101
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Yan S, Lai G, Li L, Xiao H, Zhao M, Wang M. DNA barcoding reveals mislabeling of imported fish products in Nansha new port of Guangzhou, Guangdong province, China. Food Chem 2016; 202:116-9. [PMID: 26920274 DOI: 10.1016/j.foodchem.2016.01.133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2016] [Accepted: 01/29/2016] [Indexed: 11/20/2022]
Abstract
In the present study, we employed a DNA barcoding approach to authenticate the species of fish imported via one port in China. The fish were identified as smallmouth scad based on morphological characteristics, Alepes apercna (Perciformes, Carangidae), but were labeled as Rastrelliger brachysoma (Perciformes, Scombridae). Fragments of the partial mitochondrial cytochrome c oxidase 1 (COI) gene were sequenced from 12 specimens, and their phylogenetic relationship was subsequently examined. The phylogenetic analysis demonstrated that all of the individuals formed a monophyletic cluster with high bootstrap values and were placed in a sister group with the ancestor of Alepes vari and Alepes melanoptera. The K2P genetic distances at an intraspecific level were significantly smaller than those at an interspecific level. Our results indicated that the fish were A. apercna, rather than R. brachysoma, which confirms the morphological analysis. This study presents a practical demonstration of the use of DNA barcoding to prevent fraud in international trade.
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Affiliation(s)
- Shuai Yan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Guiyan Lai
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Li Li
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Hao Xiao
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Ming Zhao
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China
| | - Ming Wang
- Nansha Entry-Exit Inspection and Quarantine Bureau, Guangzhou 511457, PR China; Guangdong Institute of Standardization, Guangzhou 510220, PR China.
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102
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Ahn JJ, Kim Y, Hong JY, Kim GW, Kim SY, Hwang SY. Probe-Based Fluorescence Melting Curve Analysis for Differentiating Larimichthys polyactis and Larimichthys crocea. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-015-0381-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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103
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Lin Y, Yanhua J, Qingjiao L, Zhe S, Lianzhu W, Yuxiu Z. A Comparison of Eight Methods for DNA Etraction from Processed Seafood Products. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2016. [DOI: 10.3136/fstr.22.751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yao Lin
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Jiang Yanhua
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Li Qingjiao
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Sui Zhe
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Wang Lianzhu
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
| | - Zhai Yuxiu
- Key Laboratory of Test and Evaluation on Quality and Safety of Aquatic Products, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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104
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The Impact of Molecular Diagnostics on Surveillance of Foodborne Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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105
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Dawnay N, Hughes R, Court DS, Duxbury N. Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications. Forensic Sci Int Genet 2015; 20:103-111. [PMID: 26561743 DOI: 10.1016/j.fsigen.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/05/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products, tested, provided a correct single species result with the remaining samples erroneously identified as containing non-target species. The data shows that the assay was quick to design and characterise and is also capable of yielding results that would be beneficial in a variety of fields, not least the authentication of food.
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Affiliation(s)
- Nick Dawnay
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Rebecca Hughes
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Nicola Duxbury
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK
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106
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Rašković B, Heinke R, Rösch P, Popp J. The Potential of Raman Spectroscopy for the Classification of Fish Fillets. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0312-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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107
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Wen J, Zeng L, Sun Y, Chen D, Xu Y, Luo P, Zhao Z, Yu Z, Fan S. Authentication and traceability of fish maw products from the market using DNA sequencing. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.02.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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108
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Muñoz-Colmenero M, Klett-Mingo M, Díaz E, Blanco O, Martínez JL, Garcia-Vazquez E. Evolution of hake mislabeling niches in commercial markets. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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109
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A handheld sensor assay for the identification of grouper as a safeguard against seafood mislabeling fraud. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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110
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Authentication of closely related scombrid, catfish and tilapia species by PCR-based analysis and isoelectric focusing of parvalbumin. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2479-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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111
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Leal MC, Pimentel T, Ricardo F, Rosa R, Calado R. Seafood traceability: current needs, available tools, and biotechnological challenges for origin certification. Trends Biotechnol 2015; 33:331-6. [DOI: 10.1016/j.tibtech.2015.03.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/09/2015] [Accepted: 03/19/2015] [Indexed: 11/27/2022]
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112
