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Ivanov AV, Popravko DS, Safenkova IV, Zvereva EA, Dzantiev BB, Zherdev AV. Rapid Full-Cycle Technique to Control Adulteration of Meat Products: Integration of Accelerated Sample Preparation, Recombinase Polymerase Amplification, and Test-Strip Detection. Molecules 2021; 26:6804. [PMID: 34833896 PMCID: PMC8622786 DOI: 10.3390/molecules26226804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022] Open
Abstract
Verifying the authenticity of food products is essential due to the recent increase in counterfeit meat-containing food products. The existing methods of detection have a number of disadvantages. Therefore, simple, cheap, and sensitive methods for detecting various types of meat are required. In this study, we propose a rapid full-cycle technique to control the chicken or pig adulteration of meat products, including 3 min of crude DNA extraction, 20 min of recombinase polymerase amplification (RPA) at 39 °C, and 10 min of lateral flow assay (LFA) detection. The cytochrome B gene was used in the developed RPA-based test for chicken and pig identification. The selected primers provided specific RPA without DNA nuclease and an additional oligonucleotide probe. As a result, RPA-LFA, based on designed fluorescein- and biotin-labeled primers, detected up to 0.2 pg total DNA per μL, which provided up to 0.001% w/w identification of the target meat component in the composite meat. The RPA-LFA of the chicken and pig meat identification was successfully applied to processed meat products and to meat after heating. The results were confirmed by real-time PCR. Ultimately, the developed analysis is specific and enables the detection of pork and chicken impurities with high accuracy in raw and processed meat mixtures. The proposed rapid full-cycle technique could be adopted for the authentication of other meat products.
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Affiliation(s)
| | | | | | | | | | - Anatoly V. Zherdev
- Research Centre of Biotechnology, A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (D.S.P.); (I.V.S.); (E.A.Z.); (B.B.D.)
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Species-specific identification of porcine blood plasma in heat-treated chicken meatballs. Saudi J Biol Sci 2021; 28:2447-2452. [PMID: 33911957 PMCID: PMC8071913 DOI: 10.1016/j.sjbs.2021.01.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/21/2022] Open
Abstract
This study was conducted to detect the presence of chicken and porcine DNA in meatballs using mitochondria DNA (mtDNA) of cytochrome b (cyt b) and nuclear DNA (nDNA) short interspersed nuclear element (SINE) species-specific primers, respectively. While, the mtDNA primers targeted transfer RNA-ATP8 (tRNA-ATP8) gene was used for 1 and 5% (w/w) chicken meatball spiked with commercial porcine blood plasm. Chicken meatballs spiked with 1% and 5% (v/w) fresh and commercial porcine blood plasma, respectively were prepared and heat-treated using five (n = 5) cooking methods: boiling, pan-frying, roasting, microwaving and autoclaving. Two pairs of mtDNA and nDNA primers used, produced 129 and 161 bp amplicons, respectively. Whereas, tRNA-ATP8 primers produced 212 bp of amplicon. Electrophoresis analysis showed positive results for porcine DNA at 1% and 5% (w/w or v/v) for all of the different cooking techniques, either for fresh or commercial blood plasma using SINE primers but not for tRNA-ATP8 primers. The present study has highlighted the useful of species-specific primers of SINE primers in PCR analysis for detecting porcine DNA blood plasma in heat-treated chicken meatballs.
