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Ripari V, Gänzle MG, Berardi E. Evolution of sourdough microbiota in spontaneous sourdoughs started with different plant materials. Int J Food Microbiol 2016; 232:35-42. [PMID: 27240218 DOI: 10.1016/j.ijfoodmicro.2016.05.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/24/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
Abstract
The preparation of sourdough in bakeries may include the use of inocula, e.g. fruits, flowers or rumen cuts to accelerate the process of selection of suitable microorganisms. The aim of this work was to investigate the effect of these inocula on the microbial evolution in sourdoughs. First, the microbiota of nineteen traditional sourdoughs that were initially started with diverse inocula was identified. Second, de novo sourdoughs were started with plant materials and the evolution of sourdough microbiota was investigated by culture, and by high-resolution melting curve quantitative PCR (HRM-qPCR). This study developed a new protocol for HRM-qPCR analysis of yeast microbiota in sourdough, and indicates this independent culture method suitable for characterization of yeasts. Microbiota of traditional sourdoughs were largely independent from the use of inoculum, however, Acetobacter spp. were identified only in sourdoughs started with apple flowers or apple pulp. In de novo sourdoughs started with plant materials, microbiota rapidly stabilized, and were characterized by Lactobacillus sanfranciscensis, Lactobacillus plantarum, Lactobacillus graminis, or Lactobacillus rossiae, and Saccharomyces cerevisiae as dominant species. Competition experiments revealed that the ecological fitness of L. plantarum, L. graminis, and L. rossiae in wheat or rye malt sourdoughs was lower when compared to L. sanfranciscensis, demonstrating that their presence in de novo sourdoughs reflects dispersal limitation. In conclusion, establishment of microbiota in de novo sourdoughs is dispersal limited. This study provides scientific support for the artisanal practice to inoculate de novo sourdoughs with flowers, berries, or related plant material.
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Affiliation(s)
- Valery Ripari
- Università Politecnica delle Marche, Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Ancona 62010, Italy; University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, AB T6G 2P5, Canada
| | - Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Science, Edmonton, AB T6G 2P5, Canada.
| | - Enrico Berardi
- Università Politecnica delle Marche, Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Ancona 62010, Italy
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102
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Salihah NT, Hossain MM, Lubis H, Ahmed MU. Trends and advances in food analysis by real-time polymerase chain reaction. Journal of Food Science and Technology 2016; 53:2196-209. [PMID: 27407185 PMCID: PMC4921084 DOI: 10.1007/s13197-016-2205-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023]
Abstract
Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.
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Affiliation(s)
- Nur Thaqifah Salihah
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | | | - Hamadah Lubis
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
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103
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Zhong Q, Tian J, Wang B, Wang L. PMA based real-time fluorescent LAMP for detection of Vibrio parahaemolyticus in viable but nonculturable state. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.11.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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104
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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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105
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Wah JLT, David C, Rudiuk S, Baigl D, Estevez-Torres A. Observing and Controlling the Folding Pathway of DNA Origami at the Nanoscale. ACS NANO 2016; 10:1978-87. [PMID: 26795025 DOI: 10.1021/acsnano.5b05972] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA origami is a powerful method to fold DNA into rationally designed nanostructures that holds great promise for bionanotechnology. However, the folding mechanism has yet to be fully resolved, principally due to a lack of data with single molecule resolution. To address this issue, we have investigated in detail, using atomic force microscopy, the morphological evolution of hundreds of individual rectangular origamis in solution as a function of temperature. Significant structural changes were observed between 65 and 55 °C both for folding and melting, and six structural intermediates were identified. Under standard conditions, folding was initiated at the edges of the rectangle and progressed toward the center. Melting occurred through the reverse pathway until the structures were significantly disrupted but ended through a different pathway involving out-of-equilibrium chainlike structures. Increasing the relative concentration of center to edge staples dramatically modified the folding pathway to a mechanism progressing from the center toward the edges. These results indicate that the folding pathway is determined by thermodynamics and suggest a way of controlling it.
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Affiliation(s)
- Jonathan Lee Tin Wah
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
| | - Christophe David
- Laboratoire de photonique et de nanostructures, CNRS, route de Nozay, 91460 Marcoussis, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - André Estevez-Torres
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
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106
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Wang H, Turechek WW. A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry. PLoS One 2016; 11:e0147122. [PMID: 26766068 PMCID: PMC4713083 DOI: 10.1371/journal.pone.0147122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×10(3) CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2-3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management.
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Affiliation(s)
- Hehe Wang
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
| | - William W. Turechek
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
- * E-mail:
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107
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Price ER, Rott KH, Caviedes-Vidal E, Karasov WH. Claudin gene expression patterns do not associate with interspecific differences in paracellular nutrient absorption. Comp Biochem Physiol B Biochem Mol Biol 2016; 191:36-45. [DOI: 10.1016/j.cbpb.2015.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
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108
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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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109
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Zarlenga D, Hoberg E, Tuo W. The Identification of Haemonchus Species and Diagnosis of Haemonchosis. ADVANCES IN PARASITOLOGY 2016; 93:145-80. [PMID: 27238005 DOI: 10.1016/bs.apar.2016.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Diagnosis is often equated with identification or detection when discussing parasitic diseases. Unfortunately, these are not necessarily mutually exclusive activities; diseases and infections are generally diagnosed and organisms are identified. Diagnosis is commonly predicated upon some clinical signs; in an effort to determine the causative agent, identification of genera and species is subsequently performed. Both identification and diagnosis play critical roles in managing an infection, and involve the interplay of direct and indirect methods of detection, particularly in light of the complex and expanding problem of drug-resistance in parasites. Accurate and authoritative identification that is cost- and time-effective, based on structural and molecular attributes of specimens, provides a foundation for defining parasite diversity and changing patterns of geographical distribution, host association and emergence of disease. Most techniques developed thus far have been grounded in assumptions based on strict host associations between Haemonchus contortus and small ruminants, that is, sheep and goats, and between Haemonchus placei and bovids. Current research and increasing empirical evidence of natural infections in the field demonstrates that this assumption misrepresents the host associations for these species of Haemonchus. Furthermore, the capacity of H. contortus to utilize a considerably broad spectrum of ungulate hosts is reflected in our understanding of the role of anthropogenic forcing, the 'breakdown' of ecological isolation, global introduction and host switching as determinants of distribution. Nuanced insights about distribution, host association and epidemiology have emerged over the past 30years, coincidently with the development of increasingly robust means for parasite identification. In this review and for the sake of argument, we would like to delineate the diagnosis of haemonchosis from the identification of the specific pathogen. As a foundation for exploring host and parasite biology, we will examine the evolution of methods for distinguishing H. contortus from other common gastrointestinal nematodes of agriculturally significant and free-ranging wild ruminants using morphological, molecular and/or immunological methods for studies at the species and genus levels.
