1
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Costantini F, Lovecchio N, Nandimandalam M, Manglli A, Faggioli F, Biasin M, Manetti C, Roversi PF, Nascetti A, de Cesare G, Caputo D. Biomolecular Monitoring Tool Based on Lab-on-Chip for Virus Detection. BIOSENSORS 2023; 13:bios13050544. [PMID: 37232905 DOI: 10.3390/bios13050544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Lab-on-Chip (LoC) devices for performing real-time PCR are advantageous compared to standard equipment since these systems allow to conduct in-field quick analysis. The development of LoCs, where the components for performing the nucleic acid amplification are all integrated, can be an issue. In this work, we present a LoC-PCR device where thermalization, temperature control and detection elements are all integrated on a single glass substrate named System-on-Glass (SoG) obtained using metal thin-film deposition. By using a microwell plate optically coupled with the SoG, real-time reverse transcriptase PCR of RNA extracted from both a plant and human virus has been carried out in the developed LoC-PCR device. The limit of detection and time of analysis for the detection of the two viruses by using the LoC-PCR were compared with those achieved by standard equipment. The results showed that the two systems can detect the same concentration of RNA; however, the LoC-PCR performs the analysis in half of the time compared to the standard thermocycler, with the advantage of the portability, leading to a point-of-care device for several diagnostic applications.
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Affiliation(s)
- Francesca Costantini
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Nicola Lovecchio
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, 00184 Rome, Italy
| | - Manasa Nandimandalam
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Ariana Manglli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Francesco Faggioli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Cesare Manetti
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Augusto Nascetti
- School of Aerospace Engineering, Sapienza University of Rome, 00138 Rome, Italy
| | - Giampiero de Cesare
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Domenico Caputo
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
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2
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Detection of porcine DNA in food using direct asymmetric PCR and catalyzed hairpin assembly fluorescent biosensor: A novel assay for halal food analysis. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Wang L, Zuo Y, Xue Z, Zuo T, Lu H, Zhang T. A simple and effective PCR assay to detect the origin of meat in food using mitochondrial DNA. J Verbrauch Lebensm 2022. [DOI: 10.1007/s00003-022-01388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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4
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Qin P, Qu W, Xu J, Qiao D, Yao L, Xue F, Chen W. A sensitive multiplex PCR protocol for simultaneous detection of chicken, duck, and pork in beef samples. Journal of Food Science and Technology 2019; 56:1266-1274. [PMID: 30956306 DOI: 10.1007/s13197-019-03591-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/11/2018] [Accepted: 01/14/2019] [Indexed: 11/30/2022]
Abstract
A rapid and sensitive multiplex PCR assay was developed for simultaneous identification of the adulteration ingredients of chicken, duck and pork in beef. Specific primers for the mitochondrial genes of Cyt b, CO III, ATPase subunit 8/6 and Cyt b of chicken, duck, pork, and beef, respectively, were adopted in the assay. DNA exaction from meat samples was carried out by using magnetic nanoparticles as rapid separation substrates. The multiplex PCR assay showed that the limit of detection was 0.05% for each species. Moreover, the multiplex PCR specifically identified five beef samples adulterated with pork and one beef samples adulterated with chicken among the 35 commercial samples examined, indicating the practicability of this multiplex PCR method for identifying adulterated ingredients of chicken, duck, and pork in commercial beef products.
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Affiliation(s)
- Panzhu Qin
- 1School of Food and Biological Engineering, Engineering Research Center of Bio-Process, MOE, Hefei University of Technology, Hefei, 230009 China
| | - Wei Qu
- 2School of Biological and Medical Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Jianguo Xu
- 1School of Food and Biological Engineering, Engineering Research Center of Bio-Process, MOE, Hefei University of Technology, Hefei, 230009 China
| | - Dongqing Qiao
- 1School of Food and Biological Engineering, Engineering Research Center of Bio-Process, MOE, Hefei University of Technology, Hefei, 230009 China
| | - Li Yao
- 1School of Food and Biological Engineering, Engineering Research Center of Bio-Process, MOE, Hefei University of Technology, Hefei, 230009 China
| | - Feng Xue
- 3College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wei Chen
- 1School of Food and Biological Engineering, Engineering Research Center of Bio-Process, MOE, Hefei University of Technology, Hefei, 230009 China
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5
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Uguz SS, Ozvural EB, Beira MJ, Oztop MH, Sebastião PJ. Use of NMR Relaxometry to identify frankfurters of different meat sources. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1542162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sirvan Sultan Uguz
- Department of Food Engineering, Middle East Technical University, Ankara, Turkey
| | - E. Burcin Ozvural
- Department of Food Engineering, Cankiri Karatekin University, Cankiri, Turkey
| | - Maria Jardim Beira
- CeFEMA – Center of Physics and Engineering of Advanced Materials and Department of Physics, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mecit Halil Oztop
- Department of Food Engineering, Middle East Technical University, Ankara, Turkey
| | - Pedro José Sebastião
- CeFEMA – Center of Physics and Engineering of Advanced Materials and Department of Physics, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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6
