1
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Manning JC, Boza JM, Cesarman E, Erickson D. Rapid, equipment-free extraction of DNA from skin biopsies for point-of-care diagnostics. Sci Rep 2024; 14:13782. [PMID: 38877073 PMCID: PMC11178891 DOI: 10.1038/s41598-024-64533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Kaposi's sarcoma (KS) is a cancer affecting skin and internal organs for which the Kaposi's sarcoma associated herpesvirus (KSHV) is a necessary cause. Previous work has pursued KS diagnosis by quantifying KSHV DNA in skin biopsies using a point-of-care (POC) device which performs quantitative loop-mediated isothermal amplification (LAMP). These previous studies revealed that extracting DNA from patient biopsies was the rate limiting step in an otherwise rapid process. In this study, a simplified, POC-compatible alkaline DNA extraction, ColdSHOT, was optimized for 0.75 mm human skin punch biopsies. The optimized ColdSHOT extraction consistently produced 40,000+ copies of DNA per 5 µl reaction from 3 mg samples-a yield comparable to standard spin column extractions-within 1 h without significant equipment. The DNA yield was estimated sufficient for KSHV detection from KS-positive patient biopsies, and the LAMP assay was not affected by non-target tissue in the unpurified samples. Furthermore, the yields achieved via ColdSHOT were robust to sample storage in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer prior to DNA extraction, and the DNA sample was stable after extraction. The results presented in this study indicate that the ColdSHOT DNA extraction could be implemented to simplify and accelerate the LAMP-based diagnosis of Kaposi's sarcoma using submillimeter biopsy samples.
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Affiliation(s)
- Jason Cade Manning
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Juan Manuel Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Ethel Cesarman
- Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14850, USA.
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14850, USA.
- Cornell University, 369 Upson Hall, Ithaca, NY, 14853, USA.
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2
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Barido FH, Desti D, Pramono A, Abdurrahman ZH, Volkandari SD, Cahyadi M. Validating duplex-PCR targeting ND2 for bovine and porcine detection in meat products. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100181. [PMID: 37637373 PMCID: PMC10457504 DOI: 10.1016/j.fochms.2023.100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/01/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023]
Abstract
Food authentication is a mandatory effort to assure the fair-trade. This study developed a duplex polymerase chain reaction (PCR) from the NADH dehydrogenase subunit 2 (ND2) gene to amplify specific segments of a cattle and porcine DNA. A universal forward primer composed of nineteen base pairs (bp) (3'-CCAAACACAACTCCGAAAA-5') and species-specific reverse primers composed of twenty (3'-CCAAACACAACTCCGAAAA-5') and twenty-one (3'-TGGCAAGAATTAGGACGGTTA-5') bp were used to limit the amplified DNA segment for porcine and cattle. The PCR reaction would generate a product with a profile of 168 and 227 bp, respectively. To investigate the accuracy and limit of detection, an in vitro experiment was conducted using simplex and duplex PCR on commercial meatballs randomly purchased from a commercial market in Surakarta, Indonesia. The findings of this study indicated that ND2 could be used as an alternative genetic marker for the identification of porcine and beef species in meat-derived products.