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Yoshinaga N, Shindo K, Matsui Y, Takiuchi Y, Fukuda H, Nagata K, Shirakawa K, Kobayashi M, Takeda S, Takaori-Kondo A. A screening for DNA damage response molecules that affect HIV-1 infection. Biochem Biophys Res Commun 2019; 513:93-98. [PMID: 30935695 DOI: 10.1016/j.bbrc.2019.03.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 01/14/2023]
Abstract
Host DNA damage response molecules affect retroviral infection, as DNA intermediates of the viruses play essential roles in the viral life cycles. Although several such molecules have been reported, interactions between HIV-1 and host DNA damage response molecules have not been fully elucidated. To screen DNA damage response molecules that might affect HIV-1 infection, a set of 32 DNA-repair-deficient DT40 isogenic mutant cells were tested for HIV-1 infectivity. Seven out of the 32 clones showed less than 50% infectivity compared to parental DT40 cells, implying that DNA repair molecules deficient in these cells might support HIV-1 infection. Of these, EXO1 -/-, TP53BP1 -/- and WRN -/- cells showed more than twofold accumulation of two long terminal repeat circles and less than 50% integrated proviral DNA in quantitative-PCR analyses, indicating that the integration step is impaired. RAD18 -/- cells showed twofold higher HIV-1 infectivity and increased reverse transcription products at earlier time points, suggesting that RAD18 suppresses reverse transcription. The HIV-1 suppressive effects of RAD18 were confirmed by over-expression and knockdown experiments in human cells. L274P, a DNA-binding-impaired mutant of RAD18, showed impaired HIV-1 suppression and DNA binding, suggesting that binding HIV-1 DNA intermediates is critical for RAD18 to suppress reverse transcription and HIV-1 infection. Our data help understand interactions between host DNA damage response molecules and viral DNA.
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Affiliation(s)
- Noriyoshi Yoshinaga
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan.
| | - Yusuke Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Yoko Takiuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Hirofumi Fukuda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Kayoko Nagata
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
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Cosenza G, Iannaccone M, Gallo D, Pauciullo A. A fast and reliable polymerase chain reaction method based on short interspersed nuclear elements detection for the discrimination of buffalo, cattle, goat, and sheep species in dairy products. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:891-895. [PMID: 30744372 PMCID: PMC6498080 DOI: 10.5713/ajas.18.0459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/29/2018] [Indexed: 11/27/2022]
Abstract
Objective Aim of present study was the set up of a fast and reliable protocol using species-specific markers for the quali-quantitative analysis of DNA and the detection of ruminant biological components in dairy products. For this purpose, the promoter of the gene coding for the α-lactoalbumin (LALBA) was chosen as possible candidate for the presence of short interspersed nuclear elements (SINEs). Methods DNA was isolated from somatic cells of 120 individual milk samples of cattle (30), Mediterranean river buffalo (30), goat (30), and sheep (30) and the gene promoter region (about 600/700 bp) of LALBA (from about 600 bp upstream of exon 1) has been sequenced. For the development of a single polymerase chain reaction (PCR) protocol that allows the simultaneous identification of DNA from the four species of ruminants, the following internal primers pair were used: 5′-CACTGATCTTAAAGCTCAGGTT-3′ (forward) and 5′-TCAGA GTAGGCCACAGAAG-3′ (reverse). Results Sequencing results of LALBA gene promoter region confirmed the presence of SINEs as monomorphic “within” and variable in size “among” the selected species. Amplicon lengths were 582 bp in cattle, 592 bp in buffalo, 655 in goat and 729 bp in sheep. PCR specificity was demonstrated by the detection of trace amounts of species-specific DNA from mixed sources (0.25 ng/μL). Conclusion We developed a rapid PCR protocol for the quali-quantitative analysis of DNA and the traceability of dairy products using a species-specific marker with only one pair of primers. Our results validate the proposed technique as a suitable tool for a simple and inexpensive (economic) detection of animal origin components in foodstuffs.
