO's elimination targets. While a few markers of viral hepatitis are already available in POC formats, tests for additional markers or using novel technologies need to be developed and validated for clinical use. Potential methods and uses for the POC testing of antibodies, antigens, and nucleic acids that relate to the diagnosis, monitoring, or surveillance of viral hepatitis infections are discussed here. Unmet needs and areas where additional research is needed are also described.
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Affiliation(s)
| | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., NE, Atlanta, GA 30329, USA;
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Iijima T, Sakai J, Kanamori D, Ando S, Nomura T, Tisi L, Kilgore PE, Percy N, Kohase H, Hayakawa S, Maesaki S, Hoshino T, Seki M. A New Method to Detect Variants of SARS-CoV-2 Using Reverse Transcription Loop-Mediated Isothermal Amplification Combined with a Bioluminescent Assay in Real Time (RT-LAMP-BART). Int J Mol Sci 2023; 24:10698. [PMID: 37445876 DOI: 10.3390/ijms241310698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), of which there are several variants. The three major variants (Alpha, Delta, and Omicron) carry the N501Y, L452R, and Q493R/Q498R mutations, respectively, in the S gene. Control of COVID-19 requires rapid and reliable detection of not only SARS-CoV-2 but also its variants. We previously developed a reverse transcription loop-mediated isothermal amplification assay combined with a bioluminescent assay in real time (RT-LAMP-BART) to detect the L452R mutation in the SARS-CoV-2 spike protein. In this study, we established LAMP primers and peptide nucleic acid probes to detect N501Y and Q493R/Q498R. The LAMP primer sets and PNA probes were designed for the N501Y and Q493R/Q498R mutations on the S gene of SARS-CoV-2. The specificities of RT-LAMP-BART assays were evaluated using five viral and four bacterial reference strains. The sensitivities of RT-LAMP-BART assays were evaluated using synthetic RNAs that included the target sequences, together with RNA-spiked clinical nasopharyngeal and salivary specimens. The results were compared with those of conventional real-time reverse transcription-polymerase chain reaction (RT-PCR) methods. The method correctly identified N501Y and Q493R/Q498R. Within 30 min, the RT-LAMP-BART assays detected up to 100-200 copies of the target genes; conventional real-time RT-PCR required 130 min and detected up to 500-3000 copies. Surprisingly, the real-time RT-PCR for N501Y did not detect the BA.1 and BA.2 variants (Omicron) that exhibited the N501Y mutation. The novel RT-LAMP-BART assay is highly specific and more sensitive than conventional real-time RT-PCR. The new assay is simple, inexpensive, and rapid; thus, it can be useful in efforts to identify SARS-CoV-2 variants of concern.
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Affiliation(s)
- Takahiro Iijima
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Moroyama 350-8550, Japan
| | - Dai Kanamori
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Shinnosuke Ando
- Division of Dental Anesthesiology, Department of Diagnostic and Therapeutic Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | - Tsutomu Nomura
- Division of Otolaryngology, Department of Comprehensive Medical Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | | | - Paul E Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | | | - Hikaru Kohase
- Division of Dental Anesthesiology, Department of Diagnostic and Therapeutic Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Moroyama 350-8550, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Mitsuko Seki
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
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8
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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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9
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Mortazavi M, Torkzadeh-Mahani M, Rahimi M, Maleki M, Lotfi S, Riahi-Madvar A. Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study. Int J Biol Macromol 2023; 235:123835. [PMID: 36870640 DOI: 10.1016/j.ijbiomac.2023.123835] [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: 11/17/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran.
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Ali Riahi-Madvar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, Kosar University of Bojnord, Bojnord, Iran
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Satalkar V, Benassi E, Mao Y, Pan X, Ran C, Chen X, Shao Y. Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs. J Photochem Photobiol A Chem 2022; 431:114018. [PMID: 36407037 PMCID: PMC9673899 DOI: 10.1016/j.jphotochem.2022.114018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.