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110
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Martin A, Bouffier L, Grant KB, Limoges B, Marchal D. Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes. Analyst 2016; 141:4196-203. [DOI: 10.1039/c6an00867d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The main objective of this study is provide guidelines in the search for ideal redox-active reporters in real-time electrochemical LAMP.
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Affiliation(s)
- Alexandra Martin
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - Laurent Bouffier
- Institut des Sciences Moléculaires
- UMR 5255 CNRS
- Université Bordeaux
- 33400 Talence
- France
| | | | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - Damien Marchal
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
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111
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Bose PP, Kumar P, Munagala N. Concurrent visual diagnosis and susceptibility profiling of the first line drug against visceral leishmaniasis by plasmonic detection of PCR amplified genetic biomarker. Acta Trop 2015; 152:208-214. [PMID: 26394185 DOI: 10.1016/j.actatropica.2015.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/01/2015] [Accepted: 09/17/2015] [Indexed: 11/26/2022]
Abstract
Visceral form of leishmaniasis (also known as Kala-azar) is a fatal neglected tropical disease affecting 95 countries worldwide. Recently, substantial proportion of resistance related treatment failure cases have been reported against its first line drug, sodium-antimony gluconate (SAG). We report an easy, fast, sensitive and cheap visual diagnosis and SAG susceptibility profiling for this disease based on recently recognized genetic biomarker and gold nanoparticle based plasmonic detection phenomenon. This is a non-gel, non-culture based detection technique, which can be used as simultaneous high throughput detection and SAG-susceptibility profiling in Leishmania endemic resource stringent countries.
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112
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Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiol Methods 2015; 119:223-7. [PMID: 26554941 DOI: 10.1016/j.mimet.2015.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.
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113
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Oscorbin IP, Boyarskikh UA, Filipenko ML. Large Fragment of DNA Polymerase I from Geobacillus sp. 777: Cloning and Comparison with DNA Polymerases I in Practical Applications. Mol Biotechnol 2015; 57:947-59. [DOI: 10.1007/s12033-015-9886-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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114
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Abstract
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCR-based mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial real-time PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
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Affiliation(s)
| | - Pavel Neužil
- 1] Kist-Europe, Saarbrücken, Saarland, 66123, Germany [2] Central European Institute of Technology, Brno University of Technology, Technická 3058/10, CZ-616 00 Brno, Czech Republic [3] Northwestern Polytechnical University, School of Mechanical Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R.China
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115
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Detection of Schistosoma mansoni and Schistosoma haematobium by Real-Time PCR with High Resolution Melting Analysis. Int J Mol Sci 2015; 16:16085-103. [PMID: 26193254 PMCID: PMC4519940 DOI: 10.3390/ijms160716085] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 06/19/2015] [Accepted: 07/01/2015] [Indexed: 12/13/2022] Open
Abstract
The present study describes a real-time PCR approach with high resolution melting-curve (HRM) assay developed for the detection and differentiation of Schistosoma mansoni and S. haematobium in fecal and urine samples collected from rural Yemen. The samples were screened by microscopy and PCR for the Schistosoma species infection. A pair of degenerate primers were designed targeting partial regions in the cytochrome oxidase subunit I (cox1) gene of S. mansoni and S. haematobium using real-time PCR-HRM assay. The overall prevalence of schistosomiasis was 31.8%; 23.8% of the participants were infected with S. haematobium and 9.3% were infected with S. mansoni. With regards to the intensity of infections, 22.1% and 77.9% of S. haematobium infections were of heavy and light intensities, respectively. Likewise, 8.1%, 40.5% and 51.4% of S. mansoni infections were of heavy, moderate and light intensities, respectively. The melting points were distinctive for S. mansoni and S. haematobium, categorized by peaks of 76.49 ± 0.25 °C and 75.43 ± 0.26 °C, respectively. HRM analysis showed high detection capability through the amplification of Schistosoma DNA with as low as 0.0001 ng/µL. Significant negative correlations were reported between the real-time PCR-HRM cycle threshold (Ct) values and microscopic egg counts for both S. mansoni in stool and S. haematobium in urine (p < 0.01). In conclusion, this closed-tube HRM protocol provides a potentially powerful screening molecular tool for the detection of S. mansoni and S. haematobium. It is a simple, rapid, accurate, and cost-effective method. Hence, this method is a good alternative approach to probe-based PCR assays.