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Affiliation(s)
- Gianfranco Cosenza
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, NA 80055, Italy
| | - Marco Iannaccone
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, NA 80055, Italy
| | - Daniela Gallo
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, NA 80055, Italy
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Science, University of Torino, Grugliasco, TO 10095, Italy
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Zhang X, Wang D, Han Y, Duan F, Lv Q, Li Z. Altered imprinted gene expression and methylation patterns in mid-gestation aborted cloned porcine fetuses and placentas. J Assist Reprod Genet 2014; 31:1511-7. [PMID: 25172095 DOI: 10.1007/s10815-014-0320-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/19/2014] [Indexed: 12/12/2022] Open
Abstract
PURPOSE To determine the expression patterns of imprinted genes and their methylation status in aborted cloned porcine fetuses and placentas. METHODS RNA and DNA were prepared from fetuses and placentas that were produced by SCNT and controls from artificial insemination. The expression of 18 imprinted genes was determined by quantitative real-time PCR (q-PCR). Bisulfite sequencing PCR (BSP) was conducted to determine the methylation status of PRE-1 short interspersed repetitive element (SINE), satellite DNA and H19 differentially methylated region 3 (DMR3). RESULTS The weight, imprinted gene expression and genome-wide DNA methylation patterns were compared between the mid-gestation aborted and normal control samples. The results showed hypermethylation of PRE-1 and satellite sequences, the aberrant expression of imprinted genes, and the hypomethylation of H19 DMR3 occurred in mid-gestation aborted fetuses and placentas. CONCLUSIONS Cloned pigs generated by somatic cell nuclear transfer (SCNT) showed a greater ratio of early abortion during mid-gestation than did normal controls because of the incomplete epigenetic reprogramming of the donor cells. Altered expression of imprinted genes and the hypermethylation profile of the repetitive regions (PRE-1 and satellite DNA) may be associated with defective development and early abortion of cloned pigs, emphasizing the importance of epigenetics during pregnancy and implications thereof for patient-specific embryonic stem cells for human therapeutic cloning and improvement of human assisted reproduction.
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Affiliation(s)
- Xiaoyang Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, China,
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Pegels N, González I, Fernández S, García T, Martín R. Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2012; 29:1402-12. [PMID: 22780087 DOI: 10.1080/19440049.2012.696284] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.
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Affiliation(s)
- N Pegels
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Wang X, Teng D, Tian F, Guan Q, Wang J. Comparison of three DNA extraction methods for feed products and four amplification methods for the 5'-junction fragment of Roundup Ready soybean. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:4586-95. [PMID: 22515503 DOI: 10.1021/jf300827q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Three methods of DNA extraction from feed products and four detection methods for the 5'-junction fragment of genetically modified (GM) Roundup Ready soybean (RRS) were compared and evaluated. The DNA extraction methods, including cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), and guanidine hydrochloride (Kit), were assessed for their yields and purity of DNA, extraction time, and reagent cost. The DNA yields of CTAB, SDS, and Kit were 52-694, 164-1750 and 23-105 ng/mg sample, and their extraction time was 2.5-3, 2-2.5, and 1.5-2 h with reagent cost about US dollar 0.24, 0.13, and 1.9 per extraction, respectively. The SDS method was generally well suited to all kinds of feed matrices tested. The limits of detection for the four amplification protocols, including loop-mediated isothermal amplification (LAMP), hyperbranched rolling circle amplification (HRCA), conventional polymerase chain reaction (PCR), and real-time PCR, were 48.5, 4.85, 485, and 9 copies of the pTLH10 plasmid, respectively. The ranked results of the four detection methods were based on multiattribute utility theory as follows (from best to worse): HRCA, LAMP, PCR, and real-time PCR. This comparative evaluation was specifically useful for selection of a highly efficient DNA extraction or amplification method for detecting different GM ingredients.