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Affiliation(s)
- Farouq Heidar Barido
- Faculty of Animal Science, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
- Halal Research Center and Services (HRCS), Institute for Research and Community Service, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
| | - Desti Desti
- Faculty of Animal Science, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
| | - Ahmad Pramono
- Faculty of Animal Science, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
| | | | - Slamet Diah Volkandari
- Research Center for Food Technology and Processing (PRTPP), National Research and Innovation Agency (BRIN), Gunung Kidul, Daerah Istimewa, Yogyakarta 55861, Indonesia
| | - Muhammad Cahyadi
- Faculty of Animal Science, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
- Halal Research Center and Services (HRCS), Institute for Research and Community Service, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
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3
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JAFAR S, KABIR F, ANJUM KM, ZAHOOR MY, SHEHZAD W, IMRAN M. Comparison of different DNA preparatory methods for development of a universal direct PCR-RFLP workflow for identification of meat origin in food products. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.65122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Girish PS, Kumari A, Gireesh‐Babu P, Karabasanavar NS, Raja B, Ramakrishna C, Barbuddhe SB. Alkaline lysis‐loop mediated isothermal amplification assay for rapid and on‐site authentication of buffalo (
Bubalus bubalis
) meat. J Food Saf 2021. [DOI: 10.1111/jfs.12955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Patil S. Girish
- ICAR – National Research Centre on Meat Hyderabad Telangana State India
| | - Aparana Kumari
- ICAR – National Research Centre on Meat Hyderabad Telangana State India
| | | | - Nagappa S. Karabasanavar
- Department of Veterinary Public Health & Epidemiology Veterinary College, Karnataka Veterinary Animal and Fisheries Sciences University Hassan Karnataka India
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5
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Zhao G, Shen X, Liu Y, Xie P, Yao C, Li X, Sun Y, Lei Y, Lei H. Direct lysis-multiplex polymerase chain reaction assay for beef fraud substitution with chicken, pork and duck. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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Mounika T, Girish PS, Shashi Kumar M, Kumari A, Singh S, Karabasanavar NS. Identification of sheep ( Ovis aries) meat by alkaline lysis-loop mediated isothermal amplification technique targeting mitochondrial D-loop region. Journal of Food Science and Technology 2021; 58:3825-3834. [PMID: 34471306 DOI: 10.1007/s13197-020-04843-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/30/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
Identification of meat species origin using reliable techniques is a critical requirement for ensuring label compliance, protection of consumer preference and prevention of fraudulence in the meat trade. Although a plethora of protein and DNA based meat species identification techniques are in vogue, need for rapid test suitable for under-resourced laboratories catering point-of-care (PoC) services was construed. Present study deals with development of rapid sheep (Ovis aries) meat identification technique using DNA extraction by alkaline lysis (AL) and loop-mediated isothermal amplification (LAMP) technique. The AL-LAMP specifically amplifies sheep-specific signal of mitochondrial D loop region under an isothermal temperature of 60 °C with an analytical sensitivity of 0.5 ng sheep DNA. The test was highly specific to sheep and performed well even in the presence of DNA of closely related meat animal species such as goat, cattle, buffalo and chicken. The novel primers designed for the AL-LAMP successfully detected sheep meat in raw and cooked meat samples heated up to 121 °C for 30 min. Sheep-specific AL-LAMP assay could detect 0.1% mutton-in-beef adulteration. Novel AL-LAMP assay being simple, rapid and reliable for sheep meat authentication in just 120 min; hence, it could be conveniently used by terminal laboratories engaged in rendering on-site or PoC services.
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Affiliation(s)
- T Mounika
- College of Veterinary Science, Rajendranagar, Hyderabad, Telangana State 500030 India
| | - P S Girish
- ICAR - National Research Centre on Meat, Chengicherla, Hyderabad, Telangana State 500092 India
| | - M Shashi Kumar
- College of Veterinary Science, Rajendranagar, Hyderabad, Telangana State 500030 India
| | - Aparana Kumari
- ICAR - National Research Centre on Meat, Chengicherla, Hyderabad, Telangana State 500092 India
| | - Sujatha Singh
- College of Veterinary Science, Rajendranagar, Hyderabad, Telangana State 500030 India
| | - Nagappa S Karabasanavar
- Karnataka Veterinary, Animal and Fisheries Sciences University, Veterinary College, Gokula Campus, Vidyanagar, Hassan, Karnataka 573202 India
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7
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Galal-Khallaf A, Hussein D, El-Sayed Hassab El-Nabi S. Single nucleotide polymorphism-based methodology for authentication of bovine, caprine, ovine, camel, and donkey meat cuts. J Food Sci 2021; 86:4444-4456. [PMID: 34431103 DOI: 10.1111/1750-3841.15885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022]
Abstract
To guarantee food safetyand sustainability, it is necessary to verify meat authenticity. This study focused on the development of single nucleotide polymorphism-based polymerase chain reaction-restriction fragment length polymorphism (SNP-based PCR-RFLP) and forensically informative nucleotide sequence (FINS) methodologies based on PCR amplification of the mitochondrial 12S rRNA gene for discrimination of six red meat species, that is, cattle, buffalo, goat, sheep, camel, and donkey. FINS allowed the unambiguous identification of all species analyzed. In addition, six SNPs, where a restriction site for TasI could be localized using a preliminary in silico analysis, gave a unique RFLP pattern for each species. The results revealed a low level of species substitution (8%) in the tested meat samples. In particular, one buffalo and goat samples have been substituted with cow and sheep, respectively. Finally, the developed techniques herein showed high potentials to be routinely used as reliable and fast tools to avoid meat species substitutions. PRACTICAL APPLICATION: This research deals with genetic techniques to trace meats. This kind of research helps the concerned agencies to build capacity to safeguard consumer sentiments as well as providing better market access and better food price and quality for the consumer.