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Scarano D, Rao R, Masi P, Corrado G. SSR fingerprint reveals mislabeling in commercial processed tomato products. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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113
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114
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A novel reliable method of DNA extraction from olive oil suitable for molecular traceability. Food Chem 2015; 172:596-602. [DOI: 10.1016/j.foodchem.2014.09.101] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/04/2014] [Accepted: 09/17/2014] [Indexed: 11/23/2022]
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115
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de Brito MA, Schneider H, Sampaio I, Santos S. DNA barcoding reveals high substitution rate and mislabeling in croaker fillets (Sciaenidae) marketed in Brazil: The case of “pescada branca” (Cynoscion leiarchus and Plagioscion squamosissimus). Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.01.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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116
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Ortea I, Gallardo JM. Investigation of production method, geographical origin and species authentication in commercially relevant shrimps using stable isotope ratio and/or multi-element analyses combined with chemometrics: An exploratory analysis. Food Chem 2015; 170:145-53. [DOI: 10.1016/j.foodchem.2014.08.049] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 06/24/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
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117
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Liu S, Xu K, Wu Z, Xie X, Feng J. Identification of five highly priced tuna species by quantitative real-time polymerase chain reaction. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3270-9. [PMID: 25714139 DOI: 10.3109/19401736.2015.1015004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tunas are economically important fishery worldwide, and are often used for commercial processed production. For effective fishery management and protection of consumers' rights, it is important to develop a molecular method to identify species in canned tuna products rapidly and reliably. Here, we have developed a duplex quantitative real-time PCR (qPCR) for identification of five highly priced tuna species (Thunnus maccoyii, Thunnus obesus, Thunnus albacares, Thunnus alalunga and Katsuwonus pelamis) from processed as well as fresh fish. After amplification and sequencing of seven genetic markers commonly used for species identification, 16S rDNA and control region (CR) of mitochondrial DNA were selected as the reference gene markers for genus Thunnus and tuna species identification, respectively. Subsequently, a 73 bp fragment of 16S rDNA and 85-99 bp fragment of CR were simultaneously amplified from each target species by qPCR. The qPCR efficiency of each reaction was calculated according to the standard curves, and the method was validated by amplification DNA extracted from single or mixed tuna specimen. The developed duplex qPCR system was applied to authenticate species of 14 commercial tuna products successfully, which demonstrated it was really a useful and academic technique to identify highly priced tuna species.
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Affiliation(s)
- Shasha Liu
- a Institute of Bioengineering, Zhejiang Sci-Tech University , Hangzhou , Zhejiang , P.R. China
| | - Kunhua Xu
- b Institute of Aquatic Products Processing, College of Food Science and Biotechnology, Zhejiang Gongshang University , Hangzhou , Zhejiang , P.R. China , and
| | - Zhigang Wu
- c Zhejiang Entry-Exit Inspection and Quarantine Bureau , Hangzhou , Zhejiang , P.R. China
| | - Xiao Xie
- c Zhejiang Entry-Exit Inspection and Quarantine Bureau , Hangzhou , Zhejiang , P.R. China
| | - Junli Feng
- a Institute of Bioengineering, Zhejiang Sci-Tech University , Hangzhou , Zhejiang , P.R. China .,b Institute of Aquatic Products Processing, College of Food Science and Biotechnology, Zhejiang Gongshang University , Hangzhou , Zhejiang , P.R. China , and
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118
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Genetic diversity of ivory shell (Babylonia areolata) in Taiwan and identification of species using DNA-based assays. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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119
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Bénard-Capelle J, Guillonneau V, Nouvian C, Fournier N, Le Loët K, Dettai A. Fish mislabelling in France: substitution rates and retail types. PeerJ 2015; 2:e714. [PMID: 28462014 PMCID: PMC5407283 DOI: 10.7717/peerj.714] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022] Open
Abstract
Market policies have profound implications for consumers as well as for the management of resources. One of the major concerns in fish trading is species mislabelling: the commercial name used does not correspond to the product, most often because the product is in fact a cheaper or a more easily available species. Substitution rates depend heavily on species, some often being sold mislabelled while others rarely or never mislabelled. Rates also vary largely depending on countries. In this study, we analyse the first market-wide dataset collected for France, the largest sea food market in Europe, for fish species substitution. We sequenced and analysed 371 samples bearing 55 commercial species names, collected in fishmonger shops, supermarkets and restaurants; the largest dataset assembled to date in an European country. Sampling included fish fillets, both fresh and frozen, and prepared meals. We found a total of 14 cases of mislabelling in five species: bluefin tuna, cod, yellowfin tuna, sole and seabream, setting the overall substitution rate at 3.7% CI [2.2-6.4], one of the lowest observed for comparable surveys with large sampling. We detected no case of species mislabelling among the frozen fillets or in industrially prepared meals, and all the substitutions were observed in products sold in fishmongers shops or restaurants. The rate of mislabelling does not differ between species, except for bluefin tuna. Despite a very small sample size (n = 6), the rate observed for this species (83.3% CI [36-99]) stands in sharp contrast with the low substitution rate observed for the other substituted species. In agreement with studies from other countries, this work shows that fish mislabelling can vary greatly within a country depending on the species. It further suggests that more efforts should be directed to the control of high value species like bluefin tuna.
