201
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Real-time PCR for specific detection of three phytoplasmas from the apple proliferation group. Methods Mol Biol 2013; 938:269-81. [PMID: 22987423 DOI: 10.1007/978-1-62703-089-2_23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this chapter, we describe a real-time PCR detection system for fast, reliable, specific, and sensitive detection and discrimination of 'Candidatus Phytoplasma mali', 'Ca. P. prunorum', and 'Ca. P. pyri' from the 16SrX (apple proliferation-AP) group. These phytoplasmas are causal agents of fruit tree diseases within the Rosaceae family, namely apple proliferation, European stone fruit yellows, and pear decline. The assays use (hydrolysis) TaqMan(®) minor groove binder probes. The panel of assays comprises the same set of primers and specific probes for species-specific amplification, and an additional set of primers and probe for 18S rRNA as an endogenous quality control of DNA extraction. The assays described can be used in routine phytoplasma surveys and in certification programmes.
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202
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Abstract
Quantitative PCR (qPCR), also called real-time PCR or quantitative real-time PCR, is a PCR-based technique that couples amplification of a target DNA sequence with quantification of the concentration of that DNA species in the reaction. This method enables calculation of the starting template concentration and is therefore a frequently used analytical tool in evaluating DNA copy number, viral load, SNP detection, and allelic discrimination. When preceded by reverse-transcription PCR, qPCR is a powerful tool to measure mRNA expression and is the gold standard for microarray gene expression data confirmation. Given the broad applications of qPCR and the many technical variations that have been developed, a brief survey of qPCR, including technical background, available chemistries, and data analysis techniques will provide a framework for both experimental design and evaluation.
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Affiliation(s)
- Jessica S Dymond
- The High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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203
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Wilbur AE, Ford SE, Gauthier JD, Gomez-Chiarri M. Quantitative PCR assay to determine prevalence and intensity of MSX (Haplosporidium nelsoni) in North Carolina and Rhode Island oysters Crassostrea virginica. DISEASES OF AQUATIC ORGANISMS 2012; 102:107-118. [PMID: 23269385 DOI: 10.3354/dao02540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The continuing challenges to the management of both wild and cultured eastern oyster Crassostrea virginica populations resulting from protozoan parasites has stimulated interest in the development of molecular assays for their detection and quantification. For Haplosporidium nelsoni, the causative agent of multinucleated sphere unknown (MSX) disease, diagnostic evaluations depend extensively on traditional but laborious histological approaches and more recently on rapid and sensitive (but not quantitative) end-point polymerase chain reaction (PCR) assays. Here, we describe the development and application of a quantitative PCR (qPCR) assay for H. nelsoni using an Applied Biosystems TaqMan® assay designed with minor groove binder (MGB) probes. The assay was highly sensitive, detecting as few as 20 copies of cloned target DNA. Histologically evaluated parasite density was significantly correlated with the quantification cycle (Cq), regardless of whether quantification was categorical (r2 = 0.696, p < 0.0001) or quantitative (r2 = 0.797, p < 0.0001). Application in field studies conducted in North Carolina, USA (7 locations), revealed widespread occurrence of the parasite with moderate to high intensities noted in some locations. In Rhode Island, USA, application of the assay on oysters from 2 locations resulted in no positives.
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Affiliation(s)
- Ami E Wilbur
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28409, USA.
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204
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Li Z, Cui L, Zhou M, Qi X, Bao C, Hu J, Shan J, Wu B, Wang S, Guo X, Jiao Y, Tang F, Wang H. Development and application of a one-step real-time RT-PCR using a minor-groove-binding probe for the detection of a novel bunyavirus in clinical specimens. J Med Virol 2012; 85:370-7. [DOI: 10.1002/jmv.23415] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2012] [Indexed: 11/06/2022]
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205
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Abstract
During the past decade many new molecular methods for DNA and RNA analysis have emerged. The most popular thus far have been SSCP, HET, CMC, DGGE, RFLP or ASA, which have now been replaced by methods that are more cost effective and less time consuming. Real-time amplification techniques and particularly those with the capacity of multiplexing have become commonly used in laboratory practice. Novel screening methods enable the very rapid examination of large patients series. Use of liquid handling robotics applied to the isolation of DNA or RNA, the normalisation of sample concentration, and standardization of target amplification by PCR have also contributed to a reduced risk of sample contamination and have resulted in laboratory analysis being easier and faster. The aim of this study is the introduction of a few modern techniques, most commonly used in detection of genetic predisposition to cancer.
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206
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Zhelev DV, Hunt M, Le A, Dupuis C, Ren S, Gibbons HS. Effect of the Bacillus atrophaeus subsp. globigii Spo0F H101R mutation on strain fitness. Appl Environ Microbiol 2012; 78:8601-10. [PMID: 23042165 PMCID: PMC3502920 DOI: 10.1128/aem.01922-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/24/2012] [Indexed: 11/20/2022] Open
Abstract
Sporulation is a critical developmental process in Bacillus spp. that, once initiated, removes the possibility of further growth until germination. Therefore, the threshold conditions triggering sporulation are likely to be subject to evolutionary constraint. Our previous studies revealed two spontaneous hypersporulating mutants of Bacillus atrophaeus subsp. globigii, both containing point mutations in the spo0F gene. One of these strains (Detrick-2; contains the spo0F101 allele with a C:T [His101Arg] substitution) had been deliberately selected in the early 1940s as an anthrax surrogate. To determine whether the experimental conditions used during the selection of the "military" strains could have supported the emergence of hypersporulating variants, the relative fitness of strain Detrick-2 was measured in several experimental settings modeled on experimental conditions employed during its development in the 1940s as a simulant. The congenic strain Detrick-1 contained a wild-type spo0F gene and sporulated like the wild-type strain. The relative fitness of Detrick-1 and Detrick-2 was evaluated in competition experiments using quantitative single nucleotide polymorphism (SNP)-specific real-time PCR assays directed at the C:T substitution. The ancestral strain Detrick-1 had a fitness advantage under all conditions tested except when competing cultures were subjected to frequent heat shocks. The hypersporulating strain gained the maximum fitness advantage when cultures were grown at low oxygen tension and when heat shock was applied soon after the formation of the first heat-resistant spores. This is interpreted as gain of fitness by the hypersporulating strain in fast-changing fluctuating environments as a result of the increased rate of switching to the sporulating phenotype.