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Affiliation(s)
- Xiumin Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing 100081, PR China
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Huang Q, Xu T, Wang GY, Huang JF, Xia H, Yin R, Tang A, Fu WL. Species-specific identification of ruminant components contaminating industrial crude porcine heparin using real-time fluorescent qualitative and quantitative PCR. Anal Bioanal Chem 2011; 402:1625-34. [PMID: 22147273 DOI: 10.1007/s00216-011-5590-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 11/01/2011] [Accepted: 11/20/2011] [Indexed: 12/19/2022]
Abstract
Ever since the emergence of bovine spongiform encephalopathy, the source of pharmaceutical heparin has been restricted to porcine intestinal mucosa. In this project, two real-time fluorescent PCR methods were developed to assist with quality control analysis. The first is a qualitative method which relies on SYBR Green I chemistry to confirm the porcine origin of industrial crude porcine heparin (ICPH), identify any ruminant contaminants, and generally control purity. The second is based on TaqMan chemistry and is able to quantitatively identify porcine, bovine, caprine, and ovine components and contaminants in ICPH. By targeting mitochondrial DNA, both PCR systems showed a detection limit of 1 pg DNA and amplification efficiencies ranging between 96% and 102%. Moreover, quantitative PCR showed a detection limit of 0.02 ppm in samples comprising porcine, bovine, caprine, and ovine DNA. The results of qualitative PCR over 27 ICPH samples showed that all samples were porcine in origin and that 17 had ruminant contaminants. The results of quantitative PCR further showed that out of all 17 samples with ruminant contaminants, seven samples had bovine, ovine, and caprine contaminants, two samples had bovine and ovine contaminants, and eight samples had only ovine contaminants. In conclusion, the qualitative PCR system was found to be a relatively inexpensive, rapid, and flexible method of identifying the porcine origin of and ruminant contaminants in ICPH, while the quantitative PCR was found suitable to accurately analyze the components and contaminants in detail. Both methods are suitable for routine control assays for the evaluation of ICPH purity and origins of contaminants.
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Affiliation(s)
- Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
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Application of species-specific polymerase chain reaction assays to verify the labeling of quail (Coturnix coturnix), pheasant (Phasianus colchicus) and ostrich (Struthio camelus) in pet foods. Anim Feed Sci Technol 2011. [DOI: 10.1016/j.anifeedsci.2011.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Pegels N, González I, García T, Martín R. Detection of banned ruminant-derived material in industrial feedstuffs by TaqMan real-time PCR Assay. J Food Prot 2011; 74:1300-8. [PMID: 21819656 DOI: 10.4315/0362-028x.jfp-11-029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A ruminant-specific real-time PCR system was designed and applied for the detection of processed animal protein from ruminants in industrial feedstuffs. The assay includes a primer pair and a TaqMan probe selectively targeting mitochondrial 16S rRNA gene sequences from the ruminant group and another primer-probe set based on the eukaryotic nuclear 18S rRNA gene (positive amplification control). Both ruminant and eukaryotic PCR systems generated short PCR amplicons of 79 and 77 bp, respectively. To evaluate the suitability of the real-time PCR assay for the detection of banned by-products of ruminant origin, 126 feed samples subjected to rendering under current European legislation regulations were analyzed. The assay achieved 100% success in classifying the samples as positive or negative in terms of qualitative ruminant composition, with a detection limit of 0.1%. The quantitative ability of the assay is however restricted by variations in the composition and treatment of the feeds, which affect the amount and quality of amplifiable DNA.
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Affiliation(s)
- Nicolette Pegels
