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Zarbali A, Djaffar I, Menyhárd A. Prediction of tensile modulus based on parameters of crystalline structure in polyethylene terephthalate with cold crystallization ability. Heliyon 2024; 10:e26122. [PMID: 38404902 PMCID: PMC10884433 DOI: 10.1016/j.heliyon.2024.e26122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
This work aims to adopt a simple modulus prediction method for the crystalline poly(ethylene-terephthalate) (PET), which has strong cold-crystallization ability. Based on a single melting curve generated by calorimetry, crystallinity and average melting temperature can easily be evaluated and consequently, tensile modulus can be predicted. Nonetheless, in the case of polymers with cold crystallization behavior, such as PET, the melting process is affected by cold crystallization, impeding the simple calculation of the aforementioned important parameters. In this paper, the techniques to eradicate cold crystallization during calorimetry are presented. Accordingly, the results of a tensile modulus prediction model are presented and discussed. The crystallization and melting characteristics of PET were measured by differential scanning calorimetry (DSC). The mechanical properties of the specimens were estimated by standardized tensile tests. The specimens, which were used for mechanical tests were fabricated using conventional injection molding. The samples were annealed at different temperatures in order to obtain different crystalline structures. The results clearly indicate that the prediction technique is capable to describe the tensile modulus of PET accurately in the case of very diverse crystalline structures.
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Affiliation(s)
- Ali Zarbali
- Laboratory of Plastics and Rubber Technology, Department of Physical Chemistry and Materials Science at Budapest University of Technology and Economics, H-1111 Budapest, Műegyetem rkp. 3., Hungary
| | - Ilies Djaffar
- Laboratory of Plastics and Rubber Technology, Department of Physical Chemistry and Materials Science at Budapest University of Technology and Economics, H-1111 Budapest, Műegyetem rkp. 3., Hungary
| | - Alfréd Menyhárd
- Laboratory of Plastics and Rubber Technology, Department of Physical Chemistry and Materials Science at Budapest University of Technology and Economics, H-1111 Budapest, Műegyetem rkp. 3., Hungary
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2
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Xu B, Lan Y, Luo D, Zheng Y, Ni R, Su G, Huang Q, Li Q. Highly Sensitive Detection of PIK3CA Mutations by Looping-Out Probes-Based Melting Curve Analysis. Biochem Genet 2024; 62:77-94. [PMID: 37249716 DOI: 10.1007/s10528-023-10408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
PIK3CA mutations have important therapeutic and prognostic implications in various cancer types. However, highly sensitive detection of PIK3CA hotspot mutations in heterogeneous tumor samples remains a challenge in clinical settings. To establish a rapid PCR assay for highly sensitive detection of multiple PIK3CA hotspot mutations. We described a novel melting curve analysis-based assay using looping-out probes that can enrich target mutations in the background of excess wild-type and concurrently reveal the presence of mutations. The analytical and clinical performance of the assay were evaluated. The developed assay could detect 10 PIK3CA hotspot mutations at a mutant allele fraction of 0.05-0.5% within 2 h in a single step. Analysis of 82 breast cancer tissue samples revealed 43 samples with PIK3CA mutations, 28 of which were confirmed by Sanger sequencing. Further testing of 175 colorectal cancer tissue samples showed that 24 samples contained PIK3CA mutations and 19 samples were confirmed by Sanger sequencing. Droplet digital PCR supported that all mutation-containing samples undetected by sequencing contained mutations with a low allele fraction. The rapidity, ease of use, high sensitivity and accuracy make the new assay a potential screening tool for PIK3CA mutations in clinical laboratories.
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Affiliation(s)
- Boheng Xu
- Department of Molecular Diagnostics, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yanping Lan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Danjiao Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yangsi Zheng
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Runfang Ni
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guoqiang Su
- The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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3
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Yin C, Pang B, Huang Y, Li J, Meng T, Zhang M, Zhang L, Gao Y, Song X. Multiplex polymerase spiral reaction for simultaneous detection of Salmonella typhimurium and Staphylococcus aureus. Anal Biochem 2023; 667:115086. [PMID: 36813221 DOI: 10.1016/j.ab.2023.115086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023]
Abstract
Salmonella typhimurium (S. typhimurium) and Staphylococcus aureus (S. aureus) are common food-borne pahogens that cause food poisoning in humans. In this study, we developed a method for the simultaneous determination of S. typhimurium and S. aureus based on multiplex polymerase spiral reaction (m-PSR) and melting curve analysis. Two pairs of primers were designed specifically to target the conserved invA gene of S. typhimurium and nuc gene of S. aureus, and the nucleic acid amplification reaction was achieved under isothermal conditions in the same reaction tube for 40 min at 61 °C, melting curve analysis of the amplification product was carried out. The distinct mean melting temperature allowed simultaneous differentiation of the two target bacteria in the m-PSR assay. The limit of detection of S. typhimurium and S. aureus that could be detected simultaneously was 4.1 × 10-4 ng genomic DNA and 2 × 101 CFU/mL pure bacterial culture. Based on this method, analysis of artificially contaminated samples showed excellent sensitivity and specificity consistent with those of pure bacterial cultures. This method is rapid, simultaneous and promises to be a useful tool for the detection of food-borne pathogens in the food industry.
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Affiliation(s)
- Caihong Yin
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China
| | - Bo Pang
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China
| | - Yanzhi Huang
- Research Laboratory, Changchun Children's Hospital, Changchun, 130061, Jilin, PR China
| | - Jinhua Li
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China
| | - Tingyu Meng
- Research Laboratory, Changchun Children's Hospital, Changchun, 130061, Jilin, PR China
| | - Mengfan Zhang
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China.
| | - Liang Zhang
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China
| | - Yanli Gao
- Department of Pediatric Ultrasound, The First Hospital of Jilin University, Changchun, 130000, PR China.
| | - Xiuling Song
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, 130021, PR China.
