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Sheu SC, Wang YJ, Huang PC, Lien YY, Lee MS. Authentication of olive oil in commercial products using specific, sensitive, and rapid loop-mediated isothermal amplification. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:1834-1840. [PMID: 37187977 PMCID: PMC10169996 DOI: 10.1007/s13197-023-05726-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/24/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Olive oil is an important and popularly used plant oil in the daily diet or chemical industry. Due to its biological benefits on human health and higher selling prices, adulteration of olive oil for commercial fraud by other plant oils is becoming a serious issue. In this study, a specific, sensitive and rapid loop-mediated isothermal amplification (LAMP) was first developed for the detection of Olea europaea DNA for olive oil authentication. The oleosin gene was used for the primer design of the LAMP assay. After primer validation, the results showed that the LAMP primers were specific and rapid to isothermally authenticate the oleosin gene of Olea europaea within 1 h at 62 °C and had no cross-reaction with other DNA of plant oils. The sensitivity of LAMP was 1 ng of genomic DNA in olive oil, and only 1% olive oil in the sample was requisite during DNA amplification. Additionally, positive detection by LAMP in all the collected commercial olive oil products was practically performed but not in PCR assays. In conclusion, herein, the established LAMP assay with specificity could not only be capable for rapid identification but also applicable for olive oil authentication for precluding adulteration in plant oil products. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05726-y.
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Affiliation(s)
- Shyang-Chwen Sheu
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
| | - Ying-Jie Wang
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
| | - Pao-Cheng Huang
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
| | - Yi-Yang Lien
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
| | - Meng-Shiou Lee
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, Taichung, 40402 Taiwan
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Tavakoli-Koopaei R, Javadi-Zarnaghi F, Aboutalebian S, Mirhendi H. Malachite Green-Based Detection of SARS-CoV-2 by One-Step Reverse Transcription Loop-Mediated Isothermal Amplification. IRANIAN JOURNAL OF SCIENCE 2023. [PMCID: PMC9898859 DOI: 10.1007/s40995-022-01392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The pandemic of severe acute respiratory syndrome 2 (SARS-CoV-2) revealed the necessity of diagnosis of the infected people to prevent the prevalence infection cycle. Many commercial pathogen diagnosis methods are based on the detection of genomic materials. Isothermal amplification methods such as loop-mediated-isothermal amplification (LAMP) are the method of choice in these cases. Reverse transcription steps are efficiently coupled to LAMP for the detection of pathogens with genomic RNAs such as SARS-CoV-2. Many detection systems for LAMP include fluorescent readout systems. Although such systems result in desirable limits of detection, the need for special instrumentation is the main dispute of such systems to become real point of care assays. In contrast, colorimetric detection methods would reduce costs and improve the applicability of the system. In this study one-step reverse transcription-LAMP reaction was established that enables visual detection of the SARS-CoV-2 genome. Nasopharyngeal RNA samples were first validated by reverse transcription quantitative polymerase chain reaction and then subjected to RT-LAMP. To lower the cost associated with the readout system equipment, malachite green (MG) was used. The color change of MG to blue allowed visual detection of the virus. Firstly, experiments were set up as two-step RT-LAMP reaction to identify the best primer sets. In addition, MG concentration was optimized with the significant colorimetric signal for the positive samples. Next, a one-step colorimetric method was developed for the detection of SARS-CoV-2 based on MG color shift in 2 h.
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Affiliation(s)
- Reyhaneh Tavakoli-Koopaei
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Shima Aboutalebian
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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Varliero G, Wray J, Malandain C, Barker G. PhyloPrimer: a taxon-specific oligonucleotide design platform. PeerJ 2021; 9:e11120. [PMID: 33986979 PMCID: PMC8098674 DOI: 10.7717/peerj.11120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/25/2021] [Indexed: 11/26/2022] Open
Abstract
Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
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Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jared Wray
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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