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Bustin SA, Kirvell S, Nolan T, Shipley GL. FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols. Int J Mol Sci 2024; 25:2773. [PMID: 38474020 DOI: 10.3390/ijms25052773] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
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Wax N, Pförtner LS, Holz N, Sterzl S, Melnik M, Kappel K, Bade P, Schröder U, Haase I, Fritsche J, Fischer M. Fast and User-Friendly Detection of Flatfish Species ( Pleuronectes platessa and Solea solea) via Loop-Mediated Isothermal Amplification (LAMP). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14795-14805. [PMID: 37751470 DOI: 10.1021/acs.jafc.3c03917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
The detection of a Cytochrome b gene (cytb) for species differentiation in fish is intensively used. A fast alternative to expensive and time-consuming DNA barcoding is loop-mediated isothermal amplification (LAMP) in combination with efficient readout systems. For this reason, we developed LAMP assays for rapid species detection of Pleuronectes platessa and Solea solea, two economically important flatfish species in Europe that are prone to mislabeling. Species-specific primer sets targeting cytb were designed, and LAMP assays were optimized. With the optimized LAMP assays, we were able to detect up to 0.1 and 0.01 ng of target DNA of P. platessa and S. solea, respectively, and in each case up to 1% (w/w) of target species in mixtures with nontarget species. For future on-site detection, a lateral flow assay and a pocket-sized lab-on-phone assay were used as readout systems. The lab-on-phone assay with the S. solea specific primer set revealed cross-reactivity to Solea senegalensis. The assay targeting P. platessa proved to be highly specific. Both assays could be performed within 45 min and provided rapid and easy detection of fish species.
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Affiliation(s)
- Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Laura Sophie Pförtner
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nathalie Holz
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Svenja Sterzl
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Melina Melnik
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Kristina Kappel
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Patrizia Bade
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Ute Schröder
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Ilka Haase
- National Reference Centre for Authentic Food, Max Rubner-Institut (MRI), E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Jan Fritsche
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut (MRI), Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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Massa B, Tagliavia M, Buzzetti FM, Fontana P, Carotti G, Bardiani M, Leandri F, Scherini R, Verde GL. A taxonomic revision of the Palaearctic genus Roeseliana (Orthoptera: Tettigoniidae: Tettigoniinae: Platycleidini): a case of ongoing Mediterranean speciation. Zootaxa 2023; 5270:351-400. [PMID: 37518157 DOI: 10.11646/zootaxa.5270.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Indexed: 08/01/2023]
Abstract
The genus Roeseliana presently includes 10 specific or subspecific taxa, but following different authors some of them are considered synonyms. However, the authors who have treated these taxa often did not agree with the synonymies, in particular, concerning some taxa, such as R. fedtschenkoi (Saussure, 1874) and R. roeselii (Hagenbach, 1822). The present authors examined hundreds of specimens of different taxa, for the first time were able to obtain the translation from the Russian of the description of R. fedtschenkoi, compared the main morphological characters used to discriminate different taxa, biometrics, bioacoustics and genetics of some taxa. This allowed them to conclude that it is possible to recognize the following taxa: 1) Roeseliana roeselii (Hagenbach, 1822) widespread in the Palaearctic Region and imported in North America; 2) Roeseliana fedtschenkoi (Saussure, 1874) in Uzbekistan and Turkmenistan; 3) Roeseliana pylnovi (Uvarov, 1924) in the Caucasian region; 4) Roeseliana bispina (Bolívar, 1899) in Turkey; 5) Roeseliana azami (Finot, 1892) from the Mediterranean France through Italian peninsula (formerly R. azami minor Nadig, 1961); 6) R. ambitiosa (Uvarov, 1924) on the Balkan peninsula; 7) Roeseliana n. sp. Lemonnier-Darcemont & Darcemont, (in press) on Epirus (Greece and Albania); 8) Roeseliana brunneri Ramme 1951 in north east Italy (Veneto, Friuli and Po Valley); 9) Roeseliana oporina (Bolívar, 1887) in Spain.