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Affiliation(s)
- Doncho V. Zhelev
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Mia Hunt
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Anna Le
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Christopher Dupuis
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Suelynn Ren
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Henry S. Gibbons
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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207
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Minor groove binder modification of widely used TaqMan probe for hepatitis E virus reduces risk of false negative real-time PCR results. J Virol Methods 2012; 186:157-60. [DOI: 10.1016/j.jviromet.2012.07.027] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/22/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022]
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208
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Gévaudan G, Hamelin J, Dabert P, Godon JJ, Bernet N. Homogeneity and synchronous dynamics of microbial communities in particulate biofilms: from major populations to minor groups. Microbes Environ 2012; 27:142-8. [PMID: 22791046 PMCID: PMC4036020 DOI: 10.1264/jsme2.me11264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Natural or engineered microbial populations often show variations over time. These variations may be due to environmental fluctuations or intrinsic factors. Thus, studying the dynamics of microbial diversity for different communities living in a spatially homogeneous landscape is of interest. As a model ecosystem, nitrifying biofilm communities were grown in a two litre inverse turbulent bed reactor (ITBR) containing an estimated 200 million small particles (about 150 μm in diameter). Each particulate biofilm is considered as a distinct community growing in the neighborhood of other similar particles, in a homogeneous and well-controlled environmental context. A molecular approach was adopted to test how microbial community structures might evolve: either in synchrony, converging or diverging. The shape of biofilm was observed by microscopy for each particle. The biomass content was evaluated by quantitative PCR and showed similar values for each particle. The microbial community structure was evaluated by Capillary Electrophoresis-Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting and showed extraordinary homogeneity between particles, even though transitory community structures were observed when reactor operating conditions were modified. This homogeneity was observed for the Bacteria primer set but, more interestingly, was also observed when minor non-nitrifying bacteria making up the biofilm, representing about 5% and 10% of total cells, were targeted.
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Affiliation(s)
- Gaëlle Gévaudan
- INRA, UR50, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, Narbonne, F-11100, France
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209
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Abstract
Technology for infectious agent detection continues to evolve, particularly molecular methods that first emerged in the mid-1970s. The goals of new technology in diagnostics, whether in humans or in animals, including poultry, are to achieve the highest sensitivity and specificity possible to accurately identify the infection status of an individual or flock in the shortest time possible. Ease of use, low cost and increased information from a single test (e.g. multiplexing) are also critical areas frequently targeted for improvement. New tests and modifications of current tests are reported often, and diagnostic tests are now commonly developed by commercial companies. As one would expect, most advances in diagnostic technology are applied first to human health, and then may be adapted to animal health if practical. In the present review the trends and novel innovative technologies in primarily viral diagnostics are reviewed and the practicality of these methods and application for poultry health are discussed briefly. Also, influenza will seem to be over-represented in viral diagnostics since it is frequently used as a proof-of-concept target for novel technology due to its importance for animal and public health. Finally, the review is intended to be a brief survey of some of the innovative diagnostic technologies reported in recent years. It is not entirely comprehensive of all technology and the author makes no claims or endorsements of any of the technology or products mentioned.
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Affiliation(s)
- Erica Spackman
- Southeast Poultry Research Laboratory, USDA-ARS, Athens, GA 30605, USA.
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210
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Fringuelli E, Gordon AW, Rodger H, Welsh MD, Graham DA. Detection of Neoparamoeba perurans by duplex quantitative Taqman real-time PCR in formalin-fixed, paraffin-embedded Atlantic salmonid gill tissues. JOURNAL OF FISH DISEASES 2012; 35:711-724. [PMID: 22804799 DOI: 10.1111/j.1365-2761.2012.01395.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The development and the application of a quantitative duplex real-time PCR for the detection of Neoparamoeba perurans and the elongation factor α 1 gene (ELF) of Atlantic salmon, Salmo salar L., and rainbow trout, Oncorhynchus mykiss (Walbaum), are described. A set of primers and probe was designed to amplify a 139-bp fragment specific to the N. perurans 18S rRNA gene. The test was shown to be very sensitive, being able to detect as little as 13.4 DNA copies per μL corresponding to 0.15 fg of template DNA. In addition, the reaction that detected N. perurans was found to have a high degree of repeatability and reproducibility, to have a linear dynamic range (R(2 ) = 0.999) extending over 5 log(10) dilutions and to have a high efficiency (104%). The assay was applied to DNA samples extracted from 48 formalin-fixed, paraffin-embedded (FFPE) salmon gill tissues showing varying degrees of gill histopathology and amoebic gill disease (AGD)-type histopathology ranging from absent to severe (each scored 0-3). Neoparamoeba perurans DNA was detected in all the blocks where AGD-type histopathology was diagnosed microscopically and in 43.6% of the blocks showing signs of gill pathology. The association between parasitic load and gill histopathology and AGD-type histopathology severity was also investigated. This study also describes the development and the application of a second real-time PCR for the generic detection of Neoparamoeba spp., Page, 1987. A set of primers and probe conserved among the Neoparamoeba spp. was designed to amplify a 150-bp fragment within the 18S rRNA gene. Applied to N. perurans-negative gill tissues, the method was used to exclude the presence of other Neoparamoeba spp. in those blocks where gill pathology was observed microscopically.
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Affiliation(s)
- E Fringuelli
- Veterinary Sciences Division, Agri-food and Biosciences Institute of Northern Ireland, Belfast, UK.
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211
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Development of TaqMan probe-based insulated isothermal PCR (iiPCR) for sensitive and specific on-site pathogen detection. PLoS One 2012; 7:e45278. [PMID: 23049781 PMCID: PMC3458002 DOI: 10.1371/journal.pone.0045278] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/15/2012] [Indexed: 12/23/2022] Open
Abstract
Insulated isothermal PCR (iiPCR), established on the basis of Ralyeigh-Bénard convection, is a rapid and low-cost platform for nucleic acid amplification. However, the method used for signal detection, namely gel electrophoresis, has limited the application of iiPCR. In this study, TaqMan probe-based iiPCR system was developed to obviate the need of post-amplification processing. This system includes an optical detection module, which was designed and integrated into the iiPCR device to detect fluorescent signals generated by the probe. TaqMan probe-iiPCR assays targeting white spot syndrome virus (WSSV) and infectious myonecrosis virus were developed for preliminary evaluation of this system. Significant elevation of fluorescent signals was detected consistently among positive iiPCR reactions in both assays, correlating with amplicon detection by gel electrophoresis analysis. After condition optimization, a threshold value of S/N (fluorescent intensityafter/fluorescent intensitybefore) for positive reactions was defined for WSSV TaqMan probe-iiPCR on the basis of 20 blank reactions. WSSV TaqMan probe-iiPCR generated positive S/Ns from as low as 101 copies of standard DNA and lightly infected Litopenaeus vannamei. Compared with an OIE-certified nested PCR, WSSV TaqMan probe-iiPCR showed a sensitivity of 100% and a specificity of 96.67% in 120 WSSV-free or lightly infected shrimp samples. Generating positive signals specifically and sensitively, TaqMan probe-iiPCR system has a potential as a low-cost and rapid on-site diagnostics method.
