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      Shining a LAMP on the applications of isothermal amplification for monitoring environmental biosecurity

      , , ,
      NeoBiota
      Pensoft Publishers

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          Abstract

          Environmental biosecurity risks associated with the transnational wildlife trade include the loss of biodiversity, threats to public health, and the proliferation of invasive alien species. To assist enforcement agencies in identifying species either intentionally (trafficked) or unintentionally (stowaway) entrained in the trade-chain pathway, rapid forensic techniques are needed to enable their detection from DNA samples when physical identification is not possible. Loop Mediated Isothermal Amplification (LAMP) is an emerging technique, with recent applications in biosecurity and forensic sciences, which has potential to function as a field-based detection tool. Here we provide an overview of current research that applies LAMP to environmental biosecurity, including identification of ornamental wildlife parts, consumer products, and invasive species monitoring and biosecurity detection. We discuss the current scope of LAMP as applied to various wildlife trade scenarios and biosecurity checkpoint monitoring, highlight the specificity, sensitivity, and robustness for these applications, and review the potential utility of LAMP for rapid field-based detection at biosecurity checkpoints. Based on our assessment of the literature we recommend broader interest, research uptake, and investment in LAMP as an appropriate field-based species detection method for a wide range of environmental biosecurity scenarios.

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          Most cited references125

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          NIH Image to ImageJ: 25 years of image analysis

          For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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            Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China.

            Y Guan (2003)
            A novel coronavirus (SCoV) is the etiological agent of severe acute respiratory syndrome (SARS). SCoV-like viruses were isolated from Himalayan palm civets found in a live-animal market in Guangdong, China. Evidence of virus infection was also detected in other animals (including a raccoon dog, Nyctereutes procyonoides) and in humans working at the same market. All the animal isolates retain a 29-nucleotide sequence that is not found in most human isolates. The detection of SCoV-like viruses in small, live wild mammals in a retail market indicates a route of interspecies transmission, although the natural reservoir is not known.
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              Loop-mediated isothermal amplification of DNA.

              T. Notomi (2000)
              We have developed a novel method, termed loop-mediated isothermal amplification (LAMP), that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. This method employs a DNA polymerase and a set of four specially designed primers that recognize a total of six distinct sequences on the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. The following strand displacement DNA synthesis primed by an outer primer releases a single-stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem-loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem-loop DNA and a new stem-loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 10(9) copies of target in less than an hour. The final products are stem-loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity.
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                Author and article information

                Contributors
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                Journal
                NeoBiota
                NB
                Pensoft Publishers
                1314-2488
                1619-0033
                February 24 2023
                February 24 2023
                : 82
                : 119-144
                Article
                10.3897/neobiota.82.97998
                6e1a2a69-c9fc-4066-bcd1-f9ca85032c2b
                © 2023

                http://creativecommons.org/licenses/by/4.0/

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