Development of a loop-mediated isothermal amplification method for the rapid detection of the dioxin-degrading bacterium Ochrobactrum anthropi in soil

Chen, Hsi-Jien; Lai, Jun-Yu; Lee, Meng-Shiou

doi:10.1016/j.jenvman.2015.06.027

Cited by 14 publications

(11 citation statements)

References 32 publications

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“…Loop-mediated isothermal amplification (LAMP) is a well-developed DNA amplification method that has been widely used for the authentication of various bioresources, such as bacteria, viruses, animals or plants ( Notomi et al, 2000 , Huang et al, 2010 , Chen et al, 2015 , Lee et al, 2017 , Lee et al, 2019 ). Theoretically, at least four LAMP primers, including two outer primers (denoted by F3 and B3) and two inner primers (denoted by FIP and BIP), were needed to perform the LAMP reaction.…”

Section: Introductionmentioning

confidence: 99%

Specific, sensitive and rapid Curcuma longa turmeric powder authentication in commercial food using loop-mediated isothermal nucleic acid amplification

Sheu¹,

Wu²,

Lien³

et al. 2021

Saudi Journal of Biological Sciences

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Turmeric ( Curcuma longa ) is a rhizomatous plant of the ginger family Zingiberaceae that is usually dried and ground into powder for use as a seasoning. Because turmeric has become increasingly popular in the functional food market, adulteration of C . longa by other turmeric species is becoming an increasingly significant problem. In this study, loop-mediated isothermal amplification (LAMP) was developed for the detection of C. longa DNA for turmeric authentication. ITS2-26S rDNA was used for the LAMP primer designation. The results demonstrated that the specific primers exhibited high specificity, authenticated C. longa DNA within 30 min at 65 °C isothermally and had no cross-reaction with other adulterants. LAMP was sensitive to 0.1 ng of turmeric C. longa DNA, and only 0.01% of C. longa turmeric powder in the sample was required for DNA amplification. The sensitivity of LAMP was 10-fold higher than that of PCR (0.1%) from a previous report. Moreover, all the collected commercial turmeric products were positively detected by LAMP and RtF-LAMP (real-time fluorescence LAMP). The developed LAMP assay not only had higher specificity and rapidity than that of other methods but could also be applied to authenticate turmeric to prevent adulteration in food products.

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Section: Introductionmentioning

confidence: 99%

Specific, sensitive and rapid Curcuma longa turmeric powder authentication in commercial food using loop-mediated isothermal nucleic acid amplification

Sheu¹,

Wu²,

Lien³

et al. 2021

Saudi Journal of Biological Sciences

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“…. As to LAMP, published literature has reported that LAMP provides a more convenient way to identify organisms such as bacteria, fungi, viruses, animals, and plants89111213. In this work, the specific aim was to develop a sensitive, specific and rapid method to detect FFVs.…”

Section: Discussionmentioning

confidence: 99%

“…At present, LAMP is extensively applied to amplify DNA for detection or diagnostic purposes. For example, many pathogens such as viruses, fungi, bacteria, and parasites are examined using the LAMP assay891011. Other bio-resource materials such as genetically modified organisms (GMOs), as well as animals or plants can be applied as detection targets using the LAMP assay12131415.…”

mentioning

confidence: 99%

The development of loop-mediated isothermal amplification (LAMP) assays for the rapid authentication of five forbidden vegetables in strict vegetarian diets

Lee

Lien

et al. 2017

Sci Rep

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Plant-based food ingredients such as garlic, Chinese leek, Chinese onion, green onion and onion are widely used in many cuisines around the world. However, these ingredients known as the “five forbidden vegetables” (FFVs) are not allowed in some vegetarian diets. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of FFVs using five respective LAMP primer sets. The specific primers targeted the ITS1-5.8S-ITS2 nuclear ribosomal DNA sequence regions among the five vegetables. The results demonstrated that the identification of FFVs using the newly developed LAMP assay is more sensitive than the traditional PCR method. Using pepper, basil, parsley, chili and ginger as references, established LAMP primer sets showed high specificity for the identification of the FFV species. Moreover, when FFVs were mixed with other plant ingredients at different ratios (100:0, 50:50, 20:80, 10:90, 5:95, 2:98, and 1:99), no cross-reactivity was evident using LAMP. Finally, genomic DNAs extracted from boiled and steamed FFVs in processed foods were used as templates; the performance of the LAMP reaction was not influenced using validated LAMP primers. Not only can FFV ingredients be identified but commercial foods containing FFVs can also be authenticated. This LAMP method will be useful for the authentication of FFVs in practical food markets in the future.

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“…Future studies are also planned with additional markers such as genes associated with biodegradation of contaminants (Chen et al, 2015), which are expected to persist in sediment samples. Future studies will also test the intI1 gene and universal 16S rRNA gene LAMP assays with minimal sample processing and explore if there are bacterial species containing intI1 gene that do not amplify.…”

Section: Discussionmentioning

confidence: 99%

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Stedtfeld¹,

Stedtfeld²,

Waseem³

et al. 2017

Journal of Environmental Management

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Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively “untrained” personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

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Development of a loop-mediated isothermal amplification method for the rapid detection of the dioxin-degrading bacterium Ochrobactrum anthropi in soil

Cited by 14 publications

References 32 publications

Specific, sensitive and rapid Curcuma longa turmeric powder authentication in commercial food using loop-mediated isothermal nucleic acid amplification

Specific, sensitive and rapid Curcuma longa turmeric powder authentication in commercial food using loop-mediated isothermal nucleic acid amplification

The development of loop-mediated isothermal amplification (LAMP) assays for the rapid authentication of five forbidden vegetables in strict vegetarian diets

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

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