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Malinin NL, Lee G, Lazzarotto CR, Li Y, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Iafrate AJ, Le LP, Aryee MJ, Joung JK, Tsai SQ. Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq. Nat Protoc 2021; 16:5592-5615. [PMID: 34773119 PMCID: PMC9331158 DOI: 10.1038/s41596-021-00626-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 10/31/2020] [Accepted: 09/02/2021] [Indexed: 12/26/2022]
Abstract
Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we describe a detailed GUIDE-seq protocol including cell transfection, library preparation, sequencing and bioinformatic analysis. The entire protocol including cell culture can be completed in 9 d. Once tag-integrated genomic DNA is isolated, library preparation, sequencing and analysis can be performed in 3 d. The result is a genome-wide catalog of off-target sites ranked by nuclease activity as measured by GUIDE-seq read counts. GUIDE-seq is one of the most sensitive cell-based methods for defining genome-wide off-target activity and has been broadly adopted for research and therapeutic use.
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Affiliation(s)
- Nikolay L Malinin
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - GaHyun Lee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zongli Zheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Nhu T Nguyen
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
| | - Matthew Liebers
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Ved V Topkar
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - A John Iafrate
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Long P Le
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Martin J Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Yu B, van Tol HTA, Stout TAE, Roelen BAJ. Reverse transcription priming methods affect normalisation choices for gene expression levels in oocytes and early embryos. Mol Hum Reprod 2021; 27:6307270. [PMID: 34152407 PMCID: PMC8314208 DOI: 10.1093/molehr/gaab040] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/05/2021] [Indexed: 11/14/2022] Open
Abstract
Mammalian oocytes and embryos rely exclusively on maternal mRNAs to accomplish early developmental processes. Since oocytes and early embryos are transcriptionally silent after meiotic resumption, most of the synthesised maternal mRNA does not undergo immediate translation but is instead stored in the oocyte. Quantitative RT-PCR is commonly used to quantify mRNA levels, and correct quantification relies on reverse transcription and the choice of reference genes. Different methods for reverse transcription may affect gene expression determination in oocytes. In this study, we examined the suitability of either random or oligo(dT) primers for reverse transcription to be used for quantitative RT-PCR. We further looked for changes in poly(A) length of the maternal mRNAs during oocyte maturation. Our data indicate that depending on the method of reverse transcription, the optimal combination of reference genes for normalisation differed. Surprisingly, we observed a shortening of the poly(A) tail lengths of maternal mRNA as oocytes progressed from germinal vesicle to metaphase II. Overall, our findings suggest dynamic maternal regulation of mRNA structure and gene expression during oocyte maturation and early embryo development.
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Affiliation(s)
- Bo Yu
- Farm Animal Health, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Helena T A van Tol
- Farm Animal Health, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Tom A E Stout
- Equine Sciences, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bernard A J Roelen
- Embryology, Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Correspondence address. Embryology, Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands. E-mail: http://orcid.org/0000-0001-9512-4708
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3
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Chowdhury IA, Yan G. Development of Real-Time and Conventional PCR Assays for Identifying a Newly Named Species of Root-Lesion Nematode ( Pratylenchus dakotaensis) on Soybean. Int J Mol Sci 2021; 22:5872. [PMID: 34070906 PMCID: PMC8197872 DOI: 10.3390/ijms22115872] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
A rapid and accurate PCR-based method was developed in this study for detecting and identifying a new species of root-lesion nematode (Pratylenchus dakotaensis) recently discovered in a soybean field in North Dakota, USA. Species-specific primers, targeting the internal transcribed spacer region of ribosomal DNA, were designed to be used in both conventional and quantitative real-time PCR assays for identification of P.dakotaensis. The specificity of the primers was evaluated in silico analysis and laboratory PCR experiments. Results showed that only P.dakotaensis DNA was exclusively amplified in conventional and real-time PCR assays but none of the DNA from other control species were amplified. Detection sensitivity analysis revealed that the conventional PCR was able to detect an equivalent to 1/8 of the DNA of a single nematode whereas real-time PCR detected an equivalent to 1/32 of the DNA of a single nematode. According to the generated standard curve the amplification efficiency of the primers in real-time PCR was 94% with a R2 value of 0.95 between quantification cycle number and log number of P.dakotaensis. To validate the assays to distinguish P.dakotaensis from other Pratylenchus spp. commonly detected in North Dakota soybean fields, 20 soil samples collected from seven counties were tested. The PCR assays amplified the DNA of P.dakotaensis and discriminated it from other Pratylenchus spp. present in North Dakota soybean fields. This is the first report of a species-specific and rapid PCR detection method suitable for use in diagnostic and research laboratories for the detection of P.dakotaensis.
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Affiliation(s)
| | - Guiping Yan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA;
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Lu X, Wang L, Sakthivel SK, Whitaker B, Murray J, Kamili S, Lynch B, Malapati L, Burke SA, Harcourt J, Tamin A, Thornburg NJ, Villanueva JM, Lindstrom S. US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2020; 26:1654-1665. [PMID: 32396505 PMCID: PMC7392423 DOI: 10.3201/eid2608.201246] [Citation(s) in RCA: 397] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the etiologic agent associated with coronavirus disease, which emerged in late 2019. In response, we developed a diagnostic panel consisting of 3 real-time reverse transcription PCR assays targeting the nucleocapsid gene and evaluated use of these assays for detecting SARS-CoV-2 infection. All assays demonstrated a linear dynamic range of 8 orders of magnitude and an analytical limit of detection of 5 copies/reaction of quantified RNA transcripts and 1 x 10-1.5 50% tissue culture infectious dose/mL of cell-cultured SARS-CoV-2. All assays performed comparably with nasopharyngeal and oropharyngeal secretions, serum, and fecal specimens spiked with cultured virus. We obtained no false-positive amplifications with other human coronaviruses or common respiratory pathogens. Results from all 3 assays were highly correlated during clinical specimen testing. On February 4, 2020, the Food and Drug Administration issued an Emergency Use Authorization to enable emergency use of this panel.
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Mögling R, Meijer A, Berginc N, Bruisten S, Charrel R, Coutard B, Eckerle I, Enouf V, Hungnes O, Korukluoglu G, Kossyvakis T, Mentis A, Molenkamp R, Muradrasoli S, Papa A, Pigny F, Thirion L, van der Werf S, Reusken C. Delayed Laboratory Response to COVID-19 Caused by Molecular Diagnostic Contamination. Emerg Infect Dis 2020; 26:1944-1946. [PMID: 32433015 PMCID: PMC7392437 DOI: 10.3201/eid2608.201843] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) created an exceptional situation in which numerous laboratories in Europe simultaneously implemented SARS-CoV-2 diagnostics. These laboratories reported in February 2020 that commercial primer and probe batches for SARS-CoV-2 detection were contaminated with synthetic control material, causing delays of regional testing roll-out in various countries.