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Affiliation(s)
- Bruno Massa
- Department of Agricultural; Food and Forest Sciences; University of Palermo; Viale delle Scienze; 13; 90128 Palermo; Italy.
| | - Marcello Tagliavia
- Institute for Biomedical Research and Innovation-National Research Council (IRIB-CNR); Via Ugo La Malfa 153; 90146 Palermo; Italy.
| | - Filippo Maria Buzzetti
- Fondazione Museo Civico di Rovereto; Zoology Section; Borgo Santa Caterina 41; 38068 Rovereto (Trento); Italy.
| | - Paolo Fontana
- Fondazione Edmund Mach di San Michele all'Adige-Centro Trasferimento Tecnologico; Via E. Mach; 39098 Trento; Italy.
| | | | - Marco Bardiani
- Centro Nazionale Carabinieri Biodiversità; Bosco Fontana; Strada Mantova 29; 46045 Marmirolo (Mantova); Italy.
| | - Fausto Leandri
- World Biodiversity Association onlus c/o Museo Civico di Storia Naturale Lungadige Porta Vittoria; 9; 37129 Verona; Italy.
| | | | - Gabriella Lo Verde
- Department of Agricultural; Food and Forest Sciences; University of Palermo; Viale delle Scienze; 13; 90128 Palermo; Italy.
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High-Performance PCR for Alleles Discrimination of Chromo-Helicase-DNA Binding Protein (CHD1) Gene in Bird Sexing. BIOLOGY 2023; 12:biology12020300. [PMID: 36829577 PMCID: PMC9953129 DOI: 10.3390/biology12020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Genetic analyses aiming at assessing the presence of specific sequences or alleles are often carried out by PCR. Sexing of most birds is nowadays based on PCR with "universal" primers and relies on the assessment of the presence of the sex-linked CHD1-Z and -W alleles. The entire workflow is relatively time-consuming, especially for batch analyses, whereas methods that allow carrying out the entire procedure in a short time are highly desirable. The only method for outdoor analyses reported so far relies on LAMP; however; it fails to work properly in Procellariiformes. Besides improving the LAMP test; we have developed a PCR-based DNA amplification procedure (named high-performance PCR); whose unique features allow it to outperform standard PCR; making possible the direct, in-tube visual reading of results. We tested it with specifically designed Procellariiformes-targeted primer sets for rapid sexing of the birds using fluorimetric detection. The protocol, combined with rapid DNA extraction, allows for fast reading of results without electrophoresis within less than 1 h from sampling. The technique could be extended to other species, as well as to many other applications.
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Deconinck D, Robbens J, Volckaert FA, Derycke S. Rapid and low-cost identification of common sole (Solea solea) in the field using a fast DNA isolation protocol and loop-mediated isothermal amplification (LAMP). J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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JAFAR S, KABIR F, ANJUM KM, ZAHOOR MY, SHEHZAD W, IMRAN M. Comparison of different DNA preparatory methods for development of a universal direct PCR-RFLP workflow for identification of meat origin in food products. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.65122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Socorro TR, Joran V, Sofie D. Evaluation of DNA metabarcoding using Oxford Nanopore sequencing for authentication of mixed seafood products. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Li Q, Cheng Y, Xu W, Cui X, Cao M, Xiong X, Wang L, Xiong X. Rapid identification of Atlantic salmon (Salmo salar) based on loop-mediated isothermal amplification (LAMP) using self-quenching fluorogenic approach. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Characterizing Billbug ( Sphenophorus spp.) Seasonal Biology Using DNA Barcodes and a Simple Morphometric Analysis. INSECTS 2021; 12:insects12100930. [PMID: 34680699 PMCID: PMC8538943 DOI: 10.3390/insects12100930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Billbugs (Sphenophorus spp.) are a group of grass-feeding weevils considered to be one of the most important and widespread insect pests of turfgrass. However, our limited understanding of regional variation in billbug species composition and inability to identify the damaging larval stage to species level, has hindered our ability to resolve the seasonal biology of many billbug species and constrained development of effective management approaches. In this study, we developed a robust DNA barcoding approach for identification of morphologically cryptic billbug larvae. Using this molecular tool combined with larval head capsule measurements we characterized regional variation in billbug species and developed larval phenology charts. Our approach provides researchers with the molecular tools necessary to fill critical gaps in our understanding of billbug seasonal biology and will facilitate the development of improved turfgrass pest management programs. Abstract Billbugs (Sphenophorus spp.) are a complex of grass-feeding weevil species that reduce the aesthetic and functional qualities of turfgrass. Effective billbug monitoring and management programs rely on a clear understanding of their seasonal biology. However, our limited understanding of regional variation in the species compositions and seasonal biology of billbugs, stemming primarily from our inability to identify the damaging larval stage to species level, has hindered efforts to