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Affiliation(s)
- Julien Bénard-Capelle
- Institut National de la Santé et de la Recherche Medicale, Unité 1001 Robustness and Evolvability of Life, Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | | | | | | | | | - Agnès Dettai
- Département Systématique et Évolution, Muséum national d’Histoire naturelle, Sorbonne Universités, UMR 7205 MNHN-CNRS-UPMC-EPHE, Paris, France
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120
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Vartak VR, Narasimmalu R, Annam PK, Singh DP, Lakra WS. DNA barcoding detected improper labelling and supersession of crab food served by restaurants in India. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:359-366. [PMID: 24796530 DOI: 10.1002/jsfa.6728] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Detection of improper labelling of raw and processed seafood is of global importance for reducing commercial fraud and enhancing food safety. Crabs are crustaceans with intricate morphological as well as genetic divergence among species and are popular as seafood in restaurants. Owing to the high number of crab species available, it can be difficult to identify those included in particular food dishes, thus increasing the chance of supersession. DNA barcoding is an advanced technology for detecting improper food labelling and has been used successfully to authenticate seafood. RESULTS This study identified 11 edible crab species from India by classical taxonomy and developed molecular barcodes with the cytochrome c oxidase I (COI) gene. These barcodes were used as reference barcodes for detecting any improper labelling of 50 restaurant crab samples. Neighbour-joining tree analysis with COI barcodes showed distinct clusters of restaurant samples with respective reference species. The study demonstrated 100% improper labelling of restaurant samples to cover up acts of inferior crab supersession. CONCLUSION DNA barcoding successfully identified 11 edible crabs in accordance with classical taxonomy and discerned improper crab food labelling in restaurants of India.
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Affiliation(s)
- Vivek Rohidas Vartak
- Khar Land Research Station (Dr. B.S. Konkan Agricultural University), Panvel 410206, Navi Mumbai, Maharashtra, India; Vellore Institute of Technology University, Vellore, 632 014, Tamil Nadu, India
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121
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Two alternative multiplex PCRs for the identification of the seven species of anglerfish (Lophius spp.) using an end-point or a melting curve analysis real-time protocol. Food Chem 2015; 166:1-9. [DOI: 10.1016/j.foodchem.2014.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 01/31/2014] [Accepted: 06/05/2014] [Indexed: 12/12/2022]
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122
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Galal-Khallaf A, Ardura A, Mohammed-Geba K, Borrell YJ, Garcia-Vazquez E. DNA barcoding reveals a high level of mislabeling in Egyptian fish fillets. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.06.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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123
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124
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125
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Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, Carvalho GR, Brutto SL, Costa FO. DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One 2014; 9:e106135. [PMID: 25222272 PMCID: PMC4164363 DOI: 10.1371/journal.pone.0106135] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 08/01/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. METHODOLOGY/PRINCIPAL FINDINGS A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species. CONCLUSION/SIGNIFICANCE We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.
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Affiliation(s)
- Monica Landi
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Mark Dimech
- Malta Centre for Fisheries Science (MCFS), Fort San Lucjan Marsaxlokk, Malta
| | - Marco Arculeo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Girolama Biondo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Rogelia Martins
- Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal
| | - Miguel Carneiro
- Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal
| | - Gary Robert Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Sabrina Lo Brutto
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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127
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Asis AMJM, Lacsamana JKM, Santos MD. Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding. ACTA ACUST UNITED AC 2014; 27:659-66. [DOI: 10.3109/19401736.2014.913138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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128
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Chairi H, Rebordinos L. A rapid method for differentiating four species of the Engraulidae (anchovy) family. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2803-2808. [PMID: 24628361 DOI: 10.1021/jf405680g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The four species of the Engraulidae family: European anchovy (Engraulis encrasicolus), Californian anchovy (Engraulis mordax), Peruvian anchoveta (Engraulis ringens), and Japanese anchovy (Engraulis japonicus) studied in this work are very similar morphologically, and it is very difficult to distinguish between them, especially when frozen or processed. We have used the 5S rDNA as a molecular marker to discriminate these four species and used specific primers designed for each species in the nontranscribed spacers (NTS) of these genes. Multiplex PCR was performed with three pairs of primers, and three different sizes were obtained: 597 bp E. encrasicolus, 598 bp E. japonicus, 380 bp E. mordax, and 250 bp E. ringens. For the species E. encrasicolus and E. japonicus, PCR-RFLP was used as an additional technique to distinguish between them because their NTS sequences showed considerable similarity.