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Affiliation(s)
- Asmaa Galal-Khallaf
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Doaa Hussein
- Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Sobhy El-Sayed Hassab El-Nabi
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
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8
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Chen XX, Chen W, Liu YL, Lin CX, Li M, Chen WJ, Xie SH, Lin DF, Cao SM. Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types. J Clin Lab Anal 2021; 35:e23962. [PMID: 34399000 PMCID: PMC8418477 DOI: 10.1002/jcla.23962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples. METHODS The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses. RESULTS The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities. CONCLUSIONS This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.
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Affiliation(s)
- Xiao-Xia Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Chen
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yi-Long Liu
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Can-Xiang Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Mengmeng Li
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Jie Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dong-Feng Lin
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
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9
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Islam A, Halder J, Rahman ATMM, Ud-Daula A, Uddin S, Hossain MK, Jahan N, Alim A, Bhuyan AA, Rubaya, Hasan M, Alam J. Meat origin differentiation by polymerase chain reaction-restriction fragment length polymorphism. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2021. [DOI: 10.1080/10942912.2021.1953068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ariful Islam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
- Department of Applied Nutrition & Food Technology, Islamic University, Kushtia, Bangladesh
| | - Joyanta Halder
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - ATM Mijanur Rahman
- Department of Applied Nutrition & Food Technology, Islamic University, Kushtia, Bangladesh
| | - Asad Ud-Daula
- Department of Applied Nutrition & Food Technology, Islamic University, Kushtia, Bangladesh
| | - Salah Uddin
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
- Department of Applied Nutrition & Food Technology, Islamic University, Kushtia, Bangladesh
| | - Mridha Kamal Hossain
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Nusrat Jahan
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Abdul Alim
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Anjuman Ara Bhuyan
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Rubaya
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Mahmud Hasan
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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10
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Khalil I, Hashem A, Nath AR, Muhd Julkapli N, Yehye WA, Basirun WJ. DNA/Nano based advanced genetic detection tools for authentication of species: Strategies, prospects and limitations. Mol Cell Probes 2021; 59:101758. [PMID: 34252563 DOI: 10.1016/j.mcp.2021.101758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/20/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Authentication, detection and quantification of ingredients, and adulterants in food, meat, and meat products are of high importance these days. The conventional techniques for the detection of meat species based on lipid, protein and DNA biomarkers are facing challenges due to the poor selectivity, sensitivity and unsuitability for processed food products or complex food matrices. On the other hand, DNA based molecular techniques and nanoparticle based DNA biosensing strategies are gathering huge attention from the scientific communities, researchers and are considered as one of the best alternatives to the conventional strategies. Though nucleic acid based molecular techniques such as PCR and DNA sequencing are getting greater successes in species detection, they are still facing problems from its point-of-care applications. In this context, nanoparticle based DNA biosensors have gathered successes in some extent but not to a satisfactory stage to mark with. In recent years, many articles have been published in the area of progressive nucleic acid-based technologies, however there are very few review articles on DNA nanobiosensors in food science and technology. In this review, we present the fundamentals of DNA based molecular techniques such as PCR, DNA sequencing and their applications in food science. Moreover, the in-depth discussions of different DNA biosensing strategies or more specifically electrochemical and optical DNA nanobiosensors are presented. In addition, the significance of DNA nanobiosensors over other advanced detection technologies is discussed, focusing on the deficiencies, advantages as well as current challenges to ameliorate with the direction for future development.