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Affiliation(s)
- Vardhan Satalkar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Enrico Benassi
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, MA 02129, USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, 117597, Singapore
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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11
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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). PLoS One 2022; 17:e0265748. [PMID: 35312732 PMCID: PMC8936440 DOI: 10.1371/journal.pone.0265748] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
The new coronavirus infection (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be fatal, and several variants of SARS-CoV-2 with mutations of the receptor-binding domain (RBD) have increased avidity for human cell receptors. A single missense mutation of U to G at nucleotide position 1355 (U1355G) in the spike (S) gene changes leucine to arginine (L452R) in the spike protein. This mutation has been observed in the India and California strains (B.1.617 and B.1.427/B.1.429, respectively). Control of COVID-19 requires rapid and reliable detection of SARS-CoV-2. Therefore, we established a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay plus a bioluminescent assay in real-time (BART) to detect SARS-CoV-2 and the L452R spike mutation. The specificity and sensitivity of the RT-LAMP-BART assay was evaluated using synthetic RNAs including target sequences and RNA-spiked clinical nasopharyngeal and saliva specimens as well as reference strains representing five viral and four bacterial pathogens. The novel RT-LAMP-BART assay to detect SARS-CoV-2 was highly specific compared to the conventional real-time RT-PCR. Within 25 min, the RT-LAMP-BART assay detected 80 copies of the target gene in a sample, whereas the conventional real-time RT-PCR method detected 5 copies per reaction within 130 min. Using RNA-spiked specimens, the sensitivity of the RT-LAMP-BART assay was slightly attenuated compared to purified RNA as a template. The results were identical to those of the conventional real-time RT-PCR method. Furthermore, using a peptide nucleic acid (PNA) probe, the RT-LAMP-BART method correctly identified the L452R spike mutation. This is the first report describes RT-LAMP-BART as a simple, inexpensive, rapid, and useful assay for detection of SARS-CoV-2, its variants of concern, and for screening of COVID-19.
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13
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Eitzmann DR, Varona M, Anderson JL. Thin Film Microextraction Enables Rapid Isolation and Recovery of DNA for Downstream Amplification Assays. Anal Chem 2022; 94:3677-3684. [DOI: 10.1021/acs.analchem.1c05380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Derek R. Eitzmann
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
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14
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Remmel MC, Coyle SM, Eshoo MW, Sweeney TE, Rawling DC. Diagnostic Host Gene Expression Analysis by Quantitative Reverse Transcription Loop-Mediated Isothermal Amplification to Discriminate between Bacterial and Viral Infections. Clin Chem 2022; 68:550-560. [PMID: 35134876 DOI: 10.1093/clinchem/hvab275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Early and accurate diagnosis of acute infections can help minimize the overprescription of antibiotics and improve patient outcomes. Discrimination between bacterial and viral etiologies in acute infection based on changes in host gene expression has been described. Unfortunately, established technologies used for gene expression profiling are typically expensive and slow, confounding integration into clinical workflows. Here we report the development of an ultra-rapid test system for host gene expression profiling from blood based on quantitative reverse transcription followed by loop-mediated isothermal amplification (qRT-LAMP). METHODS We developed 10 messenger ribonucleic acid-specific assays based on qRT-LAMP targeting 7 informative biomarkers to discriminate viral from bacterial infections and 3 housekeeping reference genes. We optimized qRT-LAMP formulations to achieve a turnaround time of 12 min without sacrificing specificity or precision. The accuracy of the test system was verified utilizing blood samples from 57 patients and comparing qRT-LAMP results to profiles obtained using an orthogonal reference technology. RESULTS We observed a Pearson coefficient of 0.90 between bacterial/viral metascores generated by qRT-LAMP and the reference technology. CONCLUSIONS qRT-LAMP assays can provide sufficiently accurate gene expression profiling data to enable discrimination between bacterial and viral etiologies using an established set of biomarkers and a classification algorithm.