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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KARABASANAVAR NAGAPPAS, SINGH S, UMAPATHI V., KUMAR DEEPAK, SHEBANNAVAR SUNILN. IDENTIFICATION OF GOAT MEAT USING HIGHLY SPECIES-SPECIFIC POLYMERASE CHAIN REACTION. J FOOD QUALITY 2011. [DOI: 10.1111/j.1745-4557.2011.00376.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Ahmed MU, Hasan Q, Mosharraf Hossain M, Saito M, Tamiya E. Meat species identification based on the loop mediated isothermal amplification and electrochemical DNA sensor. Food Control 2010. [DOI: 10.1016/j.foodcont.2009.09.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ballin NZ, Vogensen FK, Karlsson AH. Species determination – Can we detect and quantify meat adulteration? Meat Sci 2009; 83:165-74. [DOI: 10.1016/j.meatsci.2009.06.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 10/20/2022]
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Murugaiah C, Noor ZM, Mastakim M, Bilung LM, Selamat J, Radu S. Meat species identification and Halal authentication analysis using mitochondrial DNA. Meat Sci 2009; 83:57-61. [DOI: 10.1016/j.meatsci.2009.03.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 03/12/2009] [Accepted: 03/30/2009] [Indexed: 11/26/2022]
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Yoshida T, Nomura T, Shinoda N, Kusama T, Kadowaki KI, Sugiura K. Development of PCR primers for the detection of porcine DNA in feed using mtATP6 as the target sequence. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2009; 50:89-92. [PMID: 19436158 DOI: 10.3358/shokueishi.50.89] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Japan, PCR identification of species-specific, animal group-specific and plant DNA is employed as part of the audit program to ensure compliance with the feed ban in place for the control of bovine spongiform encephalopathy (BSE). Since October 2001, animal proteins other than dairy proteins, egg proteins and gelatin have been prohibited to be used in feed for ruminants. Meat-and-bone meal (MBM) derived from poultry, pig and/or fish is allowed to be used in feed for poultry, pigs and fish. Porcine MBM is permitted in feed for domestic animals other than cattle since April 2005. Given the fact that pigs and cattle are the two major sources of MBM in Japan, the identification of porcine DNA with high specificity and sensitivity has become increasingly important to ensure that MBM products are free from ruminant materials. Two PCR primer sets (PPA8 and PPA6) were newly designed using mtATP8 and mtATP6 as the target sequences, with relatively short amplification sizes. PPA8 and PPA6 were able to specifically detect porcine DNA with the detection limits of 0.01% and 0.001% of porcine MBM in feed, respectively. PPA6 was superior to PPA8 in terms of detection of DNA damaged/fragmented during rendering procedures. The PCR method using these primer sets is registered as the official analytical method for feed in Japan.
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Affiliation(s)
- Tomotaro Yoshida
- Food and Agricultural Materials Inspection Center, Chuo-ku, Saitama 3309731, Japan
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Scott M, Knight A. Quantitative PCR analysis for fruit juice authentication using PCR and laboratory-on-a-chip capillary electrophoresis according to the Hardy-Weinberg law. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:4545-4551. [PMID: 19438229 DOI: 10.1021/jf9002686] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA-based analysis for the authentication of fruit juices was evaluated using the Polymerase Chain Reaction (PCR) and laboratory-on-a-chip capillary electrophoresis (LOC). A PCR restriction fragment length polymorphism (RFLP) assay demonstrated the detection of grapefruit juice in orange juice, although the assay was relatively insensitive with a limit of detection of 10% v/v. A PCR heteroduplex assay for detecting mandarin juice in orange juice was successfully applied to the LOC system and demonstrated greater sensitivity with a limit of detection of 2.5% v/v. Results for both assays using authentic juice mixtures were consistent with that expected following the random reannealing of PCR-amplified DNA at PCR plateau according to the principles of the Hardy-Weinberg law. Calculations of theoretical and expected yields of homoduplex and heteroduplexes indicated that the heteroduplexes were underestimated by 1.5-fold on the LOC. Although the LOC can provide good quantitative end-point analytical data from PCR methods, care must be taken in data interpretation because different data interpretation applies dependent on the attainment of the PCR plateau.
