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Jeong J, Yang Y, Song MS, Won HY, Han AT, Kim S. High-Resolution Melting (HRM) analysis of DNA methylation using semiconductor chip-based digital PCR. Genes Genomics 2024:10.1007/s13258-024-01527-5. [PMID: 38849705 DOI: 10.1007/s13258-024-01527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Digital PCR (dPCR) technology allows absolute quantification and detection of disease-associated rare variants, and thus the use of dPCR technology has been increasing in clinical research and diagnostics. The high-resolution melting curve analysis (HRM) of qPCR is widely used to distinguish true positives from false positives and detect rare variants. In particular, qPCR-HRM is commonly used for methylation assessment in research and diagnostics due to its simplicity and high reproducibility. Most dPCR instruments have limited fluorescence channels available and separate heating and imaging systems. Therefore, it is difficult to perform HRM analysis using dPCR instruments. OBJECTIVE A new digital real-time PCR instrument (LOAA) has been recently developed to integrate partitioning, thermocycling, and imaging in a single dPCR instrument. In addition, a new technique to perform HRM analysis is utilized in LOAA. The aim of the present study is to evaluate the efficiency and accuracy of LOAA dPCR on HRM analysis for the detection of methylation. METHODS In this study, comprehensive comparison with Bio-Rad qRT-PCR and droplet-based dPCR equipment was performed to verify the HRM analysis-based methylation detection efficiency of the LOAA digital PCR equipment. Here, sodium bisulfite modification method was applied to detect methylated DNA sequences by each PCR method. RESULTS Melting curve analysis detected four different Tm values using LOAA and qPCR, and found that LOAA, unlike qPCR, successfully distinguished between different Tm values when the Tm values were very similar. In addition, melting temperatures increased by each methylation were about 0.5℃ for qPCR and about 0.2 ~ 0.6℃ for LOAA. The melting temperature analyses of methylated and unmethylated DNA samples were conducted using LOAA dPCR with TaqMan probes and EvaGreen, and the result found that Tm values of methylated DNA samples are higher than those of unmethylated DNA samples. CONCLUSION The present study shows that LOAA dPCR could detect different melting temperatures according to methylation status of target sequences, indicating that LOAA dPCR would be useful for diagnostic applications that require the accurate quantification and assessment of DNA methylation.
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Affiliation(s)
- Jinuk Jeong
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yongsu Yang
- Department of Microbiology, College of Bio-Convergence, Dankook University, Cheonan, 31116, Republic of Korea
| | - Min-Sik Song
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Hee-Young Won
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Andrew T Han
- BIO Institute, OPTOLANE Technologies Inc, Seongnam, South Korea
| | - Songmi Kim
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea.
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Sharma P, Tandel N, Kumar R, Negi S, Sharma P, Devi S, Saxena K, Chaudhary NR, Saini S, Kumar R, Chandel BS, Sijwali PS, Tyagi RK. Oleuropein activates autophagy to circumvent anti-plasmodial defense. iScience 2024; 27:109463. [PMID: 38562521 PMCID: PMC10982566 DOI: 10.1016/j.isci.2024.109463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Antimalarial drug resistance and unavailability of effective vaccine warrant for newer drugs and drug targets. Hence, anti-inflammatory activity of phyto-compound (oleuropein; OLP) was determined in antigen (LPS)-stimulated human THP-1 macrophages (macrophage model of inflammation; MMI). Reduction in the inflammation was controlled by the PI3K-Akt1 signaling to establish the "immune-homeostasis." Also, OLP treatment influenced the cell death/autophagy axis leading to the modulated inflammation for extended cell survival. The findings with MII prompted us to detect the antimalarial activity of OLP in the wild type (3D7), D10-expressing GFP-Atg18 parasite, and chloroquine-resistant (Dd2) parasite. OLP did not show the parasite inhibition in the routine in vitro culture of P. falciparum whereas OLP increased the antimalarial activity of artesunate. The molecular docking of autophagy-related proteins, investigations with MMI, and parasite inhibition assays indicated that the host activated the autophagy to survive OLP pressure. The challenge model of P. berghei infection showed to induce autophagy for circumventing anti-plasmodial defenses.
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Affiliation(s)
- Praveen Sharma
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG highway, Ahmedabad 382481, India
| | - Rajinder Kumar
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
| | - Sushmita Negi
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
| | - Prakriti Sharma
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
| | - Sonia Devi
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
| | - Kanika Saxena
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, India
| | - Neil Roy Chaudhary
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
| | - Sheetal Saini
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
| | - Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
| | - Bharat Singh Chandel
- Department of Animal Biotechnology, College of Veterinary Science and AH, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat 385 506, India
| | - Puran S. Sijwali
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, India
| | - Rajeev K. Tyagi
- Division of Cell Biology and Immunology, Biomedical Parasitology and Translational-immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Sec-39A, Chandigarh 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
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Ruengdit C, Punyamung M, Intasai N, Pornprasert S. Single-tube multiplex real-time PCR with EvaGreen and high-resolution melting analysis for diagnosis of α0-thalassemia--SEA,--THAI, and--CR type deletions. PLoS One 2023; 18:e0293838. [PMID: 37930985 PMCID: PMC10627449 DOI: 10.1371/journal.pone.0293838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Regions with a high prevalence of α-thalassemia (α-thal) require simple, rapid, and accurate tests for carrier screening and prenatal diagnosis. Diagnosis of multiple deletions in a single tube is necessary to clearly identify individuals with α0-thalassemia in the routine setting, especially in at-risk couples. Therefore, we aimed to develop a single-tube multiplex real-time PCR with EvaGreen and high-resolution melting (HRM) analysis for the identification of α0-thalassemia Southeast Asian (SEA), Thai and Chiang Rai (CR) type deletions. The results of the HRM analysis indicated that the amplified fragments from α0-thal--CR,--THAI,--SEA, and the wild-type α-globin gene had specific peak heights at mean melting temperature (Tm) values of 85.40°C, 86.50°C, 87.65°C, and 91.04°C, respectively. The frequencies of α0-thal--SEA,--THAI,--CR obtained from routine testing in 2,135 samples were 17.89%, 0.19% and 0.19%, respectively. This method would be useful for preventing Hb Bart's hydrops fetalis. Detection of multiple deletions in a single run is cost-effective, highly accurate and timesaving. This technique could enable wider α-thalassemia diagnosis in high prevalence areas and served as an example for thalassemia routine setting.
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Affiliation(s)
- Chedtapak Ruengdit
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Manoo Punyamung
- Associated Medical Sciences Clinical Service Center, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Nutjeera Intasai
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sakorn Pornprasert
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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Chang M, Jung JK, Park JH, Jung JY, Lee WH, Kim JY. Amplification Failure of the Amelogenin X Gene Caused by a Rare Mutation in the Primer-Binding Region. Genes (Basel) 2023; 14:1986. [PMID: 38002929 PMCID: PMC10670841 DOI: 10.3390/genes14111986] [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: 09/11/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
The study of gender markers is essential in forensic genetic analysis. Mutations in the X or Y homologs of the amelogenin gene can be misleading, resulting in serious mistakes in forensic genetic analysis. We recently discovered two male cases of the X homolog of the amelogenin (AMELX) allelic dropout while analyzing short tandem repeat genotypes obtained from crime scene evidence. Subsequently, we evaluated the molecular characteristics of AMELX allelic dropout in this study. We used two previously reported amelogenin primers to verify a half level of amelogenin gene amplification intensity in the two male cases, which we confirmed was caused by AMELX allelic dropout. We then characterized the point mutation using Sanger sequencing and designed mutation-specific primers that could overcome AMELX allelic dropout. Short tandem repeat genotyping analysis confirmed that the AMELX allelic dropout was recovered by the mutation-specific primer designed specifically for this case. The sequencing of the AMELX allele revealed a single-point variant from A→G at base position 7 downstream from the 3' end in the amelogenin forward primer-binding region. This point mutation was identically found in two different male cases, resulting in AMELX allelic dropout. To our knowledge, these mutations and the X homolog amplification failure of amelogenin have not been reported in the Korean population. Our study provides a reliable approach to AMELX allelic dropout due to rare case mutations and could enable the better interpretation of gender markers for forensic samples.
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Affiliation(s)
- Miwha Chang
- Forensic DNA Division, National Forensic Service, Wonju-si 26460, Republic of Korea; (M.C.); (J.H.P.)
- Division of Laboratory Diagnosis Management, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea
| | - Jong Keun Jung
- National Forensic Service, Busan Institute, Yangsan-si 50612, Republic of Korea;
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, Wonju-si 26460, Republic of Korea; (M.C.); (J.H.P.)
| | - Ju Yeon Jung
- Jeju Branch, National Forensic Service, Jeju-si 63309, Republic of Korea;
| | - Won-Hae Lee
- National Forensic Service, Seoul Institute, Seoul 08036, Republic of Korea;
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju-si 26460, Republic of Korea; (M.C.); (J.H.P.)