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212
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López-Andreo M, Aldeguer M, Guillén I, Gabaldón JA, Puyet A. Detection and quantification of meat species by qPCR in heat-processed food containing highly fragmented DNA. Food Chem 2012. [DOI: 10.1016/j.foodchem.2012.02.111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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213
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Fringuelli E, Savage PD, Gordon A, Baxter EJ, Rodger HD, Graham DA. Development of a quantitative real-time PCR for the detection of Tenacibaculum maritimum and its application to field samples. JOURNAL OF FISH DISEASES 2012; 35:579-590. [PMID: 22724390 DOI: 10.1111/j.1365-2761.2012.01377.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The development and the application of a quantitative real-time PCR for the detection of Tenacibaculum maritimum are described. A set of primers and probe was designed to amplify a 155-bp fragment specific to the T. maritimum 16S rRNA gene. The test was shown to be very sensitive, able to detect as little as 4.8 DNA copies number μL(-1) . In addition, the assay was found to have a high degree of repeatability and reproducibility, with a linear dynamic range (R(2) = 0.999) extending over 6 log(10) dilutions and a high efficiency (100%). The assay was applied to DNA samples extracted from 48 formalin-fixed paraffin-embedded (FFPE) Atlantic salmon, Salmo salar, gill tissues showing varying degrees of gill pathology (scored 0-3) and from 26 jellyfish samples belonging to the species Phialella quadrata and Muggiaea atlantica. For each sample, the bacterial load was normalised against the level of the salmonid elongation factor alpha 1 (ELF) detected by a second real-time PCR using previously published primers and probe. Tenacibaculum maritimum DNA was detected in 89% of the blocks with no signs of gill disease as well as in 95% of the blocks with mild-to-severe gill pathology. Association between bacterial load and gill pathology severity was investigated. T. maritimum DNA was detected at low level in four of the 26 jellyfish tested.
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Affiliation(s)
- E Fringuelli
- Veterinary Sciences Division, Agri-food and Biosciences Institute of Northern Ireland, Stormont, Belfast, UK.
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214
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Miszczycha SD, Ganet S, Duniere L, Rozand C, Loukiadis E, Thevenot-Sergentet D. Novel real-time PCR method to detect Escherichia coli O157:H7 in raw milk cheese and raw ground meat. J Food Prot 2012; 75:1373-81. [PMID: 22856560 DOI: 10.4315/0362-028x.jfp-11-498] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Raw milk, raw milk cheeses, and raw ground meat have been implicated in Escherichia coli O157:H7 outbreaks. Developing methods to detect these bacteria in raw milk and meat products is a major challenge for food safety. The aim of our study was to develop a real-time PCR assay to detect E. coli O157:H7 in raw milk cheeses and raw ground meat. Well-known primers targeting a mutation at position +93 of the uidA gene in E. coli O157:H7 were chosen, and a specific TaqMan-minor groove binder probe was designed. This probe targets another mutation, at position +191 of the uidA gene in E. coli O157:H7. The first step in the study was to evaluate the specificity of this probe with 156 different O157:H7/NM strains and 48 non-O157:H7/NM strains of E. coli. The sensitivity of the method was evaluated by pre- and postinoculation of cheeses and meat enrichments with different E. coli O157:H7 strains. All the E. coli O157:H7 isolates tested were positive, and none of the other bacteria were detected. Our results indicate that this method is sensitive enough to detect 10(2) E. coli O157:H7 isolates per ml of cheese or meat enrichment broth (24 h at 41.5° C) and is more sensitive than the International Organization for Standardization reference method. We can conclude that this new real-time PCR protocol is a useful tool for rapid, specific, and sensitive detection of E. coli O157:H7 in raw milk and raw ground meat products.
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Affiliation(s)
- Stéphane D Miszczycha
- Unité de Recherche CALITYSS/Equipe EMSA, VetAgro Sup, Université de Lyon, 1 avenue Claude Bourgelat, Marcy l'Etoile, France.
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215
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Multiplex real-time PCR assay for simultaneous detection of Omphalotus guepiniformis and Lentinula edodes. Biosci Biotechnol Biochem 2012; 76:1343-9. [PMID: 22785476 DOI: 10.1271/bbb.120090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A rapid multiplex real-time PCR assay was developed to achieve highly specific, simultaneous detection of two kinds of mushrooms, Omphalotus guepiniformis and Lentinula edodes. Primers and TaqMan minor groove binder probes were designed according to the internal transcribed spacers 1-5.8S region of rDNA and evaluated by the specificity for fruiting bodies of 17 O. guepiniformis, 16 L. edodes and samples from 57 other species. DNA extracts of all the target species had positive signals with no cross-reaction, the limit of detection being 0.00025 ng of DNA. Threshold cycle (Ct) values for raw and processed fruiting bodies and for fruiting bodies (1% (w/w)) mixed with foodstuffs or artificial gastric juice contents ranged from 17.16 to 26.60 for both examined species. This new assay proved specific to the target species, highly sensitive, and applicable to processed food samples and gastric juice contents, making it useful for rapidly identifying O. guepiniformis and L. edodes.
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216
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Kumar A, Zhang M, Zhu L, Liao RP, Mutai C, Hafsat S, Sherman DR, Wang MW. High-throughput screening and sensitized bacteria identify an M. tuberculosis dihydrofolate reductase inhibitor with whole cell activity. PLoS One 2012; 7:e39961. [PMID: 22768185 PMCID: PMC3386958 DOI: 10.1371/journal.pone.0039961] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 05/30/2012] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is a bacterial pathogen that claims roughly 1.4 million lives every year. Current drug regimens are inefficient at clearing infection, requiring at least 6 months of chemotherapy, and resistance to existing agents is rising. There is an urgent need for new drugs that are more effective and faster acting. The folate pathway has been successfully targeted in other pathogens and diseases, but has not yielded a lead drug against tuberculosis. We developed a high-throughput screening assay against Mtb dihydrofolate reductase (DHFR), a critical enzyme in the folate pathway, and screened a library consisting of 32,000 synthetic and natural product-derived compounds. One potent inhibitor containing a quinazoline ring was identified. This compound was active against the wild-type laboratory strain H37Rv (MIC99 = 207 µM). In addition, an Mtb strain with artificially lowered DHFR levels showed increased sensitivity to this compound (MIC99 = 70.7 µM), supporting that the inhibition was target-specific. Our results demonstrate the potential to identify Mtb DHFR inhibitors with activity against whole cells, and indicate the power of using a recombinant strain of Mtb expressing lower levels of DHFR to facilitate the discovery of antimycobacterial agents. With these new tools, we highlight the folate pathway as a potential target for new drugs to combat the tuberculosis epidemic.