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Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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Chen C, Chen Y, Huang W, Jiang Y, Zhang H, Wu W. Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica. PLoS One 2019; 14:e0221040. [PMID: 31437239 PMCID: PMC6706007 DOI: 10.1371/journal.pone.0221040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/29/2019] [Indexed: 11/18/2022] Open
Abstract
Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.
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Affiliation(s)
- Chen Chen
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Youjun Chen
- Key Laborary of Superior Forage Germplasm in the Qinghai-Tibetan Plateau (2017-ZJ-Y12), Qinghai University, Xining, Qinghai Province, China
| | - Wenjuan Huang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Yijie Jiang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Huihui Zhang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Wei Wu
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
- * E-mail:
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Cai G, Fleury TJ, Zhang N. Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen. Sci Rep 2019; 9:7969. [PMID: 31138887 PMCID: PMC6538632 DOI: 10.1038/s41598-019-44411-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/28/2018] [Accepted: 05/16/2019] [Indexed: 11/30/2022] Open
Abstract
Microsatellites are a tract of repetitive, short DNA motifs (usually 1 to 6 bp) abundant in eukaryotic genomes. They are robust molecular markers in many areas of studies. Development of microsatellite markers usually involves three steps: (1) obtaining microsatellite-containing sequences, (2) primer design, and (3) screening microsatellite loci for polymorphism. The first and third steps require considerable resources. Next generation sequencing technologies have greatly alleviated the constraint of the first step. In this study, we leveraged the availability of genome assemblies of multiple individuals in many species and designed a comparative genomics approach to bioinformatically identify polymorphic loci. Our approach can eliminate or greatly reduce the need of experimental screening for polymorphism and ensure that the flanking regions do not have length difference that would confound interpretation of genotyping results using microsatellite markers. We applied this approach on Phytophthora sojae, a soybean pathogen, and identified 157 high-quality, informative microsatellite markers in this oomycete. Experimental validation of 20 loci supported bioinformatics predictions. Our approach can be readily applied to other organisms of which the genomes of multiple individuals have been sequenced.
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Affiliation(s)
- Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, 47907, West Lafayette, IN, USA.
- Botany and Plant Pathology Department, Purdue University, 47907, West Lafayette, IN, USA.
| | - Tomara J Fleury
- Crop Production and Pest Control Research Unit, USDA-ARS, 47907, West Lafayette, IN, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, 08901, New Brunswick, NJ, USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 08901, New Brunswick, NJ, USA
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9
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Bosma TJ, Karagiannis K, Santana-Quintero L, Ilyushina N, Zagorodnyaya T, Petrovskaya S, Laassri M, Donnelly RP, Rubin S, Simonyan V, Sauder CJ. Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm. PLoS One 2019; 14:e0216944. [PMID: 31100083 PMCID: PMC6524942 DOI: 10.1371/journal.pone.0216944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Most viruses are known to spontaneously generate defective viral genomes (DVG) due to errors during replication. These DVGs are subgenomic and contain deletions that render them unable to complete a full replication cycle in the absence of a co-infecting, non-defective helper virus. DVGs, especially of the copyback type, frequently observed with paramyxoviruses, have been recognized to be important triggers of the antiviral innate immune response. DVGs have therefore gained interest for their potential to alter the attenuation and immunogenicity of vaccines. To investigate this potential, accurate identification and quantification of DVGs is essential. Conventional methods, such as RT-PCR, are labor intensive and will only detect primer sequence-specific species. High throughput sequencing (HTS) is much better suited for this undertaking. Here, we present an HTS-based algorithm called DVG-profiler to identify and quantify all DVG sequences in an HTS data set generated from a virus preparation. DVG-profiler identifies DVG breakpoints relative to a reference genome and reports the directionality of each segment from within the same read. The specificity and sensitivity of the algorithm was assessed using both in silico data sets as well as HTS data obtained from parainfluenza virus 5, Sendai virus and mumps virus preparations. HTS data from the latter were also compared with conventional RT-PCR data and with data obtained using an alternative algorithm. The data presented here demonstrate the high specificity, sensitivity, and robustness of DVG-profiler. This algorithm was implemented within an open source cloud-based computing environment for analyzing HTS data. DVG-profiler might prove valuable not only in basic virus research but also in monitoring live attenuated vaccines for DVG content and to assure vaccine lot to lot consistency.
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Affiliation(s)
- Trent J. Bosma
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Konstantinos Karagiannis
- Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC, United States of America
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Luis Santana-Quintero
- Office of Hematology and Oncology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Natalia Ilyushina
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Tatiana Zagorodnyaya
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Svetlana Petrovskaya
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Steven Rubin
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Vahan Simonyan
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Christian J. Sauder
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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Escobedo-Guerra MR, Katoku-Herrera M, Lopez-Hurtado M, Gutierrez-Trujillo R, Guerra-Infante FM. Use of the mtrR Gene for Rapid Molecular Diagnosis of Neisseria gonorrhoeae and Identification of the Reduction of Susceptibility to Antibiotics in Endocervical Swabs. Mol Diagn Ther 2018; 22:361-368. [PMID: 29589256 DOI: 10.1007/s40291-018-0328-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Neisseria gonorrhoeae is one of the main etiological agents of sexually transmitted diseases. The asymptomatic course of the infection and its resistance to antibiotics can lead to pelvic inflammatory disease and infertility. OBJECTIVES We developed a polymerase chain reaction (PCR) test using the methyltetrahydrofolate homocysteine methyltransferase reductase (mtrR) gene to identify N. gonorrhoeae and detect reduced susceptibility to antibiotics. MATERIAL AND METHODS We analysed 250 samples of endocervical exudate from infertile women with a negative diagnosis of N. gonorrhoeae. We designed NGmtr primers to detect N. gonorrhoeae and identify the antibiotic-resistant strain. RESULTS Of the 250 samples, 60 (24%) tested positive for N. gonorrhoeae using real-time PCR. Our study was validated using the HO primers and the Seeplex STD6 ACE System, with a 100% correlation. Furthermore, the NGmtr primers are specific for N. gonorrhoeae and not for other species. Additionally, the curves generated by real-time PCR differed between wild and variant strains (10.93%). The dissociation temperatures for the wild and variant strains were 86.5 and 89 °C, respectively. CONCLUSIONS The NGmtr primers enabled us to identify N. gonorrhoeae strains with or without reduction of susceptibility to antibiotics. Therefore, this work constitutes a tool that will facilitate the diagnosis of this infection for a low cost and improve patient quality of life.