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Ahrberg CD. Modeling of PCR: Kinetic Explanation for Short-Chained Side Products. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201700132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christian D. Ahrberg
- Sogang University; Department of Mechanical Engineering; 35 Baekbeom-ro 04107 Seoul Korea
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7
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Species Identification of Fox-, Mink-, Dog-, and Rabbit-Derived Ingredients by Multiplex PCR and Real-Time PCR Assay. Appl Biochem Biotechnol 2017; 185:1-12. [DOI: 10.1007/s12010-017-2621-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/02/2017] [Indexed: 11/27/2022]
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8
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Meat species identification by two direct-triplex real-time PCR assays using low resolution melting. Food Chem 2017; 233:144-150. [DOI: 10.1016/j.foodchem.2017.04.090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 01/02/2017] [Accepted: 04/16/2017] [Indexed: 11/19/2022]
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9
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Feng T, Li S, Wang S, Pan J. Cross priming amplification with nucleic acid test strip analysis of mutton in meat mixtures. Food Chem 2017; 245:641-645. [PMID: 29287420 DOI: 10.1016/j.foodchem.2017.08.107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/24/2017] [Accepted: 08/30/2017] [Indexed: 11/28/2022]
Abstract
A simple, sensitive, accurate and affordable rapid detection of meat species authentication is urgently needed in food industry. In this study, a cross priming amplification (CPA) combining nucleic acid test strip (CPA-Strip) assay for rapid detection of mutton from meat mixture were developed and its feasibility was investigated. In an isothermal CPA system, cytochrome b (cytb) gene as target was amplified at 63°C for 60min. The nucleic acid strip was able to show the corresponding test line in the presence of target gens in 5min. Non-targeting gene interference was not evident. The CPA-Strip has been applied for the detection of 0.1-100% mutton in a thermal treated meat mixtures with a detection limit of a detect limit of 1%. CPA-Strip assay would be a promising simple, rapid and sensitive method for identification of target species in raw and processed meat mixtures.
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Affiliation(s)
- Tao Feng
- College of Life Sciences, China Jiliang University, 258 Xueyuan Street, Xiasha High Education Area, Hangzhou 310018, PR China
| | - Sufang Li
- College of Life Sciences, China Jiliang University, 258 Xueyuan Street, Xiasha High Education Area, Hangzhou 310018, PR China.
| | - Sunan Wang
- Canadian Food and Wine Institute, Niagara College, 135 Taylor Road, Niagara-on-the-Lake, Ontario L0S 1J0, Canada
| | - Jiarong Pan
- College of Life Sciences, China Jiliang University, 258 Xueyuan Street, Xiasha High Education Area, Hangzhou 310018, PR China.
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10
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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11
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Safdar M, Junejo Y. The development of a hexaplex-conventional PCR for identification of six animal and plant species in foodstuffs. Food Chem 2016; 192:745-9. [PMID: 26304406 DOI: 10.1016/j.foodchem.2015.07.082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/08/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
A hexaplex-conventional PCR assay was developed for identification of five meat and one plant species origins in foodstuffs simultaneously. The method merges the use of horse (Equus caballus), soybean (Glycine max), sheep (Ovis aries), poultry (Meleagris meleagris), pork (Sus scrofa), and cow (Bos taurus) specific primers that amplify fragments (horse; 85 bp, soybean; 100 bp, sheep; 119 bp, poultry; 183 bp, pork; 212 bp and cow; 271 bp) of the mitochondrial cyt b, lectin, 12S rRNA, 12S rRNA, ATPase subunit 6 genes and ATPase subunit 8 genes respectively, and a universal 18S rRNA primers that amplifies a 141 bp. Multiplex analysis of the reference food samples showed that detection limit of the hexaplex assay was 0.01% for each species. Taken together, all data indicated that this hexaplex PCR assay was a simple, fast, sensitive, specific, and cost-effective detection method for horse, soybean, sheep, poultry, pork and cow species in foodstuffs.
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Affiliation(s)
- Muhammad Safdar
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey.
| | - Yasmeen Junejo
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey; National Center of Excellence in Analytical Chemistry, University of Sindh Jamshoro, Jamshoro 76080, Pakistan
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12
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Safdar M, Junejo Y, Arman K, Abasıyanık MF. Rapid bovine and caprine species identification in ruminant feeds by duplex real-time PCR melting curve analysis using EvaGreen fluorescence dye. Mol Biotechnol 2015; 56:770-6. [PMID: 24770990 DOI: 10.1007/s12033-014-9756-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A duplex real-time PCR assay with melting curve analysis, using the EvaGreen fluorescence dye, was developed for rapid and reliable identification of bovine and caprine in ruminant feeds. The method merges the use of bovine (Bos taurus) and caprine (Capra hircus) specific primers that amplify small fragments (bovine 96 bp and caprine 142 bp) of the mitochondrial 16S rRNA and 12S rRNA genes, respectively. DNA was isolated from heat-treated meats (133 °C/3 bar for 20 min) mixtures of bovine and caprine and was used to optimize the assay. Gene products of caprine and bovine produced two distinct melting peaks simultaneously at 82 and 86.8 °C, respectively. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The aim of this study was to develop a duplex real-time PCR assay followed by a melt curve step for sensitive, rapid, specific, and cost-effective detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies.