articulate efficient IPM strategies to growers. We used a combination of DNA barcoding methods and morphometric measures to begin filling critical gaps in our understanding of the seasonal biology of the billbug species complex across a broad geographic range. First, we developed a DNA barcoding reference library using cytochrome oxidase subunit 1 (COI) sequences from morphologically identified adult billbugs collected across Indiana, Missouri, Utah and Arizona. Next, we used our reference library for comparison and identification of unknown larval specimens collected across the growing season in Utah and Indiana. Finally, we combined our DNA barcoding approach with larval head capsule diameter, a proxy for developmental instar, to develop larval phenology charts. Adult COI sequences varied among billbug species, but variation was not influenced by geography, indicating that this locus alone was useful for resolving larval species identity. Overlaid with head capsule diameter data from specimens collected across the growing season, a better visualization of billbug species composition and seasonal biology emerged. This approach will provide researchers with the tools necessary to fill critical gaps in our understanding of billbug biology and facilitate the development of turfgrass pest management programs.
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Development of loop-mediated isothermal amplification (LAMP) assay for rapid screening of skipjack tuna (Katsuwonus pelamis) in processed fish products. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Distribution of organochlorine pesticide pollution in water, sediment, mollusk, and fish at Saguling Dam, West Java, Indonesia. Toxicol Res 2021; 38:149-157. [PMID: 35419272 PMCID: PMC8960551 DOI: 10.1007/s43188-021-00094-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022] Open
Abstract
This study aims to determine the distribution of organochlorine pesticide pollution in water, sediments, mollusks, and fish at Saguling Dam as baseline data of organochlorine pollution. Samples were obtained from 12 locations, with 9 and 3 sampling points inside and outside the dam, respectively. Measurement of organochlorine residues was carried out using methods of extraction, purification, evaporation, and gas chromatography. Results showed the presence of several types of organochlorine compounds, namely, lindane, aldrin, dieldrin, heptachlor, dichlorodiphenyltrichloroethane (DDT), and endosulfan. Aldrin was dominant in water (2-37 μg/L) and sediments (2-1438 μg/L), while DDT and heptachlor were dominant organochlorine compounds in mollusks (13-2758 µg/L) and fish (11-104 μg/L), respectively. Sediments demonstrated higher organochlorine concentrations than water, mollusk, and fish. The distribution of organochlorine was affected by land use around the Citarum watershed and pollutant input from tributaries.
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12
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DNA-based techniques for seafood species authentication. ADVANCES IN FOOD AND NUTRITION RESEARCH 2020; 95:207-255. [PMID: 33745513 DOI: 10.1016/bs.afnr.2020.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.
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13
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Lo YT, Shaw PC. Application of next-generation sequencing for the identification of herbal products. Biotechnol Adv 2019; 37:107450. [DOI: 10.1016/j.biotechadv.2019.107450] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022]
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14
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Kang TS. Basic principles for developing real-time PCR methods used in food analysis: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Tagliavia M, Salamone M, Bennici C, Quatrini P, Cuttitta A. A modified culture medium for improved isolation of marine vibrios. Microbiologyopen 2019; 8:e00835. [PMID: 31318499 PMCID: PMC6741135 DOI: 10.1002/mbo3.835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022] Open
Abstract
Marine Vibrio members are of great interest for both ecological and biotechnological research, which often relies on their isolation. Whereas many efforts have been made for the detection of food‐borne pathogenic species, much less is known about the performances of standard culture media toward environmental vibrios. We show that the isolation/enumeration of marine vibrios using thiosulfate‐citrate‐bile salts‐sucrose agar (TCBS) as selective medium may be hampered by the variable adaptability of different taxa to the medium, which may result even in isolation failure and/or in substantial total count underestimation. We propose a modified TCBS as isolation medium, adjusted for marine vibrios requirements, which greatly improved their recovery in dilution plate counts, compared with the standard medium. The modified medium offers substantial advantages over TCBS, providing more accurate and likely estimations of the actual presence of vibrios. Modified TCBS allowed the recovery of otherwise undetected vibrios, some of which producing biotechnologically valuable enzymes, thus expanding the isolation power toward potentially new enzyme‐producers Vibrio taxa. Moreover, we report a newly designed Vibrio‐specific PCR primers pair, targeting a unique rpoD sequence, useful for rapid confirmation of isolates as Vibrio members and subsequent genetic analyses.