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Affiliation(s)
- Ibrahim Khalil
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia; Healthcare Pharmaceuticals Ltd., Rajendrapur, Gazipur, Bangladesh
| | - Abu Hashem
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia; Microbial Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Amit R Nath
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia; Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, 518055, China
| | - Nurhidayatullaili Muhd Julkapli
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wageeh A Yehye
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wan Jeffrey Basirun
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute for Advanced Studies (IAS), Universiti Malaya, 50603, Kuala Lumpur, Malaysia; Department of Chemistry, Universiti Malaya, Malaysia
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11
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Paper-Based Molecular Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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12
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Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source. Foods 2020; 9:foods9101392. [PMID: 33019679 PMCID: PMC7600754 DOI: 10.3390/foods9101392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Detection of animal species in meat product is crucial to prevent adulterated and unnecessary contamination during processing, in addition to avoid allergy and religious consequences. Gold standard is the real-time PCR assays, which has a limited target capability. In this study, we have established a rapid sequencing protocol to identify animal species within hours. Sequencing was achieved by nanopore sequencing and data analysis via offline BLAST search. The whole procedure was conducted in a mobile suitcase lab. As per national and international regulations, the developed assay detected adulteration of pork meat with 0.1% of horse, chicken, turkey, cattle, sheep, duck, rabbit, goat, and donkey. The developed test could be used on-site as a rapid and mobile detection system to determine contamination of meat products.
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13
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Girish P, Barbuddhe S, Kumari A, Rawool DB, Karabasanavar NS, Muthukumar M, Vaithiyanathan S. Rapid detection of pork using alkaline lysis- Loop Mediated Isothermal Amplification (AL-LAMP) technique. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Development of a real-time PCR assay for the identification and quantification of bovine ingredient in processed meat products. Sci Rep 2020; 10:2052. [PMID: 32029865 PMCID: PMC7004997 DOI: 10.1038/s41598-020-59010-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 01/22/2020] [Indexed: 01/22/2023] Open
Abstract
In order to find fraudulent species substitution in meat products, a highly sensitive and rapid assay for meat species identification and quantification is urgently needed. In this study, species-specific primers and probes were designed from the mitochondrial cytb (cytochrome b) fragment for identification and quantification of bovine ingredient in commercial meat products. Bovine samples and non-bovine ones were used to identify the specificity, sensitivity, and applicability of established assay. Results showed that the primers and probes were highly specific for bovine ingredient in meat products. The absolute detection limit of the real-time PCR method was 0.025 ng DNA, and the relative detection limit was 0.002% (w/w) of positive samples. The quantitative real-time PCR assay was validated on simulated meat samples and high in the precision and accuracy. In order to demonstrate the applicability and reliability of the proposed assay in practical products, the 22 commercial meat products including salted, jerkies, and meatball were used. The results indicated the established method has a good stability in detection of bovine ingredient in real food. The established method in this study showed specificity and sensitivity in identification and quantification of beef meat in processed meat products.