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Liu Y, Sheng C, Zhou Y, Li J, Gong Q, Shi K, Liu F, Xu L, Cui Z, Leng X, Du R. Application of quantitative real-time PCR to detect Mink Circovirus in minks, foxes and raccoon dogs in northern China. Front Microbiol 2023; 14:1205297. [PMID: 37588885 PMCID: PMC10426742 DOI: 10.3389/fmicb.2023.1205297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
Mink circovirus disease caused by Mink Circovirus (MiCV) is a serious infectious disease of mink that has become prevalent in recent years in China, severely affecting the reproductive performance of mink and causing significant economic losses to farms. To date, there have been few studies on MiCV, its pathogenic mechanism is not clear, and there is no effective vaccine or drug to prevent and control the disease. Therefore, it is necessary to establish a rapid and reliable molecular diagnostic method, which would aid future studies of this novel virus. In our study, we developed a sensitive and specific TaqMan-based quantitative real-time PCR assay targeting the MiCV Cap gene. The assay showed no cross-reaction with other tested animal viruses. The assay is highly sensitive, with a detection limit of as low as 10 plasmid DNA copies and 2.38 × 10-2 pg of viral DNA. The intra and inter--assay coefficients of variation were both low. The positive detection rate of MiCV in clinical samples from minks, foxes, and raccoon dogs were 58.8% (133/226), 50.7% (72/142), and 42.2% (54/128), respectively, giving a total positive detection rate of 52.2% (259/496). Higher contamination levels were observed in samples from the environment in direct or indirect contact with animals, with a total positive detection rate of 75.1% (220/293). These epidemiological results showed that minks, foxes, and raccoon dogs had high infection rates of MiCV. This was also the first study to detect MiCV on the ground and equipment of fur-bearing animal farms. Our assay is highly sensitive and specific for the diagnosis and quantification of MiCV, and should provide a reliable real-time tool for epidemiological and pathogenetic study of MiCV infection.
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Affiliation(s)
- Yingyu Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Chenyan Sheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yu Zhou
- Huizhou Customs District P.R. China, Huizhou, China
| | - Jianming Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Qinglong Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Kun Shi
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Fei Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lihui Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zhenzhen Cui
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Xue Leng
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Rui Du
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses. PLoS One 2023; 18:e0272980. [PMID: 37155676 PMCID: PMC10166557 DOI: 10.1371/journal.pone.0272980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/30/2022] [Indexed: 05/10/2023] Open
Abstract
Twenty-four species of RNA viruses contain members infecting economically important crops that are classified within the genus Emaravirus, family Fimoviridae. There are at least two other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. This research aimed to explore the ability to predict HRM outputs coupled to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). To approach this goal a pair of degenerate genus-specific primers were designed for endpoint RT-PCR and RT-qPCR-HRM and the species in the genus Emaravirus were selected to framework the development of the assays. Both nucleic acid amplification methods were able to detect in-vitro several members of seven Emaravirus species with sensitivity up to one fg of cDNA. Specific parameters for in-silico prediction of the melting temperatures of each expected emaravirus amplicon are compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The high-resolution DNA melting curves of the RT-PCR products predicted in-silico using uMeltSM allowed saving time while designing and developing the RT-qPCR-HRM assay since the approach avoided extensive searching for optimal HRM assay regions and rounds of HRM tests in-vitro for optimization. The resultant assay provides sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Adriana E Larrea-Sarmiento
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses. J Virol Methods 2021:114425. [PMID: 34902460 DOI: 10.1016/j.jviromet.2021.114425] [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: 07/13/2020] [Revised: 03/09/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023]
Abstract
High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. The aim of this research was to explore the ability to predict HRM outputs when coupled to reverse transcription quantitative polymerase chain reaction (RT-qPCR). This research used the species in the Emaravirus genus as model to framework the development of genus-specific RT-qPCR-HRM assays. A pair of degenerate genus-specific primers were designed for use in endpoint RT-PCR and RT-qPCR-HRM detection of emaraviruses. Eleven species of RNA viruses infecting economically important crops are classified within the genus Emaravirus, family Fimoviridae. There are at least fifteen other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. RT-PCR and RT-qPCR-HRM were able to detect seven emaravirus species in-vitro with sensitivity up to one fg of cDNA. Specific parameters for prediction in-silico of the melting temperatures of each expected emaravirus amplicon are provided and compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The prediction in-silico of fluorescence of high-resolution DNA melting curves of predicted RT-PCR products using uMeltSM speeded the design and development of RT-qPCR-HRM assay. This approach avoided rounds of HRM tests in-vitro when searching for the optimal regions that provides accurate diagnosis. The resultant assay provided sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA; Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA.
| | - Adriana E Larrea-Sarmiento
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador; Universidad UTE, Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Quito, Ecuador
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Development of DNA Melt Curve Analysis for the Identification of Lepidopteran Pests in Almonds and Pistachios. INSECTS 2021; 12:insects12060553. [PMID: 34203602 PMCID: PMC8232234 DOI: 10.3390/insects12060553] [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: 05/11/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Almonds and pistachios are fed upon by a diverse assemblage of lepidopteran insects, several of which are economically important pests. Unfortunately, identification of these pests can be difficult, as specimens are frequently damaged during collection, occur in traps with non-target species, and are morphologically similar up to their third instar. Here, we present a quantitative PCR based melt curve analysis for simple, rapid, and accurate identification of six lepidopteran pests of almonds and pistachios: navel orangeworm, peach twig borer, oriental fruit moth, obliquebanded leafroller, raisin moth, and Indian meal moth. We demonstrate that the dissociation or the “melt” temperature(s) of a 658 bp section of cytochrome c oxidase subunit 1 provides unambiguous species level identification of these six species and is reproducible in field specimens collected following conventional orchard practices. The melt curve’s simplicity allows it to be performed in any basic molecular biology laboratory with a quantitative PCR. Abstract Almonds and pistachios are fed upon by a diverse assemblage of lepidopteran insects, several of which are economically important pests. Unfortunately, identification of these pests can be difficult, as specimens are frequently damaged during collection, occur in traps with non-target species, and are morphologically similar up to their third instar. Here, we present a quantitative PCR based melt curve analysis for simple, rapid, and accurate identification of six lepidopteran pests of almonds and pistachios: navel orangeworm (Amyelois transitella), peach twig borer (Anarsia lineatella), oriental fruit moth (Grapholita molesta), obliquebanded leafroller (Choristoneura rosaceana), raisin moth (Cadra figulilella), and Indian meal moth (Plodia interpunctella). In this approach, the dissociation (melt) temperature(s) of a 658 bp section of cytochrome c oxidase subunit 1 was determined using quantitative PCR (qPCR). Within these six species, the distribution and the number of melt peak temperatures provide an unambiguous species level identification that is reproducible when unsheared DNA can be extracted. The test is robust across a variety of sampling approaches including insects removed from sticky card traps, museum specimens, and samples that were left in the field for up to 7 days. The melt curve’s simplicity allows it to be performed in any basic molecular biology laboratory with a quantitative PCR.
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A Real-Time PCR Assay for Simultaneous Detection and Differentiation of Four Common Entamoeba Species That Infect Humans. J Clin Microbiol 2020; 59:JCM.01986-20. [PMID: 33115843 DOI: 10.1128/jcm.01986-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 11/20/2022] Open
Abstract
There are over 40 species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, and yet differentiation is important for appropriate treatment decisions. Here, we developed a hydrolysis probe-based tetraplex real-time PCR assay that can simultaneously detect and differentiate these four species in clinical samples. In this assay, multicopy small-subunit (SSU) ribosomal DNA (rDNA) sequences were used as targets. We determined that the tetraplex real-time PCR can detect amebic DNA corresponding to as little as a 0.1 trophozoite equivalent of any of these species. We also determined that this assay can detect E. histolytica DNA in the presence of 10-fold more DNA from another Entamoeba species in mixed-infection scenarios. With a panel of more than 100 well-characterized clinical samples diagnosed and confirmed using a previously published duplex real-time PCR (capable of detecting E. histolytica and E. dispar), our tetraplex real-time PCR assay demonstrated levels of sensitivity and specificity comparable with those demonstrated by the duplex real-time PCR assay. The advantage of our assay over the duplex assay is that it can specifically detect two additional Entamoeba species and can be used in conventional PCR format. This newly developed assay will allow further characterization of the epidemiology and pathogenicity of the four morphologically identical Entamoeba species, especially in low-resource settings.
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Tan LL, Ahmed SA, Ng SK, Citartan M, Raabe CA, Rozhdestvensky TS, Tang TH. Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay. Food Chem 2020; 309:125654. [PMID: 31678669 DOI: 10.1016/j.foodchem.2019.125654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/02/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
A specialized DNA extraction method and a SYBR Green quantitative polymerase chain reaction (SyG-qPCR) assay were combined to generate a ready-to-use kit for rapid detection of porcine admixtures in processed meat products. Our qPCR assay utilized repetitive LINE-1 elements specific to the genome of Sus scrofa domesticus (pig) as a target and incorporated internal controls. We improved the genomic DNA extraction method, and reduced extraction times to the minimum. The method was validated for specificity, sensitivity (0.001% w/w) and robustness, and values were compared with those of a commercially available kit. We also tested our method using 121 processed food products and consistently detected amplification only in samples containing pork. Due to its efficiency and cost-effectiveness, our method represents a valuable new method for detecting food adulteration with pork that is superior to existing quality control approaches.