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Affiliation(s)
- Anuradha Kumar
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Meng Zhang
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Linyun Zhu
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Reiling P. Liao
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Charles Mutai
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Shittu Hafsat
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- * E-mail: (DRS); (MWW)
| | - Ming-Wei Wang
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
- * E-mail: (DRS); (MWW)
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217
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Tomás G, Hernández M, Marandino A, Panzera Y, Maya L, Hernández D, Pereda A, Banda A, Villegas P, Aguirre S, Pérez R. Development and validation of a TaqMan-MGB real-time RT-PCR assay for simultaneous detection and characterization of infectious bursal disease virus. J Virol Methods 2012; 185:101-7. [PMID: 22728272 DOI: 10.1016/j.jviromet.2012.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/26/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
Rapid and reliable detection and classification of infectious bursal disease viruses (IBDVs) is of crucial importance for disease surveillance and control. This study presents the development and validation of a real-time RT-PCR assay to detect and discriminate very virulent (vv) from non-vv (classic and variant) IBDV strains. The assay uses two fluorogenic, minor groove-binding (MGB) TaqMan probes targeted to a single nucleotide polymorphism (SNP) embedded in a highly conserved genomic region. The analytical sensitivity of the assay was determined using serial dilutions of in vitro-transcribed RNA. The assay demonstrated a wide dynamic range between 10(2) and 10(8) standard RNA copies per reaction. Good reproducibility was also detected, with intra- and inter-assay coefficients of variation ranging from 0.13% to 2.23% and 0.26% to 1.92%, respectively. The assay detected successfully all the assessed vv, classical, and variant field and vaccine strains and correctly discriminated all vvIBDV strains from non-vvIBDV strains. Other common avian RNA viruses tested negative, indicating high specificity of the assay. The high sensitivity, rapidity, reproducibility, and specificity of the real-time RT-PCR assay make this method suitable for general and genotype-specific detection and quantitation.
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Affiliation(s)
- Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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218
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Wozney KM, Wilson PJ. Real-time PCR detection and quantification of elephantid DNA: Species identification for highly processed samples associated with the ivory trade. Forensic Sci Int 2012; 219:106-12. [DOI: 10.1016/j.forsciint.2011.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 12/12/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
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219
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Becker CAM, Ramos F, Sellal E, Moine S, Poumarat F, Tardy F. Development of a multiplex real-time PCR for contagious agalactia diagnosis in small ruminants. J Microbiol Methods 2012; 90:73-9. [PMID: 22579581 DOI: 10.1016/j.mimet.2012.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/23/2012] [Accepted: 04/25/2012] [Indexed: 10/28/2022]
Abstract
Contagious agalactia is an important disease worldwide that affects small ruminants. Clinical manifestations vary from mastitis, pneumonia, arthritis and keratoconjunctivitis to septicemia. Four mycoplasmal etiological agents have been identified: Mycoplasma (M.) agalactiae, M. mycoides subsp. capri, M. capricolum subsp. capricolum and M. putrefaciens. The current procedure for direct diagnosis, recommended by the World Organization for Animal Health, involves the isolation of one or several causative agents from clinical specimens and further time-consuming identification steps. The present study reports the development of a new multiplex real-time PCR (including an internal positive control) that detects all four pathogens simultaneously and distinguishes M. agalactiae from the others. First, intra- and inter-species polymorphisms of the two target house-keeping genes, namely polC and fusA, were analyzed to design primers and probes adapted to the diversity of currently circulating strains. The specificity and the sensitivity of the assay were then challenged and the limit of detection was found to be as low as 6 to 12 copies of the target genes. The assay requires further assessment on clinical specimens but its performances (notably low intra- and inter-assay variability) are already very promising for use in large-scale diagnosis and prophylactic surveys of contagious agalactia.
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Affiliation(s)
- Claire A M Becker
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants Anses VetAgro Sup, F-69280, Marcy l'Etoile, France.
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Yun T, Ni Z, Hua J, Ye W, Chen L, Zhang S, Zhang Y, Zhang C. Development of a one-step real-time RT-PCR assay using a minor-groove-binding probe for the detection of duck Tembusu virus. J Virol Methods 2012; 181:148-54. [DOI: 10.1016/j.jviromet.2012.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 11/15/2022]
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221
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Nübel U, Nitsche A, Layer F, Strommenger B, Witte W. Single-nucleotide polymorphism genotyping identifies a locally endemic clone of methicillin-resistant Staphylococcus aureus. PLoS One 2012; 7:e32698. [PMID: 22427866 PMCID: PMC3302872 DOI: 10.1371/journal.pone.0032698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/29/2012] [Indexed: 11/18/2022] Open
Abstract
We developed, tested, and applied a TaqMan real-time PCR assay for interrogation of three single-nucleotide polymorphisms that differentiate a clade (termed 't003-X') within the radiation of methicillin-resistant Staphylococcus aureus (MRSA) ST225. The TaqMan assay achieved 98% typeability and results were fully concordant with DNA sequencing. By applying this assay to 305 ST225 isolates from an international collection, we demonstrate that clade t003-X is endemic in a single acute-care hospital in Germany at least since 2006, where it has caused a substantial proportion of infections. The strain was also detected in another hospital located 16 kilometers away. Strikingly, however, clade t003-X was not found in 62 other hospitals throughout Germany nor among isolates from other countries, and, hence, displayed a very restricted geographical distribution. Consequently, our results show that SNP-typing may be useful to identify and track MRSA clones that are specific to individual healthcare institutions. In contrast, the spatial dissemination pattern observed here had not been resolved by other typing procedures, including multilocus sequence typing (MLST), spa typing, DNA macrorestriction, and multilocus variable-number tandem repeat analysis (MLVA).
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Affiliation(s)
- Ulrich Nübel
- Fachgebiet Nosokomiale Infektionen, Robert Koch-Institut, Wernigerode, Germany.
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Cammà C, Di Domenico M, Monaco F. Development and validation of fast Real-Time PCR assays for species identification in raw and cooked meat mixtures. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.08.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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223
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Wang LF, Daniels P. Diagnosis of henipavirus infection: current capabilities and future directions. Curr Top Microbiol Immunol 2012; 359:179-96. [PMID: 22481141 DOI: 10.1007/82_2012_215] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since the last major review on diagnosis of henipavirus infection about a decade ago, significant progress has been made in many different areas of test development, especially in the development of molecular tests using real-time PCR and many novel serological test platforms. In addition to provide an updated review of the current test capabilities, this review also identifies key future challenges in henipavirus diagnosis.
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Affiliation(s)
- Lin-Fa Wang
- CSRIO Livestock Industries, Australian Animal Health Laboratory, Geelong, VIC, Australia.