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15
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WANG L, HANG X, GENG R. Molecular detection of adulteration in commercial buffalo meat products by multiplex PCR assay. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.28717] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Seok Y, Jang H, Oh J, Joung HA, Kim MG. A handheld lateral flow strip for rapid DNA extraction from staphylococcus aureus cell spiked in various samples. Biomed Phys Eng Express 2019. [DOI: 10.1088/2057-1976/aaf3be] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes J. Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. eLife 2018; 7:37090. [PMID: 30322445 PMCID: PMC6237439 DOI: 10.7554/elife.37090] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than those in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depends on the initial conditions. Our work has important implications for gut microbial community modeling as well as for ecological interaction detection from batch cultures. Our gut is home to trillions of microorganisms, most of them bacteria, which have an important impact on our body. During healthy periods, these microorganisms help our digestion, protect our cells, and compete against disease-causing bacteria. But specific communities of gut bacteria are linked to many diseases. We already have a good knowledge of the bacterial composition present in a wide range of human guts, but how the different bacterial species within such communities affect each other, has so far been unclear. Future disease treatments may be able to steer ‘bad’ communities to healthier mixtures. For this to happen we need to know how species interact and how these interactions change the behavior of the whole community. To investigate this further, D'hoe, Vet, Faust et al. studied three common species of gut bacteria under controlled conditions in the laboratory. The different species were either grown alone, in pairs or together, and the number of bacteria and the concentration of nutrients were measured over time. The results showed that when grown alone or together, their behavior changed. D'hoe et al. then used a mathematical model to estimate the rates at which species multiplied and consumed nutrients. This model was able to predict the dynamics of each of the species grown alone. However, the data from bacteria grown in pairs was needed to predict the dynamics of bacteria grown as a group of three. Next, D'hoe et al. compared the activity of genes between bacteria grown alone or together, and discovered several differences. This suggests that bacterial species affect each other greatly, and community behavior cannot be predicted from knowledge of its members alone. Therefore, studying bacteria in isolation is not enough to understand the complex environments of our guts, which are inhabited not by three but hundreds of bacterial species. In future, interactions between bacteria will need to be studied to ultimately be able to shift the gut community into better shapes.
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Affiliation(s)
- Kevin D'hoe
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Vet
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.,Unité de Chronobiologie Théorique, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
| | - Frédéric Moens
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Verónica Lloréns-Rico
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, KU Leuven, Leuven, Belgium
| | - Jan Danckaert
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium.,Jeroen Raes Lab, VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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18
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Ahmad Nizar NN, Sultana S, Hossain MM, Johan MR, Ali ME. Double gene targeting multiplex PCR-RFLP detects Crocodylus porosus in chicken meatball and traditional medicine. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2018.1508164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nina Naquiah Ahmad Nizar
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Sharmin Sultana
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - M.A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Md. Eaqub Ali
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Halal Research Centre (UMHRC), University of Malaya, Kuala Lumpur, Malaysia
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19
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Zhao J, Zhang T, Liu Y, Wang X, Zhang L, Ku T, Quek SY. Qualitative and quantitative assessment of DNA quality of frozen beef based on DNA yield, gel electrophoresis and PCR amplification and their correlations to beef quality. Food Chem 2018; 260:160-165. [PMID: 29699657 DOI: 10.1016/j.foodchem.2018.03.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 02/14/2018] [Accepted: 03/17/2018] [Indexed: 10/17/2022]
Abstract
Freezing is a practical method for meat preservation but the quality of frozen meat can deteriorate with storage time. This research investigated the effect of frozen storage time (up to 66 months) on changes in DNA yield, purity and integrity in beef, and further analyzed the correlation between beef quality (moisture content, protein content, TVB-N value and pH value) and DNA quality in an attempt to establish a reliable, high-throughput method for meat quality control. Results showed that frozen storage time influenced the yield and integrity of DNA significantly (p < 0.05). The DNA yield decreased as frozen storage time increased due to DNA degradation. The half-life (t1/2 = ln2/0.015) was calculated as 46 months. The DNA quality degraded dramatically with the increased storage time based on gel electrophoresis results. Polymerase chain reaction (PCR) products from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) were observed in all frozen beef samples. Using real-time PCR for quantitative assessment of DNA and meat quality revealed that correlations could be established successfully with mathematical models to evaluate frozen beef quality.