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Affiliation(s)
- Marcos R Escobedo-Guerra
- Departamento de Infectología, Instituto Nacional de Perinatología, Montes Urales No. 800, Colonia Lomas de Virreyes, Miguel Hidalgo, CP 11000, Mexico City, Mexico
| | - Mitzuko Katoku-Herrera
- Departamento de Infectología, Instituto Nacional de Perinatología, Montes Urales No. 800, Colonia Lomas de Virreyes, Miguel Hidalgo, CP 11000, Mexico City, Mexico
| | - Marcela Lopez-Hurtado
- Departamento de Infectología, Instituto Nacional de Perinatología, Montes Urales No. 800, Colonia Lomas de Virreyes, Miguel Hidalgo, CP 11000, Mexico City, Mexico
| | - Rodrigo Gutierrez-Trujillo
- Departamento de Infectología, Instituto Nacional de Perinatología, Montes Urales No. 800, Colonia Lomas de Virreyes, Miguel Hidalgo, CP 11000, Mexico City, Mexico
| | - Fernando M Guerra-Infante
- Departamento de Infectología, Instituto Nacional de Perinatología, Montes Urales No. 800, Colonia Lomas de Virreyes, Miguel Hidalgo, CP 11000, Mexico City, Mexico.
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Flores-Herrera P, Arredondo-Zelada O, Marshall SH, Gómez FA. Selection and validation of reliable housekeeping genes to evaluate Piscirickettsia salmonis gene expression. Infect Genet Evol 2018; 63:151-157. [PMID: 29860100 DOI: 10.1016/j.meegid.2018.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/15/2018] [Accepted: 05/30/2018] [Indexed: 12/30/2022]
Abstract
Piscirickettsia salmonis is a highly aggressive facultative intracellular bacterium that challenges the sustainability of Chilean salmon production. Due to the limited knowledge of its biology, there is a need to identify key molecular markers that could help define the pathogenic potential of this bacterium. We think a model system should be implemented that efficiently evaluates the expression of putative bacterial markers by using validated, stable, and highly specific housekeeping genes to properly select target genes, which could lead to identifying those responsible for infection and disease induction in naturally infected fish. Here, we selected a set of validated reference or housekeeping genes for RT-qPCR expression analyses of P. salmonis under different growth and stress conditions, including an in vitro infection kinetic. After a thorough screening, we selected sdhA as the most reliable housekeeping gene able to represent stable and highly specific host reference genes for RT-qPCR-driven P. salmonis analysis.
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Affiliation(s)
- Patricio Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
| | - Oscar Arredondo-Zelada
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
| | - Fernando A Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330 Curauma, Valparaíso, Chile.
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Defosse TA, Le Govic Y, Vandeputte P, Courdavault V, Clastre M, Bouchara JP, Chowdhary A, Giglioli-Guivarc'h N, Papon N. A synthetic construct for genetic engineering of the emerging pathogenic yeast Candida auris. Plasmid 2018; 95:7-10. [PMID: 29170093 DOI: 10.1016/j.plasmid.2017.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 08/28/2017] [Revised: 11/16/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022]
Abstract
Candida auris has recently emerged as a global cause of severe hospital-acquired fungal infections. To enable functional genomic approaches for this prominent pathogen, we designed a synthetic construct that can be used to genetically transform the genome-sequenced strain VPCI 479/P/13 of C. auris following an efficient electroporation procedure.
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Affiliation(s)
- Tatiana A Defosse
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), GEIHP, UNIV. Angers, Université Bretagne-Loire, Angers, France; Université François-Rabelais de Tours, Biomolécules et Biotechnologies Végétales, Tours EA 2106, France
| | - Yohann Le Govic
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), GEIHP, UNIV. Angers, Université Bretagne-Loire, Angers, France; Laboratoire de Parasitologie - Mycologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Patrick Vandeputte
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), GEIHP, UNIV. Angers, Université Bretagne-Loire, Angers, France; Laboratoire de Parasitologie - Mycologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Vincent Courdavault
- Université François-Rabelais de Tours, Biomolécules et Biotechnologies Végétales, Tours EA 2106, France
| | - Marc Clastre
- Université François-Rabelais de Tours, Biomolécules et Biotechnologies Végétales, Tours EA 2106, France
| | - Jean-Philippe Bouchara
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), GEIHP, UNIV. Angers, Université Bretagne-Loire, Angers, France; Laboratoire de Parasitologie - Mycologie, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (EA 3142), GEIHP, UNIV. Angers, Université Bretagne-Loire, Angers, France.
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Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L. Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase. Nucleic Acids Res 2017; 45:9046-9058. [PMID: 28911121 PMCID: PMC5587808 DOI: 10.1093/nar/gkx633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.
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Affiliation(s)
- Rubén Agudo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
| | - Patricia A. Calvo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | | | - Luis Blanco
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
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14
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Ma Y, Lu Y, Guan G, Luo J, Niu Q, Liu J, Yin H, Liu G. Flower-like ZnO nanostructure assisted loop-mediated isothermal amplification assay for detection of Japanese encephalitis virus. Virus Res 2017; 232:34-40. [PMID: 28137456 DOI: 10.1016/j.virusres.2017.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/24/2016] [Accepted: 01/23/2017] [Indexed: 11/20/2022]
Abstract
In this study, we described a novel and effective flower-like ZnO nanostructure assisted Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) method to detect Japanese Encephalitis Virus (JEV). The effects of different concentrations of ZnO nanoflower on the RT-LAMP reaction were investigated. With the increase of concentration of ZnO nanoflower, RT-LAMP reaction obtained optimization, until the concentration exceeded 1.5nM, RT-LAMP reaction was inhibited. Made 1nM as optimum concentration of ZnO nanoflower, we found that optimum RT-LAMP reaction temperature and time were 60°C and 30min, respectively. The optimization might be connected with good adsorption to DNA and thermal conductivity of ZnO nanoflower, but mechanism of the RT-LAMP reaction affected by ZnO nanoflower needs to be explored further.
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Affiliation(s)
- Yonghua Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China; Toxicology Laboratory, Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730030, China
| | - Yan Lu
- Key Laboratory of Atomic and Molecular Physics & Functional Materials of Gansu Province, College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China.
| | - Qingli Niu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, China
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15
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Kuznetsova TV, Smimova MS, Leonovich OA, Gordeichuk IV, Biriukova IK, Zylkova MV, Tyn'o YY, Belyakova AV, Shevelev AB. A new method of producing NS5A antigen of hepatitis C virus. Vopr Virusol 2017; 62:17-25. [PMID: 29323842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A task of creating a universal platform for engineering affordable recombinant producers of viral proteins conserving immunogenicity has not been solved yet. High toxicity of the viral proteins for the host cells, low yield and abnormal folding of the products often present severe obstacles to obtaining producers of the viral proteins. In this work, we report a new method of engineering and screening of deletion libraries from the viral antigen genes. This method allows selection of artificial derivatives of these genes adapted for expression in microbial producer cells. The method involves PCR amplification of the gene fragments using a system of randomized and adapter primers, which allows the spontaneous formation of duplexes from the random primers in the absence of the template DNA to be prevented. For selecting variants capable of in vivo expression, the obtained PCR products are cloned to a special vector of a direct phenotypical selection pQL30. It contains E. coli β-galactosidase gene with an inserted polylinker producing a frame-shift mutation. Using this screening method, an artificial variant of hepatitis C (HCV) NS5a gene with optimal biotechnological properties was established. 27 clinical specimens of 1670 bp long HCV1b NS5a fragments were used as a source gene. A PCR bank of the deletion derivatives was produced. 40 LacZ-positive clones based on pQL30 vector with a 50-700 bp long insertion were selected. The LacZ activity of the cell lysates and the immunogenicity of the products were tested. As a result, a single clone encoding a soluble protein with Mr = 114 kDa was selected. Its yield reached 0.3% of the total cell protein. It was highly reactive with sera of HCV 1b infected patients but not with sera of the healthy donors.