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224
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Pepino MY, Love-Gregory L, Klein S, Abumrad NA. The fatty acid translocase gene CD36 and lingual lipase influence oral sensitivity to fat in obese subjects. J Lipid Res 2011; 53:561-566. [PMID: 22210925 DOI: 10.1194/jlr.m021873] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The precise orosensory inputs engaged for dietary lipids detection in humans are unknown. We evaluated whether a common single nucleotide polymorphism (rs1761667) in the CD36 gene that reduces CD36 expression and the addition of orlistat, a lipase inhibitor, to reduce FA release from triacylglycerols (TGs), the main component of dietary fats, would attenuate fat orosensory sensitivity in humans. Twenty-one obese subjects with different rs1761667 genotypes (6 AA, 7 AG, and 8 GG) were studied on two occasions in which oleic acid and triolein orosensory detection thresholds were measured using emulsions prepared with and without orlistat. Subjects homozygous for the G-allele had 8-fold lower oral detection thresholds for oleic acid and triolein than subjects homozygous for the A allele, which associates with lower CD36 expression (P = 0.03). Thresholds for heterozygous subjects were intermediate. The addition of orlistat increased detection thresholds for triolein (log threshold = -0.3 ± 0.2 vs. 0.3 ± 0.1; P < 0.001) but not oleic acid (log threshold = -1.0 ± 0.2 vs. -0.8 ± 0.2; P > 0.2). In conclusion, this is the first experimental evidence for a role of CD36 in fat gustatory perception in humans. The data also support involvement of lingual lipase and are consistent with the concept that FA and not TG is the sensed stimulus.
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Affiliation(s)
- Marta Yanina Pepino
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110.
| | - Latisha Love-Gregory
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110
| | - Nada A Abumrad
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110
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225
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Wang Q, Wang X, Zhang J, Song G. LNA real-time PCR probe quantification of hepatitis B virus DNA. Exp Ther Med 2011; 3:503-508. [PMID: 22969919 DOI: 10.3892/etm.2011.442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 11/22/2011] [Indexed: 12/28/2022] Open
Abstract
In the present study, we standardized a TaqMan locked nucleic acid (LNA) real-time polymerase chain reaction (PCR) probe for the accurate quantification and detection of hepatitis B virus (HBV) DNA in serum (plasma), and evaluated its methodology. LNA probe technology had a much better detection performance in HBV DNA than the common TaqMan probe. The assay based on the LNA probe had a wider linear detection range, higher sensitivity, stability and amplification efficiency, and a lower concentration of probes than the TaqMan probe. Among the 15 cases with chronic hepatitis B surface antigen (HBsAg) (+) alone, only 4 cases that were detected by TaqMan real-time PCR were negative; however, the same samples were positive by LNA real-time PCR (p<0.05). A positive correlation between viral load measurements for the 35 samples with HBV-positive DNA was detected in both LNA and TaqMan real-time PCR.
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Affiliation(s)
- Qing Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University Medical College
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226
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Evaluation of real-time reverse transcriptase PCR assays for detection of pandemic influenza A/H1N1 2009 virus. J Clin Microbiol 2011; 49:3444-5. [PMID: 21878586 DOI: 10.1128/jcm.00974-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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227
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Koch W, Wolferstetter H, Schatke A, Schömig A, Kastrati A. Interleukin 18 gene variation and risk of acute myocardial infarction. Cytokine 2011; 56:786-91. [DOI: 10.1016/j.cyto.2011.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/18/2011] [Accepted: 09/10/2011] [Indexed: 12/25/2022]
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228
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The challenge of merging food safety diagnostic needs with quantitative PCR platforms. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.02.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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229
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Wen G, Zhang T, Yang J, Luo Q, Liao Y, Hu Z, Zhang R, Wang H, Ai D, Luo L, Song N, Shao H. Evaluation of a real-time RT-PCR assay using minor groove binding probe for specific detection of Chinese wild-type classical swine fever virus. J Virol Methods 2011; 176:96-102. [DOI: 10.1016/j.jviromet.2011.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 01/09/2023]
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230
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Detection, discrimination and absolute quantitation of Tomato spotted wilt virus isolates using real time RT-PCR with TaqMan®MGB probes. J Virol Methods 2011; 176:32-7. [DOI: 10.1016/j.jviromet.2011.05.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 04/28/2011] [Accepted: 05/17/2011] [Indexed: 11/15/2022]
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231
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Lins AK, Lima RA, Magalhães M. Clarithromycin-resistant Helicobacter pylori in Recife, Brazil, directly identified from gastric biopsies by polymerase chain reaction. ARQUIVOS DE GASTROENTEROLOGIA 2011; 47:379-82. [PMID: 21225149 DOI: 10.1590/s0004-28032010000400011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 07/20/2010] [Indexed: 12/12/2022]
Abstract
CONTEXT Clarithromycin is the most effective drug used in the eradication of infection by Helicobacter pylori. Due to worldwide increase in resistance, pre-treatment susceptibility testing for clarithromycin is recommended. OBJECTIVES To evaluate the prevalence of clarithromycin resistance of H. pylori in Recife, a city in Northeast Brazil. METHODS From January 2006 to December 2007, 114 gastric biopsy samples positive for H. pylori at culture were directly assayed by polymerase chain reaction (PCR) to detect the most frequent point mutations involved in clarithromycin resistance. Results were compared with those obtained by Etests. RESULT Molecular and phenotypic methods showed 111 (97.4%) susceptible or resistant concordant results. PCR detected 3 (2.6%) biopsy specimens with H. pylori-resistant genotypes, which were misdiagnosed as susceptible by Etests. In Recife, based on PCR results, primary clarithromycin resistance was found in 15 (16.5%) patients, prevalence close to that observed in Southeast Brazil. Resistance increased to 52% among previously treated patients. The point mutation A2143G was present in 20 (71.4%) of specimens and A2142G, in 8 (28.6%) of specimens. A2142C was not found. CONCLUSION In Recife, the prevalence of primary clarithromycin resistance, 16.5%, showed the need for pretreatment susceptibility testing in H. pylori infections.
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232
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Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol 2011; 11:80. [PMID: 21831278 PMCID: PMC3224242 DOI: 10.1186/1472-6750-11-80] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.
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Affiliation(s)
- Joseph R Dobosy
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 5224, USA
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233
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Ferriol I, Ruiz-Ruiz S, Rubio L. Detection and absolute quantitation of Broad bean wilt virus 1 (BBWV-1) and BBWV-2 by real time RT-PCR. J Virol Methods 2011; 177:202-5. [PMID: 21855578 DOI: 10.1016/j.jviromet.2011.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/25/2011] [Accepted: 08/01/2011] [Indexed: 01/01/2023]
Abstract
Broad bean wilt virus 1 (BBWV-1) and BBWV-2 are the two most significant viruses in the genus Fabavirus, causing damage to many economically important agricultural crops worldwide. A quantitative real-time reverse transcription-polymerase chain reaction (RT-qPCR) procedure using two TaqMan(®)MGB probes was developed for sensitive and specific detection and quantitation of BBWV-1 and BBWV-2. Primers and probes were designed from conserved sequence stretches to detect all isolates of each virus. Standard curves using RNA transcripts identical to both TaqMan(®)MGB probes enabled absolute quantitation, with a wide dynamic range and high sensitivity (10(3)-10(10) RNA molecules). RT-qPCR was assayed with genetically divergent BBWV-1 and BBWV-2 isolates from different plant hosts and countries, and was used to evaluate the temporal accumulation of BBWV-1 RNA in two plant hosts.