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Affiliation(s)
- Jing Zhao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China
| | - Ting Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China
| | - Yongfeng Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China.
| | - Xingyu Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China
| | - Lan Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China
| | - Ting Ku
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, 710062 Xi'an, Shaanxi, PR China
| | - Siew Young Quek
- Food Science, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand; Riddet Institute, Palmerston North, New Zealand.
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20
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Guan F, Jin YT, Zhao J, Xu AC, Luo YY. A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:5890140. [PMID: 29629212 PMCID: PMC5832126 DOI: 10.1155/2018/5890140] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/23/2017] [Indexed: 06/08/2023]
Abstract
There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.
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Affiliation(s)
- Feng Guan
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yu-Ting Jin
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Jin Zhao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Ai-Chun Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yuan-Yuan Luo
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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21
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Hossain MM, Ali ME, Hamid SBA, Hossain SA, Asing, Nizar NNA, Uddin MN, Ali L, Asaduzzaman M, Akanda MJH. Tetraplex PCR assay involving double gene-sites discriminates beef and buffalo in Malaysian meat curry and burger products. Food Chem 2017; 224:97-104. [DOI: 10.1016/j.foodchem.2016.12.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/13/2016] [Accepted: 12/18/2016] [Indexed: 11/29/2022]
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22
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Hossain MAM, Ali ME, Sultana S, Bonny SQ, Kader MA, Rahman MA. Quantitative Tetraplex Real-Time Polymerase Chain Reaction Assay with TaqMan Probes Discriminates Cattle, Buffalo, and Porcine Materials in Food Chain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3975-3985. [PMID: 28481513 DOI: 10.1021/acs.jafc.7b00730] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.
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Affiliation(s)
- M A Motalib Hossain
- Nanotechnology and Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya , Kuala Lumpur 50603, Malaysia
| | - Md Eaqub Ali
- Nanotechnology and Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya , Kuala Lumpur 50603, Malaysia
- Institute of Halal Research University Malaya (IHRUM), University of Malaya , 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya , Kuala Lumpur 50603, Malaysia
| | - Sharmin Sultana
- Nanotechnology and Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya , Kuala Lumpur 50603, Malaysia
| | - Sharmin Quazi Bonny
- Nanotechnology and Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya , Kuala Lumpur 50603, Malaysia
| | - Md Abdul Kader
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu , 21030 Kuala Terengganu, Terengganu, Malaysia
| | - M Aminur Rahman
- Laboratory of Marine Biotechnology, Institute of Bioscience (IBS), Universiti Putra Malaysia , 43400 UPM Serdang, Selangor, Malaysia
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23
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Sharma V, Hazra T, Kandhol R, Sharma R, Arora S. Confirmation of buffalo tallow in anhydrous cow milk fat using gas liquid chromatography in tandem with species-specific polymerase chain reaction. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vivek Sharma
- Dairy Chemistry Division; National Dairy Research Institute (NDRI); Karnal Haryana 132001 India
| | - Tanmay Hazra
- Dairy Chemistry Division; National Dairy Research Institute (NDRI); Karnal Haryana 132001 India
| | - Rakesh Kandhol
- Dairy Chemistry Division; National Dairy Research Institute (NDRI); Karnal Haryana 132001 India
| | - Rekha Sharma
- National Bureau of Animal Genetic Resources (NBAGR); Karnal Haryana 132001 India
| | - Sumit Arora
- Dairy Chemistry Division; National Dairy Research Institute (NDRI); Karnal Haryana 132001 India
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24