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Ooi KH, Liu MM, Moo JR, Nimsamer P, Payungporn S, Kaewsapsak P, Tan MH. A Sensitive and Specific Fluorescent RT-LAMP Assay for SARS-CoV-2 Detection in Clinical Samples. ACS Synth Biol 2022; 11:448-463. [PMID: 34981924 DOI: 10.1021/acssynbio.1c00538] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because it can be performed with simple instrumentation. However, isothermal amplification methods frequently yield spurious amplicons even in the absence of a template. Consequently, RT-LAMP assays can produce false positive results when they are based on generic intercalating dyes or pH-sensitive indicators. Here, we report the development of a sensitive RT-LAMP assay that leverages on a novel sequence-specific probe to guard against spurious amplicons. We show that our optimized fluorescent assay, termed LANTERN, takes only 30 min to complete and can be applied directly on swab or saliva samples. Furthermore, utilizing clinical RNA samples from 52 patients with COVID-19 infection and 21 healthy individuals, we demonstrate that our diagnostic test exhibits a specificity and positive predictive value of 95% with a sensitivity of 8 copies per reaction. Hence, our new probe-based RT-LAMP assay can serve as an inexpensive method for point-of-need diagnosis of COVID-19 and other infectious diseases.
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Affiliation(s)
- Kean Hean Ooi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
| | - Mengying Mandy Liu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
| | - Jia Rong Moo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
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16
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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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17
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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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18
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Rajagopal R, Barnes CA, David JM, Goseland J, Goseland J. Evaluation of a commercial loop-mediated isothermal amplification assay, 3M TM Molecular Detection Assay 2 - Campylobacter, for the detection of Campylobacter from poultry matrices. Br Poult Sci 2021; 62:404-413. [PMID: 33517711 DOI: 10.1080/00071668.2021.1879992] [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] [Indexed: 12/11/2022]
Abstract
1. The objective of this study was to evaluate performance of a commercial loop-mediated isothermal amplification (LAMP) method as an alternative method for the detection of Campylobacter spp. in primary production samples, poultry rinses and raw poultry products, as compared to the US Department of Agriculture Food Inspection Service Microbiology Laboratory Guide Book PCR reference method, MLG 41A.2. The Campylobacter spp. LAMP was used in conjunction with a ready-to-use enrichment broth that does not require microaerophilic incubation. After enrichment, boot swabs from poultry farms, carcase rinses and raw poultry products were tested by the LAMP method and the MLG 41A PCR method.3. The ready-to-use enrichment broth enabled the growth of Campylobacter spp. within 22 to 28 hours under aerobic incubation conditions. The LAMP method enabled Campylobacter detection in the enriched samples of various poultry matrices and had equivalent sensitivity and specificity to the MLG 41A PCR method.4. No significant difference (95% confidence interval) was found between the alternative and the MLG 41A PCR method, as determined by probability of detection analysis, except for neutralising buffered peptone water post-chill rinsates. For the post-chill neutralising buffered peptone water rinsates, the LAMP method had significantly higher confirmed portions.
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Affiliation(s)
| | | | | | - J Goseland
- WBA Analytical Laboratories, Inc., Springdale, AR, USA
| | - J Goseland
- WBA Analytical Laboratories, Inc., Springdale, AR, USA
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19
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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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20
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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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21
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Khafizov KF, Petrov VV, Krasovitov KV, Zolkina MV, Akimkin VG. [Rapid diagnostics of novel coronavirus infection by loop-mediated isothermal amplification]. Vopr Virusol 2021; 66:17-28. [PMID: 33683062 DOI: 10.36233/0507-4088-42] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/07/2021] [Indexed: 12/20/2022]
Abstract
This review presents the basic principles of application of the loop-mediated isothermal amplification (LAMP) reaction for the rapid diagnosis of coronavirus infection caused by SARS-CoV-2. The basic technical details of the method, and the most popular approaches of specific and non-specific detection of amplification products are briefly described. We also discuss the first published works on the use of the method for the detection of the nucleic acid of the SARS-CoV-2 virus, including those being developed in the Russian Federation. For commercially available and published LAMP-based assays, the main analytical characteristics of the tests are listed, which are often comparable to those based on the method of reverse transcription polymerase chain reaction (RT-PCR), and in some cases are even superior. The advantages and limitations of this promising methodology in comparison to other methods of molecular diagnostics, primarily RT-PCR, are discussed, as well as the prospects for the development of technology for the detection of other infectious agents.