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Affiliation(s)
- Mary Scott
- Leatherhead Food International, Randalls Road, Leatherhead, Surrey, United Kingdom
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18
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Electrochemical detection of the neomycin phosphotransferase gene (NPT-II) in transgenic plants with a novel DNA biosensor. J APPL ELECTROCHEM 2009. [DOI: 10.1007/s10800-008-9775-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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A method of isolating the collagen (I) α2 chain carboxytelopeptide for species identification in bone fragments. Anal Biochem 2008; 374:325-34. [DOI: 10.1016/j.ab.2007.12.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 11/30/2007] [Accepted: 12/01/2007] [Indexed: 11/16/2022]
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Prado M, Berben G, Fumière O, van Duijn G, Mensinga-Kruize J, Reaney S, Boix A, von Holst C. Detection of ruminant meat and bone meals in animal feed by real-time polymerase chain reaction: result of an interlaboratory study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:7495-501. [PMID: 17725317 DOI: 10.1021/jf0707583] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The commercialization of animal feeds infected by prions proved to be the main cause of transmission of bovine spongiform encephalopathy (BSE). Therefore, feed bans were enforced, initially for ruminant feeds, and later for all feeds for farmed animals. The development and validation of analytical methods for the species-specific detection of animal proteins in animal feed has been indicated in the TSE (Transmissible Spongiform Encephalopathies) Roadmap (European Commission. The TSE (Transmissible Spongiform Encephalopathy) roadmap. URL: http://europa.eu.int/comm/food/food/biosafety/bse/roadmap_en.pdf, 2005) as the main condition for lifting the extended feed ban. Methods based on polymerase chain reaction (PCR) seem to be a promising solution for this aim. The main objective of this study was to determine the applicability of four different real-time PCR methods, developed by three National expert laboratories from the European Union (EU), for the detection and identification of cattle or ruminant species in typical compound feeds, fortified with meat and bone meals (MBM) from different animal species at different concentration levels. The MBM samples utilized in this study have been treated using the sterilization condition mandatory within the European Union (steam pressure sterilization at 133 degrees C, 3 bar, and 20 min), which is an additional challenge to the PCR methods evaluated in this study. The results indicate that the three labs applying their PCR methods were able to detect 0.1% of cattle MBM, either alone or in mixtures with different materials such as fishmeal, which demonstrates the improvement made by this technique, especially when compared with results from former interlaboratory studies.
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Affiliation(s)
- Marta Prado
- European Commission, Directorate General Joint Research Centre, Institute of Reference Materials and Measurements, Geel, Belgium.
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Onami JI, Nikaido M, Mannen H, Okada N. Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management. Mamm Genome 2007; 18:187-96. [PMID: 17436038 DOI: 10.1007/s00335-007-9000-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
Bov-A2 is a retroposon that is widely distributed among the genomes of ruminants (e.g., cow, deer, giraffe, pronghorn, musk deer, and chevrotain). This retroposon is composed of two monomers, called Bov-A units, which are joined by a linker sequence. The structure and origin of Bov-A2 has been well characterized but a genome-level exploration of this retroposon has not been implemented. In this study we performed an extensive search for Bov-A2 using all available genome sequence data on Bos taurus. We found unique Bov-A2-derived sequences that were longer than Bov-A2 due to amplification of three to six Bov-A units arranged in tandem. Detailed analysis of these elongated Bov-A2-derived sequences revealed that they originated through unequal crossing-over of Bov-A2. We found a large number of these elongated Bov-A2-derived sequences in cattle genomes, indicating that unequal crossing-over of Bov-A2 occurred very frequently. We found that this type of elongation is not observed in wild bovine and is therefore specific to the domesticated cattle genome. Furthermore, at specific loci, the number of Bov-A units was also polymorphic between alleles, implying that the elongation of Bov-A units might have occurred very recently. For these reasons, we speculate that genomic instability in bovine genomes can lead to extensive unequal crossing-over of Bov-A2 and levels of polymorphism might be generated in part by repeated outbreeding.
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Affiliation(s)
- Jun-ichi Onami
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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22
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Santaclara FJ, Espiñeira M, Cabado AG, Vieites JM. Detection of land animal remains in fish meals by the polymerase chain reaction-restriction fragment length polymorphism technique. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:305-10. [PMID: 17227058 DOI: 10.1021/jf061840l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the present study a technique was developed with the aim of guaranteeing the composition and security of fish meals, since it allows verification of whether these meals contain land animal remains. The method is based on polymerase chain reaction (PCR) and length polymorphism, followed by a restriction fragment length polymorphism (RFLP). Specific primers for every species were designed and calibrated, generating exclusively a PCR product with a specific size when DNA for each species was present in the sample. This technique allows the detection of land animal remains in fish meals, specifically cow, chicken, pig, horse, sheep, and goat. The identity of the PCR products can be confirmed by RFLP analysis using only one restriction enzyme. The selected restrictase generated one characteristic restriction profile for every species included in this study. The detection limit of this method was calculated by using mixtures of fish meals in different proportions and meal that exclusively contained remains of one of these land species studied. The analytical strategy herein proposed was applied to fish and meat meals, giving good results, both in the analyzed standards and in commercial samples.