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Affiliation(s)
- Lee Lee Tan
- Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Malaysia.
| | - Siti Aminah Ahmed
- Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Malaysia.
| | - Siew Kit Ng
- Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Malaysia.
| | - Carsten A Raabe
- Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany; Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany; Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany.
| | - Timofey S Rozhdestvensky
- Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University Hospital of Muenster, D-48149 Muenster, Germany.
| | - Thean Hock Tang
- Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Malaysia.
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11
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Farhad SZ, Siadat A, Sadeghian N, Abrishamkar S, Khosraviani F, Khazaei P, Saberi-Demneh A. The effect of low-level laser radiation and doxycycline on the levels of osteoprotegerin and receptor activator of nuclear factor kappa-B ligand. Lasers Med Sci 2020; 35:1975-1979. [PMID: 32221769 DOI: 10.1007/s10103-020-02993-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 03/01/2020] [Indexed: 11/25/2022]
Abstract
The present in vitro study was conducted to investigate the effect of low-level laser (LLL) radiation and doxycycline on the levels of osteoprotegerin (OPG) and receptor activator of nuclear factor kappa-B ligand (RANKL) derived from MG-63 osteosarcoma cell line. MG-63 cells were divided into four groups. In the first group, 2 mg/mL of doxycycline was injected into the cell culture medium. Diode laser (810 nm, 100 mw, 75 s) was radiated to the culture medium of the second group. The third group received both doxycycline and laser radiation. In the fourth group (control), the culture medium was replaced daily, similar to the above three groups. Mentioned interventions were performed once a day for 4 consecutive days. Then, on the sixth day, the levels of OPG and RANKL mediators were measured using real-time polymerase chain reaction by isolating the cells from the samples. OPG expression had the highest to lowest levels in the laser + doxycycline, doxycycline, laser, and control groups, respectively. The level of OPG was significantly different between all the study groups (p < 0.05) except in the doxycycline + laser and doxycycline groups (p = 0.061). The highest to lowest levels of RANKL was observed in the doxycycline, laser + doxycycline, control, and laser groups, respectively. The RANKL expression was not significantly different between all the study groups (p > 0.05). The results of this study revealed that LLL and doxycycline reduced the RANKL/OPG ratio derived from the MG-63 osteosarcoma cell line, which may result in the diminished activity of osteoclasts and osteoclastogenesis.
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Affiliation(s)
- Shirin Zahra Farhad
- School of Dentistry, Islamic Azad University, Khorasgan Branch, Isfahan, Iran
| | - Amir Siadat
- School of Dentistry, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Neda Sadeghian
- School of Dentistry, Islamic Azad University, Khorasgan Branch, Isfahan, Iran
| | - Sourena Abrishamkar
- School of Dentistry, Islamic Azad University, Khorasgan Branch, Isfahan, Iran.
| | | | - Pegah Khazaei
- School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
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12
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Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:2697230. [PMID: 32184908 PMCID: PMC7061119 DOI: 10.1155/2020/2697230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 01/23/2023]
Abstract
Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.
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13
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Vishwakarma G, Sanyal RP, Saini A, Sahu PK, Singh Patel RR, Sharma D, Tiwari R, Das BK. GLADS: A gel-less approach for detection of STMS markers in wheat and rice. PLoS One 2019; 14:e0224572. [PMID: 31689318 PMCID: PMC6830750 DOI: 10.1371/journal.pone.0224572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 11/18/2022] Open
Abstract
Sequence tagged microsatellite site (STMS) are useful PCR based DNA markers. Wide genome coverage, high polymorphic index and co-dominant nature make STMS a preferred choice for marker assisted selection (MAS), genetic diversity analysis, linkage mapping, seed genetic purity analysis etc. Routine STMS analysis involving low-throughput, laborious and time-consuming polyacrylamide/agarose gels often limit their full utility in crop breeding experiments that involve large populations. Therefore, convenient, gel-less marker detection methods are highly desirable for STMS markers. The present study demonstrated the utility of SYBR Green dye based melt-profiling as a simple and convenient gel-less approach for detection of STMS markers (referred to as GLADS) in bread wheat and rice. The method involves use of SYBR Green dye during PCR amplification (or post-PCR) of STMS markers followed by generation of a melt-profile using controlled temperature ramp rate. The STMS amplicons yielded characteristic melt-profiles with differences in melting temperature (Tm) and profile shape. These characteristic features enabled melt-profile based detection and differentiation of STMS markers/alleles in a gel-less manner. The melt-profile approach allowed assessment of the specificity of the PCR assay unlike the end-point signal detection assays. The method also allowed multiplexing of two STMS markers with non-overlapping melt-profiles. In principle, the approach can be effectively used in any crop for STMS marker analysis. This SYBR Green melt-profiling based GLADS approach offers a convenient, low-cost (20–51%) and time-saving alternative for STMS marker detection that can reduce dependence on gel-based detection, and exposure to toxic chemicals.
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Affiliation(s)
- Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
| | - Ravi Prakash Sanyal
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Ajay Saini
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
| | - Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ravi Raj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ratan Tiwari
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, Maharashtra, India
- * E-mail:
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14
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Dong J, Xu Q, Li CC, Zhang CY. Single-color multiplexing by the integration of high-resolution melting pattern recognition with loop-mediated isothermal amplification. Chem Commun (Camb) 2019; 55:2457-2460. [PMID: 30734782 DOI: 10.1039/c8cc09741k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We develop a single-color multiplexing strategy by the integration of high-resolution melting pattern recognition with loop-mediated isothermal amplification (LAMP). This strategy can identify multiple amplicons with a small DNA melting temperature (Tm) difference (∼0.2 °C) without the involvement of either multicolor labels or parallelized multiplexing, and it can sensitively detect LAMP amplicons with the initial DNA concentrations ranging from 10 to 108 copies.
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Affiliation(s)
- Jing Dong
- School of Food and Biological Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, 710021, China.
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15
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Development of one-tube real-time RT-qPCR for the universal detection and quantification of Plum pox virus (PPV). J Virol Methods 2019; 263:10-13. [DOI: 10.1016/j.jviromet.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/30/2018] [Accepted: 10/12/2018] [Indexed: 12/22/2022]
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16
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Okino CH, Giglioti R, Silva PC, de Oliveira HN, de Sena Oliveira MC. Comparative evaluation of DNA extraction kit, matrix sample and qPCR assays for bovine babesiosis monitoring. Mol Biol Rep 2018; 45:2671-2680. [DOI: 10.1007/s11033-018-4436-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/10/2018] [Indexed: 10/28/2022]
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17
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Ahmed FE, Gouda MM, Hussein LA, Ahmed NC, Vos PW, Mohammad MA. Role of Melt Curve Analysis in Interpretation of Nutrigenomics' MicroRNA Expression Data. Cancer Genomics Proteomics 2018; 14:469-481. [PMID: 29109097 DOI: 10.21873/cgp.20057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/05/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
This article illustrates the importance of melt curve analysis (MCA) in interpretation of mild nutrogenomic micro(mi)RNA expression data, by measuring the magnitude of the expression of key miRNA molecules in stool of healthy human adults as molecular markers, following the intake of Pomegranate juice (PGJ), functional fermented sobya (FS), rich in potential probiotic lactobacilli, or their combination. Total small RNA was isolated from stool of 25 volunteers before and following a three-week dietary intervention trial. Expression of 88 miRNA genes was evaluated using Qiagen's 96 well plate RT2 miRNA qPCR arrays. Employing parallel coordinates plots, there was no observed significant separation for the gene expression (Cq) values, using Roche 480® PCR LightCycler instrument used in this study, and none of the miRNAs showed significant statistical expression after controlling for the false discovery rate. On the other hand, melting temperature profiles produced during PCR amplification run, found seven significant genes (miR-184, miR-203, miR-373, miR-124, miR-96, miR-373 and miR-301a), which separated candidate miRNAs that could function as novel molecular markers of relevance to oxidative stress and immunoglobulin function, for the intake of polyphenol (PP)-rich, functional fermented foods rich in lactobacilli (FS), or their combination. We elaborate on these data, and present a detailed review on use of melt curves for analyzing nutigenomic miRNA expression data, which initially appear to show no significant expressions, but are actually more subtle than this simplistic view, necessitating the understanding of the role of MCA for a comprehensive understanding of what the collective expression and MCA data collectively imply.