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Affiliation(s)
- K F Khafizov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - V V Petrov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - K V Krasovitov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - M V Zolkina
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - V G Akimkin
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
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22
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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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23
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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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24
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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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25
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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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26
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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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27
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Rosen DK, Gallardo M, Vail M, Hellberg RS. Microplate immunocapture coupled with the 3M molecular detection system and selective plating for the rapid detection of Salmonella infantis in dry dog food and treats. J Microbiol Methods 2020; 172:105881. [PMID: 32119958 DOI: 10.1016/j.mimet.2020.105881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
The objective of this study was to use microplate immunocapture (IC) to reduce the enrichment time required for detection of Salmonella in pet food with the 3 M Molecular Detection System (MDS) or selective plating on XLD. Dog food and pig ear treats were inoculated with Salmonella Infantis at concentrations of 100-104 CFU/25 g, followed by a 3-h enrichment, then microplate IC and 3 M MDS or microplate IC and selective plating on XLD. Another set of samples underwent a traditional 24-h enrichment followed by 3 M MDS or selective plating. Based on the results of three independent trials, microplate IC followed by selective plating enabled detection of Salmonella in 100% of dog food and treat samples tested, including at levels as low as 100 CFU/25 g. Microplate IC coupled with 3 M MDS enabled detection of Salmonella in dog food and treat samples down to levels of 100 CFU/25 g, with an overall detection rate of 92%. These results indicate high potential for microplate IC to be used in place of the traditional 24-h enrichment step, enabling detection of Salmonella in complex matrices when coupled with 3 M MDS or selective plating.
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Affiliation(s)
- Danielle K Rosen
- Schmid College of Science and Technology, Food Science Program, Chapman University, One University Drive, Orange, CA 92866, USA
| | - Miguel Gallardo
- Schmid College of Science and Technology, Food Science Program, Chapman University, One University Drive, Orange, CA 92866, USA
| | - McClain Vail
- Schmid College of Science and Technology, Food Science Program, Chapman University, One University Drive, Orange, CA 92866, USA
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, One University Drive, Orange, CA 92866, USA.
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28
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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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29
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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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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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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: 91] [Impact Index Per Article: 18.2] [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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Ding X, Mauk MG, Yin K, Kadimisetty K, Liu C. Interfacing Pathogen Detection with Smartphones for Point-of-Care Applications. Anal Chem 2019; 91:655-672. [PMID: 30428666 PMCID: PMC6867037 DOI: 10.1021/acs.analchem.8b04973] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Karteek Kadimisetty
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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Eboigbodin KE. Application of Loop-Mediated Isothermal Amplification Assay for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Methods Mol Biol 2019; 2042:19-25. [PMID: 31385267 DOI: 10.1007/978-1-4939-9694-0_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The loop-mediated isothermal amplification (LAMP) is one of the most widely used isothermal nucleic acid amplification techniques due to it its simplicity and adaptability within limited resource or point-of-care settings. Here, LAMP was utilized for the rapid amplification and detection of Chlamydia trachomatis and Neisseria gonorrhoeae.
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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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Yang Q, Domesle KJ, Ge B. Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions. Foodborne Pathog Dis 2018; 15:309-331. [PMID: 29902082 PMCID: PMC6004089 DOI: 10.1089/fpd.2018.2445] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed.