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4
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Almendras K, Iannuzzi S, Carú M, Orlando J. Diversity of Microbial Functional Genes Should Be Considered During the Interpretation of the qPCR Melting Curves. Microb Ecol 2022; 84:935-940. [PMID: 34599356 DOI: 10.1007/s00248-021-01883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Soil microorganisms play an essential role in biogeochemical cycles. One approach to study these microbial communities is quantifying functional genes by quantitative PCR (qPCR), in which a melting curve analysis is usually assessed to confirm that a single PCR product is being quantified. However, the high diversity of functional genes in environmental samples could generate more than one peak in those curves, so the presence of two or multiple peaks does not always indicate nonspecific amplification. Here, we analyzed the taxonomic diversity of soil microorganisms harboring functional genes involved in nitrogen (N) and phosphorus (P) cycles, based on a database of genomes and metagenomes, and predicted the melting curve profiles of these genes. These functional genes were spread across many bacterial phyla, but mainly Proteobacteria and Actinobacteria. In general, the melting curves exhibited more than one peak or peaks with shoulders, mainly related to the variation of the nucleotide composition of the genes and the expected size of the amplicons. These results indicate that the melting curves of functional genes from environmental samples should be carefully evaluated, being in silico analyses a cost-effective way to identify inherent sequence diversity and avoid interpreting multiple peaks always as unspecific amplifications.
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Affiliation(s)
- Katerin Almendras
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Stefania Iannuzzi
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Margarita Carú
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile.
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5
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Ghorbani J, Hashemi FB, Jabalameli F, Emaneini M, Beigverdi R. Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis. BMC Microbiol 2022; 22:141. [PMID: 35590256 PMCID: PMC9118692 DOI: 10.1186/s12866-022-02558-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Background The study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples. Results Our MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8–100%, respectively. Conclusions Our MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02558-2.
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Affiliation(s)
- Jaber Ghorbani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Farhad Bonakdar Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran.,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran. .,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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6
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Zhang L, Liu D, Li B, Xie J, Liu J, Zhang Z. Single nucleotide polymorphism genotyping of ALDH2 gene based on asymmetric PCR and fluorescent probe-mediated melting curves. Anal Biochem 2021; 642:114509. [PMID: 34864041 DOI: 10.1016/j.ab.2021.114509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/15/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is of great value in precision medicine. The polymorphism of the aldehyde dehydrogenase 2 (ALDH2) gene is caused by a G1510A transition, resulting in the substitution of glutamic acid by lysine at position 487. People of different ALDH2 genotypes show different susceptibility to cancer, metabolic diseases, etc. SNP analysis based on fluorescent probe-mediated melting curves is a relatively efficient and cost-effective method. Genomic DNA extracted from 100 whole blood samples was subjected to polymorphisms mutational analysis using asymmetric PCR and probe-mediated melting curves. Then a certain number of samples from each genotype were randomly selected for direct sequencing verification. The new assay can be performed in 2 h without post-PCR processing such as gel electrophoresis and validated by direct sequencing in a blind study with 100% concordance. Moreover, comparing the detection of polymorphisms of ALDH2 with the clinics, and an overall agreement of 100% (100/100) was demonstrated. Our study has shown a high level of concordance between DNA sequencing, which is suitable for the detection of clinical specimens. Based on the concept of probe-mediated melting curves, we further developed this platform as a universal strategy for the detection of polymorphisms related to folate metabolism.
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Affiliation(s)
- Limei Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, PR China
| | - Dan Liu
- Department of Clinical Laboratory, Zigong Fourth People' Hospital, Zigong, 643099, PR China
| | - Baolin Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, PR China
| | - Jingling Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, PR China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, PR China.
| | - Zhang Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, PR China; Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, PR China.
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7
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Untergasser A, Ruijter JM, Benes V, van den Hoff MJB. Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. BMC Bioinformatics 2021; 22:398. [PMID: 34433408 PMCID: PMC8386043 DOI: 10.1186/s12859-021-04306-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable and reproducible quantitative results. IMPLEMENTATION The main steps in the amplification curve analysis are (1) a unique baseline subtraction, not using the ground phase cycles, (2) PCR efficiency determination from the exponential phase of the individual reactions, (3) setting a common quantification threshold and (4) calculation of the efficiency-corrected target quantity with the common threshold, efficiency per assay and Cq per reaction. The melting curve analysis encompasses smoothing of the observed fluorescence data, normalization to remove product-independent fluorescence loss, peak calling and assessment of the correct peak by comparing its melting temperature with the known melting temperature of the intended amplification product. RESULTS The LinRegPCR web application provides visualization and analysis of a single qPCR run. The user interface displays the analysis results on the amplification curve analysis and melting curve analysis in tables and graphs in which deviant reactions are highlighted. The annotated results in the tables can be exported for calculation of gene-expression ratios, fold-change between experimental conditions and further statistical analysis. Web-based LinRegPCR addresses two types of users, wet-lab scientists analyzing the amplification and melting curves of their own qPCR experiments and bioinformaticians creating pipelines for analysis of series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization, analysis and interactive access. The use of the RDML data standard enables machine independent storage and exchange of qPCR data and the RDML-Tools assist with the import of qPCR data from the files exported by the qPCR instrument. CONCLUSIONS The combined implementation of these analyses in the newly developed web-based LinRegPCR ( https://www.gear-genomics.com/rdml-tools/ ) is platform independent and much faster than the original Windows-based versions of the LinRegPCR program. Moreover, web-based LinRegPCR includes a novel statistical outlier detection and the combination of amplification and melting curve analyses allows direct validation of the amplification product and reporting of reactions that amplify artefacts.