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Affiliation(s)
- Marcello Tagliavia
- IAS-CNR, Campobello di Mazara, Italy.,Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | | | | | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
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17
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Tagliavia M, Nicosia A. Advanced Strategies for Food-Grade Protein Production: A New E. coli/Lactic Acid Bacteria Shuttle Vector for Improved Cloning and Food-Grade Expression. Microorganisms 2019; 7:microorganisms7050116. [PMID: 31035573 PMCID: PMC6560424 DOI: 10.3390/microorganisms7050116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Food-grade production of recombinant proteins in Gram-positive bacteria, especially in LAB (i.e., Lactococcus, Lactobacillus, and Streptococcus), is of great interest in the areas of recombinant enzyme production, industrial food fermentation, gene and metabolic engineering, as well as antigen delivery for oral vaccination. Food-grade expression relies on hosts generally considered as safe organisms and on clone selection not dependent on antibiotic markers, which limit the overall DNA manipulation workflow, as it can be carried out only in the expression host and not in E. coli. Moreover, many commercial expression vectors lack useful elements for protein purification. We constructed a “shuttle” vector containing a removable selective marker, which allows feasible cloning steps in E. coli and subsequent protein expression in LAB. In fact, the cassette can be easily excised from the selected recombinant plasmid, and the resulting marker-free vector transformed into the final LAB host. Further useful elements, as improved MCS, 6xHis-Tag, and thrombin cleavage site sequences were introduced. The resulting vector allows easy cloning in E. coli, can be quickly converted in a food-grade expression vector and harbors additional elements for improved recombinant protein purification. Overall, such features make the new vector an improved tool for food-grade expression.
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Affiliation(s)
- Marcello Tagliavia
- National Research Council-Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment (IAS-CNR), Capo Granitola, Via del mare, Campobello di Mazara (TP), 91021 Sicily, Italy.
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Ed.16, 90128 Palermo, Italy.
| | - Aldo Nicosia
- National Research Council-Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment (IAS-CNR), Capo Granitola, Via del mare, Campobello di Mazara (TP), 91021 Sicily, Italy.
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Ed.16, 90128 Palermo, Italy.
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Ying Hwa G, Yih Hui B, Jairaj Moses E, Shahriman MS, Md Yusoff M, Yahaya N, Sambasevam KP, Surikumaran H, Chandrasekaram K, Raoov M. Smart combination of β-cyclodextrin polymer-conjugated magnetic nanosorbent for potential adsorption of deoxyribonucleic acid. SEP SCI TECHNOL 2019. [DOI: 10.1080/01496395.2018.1524485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Goh Ying Hwa
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Boon Yih Hui
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Emmanuel Jairaj Moses
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Mohamad Shariff Shahriman
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Masrudin Md Yusoff
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Noorfatimah Yahaya
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | | | - Hemavathy Surikumaran
- Faculty of Bioeconomic and Health Sciences, Geomatika University College, Kuala Lumpur, Malaysia
| | - Kumuthini Chandrasekaram
- Department of Chemistry, Faculty of Science, Universiti of Malaya, Kuala Lumpur, Malaysia
- University Malaya Centre for Ionic Liquids (UMCiL), Universiti of Malaya, Kuala Lumpur, Malaysia
| | - Muggundha Raoov
- Department of Chemistry, Faculty of Science, Universiti of Malaya, Kuala Lumpur, Malaysia
- University Malaya Centre for Ionic Liquids (UMCiL), Universiti of Malaya, Kuala Lumpur, Malaysia
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Vidic J, Vizzini P, Manzano M, Kavanaugh D, Ramarao N, Zivkovic M, Radonic V, Knezevic N, Giouroudi I, Gadjanski I. Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1100. [PMID: 30836707 PMCID: PMC6427207 DOI: 10.3390/s19051100] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
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Affiliation(s)
- Jasmina Vidic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Priya Vizzini
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Devon Kavanaugh
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Milica Zivkovic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, 11000 Belgrade, Serbia.