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116
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Hünniger T, Felbinger C, Wessels H, Mast S, Hoffmann A, Schefer A, Märtlbauer E, Paschke-Kratzin A, Fischer M. Food Targeting: A Real-Time PCR Assay Targeting 16S rDNA for Direct Quantification of Alicyclobacillus spp. Spores after Aptamer-Based Enrichment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4291-4296. [PMID: 25880790 DOI: 10.1021/acs.jafc.5b00874] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Spore-forming Alicyclobacillus spp. are able to form metabolites that induce even in small amounts an antiseptical or medicinal off-flavor in fruit juices. Microbial contaminations could occur by endospores, which overcame the pasteurization process. The current detection method for Alicyclobacillus spp. can take up to 1 week because of microbiological enrichment. In a previous study, DNA aptamers were selected and characterized for an aptamer-driven rapid enrichment of Alicyclobacillus spp. spores from orange juice by magnetic separation. In the present work, a direct quantification assay for Alicyclobacillus spp. spores was developed to complete the two-step approach of enrichment and detection. After mechanical treatment of the spores, the isolated DNA was quantified in a real-time PCR-assay targeting 16S rDNA. The assay was evaluated by the performance requirements of the European Network of Genetically Modified Organisms Laboratories (ENGL). Hence, the presented method is applicable for direct spore detection from orange juice in connection with an enrichment step.
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Affiliation(s)
- Tim Hünniger
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Christine Felbinger
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Hauke Wessels
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sophia Mast
- ‡Lehrstuhl für Hygiene und Technologie der Milch, Tierärtzliche Fakultät, Ludwig-Maximilians-Universität, Schönleutnerstraße 8/219, 85764 Oberschleißheim, Germany
| | - Antonia Hoffmann
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Anna Schefer
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Erwin Märtlbauer
- ‡Lehrstuhl für Hygiene und Technologie der Milch, Tierärtzliche Fakultät, Ludwig-Maximilians-Universität, Schönleutnerstraße 8/219, 85764 Oberschleißheim, Germany
| | - Angelika Paschke-Kratzin
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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117
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Sun Y, Quyen TL, Hung TQ, Chin WH, Wolff A, Bang DD. A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples. LAB ON A CHIP 2015; 15:1898-904. [PMID: 25715949 DOI: 10.1039/c4lc01459f] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.
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Affiliation(s)
- Yi Sun
- Department of Micro and Nanotechnology (DTU-Nanotech), Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
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Japaridze A, Benke A, Renevey S, Benadiba C, Dietler G. Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy. Macromolecules 2015. [DOI: 10.1021/ma502537g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Alexander Benke
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Sylvain Renevey
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Carine Benadiba
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
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119
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Comparison of different DNA binding fluorescent dyes for applications of high-resolution melting analysis. Clin Biochem 2015; 48:609-16. [PMID: 25641335 DOI: 10.1016/j.clinbiochem.2015.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Different applications of high-resolution melting (HRM) analysis have been adopted for a wide range of research and clinical applications. This study compares the performance of selected DNA binding fluorescent dyes for their possible application in HRM. DESIGN AND METHODS We compared twelve dyes with basic properties considered relevant for PCR amplification and melting curve analysis. These included PCR inhibition, fluorescence intensity, the ability to generate melting curves and their effect on melting temperature (Tm). Seven of these dyes with promising properties were then evaluated for possible use in basic HRM applications; such as small amplicon genotyping, genotyping of a 1 kb insertion/deletion polymorphism, probe-based genotyping and mutation screening. RESULTS Five dyes failed to exhibit promising properties during the first part of the study, and these were excluded from further testing. Of the remaining dyes, SYTO11, SYTO13 and SYTO16 showed better PCR inhibitory and Tm affecting properties compared to commercial HRM dyes LCGreen Plus, EvaGreen and ResoLight. Although the SYTO dyes generally exhibited good discrimination powers in HRM applications, SYTO11 and SYTO14 gave low signal intensity and lower quality results. CONCLUSIONS Our results suggest that the best performing dyes for HRM are those commercially offered for HRM analyses. However, the performance of SYTO16 and SYTO13 was comparable to the HRM dyes in the majority of our assays, thus demonstrating that they are also quite suitable for both real-time PCR and HRM applications.
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Bhakta MS, Jones VA, Vallejos CE. Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L. PLoS One 2015; 10:e0116822. [PMID: 25629314 PMCID: PMC4309454 DOI: 10.1371/journal.pone.0116822] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022] Open
Abstract
High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome.
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Affiliation(s)
- Mehul S. Bhakta
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - Valerie A. Jones
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - C. Eduardo Vallejos
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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121
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Mohamed Zahidi J, Bee Yong T, Hashim R, Mohd Noor A, Hamzah SH, Ahmad N. Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis. Diagn Microbiol Infect Dis 2015; 81:227-33. [PMID: 25641125 DOI: 10.1016/j.diagmicrobio.2014.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/10/2014] [Accepted: 12/28/2014] [Indexed: 11/18/2022]
Abstract
Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level.
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Affiliation(s)
| | - Tay Bee Yong
- Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Rohaidah Hashim
- Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Azura Mohd Noor
- Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Siti Hawa Hamzah
- Microbiology Unit, Department of Pathology, Hospital Pulau Pinang, Jalan Residensi, 10990 Georgetown, Pulau Pinang, Malaysia
| | - Norazah Ahmad
- Bacteriology Unit, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
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122
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Mauk MG, Liu C, Sadik M, Bau HH. Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection. Methods Mol Biol 2015; 1256:15-40. [PMID: 25626529 PMCID: PMC6540113 DOI: 10.1007/978-1-4939-2172-0_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Molecular (nucleic acid)-based diagnostics tests have many advantages over immunoassays, particularly with regard to sensitivity and specificity. Most on-site diagnostic tests, however, are immunoassay-based because conventional nucleic acid-based tests (NATs) require extensive sample processing, trained operators, and specialized equipment. To make NATs more convenient, especially for point-of-care diagnostics and on-site testing, a simple plastic microfluidic cassette ("chip") has been developed for nucleic acid-based testing of blood, other clinical specimens, food, water, and environmental samples. The chip combines nucleic acid isolation by solid-phase extraction; isothermal enzymatic amplification such as LAMP (Loop-mediated AMPlification), NASBA (Nucleic Acid Sequence Based Amplification), and RPA (Recombinase Polymerase Amplification); and real-time optical detection of DNA or RNA analytes. The microfluidic cassette incorporates an embedded nucleic acid binding membrane in the amplification reaction chamber. Target nucleic acids extracted from a lysate are captured on the membrane and amplified at a constant incubation temperature. The amplification product, labeled with a fluorophore reporter, is excited with a LED light source and monitored in situ in real time with a photodiode or a CCD detector (such as available in a smartphone). For blood analysis, a companion filtration device that separates plasma from whole blood to provide cell-free samples for virus and bacterial lysis and nucleic acid testing in the microfluidic chip has also been developed. For HIV virus detection in blood, the microfluidic NAT chip achieves a sensitivity and specificity that are nearly comparable to conventional benchtop protocols using spin columns and thermal cyclers.