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Affiliation(s)
- I Ferriol
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain
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234
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Hong J, Kang B, Kim A, Hwang S, Ahn J, Lee S, Kim J, Park JH, Cheon DS. Development of a highly sensitive real-time one step RT-PCR combined complementary locked primer technology and conjugated minor groove binder probe. Virol J 2011; 8:330. [PMID: 21714898 PMCID: PMC3142241 DOI: 10.1186/1743-422x-8-330] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 06/29/2011] [Indexed: 11/25/2022] Open
Abstract
Background Enterovirus (EV) infections are commonly associated with encephalitis and meningitis. Detection of enteroviral RNA in clinical specimens has been demonstrated to improve the management of patients, by ruling out other causes of disease. Method To develop a sensitive and reliable assay for routine laboratory diagnosis, we developed a real-time one step reverse transcription polymerase chain reaction (RT-PCR) assay with minor groove binder probes and primers modified with complementary locked primer technology (TMC-PCR). We checked the sensitivity of the developed assay by comparing it to a previously published TaqMan probe real-time one-step RT-PCR (TTN-PCR) procedure using enteroviral isolates, Enterovirus Proficiency panels from Quality Control on Molecular Diagnostics (QCMD-2007), and clinical specimens from patients with suspected EV infections. Results One hundred clinical specimens from 158 suspected viral meningitis cases were determined to be positive by the TMC-PCR assay (63.29%), whereas only 60 were found to be positive by the TTN-PCR assay (37.97%). The positive and negative agreements between the TMC-PCR and TTN-PCR assays were 100% and 59.2%, respectively. Conclusion This data suggest that the TMC-PCR assay may be suitable for routine diagnostic screening from patient suspected EV infection.
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Affiliation(s)
- JiYoung Hong
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institute of Health, Korea Center for Disease Control and Prevention, Chungcheongbuk-do 363-951, Korea
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235
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Guimaraes AMS, Vieira RFC, Poletto R, Vemulapalli R, Santos AP, de Moraes W, Cubas ZS, Santos LC, Marchant-Forde JN, Timenetsky J, Biondo AW, Messick JB. A quantitative TaqMan PCR assay for the detection of Mycoplasma suis. J Appl Microbiol 2011; 111:417-25. [PMID: 21575112 DOI: 10.1111/j.1365-2672.2011.05053.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM To develop a TaqMan probe-based, highly sensitive and specific quantitative PCR (qPCR) assay for the detection and quantification of Mycoplasma suis in the blood of pigs. METHODS AND RESULTS Primers and probes specific to Myc. suis 16S rRNA gene were designed. The qPCR assay's specificity, detection limit, intra- and inter-assay variability were evaluated and its performance was compared with a Myc. suis conventional PCR assay (cPCR). Blood of two experimentally infected pigs, 40 Indiana pigs, 40 Brazilian sows and 28 peccaries were tested. The assay detected as few as ten copies of Myc. suis plasmids and was 100-fold more sensitive than the cPCR. No cross-reactivity with nontarget pig mycoplasmas was observed. An average of 1·62 × 10(11) and 2·75 × 10(8) target copies ml(-1) of blood were detected in the acutely and chronically infected pigs, respectively. Three (7·5%) pigs and 32 (80·0%) sows were positive while all peccaries were negative for Myc. suis. CONCLUSION The developed qPCR assay is highly sensitive and specific for Myc. suis detection and quantification. SIGNIFICANCE AND IMPACT OF THE STUDY TaqMan qPCR is an accurate and quick test for detection of Myc. suis infected pigs, which can be used on varied instrumentation platforms.
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Affiliation(s)
- A M S Guimaraes
- Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
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A duplex real-time RT-PCR assay for the simultaneous genogroup-specific detection of noroviruses in both clinical and environmental specimens. Virus Genes 2011; 43:192-200. [PMID: 21643768 DOI: 10.1007/s11262-011-0626-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/17/2011] [Indexed: 12/21/2022]
Abstract
Norovirus (NoV) is the major etiological agent causing foodborne and waterborne outbreaks worldwide. We developed a novel duplex real-time quantitative RT-PCR assay designed for the simultaneous detection of and discrimination between NoV genogroups GI and GII, by targeting the short junction region between ORF1 and ORF2, with sensitivity and efficiency comparable to those of each simplex RT-PCR assay. This new duplex assay was evaluated against clinical stool (n = 82) and environmental (groundwater or surface water, n = 60) specimens from South Korea, and the results were compared with those of conventional RT-PCR (cRT-PCR) assays. The duplex assay detected more positive samples than did the cRT-PCR for both clinical (74 vs. 71) and, more strikingly, environmental (24 vs. 10) specimens. No cross-reactivity against specimens containing other enteric viruses such as rotavirus, adenovirus, and poliovirus were observed. These results suggest that this newly developed duplex real-time RT-PCR assay can be used for the sensitive and simultaneous genogroup-specific detection of NoV in both clinical and environmental specimens.
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239
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Blanco-Meneses M, Ristaino JB. Detection and Quantification of Peronospora tabacina Using a Real-Time Polymerase Chain Reaction Assay. PLANT DISEASE 2011; 95:673-682. [PMID: 30731912 DOI: 10.1094/pdis-05-10-0333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Peronospora tabacina is an obligate plant pathogen that causes blue mold of tobacco. The disease is difficult to diagnose before the appearance of symptoms and can be easily spread in nonsymptomatic tobacco seedlings. We developed a real-time polymerase chain reaction (PCR) assay for P. tabacina that uses 5' fluorogenic exonuclease (TaqMan) chemistry to detect and quantify pathogen DNA from diseased tissue. The primers and probe were designed using 5.8S ribosomal DNA sequences from 12 fungal and oomycete tobacco pathogens and 24 Peronospora spp. The PtabBM TaqMan assay was optimized and performed with a final concentration of 450 nM primers and 125 nM probe. The real-time TaqMan assay was assessed for sensitivity and the lower detection limit was 1 fg of DNA. The assay was specific for P. tabacina. None of the DNA from other tobacco pathogens, nonpathogens, or the host were amplified. The PtabBM TaqMan assay was useful for detection of P. tabacina in field samples, artificially inoculated leaves, roots, and systemically infected tobacco seedlings. The assay was used to quantify host resistance and it was possible to detect the pathogen 4 days postinoculation in both medium-resistant and susceptible tobacco cultivars. The real-time PCR assay for P. tabacina will be a valuable tool for the detection of the pathogen and of use to regulatory agencies interested in preventing the spread of blue mold.