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Affiliation(s)
- Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Kelly J Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
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Song J, Pandian V, Mauk MG, Bau HH, Cherry S, Tisi LC, Liu C. Smartphone-Based Mobile Detection Platform for Molecular Diagnostics and Spatiotemporal Disease Mapping. Anal Chem 2018; 90:4823-4831. [PMID: 29542319 PMCID: PMC5928517 DOI: 10.1021/acs.analchem.8b00283] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Rapid and quantitative molecular diagnostics in the field, at home, and at remote clinics is essential for evidence-based disease management, control, and prevention. Conventional molecular diagnostics requires extensive sample preparation, relatively sophisticated instruments, and trained personnel, restricting its use to centralized laboratories. To overcome these limitations, we designed a simple, inexpensive, hand-held, smartphone-based mobile detection platform, dubbed "smart-connected cup" (SCC), for rapid, connected, and quantitative molecular diagnostics. Our platform combines bioluminescent assay in real-time and loop-mediated isothermal amplification (BART-LAMP) technology with smartphone-based detection, eliminating the need for an excitation source and optical filters that are essential in fluorescent-based detection. The incubation heating for the isothermal amplification is provided, electricity-free, with an exothermic chemical reaction, and incubation temperature is regulated with a phase change material. A custom Android App was developed for bioluminescent signal monitoring and analysis, target quantification, data sharing, and spatiotemporal mapping of disease. SCC's utility is demonstrated by quantitative detection of Zika virus (ZIKV) in urine and saliva and HIV in blood within 45 min. We demonstrate SCC's connectivity for disease spatiotemporal mapping with a custom-designed website. Such a smart- and connected-diagnostic system does not require any lab facilities and is suitable for use at home, in the field, in the clinic, and particularly in resource-limited settings in the context of Internet of Medical Things (IoMT).
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vikram Pandian
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sara Cherry
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Song J, Liu C, Mauk MG, Peng J, Schoenfeld T, Bau HH. A Multifunctional Reactor with Dry-Stored Reagents for Enzymatic Amplification of Nucleic Acids. Anal Chem 2018; 90:1209-1216. [PMID: 29226671 PMCID: PMC6310013 DOI: 10.1021/acs.analchem.7b03834] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To enable inexpensive molecular detection at the point-of-care and at home with minimal or no instrumentation, it is necessary to streamline unit operations and store reagents refrigeration-free. To address this need, a multifunctional enzymatic amplification reactor that combines solid-phase nucleic acid extraction, concentration, and purification; refrigeration-free storage of reagents with just-in-time release; and enzymatic amplification is designed, prototyped, and tested. A nucleic acid isolation membrane is placed at the reactor's inlet, and paraffin-encapsulated reagents are prestored within the reactor. When a sample mixed with chaotropic agents is filtered through the nucleic acid isolation membrane, the membrane binds nucleic acids from the sample. Importantly, the sample volume is decoupled from the reaction volume, enabling the use of relatively large sample volumes for high sensitivity. When the amplification reactor's temperature increases to its operating level, the paraffin encapsulating the reagents melts and moves out of the way. The reagents are hydrated, just-in-time, and the polymerase reaction proceeds. The amplification process can be monitored, in real-time. We demonstrate our reactors' ability to amplify both DNA and RNA targets using polymerase with both reverse-transcriptase and strand displacement activities to obtain sensitivities on-par with benchtop equipment and a shelf life exceeding 6 months.
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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39
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Kumar Y, Bansal S, Jaiswal P. Loop-Mediated Isothermal Amplification (LAMP): A Rapid and Sensitive Tool for Quality Assessment of Meat Products. Compr Rev Food Sci Food Saf 2017; 16:1359-1378. [DOI: 10.1111/1541-4337.12309] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yogesh Kumar
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Sangita Bansal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Pranita Jaiswal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
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40
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Hu C, Kalsi S, Zeimpekis I, Sun K, Ashburn P, Turner C, Sutton JM, Morgan H. Ultra-fast electronic detection of antimicrobial resistance genes using isothermal amplification and Thin Film Transistor sensors. Biosens Bioelectron 2017; 96:281-287. [DOI: 10.1016/j.bios.2017.05.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
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41
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Anklam K, Kulow M, Yamazaki W, Döpfer D. Development of real-time PCR and loop-mediated isothermal amplification (LAMP) assays for the differential detection of digital dermatitis associated treponemes. PLoS One 2017; 12:e0178349. [PMID: 28542573 PMCID: PMC5444799 DOI: 10.1371/journal.pone.0178349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
Bovine digital dermatitis (DD) is a severe infectious cause of lameness in cattle worldwide, with important economic and welfare consequences. There are three treponeme phylogroups (T. pedis, T. phagedenis, and T. medium) that are implicated in playing an important causative role in DD. This study was conducted to develop real-time PCR and loop-mediated isothermal amplification (LAMP) assays for the detection and differentiation of the three treponeme phylogroups associated with DD. The real-time PCR treponeme phylogroup assays targeted the 16S-23S rDNA intergenic space (ITS) for T. pedis and T. phagedenis, and the flagellin gene (flaB2) for T. medium. The 3 treponeme phylogroup LAMP assays targeted the flagellin gene (flaB2) and the 16S rRNA was targeted for the Treponeme ssp. LAMP assay. The real-time PCR and LAMP assays correctly detected the target sequence of all control strains examined, and no cross-reactions were observed, representing 100% specificity. The limit of detection for each of the three treponeme phylogroup real-time PCR and LAMP assays was ≤ 70 fg/μl. The detection limit for the Treponema spp. LAMP assay ranged from 7-690 fg/μl depending on phylogroup. Treponemes were isolated from 40 DD lesion biopsies using an immunomagnetic separation culture method. The treponeme isolation samples were then subjected to the real-time PCR and LAMP assays for analysis. The treponeme phylogroup real-time PCR and LAMP assay results had 100% agreement, matching on all isolation samples. These results indicate that the developed assays are a sensitive and specific test for the detection and differentiation of the three main treponeme phylogroups implicated in DD.