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Affiliation(s)
- Andreas Untergasser
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany. .,European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany.
| | - Jan M Ruijter
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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8
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Ong DSY, Koeleman JGM, Vaessen N, Breijer S, Paltansing S, de Man P. Rapid screening method for the detection of SARS-CoV-2 variants of concern. J Clin Virol 2021; 141:104903. [PMID: 34182300 PMCID: PMC8213512 DOI: 10.1016/j.jcv.2021.104903] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/18/2022]
Abstract
Background Comprehensive and up-to-date monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) is crucial as these are characterized by their increased transmissibility, immune evasion and virulence. Objectives To describe the wide-scale implementation of a reverse transcriptase polymerase chain reaction (RT-PCR) multiple variants assay with melting curve analysis as a routine procedure. Study design We prospectively performed multiple variants RT-PCR on consecutive SARS-CoV-2 RT-PCR positive samples from patients, healthcare workers and nursing home residents from our hospital catchment area. This technique was implemented in our automated Roche FLOW system with a turn-around time of 6 h. Results Between February 1 and May 2, 2021, 989 samples were tested by the variant RT-PCR. Our method was validated by comparison of variant RT-PCR to whole genome sequencing testing. We observed an increase over time in the proportion of UK variant that became the dominant variant, and the concurrent emergence of the South-African and Brazilian variants. Prompt public health responses for infection control were possible because of this rapid screening method, resulting in early detection and reduction of unnoticed spread of VOC as early as possible. Conclusion A variant RT-PCR with additional melting curve analyses is a feasible, rapid and efficient screening strategy that can be implemented in routine microbiological laboratories.
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Affiliation(s)
- David S Y Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Johannes G M Koeleman
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - Norbert Vaessen
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - Simone Breijer
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - Sunita Paltansing
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
| | - Peter de Man
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands
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9
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Li Y, Wan Z, Zuo L, Li S, Liu H, Ma Y, Zhou L, Jin X, Li Y, Zhang C. A Novel 2-dimensional Multiplex qPCR Assay for Single-Tube Detection of Nine Human Herpesviruses. Virol Sin 2021; 36:746-754. [PMID: 33635517 DOI: 10.1007/s12250-021-00354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human herpesviruses are double-stranded DNA viruses that are classified into nine species. More than 90% of adults are ever infected with one or more herpesviruses. The symptoms of infection with different herpesviruses are diverse ranging from mild or asymptomatic infections to deadly diseases such as aggressive lymphomas and sarcomas. Timely and accurate detection of herpesvirus infection is critical for clinical management and treatment. In this study, we established a single-tube nonuple qPCR assay for detection of all nine herpesviruses using a 2-D multiplex qPCR method with a house-keeping gene as the internal control. The novel assay can detect and distinguish different herpesviruses with 30 to 300 copies per 25 µL single-tube reaction, and does not cross-react with 20 other human viruses, including DNA and RNA viruses. The robustness of the novel assay was evaluated using 170 clinical samples. The novel assay showed a high consistency (100%) with the single qPCR assay for HHVs detection. The features of simple, rapid, high sensitivity, specificity, and low cost make this assay a high potential to be widely used in clinical diagnosis and patient treatment.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Lulu Zuo
- Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, China
| | - Honglian Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lianqun Zhou
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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10
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Chen KY, Xu JX, Wang MM, Hu D, Xie F, Huang D, Chen J, Yang T, Zhang J, Song F, Huang S, Zhong T. Single probe PCR melting curve analysis MTHFR C677T SNP sites. Anal Biochem 2021; 619:114102. [PMID: 33450284 DOI: 10.1016/j.ab.2021.114102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND The detection and analysis of methylene tetrahydrofolate reductase (MTHFR) C677T single nucleotide polymorphism (SNP) from blood samples is time-consuming and costly. We aimed to establish a method to detect these SNPs by direct whole blood PCR and without DNA extraction. METHODS Probes modified by different fluorescent groups on the same sequence were designed. Various MTHFR genotypes from direct blood PCR experiments were used to verify the similarity of the obtained and sequencing results. The SNP sites adjacent to the MTHFR C677T SNP were used to verify whether the method can accurately distinguish these sites. RESULTS The ROX probe was found to be the most suitable for this study. We tested 291 samples with 1 μL whole blood as a template, and obtained 126, 43, and 122 cases of C677C, C677T, and C677 C/T genotypes, respectively. The melting curve was consistent with the sequencing results. The detection limit was approximately 1000 white blood cells/μL. Through PCR and the melting curve method, the adjacent sites were accurately distinguished. CONCLUSION We established a reliable, simple, rapid, and low-cost direct blood PCR method for the detection of MTHFR C677T SNPs. This could also be used as a potential diagnostic tool for a variety of diseases.
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Affiliation(s)
- Kai-Yun Chen
- Department of Drug Clinical Trial, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Jiang-Xia Xu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Meng-Meng Wang
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Die Hu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Fangfang Xie
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Defa Huang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Jie Chen
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, Jiangxi Province, China
| | | | | | | | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, China.
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11
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Abstract
Quantitative-PCR (qPCR) enables the quantification of specific DNA targets, such as functional or phylogenetic marker genes associated with environmental samples. During each qPCR cycle, the number of copies of a gene (or region) of interest in DNA samples is determined in real time using a fluorescence-based label and compared to a standard serial dilution. Here, we describe a qPCR method to quantify the ammonia oxidizing bacteria involved in the first step of nitrification, using the amoA gene as a proxy of their abundance. The preparation of the standards from environmental samples and qPCR is presented in detail for specifically quantifying microbial abundance in environmental samples such as soil.