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16
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Mansour H, Bryngelsson T, Garkava-Gustavsson L. Development, characterization and transferability of 10 novel microsatellite markers in Cotoneaster orbicularis Schltdl. (Rosaceae). J Genet 2016; 95:e9-e12. [PMID: 27659209 DOI: 10.1007/s12041-016-0687-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Hassan Mansour
- Faculty of Science, Department of Botany, Suez Canal University, 41522 Ismailia, Egypt.
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Khorosheva EM, Karymov MA, Selck DA, Ismagilov RF. Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP. Nucleic Acids Res 2016; 44:e10. [PMID: 26358811 PMCID: PMC4737171 DOI: 10.1093/nar/gkv877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions.
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Affiliation(s)
- Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Mikhail A Karymov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
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18
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Coudray-Meunier C, Fraisse A, Martin-Latil S, Delannoy S, Fach P, Perelle S. A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System. PLoS One 2016; 11:e0147832. [PMID: 26824897 PMCID: PMC4732599 DOI: 10.1371/journal.pone.0147832] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/08/2016] [Indexed: 12/23/2022] Open
Abstract
Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health.
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Affiliation(s)
- Coralie Coudray-Meunier
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
- * E-mail:
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19
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Ostankova YV, Semenov AV, Stoyanova NA, Tokarevich NK, Lyubimova NE, Petrova OA, Ananina YV, Petrov EM. [TYPING OF LEPTOSPIRA SPP. STRAINS BASED ON 16S rRNA]. Zh Mikrobiol Epidemiol Immunobiol 2016:35-39. [PMID: 27029114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
AIM Comparative typing of Leptospira spp. strain collection based on analysis of 16S RNA fragment. MATERIALS AND METHODS 2 pairs of primers were used for PCR, that jointly flank 1423b.p. sized fragment. Sequences of Leptospira spp. strain 16S rRNA, presented in the international database, were used for phylogenetic analysis. RESULTS A high similarity, including interspecies, of the 16S fragment in Leptospira spp. strains was shown independently of the source, serovar and serogroup. Heterogeneity of the primary matrix, spontaneous mutations of hotspots and erroneous nucleotide couplings, characteristic for 16S sequence of pathogenic Leptospira spp. strains, are discussed. Molecular-genetic characteristic of certain reference Leptospira spp. strains by 16S sequence is obtained. CONCLUSION Results of the studies give evidence on expedience of introduction into clinical practice of identification of Leptospira spp. by 16S sequence directly from the clinical material, that would allow to significantly reduce identification time, dismiss complex type-specific sera and other labor-intensive methods.
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20
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Dedkov VG, Deviatkin AA, Poleschuk EM, Safonova MV, Markelov ML, Shipulin GA. Development and evaluation of the RT-PCR kit for the rabies virus diagnosis. Vopr Virusol 2016; 61:235-240. [PMID: 29323857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To improve the diagnosis, surveillance, and control for the rabies virus, a kit for hybridization-triggered fluorescence detection of rabies virus DNA by the RT-PCR technique was developed and evaluated. The analytical sensitivity of the kit was 4*10 GE per ml. High specificity of the kit was shown using representative sampling of viral, bacterial, and human nucleic acids.
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21
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Kartashov MY, Mikryukova TP, Ternovoi VA, Moskvitina NS, Loktev VB. [THE HIGHLY EFFECTIVE DETECTION OF DNA RICKETTSIA USING TECHNIQUE OF POLYMERASE CHAIN REACTION IN REAL-TIME]. Klin Lab Diagn 2015; 60:39-43. [PMID: 27032252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The article considers development of highly effective technique of detection of genetic material of ricketsia based on polymerase chain reaction in real-time using original primers to the most conservative sites of gene of citrate synthase (gItA). The analytical sensitivity of the developed polymerase chain reaction in real-time test permits to detect from 80 genome equivalents in analyzed sample during three hours. The high specificity of test-system is substantiated by detection of nucleotide sequences of amplificated fragments of gene gltA. The approbation ofthe polymerase chain reaction in real-time test is carried out on collection of 310 ticks of species I. persulcatus, I. pavlovskyi, D. reticulatus. It is demonstrated that the developed alternate ofprimers and probe permits with high degree of sensitivity and specifcity to detect DNA of different species of ricketsia widespread on territory of Russia (R. sibirica, R. raoultii, R. helvetica, R. tarasevichiae). The proposed polymerase chain reaction in real-time test can be appliedfor isolation of fragment of gene gltA with purpose for detecting nucleotide sequence and subsequent genetic typing of ricketsia. The application ofthe proposed technique can facilitate task of monitoring hot spots of ricketsiosis.
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22
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Randhawa GJ, Chhabra R, Bhoge RK, Singh M. Visual and Real-Time Event-Specific Loop-Mediated Isothermal Amplification Based Detection Assays for Bt Cotton Events MON531 and MON15985. J AOAC Int 2015; 98:1207-14. [PMID: 26525238 DOI: 10.5740/jaoacint.14-269] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bt cotton events MON531 and MON15985 are authorized for commercial cultivation in more than 18 countries. In India, four Bt cotton events have been commercialized; more than 95% of total area under genetically modified (GM) cotton cultivation comprises events MON531 and MON15985. The present study reports on the development of efficient event-specific visual and real-time loop-mediated isothermal amplification (LAMP) assays for detection and identification of cotton events MON531 and MON15985. Efficiency of LAMP assays was compared with conventional and real-time PCR assays. Real-time LAMP assay was found time-efficient and most sensitive, detecting up to two target copies within 35 min. The developed real-time LAMP assays, when combined with efficient DNA extraction kit/protocol, may facilitate onsite GM detection to check authenticity of Bt cotton seeds.