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Affiliation(s)
- Francisco J Santaclara
- Area of Molecular Biology and Biotechnology, ANFACO-CECOPESCA, Vigo, 36310 Pontevedra, Spain.
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23
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Abstract
Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.
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Affiliation(s)
- David A Ray
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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24
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Huang Q, Yao CY, Chen B, Wang F, Huang JF, Zhang X, Fu WL. Species-specific identification by inhibitor-controlled PCR of ruminant components contaminating industrial crude porcine heparin. Mol Cell Probes 2006; 20:250-8. [PMID: 16563696 DOI: 10.1016/j.mcp.2006.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 01/11/2006] [Indexed: 11/26/2022]
Abstract
With the emergence of bovine spongiform encephalopathy, the source of pharmaceutical heparin is currently restricted to porcine intestinal mucosa. To control the species origin of industrial crude heparin, molecular biology methods relying on species-specific protein or DNA analysis should be developed to identify the ruminant components that might be contaminants in industrial crude porcine heparin (ICPH). Because heparin contained in ICPH is a strong PCR inhibitory substance, it is necessary to explore DNA extraction methods specific for ICPH and develop analysis methods that could monitor the presence of PCR inhibitory substances. In the present studies, DNA was extracted from ICPH by seven methods, and their abilities to remove the PCR inhibitory substances were compared using inhibitory-controlled PCR (IC-PCR). The results showed that, based on the optimization of the final concentration of the internal processing control (IPC), IC-PCR was a rapid, sensitive and efficient way to monitor the presence of PCR inhibitory substances contained in DNA extracted from ICPH, and only the agarose gel purification method could be used to completely eliminate the PCR inhibitory substances contained in ICPH.
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Affiliation(s)
- Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, The Third Military Medical University, Chongqing 400038, People's Republic of China
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25
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Abstract
A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species-derived material in concentrate feed mixtures and fish meals.
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Affiliation(s)
- Pavel Krcmar
- Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic.
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26
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Toyoda A, Nakajo M, Kawachi H, Matsui T, Yano H. PCR detection of bovine mitochondrial DNA derived from meat and bone meal in feed. J Food Prot 2004; 67:2829-32. [PMID: 15633697 DOI: 10.4315/0362-028x-67.12.2829] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Because bovine meat and bone meal (MBM) is thought to be a major source of bovine spongiform encephalopathy, we developed a PCR-based method for detection of bovine MBM in animal feed. We isolated bone particles from feed containing bovine MBM using a separation technique based on specific gravity and then washed bone particles with sodium hypochlorite solution and an EDTA-proteinase K solution. The mitochondrial DNA was extracted from bone particles and amplified using PCR with cattle-specific primers. Bovine DNA was not detected in a milk replacer containing dried skim milk and dried whey, but bovine DNA was detected in the milk replacer that was mixed with bovine MBM. Other cattle-derived materials in feeds did not interfere with the selective detection of bovine MBM. This method allowed detection of bovine mitochondrial DNA in feed with 0.1% added bovine MBM. When the treatment with sodium hypochlorite was excluded, bovine DNA derived from MBM could not be distinguished from bovine DNA derived from other bovine materials. However, the exclusion of this treatment improved the detection limit of bovine MBM in feed. This method appears suitable for the selective detection of bovine MBM in feed.
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Affiliation(s)
- Atsushi Toyoda
- College of Agriculture, Ibaraki University, Ibaraki 300-0393, Japan.
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27
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Mendoza-Romero L, Verkaar ELC, Savelkoul PH, Catsburg A, Aarts HJM, Buntjer JB, Lenstra JA. Real-time PCR detection of ruminant DNA. J Food Prot 2004; 67:550-4. [PMID: 15035372 DOI: 10.4315/0362-028x-67.3.550] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To control the spread of bovine spongiform encephalopathy, several DNA methods have been described for the detection of the species origin of meat and bone meal. Most of these methods are based on the amplification of a mitochondrial DNA segment. We have developed a semiquantitative method based on real-time PCR for detection of ruminant DNA, targeting an 88-bp segment of the ruminant short interspersed nuclear element Bov-A2. This method is specific for ruminants and is able to detect as little as 10 fg of bovine DNA. Autoclaving decreased the amount of detectable DNA, but positive signals were observed in feeding stuff containing 10% bovine material if this had not been rendered in accordance with the regulations, i.e., heated at 134 degrees C for 3 instead of 20 min.