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Affiliation(s)
- Aimeric Blaud
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK.
| | - Abadie Maïder
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Herts, UK
| | - Ian M Clark
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Herts, UK
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12
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Li Y, Xu P, Wan Z, Du H, Jin X, Zhang C. Single-tube detection of nine bacterial antibiotic-resistance genes by a 2-dimensional multiplex qPCR assay based on fluorescence and melting temperature. Mol Biol Rep 2020; 47:7341-7348. [PMID: 32888129 DOI: 10.1007/s11033-020-05789-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/28/2020] [Indexed: 12/21/2022]
Abstract
Simple, multiplex qPCR methods are advantages for rapid molecular diagnosis of multiple antibiotics-resistant genes simultaneously. However, the number of genes can be detected in a single reaction tube is often limited by the fluorescence channels of a real-time PCR instrument. In this study, we developed a simple 2-D multiplex qPCR method by combining the probe colors and amplicon Tm values to overcome the mechanical limit of the machine. The principle of the novel assay was validated by detection of nine bacterial antibiotic-resistance genes (KPC, NDM, VIM, OXA-48, GES, CIT, EBC, ACC and DHA) in a single reaction tube. This assay is highly sensitive within a range of 30-3000 copies per reaction. The simplicity, rapidity, high sensitivity and specificity, and low cost of the novel method make it a promising tool for developing clinical diagnostic kits for monitoring resistance and other genetic determinants of infectious diseases.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, Suzhou, 215000, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China.
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13
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Drogou C, Sauvet F, Erblang M, Detemmerman L, Derbois C, Erkel MC, Boland A, Deleuze JF, Gomez-Merino D, Chennaoui M. Genotyping on blood and buccal cells using loop-mediated isothermal amplification in healthy humans. ACTA ACUST UNITED AC 2020; 26:e00468. [PMID: 32461926 PMCID: PMC7240324 DOI: 10.1016/j.btre.2020.e00468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/23/2020] [Accepted: 05/10/2020] [Indexed: 12/11/2022]
Abstract
Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt. LAMP-MC is a recently developed method to characterize Single Nucleotide Polymorphism. Detection is performed directly from whole blood or buccal cells. LAMP-MC method produced specific melting curves for 5 sleep debt-related SNPs. High concordance of results was observed between LAMP-MC and Taqman referent method.
Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt, particularly for five single nucleotide polymorphisms (SNPs). Loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) is a recently developed method to characterize SNPs. The aim of present study was to evaluate the LAMP-MC method on blood and buccal cells for detection of five SNPs of interest in healthy humans. We first analyzed signals obtained from LAMP-MC method on 42 samples. Then we compared the results with those of referent TaqMan method. The LAMP-MC method produced specific melting curves for the five SNPs. A high concordance of genotyping results was observed between the two methods for rs5751876_ADORA2A, rs1800629_TNF-α, rs73598374_ADA and rs228697_PER3 in blood and saliva (Cohen’s kappa coefficient >0.80). A good agreement ( = 0.61) was observed for rs4680_COMT in blood only. LAMP-MC is a simple and reliable method to study genetic influences on health, sleep debt-related performance impairments and countermeasures.
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Affiliation(s)
- Catherine Drogou
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Fabien Sauvet
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Mégane Erblang
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | | | - Céline Derbois
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Marie Claire Erkel
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Danielle Gomez-Merino
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Mounir Chennaoui
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
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14
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Laconi A, Berends AJ, de Laat ECH, Urselmann TAPMP, Verheije HM. Infectious bronchitis virus Mass-type (GI-1) and QX-like (GI-19) genotyping and vaccine differentiation using SYBR green RT-qPCR paired with melting curve analysis. J Virol Methods 2019; 275:113771. [PMID: 31712091 PMCID: PMC7113787 DOI: 10.1016/j.jviromet.2019.113771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/15/2019] [Accepted: 11/06/2019] [Indexed: 01/24/2023]
Abstract
Infectious Bronchitis Virus (IBV) is a highly contagious virus of chicken, causing huge economic losses in the poultry industry. Many genotypes circulate in a given area, and optimal protection relies on vaccination with live attenuated vaccines of the same genotype. As these live vaccines are derived from field viruses and circulate, understanding the prevalence of different IBV genotypes in any area is complex. In a recent study, the genome comparison of an IBV QX vaccine and its progenitor field strain led to the identification of vaccine markers. Here we developed a simplex SYBRgreen RT-qPCR assay for differentiation between QX-like field and vaccine strains and a multiplex SYBRgreen RT-qPCR assay for IBV genotyping with melting curve analysis, as each virus produced distinct and reliable melting peaks. Both the simplex and the multiplex assays showed excellent efficiency, sensitivity and specificity representing a low cost diagnostic tool for IBV genotyping and vaccine differentiation.
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Affiliation(s)
- Andrea Laconi
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Alinda J Berends
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Esther C H de Laat
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tara A P M P Urselmann
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Hélène M Verheije
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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15
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Liu P, Lu L, Xu M, Zhong H, Jia R, Su L, Cao L, Dong Z, Dong N, Zhou L, Xu J. A novel multiplex PCR for virus detection by melting curve analysis. J Virol Methods 2018; 262:56-60. [PMID: 30267725 PMCID: PMC7113878 DOI: 10.1016/j.jviromet.2018.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022]
Abstract
Taqman probe based melting curve analysis can detect and distinguish six respiratory viruses simultaneously. The multiplex PCR established here has a good analytical sensitivity and specificity. The accordance rate between the multiplex PCR and direct fluorescent antibody testing was high. Taqman probe based melting curve analysis is well suited to multiple virus detection.