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Affiliation(s)
- Farid E Ahmed
- GEM Tox Labs, Institute for Research in Biotechnology, Greenville, NC, U.S.A.
| | - Mostafa M Gouda
- Department of Nutrition & Food Science, National Research Centre, Dokki, Cairo, Egypt
| | - Laila A Hussein
- Department of Nutrition & Food Science, National Research Centre, Dokki, Cairo, Egypt
| | - Nancy C Ahmed
- GEM Tox Labs, Institute for Research in Biotechnology, Greenville, NC, U.S.A
| | - Paul W Vos
- Department of Biostatistics, College of Allied Health Sciences, East Carolina University, Greenville, NC, U.S.A
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18
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Cui X, Shi Y, Zhao L, Gu S, Wei C, Yang Y, Wen S, Chen H, Ge J. Application of Real-Time Quantitative PCR to Detect Mink Circovirus in Naturally and Experimentally Infected Minks. Front Microbiol 2018; 9:937. [PMID: 29867846 PMCID: PMC5960700 DOI: 10.3389/fmicb.2018.00937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
The mink circovirus (MiCV), a newly discovered pathogen, is associated with diarrhea in farmed minks. The prevalence and economic importance of this virus remain poorly understood, and a quantitative method for diagnosis of MiCV infection has not been established. This research aims to develop a highly specific, sensitive, and quantitative assay for MiCV. A Real-Time quantitative polymerase chain reaction (qPCR) assay was developed to detect different isolates of the MiCV in mink samples. The qPCR system is highly sensitive with a detection limit of as low as 10 viral DNA copies. The specificity of this qPCR assay was supported by the absence of cross-reaction with other pathogens. The coefficients of variation were low for both inter-assay and intra-assay variabilities. In addition, the results also expressed the distribution of MiCV in infectious mink tissues with high levels of virus in the skeletal muscle and heart. The heart occupied a higher proportion than other tissues, which can be considered the primary source of test material. This qPCR method could be a useful tool for epidemiological studies and disease management. This method for MiCV is highly specific, sensitive, repeatable, quantitative, and can rapidly determine viral load levels in different tissues samples.
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Affiliation(s)
- Xingyang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yunjia Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Lili Zhao
- Laboratory Animal and Comparative Medicine Unit, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shanshan Gu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Chengwei Wei
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yan Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Shanshan Wen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hongyan Chen
- Laboratory Animal and Comparative Medicine Unit, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
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19
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Okino CH, Montassier MDFS, Oliveira APD, Montassier HJ. Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I. J Vet Med Sci 2018; 80:725-730. [PMID: 29491226 PMCID: PMC5938207 DOI: 10.1292/jvms.17-0566] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene
within a RT-qPCR was developed to detect different genotypes of avian infectious
bronchitis virus (IBV) and identify the Mass genotype. The method was able to rapidly
identify the Mass genotype among IBV field isolates, vaccine attenuated strains and
reference M41 strain in allantoic liquid and also directly in tissues. The RT-qPCR
developed detected the virus in both tracheal and pulmonary samples from M41-infected or
H120-infected birds, in a larger post-infection period compared to detection by standard
method of virus isolation. RT-qPCR method tested provided a sensitivity and rapid approach
for screening on IBV detection and Mass genotyping from IBV isolates.
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Affiliation(s)
- Cintia Hiromi Okino
- Laboratory of Immunology and Virology, Department of Veterinary Pathology, Universidade Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil.,Current affiliation: Embrapa Pecuária Sudeste, Rodovia Washington Luiz km 234 s/n, São Carlos, SP, 13560-970, Brazil
| | - Maria de Fátima Silva Montassier
- Laboratory of Immunology and Virology, Department of Veterinary Pathology, Universidade Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Andressa Peres de Oliveira
- Laboratory of Immunology and Virology, Department of Veterinary Pathology, Universidade Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Helio José Montassier
- Laboratory of Immunology and Virology, Department of Veterinary Pathology, Universidade Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, 14884-900, Brazil
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20
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Lubis H, Salihah NT, Norizan NA, Hossain MM, Ahmed MU. Fast and Sensitive Real-time PCR-based Detection of Porcine DNA in Food Samples by Using EvaGreen Dye. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2018. [DOI: 10.3136/fstr.24.803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hamadah Lubis
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam
| | - Nur Thaqifah Salihah
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam
| | - Nur Aqirah Norizan
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam
| | | | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam
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21
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Kouhpayeh S, Hejazi Z, Khanahmad H, Rezaei A. Real-Time PCR: an Appropriate Approach to Confirm ssDNA Generation from PCR Product in SELEX Process. IRANIAN JOURNAL OF BIOTECHNOLOGY 2017; 15:143-148. [PMID: 29845062 DOI: 10.15171/ijb.1550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/09/2017] [Accepted: 06/20/2017] [Indexed: 01/12/2023]
Abstract
Background: Aptamers are single stranded DNA (ssDNA) or RNA molecules. The potential of aptamers for binding to the different targets has made them be widely used as the preferred diagnostic and therapeutic tools. DNA aptamers present several advantages over the RNA oligonucleotides due to their higher stability, easier selection, and production. Selection of DNA aptamers which is facilitated through a systematic evolution of ligand by exponential enrichment (SELEX) method is much dependent on the successful conversion of double stranded DNA (dsDNA) to ssDNA. Objective: There are different methods available for ssDNA generation. While visualization of ssDNA is limited to the gelbased method, the method is not applicable in the initial rounds of SELEX due to more than 1015 different sequences. This study was designed to evaluate the effi ciency of another technique for confi rming the ssDNA generation in comparison to the polyacrylamide electrophoresis (PAGE) analysis. Materials and Methods: Real-time PCR was employed in the present study for PCR amplifi cation of the initial library that was followed by enzymatic digestion of the dsDNA. Subsequently melting curve analysis was carried out to evaluate ssDNA generation from dsDNA. Moreover, PAGE analysis was performed and the results were compared with the melt curve analysis. Results: The melt curves, revealed dsDNA conversion to the ssDNA based on a significant reduction of Tm from 73.8 to 41.5 °C. Applying PAGE analysis, it was not effectively feasible to show ssDNA generation from the corresponding initial dsDNA library, while, it was effi cient enough to confirm ssDNA generation in accordance with the increasing the number of SELEX rounds. Conclusion: The present study has proven the applicability of the real-time PCR as a suitable confirmatory technique for validating ssDNA generation in the DNA aptamer selection process for the initial library preparation.
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Affiliation(s)
- Shirin Kouhpayeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 313, Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 313, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 313, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable disease, Isfahan University of Medical Sciences, Isfahan, 313, Iran
| | - Abbas Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 313, Iran
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22
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Bahder BW, Helmick EE, Harrison NA. Detecting and Differentiating Phytoplasmas Belonging to Subgroups 16SrIV-A and 16SrIV-D Associated With Lethal Declines of Palms in Florida Using qPCR and High-Resolution Melt Analysis (HRMA). PLANT DISEASE 2017; 101:1449-1454. [PMID: 30678590 DOI: 10.1094/pdis-01-17-0023-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lethal yellowing (LY) and Texas Phoenix palm decline (TPPD) are two important phytoplasma diseases of palms in Florida. Both have been responsible for major economic losses historically and remain a constant threat to the sustainability of palm production in the landscaping and nursery industries in Florida. These two diseases cause rapid, lethal decline in afflicted palms, so rapid detection and identification is crucial to implement appropriate management strategies to reduce further spread and losses. In this study, a qPCR assay was developed to detect and identify the causal agents of LY and TPPD. Based on sequence data of the 16S gene for the 16SrIV-A phytoplasma (LY) and the 16SrIV-D phytoplasma (TPPD), two regions were identified in the gene that possessed sufficient variation to yield amplicons with measurable differences in melting temperature based on high resolution melt analysis (HRMA). One region was in the 5' region and the other was located in the 3' region of the gene. Products from both regions yielded amplicons with significantly different melting temperatures between the two phytoplasma strains. This research allows for the detection and identification of phytoplasmas in palms rapidly by eliminating many lengthy and post-PCR steps commonly used in phytoplasma identification.
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Affiliation(s)
- Brian W Bahder
- Department of Entomology and Nematology, University of Florida, Davie, 33314-7719
| | - Ericka E Helmick
- Department of Entomology and Nematology, University of Florida, Davie, 33314-7719
| | - Nigel A Harrison
- Department of Plant Pathology, University of Florida, Davie, 33314-7719
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23
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Lieveld M, Carregosa A, Benoy I, Redzic N, Berth M, Vanden Broeck D. A high resolution melting (HRM) technology-based assay for cost-efficient clinical detection and genotyping of herpes simplex virus (HSV)-1 and HSV-2. J Virol Methods 2017; 248:181-186. [PMID: 28734843 DOI: 10.1016/j.jviromet.2017.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
Abstract
Genital herpes can be caused by two very similar viruses, herpes simplex virus (HSV)-1 or HSV-2. These two HSV types cannot be distinguished clinically, but genotyping is recommended in the first-episodes of genital herpes to guide counselling and management. Quantitative polymerase chain reaction (qPCR) is the preferred diagnostic method for HSV typing. However, commercial qPCR methods use expensive fluorescent labeled probes for detection. Furthermore, most low-cost methods are not able to differentiate between HSV-1 and -2. The aim of this study was to develop a high resolution melting (HRM) technology-based assay for sensitive HSV-1 and HSV-2 detection and genotyping. Using a panel of 46 clinical specimens, the performance of the HRM assay was compared to two commercial HSV tests: the HRM assay detected HSV in all 23 positive samples, with no false positive results (100% concordance with HSV I/II Real-TM assay). Additionally, the HRM assay correctly genotyped both HSV types in a subset of these clinical samples, as determined by the Realstar HSV PCR Kit. The HSV HRM assay provides a cost-effective alternative method to conventional more expensive assays and can be used in routine clinical specimens, in cases where it is particularly necessary to detect and distinguish HSV-1 from -2.