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23
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Xu CCY, Yen IJ, Bowman D, Turner CR. Spider Web DNA: A New Spin on Noninvasive Genetics of Predator and Prey. PLoS One 2015; 10:e0142503. [PMID: 26606730 PMCID: PMC4659541 DOI: 10.1371/journal.pone.0142503] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 10/22/2015] [Indexed: 01/06/2023] Open
Abstract
Noninvasive genetic sampling enables biomonitoring without the need to directly observe or disturb target organisms. This paper describes a novel and promising source of noninvasive spider and insect DNA from spider webs. Using black widow spiders (Latrodectus spp.) fed with house crickets (Acheta domesticus), we successfully extracted, amplified, and sequenced mitochondrial DNA from spider web samples that identified both spider and prey to species. Detectability of spider DNA did not differ between assays with amplicon sizes from 135 to 497 base pairs. Spider and prey DNA remained detectable at least 88 days after living organisms were no longer present on the web. Spider web DNA as a proof-of-concept may open doors to other practical applications in conservation research, pest management, biogeography studies, and biodiversity assessments.
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Affiliation(s)
- Charles C. Y. Xu
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
| | - Ivy J. Yen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Dean Bowman
- Potawatomi Zoo, South Bend, Indiana, United States of America
| | - Cameron R. Turner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
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24
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Liang ML, Yan JL, Yang YQ, Liu L, Li CY, Yang J. Construction of overexpression vectors of Magnaporthe oryzae genes BAS1 and BAS4 fusion to mCherry and screening of overexpression strains. Genet Mol Res 2015; 14:7068-78. [PMID: 26125917 DOI: 10.4238/2015.june.26.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this study was to construct overexpression vectors and selecting strains of the Magnaporthe oryzae effectors BAS1 and BAS4. Primer pairs of BAS1, BAS4, and mCherry were designed based on their known nucleotide sequences. The coding sequences of BAS1 and BAS4 were amplified, and the pXY201 plasmid was selected as a template to amplify the mCherry sequence. Fragments of BAS1 and mCherry, and BAS4 and mCherry were ligated into the pCAMBIA1302 vector. The recombinant pCAMBIA-BAS1-mCherry and pCAMBIA-BAS4-mCherry plasmids were transformed into E. coli DH5α competent cells. Transformants were screened by PCR, and plasmids from the positive transformants were extracted by enzymatic digestion to obtain pCAMBIA-BAS1-mCherry and pCAMBIA-BAS4-mCherry. The pCAMBIA-BAS1-mCherry and pCAMBIA-BAS4-mCherry plasmids were transformed into protoplasts of rice blast strains and the transformed strains were screened by PCR using primer pairs against the hygromycin gene. The result showed that the PCR products corresponded with the theoretical sizes. RT-PCR was used to analyze the expression of BAS1 and BAS4 in five transformed strains of BAS1 and BAS4, and the result showed that the higher expression level of the two genes was occurred in five transformant strains comparing to wild-type strain A3467-40 (the strain containing BAS1 and BAS4), but there was no difference among the five overexpression strains. The sporulation and spore germination of transformed strains was higher than in wild type strain, and there was no difference in the germination time. Construction of overexpression vectors and strains of M. oryzae effectors BAS1 and BAS4 provide reference material for other new effectors.
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Affiliation(s)
- M L Liang
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
| | - J L Yan
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
| | - Y Q Yang
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
| | - L Liu
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
| | - C Y Li
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
| | - J Yang
- Key Laboratory for Agricultural Biodiversity and Pest Management of China Education Ministry, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan, China
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25
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Abstract
Ion Torrent is a next generation sequencing technology based on the detection of hydrogen ions produced during DNA chain elongation; this technology allows analyzing and characterizing genomes, genes, and species. Here, we describe an Ion Torrent procedure applied to the metagenomic analysis of 16S rRNA gene amplicons to study the bacterial diversity in food and environmental samples.
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Affiliation(s)
- Elio Fantini
- Italian National Agency for New technologies, Energy and Sustainable development, Roma, Italy
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26
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Gerasymenko IM, Mazur MG, Sheludko YV, Kuchuk NV. MULTIPLEX PCR ASSAY FOR DETECTION OF HUMAN SOMATOTROPIN AND INTERFERON ALPHA2b GENES IN PLANT MATERIAL. Tsitol Genet 2015; 49:3-8. [PMID: 26214899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Using transgenic plants as factories for production of physiologically active human proteins arouses special concern because occasional escape of such transgenes into environment may cause health problems. Creation of plant varieties producing pharmaceutically valuable proteins should be accompanied by development of detection methods suitable for controlling the transgene behavior. Here we describe a multiplex PCR protocol for revealing of two human genes (encoding growth hormone and interferon alpha2b) that have been successfully introduced into plant genomes. The primer pair designed for detection of human growth hormone coding sequence amplifies fragments of different size from the full-length gene in the human genome and the intronless coding sequence usually used for plant transformation. Application of this primer pair may be recommended for ruling out false positive results due to sample contamination with human DNA. Such a control may be useful also in PCR analysis during establishing of transgenic plants carrying genes of human origin.
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27
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De Spiegelaere W, Philippé J, Vervisch K, Verhofstede C, Malatinkova E, Kiselinova M, Trypsteen W, Bonczkowski P, Vogelaers D, Callens S, Ruelle J, Kabeya K, De Wit S, Van Acker P, Van Sandt V, Emonds MP, Coucke P, Sermijn E, Vandekerckhove L. Comparison of methods for in-house screening of HLA-B*57:01 to prevent abacavir hypersensitivity in HIV-1 care. PLoS One 2015; 10:e0123525. [PMID: 25874872 PMCID: PMC4398410 DOI: 10.1371/journal.pone.0123525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 03/04/2015] [Indexed: 12/27/2022] Open
Abstract
Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting.