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Affiliation(s)
- Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 220 South 33rd Street, 107 towne building, Philadelphia, PA, 19104-6315, USA
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Tong Y, Jiang C, Yuan Y, Jin Y, Cui ZH, Huang L. Molecular identification of antelope horn by melting curve analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3945-3951. [PMID: 25541315 DOI: 10.3109/19401736.2014.989500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Antelope horn is a valuable Chinese traditional medicine and widely used in clinic. However, with the deterioration of antelope's living environment and a lot of killing, the saiga population begins falling and in some places plummet. Since the increasing demand of this expensive and good bioactive medicine, the horn of artiodactyla animals is often used as the antelope horn. The adulterated or impostor not only cause damage to clinical medicine but also affect the antelope resources protection and sustainable development. Here, in order to establish a melting curve analysis (MCA) method to distinguish the antelope horn from other animal horns and identify the decoction pieces and Chinese patent medicine in a fast and easy way, animal horns and its decoction pieces, Chinese patent medicines were collected from the market and the DNA of all the collected samples were extracted. The melting curve of two universal fragments (COI and Cyt b) was scanned and Cyt b was selected as feasibility fragment for identifying authentic antelope horn from eight adulterant animal horns. After optimizing the condition for MCA, inspecting the precision and the replication of the method, a reference melting curve modern was established and we performed MCA on the antelope horns, fakes, and adulterants on a 1:1 mix, decoction pieces, and Chinese patent medicine. Thus, this study provides fast and easy methods so that MCA can detect the truth, fakes, and adulterations of antelope horns.
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Affiliation(s)
- Yuru Tong
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
| | - Chao Jiang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yuan Yuan
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yan Jin
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Zhan-Hu Cui
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Luqi Huang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
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Rao P, Wu H, Jiang Y, Opriessnig T, Zheng X, Mo Y, Yang Z. Development of an EvaGreen-based multiplex real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of six viral pathogens of porcine reproductive and respiratory disorder. J Virol Methods 2014; 208:56-62. [DOI: 10.1016/j.jviromet.2014.06.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/17/2014] [Accepted: 06/20/2014] [Indexed: 11/27/2022]
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125
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Mathematical tools to optimize the design of oligonucleotide probes and primers. Appl Microbiol Biotechnol 2014; 98:9595-608. [PMID: 25359473 DOI: 10.1007/s00253-014-6165-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022]
Abstract
The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose.
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126
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Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
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Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
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127
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Wang LJ, Zhang Y, Zhang CY. A target-triggered exponential amplification-based DNAzyme biosensor for ultrasensitive detection of folate receptors. Chem Commun (Camb) 2014; 50:15393-6. [DOI: 10.1039/c4cc07230h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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128
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Griffis JW, Safranovitch MM, Vyas SP, Gerrin S, Protozanova E, Malkin G, Meltzer RH. Single molecule DNA intercalation in continuous homogenous elongational flow. LAB ON A CHIP 2014; 14:3881-3893. [PMID: 25133764 DOI: 10.1039/c4lc00781f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sequence-nonspecific staining of DNA with intercalating fluorophores is required for fluorescence-based length estimation of elongated DNA in optical mapping techniques. However, the observed length of a DNA molecule is affected by the relative concentrations of DNA and dye. In some applications, predetermination of DNA concentration may not be possible. Here we present a microfluidic approach in which individual DNA molecules are entrained by converging laminar sheath flows containing the intercalating dye PO-PRO-1. This provides uniform staining regardless of DNA concentration, and uniform elastic stretching of DNA in continuous elongational flow. On-chip intercalation provides a unique process for concentration-independent staining of long DNA fragments for the optical mapping method Genome Sequence Scanning (GSS), and normalizes intramolecular elasticity across a broad range of molecule lengths. These advances permit accurate mapping of observed molecules to sequence derived templates, thus improving detection of complex bacterial mixtures using GSS.