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Affiliation(s)
- M Lieveld
- International Centre for Reproductive Health, Department of Urogynaecology, Ghent University Hospital, Ghent, Belgium.
| | - A Carregosa
- International Centre for Reproductive Health, Department of Urogynaecology, Ghent University Hospital, Ghent, Belgium.
| | - I Benoy
- Algemeen Medisch Laboratorium, Sonic Healthcare, Antwerp, Belgium.
| | - N Redzic
- Algemeen Medisch Laboratorium, Sonic Healthcare, Antwerp, Belgium; AMBIOR, Laboratory for Cell Biology & Histology, University of Antwerp, Antwerp, Belgium.
| | - M Berth
- Algemeen Medisch Laboratorium, Sonic Healthcare, Antwerp, Belgium.
| | - D Vanden Broeck
- International Centre for Reproductive Health, Department of Urogynaecology, Ghent University Hospital, Ghent, Belgium; Algemeen Medisch Laboratorium, Sonic Healthcare, Antwerp, Belgium.
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24
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Satta E, Nanni IM, Contaldo N, Collina M, Poveda JB, Ramírez AS, Bertaccini A. General phytoplasma detection by a q-PCR method using mycoplasma primers. Mol Cell Probes 2017; 35:1-7. [PMID: 28558918 DOI: 10.1016/j.mcp.2017.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 11/24/2022]
Abstract
Phytoplasmas and mycoplasmas are bacteria belonging to the class Mollicutes. In this study, a fine tuning of quantitative polymerase chain reaction (qPCR) with a universal mycoplasma primer pair (GPO3F/MGSO) targeting the 16S rRNA gene was carried out on phytoplasmas. The dissociation curves of DNAs from Catharanthus roseus phytoplasma-infected micropropagated shoots and from phytoplasma field-infected plant samples showed a single peak at 82.5 °C (±0.5) specifically detecting phytoplasmas belonging to several ribosomal groups. Assay specificity was determined with DNA of selected bacteria: 'Candidatus Liberibacter solanacearum', Xylella fastidiosa, Ralstonia solanacearum and Clavibacter michiganensis. No amplification curves were observed with any of these tested bacteria except 'Ca. L. solanacearum' that was amplified with a melting temperature at 85 °C. Absolute quantification of phytoplasma titer was calculated using standard curves prepared from serial dilutions of plasmids containing the cloned fragment GPO3F/MGSO from European stone fruit yellows phytoplasma. Phytoplasma copy number ranged from 106 to 103 according with the sample. The sensitivity evaluated comparing plasmid serial dilutions resulted 10-6 for conventional PCR and 10-7 for qPCR. The latter method resulted therefore able to detect very low concentrations of phytoplasma in plant material.
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Affiliation(s)
- Eleonora Satta
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy.
| | - Irene M Nanni
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Nicoletta Contaldo
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Marina Collina
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - José B Poveda
- Unidad de Epidemiologia y Medicina Preventiva, Universidad de Las Palmas de Gran Canaria, (IUSA), Arucas, Spain
| | - Ana S Ramírez
- Unidad de Epidemiologia y Medicina Preventiva, Universidad de Las Palmas de Gran Canaria, (IUSA), Arucas, Spain
| | - Assunta Bertaccini
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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Fernández-Álvarez C, González SF, Santos Y. Development of a SYBR green I real-time PCR assay for specific identification of the fish pathogen Aeromonas salmonicida subspecies salmonicida. Appl Microbiol Biotechnol 2016; 100:10585-10595. [PMID: 27838837 DOI: 10.1007/s00253-016-7929-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
A SYBR Green I real-time polymerase chain reaction protocol for specific detection of the fish pathogen Aeromonas salmonicida subsp. salmonicida was developed and validated for rapid diagnosis of typical furunculosis. The sequence of the aopO gene of A. salmonicida subsp. salmonicida, which encodes for a serine/threonine protein kinase linked to virulence, was chosen for primer design. The selected primers amplified a 119-bp internal fragment of the aopO gene. The specificity test proved that 100 % (40/40) of the A. salmonicida subsp. salmonicida strains tested showed a positive amplification with subspecies-specific melting temperatures (Tm) of 80.75 ± 0.35 °C. Atypical A. salmonicida subspecies and other non-related bacterial fish pathogens did not amplify or showed unspecific melting profiles, except for one strain of A. salmonicida subsp. achromogenes and one strain of A. salmonicida subsp. smithia. The detection sensitivity was 21 fg of purified bacterial DNA per reaction, corresponding to 1-2 bacterial cells and 6-60 bacteria per reaction for seeded kidney and blood. The assay was highly reproducible with low variation coefficient values for intra-run and inter-run assays. The assay also allowed the specific detection of A. salmonicida subsp. salmonicida in tissues of fish naturally and experimentally infected. No amplification was detected when tissues from healthy fish or fish affected by other diseases were tested. The SYBR Green real-time PCR and melt curve analysis developed in this study is a rapid and accurate method for the specific identification of A. salmonicida subsp. salmonicida isolates and its detection on tissues of fish affected by furunculosis.
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Affiliation(s)
- Clara Fernández-Álvarez
- Departamento de Microbiología y Parasitología, Edificio CIBUS Facultad de Biología and Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
| | - Santiago F González
- Institute for Research in Biomedicine, Università della Suvizzera Italiana, 6500, Bellinzona, Switzerland
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Edificio CIBUS Facultad de Biología and Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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26
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Asing, Ali E, Hamid SBA, Hossain M, Ahamad MNU, Hossain SMA, Naquiah N, Zaidul ISM. Duplex real-time PCR assay using SYBR Green to detect and quantify Malayan box turtle (Cuora amboinensis) materials in meatballs, burgers, frankfurters and traditional Chinese herbal jelly powder. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2016; 33:1643-1659. [DOI: 10.1080/19440049.2016.1236403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Asing
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Eaqub Ali
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Sharifah Bee Abd Hamid
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Motalib Hossain
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | | | - S. M. Azad Hossain
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Nina Naquiah
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - I. S. M. Zaidul
- Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University, Kuantan, Malaysia
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Nagy A, Černíková L, Vitásková E, Křivda V, Dán Á, Dirbáková Z, Jiřincová H, Procházka B, Sedlák K, Havlíčková M. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS One 2016; 11:e0151204. [PMID: 27031831 PMCID: PMC4816343 DOI: 10.1371/journal.pone.0151204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 12/05/2022] Open
Abstract
In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.
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Affiliation(s)
- Alexander Nagy
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
| | - Lenka Černíková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Eliška Vitásková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Vlastimil Křivda
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Ádám Dán
- National Food Chain Safety Office, Veterinary Diagnostic Directorate, Molecular Biology Laboratory, Budapest, Hungary
| | - Zuzana Dirbáková
- Department of Virology, State Veterinary Institute Zvolen, Zvolen, Slovak Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
| | - Bohumír Procházka
- Department of Informatics and Biostatistics, National Institute of Public Health, Prague, Czech Republic
| | - Kamil Sedlák
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Martina Havlíčková
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
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Two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites. Biosens Bioelectron 2016; 82:1-8. [PMID: 27031184 DOI: 10.1016/j.bios.2016.03.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 01/07/2023]
Abstract
Rapid, early, and accurate diagnosis of malaria is essential for effective disease management and surveillance, and can reduce morbidity and mortality associated with the disease. Although significant advances have been achieved for the diagnosis of malaria, these technologies are still far from ideal, being time consuming, complex and poorly sensitive as well as requiring separate assays for sample processing and detection. Therefore, the development of a fast and sensitive method that can integrate sample processing with detection of malarial infection is desirable. Here, we report a two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites. It combines the Dimethyl adipimidate (DMA)/Thin film Sample processing (DTS) technique as a first stage and the Mach-Zehnder Interferometer-Isothermal solid-phase DNA Amplification (MZI-IDA) sensing technique as a second stage. The system can extract DNA from malarial parasites using DTS technique in a closed system, not only reducing sample loss and contamination, but also facilitating the multiplexed malarial DNA detection using the fast and accurate MZI-IDA technique. Here, we demonstrated that this system can deliver results within 60min (including sample processing, amplification and detection) with high sensitivity (<1 parasite μL(-1)) in a label-free and real-time manner. The developed system would be of great potential for better diagnosis of malaria in low-resource settings.