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Affiliation(s)
- M Safdar
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey,
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13
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Abstract
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCR-based mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial real-time PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
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Affiliation(s)
| | - Pavel Neužil
- 1] Kist-Europe, Saarbrücken, Saarland, 66123, Germany [2] Central European Institute of Technology, Brno University of Technology, Technická 3058/10, CZ-616 00 Brno, Czech Republic [3] Northwestern Polytechnical University, School of Mechanical Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R.China
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14
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Development and validation of fast duplex real-time PCR assays based on SYBER Green florescence for detection of bovine and poultry origins in feedstuffs. Food Chem 2015; 173:660-4. [DOI: 10.1016/j.foodchem.2014.10.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 06/15/2014] [Accepted: 10/17/2014] [Indexed: 11/15/2022]
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15
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Safdar M, Junejo Y. A multiplex-conventional PCR assay for bovine, ovine, caprine and fish species identification in feedstuffs: Highly sensitive and specific. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.08.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Safdar M, Junejo Y, Arman K, Abasıyanık MF. A highly sensitive and specific tetraplex PCR assay for soybean, poultry, horse and pork species identification in sausages: development and validation. Meat Sci 2014; 98:296-300. [PMID: 24980471 DOI: 10.1016/j.meatsci.2014.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 05/26/2014] [Accepted: 06/05/2014] [Indexed: 10/25/2022]
Abstract
A tetraplex PCR assay was developed for a rapid and reliable identification of horse, soybean, poultry, and pork species in sausages simultaneously. The method merges the use of horse (Equus caballus), soybean (Glycine max), poultry (Gallus gallus), and pork (Sus scrofa) specific primers that amplify small fragments (horse; 85bp, soybean; 100bp, poultry; 183bp and pork; 212bp) of the mitochondrial cyt b, lectin, 12S rRNA and ATPase subunit 6 genes respectively. Good quality DNA was isolated from reference sausage to optimize the assay. Tetraplex analysis of the reference sausage samples showed that the detection limit of the assay was 0.01% for each species. Taken together, all data indicated that this tetraplex PCR assay was a simple, rapid, sensitive, specific, and cost-effective detection method for horse, soybean, poultry, and pork species in commercial sausages.
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Affiliation(s)
- M Safdar
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey.
| | - Y Junejo
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey; National Center of Excellence in Analytical Chemistry, University of Sindh Jamshoro, Jamshoro 76080, Pakistan
| | - Kaifee Arman
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey
| | - M F Abasıyanık
- Department of Genetics and Bioengineering, Faculty of Engineering, Fatih University, Büyükçekmece, 34500 Istanbul, Turkey
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17
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Hu Z, Zhu C, Chang H, Guo W, Liu D, Xiang W, Wang X. Development of a single-tube duplex EvaGreen real-time PCR for the detection and identification of EHV-1 and EHV-4. Appl Microbiol Biotechnol 2014; 98:4179-86. [PMID: 24615388 DOI: 10.1007/s00253-014-5626-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/15/2014] [Accepted: 02/17/2014] [Indexed: 12/24/2022]
Abstract
The objective of this study was to develop a novel EvaGreen (EG) based real-time PCR technique for the simultaneous detection of Equine herpesvirus 1 (EHV-1) and Equine herpesvirus 4 (EHV-4) genomes from equine nasal swabs. Viral genomes were identified based on their specific melting temperatures (T m), which are 88.0 and 84.4 °C for EHV-1 and EHV-4, respectively. The detection limitation of this method was 50 copies/μl or 0.15 pg/μl for EHV-1 and 5 copies/μl or 2.5 fg/μl for EHV-4. This assay was 50-1,000 times more sensitive than the SYBR Green (SG)-based assay using the same primer pairs and as sensitive as the TaqMan-MGB probe-based assay. The validity of the real-time PCR assays was confirmed by testing 13 clinical samples. When all results of the EG, SG, and TaqMan probe-based singleplex and duplex real-time PCRs were considered together, a total of 84.6 % (11/13) horses and donkeys were positive for at least one virus. EHV-1 and EHV-4 coexisted in 81.8 % (9/11) horses. Overall, we report that the EvaGreen duplex real-time PCR is an economical and alternative diagnostic method for the rapid differentiation of EHV-1 and EHV-4 in nasal swabs.
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Affiliation(s)
- Zhe Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 427 Maduan Street, Harbin, 150001, People's Republic of China
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18
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Safdar M, Abasıyanık M. Development of fast multiplex real-time PCR assays based on EvaGreen fluorescence dye for identification of beef and soybean origins in processed sausages. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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