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129
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Zhang R, He YF, Chen M, Chen CM, Zhu QJ, Lu H, Wei ZH, Li F, Zhang XX, Xu CJ, Yu L. Diagnosis of 25 genotypes of human papillomaviruses for their physical statuses in cervical precancerous/cancerous lesions: a comparison of E2/E6E7 ratio-based vs. multiple E1-L1/E6E7 ratio-based detection techniques. J Transl Med 2014; 12:282. [PMID: 25269554 PMCID: PMC4192431 DOI: 10.1186/s12967-014-0282-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 09/24/2014] [Indexed: 01/15/2023] Open
Abstract
Background Cervical lesions caused by integrated human papillomavirus (HPV) infection are highly dangerous because they can quickly develop into invasive cancers. However, clinicians are currently hampered by the lack of a quick, convenient and precise technique to detect integrated/mixed infections of various genotypes of HPVs in the cervix. This study aimed to develop a practical tool to determine the physical status of different HPVs and evaluate its clinical significance. Methods The target population comprised 1162 women with an HPV infection history of > six months and an abnormal cervical cytological finding. The multiple E1-L1/E6E7 ratio analysis, a novel technique, was developed based on determining the ratios of E1/E6E7, E2/E6E7, E4E5/E6E7, L2/E6E7 and L1/E6E7 within the viral genome. Any imbalanced ratios indicate integration. Its diagnostic and predictive performances were compared with those of E2/E6E7 ratio analysis. The detection accuracy of both techniques was evaluated using the gold-standard technique “detection of integrated papillomavirus sequences” (DIPS). To realize a multigenotypic detection goal, a primer and probe library was established. Results The integration rate of a particular genotype of HPV was correlated with its tumorigenic potential and women with higher lesion grades often carried lower viral loads. The E1-L1/E6E7 ratio analysis achieved 92.7% sensitivity and 99.0% specificity in detecting HPV integration, while the E2/E6E7 ratio analysis showed a much lower sensitivity (75.6%) and a similar specificity (99.3%). Interference due to episomal copies was observed in both techniques, leading to false-negative results. However, some positive results of E1-L1/E6E7 ratio analysis were missed by DIPS due to its stochastic detection nature. The E1-L1/E6E7 ratio analysis is more efficient than E2/E6E7 ratio analysis and DIPS in predicting precancerous/cancerous lesions, in which both positive predictive values (36.7%-82.3%) and negative predictive values (75.9%-100%) were highest (based on the results of three rounds of biopsies). Conclusions The multiple E1-L1/E6E7 ratio analysis is more sensitive and predictive than E2/E6E7 ratio analysis as a triage test for detecting HPV integration. It can effectively narrow the range of candidates for colposcopic examination and cervical biopsy, thereby lowering the expense of cervical cancer prevention. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0282-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
| | - Yi-feng He
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China. .,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Mo Chen
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Road, Shanghai, 200011, China.
| | - Chun-mei Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.
| | - Qiu-jing Zhu
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Huan Lu
- Department of Obstetrics and Gynecology, Fengxian Hospital, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
| | - Zhen-hong Wei
- Department of Obstetrics and Gynecology, Fengxian Hospital, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
| | - Fang Li
- Department of Obstetrics and Gynecology, Fengxian Hospital, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
| | - Xiao-xin Zhang
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Cong-jian Xu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Road, Shanghai, 200011, China.
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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Marzenell P, Hagen H, Blechinger J, Erfle H, Mokhir A. Terminally modified, short phosphorothioate oligonucleotides as inhibitors of gene expression in cells. Bioorg Med Chem Lett 2014; 24:4694-4698. [PMID: 25176331 DOI: 10.1016/j.bmcl.2014.08.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 11/24/2022]
Abstract
Phosphorothioates are excellent antisense inhibitors, which are active both in cells and in vivo. Since their affinity to complementary ribonucleic acids is rather low, long strands (⩾20-mers) are typically required to achieve the desired biological activity. However, mismatch discrimination of long inhibitors is reduced. In contrast, shorter phosphorothioates exhibit better sequence specificity, but have in most cases too low affinity for practical applications in cells. We screened a range of terminal modifiers of a 14-mer phosphorothioate sequence, which is complementary to mRNA of a representative gene, whose protein product is fluorescent (DsRed2) and easy to monitor in cells. We found that optimal combinations of 5'- and 3'-modifications include 5'-trimethoxystilbene with 3'-uracil(anthraquinone)-cap, 5'-chloic acid derivative with 3'-uracyl(anthraquinone)-cap and 5'-cholic acid derivative with three 3'-LNA moieties. In contrast to the LNA, stabilizing and activity-enhancing effects of other mentioned modifiers for PTO/RNA duplexes have not been previously reported. We observed that the 14-mer inhibitor carrying 5'-cholic acid derivative with three 3'-LNA moieties inhibits expression of DsRed2 in cells stronger than the unmodified 21-mer. Mismatch discrimination of this inhibitor was found to be comparable to that of the unmodified 14-mer.
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Affiliation(s)
- Paul Marzenell
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany; Ruprecht-Karls University of Heidelberg, Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Helen Hagen
- Ruprecht-Karls University of Heidelberg, Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jenny Blechinger
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany
| | - Holger Erfle
- Ruprecht-Karls University of Heidelberg, BioQuant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Andriy Mokhir
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany
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Hsu CY, Hsu BM, Chang TY, Hsu TK, Shen SM, Chiu YC, Wang HJ, Ji WT, Fan CW, Chen JL. Evaluation of immunomagnetic separation for the detection of Salmonella in surface waters by polymerase chain reaction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:9811-21. [PMID: 25243887 PMCID: PMC4199051 DOI: 10.3390/ijerph110909811] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 11/17/2022]
Abstract
Salmonella spp. is associated with fecal pollution and capable of surviving for long periods in aquatic environments. Instead of the traditional, time-consuming biochemical detection, polymerase chain reaction (PCR) allows rapid identification of Salmonella directly concentrated from water samples. However, prevalence of Salmonella may be underestimated because of the vulnerability of PCR to various environmental chemicals like humic acid, compounded by the fact that various DNA polymerases have different susceptibility to humic acid. Because immunomagnetic separation (IMS) theoretically could isolate Salmonella from other microbes and facilitate removal of aquatic PCR inhibitors of different sizes, this study aims to compare the efficiency of conventional PCR combined with immunomagnetic separation (IMS) for Salmonella detection within a moderately polluted watershed. In our study, the positive rate was increased from 17.6% to 47% with nearly ten-fold improvement in the detection limit. These results suggest the sensitivity of Salmonella detection could be enhanced by IMS, particularly in low quality surface waters. Due to its effects on clearance of aquatic pollutants, IMS may be suitable for most DNA polymerases for Salmonella detection.
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Affiliation(s)
- Chao-Yu Hsu
- Division of Urology, Department of Surgery, Tungs' Taichung MetroHarbor Hospital, Taichung 435, Taiwan.