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29
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Advance Detection Techniques of Phytopathogenic Fungi: Current Trends and Future Perspectives. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Rath S, Salinas M, Villegas AG, Ramaswamy S. Differentiation and Distribution of Marrow Stem Cells in Flex-Flow Environments Demonstrate Support of the Valvular Phenotype. PLoS One 2015; 10:e0141802. [PMID: 26536240 PMCID: PMC4633293 DOI: 10.1371/journal.pone.0141802] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
For treatment of critical heart valve diseases, prosthetic valves perform fairly well in most adults; however, for pediatric patients, there is the added requirement that the replacement valve grows with the child, thus extremely limiting current treatment options. Tissue engineered heart valves (TEHV), such as those derived from autologous bone marrow stem cells (BMSCs), have the potential to recapitulate native valve architecture and accommodate somatic growth. However, a fundamental pre-cursor in promoting directed integration with native tissues rather than random, uncontrolled growth requires an understanding of BMSC mechanobiological responses to valve-relevant mechanical environments. Here, we report on the responses of human BMSC-seeded polymer constructs to the valve-relevant stress states of: (i) steady flow alone, (ii) cyclic flexure alone, and (iii) the combination of cyclic flexure and steady flow (flex-flow). BMSCs were seeded onto a PGA: PLLA polymer scaffold and cultured in static culture for 8 days. Subsequently, the aforementioned mechanical conditions, (groups consisting of steady flow alone-850ml/min, cyclic flexure alone-1 Hz, and flex-flow-850ml/min and 1 Hz) were applied for an additional two weeks. We found samples from the flex-flow group exhibited a valve-like distribution of cells that expressed endothelial (preference to the surfaces) and myofibroblast (preference to the intermediate region) phenotypes. We interpret that this was likely due to the presence of both appreciable fluid-induced shear stress magnitudes and oscillatory shear stresses, which were concomitantly imparted onto the samples. These results indicate that flex-flow mechanical environments support directed in vitro differentiation of BMSCs uniquely towards a heart valve phenotype, as evident by cellular distribution and expression of specific gene markers. A priori guidance of BMSC-derived, engineered tissue growth under flex-flow conditions may serve to subsequently promote controlled, engineered to native tissue integration processes in vivo necessary for successful long-term valve remodeling.
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Affiliation(s)
- Sasmita Rath
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, United States of America
| | - Manuel Salinas
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, United States of America
| | - Ana G. Villegas
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, United States of America
| | - Sharan Ramaswamy
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33174, United States of America
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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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32
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Keller M, Naue J, Zengerle R, von Stetten F, Schmidt U. Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment. PLoS One 2015; 10:e0131845. [PMID: 26147196 PMCID: PMC4492497 DOI: 10.1371/journal.pone.0131845] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/05/2015] [Indexed: 11/19/2022] Open
Abstract
Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols.
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Affiliation(s)
- Mark Keller
- Laboratory for MEMS Applications, IMTEK–Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK–Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
- BIOSS–Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK–Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - Ulrike Schmidt
- Institute of Legal Medicine, Freiburg University Medical Center, Freiburg, Germany
- * E-mail:
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33
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Development and validation of a multiplex reverse transcription quantitative PCR (RT-qPCR) assay for the rapid detection of Citrus tristeza virus, Citrus psorosis virus, and Citrus leaf blotch virus. J Virol Methods 2015; 220:64-75. [PMID: 25907469 DOI: 10.1016/j.jviromet.2015.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 11/20/2022]
Abstract
A single real-time multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay for the simultaneous detection of Citrus tristeza virus (CTV), Citrus psorosis virus (CPsV), and Citrus leaf blotch virus (CLBV) was developed and validated using three different fluorescently labeled minor groove binding qPCR probes. To increase the detection reliability, coat protein (CP) genes from large number of different isolates of CTV, CPsV and CLBV were sequenced and a multiple sequence alignment was generated with corresponding CP sequences from the GenBank and a robust multiplex RT-qPCR assay was designed. The capacity of the multiplex RT-qPCR assay in detecting the viruses was compared to singleplex RT-qPCR designed specifically for each virus and was assessed using multiple virus isolates from diverse geographical regions and citrus species as well as graft-inoculated citrus plants infected with various combination of the three viruses. No significant difference in detection limits was found and specificity was not affected by the inclusion of the three assays in a multiplex RT-qPCR reaction. Comparison of the viral load for each virus using singleplex and multiplex RT-qPCR assays, revealed no significant differences between the two assays in virus detection. No significant difference in Cq values was detected when using one-step and two-step multiplex RT-qPCR detection formats. Optimizing the RNA extraction technique for citrus tissues and testing the quality of the extracted RNA using RT-qPCR targeting the cytochrome oxidase citrus gene as an RNA specific internal control proved to generate better diagnostic assays. Results showed that the developed multiplex RT-qPCR can streamline viruses testing of citrus nursery stock by replacing three separate singleplex assays, thus reducing time and labor while retaining the same sensitivity and specificity. The three targeted RNA viruses are regulated pathogens for California's mandatory "Section 3701: Citrus Nursery Stock Pest Cleanliness Program". Adopting a compatible multiplex RT-qPCR testing protocol for these viruses as well as other RNA and DNA regulated pathogens will provide a valuable alternative tool for virus detection and efficient program implementation.
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34
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Tsakogiannis D, Papacharalampous M, Toska E, Kyriakopoulou Z, Dimitriou TG, Ruether IGA, Komiotis D, Markoulatos P. Duplex Real-time PCR assay and SYBR green I melting curve analysis for molecular identification of HPV genotypes 16, 18, 31, 35, 51 and 66. Mol Cell Probes 2014; 29:13-8. [PMID: 25281890 DOI: 10.1016/j.mcp.2014.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/03/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
Long-term infection with high-risk HPV genotypes is the leading cause of cervical cancer. In the present study a Duplex Real-time PCR assay was developed in order to identify HPV types 16, 18, 31, 35, 51 and 66 in three reactions, through SYBR green I melting curve analysis. The method utilizes type-specific primer sets that allowed the amplification of highly conserved regions of L1 gene. Reconstitution experiments were conducted by using HPV DNA plasmids in order to determine the sensitivity of the assay. The newly designed assay has a limit of detection of 10 copies per reaction. The most prevalent HPV genotype in single and in multiple HPV infections was HPV16 followed by HPV18, HPV51, HPV31, HPV35 and HPV66. The proposed method is a simple, specific, sensitive and cost-effective assay that can be easily incorporated in small and medium size laboratories for the rapid identification of the most clinically important HPV genotypes.
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Affiliation(s)
- D Tsakogiannis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - M Papacharalampous
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - E Toska
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - Z Kyriakopoulou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - T G Dimitriou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - I G A Ruether
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - D Komiotis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - P Markoulatos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece.
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Álvarez-Sandoval BA, Manzanilla LR, Montiel R. Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis. PLoS One 2014; 9:e104629. [PMID: 25098828 PMCID: PMC4123986 DOI: 10.1371/journal.pone.0104629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.
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Affiliation(s)
- Brenda A. Álvarez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Linda R. Manzanilla
- Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
- * E-mail:
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36
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Burchard PR, Abou Tayoun AN, Scherer A, Tsongalis GJ. A rapid RT-PCR assay for the detection of HIV-1 in human plasma specimens. Exp Mol Pathol 2014; 97:111-5. [PMID: 24945443 DOI: 10.1016/j.yexmp.2014.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 10/25/2022]
Abstract
INTRODUCTION The CDC estimates that there are currently over 1million people living with human immunodeficiency virus (HIV-1) in the United States, with new cases increasing by approximately 50,000 each year. HIV-1 consists of four distinct groups: the major M group, and the rare N, O, and P groups, each comprising of various subtypes. Without proper care, HIV-1 can lead to cardiovascular, kidney, and liver diseases, cancer, and rapid progression into acquired immune deficiency syndrome (AIDS). Here, we describe a novel, rapid, and highly sensitive assay for the detection of HIV-1 using intercalating dye based RT-PCR and melt curve analysis. MATERIALS AND METHODS We designed an RT-PCR assay for the detection of the major M subtypes in addition to the rare (O, N, and P) HIV-1 groups, as well as an extraction/RT-PCR control, using melt curve analysis. Viral RNA was extracted using the automated Qiagen EZ1 robotic system (Qiagen, Valencia, CA). To establish the limit of detection (LOD) for this assay, we diluted the AcroMetrix HIV-1 panel (LifeTechnologies, Grand Island, NY) to concentrations ranging from 25 to 500 copies/ml. Armored RNA BCR/ABL b3/a2 (Asuragen, Austin, Texas) was used as our extraction and RT-PCR control. Specificity and accuracy were assessed by testing plasma specimens from 48 anonymized patients negative for HIV-1. RESULTS This assay has a turnaround time of less than 2.5h and has a limit of detection of 50 copies/ml of plasma. Our assay also demonstrated 100% concordance with 53 previously quantified plasma patient specimens, including 48 negative samples and 5 positive samples. HIV-1 and our extraction/RT-PCR control were consistently identified at 79 °C and 82.5 °C, respectively. CONCLUSIONS We developed a comprehensive, easy to use assay for the detection of HIV-1 in human plasma. Our assay combines a rapid and cost-effective method for molecular diagnostics with the versatility necessary for widespread laboratory use. These performance characteristics make this HIV-1 detection assay highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Paul R Burchard
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Ahmad N Abou Tayoun
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Axel Scherer
- Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Gregory J Tsongalis
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States.