Background Rapid and accurate laboratory diagnoses of viral infections are crucial for the management and treatment of patients with viral infections. Conventional methods for virus detection are labourious, time consuming, and only a single virus can be analysed in one assay. Objectives The objective of this study was to develop a novel real-time PCR method for multiple virus detection by melting curve analysis using Taqman probes in a single reaction. Study design As a model, six respiratory viruses were detected in one tube using three fluorophores. The specificity was assessed by cross-reaction tests with other common respiratory pathogens. The analytical sensitivity was assessed by testing the limit of detection of the assay using artificial plasmids as the positive template. The clinical evaluation of the established assay was evaluated for the detection of respiratory viruses in clinical samples, and the results were compared with direct fluorescent antibody testing (DFA). Results The six respiratory viruses were clearly distinguished by their respective melting temperature values in the corresponding fluorescence detection channels. No cross reactions were observed by cross reaction tests. The detection limits of this assay were 2 to 2 × 103 copies per reaction for each virus. The clinical evaluation of this assay was demonstrated by analysing 352 clinical samples, and 67(19.0%) samples were positive for at least one virus. The accordance rate between the established PCR and DFA testing was high, and ranged from 94.57% to 100%. Conclusions Taqman probe-based melting curve analysis is well suited for detection of multiple viruses in clinical and research laboratories because of its high throughput, reliability, and cost savings.
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Affiliation(s)
- Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Zuoquan Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Niuniu Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Linfu Zhou
- Medical Biotechnology Laboratory, Zhejiang University, Hangzhou, China.
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China.
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16
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Otaguiri ES, Morguette AEB, Morey AT, Tavares ER, Kerbauy G, de Almeida Torres RSL, Chaves Júnior M, Tognim MCB, Góes VM, Krieger MA, Perugini MRE, Yamauchi LM, Yamada-Ogatta SF. Development of a melting-curve based multiplex real-time PCR assay for simultaneous detection of Streptococcus agalactiae and genes encoding resistance to macrolides and lincosamides. BMC Pregnancy Childbirth 2018; 18:126. [PMID: 29724169 PMCID: PMC5934892 DOI: 10.1186/s12884-018-1774-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/25/2018] [Indexed: 01/25/2023] Open
Abstract
Background Streptococcus agalactiae or Group B Streptococcus (GBS) remains the leading cause of infections in newborns worldwilde. Prenatal GBS screening of pregnant women for vaginal-rectal colonization is recommended in many countries to manage appropriate intrapartum antimicrobial prophylaxis for those identified as carriers. In this study, a novel melting-curve based multiplex real-time PCR assay for the simultaneous detection of GBS and macrolide and lincosamide resistance markers was developed. The usefulness of the assay was evaluated for rapid and accurate prenatal GBS screening. Methods One hundred two pregnant women who were at 35–37 weeks of gestation were enrolled in this study. The analytical performance of the multiplex real-time PCR was first tested using a panel of reference and clinical bacterial and fungal strains. To test the clinical performance, vaginal-rectal swabs were obtained from pregnant women who were seen at the teaching hospital for regular prenatal care. The results of real-time were compared with those obtained from microbiological analyses. Results The real-time PCR assay showed 100% specificity and a limit of detection of 104 colony forming units equivalent per reaction. The prevalence of GBS colonization among the population studied was 15.7% (16/102) based on a positive culture and the real-time PCR results. Agreement between the two assays was found for 11 (68.75%) GBS colonized women. Using the culture-based results as a reference, the multiplex real-time PCR had a sensitivity of 91.7% (11/12, CI 59.7–99.6%), a specificity of 95.5% (86/90, CI 89.8–98.7%), a positive predictive value of 73.3% (11/15, CI 44.8–91.1%) and a negative predictive value of 98.9% (86/87, CI 92.9–99.9%). Conclusion The multiplex real-time PCR is a rapid, affordable and sensitive assay for direct detection of GBS in vaginal-rectal swabs. Electronic supplementary material The online version of this article (10.1186/s12884-018-1774-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliane Saori Otaguiri
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Ana Elisa Belotto Morguette
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alexandre Tadachi Morey
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Eliandro Reis Tavares
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Gilselena Kerbauy
- Departamento de Enfermagem, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Rosângela S L de Almeida Torres
- Laboratory of Bacteriology, Epidemiology Laboratory and Disease Control Division, Laboratório Central do Estado do Paraná - LACEN, Curitiba, PR, Brazil
| | - Mauricio Chaves Júnior
- Departamento de Medicina, Hospital Universitário de Maringá, Universidade Estadual de Maringá, Maringá, Brazil
| | | | | | | | - Marcia Regina Eches Perugini
- Departamento de Patologia, Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Lucy Megumi Yamauchi
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil. .,Departamento de Microbiologia, Universidade Estadual de Londrina, Centro de Ciências Biológicas, Rodovia Celso Garcia Cid, PR 445, km 380. CEP, Londrina, 86057-970, Brazil.