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan.
| | - Tien-Yu Chang
- Department of Radiology, Cheng Hsin General Hospital, Taipei 112, Taiwan.
| | - Tsui-Kang Hsu
- Department of Ophthalmology, Cheng Hsin General Hospital, Taipei 112, Taiwan.
| | - Shu-Min Shen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan.
| | - Yi-Chou Chiu
- General Surgery, Surgical Department, Cheng Hsin General Hospital, Taipei 112, Taiwan.
| | - Hung-Jen Wang
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan.
| | - Wen-Tsai Ji
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan.
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan.
| | - Jyh-Larng Chen
- Department of Environmental Engineering and Health, Yuan-Pei University, Hsinchu 300, Taiwan.
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Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A. A survey of tools for the analysis of quantitative PCR (qPCR) data. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 1:23-33. [PMID: 27920994 PMCID: PMC5129434 DOI: 10.1016/j.bdq.2014.08.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/26/2014] [Accepted: 08/26/2014] [Indexed: 01/12/2023]
Abstract
Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.
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Affiliation(s)
- Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Stefan Rödiger
- Faculty of Natural Sciences, InnoProfile Group "Image-based Assays", Brandenburg University of Technology Cottbus - Senftenberg, Großenhainer Straße 57, 01968 Senftenberg, Germany
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Klemens Vierlinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
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133
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Ye LP, Hu J, Liang L, Zhang CY. Surface-enhanced Raman spectroscopy for simultaneous sensitive detection of multiple microRNAs in lung cancer cells. Chem Commun (Camb) 2014; 50:11883-6. [DOI: 10.1039/c4cc05598e] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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134
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Salm E, Zhong Y, Reddy B, Duarte-Guevara C, Swaminathan V, Liu YS, Bashir R. Electrical detection of nucleic acid amplification using an on-chip quasi-reference electrode and a PVC REFET. Anal Chem 2014; 86:6968-75. [PMID: 24940939 PMCID: PMC4215847 DOI: 10.1021/ac500897t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/18/2014] [Indexed: 11/29/2022]
Abstract
Electrical detection of nucleic acid amplification through pH changes associated with nucleotide addition enables miniaturization, greater portability of testing apparatus, and reduced costs. However, current ion-sensitive field effect transistor methods for sensing nucleic acid amplification rely on establishing the fluid gate potential with a bulky, difficult to microfabricate reference electrode that limits the potential for massively parallel reaction detection. Here we demonstrate a novel method of utilizing a microfabricated solid-state quasi-reference electrode (QRE) paired with a pH-insensitive reference field effect transistor (REFET) for detection of real-time pH changes. The end result is a 0.18 μm, silicon-on-insulator, foundry-fabricated sensor that utilizes a platinum QRE to establish a pH-sensitive fluid gate potential and a PVC membrane REFET to enable pH detection of loop mediated isothermal amplification (LAMP). This technique is highly amendable to commercial scale-up, reduces the packaging and fabrication requirements for ISFET pH detection, and enables massively parallel droplet interrogation for applications, such as monitoring reaction progression in digital PCR.
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Affiliation(s)
- Eric Salm
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
| | - Yu Zhong
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Bobby Reddy
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Carlos Duarte-Guevara
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Vikhram Swaminathan
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
- Department
of Mechanical Science and Engineering, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi-Shao Liu
- Taiwan
Semiconductor Manufacturing Company, Hsinchu, Taiwan
| | - Rashid Bashir
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Micro
and Nanotechnology Laboratory, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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135
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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136
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Affiliation(s)
| | - Tea Meulia
- Ohio Agricultural Research and Development Center Wooster Ohio
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137
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Yu MH, Huang YC, Chang PL. Rapid screening of the heterogeneity of DNA methylation by single-strand conformation polymorphism and CE-LIF in the presence of electro-osmotic flow. Electrophoresis 2014; 35:2378-85. [DOI: 10.1002/elps.201300502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/14/2013] [Accepted: 12/16/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Meng-Hsuan Yu
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Ya-Chi Huang
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Po-Ling Chang
- Department of Chemistry; Tunghai University; Taichung Taiwan
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138
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Wojdacz TK. Methylation-sensitive high-resolution melting in the context of legislative requirements for validation of analytical procedures for diagnostic applications. Expert Rev Mol Diagn 2014; 12:39-47. [DOI: 10.1586/erm.11.88] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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139
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Takei F, Tani H, Matsuura Y, Nakatani K. Detection of hepatitis C virus by single-step hairpin primer RT-PCR. Bioorg Med Chem Lett 2014; 24:394-6. [DOI: 10.1016/j.bmcl.2013.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
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140
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Lehle S, Hildebrand DG, Merz B, Malak PN, Becker MS, Schmezer P, Essmann F, Schulze-Osthoff K, Rothfuss O. LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis. Nucleic Acids Res 2013; 42:e41. [PMID: 24371283 PMCID: PMC3973301 DOI: 10.1093/nar/gkt1349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify DNA lesions, and these techniques are tedious or only detect global DNA damage. In this study, we present a high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) in both the mitochondrial and nuclear genome. While most conventional methods are of low-sensitivity or restricted to abundant mitochondrial DNA samples, we established a protocol that enables the accurate sequence-specific quantification of DNA damage in >3-kb probes for any mitochondrial or nuclear DNA sequence. In order to validate the sensitivity of this method, we compared LORD-Q with a previously published qPCR-based method and the standard single-cell gel electrophoresis assay, demonstrating a superior performance of LORD-Q. Exemplarily, we monitored induction of DNA damage and repair processes in human induced pluripotent stem cells and isogenic fibroblasts. Our results suggest that LORD-Q provides a sequence-specific and precise method to quantify DNA damage, thereby allowing the high-throughput assessment of DNA repair, genotoxicity screening and various other processes for a wide range of life science applications.