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Affiliation(s)
| | - Jan Philippé
- Ghent University, Department of Clinical Chemistry, Microbiology and Immunology, Ghent, Belgium
| | - Karen Vervisch
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Chris Verhofstede
- Ghent University, Department of Clinical Chemistry, Microbiology and Immunology, Ghent, Belgium
| | - Eva Malatinkova
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Maja Kiselinova
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Wim Trypsteen
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | | | - Dirk Vogelaers
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Steven Callens
- Ghent University, Department of Internal Medicine, Ghent, Belgium
| | - Jean Ruelle
- Université Catholique de Louvain, IREC, AIDS Reference Laboratory, Brussels, Belgium
| | - Kabamba Kabeya
- Saint-Pierre University Hospital, Department of Infectious Diseases, Bruxelles, Belgium
| | - Stephane De Wit
- Saint-Pierre University Hospital, Department of Infectious Diseases, Bruxelles, Belgium
| | - Petra Van Acker
- Ghent University, Center for Medical Genetics, Ghent, Belgium
| | - Vicky Van Sandt
- HILA, Laboratory for Histocompatibility & Immunogenetics Red Cross Flanders, Mechelen, Belgium
| | - Marie-Paule Emonds
- HILA, Laboratory for Histocompatibility & Immunogenetics Red Cross Flanders, Mechelen, Belgium
| | - Paul Coucke
- Ghent University, Center for Medical Genetics, Ghent, Belgium
| | - Erica Sermijn
- Ghent University, Department of Internal Medicine, Ghent, Belgium
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Gao S, Zhang J, Miao T, Ma D, Su Y, An Y, Zhang Q. A simple and convenient sticky/blunt-end ligation method for fusion gene construction. Biochem Genet 2015; 53:42-8. [PMID: 25820211 DOI: 10.1007/s10528-015-9669-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/27/2015] [Indexed: 11/26/2022]
Abstract
Here we present a simple and convenient sticky/blunt-end ligation method for fusion gene construction. The fusion gene is constructed by seamless ligation of 5'-end phosphorylated blunt ends instead of by overlap extension PCR (OE-PCR). Therefore, the challenge of amplifying large DNA fragments (e.g., the large bifunctional enzyme gene constructed by fusion of two monofunctional enzyme genes) by PCR can be avoided. In addition, synthesis of the inner primers for OE-PCR is not necessary, indicating that this method should be especially convenient for construction of fusion genes with various combinations of multiple fragments (e.g., chimeric gene libraries, fusion gene libraries). As a modification of the commonly used fusion gene construction technique, this method may find a wide range of applications in bioscience and biotechnology.
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Affiliation(s)
- Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, No. 120 Dongling Road, Shenyang, 110161, People's Republic of China
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Korotaieva N V, Limanska N V. [Detection of pathogenic bacteria Rhizobium vitis in vineyards of the south of Ukraine]. Mikrobiol Z 2015; 77:28-32. [PMID: 26036030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The total number of microbiota from grape crown gall tissues ranged from (2,3 ± 0.8) x 10(3) to (7.3 ± 0.4) x 10(5) CFU/g. The amount of bacteria from Rhizobium genus reached from (1.2 ±0.2) x 10(2) to (2.1 ± 0.2) x 10(4) CFU/g depending on a tested plant. It was found out that only a small percentage of the strains (3.1 - 4.9%) were oncogenic. New pathogenic strains (R. vitis ONU388, R. vitis ONU389 and R. vitis ONU390) possessing plasmid genes of pathogenicity virC, ipt and virD2 were isolated.
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Sokolenko GG, Karpechenko NA. [Expression of inulinase genes in the yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus]. Mikrobiologiia 2015; 84:37-42. [PMID: 25916145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Expression of the genes encoding the enzymes involved in inulin, sucrose, and glucose metabolism in the yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus was studied. The exon-intron structure of the relevant genes was identified and the primers for quantitative PCR were optimized. Expression of the genes was found to depend on the carbon source. Glucose was shown to exhibit a repressive effect on inulinase synthesis by K. marxianus, while in S. cerevisiae glucose and sucrose were inulinase inducer and repressor, respectively.
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Duan Y, Zhang X, Ge C, Wang Y, Cao J, Jia X, Wang J, Zhou M. Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum. Sci Rep 2014; 4:7094. [PMID: 25403277 PMCID: PMC4235284 DOI: 10.1038/srep07094] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/29/2014] [Indexed: 11/24/2022] Open
Abstract
Resistance of Fusarium graminearum to carbendazim is caused by point mutations in the β2-tubulin gene. The point mutation at codon 167 (TTT → TAT, F167Y) occurs in more than 90% of field resistant isolates in China. To establish a suitable method for rapid detection of the F167Y mutation in F. graminearum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed and optimized to specially distinguish the F167Y mutation genotype. The LAMP reaction was optimal at 63 °C for 60 min. When hydroxynaphthol blue dye (HNB) was added prior to amplification, samples with DNA of the F167Y mutation developed a characteristic sky blue color after the reaction but those without DNA or with different DNA did not. Results of HNB staining method were reconfirmed by gel electrophoresis. The developed LAMP had good specificity, stability and repeatability and was suitable for monitoring carbendazim-resistance populations of F. graminearum in agricultural production.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changyan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhong Cao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Jia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
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Thanchomnang T, Tantrawatpan C, Intapan PM, Sanpool O, Janwan P, Lulitanond V, Tourtip S, Yamasaki H, Maleewong W. Rapid molecular identification of human taeniid cestodes by pyrosequencing approach. PLoS One 2014; 9:e100611. [PMID: 24945530 PMCID: PMC4063941 DOI: 10.1371/journal.pone.0100611] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 05/28/2014] [Indexed: 11/19/2022] Open
Abstract
Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.
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Affiliation(s)
- Tongjit Thanchomnang
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Faculty of Medicine, Mahasarakham University, Mahasarakham, Thailand
| | - Chairat Tantrawatpan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Division of Cell Biology, Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Rangsit Campus, Pathum Thani, Thailand
| | - Pewpan M. Intapan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Oranuch Sanpool
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Penchom Janwan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, School of Allied Health Sciences and Public Health, Walailak University, Thasala, Nakhon Si Thammarat, Thailand
| | - Viraphong Lulitanond
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Hiroshi Yamasaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Wanchai Maleewong
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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Morozov EN, Supriaga VG, Rakova VM, Morozova LF, Zhukova LA. [Human dirofilariasis: clinical and diagnostic signs and diagnostic methods]. Med Parazitol (Mosk) 2014:13-17. [PMID: 25296420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The clinical and diagnostic signs caused by the tissue location and migration of adult Dirofilaria in the human body determine the use of different methods for the diagnosis of dirofilariasis. During their investigations, the authors modified polymerase chain reaction (PCR): they chose and synthesized primers and selected amplification regimens for them and obtained agarose gel bands that corresponded to PCR fragment length nucleotide sequences that were equal to 245 bp for D. (N.) repens and 656 bp for D. immitis. There was 100% agreement in the results of PCR and microscopic examination of sera from 32 dogs and 1 female patient with low parasitemia and in the blood nucleotide sequence characteristic of D. repens.
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Latyshev OE, Eliseeva OV, Grebennikova TV, Verkhovskiĭ OA, Tsibezov VV, Chernykh OI, Dzhailidi GA, Aliper TI. [Real-time PCR kits for the detection of the African Swine Fever virus]. Vopr Virusol 2014; 59:47-49. [PMID: 25895212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The results obtained using the diagnostic kit based on real-time polymerase chain reaction to detect the DNA of the African Swine Fever in the pathological material, as well as in the culture fluid, are presented. A high sensitivity and specificity for detection of the DNA in the organs and tissues of animals was shown to be useful for detection in the European Union referentiality reagent kits for DNA detection by real time PCR of ASFV. More rapid and effective method of DNA extraction using columns mini spin Quick gDNA(TM) MiniPrep was suggested and compared to the method of DNA isolation on the inorganic sorbent. High correlation of the results of the DNA detection of ASFV by real-time PCR and antigen detection results ASFV by competitive ELISA obtained with the ELISA SEROTEST/INGEZIM COMRAC PPA was demonstrated. The kit can be used in the veterinary services for effective monitoring of ASFV to contain, eliminate and prevent further spread of the disease.