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17
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Rozej-Bielicka W, Masny A, Golab E. High-resolution melting PCR assay, applicable for diagnostics and screening studies, allowing detection and differentiation of several Babesia spp. infecting humans and animals. Parasitol Res 2017; 116:2671-2681. [PMID: 28795223 PMCID: PMC5599466 DOI: 10.1007/s00436-017-5576-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/28/2017] [Indexed: 12/24/2022]
Abstract
The goal of the study was to design a single tube PCR test for detection and differentiation of Babesia species in DNA samples obtained from diverse biological materials. A multiplex, single tube PCR test was designed for amplification of approximately 400 bp region of the Babesia 18S rRNA gene. Universal primers were designed to match DNA of multiple Babesia spp. and to have low levels of similarity to DNA sequences of other intracellular protozoa and Babesia hosts. The PCR products amplified from Babesia DNA isolated from human, dog, rodent, deer, and tick samples were subjected to high-resolution melting analysis for Babesia species identification. The designed test allowed detection and differentiation of four Babesia species, three zoonotic (B. microti, B. divergens, B. venatorum) and one that is generally not considered zoonotic—Babesia canis. Both detection and identification of all four species were possible based on the HRM curves of the PCR products in samples obtained from the following: humans, dogs, rodents, and ticks. No cross-reactivity with DNA of Babesia hosts or Plasmodium falciparum and Toxoplasma gondii was observed. The lack of cross-reactivity with P. falciparum DNA might allow using the assay in endemic malaria areas. The designed assay is the first PCR-based test for detection and differentiation of several Babesia spp. of medical and veterinary importance, in a single tube reaction. The results of the study show that the designed assay for Babesia detection and identification could be a practical and inexpensive tool for diagnostics and screening studies of diverse biological materials.
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Affiliation(s)
- Wioletta Rozej-Bielicka
- Department of Parasitology, National Institute of Public Health – National Institute of Hygiene, Warszawa, Poland
| | - Aleksander Masny
- Department of Parasitology, National Institute of Public Health – National Institute of Hygiene, Warszawa, Poland
| | - Elzbieta Golab
- Department of Parasitology, National Institute of Public Health – National Institute of Hygiene, Warszawa, Poland
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18
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Hasanpour M, Najafi A. Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli. J Microbiol Methods 2017; 137:25-29. [PMID: 28359738 DOI: 10.1016/j.mimet.2017.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 11/15/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (Tm) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.
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Affiliation(s)
- Mojtaba Hasanpour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran.
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19
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Gokulan K, Williams K, Khare S. Silver ion-mediated killing of a food pathogen: Melting curve analysis data of silver resistance genes and growth curve data. Data Brief 2017; 11:49-53. [PMID: 28127583 PMCID: PMC5247281 DOI: 10.1016/j.dib.2017.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 11/25/2022] Open
Abstract
Limited antibacterial activity of silver ions leached from silver-impregnated food contact materials could be due to: 1) the presence of silver resistance genes in tested bacteria; or 2) lack of susceptibility to silver ion-mediated killing in the bacterial strain (K. Williams, L. Valencia, K. Gokulan, R. Trbojevich, S. Khare, 2016 [1]). This study contains data to address the specificity of silver resistance genes in Salmonella Typhimurium during the real time PCR using melting curve analysis and an assessment of the minimum inhibitory concentration of silver ions for Salmonella.
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Affiliation(s)
- Kuppan Gokulan
- Division of Microbiology National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Katherine Williams
- Division of Microbiology National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sangeeta Khare
- Division of Microbiology National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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20
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Satoh H, Imai D, Sato S, Furuhama K, Harasawa R. Molecular detection of Mycoplasma haemomuris subspecies using dnaK-targeted real-time PCR with SYBR Green I and melting curve analysis. Mol Cell Probes 2016; 30:291-293. [PMID: 27720908 DOI: 10.1016/j.mcp.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 11/28/2022]
Abstract
Hemoplasmas cause severe infections in mammals, but these pathogens are difficult to detect and identify at the species and subspecies level because of the need for time-consuming sequence based methods. Here, we used real-time PCR with SYBR Green I targeting of the dnaK gene followed by standard melting curve analysis to achieve rapid detection and differentiation of the Mycoplasma haemomuris subspecies 'Candidatus Mycoplasma haemomuris subsp. musculi' and 'Candidatus M. haemomuris subsp. ratti'. The melting temperatures of the PCR products, 84.63 ± 0.14 °C for 'Candidatus M. haemomuris subsp. musculi', and 80.72 ± 0.16 °C for 'Candidatus M. haemomuris subsp. ratti', provided clear differentiation between them. Murine hemoplasma DNA samples, which were used as references, were confirmed for species by an analysis of 16S rRNA sequences. The protocol described herein provides a new rapid detection and identification method suitable for use with two recognized subspecies of M. haemomuris.
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Affiliation(s)
- Hiroshi Satoh
- Cooperative Department of Veterinary Medicine, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
| | - Daiki Imai
- Cooperative Department of Veterinary Medicine, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Shigeru Sato
- Cooperative Department of Veterinary Medicine, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Kazuhisa Furuhama
- The Iwate Research Center for Wildlife Diseases, 1-17-4 Nakano, Morioka, Iwate, 020-0816, Japan
| | - Ryô Harasawa
- The Iwate Research Center for Wildlife Diseases, 1-17-4 Nakano, Morioka, Iwate, 020-0816, Japan
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21
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Zheng X, Liu G, Opriessnig T, Wang Z, Yang Z, Jiang Y. Rapid detection and grouping of porcine bocaviruses by an EvaGreen(®) based multiplex real-time PCR assay using melting curve analysis. Mol Cell Probes 2016; 30:195-204. [PMID: 27180269 DOI: 10.1016/j.mcp.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 01/20/2023]
Abstract
Several novel porcine bocaviruses (PBoVs) have been identified in pigs in recent years and association of these viruses with respiratory signs or diarrhea has been suggested. In this study, an EvaGreen(®)-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed for simultaneous detection and grouping of novel PBoVs into the same genogroups G1, G2 and G3. Each target produced a specific amplicon with a melting peak of 81.3 ± 0.34 °C for PBoV G1, 78.2 ± 0.37 °C for PBoV G2, and 85.0 ± 0.29 °C for PBoV G3. Non-specific reactions were not observed when other pig viruses were used to assess the EG-mPCR assay. The sensitivity of the EG-mPCR assay using purified plasmid constructs containing the specific viral target fragments was 100 copies for PBoV G1, 50 for PBoV G2 and 100 for PBoV G3. The assay is able to detect and distinguish three PBoV groups with intra-assay and inter-assay variations ranging from 0.13 to 1.59%. The newly established EG-mPCR assay was validated with 227 field samples from pigs. PBoV G1, G2 and G3 was detected in 15.0%, 25.1% and 41.9% of the investigated samples and coinfections of two or three PBoV groups were also detected in 25.1% of the cases, indicating that all PBoV groups are prevalent in Chinese pigs. The agreement of the EG-mPCR assay with an EvaGreen-based singleplex real-time PCR (EG-sPCR) assay was 99.1%. This EG-mPCR will serve as a rapid, sensitive, reliable and cost effective alternative for routine surveillance testing of multiple PBoVs in pigs and will enhance our understanding of the epidemiological features and possible also pathogenetic changes associated with these viruses in pigs.