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Affiliation(s)
- Hicham Chairi
- Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, CACYTMAR, Universidad de Cádiz , Polígono Río San Pedro, s/n, 11510, Puerto Real, Cádiz, Spain
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129
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De Battisti C, Marciano S, Magnabosco C, Busato S, Arcangeli G, Cattoli G. Pyrosequencing as a tool for rapid fish species identification and commercial fraud detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:198-205. [PMID: 24350776 DOI: 10.1021/jf403545m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The increased consumption of fish products, as well as the occurrence of exotic fish species in the Mediterranean Sea and in the fish market, has increased the risk of commercial fraud. Furthermore, the great amount of processed seafood products has greatly limited the application of classic identification systems. DNA-based identification allows a clear and unambiguous detection of polymorphisms between species, permitting differentiation and identification of both commercial fraud and introduction of species with potential toxic effects on humans. In this study, a novel DNA-based approach for differentiation of fish species based on pyrosequencing technology has been developed. Raw and processed fish products were tested, and up to 25 species of fish belonging to Clupeiformes and Pleuronectiformes groups were uniquely and rapidly identified. The proper identification based on short and unique genetic sequence signatures demonstrates that this approach is promising and cost-effective for large-scale surveys.
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Affiliation(s)
- Cristian De Battisti
- Research & Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie , Viale dell'Università 10, 35020 Legnaro, Padova, Italy
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130
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Ardura A, Planes S, Garcia-Vazquez E. Applications of DNA barcoding to fish landings: authentication and diversity assessment. Zookeys 2013; 365:49-65. [PMID: 24453550 PMCID: PMC3890670 DOI: 10.3897/zookeys.365.6409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/23/2013] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches.
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Affiliation(s)
- Alba Ardura
- University of Oviedo, Department of Functional Biology. C/ Julian Claveria s/n. 33006-Oviedo, Spain
| | - Serge Planes
- USR 3278 CNRS – EPHE. Centre de Recherche Insulaire et Observatoire de l’Environnement (CRIOBE) BP 1013 - 98 729, Papetoai, Moorea, Polynésie française
- Centre de Biologie et d’Ecologie Tropicale et Méditerranéenne, Université de Perpignan, 52 Av. Paul Alduy - 66860 Perpignan cedex, France
| | - Eva Garcia-Vazquez
- University of Oviedo, Department of Functional Biology. C/ Julian Claveria s/n. 33006-Oviedo, Spain
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131
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Dalmasso A, Chiesa F, Civera T, Bottero MT. A novel minisequencing test for species identification of salted and dried products derived from species belonging to Gadiformes. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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132
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Matrix-assisted laser desorption ionization mass spectrometry for identification of shrimp. Anal Chim Acta 2013; 794:55-9. [DOI: 10.1016/j.aca.2013.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022]
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133
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Ensuring seafood identity: Grouper identification by real-time nucleic acid sequence-based amplification (RT-NASBA). Food Control 2013. [DOI: 10.1016/j.foodcont.2012.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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134
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Di Pinto A, Di Pinto P, Terio V, Bozzo G, Bonerba E, Ceci E, Tantillo G. DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks. Food Chem 2013; 141:1757-62. [PMID: 23870888 DOI: 10.1016/j.foodchem.2013.05.093] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 02/06/2013] [Accepted: 05/16/2013] [Indexed: 10/26/2022]
Abstract
The Italian Ministry of Agricultural, Food and Forestry Policies (MiPAAF) Decree dated 31 January 2008, which reports the Italian name for fish species of commercial interest, establishes that baccalà can be obtained exclusively from G. macrocephalus (Pacific cod) and G. morhua (Atlantic cod). This paper describes the COI-based DNA identification system to verify the substitution or misbranding of gadoid fish species and, consequently, its concordance with the labels on salted cod fillets shown as baccalà and on battered cod chunks labelled as bocconcini di baccalà. The analysis of interpretable sequences revealed that 55/65 dried salted cod fillet samples were detected as belonging to the family Gadidae, while 10/65 samples appeared to belong to the Lotidae family, while among battered cod chunks labelled as bocconcini di baccalà, the post-sequencing data analysis shows that the labels were completely wrong, with 28/40 samples from Pollachius virens and 12/40 samples from Brosme brosme. The substitution rate for products labelled on the market as baccalà in this study raises significant issues relating to food safety and consumer protection.