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Affiliation(s)
- Luis Mendoza-Romero
- Labocor, S. L. Poligono Industrial La Mina Nave, 38 Colmenar Viejo, Madrid, Spain
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28
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Walker JA, Hughes DA, Hedges DJ, Anders BA, Laborde ME, Shewale J, Sinha SK, Batzer MA. Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements. Genomics 2004; 83:518-27. [PMID: 14962678 DOI: 10.1016/j.ygeno.2003.09.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Accepted: 09/04/2003] [Indexed: 11/24/2022]
Abstract
We have designed and evaluated a series of class-specific (Aves), order-specific (Rodentia), and species-specific (equine, canine, feline, rat, hamster, guinea pig, and rabbit) polymerase chain reaction (PCR)-based assays for the identification and quantitation of DNA using amplification of genome-specific short and long interspersed elements. Using SYBR Green-based detection, the minimum effective quantitation levels of the assays ranged from 0.1 ng to 0.1 pg of starting DNA template. Background cross-amplification with DNA templates derived from sixteen other species was negligible prior to 30 cycles of PCR. The species-specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect known quantities of species-specific DNA from mixed (complex) sources. The 10 assays reported here will help facilitate the sensitive detection and quantitation of common domestic animal and bird species DNA from complex biomaterials.
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Affiliation(s)
- Jerilyn A Walker
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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29
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Krcmar P, Rencova E. Identification of species-specific DNA in feedstuffs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2003; 51:7655-7658. [PMID: 14664524 DOI: 10.1021/jf034167y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Due to the menace of transmission of spongiform encephalopathies, feed components intended for ruminant nutrition must be checked for the presence of ruminant-derived materials. A sensitive method for the identification of bovine- and ovine- and also swine- and chicken-specific mitochondrial DNA sequences based on Polymerase Chain Reaction (PCR) has been developed. The specificity of the primers for PCR has been tested using samples of DNA of other vertebrate species, which may also be present in rendering plant products intended for feed manufacture. The method allows the detection in concentrate mixtures of 0.01% of the target species derived material. The identity of a sample containing 0.1% of bovine, ovine, swine, and chicken meat-and-bone meal has further been confirmed by sequencing.
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Affiliation(s)
- Pavel Krcmar
- Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic.
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30
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Walker JA, Hughes DA, Anders BA, Shewale J, Sinha SK, Batzer MA. Quantitative intra-short interspersed element PCR for species-specific DNA identification. Anal Biochem 2003; 316:259-69. [PMID: 12711348 DOI: 10.1016/s0003-2697(03)00095-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We have designed and evaluated four assays based upon PCR amplification of short interspersed elements (SINEs) for species-specific detection and quantitation of bovine, porcine, chicken, and ruminant DNA. The need for these types of approaches has increased drastically in response to the bovine spongiform encephalopathy epidemic. Using SYBR Green-based detection, the minimum effective quantitation levels were 0.1, 0.01, 5, and 1 pg of starting DNA template using our bovine, porcine, chicken, and ruminant species-specific SINE-based PCR assays, respectively. Background cross-amplification with DNA templates derived from 14 other species was negligible. Species specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect trace quantities of species-specific DNA from mixed (complex) sources. Bovine DNA was detected at 0.005% (0.5 pg), porcine DNA was detected at 0.0005% (0.05 pg), and chicken DNA was detected at 0.05% (5 pg) in a 10-ng mixture of bovine, porcine, and chicken DNA templates. We also tested six commercially purchased meat products using these assays. The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species.
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Affiliation(s)
- Jerilyn A Walker
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge 70803, USA
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