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Affiliation(s)
- Xiaowen Zheng
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gaopeng Liu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Zining Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zongqi Yang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
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Nath-Chowdhury M, Sangaralingam M, Bastien P, Ravel C, Pratlong F, Mendez J, Libman M, Ndao M. Real-time PCR using FRET technology for Old World cutaneous leishmaniasis species differentiation. Parasit Vectors 2016; 9:255. [PMID: 27141967 PMCID: PMC4855858 DOI: 10.1186/s13071-016-1531-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/24/2016] [Indexed: 02/06/2023] Open
Abstract
Background Recently, there has been a re-emergence of cutaneous leishmaniasis in endemic countries and an increase in imported cases in non-endemic countries by travelers, workers, expatriates, immigrants, and military force personnel. Old World cutaneous leishmaniasis is caused primarily by Leishmania major, L. tropica and L. aethiopica. Despite their low sensitivity, diagnosis traditionally includes microscopic and histopathological examinations, and in vitro cultivation. Several conventional PCR techniques have been developed for species identification, which are time-consuming and labour-intensive. Real-time PCR using SYBR green dye, although provides rapid detection, may generate false positive signals. Therefore, a rapid and easy method such as a FRET-based real-time PCR would improve not only the turn-around time of diagnosing Old World cutaneous Leishmania species but will also increase its specificity and sensitivity. Methods A FRET-based real-time PCR assay which amplifies the cathepsin L-like cysteine protease B gene encoding a major Leishmania antigen was developed to differentiate L. major, L. tropica, and L. aethiopica in one single step using one set of primers and probes. Assay performance was tested on cutaneous and visceral strains of Leishmania parasite cultures and isolates of other protozoan parasites as well as human biopsy specimen. Results The assay readily differentiates between the three Old World cutaneous leishmaniasis species based on their melting curve characteristics. A single Tm at 55.2 ± 0.5 °C for L. aethiopica strains was distinguished from a single Tm at 57.4 ± 0.2 °C for L. major strains. A double curve with melting peaks at 66.6 ± 0.1 °C and 48.1 ± 0.5 °C or 55.8 ± 0.6 °C was observed for all L. tropica strains. The assay was further tested on biopsy specimens, which showed 100 % agreement with results obtained from isoenzyme electrophoresis and Sanger sequencing. Conclusion Currently, there are no published data on real-time PCR using FRET technology to differentiate between Old World cutaneous Leishmania species. In summary, our assay based on specific hybridization addresses the limitations of previous PCR technology and provides a single step, reliable method of species identification and rapid diagnostic applications.
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Affiliation(s)
- Milli Nath-Chowdhury
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mugundhine Sangaralingam
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Patrick Bastien
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Christophe Ravel
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Francine Pratlong
- Department of Parasitology-Mycology, Centre National de Référence des Leishmanioses, Centre Hospitalier Régional Universitaire of Montpellier and University Montpellier I (Faculty of Medicine), UMR CNRS 5290-IRD 224- UM1 et 2 "MIVEGEC", Montpellier, France
| | - Juan Mendez
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Libman
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,J.D. MacLean Centre for Tropical Diseases at McGill University, Montreal, QC, Canada
| | - Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC, Canada. .,J.D. MacLean Centre for Tropical Diseases at McGill University, Montreal, QC, Canada.
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Zhang C, Niu P, Hong Y, Wang J, Zhang J, Ma X. A probe-free four-tube real-time PCR assay for simultaneous detection of twelve enteric viruses and bacteria. J Microbiol Methods 2015; 118:93-8. [PMID: 26342434 DOI: 10.1016/j.mimet.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVES We aim to develop a multiplex real-time PCR assay to detect the most common pathogens causing community outbreaks of diarrhea. METHODS Four reaction systems of fluorescence dye-based real-time PCR assay were performed to amplify genes of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, Campylobacter jejuni, Yersinia enterocolitica, Vibrio parahaemolyticus, Salmonella spp., Escherichia coli, and Shigella spp. PCR products of each pathogen were identified by characteristic peaks in melting curves. RESULTS The assay was able to achieve detection limit of 50 copies/reaction for each individual virus target, and 140-500CFU/mL for each individual bacterium target. A total of 122 clinical specimens from hospitalized children with acute diarrhea were used to evaluate the assay. The clinical sensitivity was very similar to that of reference methods. Norovirus genogroup II revealed the highest detectable rate (45/122, 36.9%). Coinfection was found in 28 out of 122 (23%) clinical specimens. CONCLUSION This assay proved to be a cost-effective, sensitive and reliable method for simultaneous detection of enteric viruses and bacteria.