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Affiliation(s)
- Angela Di Pinto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, Prov. le per Casamassima, km 3, 70010 Valenzano, Bari, Italy.
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135
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Schiefenhövel K, Rehbein H. Differentiation of Sparidae species by DNA sequence analysis, PCR-SSCP and IEF of sarcoplasmic proteins. Food Chem 2013; 138:154-60. [DOI: 10.1016/j.foodchem.2012.10.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 06/21/2012] [Accepted: 10/17/2012] [Indexed: 11/30/2022]
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136
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137
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Ben-Ayed R, Kamoun-Grati N, Rebai A. An Overview of the Authentication of Olive Tree and Oil. Compr Rev Food Sci Food Saf 2013. [DOI: 10.1111/1541-4337.12003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Ahmed Rebai
- Centre of Biotechnology of Sfax; P.O.Box 1177; 3018 Sfax; Tunisia
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138
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De Battisti C, Salomoni A, Ormelli S, Monne I, Capua I, Cattoli G. Rapid pathotyping of Newcastle Disease Virus by pyrosequencing. J Virol Methods 2013. [DOI: 10.1016/j.jviromet.2012.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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139
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Horreo JL, Ardura A, Pola IG, Martinez JL, Garcia-Vazquez E. Universal primers for species authentication of animal foodstuff in a single polymerase chain reaction. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:354-361. [PMID: 22740422 DOI: 10.1002/jsfa.5766] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 04/20/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND There are many DNA-based systems for detecting animal species present in food and food products, applicable for food quality control and authentication. However, most (if not all) methods require more than one pair of primers and cannot be applied over a wide taxonomic range, e.g. identifying vertebrates and invertebrates with the same primers and protocols. RESULTS A pair of primers is described here that allows in a single polymerase chain reaction the identification of animal species in food and processed (precooked, canned or smoked) food products over a wide taxonomic range. CONCLUSION These primers permit the identification of most animal taxa employed in human nutrition, from invertebrates such as molluscs to higher vertebrates, distinguishing between species of the same genus. The short fragment amplified within the 16S rDNA exhibits phylogenetic value and could be considered universal based on the wide taxonomic range assayed. The primers are easy to use and accessible for laboratories with a modest budget, as well as being valuable for consumer information and to reveal food fraud.
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Affiliation(s)
- Jose L Horreo
- Department of Functional Biology, University of Oviedo. C/Julian Claveria s/n, E-33006 Oviedo, Spain.
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140
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Galimberti A, De Mattia F, Losa A, Bruni I, Federici S, Casiraghi M, Martellos S, Labra M. DNA barcoding as a new tool for food traceability. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.036] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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141
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Ortea I, Pascoal A, Cañas B, Gallardo JM, Barros-Velázquez J, Calo-Mata P. Food authentication of commercially-relevant shrimp and prawn species: From classical methods to Foodomics. Electrophoresis 2012; 33:2201-11. [DOI: 10.1002/elps.201100576] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ignacio Ortea
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Ananías Pascoal
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Benito Cañas
- Department of Analytical Chemistry; University Complutense of Madrid; Madrid; Spain
| | - José M. Gallardo
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
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142
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Chuang PS, Chen MI, Shiao JC. Identification of tuna species by a real-time polymerase chain reaction technique. Food Chem 2012. [DOI: 10.1016/j.foodchem.2012.01.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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143
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Armani A, Castigliego L, Tinacci L, Gianfaldoni D, Guidi A. Multiplex conventional and real-time PCR for fish species identification of Bianchetto (juvenile form of Sardina pilchardus), Rossetto (Aphia minuta), and Icefish in fresh, marinated and cooked products. Food Chem 2012. [DOI: 10.1016/j.foodchem.2011.12.076] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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144
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Leitfaden für die Lebensmittelüberwachung zur Identifizierung der Fischart durch DNA-Sequenzierung von PCR-Produkten. J Verbrauch Lebensm 2012. [DOI: 10.1007/s00003-012-0773-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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145
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Besbes N, Fattouch S, Sadok S. Differential detection of small pelagic fish in Tunisian canned products by PCR-RFLP: An efficient tool to control the label information. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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146
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147
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Rehbein H, Schiefenhövel K. Evaluation of a Rapid PCR-Based Method for Species Identification of Raw and Processed Fish and Shrimps. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2012. [DOI: 10.1080/10498850.2011.584017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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148
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149
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Alaskan flatfishes on the German market: part 1: identification by DNA and protein analytical methods. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1629-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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150
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Development of real-time PCR assays for the detection of Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar) and European plaice (Pleuronectes platessa) in complex food samples. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1596-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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