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Hanaki KI, Ike F, Kajita A, Yasuno W, Yanagiba M, Goto M, Sakai K, Ami Y, Kyuwa S. A broadly reactive one-step SYBR Green I real-time RT-PCR assay for rapid detection of murine norovirus. PLoS One 2014; 9:e98108. [PMID: 24847970 PMCID: PMC4029972 DOI: 10.1371/journal.pone.0098108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/28/2014] [Indexed: 11/20/2022] Open
Abstract
A one-step SYBR Green I real-time RT-PCR assay was developed for the detection and quantification of a broad range of murine noroviruses (MNVs). The primer design was based on the multiple sequence alignments of 101 sequences of the open reading frame (ORF)1−ORF2 junction of MNV. The broad reactivity and quantitative capacity of the assay were validated using 7 MNV plasmids. The assay was completed within 1 h, and the reliable detection limit was 10 copies of MNV plasmid or 0.063 median tissue culture infective doses per milliliter of RAW264 cell culture-propagated viruses. The diagnostic performance of the assay was evaluated using 158 mouse fecal samples, 91 of which were confirmed to be positive. The melting curve analysis demonstrated the diversity of MNV in the samples. This is the first report of a broadly reactive one-step SYBR Green I real-time RT-PCR assay for detecting of MNVs. The rapid and sensitive performance of this assay makes it a powerful tool for diagnostic applications.
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Affiliation(s)
- Ken-Ichi Hanaki
- Department of Laboratory Animal Medicine, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
- Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
- * E-mail:
| | - Fumio Ike
- Experimental Animal Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Ayako Kajita
- Experimental Animal Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Wataru Yasuno
- Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
| | - Misato Yanagiba
- Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
| | - Motoki Goto
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kouji Sakai
- Department of Virology III, National Institute of Infectious Diseases (NIID), Musashimurayama, Tokyo, Japan
| | - Yasushi Ami
- Division of Experimental Animal Research, NIID, Shinjuku, Tokyo, Japan
| | - Shigeru Kyuwa
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
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Simultaneous Detection of Salmonella, Listeria monocytogenes, and Staphylococcus aureus by Multiplex Real-Time PCR Assays Using High-Resolution Melting. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9875-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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García JA, Glasa M, Cambra M, Candresse T. Plum pox virus and sharka: a model potyvirus and a major disease. MOLECULAR PLANT PATHOLOGY 2014; 15:226-41. [PMID: 24102673 PMCID: PMC6638681 DOI: 10.1111/mpp.12083] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
TAXONOMIC RELATIONSHIPS Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains. GEOGRAPHICAL DISTRIBUTION First discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents. GENOMIC STRUCTURE Typical of potyviruses, the PPV genome is a positive-sense single-stranded RNA (ssRNA), with a protein linked to its 5' end and a 3'-terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N-PIPO is predicted to be produced by a translational frameshift. PATHOGENICITY FEATURES PPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner. SOURCES OF RESISTANCE A few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, 'HoneySweet', transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.
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Affiliation(s)
- Juan Antonio García
- Departmento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Okino CH, Alessi AC, Montassier MDFS, Rosa AJDM, Wang X, Montassier HJ. Humoral and cell-mediated immune responses to different doses of attenuated vaccine against avian infectious bronchitis virus. Viral Immunol 2013; 26:259-67. [PMID: 23865943 DOI: 10.1089/vim.2013.0015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The antibody and cellular immune responses against infectious bronchitis virus (IBV) were evaluated at mucosal sites of chickens after immunization with various doses of an attenuated vaccine at 1 day of age. The correlation of these immune responses with protection of tracheal tissues was evaluated after experimental infection of these birds. Significantly reduced tracheal pathologic effects, measured according to ciliostasis and histology lesions, and reduced viral load were observed only in the full-dose vaccinated group at 5 days post-infection (dpi), while incomplete protection was observed for the subdose vaccinated groups. Moreover, birds of vaccinated groups, especially with full dose, developed higher levels of lachrymal IBV-specific IgG and IgA and increased the expression of cell-mediated immunity (CMI) genes, such as gamma interferon (IFNγ), CD8+ T cell marker, and granzyme homolog A more rapidly. In addition, these humoral and cellular immune responses evaluated at mucosal sites correlated significantly with tracheal protection against homologous IBV challenge in a vaccine dose-dependent manner. The results indicate that IgG, IgA and CD8+ T cell responses developed at mucosal sites after IBV vaccination of day-old chicks, could be taken as good correlates of protection against this virus.
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Affiliation(s)
- Cintia Hiromi Okino
- Laboratory of Immunology and Virology, Department of Veterinary Pathology, Universidade Estadual Paulista, Jaboticabal, SP, Brazil.
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41
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Use of tissue culture techniques for producing virus-free plant in garlic and their identification through real-time PCR. ScientificWorldJournal 2013; 2013:781282. [PMID: 23935432 PMCID: PMC3725790 DOI: 10.1155/2013/781282] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/09/2013] [Indexed: 11/17/2022] Open
Abstract
This study was performed for comparison of meristem culture technique with shoot tip culture technique for obtaining virus-free plant, comparison of micropropagation success of two different nutrient media, and determination of effectiveness of real-time PCR assay for the detection of viruses. Two different garlic species (Allium sativum and Allium tuncelianum) and two different nutrient media were used in this experiment. Results showed that Medium 2 was more successful compared to Medium 1 for both A. tuncelianum and A. sativum (Kastamonu garlic clone). In vitro plants obtained via meristem and shoot tip cultures were tested for determination of onion yellow dwarf virus (OYDV) and leek yellow stripe virus (LYSV) through real-time PCR assay. In garlic plants propagated via meristem culture, we could not detect any virus. OYDV and LYSV viruses were detected in plants obtained via shoot tip culture. OYDV virus was observed in amount of 80% and 73% of tested plants for A. tuncelianum and A. sativum, respectively. LYSV virus was found in amount of 67% of tested plants of A. tuncelianum and in amount of 87% of tested plants of A. sativum in this study.
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Acevedo AM, Perera CL, Vega A, Ríos L, Coronado L, Relova D, Frías MT, Ganges L, Núñez JI, Pérez LJ. A duplex SYBR Green I-based real-time RT-PCR assay for the simultaneous detection and differentiation of Massachusetts and non-Massachusetts serotypes of infectious bronchitis virus. Mol Cell Probes 2013; 27:184-92. [PMID: 23810983 DOI: 10.1016/j.mcp.2013.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/13/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
Infectious bronchitis is a highly contagious viral disease of poultry caused by infectious bronchitis virus (IBV) and is considered one of the most economically important viral diseases of chickens. Control of IBV has been attempted using live attenuated and inactivated vaccines. Live attenuated vaccines of the Massachusetts (Mass.) serotype are the most commonly used for this purpose. Due to the continuous emergence of new variants of the infectious bronchitis virus, the identification of the type of IBV causing an outbreak in commercial poultry is important in the selection of the appropriate vaccine(s) capable of inducing a protective immune response. The present work was aimed at developing and evaluating a duplex SYBR Green I-based real-time RT-PCR (rRT-PCR) assay for the simultaneous detection and differentiation of Mass. and non-Mass. serotypes of IBV. The duplex rRT-PCR yielded curves of amplification with two specific melting curves (Tm1 = 83 °C ± 0.5 °C and Tm2 = 87 °C ± 0.5 °C) and only one specific melting peak (Tm = 87 °C ± 0.5 °C) when the IBV Mass. serotype and IBV non-Mass. serotype strains were evaluated, respectively. The detection limit of the assay was 8.2 gene copies/μL based on in vitro transcribed RNA and 0.1 EID50/mL. The assay was able to detect all the IBV strains assessed and discriminated well among the IBV Mass. and the IBV non-Mass. serotypes strains. In addition, amplification curves were not obtained with any of the other viruses tested. From the 300 field samples tested, the duplex rRT-PCR yielded a total of 80 samples that were positive for IBV (26.67%), 73 samples identified as the IBV Mass. serotype and seven samples as identified as the IBV non-Mass. serotype. A comparison of the performance of test as assessed with field samples revealed that the duplex rRT-PCR detected a higher number of IBV-positive samples than when conventional RT-PCR or virus isolation tests were used. The duplex rRT-PCR presented here is a useful tool for the rapid identification of outbreaks and for surveillance programmes during IB-suspected cases, particularly in countries with a vaccination control programme.