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Affiliation(s)
- Simon Lehle
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen, 72076 Tübingen, Germany, Division of Immunogenetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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141
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Watts MR, James G, Sultana Y, Ginn AN, Outhred AC, Kong F, Verweij JJ, Iredell JR, Chen SCA, Lee R. A loop-mediated isothermal amplification (LAMP) assay for Strongyloides stercoralis in stool that uses a visual detection method with SYTO-82 fluorescent dye. Am J Trop Med Hyg 2013; 90:306-11. [PMID: 24323513 DOI: 10.4269/ajtmh.13-0583] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An assay to detect Strongyloides stercoralis in stool specimens was developed using the loop-mediated isothermal amplification (LAMP) method. Primers were based on the 28S ribosomal subunit gene. The reaction conditions were optimized and SYTO-82 fluorescent dye was used to allow real-time and visual detection of the product. The product identity was confirmed with restriction enzyme digestion, cloning, and sequence analysis. The assay was specific when tested against DNA from bacteria, fungi and parasites, and 30 normal stool samples. Analytical sensitivity was to < 10 copies of target sequence in a plasmid and up to a 10(-2) dilution of DNA extracted from a Strongyloides ratti larva spiked into stool. Sensitivity was increased when further dilutions were made in water, indicative of reduced reaction inhibition. Twenty-seven of 28 stool samples microscopy and polymerase chain reaction positive for S. stercoralis were positive with the LAMP method. On the basis of these findings, the assay warrants further clinical validation.
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Affiliation(s)
- Matthew R Watts
- Centre for Infectious Diseases and Microbiology Public Health; Pathology West - Institute of Clinical Pathology and Medical Research, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity and Centre for Research Excellence in Critical Infection, University of Sydney, New South Wales, Australia; Department of Zoology, University of Dhaka, Dhaka, Bangladesh; Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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142
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Lin YZ, Chang PL. Colorimetric determination of DNA methylation based on the strength of the hydrophobic interactions between DNA and gold nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2013; 5:12045-12051. [PMID: 24199674 DOI: 10.1021/am403863w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A simple, novel colorimetric nanosensor for DNA methylation based on the strength of hydrophobic interaction between DNA and gold nanoparticles was proposed. The nanosensing of oligonucleotides with four nitrogen bases was first demonstrated by dividing the bases into two groups (A/T and C/G) using the representative colors that correspond to Watson-Crick base pairing. By treatment of the genomic DNA with sodium bisulfite followed by PCR amplification, the methylation level of nasopharyngeal carcinoma cells treated with 5-aza-2'-deoxycytidine for up to 5 days could be discriminated by naked eye observation. Furthermore, 12 cancer cell lines that demonstrate heterogeneity with respect to DNA methylation could also be distinguished using the nanosensor, even for amplicons as long as 342 bp. These results demonstrate that the proposed colorimetric nanosensor could potentially be useful in epigenetic studies.
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Affiliation(s)
- Yi-Zhen Lin
- Department of Chemistry, Tunghai University , Taichung 40704, Taiwan
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143
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Santos GB, Espínola SM, Ferreira HB, Margis R, Zaha A. Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach. Parasit Vectors 2013; 6:327. [PMID: 24517106 PMCID: PMC4029041 DOI: 10.1186/1756-3305-6-327] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/05/2013] [Indexed: 12/27/2022] Open
Abstract
Background High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. Findings For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. Conclusions In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family.
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Affiliation(s)
| | | | | | | | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970, Porto Alegre, RS, Brazil.
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144
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Soop A, Hållström L, Frostell C, Wallén H, Mobarrez F, Pisetsky DS. Effect of lipopolysaccharide administration on the number, phenotype and content of nuclear molecules in blood microparticles of normal human subjects. Scand J Immunol 2013; 78:205-13. [PMID: 23679665 DOI: 10.1111/sji.12076] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/11/2013] [Indexed: 01/11/2023]
Abstract
Microparticles (MPs) are small membrane-bound vesicles that arise from activated and dying cells and promote inflammation and thrombosis. To characterize the in vivo release of MPs, we used flow cytometry to measure MPs in the blood of 15 healthy volunteers administered bacterial endotoxin (lipopolysaccharide or LPS) in the presence of a low dose of hydrocortisone with or without inhaled nitric oxide. MPs, defined as particles less than 1.0 μm in size, were assessed following labelling for CD42a, CD14 and CD62E or CD144 antibodies to identify MPs from platelets (PMPs), monocytes (MMPs) and endothelial cells (EMPs). In addition, PMPs and MMPs were labelled with anti-HMGB1 and stained with SYTO13 to assess nuclear acid content. Administration of LPS led to an increase in the numbers of PMPs, MMPs and EMPs as defined by CD62E, as well as the number of MMPs and PMPs staining with anti-HMGB1 and SYTO13. Inhalation of NO did not influence these findings. Together, these studies show that LPS can increase levels of blood MPs and influence phenotype, including nuclear content. As such, particles may be a source of HMGB1 and other nuclear molecules in the blood during inflammation.