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Affiliation(s)
- Kelly Anklam
- Department of Medical Science, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Megan Kulow
- Department of Medical Science, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Wataru Yamazaki
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Dörte Döpfer
- Department of Medical Science, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
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Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. LAB ON A CHIP 2017; 17:382-394. [PMID: 28092381 PMCID: PMC5285266 DOI: 10.1039/c6lc01239f] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.
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Affiliation(s)
- Michael Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert Gross
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Martineau RL, Murray SA, Ci S, Gao W, Chao SH, Meldrum DR. Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming. Anal Chem 2016; 89:625-632. [PMID: 27809497 DOI: 10.1021/acs.analchem.6b02578] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.
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Affiliation(s)
- Rhett L Martineau
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Sarah A Murray
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shufang Ci
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Weimin Gao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shih-Hui Chao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Deirdre R Meldrum
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus. J Virol Methods 2016; 236:54-61. [PMID: 27421627 PMCID: PMC5010982 DOI: 10.1016/j.jviromet.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/17/2016] [Accepted: 07/12/2016] [Indexed: 11/21/2022]
Abstract
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA.
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Si M, Xu Q, Jiang L, Huang H. SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase. PLoS One 2016; 11:e0162318. [PMID: 27658030 PMCID: PMC5033358 DOI: 10.1371/journal.pone.0162318] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022] Open
Abstract
SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.
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Affiliation(s)
- Meng Si
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Qing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ling Jiang
- College of Food Sciences and Light Industry, Nanjing Tech University, Nanjing, 211816, China
- * E-mail: (LJ); (HH)
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China
- * E-mail: (LJ); (HH)
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Yang Q, Domesle KJ, Wang F, Ge B. Rapid detection of Salmonella in food and feed by coupling loop-mediated isothermal amplification with bioluminescent assay in real-time. BMC Microbiol 2016; 16:112. [PMID: 27316515 PMCID: PMC4912795 DOI: 10.1186/s12866-016-0730-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 06/06/2016] [Indexed: 11/15/2022] Open
Abstract
Background Salmonella is among the most significant pathogens causing food and feed safety concerns. This study examined the rapid detection of Salmonella in various types of food and feed samples by coupling loop-mediated isothermal amplification (LAMP) with a novel reporter, bioluminescent assay in real-time (BART). Performance of the LAMP-BART assay was compared to a conventional LAMP and the commercially available 3M Molecular Detection Assay (MDA) Salmonella. Results The LAMP-BART assay was 100 % specific among 178 strains (151 Salmonella and 27 non-Salmonella) tested. The detection limits were 36 cells per reaction in pure culture and 104 to 106 CFU per 25 g in spiked food and feed samples without enrichment, which were comparable to those of the conventional LAMP and 3M MDA Salmonella but 5–10 min faster. Ground turkey showed a strong inhibition on 3M MDA Salmonella, requiring at least 108 CFU per 25 g for detection. The correlation between Salmonella cell numbers and LAMP-BART signals was high (R2 = 0.941–0.962), suggesting good quantification capability. After 24 h enrichment, all three assays accurately detected 1 to 3 CFU per 25 g of Salmonella among five types of food (cantaloupe, ground beef, ground turkey, shell eggs, and tomato) and three types of feed (cattle feed, chicken feed, and dry dog food) examined. However, 101 CFU per 25 g was required for cattle feed when tested by 3M MDA Salmonella. Conclusions The Salmonella LAMP-BART assay was rapid, specific, sensitive, quantitative, and robust. Upon further validation, it may become a valuable tool for routine screening of Salmonella in various types of food and feed samples.