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240
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Strategies to quantify unspliced and multiply spliced mRNA expression in HIV-2 infection. J Virol Methods 2011; 175:38-45. [PMID: 21540056 DOI: 10.1016/j.jviromet.2011.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/11/2011] [Accepted: 04/14/2011] [Indexed: 01/25/2023]
Abstract
HIV-2 infection is associated with a slower rate of disease progression with limited impact on the survival of the majority of infected adults, and much lower plasma viral load than HIV-1. In spite of the major differences in viremia, the quantitative assessment of HIV-2 proviral load documented levels similar to those observed in HIV-1 infected individuals, suggesting an equivalent number of circulating infected cells in both infections. It remains unclear whether this apparent paradox results from a contribution of latent/quiescent viruses or from transcriptional and/or post-transcriptional control of HIV-2 replication. In order to investigate these possibilities, a one-step and two-step reverse transcription quantitative real-time PCR based methods (RT-qPCR) for gag and tat mRNA HIV-2 transcripts were developed. These methods were validated and compared to assess the expression of HIV-2 gag and tat transcripts in parallel with proviral DNA and viral production. The results suggest that the two-step approach may allow a better detection of low level gag and tat mRNA HIV-2 transcripts.
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241
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Diallo IS, Corney BG, Rodwell BJ. Detection and differentiation of bovine herpesvirus 1 and 5 using a multiplex real-time polymerase chain reaction. J Virol Methods 2011; 175:46-52. [PMID: 21540057 DOI: 10.1016/j.jviromet.2011.04.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/29/2011] [Accepted: 04/14/2011] [Indexed: 11/28/2022]
Abstract
A multiplex real-time PCR was developed for the detection and differentiation of two closely related bovine herpesviruses 1 (BoHV-1) and 5 (BoHV-5). The multiplex real-time PCR combines a duplex real-time PCR that targets the DNA polymerase gene of BoHV-1 and BoHV-5 and a real-time PCR targeting mitochondrial DNA, as a house-keeping gene, described previously by Cawthraw et al. (2009). The assay correctly identified 22 BoHV-1 and six BoHV-5 isolates from the Biosecurity Sciences Laboratory virus collection. BoHV-1 and BoHV-5 were also correctly identified when incorporated in spiked semen and brain tissue samples. The detection limits of the duplex assay were 10 copies of BoHV-1 and 45 copies of BoHV-5. The multiplex real-time PCR had reaction efficiencies of 1.04 for BoHV-1 and 1.08 for BoHV-5. Standard curves relating Ct value to template copy number had correlation coefficients of 0.989 for BoHV-1 and 0.978 for BoHV-5. The assay specificity was demonstrated by testing bacterial and viral DNA from pathogens commonly isolated from bovine respiratory and reproductive tracts. The validated multiplex real-time PCR was used to detect and differentiate BoHV-1 and BoHV-5 in bovine clinical samples with known histories.
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Affiliation(s)
- Ibrahim S Diallo
- Biosecurity Sciences Laboratory, Health and Food Sciences Precinct, Biosecurity Queensland, Department of Employment, Economic Development and Innovation, PO Box 156, Brisbane, Archerfield, Qld 4108, Australia.
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242
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Price EP, Matthews MA, Beaudry JA, Allred JL, Schupp JM, Birdsell DN, Pearson T, Keim P. Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis. Electrophoresis 2011; 31:3881-8. [PMID: 21064143 DOI: 10.1002/elps.201000379] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ability to characterize SNPs is an important aspect of many clinical diagnostic, genetic and evolutionary studies. Here, we designed a multiplexed SNP genotyping method to survey a large number of phylogenetically informative SNPs within the genome of the bacterium Bacillus anthracis. This novel method, CE universal tail mismatch amplification mutation assay (CUMA), allows for PCR multiplexing and automatic scoring of SNP genotypes, thus providing a rapid, economical and higher throughput alternative to more expensive SNP genotyping techniques. CUMA delivered accurate B. anthracis SNP genotyping results and, when multiplexed, saved reagent costs by more than 80% compared with TaqMan real-time PCR. When real-time PCR technology and instrumentation is unavailable or the reagents are cost-prohibitive, CUMA is a powerful alternative for SNP genotyping.
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Affiliation(s)
- Erin P Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA
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243
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van Eijk R, Licht J, Schrumpf M, Talebian Yazdi M, Ruano D, Forte GI, Nederlof PM, Veselic M, Rabe KF, Annema JT, Smit V, Morreau H, van Wezel T. Rapid KRAS, EGFR, BRAF and PIK3CA mutation analysis of fine needle aspirates from non-small-cell lung cancer using allele-specific qPCR. PLoS One 2011; 6:e17791. [PMID: 21408138 PMCID: PMC3050927 DOI: 10.1371/journal.pone.0017791] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 02/11/2011] [Indexed: 12/30/2022] Open
Abstract
Endobronchial Ultrasound Guided Transbronchial Needle Aspiration (EBUS-TBNA) and Trans-esophageal Ultrasound Scanning with Fine Needle Aspiration (EUS-FNA) are important, novel techniques for the diagnosis and staging of non-small cell lung cancer (NSCLC) that have been incorporated into lung cancer staging guidelines. To guide and optimize treatment decisions, especially for NSCLC patients in stage III and IV, EGFR and KRAS mutation status is often required. The concordance rate of the mutation analysis between these cytological aspirates and histological samples obtained by surgical staging is unknown. Therefore, we studied the extent to which allele-specific quantitative real-time PCR with hydrolysis probes could be reliably performed on EBUS and EUS fine needle aspirates by comparing the results with histological material from the same patient. We analyzed a series of 43 NSCLC patients for whom cytological and histological material was available. We demonstrated that these standard molecular techniques can be accurately applied on fine needle cytological aspirates from NSCLC patients. Importantly, we show that all mutations detected in the histological material of primary tumor were also identified in the cytological samples. We conclude that molecular profiling can be reliably performed on fine needle cytology aspirates from NSCLC patients.
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Affiliation(s)
- Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jappe Licht
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Melanie Schrumpf
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Giusi I. Forte
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra M. Nederlof
- Department of Pathology, Netherlands Cancer Institute NKI-AVL, Amsterdam, The Netherlands
| | - Maud Veselic
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Klaus F. Rabe
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jouke T. Annema
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Vincent Smit
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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244
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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Abstract
Asynchronous PCR (aPCR) is a new PCR method that directs an ordered and sequential amplification of the + and - strands of DNA amplicons. There are several unique characteristics of aPCR that generate new application opportunities. The melting temperature (Tm) of the forward and reverse aPCR primers differ by at least 15°C. The concentration of the lower Tm primer is reduced from 900 to 100 nM, thereby allowing for asynchronous or asymmetric strand-specific amplification. Furthermore, unique thermocycling parameter strategy dictates the + and - strand amplification cue. Each aPCR cycle includes two annealing and extension steps. Sequential annealing and extension of forward and reverse primers during each cycle produce transient single-stranded DNA (ssDNA) amplicons which help hybridization-based probes such as peptide nucleic acid (PNA) bind to the target sequences more effectively. This new method can be used in real-time quantitative PCR (qPCR) for gene expression analyses as well as production of robust ssDNA targets for microarray and other hybridization-based applications.