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Affiliation(s)
- Ana M Acevedo
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of The Caribean Region, Carretera de Jamaica, San José de las Lajas, La Habana 32700, Cuba
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43
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Real-time multiplex RT-PCR for the simultaneous detection of the five main grapevine viruses. J Virol Methods 2013; 188:21-4. [DOI: 10.1016/j.jviromet.2012.11.034] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/14/2012] [Accepted: 11/26/2012] [Indexed: 11/21/2022]
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44
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Sochor J, Babula P, Adam V, Krska B, Kizek R. Sharka: the past, the present and the future. Viruses 2012; 4:2853-901. [PMID: 23202508 PMCID: PMC3509676 DOI: 10.3390/v4112853] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 10/25/2012] [Accepted: 10/30/2012] [Indexed: 12/16/2022] Open
Abstract
Members the Potyviridae family belong to a group of plant viruses that are causing devastating plant diseases with a significant impact on agronomy and economics. Plum pox virus (PPV), as a causative agent of sharka disease, is widely discussed. The understanding of the molecular biology of potyviruses including PPV and the function of individual proteins as products of genome expression are quite necessary for the proposal the new antiviral strategies. This review brings to view the members of Potyviridae family with respect to plum pox virus. The genome of potyviruses is discussed with respect to protein products of its expression and their function. Plum pox virus distribution, genome organization, transmission and biochemical changes in infected plants are introduced. In addition, techniques used in PPV detection are accentuated and discussed, especially with respect to new modern techniques of nucleic acids isolation, based on the nanotechnological approach. Finally, perspectives on the future of possibilities for nanotechnology application in PPV determination/identification are outlined.
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Affiliation(s)
- Jiri Sochor
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; (J.S.); (P.B.); (V.A.); (R.K.)
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1-3, CZ-612 42, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Petr Babula
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; (J.S.); (P.B.); (V.A.); (R.K.)
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1-3, CZ-612 42, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; (J.S.); (P.B.); (V.A.); (R.K.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Boris Krska
- Department of Fruit Growing, Faculty of Horticulture, Mendel University in Brno, Valticka 337, CZ-691 44 Lednice, Czech Republic;
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; (J.S.); (P.B.); (V.A.); (R.K.)
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
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Cheng J, Jiang Y, Rao P, Wu H, Dong Q, Wu Z, Ding X, Guo J. Development of a single-tube multiplex real-time PCR for detection and identification of five pathogenic targets by using melting-curve analysis with EvaGreen. Arch Virol 2012; 158:379-86. [PMID: 23053522 DOI: 10.1007/s00705-012-1493-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/21/2012] [Indexed: 12/18/2022]
Abstract
SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye. Preferential binding of SG during PCR and inhibition of PCR often result in failure to detect multiple amplicons in multiplex reactions. In the present study, a novel single-tube, multiplex real-time PCR with EvaGreen dye (EG) was developed and evaluated for simultaneous detection of pathogenic targets by using five potato viruses as models. The PCR products obtained using five sets of specific primers were analyzed by melting curve analysis. The assay could specifically detect and differentiate the five potato viruses by producing a distinct peak for each amplification product and exhibited a high reproducibility with coefficients of variation from 0.01 to 0.25 %. Detection sensitivity of the assay ranged from 100 to 500 copies/μL for each virus. The results of this study demonstrate that multiplex real-time PCR and melting-curve analysis with EG is a sensitive, specific and inexpensive method for simultaneous detection of multiple pathogens.
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Affiliation(s)
- Juhui Cheng
- College of Life Sciences, Zhejiang Sci-Tech University, 2nd street, Xiasha, Hangzhou, 310018, China
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46
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Pérez LJ, Perera CL, Frías MT, Núñez JI, Ganges L, de Arce HD. A multiple SYBR Green I-based real-time PCR system for the simultaneous detection of porcine circovirus type 2, porcine parvovirus, pseudorabies virus and Torque teno sus virus 1 and 2 in pigs. J Virol Methods 2011; 179:233-41. [PMID: 22119629 DOI: 10.1016/j.jviromet.2011.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 10/26/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
Abstract
Multiple viral infections are common in pigs under intensive production conditions. All five of the viruses included in this study are associated with multifactorial diseases that cause significant economic losses in swine farming worldwide. The development is described of a novel multiple real-time PCR system based on the use of SYBR Green I that allows the simultaneous detection and differentiation of porcine circovirus 2 (PCV-2), porcine parvovirus (PPV), pseudorabies virus (PRV) and Torque teno sus virus species 1 and 2 (TTSuV1 and TTSuV2) in pigs. The method was able to distinguish between all five viral agents, and tests of other DNA viruses proved the specificity of the system. The multiple real-time PCR system was sensitive, as the limits of detection ranged from 3.65×10(3) to 5.04×10(3) copies of DNA template per reaction. The coefficients of variation were low for both intra-assay and inter-assay variability. In addition, the results of the multiple real-time PCR system tests were 100% consistent with previous results based on specific PCR assay testing of field samples. This method could be a useful tool for epidemiological studies and disease management.
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Affiliation(s)
- Lester J Pérez
- Centro Nacional de Sanidad Agropecuria (CENSA), La Habana, Cuba
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47
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Mutant enrichment with 3'-modified oligonucleotides a practical PCR method for detecting trace mutant DNAs. J Mol Diagn 2011; 13:657-68. [PMID: 21979247 DOI: 10.1016/j.jmoldx.2011.07.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Revised: 06/04/2011] [Accepted: 07/06/2011] [Indexed: 01/16/2023] Open
Abstract
Many clinical situations necessitate highly sensitive and reliable molecular assays; however, the achievement of such assays remains a challenge due to the inherent limitations of molecular testing methods. Here, we describe a simple and inexpensive enrichment technique that we call mutant enrichment with 3'-modified oligonucleotides (MEMO). The method is based on the use of a 3'-modified oligonucleotide primer that blocks extension of the normal allele but enables extension of the mutated allele. The performance of the technique was evaluated with respect to its ability to detect common cancer mutations in the EGFR, KRAS, BRAF, TP53, JAK2, and NPM1 genes. We achieved sensitivities of 10(-2) to 10(-6) using downstream Sanger sequencing, depending on the concentrations and thermodynamics of the primers. MEMO may be applicable to the quantitative real-time PCR platform and other downstream assays. This technique may be practically applicable to various medical situations.
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Kozina V, Cappallo-Obermann H, Gromoll J, Spiess AN. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis. PLoS One 2011; 6:e23174. [PMID: 21887237 PMCID: PMC3161745 DOI: 10.1371/journal.pone.0023174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 07/11/2011] [Indexed: 12/03/2022] Open
Abstract
Backgound Y-chromosomal microdeletions (YCMD) are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR) is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. Principal Findings The widely established “EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004)” were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. Significance With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.
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Affiliation(s)
- Viviana Kozina
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Jörg Gromoll
- Center for Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Andrej-Nikolai Spiess
- Department of Andrology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- * E-mail:
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Gias E, Johnston C, Keeling S, Spence RP, McDonald WL. Development of real-time PCR assays for detection of megalocytiviruses in imported ornamental fish. JOURNAL OF FISH DISEASES 2011; 34:609-618. [PMID: 21762172 DOI: 10.1111/j.1365-2761.2011.01274.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Megalocytiviruses have been associated globally with severe systemic disease and economic loss in farmed food fish and ornamental fish. The viruses have been spread internationally by translocation of live fish. In New Zealand, megalocytiviruses are regarded as exotic. A potential pathway for introduction has been identified, namely imported ornamental fish. In the present study, real-time PCR assays were developed for detection of megalocytiviruses using a conserved major capsid protein gene. A SYBR green assay was developed to target all known megalocytiviruses. A second real-time PCR assay using a molecular beacon was developed to specifically target gourami, Trichogaster trichopterus, iridovirus, a species of iridovirus previously linked to ornamental fish imports in Australia. The analytical sensitivity for the SYBR green and molecular beacon assays were 10 and 100 fg, respectively. The analytical specificity of the real-time PCR assays determined using genomic DNA templates from three target viruses, 12 non-target viruses and 25 aquatic bacterial species were 100%. The intra-run and inter-run coefficients of variation of both assays were <5%. The real-time PCR assays developed in this study provide rapid, sensitive, and specific detection of megalocytiviruses and gourami iridovirus.
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Affiliation(s)
- E Gias
- Investigation & Diagnostic Centre, Biosecurity New Zealand, Ministry of Agriculture and Forestry, New Zealand.
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50
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SYTO dyes and EvaGreen outperform SYBR Green in real-time PCR. BMC Res Notes 2011; 4:263. [PMID: 21798028 PMCID: PMC3162529 DOI: 10.1186/1756-0500-4-263] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/28/2011] [Indexed: 11/22/2022] Open
Abstract
Background Real-time PCR can be carried out using either probes or DNA dyes. SYBR Green has been used the most, but it suffers from several drawbacks. Numerous other DNA dyes are commercially available, but with limited structural information. Dye behavior in real time PCR is difficult to predict, so empirical data are needed. In the work described here, a panel of 23 different DNA dyes--including green, orange, and red SYTO dyes, EvaGreen, and SYBR Green--were evaluated with respect to their performance in real time PCR. Findings Data were analyzed for reaction inhibition, effects on amplicon melting temperature, fluorescent signal strength, and reaction efficiency. This is the first report of reaction efficiency using alternatives to SYBR Green. Results indicated substantial variation in performance even within the SYTO dye family. EvaGreen and the SYTO dyes 13, 16, 80, and 82 performed better than SYBR Green in general, and high reaction efficiencies can be achieved using these dyes. Conclusions Empirical data were generated for 23 DNA dyes. This paper confirms and extends previous findings that among commercially available DNA dyes, EvaGreen and certain SYTO dyes are the most desirable alternatives to the commonly used SYBR Green in real-time PCR.
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