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Hossain MM, Ali ME, Hamid SBA, Asing, Mustafa S, Desa MNM, Zaidul I. Targeting double genes in multiplex PCR for discriminating bovine, buffalo and porcine materials in food chain. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Hossain MAM, Ali ME, Abd Hamid SB, Mustafa S, Mohd Desa MN, Zaidul ISM. Double Gene Targeting Multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay Discriminates Beef, Buffalo, and Pork Substitution in Frankfurter Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:6343-6354. [PMID: 27501408 DOI: 10.1021/acs.jafc.6b02224] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Beef, buffalo, and pork adulteration in the food chain is an emerging and sensitive issue. Current molecular techniques to authenticate these species depend on polymerase chain reaction (PCR) assays involving long and single targets which break down under natural decomposition and/or processing treatments. This novel multiplex polymerase chain reaction-restriction fragment length polymorphism assay targeted two different gene sites for each of the bovine, buffalo, and porcine materials. This authentication ensured better security, first through a complementation approach because it is highly unlikely that both sites will be missing under compromised states, and second through molecular fingerprints. Mitochondrial cytochrome b and ND5 genes were targeted, and all targets (73, 90, 106, 120, 138, and 146 bp) were stable under extreme boiling and autoclaving treatments. Target specificity and authenticity were ensured through cross-amplification reaction and restriction digestion of PCR products with AluI, EciI, FatI, and CviKI-1 enzymes. A survey of Malaysian frankfurter products revealed rampant substitution of beef with buffalo but purity in porcine materials.
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Affiliation(s)
| | | | | | - Shuhaimi Mustafa
- Institute of Halal Products Research, Universiti Putra Malaysia , 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Institute of Halal Products Research, Universiti Putra Malaysia , 43400 UPM Serdang, Selangor, Malaysia
| | - I S M Zaidul
- Deparment of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University , Kuantan 25200, Pahang, Malaysia
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26
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Nishio T, Ohtsuka K, Oda M, Sugiyama K, Hara-Kudo Y. [Molecular Detection Methods for Vibrio parahaemolyticus in Seafood]. KANSENSHOGAKU ZASSHI. THE JOURNAL OF THE JAPANESE ASSOCIATION FOR INFECTIOUS DISEASES 2015; 89:445-451. [PMID: 26554219 DOI: 10.11150/kansenshogakuzasshi.89.445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To detect Vibrio parahaemolyticus in seafood, we evaluated efficient combinations of molecular methods with DNA extraction methods using heat extraction and alkaline heat extraction, and PCR, real-time PCR and loop-mediated isothermal amplification (LAMP) assays were performed targeting V parahaemolyticus species-specific genes (tlh and rpoD) and pathogenic factors genes (tdh and trh). The species-specific genes were detected in all combinations of two strains (a tdh * trh1-positive strain and a trh2-positive strain), two kinds of shellfish (oyster and bloody clams) and molecular methods with tlh-real time PCR or rpoD-LAMP assays with DNA of alkaline heat extraction at 85-145cfu/test level. tdh was detected in both seafoods with real time PCR assay with DNA of heat extraction at 85cfu/test level, and detected with the LAMP and real time PCR assays with DNA of alkaline heat extraction at 85cfu/test level. Detection of both trh1 and trh2 with the PCR assay with DNA of alkaline heat extraction was comparatively high though trh2 was detected with the LAMP assay with DNA of alkaline heat extraction at 145cfu/test level. It, however, is necessary to investigate more sensitive trh-detection methods. In this study, the results indicated that tlh-real time PCR or rpoD-LAMP, tdh-real time PCR and tdh-LAMP assays with DNA of alkaline heat extraction are relatively-sensitive methods to detect V. parahaemolyticus in seafood.
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27
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Iwobi A, Sebah D, Kraemer I, Losher C, Fischer G, Busch U, Huber I. A multiplex real-time PCR method for the quantification of beef and pork fractions in minced meat. Food Chem 2015; 169:305-13. [DOI: 10.1016/j.foodchem.2014.07.139] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022]
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28
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A nuclear DNA-based species determination and DNA quantification assay for common poultry species. Journal of Food Science and Technology 2012; 51:4060-5. [PMID: 25477681 DOI: 10.1007/s13197-012-0893-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/24/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.
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