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246
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A new duplex real-time RT-PCR assay for sensitive and specific detection of African horse sickness virus. Mol Cell Probes 2011; 25:87-93. [PMID: 21315146 DOI: 10.1016/j.mcp.2011.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 01/18/2011] [Accepted: 01/21/2011] [Indexed: 11/23/2022]
Abstract
A new real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for a simple and rapid diagnosis of African Horse Sickness (AHS) was developed. Primers and FAM-labeled TaqMan-MGB probes specific for African horse sickness virus (AHSV) were selected from the consensus sequence of the segment 8 of all 9 serotypes of AHSV reference strains. For the determination of the analytical sensitivity, an in vitro transcript (AHS_ns2T7) of the target region was constructed and tested. Furthermore, the AHS_ns2T7 transcript was used either as positive control or as a standard for quantifying target copies. A commercial heterologous Armored RNA was used as an internal positive control (IPC) for both RNA isolation and RT-PCR steps. The qRT-PCR AHS_ns2 was able to amplify the target sequence up to 0.71 copies/reaction. Its flexibility allowed to amplify a wide dynamic range of RNA copies from 1.5 to 0.001fg. Within this range, the Ct values varied from 18 to 38 cycles with SD values always lower than 0.5 confirming their strong and constant linear correlation with the RNA target. Furthermore the newly designed duplex real-time RT-PCR proved to be strictly AHSV-specific as it did not amplify close related viruses.
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247
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Zu Y, Ting AL, Gao Z. Visualizing low-level point mutations: enzyme-like selectivity offered by nanoparticle probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:306-310. [PMID: 21294256 DOI: 10.1002/smll.201001774] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Yanbing Zu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore 138669.
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248
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Advances in DNA-based techniques for the detection of seafood species substitution on the commercial market. ACTA ACUST UNITED AC 2011; 16:308-21. [PMID: 21764026 DOI: 10.1016/j.jala.2010.07.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Indexed: 02/07/2023]
Abstract
Increased worldwide trade and processing of seafood has increased the potential for species substitution on the commercial market. To detect and prevent species substitution, several deoxyribonucleic acid (DNA)-based methods have been developed that can be used to identify species in a variety of food types. For large-scale applications, such as regulatory screening, these methods must be rapid, cost-effective, reliable, and have high potential for automation. This review highlights recent technological advances in DNA-based identification methods, with a focus on seafood species identification in automated, high-throughput settings. Advances in DNA isolation methods include silica-based columns for use in high-throughput operations and magnetic bead particles for increased and targeted recovery of DNA. The three most widely used methods for seafood species identification (polymerase chain reaction [PCR] sequencing, PCR-restriction fragment length polymorphism, and species-specific PCR) will be discussed, with a focus on the incorporation of technologies such as rapid PCR cycling, microfluidic chips, and real-time PCR. Emerging methods, including DNA microarrays and next-generation sequencing will also be explored for their potential to identify seafood species on a large scale. Overall, many of the technological advances discussed here offer complementary properties that will enable species identification in a variety of settings and with a range of products.
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249
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Koch W, Schatke A, Wolferstetter H, Mueller JC, Schömig A, Kastrati A. Extended evidence for association between the melanoma inhibitory activity 3 gene and myocardial infarction. Thromb Haemost 2011; 105:670-5. [PMID: 21264445 DOI: 10.1160/th10-10-0641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/31/2010] [Indexed: 01/19/2023]
Abstract
In a genome-wide scan, isolated single nucleotide polymorphisms (SNPs), including rs17465637, in the melanoma inhibitory activity 3 gene (MIA3) on chromosome 1 were identified to be associated with coronary artery disease and myocardial infarction (MI). Because the role of common variation at the MIA3 locus has not yet been investigated, the aim of this case-control study was to determine the impact of haplotype-tagging SNPs and haplotypes in the MIA3 region on the risk of MI. In a set of nine haplotype-tagging SNPs, rs17465637, but none of the other SNPs, was associated with MI. After adjustments were made for age, gender, history of arterial hypertension, history of hypercholesterolaemia, current cigarette smoking and diabetes mellitus, multiple logistic regression analyses showed an increased risk in the carriers of one or two C alleles [adjusted odds ratio (OR) 1.17, 95% confidence interval (CI) 1.04-1.32, and 1.37, 95% CI 1.08-1.74, respectively]. Nine common haplotypes (frequency >1%) were established across the MIA3 region. Two of the haplotypes were associated with an increased risk of MI: the frequent (48%) TGACCAAAG haplotype and the rare (2%) CGACCAAAG haplotype (adjusted OR 1.102, 95% CI 1.002-1.212, and 1.574, 95% CI 1.077-2.298, respectively). Showing association between rs17465637 and MI, this work was consistent with results from the original detection study and most prior replication studies addressing this issue. In addition to correspond with such isolated evidence of association with MI, the present study identified specific haplotypes capturing the risk-related variation in the entire MIA3 region.
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Affiliation(s)
- Werner Koch
- Deutsches Herzzentrum München and 1. Medizinische Klinik, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
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Abstract
More than 99% of genomic DNA sequence is identical among humans, and not surprisingly, slight variations in sequence can often produce a major effect on phenotype. Sequence variants may also mediate the manner in which humans are susceptible to disease or respond to environmental factors such as bacteria, viruses, toxins, chemicals, drugs, and therapeutic interventions. Single-nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single base in the genome sequence can be represented by at least two different nucleotides. In the last decade, numerous SNPs have been identified that explain, at least partially, the genetic architecture of complex diseases such as cancer, diabetes, vascular complications, some forms of mental illness, and a multitude of other disorders. Disease-related SNPs are commonly identified through candidate gene approaches, or more recently, through genome-wide association studies. In either case, findings of association require verification in independent, population-based, study samples, usually consisting of several hundreds/thousands of individuals. A convenient technique to genotype a moderate number of markers in this kind of study is available with the TaqMan® platform (Applied Biosystems; Foster City, CA), which utilizes polymerase chain reaction amplification and allelic discrimination to easily and efficiently generate genotype data in a cost-effective way. Here, we introduce and describe this commonly used technique and include protocols that can be directly used in laboratories aiming to perform moderate- to large-scale genotyping studies.
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