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Gadkar VYJ, Filion M. New Developments in Quantitative Real-time Polymerase Chain Reaction Technology. Curr Issues Mol Biol 2013; 16:1-6. [PMID: 23562919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
Real time-quantitative PCR (RT-qPCR) technology has revolutionized the detection landscape in every area of molecular biology. The fundamental basis of this technology has remained unchanged since its inception, however various modifications have enhanced the overall performance of this highly versatile technology. These improvements have ranged from changes in the individual components of the enzymatic reaction cocktail (polymerizing enzymes, reaction buffers, probes, etc.) to the detection system itself (instrumentation, software, etc.). The RT-qPCR technology currently available to researchers is more sensitive, faster and affordable than when this technology was first introduced. In this article, we summarize the developments of the last few years in RT-qPCR technology and nucleic acid amplification.
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Affiliation(s)
- Vija yJ Gadkar
- Department of Biology, Universite de Moncton, 18 Antonine-Maillet, Moncton, NB E1A 3E9 Canada
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Kuzuya A, Tanaka K, Katada H, Komiyama M. Enzyme treatment-free and ligation-independent cloning using caged primers in polymerase chain reactions. Molecules 2011; 17:328-40. [PMID: 22210171 PMCID: PMC6290560 DOI: 10.3390/molecules17010328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/26/2011] [Accepted: 12/27/2011] [Indexed: 11/29/2022] Open
Abstract
A new simple scheme for constructing recombinant vectors that does not require any restriction enzyme, ligase, or any other special enzyme treatment has been developed. By using caged primers in PCR, unnatural sticky-ends of any sequence, which are sufficiently long for ligation-independent cloning (LIC), are directly prepared on the product after a brief UVA irradiation. Target genes and vectors amplified by this light-assisted cohesive-ending (LACE) PCR join together in the desired arrangement in a simple mixture of them, tightly enough to be repaired and ligated in competent cells.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
- Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
- Author to whom correspondence should be addressed; (A.K.); (M.K.); Tel.: +81-6-6368-0829 (A.K.); Fax: +81-6-6368-0829 (A.K.); Tel.: +81-3-5452-5200 (M.K.); Fax: +81-3-5452-5209 (M.K.)
| | - Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
| | - Hitoshi Katada
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; (K.T.); (H.K.)
- Author to whom correspondence should be addressed; (A.K.); (M.K.); Tel.: +81-6-6368-0829 (A.K.); Fax: +81-6-6368-0829 (A.K.); Tel.: +81-3-5452-5200 (M.K.); Fax: +81-3-5452-5209 (M.K.)
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Lymans'ka OI, Lymans'kyĭ OP. [Molecular technologies in detecting sensitive and isoniazid-resistant Mycobacterium tuberculosis]. Tsitol Genet 2011; 45:34-47. [PMID: 22329161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two types of techniques for detection of single nucleotide polymorphism in 315 codon of katG gene of MTB are developed. Isoniazid resistance of MTB is associated with point mutations in the mentioned codon. Two primer sets with additional competitive blocking primer containing 3'-terminal phosphate group (for elimination of unspecific amplification) allow detecting the most frequent point mutations AGC --> ACC and AGC --> AGA in 315 codon of katG gene. PCR with primer set of two primers one of which contains five LNA-monomers allows to determine an occurrence of any type from six known mutations in 315 codon of katG gene, i.e. to differentiate wild type and isoniazid-resistant MTB. Purity and structure of 17 bp long primers with LNA-modified nucleotides were characterized by time-of-flight MALDI-mass spectrometry. Duplex of 17 bp length formed by two complementary oligonucleotides with LNA-monomers was studied using melting.
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Martín I, García T, Rojas M, Pegels N, Pavón MA, Hernández PE, González I, Martín R. Real-time polymerase chain reaction detection of fishmeal in feedstuffs. J AOAC Int 2010; 93:1768-1777. [PMID: 21313802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A SYBR Green PCR system was developed for detection of fishmeal in feedstuffs. The real-time PCR method combines the use of fish-specific primers that amplify an 87 base pair (bp) fragment of the mitochondrial 12S ribosomal RNA gene from fish species, and a positive control primer pair that amplifies a 99 bp fragment of the nuclear 18S ribosomal RNA gene in all eukaryotic organisms. The specificity of the primers was tested against 52 animal species and six plant species. Reference feedstuff samples were successfully tested for the presence of fishmeal, demonstrating the applicability of the assay to feedstuffs.
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Affiliation(s)
- Irene Martín
- Universidad Complutense de Madrid, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, 28040 Madrid, Spain
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Saha SK, Darmstadt GL, Baqui AH, Hossain B, Islam M, Foster D, Al-Emran H, Naheed A, Arifeen SE, Luby SP, Santosham M, Crook D. Identification of serotype in culture negative pneumococcal meningitis using sequential multiplex PCR: implication for surveillance and vaccine design. PLoS One 2008; 3:e3576. [PMID: 18974887 PMCID: PMC2571985 DOI: 10.1371/journal.pone.0003576] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/29/2008] [Indexed: 11/19/2022] Open
Abstract
Background PCR-based serotyping of Streptococcus pneumoniae has been proposed as a simpler approach than conventional methods, but has not been applied to strains in Asia where serotypes are diverse and different from other part of the world. Furthermore, PCR has not been used to determine serotype distribution in culture-negative meningitis cases. Methodology Thirty six serotype-specific primers, 7 newly designed and 29 previously published, were arranged in 7 multiplex PCR sets, each in new hierarchies designed for overall serotype distribution in Bangladesh, and specifically for meningitis and non-meningitis isolates. Culture-negative CSF specimens were then tested directly for serotype-specific sequences using the meningitis-specific set of primers. PCR-based serotyping of 367 strains of 56 known serotypes showed 100% concordance with quellung reaction test. The first 7 multiplex reactions revealed the serotype of 40% of all, and 31% and 48% non-meningitis and meningitis isolates, respectively. By redesigning the multiplex scheme specifically for non-meningitis or meningitis, the quellung reaction of 43% and 48% of respective isolates could be identified. Direct examination of 127 culture-negative CSF specimens, using the meningitis-specific set of primers, yielded serotype for 51 additional cases. Conclusions This PCR approach, could improve ascertainment of pneumococcal serotype distributions, especially for meningitis in settings with high prior use of antibiotics.
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Affiliation(s)
- Samir K Saha
- Department of Microbiology, Bangladesh Institute of Child Health, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh.