| | - Vasa Radonic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Nikola Knezevic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ioanna Giouroudi
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ivana Gadjanski
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
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Guan F, Jin Y, Zhao J, Ai J, Luo Y. A Novel Direct PCR Lysis Buffer Can Improve PCR from Meat Matrices. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-018-1342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Kang TS. Rapid and simple identification of two closely-related snow crabs (Chionoecetes opilio and C. japonicus) by direct triplex PCR. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.09.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Development of four PCR-based methods to differentiate tilefish species (Branchiostegus japonicus and B. albus). Food Chem 2019; 271:1-8. [DOI: 10.1016/j.foodchem.2018.07.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/05/2018] [Accepted: 07/20/2018] [Indexed: 11/19/2022]
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Sajali N, Wong SC, Hanapi UK, Abu Bakar Jamaluddin S, Tasrip NA, Mohd Desa MN. The Challenges of DNA Extraction in Different Assorted Food Matrices: A Review. J Food Sci 2018; 83:2409-2414. [DOI: 10.1111/1750-3841.14338] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Nurhayatie Sajali
- School of Engineering and Technology; University College of Technology Sarawak; 868 Persiaran Brooke 96000 Sibu Sarawak Malaysia
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Sie Chuong Wong
- Department of Basic Science and Engineering, Faculty of Agriculture and Food Sciences; Universiti Putra Malaysia Bintulu Sarawak Campus; P.O. Box 396, Nyabau Road 97008 Bintulu Sarawak Malaysia
| | - Ummi Kalthum Hanapi
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Suhaili Abu Bakar Jamaluddin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia; 43400, Selangor Darul Ehsan Malaysia
| | - Nor Asmara Tasrip
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute; Universiti Putra Malaysia; 43400 Serdang Selangor Darul Ehsan Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia; 43400, Selangor Darul Ehsan Malaysia
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25
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High resolution melting analysis of a COI mini-barcode as a new approach for Penaeidae shrimp species discrimination. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Sun Y, Li J, Wang Y, Ding C, Lin Y, Sun W, Luo C. A chemiluminescence biosensor based on the adsorption recognition function between Fe 3O 4@SiO 2@GO polymers and DNA for ultrasensitive detection of DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 178:1-7. [PMID: 28147299 DOI: 10.1016/j.saa.2017.01.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
In this work, a chemiluminescence (CL) biosensor was prepared for ultrasensitive determination of deoxyribonucleic acid (DNA) based on the adsorption recognition function between core-shell Fe3O4@SiO2 - graphene oxide (Fe3O4@SiO2@GO) polymers and DNA. The Fe3O4@SiO2@GO polymers were composed by GO and magnetite nanoparticles. And the core-shell polymers were confirmed by Scanning Electron Microscope (SEM), X-Ray Powder Diffraction (XRD) and Fourier Transform Infrared (FTIR). Then Fe3O4@SiO2@GO was modified by DNA. Based on the principle of complementary base, Fe3O4@SiO2@GO-DNA was introduced to the CL system and the selectivity, sensitivity of DNA detection was significantly improved. The adsorption properties of Fe3O4@SiO2@GO to DNA were researched through the adsorption equilibrium, adsorption kinetic and thermodynamics. Under optimized CL conditions, DNA could be assayed with the linear concentration range of 5.0×10-12-2.5×10-11mol/L. The detection limit was 1.7×10-12mol/L (3δ) and the relative standard deviation (RSD) was 3.1%. The biosensor was finally used for the determination of DNA in laboratory samples and recoveries ranged from 99% to 103%. The satisfactory results revealed the potential application of Fe3O4@SiO2@GO-DNA-CL biosensor in the diagnosis and the treatment of human genetic diseases.
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Affiliation(s)
- Yuanling Sun
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Jianbo Li
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yanhui Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Chaofan Ding
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yanna Lin
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Weiyan Sun
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Chuannan Luo
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
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