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Affiliation(s)
- Chen Zhang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Peihua Niu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanying Hong
- Beijing Traditional Chinese Medicine Hospital, Capital Medical University Medical Laboratory, Beijing, China
| | - Ji Wang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingyun Zhang
- National Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuejun Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Gao L, Liu Y, Sun M, Zhao Y, Xie R, He Y, Xu W, Liu J, Lin Y, Lou J. Rapid detection of α-thalassaemia alleles of --(SEA)/, -α(3.7)/ and -α(4.2)/ using a dual labelling, self-quenching hybridization probe/ melting curve analysis. Mol Cell Probes 2015; 29:438-441. [PMID: 26190814 DOI: 10.1016/j.mcp.2015.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/17/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES The aim of the study was to set up an alternative automatic molecular diagnostic method for deletional α-thalassaemia mutations without gel electrophoresis. METHODS Based on the sequence variation within the two Z boxes and melting curve analysis of dually labelled probes, a real-time PCR assay was developed and validated for the rapid detection of major α-genotypes (--(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), --(SEA)/--(SEA), -α(3.7)/-α(3.7) and -α(4.2)/-α(4.2)). RESULTS Samples with the -α(3.7)/-α(3.7), -α(4.2)/-α(4.2), --(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), and --(SEA)/--(SEA) genotypes could be clearly distinguished. The accuracy of this technique for these samples was 100% sensitivity and specificity. CONCLUSION This technique is rapid and reliable, demonstrating feasibility for use in large-scale population screening and prenatal diagnosis of deletional Hb H disease and Hb Bart's hydrops fetalis.
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Affiliation(s)
- Lan Gao
- Department of Clinical Laboratory, Henan Province People's Hospital, Zhengzhou, Henan, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Manna Sun
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Ying Zhao
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Rungui Xie
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Yi He
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Wanfang Xu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Jianxin Liu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Yangyang Lin
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Jiwu Lou
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, Guangdong, China.
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Decremps F, Gauthier M, Ayrinhac S, Bove L, Belliard L, Perrin B, Morand M, Le Marchand G, Bergame F, Philippe J. Picosecond acoustics method for measuring the thermodynamical properties of solids and liquids at high pressure and high temperature. Ultrasonics 2015; 56:129-140. [PMID: 24852260 DOI: 10.1016/j.ultras.2014.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/13/2014] [Accepted: 04/02/2014] [Indexed: 06/03/2023]
Abstract
Based on the original combination of picosecond acoustics and diamond anvils cell, recent improvements to accurately measure hypersonic sound velocities of liquids and solids under extreme conditions are described. To illustrate the capability of this technique, results are given on the pressure and temperature dependence of acoustic properties for three prototypical cases: polycrystal (iron), single-crystal (silicon) and liquid (mercury) samples. It is shown that such technique also enables the determination of the density as a function of pressure for liquids, of the complete set of elastic constants for single crystals, and of the melting curve for any kind of material. High pressure ultrafast acoustic spectroscopy technique clearly opens opportunities to measure thermodynamical properties under previously unattainable extreme conditions. Beyond physics, this state-of-the-art experiment would thus be useful in many other fields such as nonlinear acoustics, oceanography, petrology, in of view. A brief description of new developments and future directions of works conclude the article.
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Affiliation(s)
- F Decremps
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France.
| | - M Gauthier
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
| | - S Ayrinhac
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
| | - L Bove
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France; Ecole Polytech. Fed. Lausanne, Inst. Condensed Matter Phys., EPSL, CH-1015 Lausanne, Switzerland
| | - L Belliard
- Institut des NanoSciences de Paris, Université Pierre et Marie Curie, 75252 Paris, France
| | - B Perrin
- Institut des NanoSciences de Paris, Université Pierre et Marie Curie, 75252 Paris, France
| | - M Morand
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
| | - G Le Marchand
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
| | - F Bergame
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
| | - J Philippe
- Institut de Minéralogie et Physique des Milieux Condensés, Université Pierre et Marie Curie, 75252 Paris, France
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Niu PH, Zhang C, Wang J, Tan WJ, Ma XJ. Detection and Identification of Six Foodborne Bacteria by Two-tube Multiplex Real Time PCR and Melting Curve Analysis. Biomed Environ Sci 2014; 27:770-778. [PMID: 25341812 DOI: 10.3967/bes2014.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/19/2014] [Indexed: 06/04/2023]
Abstract
OBJECTIVE This study is aimed to develop a two-tube melting curve-based multiplex real time PCR assay (MCMRT-PCR) for the simultaneous detection of six common foodborne pathogenic bacteria (diarrhoeagenic Escherichia coli, Salmonella, and Shigella in tube 1, Staphylococcus aureus, Vibrio parahaemolyticus, and Listeria monocytogenes in tube 2). METHODS A two-tube MCMRT-PCR assay was performed on 7900HT Fast Real-Time PCR System (Applied Biosystems, USA). Amplification by PCR was optimized to obtain high efficiency. The sensitivity and specificity of assays were investigated. RESULTS The detection limit of optimized MCMRT-PCR assay was 3.9×102 CFU/mL for S. aureus, 4.4×102 CFU/mL for L. monocytogenes, 3.0×102 CFU/mL for Salmonella, 2.5×102 CFU/mL for Shigella, 2.1×102 CFU/mL for V. parahaemolyticus, and 1.2×102 CFU/mL for E. coli. The feasibility of MCMRT-PCR was further evaluated using artificially contaminated milk, the sensitivity was at the level of 105 CFU/mL. CONCLUSION A two-tube MCMRT-PCR assay using six primer sets was developed for detection of multiple pathogens. Our findings demonstrates that the proposed two-tube assay is reliable, useful and rapid for simultaneous detection of six foodborne pathogenic bacteria with an intended application in provincial Centers for Diseases Control and Prevention (CDC).
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Affiliation(s)
- Pei Hua Niu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chen Zhang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ji Wang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wen Jie Tan
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xue Jun Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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