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Affiliation(s)
- Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA.,Department of Food Science, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Kelly J Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Fei Wang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA.,Department of Nutrition and Food Science, University of Maryland, College Park, MD, 20742, USA
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA.
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Eboigbodin KE, Hoser MJ. Multiplex Strand Invasion Based Amplification (mSIBA) assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Sci Rep 2016; 6:20487. [PMID: 26837460 PMCID: PMC4738295 DOI: 10.1038/srep20487] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022] Open
Abstract
Nucleic acid amplification tests have become a common method for diagnosis of STIs due to their improved sensitivity over immunoassays and traditional culture-based methods. Isothermal nucleic acid amplification methods offer significant advantages over polymerase chain reaction (PCR) because they do not require sophisticated instruments needed for thermal cycling of PCR. We recently reported a novel isothermal nucleic acid amplification method, Strand Invasion-Based Amplification (SIBA), which exhibited high analytical sensitivity and specificity for amplification of DNA. However, because the reactions were detected using an intercalating dye, this method was only suitable for amplifying a single genomic target. Here, we report the development of multiplexed SIBA (mSIBA) that allows simultaneous detection of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and an internal control in the same reaction tube. SIBA is compatible with probes, allowing the detection of multiple DNA targets in the same reaction tube. The IC was developed to assess the quality of the isolated DNA and the integrity of the enzyme system, as well as to test oligonucleotides. The mSIBA assay retained high analytical sensitivity and specificity for the detection of CT and NG. The development of mSIBA enables rapid screening for CT and NG within point-of-care or central laboratory settings.
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Affiliation(s)
| | - Mark J Hoser
- Molecular Biology, GeneForm Technologies, Broadstairs, United Kingdom
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Gharanlar J, Hosseinkhani S, Sajedi RH, Yaghmaei P. The Effect of Surface Charge Saturation on Heat-induced Aggregation of Firefly Luciferase. Photochem Photobiol 2015; 91:1156-64. [PMID: 25989897 DOI: 10.1111/php.12467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal-induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat-induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat-induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat-induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.
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Affiliation(s)
- Jamileh Gharanlar
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parichehr Yaghmaei
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
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Stevens W, Gous N, Ford N, Scott LE. Feasibility of HIV point-of-care tests for resource-limited settings: challenges and solutions. BMC Med 2014; 12:173. [PMID: 25197773 PMCID: PMC4157150 DOI: 10.1186/s12916-014-0173-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/11/2014] [Indexed: 11/10/2022] Open
Abstract
Improved access to anti-retroviral therapy increases the need for affordable monitoring using assays such as CD4 and/or viral load in resource-limited settings. Barriers to accessing treatment, high rates of loss to initiation and poor retention in care are prompting the need to find alternatives to conventional centralized laboratory testing in certain countries. Strong advocacy has led to a rapidly expanding repertoire of point-of-care tests for HIV. point-of-care testing is not without its challenges: poor regulatory control, lack of guidelines, absence of quality monitoring and lack of industry standards for connectivity, to name a few. The management of HIV increasingly requires a multidisciplinary testing approach involving hematology, chemistry, and tests associated with the management of non-communicable diseases, thus added expertise is needed. This is further complicated by additional human resource requirements and the need for continuous training, a sustainable supply chain, and reimbursement strategies. It is clear that to ensure appropriate national implementation either in a tiered laboratory model or a total decentralized model, clear country-specific assessments need to be conducted.
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Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 2014; 186:20-31. [DOI: 10.1016/j.virusres.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023]
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