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Affiliation(s)
- A Soop
- Department of Clinical Science Intervention and Technology, Karolinska University Hospital, Huddinge, Sweden
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145
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Montgomery JL, Rejali N, Wittwer CT. Stopped-flow DNA polymerase assay by continuous monitoring of dNTP incorporation by fluorescence. Anal Biochem 2013; 441:133-9. [PMID: 23872003 DOI: 10.1016/j.ab.2013.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 11/29/2022]
Abstract
DNA polymerase activity was measured by a stopped-flow assay that monitors polymerase extension using an intercalating dye. Double-stranded DNA formation during extension of a hairpin substrate was monitored at 75°C for 2 min. Rates were determined in nucleotides per second per molecule of polymerase (nt/s) and were linear with time and polymerase concentration from 1 to 50 nM. The concentrations of 15 available polymerases were quantified and their extension rates determined in 50 mM Tris, pH 8.3, 0.5 mg/ml BSA, 2 mM MgCl₂, and 200 μM each dNTP as well as their commercially recommended buffers. Native Taq polymerases had similar extension rates of 10-45 nt/s. Three alternative polymerases showed faster speeds, including KOD (76 nt/s), Klentaq I (101 nt/s), and KAPA2G (155 nt/s). Fusion polymerases including Herculase II and Phusion were relatively slow (3-13 nt/s). The pH optimum for Klentaq extension was between 8.5 and 8.7 with no effect of Tris concentration. Activity was directly correlated to the MgCl2 concentration and inversely correlated to the KCl concentration. This continuous assay is relevant to PCR and provides accurate measurement of polymerase activity using a defined template without the need of radiolabeled substrates.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, USA
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146
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Epigenetic alteration: new insights moving from tissue to plasma - the example of PCDH10 promoter methylation in colorectal cancer. Br J Cancer 2013; 109:807-13. [PMID: 23839493 PMCID: PMC3738140 DOI: 10.1038/bjc.2013.351] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 12/13/2022] Open
Abstract
Background: Tumour-released DNA in blood represents a promising biomarker for cancer detection. Although epigenetic alterations such as aberrant promoter methylation represent an appealing perspective, the discordance existing between frequencies of alterations found in DNA extracted from tumour tissue and cell-free DNA (cfDNA) has challenged their practical clinical application. With the aim to explain this bias of agreement, we investigated whether protocadherin 10 (PCDH10) promoter methylation in tissue was associated with methylation pattern in matched cfDNA isolated from plasma of patients with colorectal cancer (CRC), and whether the strength of concordance may depend on levels of cfDNA, integrity index, as well as on different clinical–pathological features. Methods: A quantitative methylation-specific PCR was used to analyse a selected CpG site in the PCDH10 promoter of 67 tumour tissues, paired normal mucosae, and matched plasma samples. The cfDNA integrity index and cfDNA concentration were assessed using a real-time PCR assay. Results: The PCDH10 promoter methylation was detected in 63 out of 67 (94.0%) surgically resected colorectal tumours and in 42 out of 67 (62.7%) plasma samples. The median methylation rate in tumour tissues and plasma samples was 43.5% (6.3–97.8%) and 5.9% (0–80.9%), respectively. There was a significant correlation between PCDH10 methylation in cfDNA and tumour tissue in patients with early CRC (P<0.0001). The ratio between plasma and tissue methylation rate increases with increasing cfDNA integrity index in early-stage cancers (P=0.0299) and with absolute cfDNA concentration in advanced cancers (P=0.0234). Conclusion: Our findings provide new insight into biological aspects modulating the concordance between tissues and plasma methylation profiles.
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147
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Saka K, Kawahara M, Nagamune T. Reconstitution of a cytokine receptor scaffold utilizing multiple different tyrosine motifs. Biotechnol Bioeng 2013; 110:3197-204. [DOI: 10.1002/bit.24973] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/20/2013] [Accepted: 06/03/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Koichiro Saka
- Department of Chemistry and Biotechnology, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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148
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Jothikumar N, Hill VR. A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp. Biochem Biophys Res Commun 2013; 436:134-9. [PMID: 23727382 DOI: 10.1016/j.bbrc.2013.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/08/2013] [Indexed: 11/29/2022]
Abstract
We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3'-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5'-end forms a hairpin structure. A fluorescent dye is attached to 5'-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3' dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000-0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource-limited environments.
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Affiliation(s)
- N Jothikumar
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Waterborne Disease Prevention Branch, 1600 Clifton Road, Atlanta, GA 30329, USA.
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149
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Zapparoli GV, Jorissen RN, Hewitt CA, McBean M, Westerman DA, Dobrovic A. Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection. BMC Cancer 2013; 13:206. [PMID: 23617802 PMCID: PMC3658971 DOI: 10.1186/1471-2407-13-206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/26/2013] [Indexed: 02/03/2023] Open
Abstract
Background The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. Methods We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. Results We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. Conclusions QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.
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Affiliation(s)
- Giada V Zapparoli
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia
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Abstract
PCR is an important and powerful tool in several fields, including clinical diagnostics, food analysis, and forensic analysis. In theory, PCR enables the detection of one single cell or DNA molecule. However, the presence of PCR inhibitors in the sample affects the amplification efficiency of PCR, thus lowering the detection limit, as well as the precision of sequence-specific nucleic acid quantification in real-time PCR. In order to overcome the problems caused by PCR inhibitors, all the steps leading up to DNA amplification must be optimized for the sample type in question. Sampling and sample treatment are key steps, but most of the methods currently in use were developed for conventional diagnostic methods and not for PCR. Therefore, there is a need for fast, simple, and robust sample preparation methods that take advantage of the accuracy of PCR. In addition, the thermostable DNA polymerases and buffer systems used in PCR are affected differently by inhibitors. During recent years, real-time PCR has developed considerably and is now widely used as a diagnostic tool. This technique has greatly improved the degree of automation and reduced the analysis time, but has also introduced a new set of PCR inhibitors, namely those affecting the fluorescence signal. The purpose of this chapter is to view the complexity of PCR inhibition from different angles, presenting both molecular explanations and practical ways of dealing with the problem. Although diagnostic PCR brings together scientists from different diagnostic fields, end-users have not fully exploited the potential of learning from each other. Here, we have collected knowledge from archeological analysis, clinical diagnostics, environmental analysis, food analysis, and forensic analysis. The concept of integrating sampling, sample treatment, and the chemistry of PCR, i.e., pre-PCR processing, will be addressed as a general approach to overcoming real-time PCR inhibition and producing samples optimal for PCR analysis.
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Affiliation(s)
- Johannes Hedman
- Swedish National Laboratory of Forensic Science, Linköping, Sweden.
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