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Fan Z, Yue C, Tang Y, Zhang Y. Cloning, sequence analysis and expression of bacterial lipase-coding DNA fragments from environment in Escherichia coli. Mol Biol Rep 2008; 36:1515-9. [PMID: 18773306 DOI: 10.1007/s11033-008-9344-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2008] [Accepted: 08/12/2008] [Indexed: 11/26/2022]
Abstract
Thirteen pairs of primers were designed, synthesized and used to clone the whole coding sequences or mature peptide-coding sequences of lipases. Bacteria producing extracellular lipases were enriched for the extraction of total DNAs. Eight fragments with 500-1,200 bp in length were obtained by using touchdown PCR and sequenced. Five of them were found to be lipase-coding DNAs. One fragment called BL9 that was 95.9% similar to a coding sequence of putative lipase. This lipase contained a Gly-His-Ser-Met-Gly motif which is matched to the consensus Gly-X-Ser-X-Gly conserved among lipolytic enzymes. The BL9 DNA fragment was inserted into the expression vector pET32a(+) of Escherichia coli. A functional product was yielded in the supernatant and produced a hydrolyzed zone on the tributyrin agar.
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Affiliation(s)
- Zhaoxin Fan
- College of Life Science, Sichuan University, Sichuan Key Laboratory of Molecular Biology & Biotechnology, Chengdu, 610064, China.
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41
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Bruno JG, Crowell R. Selective glutaraldehyde-mediated coupling of proteins to the 3'-adenine terminus of polymerase chain reaction products. J Biomol Tech 2008; 19:177-183. [PMID: 19137104 PMCID: PMC2563924] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Attachment of proteins to the 3' end of DNA increases stability of the DNA in serum and retards clearance of DNA by major organs, thereby enhancing in vivo half-life and therapeutic potential of DNA. Unfortunately, the length of DNA molecules that can be produced with 3 ' modifications by solid-phase synthesis for protein attachment is limited to 45-60 nucleotides due to uncertainties about sequence fidelity for longer oligonucleotides. Here we describe selective covalent coupling of proteins or other molecules to the 3'-adenine overhang of unlabeled and fluorophore-labeled double-stranded polymerase chain reaction products putatively at the N6 position of adenine using 2.5% glutaraldehyde at pH 6.0 and 4 degrees C for at least 16 h. Gel mobility shift analyses and fluorescence analyses of the shifted bands supported conjugate formation between double-stranded polymerase chain reaction products and beta2-microglobulin. In addition, blunt-ended DNA ladder fragments treated with glutaraldehyde at 4 degrees C showed no evidence of DNA-DNA or DNA-protein conjugate formation. With the present cold glutaraldehyde technique, longer DNA-3'-protein conjugates might be easily mass-produced. The protein portion of a DNA-3'-protein conjugate could possess functionality as well, such as receptor binding for cell entry, cytotoxicity, or opsonization.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, San Antonio, TX 78229, USA.
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Abstract
Background In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. Results This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. Conclusion Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds. primique can be reached via this web address:
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Affiliation(s)
- Jakob Fredslund
- BiRC – Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Building 1090, DK-8000 Århus C, Denmark
| | - Mette Lange
- Research Centre Flakkebjerg, Dept. of Genetics and Biotechnology, University of Aarhus, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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Abstract
BACKGROUND DNA-based methods are useful for enhancing immunohematology typings. Ready-to-use Conformité Européenne (CE)-marked test kits based on polymerase chain reaction with sequence-specific priming (PCR-SSP) have been developed, which enable the examination of weak, unexpected, or unclear serologic findings. DEVELOPMENT AND VALIDATION: Primers were designed according to established mutation databases. Proficiency testing for CE marking was performed in accordance with Directive 98/79EC of the European Parliament and of the Council of October 27, 1998 on in vitro diagnostic medical devices using pretyped in-house and external samples. INTENDED USE: BAGene PCR-SSP kits are in vitro diagnostic devices. Genotyping of ABO and RHD/RHCE as well as HPA and KEL, JK, and FY specificities has to be performed after the conclusion of the serologic determination. APPLICATION Ready-to-use PCR-SSP typing kits allow the determination of common, rare, or weak alleles of the ABO blood group, Rhesus, and Kell/Kidd/Duffy systems as well as alleles of the human platelet antigens. RESULTS The investigations showed clear-cut results in accordance with serology or molecular genetic pretyping. CONCLUSION PCR-SSP is a helpful supplementary technique for resolving most of the common problems caused by discrepant or doubtful serologic results, and it is an easy-to-handle robust method. Questionable cases in donor, recipient, and patient typing can be examined with acceptable cost.
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Affiliation(s)
- Martina Prager
- Department of Production Molecular Genetics, BAG--BiologischeAnalysensystemGmbH, Lich, Germany.
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Brandes JC, Carraway H, Herman JG. Optimal primer design using the novel primer design program: MSPprimer provides accurate methylation analysis of the ATM promoter. Oncogene 2007; 26:6229-37. [PMID: 17384671 DOI: 10.1038/sj.onc.1210433] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methylation-specific polymerase chain reaction (PCR) (MSP) is frequently used to study gene silencing by promoter hypermethylation. However, non-specific primer design can lead to false-positive detection of methylation. We present a novel, web-based algorithm for the design of primers for bisulfite-PCRs (MSP, sequencing, COBRA and multiplex-MSP), allowing the determination of a specificity score, which is based on the thermodynamic characteristics of the primer 3'-end. PCR amplification with primers not reaching a high specificity score can result in false-positive findings. We used MSPprimer to design MSP primers for analysis of the ATM promoter. In 37 non-small cell lung cancer (NSCLC) samples and 43 breast cancer samples no promoter methylation was detected. Conversely, published MSP primers not reaching the required specificity score led to non-specific amplification of DNA not converted by bisulfite. The result was a false-positive incidence of ATM promoter methylation of 24% in NSCLC and 48% in breast cancers, similar to published studies. This highlights the critical need for specific primer design for MSP. MSPprimer is a convenient tool to achieve this goal, which is available free of charge to the scientific community.
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Affiliation(s)
- J C Brandes
- Cancer Biology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer, Center at Johns Hopkins, Baltimore, MD 21231-1000, USA
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Afonina IA, Mills A, Sanders S, Kulchenko A, Dempcy R, Lokhov S, Vermeulen NMJ, Mahoney W. Improved biplex quantitative real-time polymerase chain reaction with modified primers for gene expression analysis. Oligonucleotides 2007; 16:395-403. [PMID: 17155914 DOI: 10.1089/oli.2006.16.395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Stabilizing modified bases incorporated in primers allows the reduction of housekeeping gene primer concentration not possible with regular primers without sacrificing amplification efficiency. Low primer concentration allows coamplification of the most abundant housekeeping genes with very rare templates without mutual inhibition. Real-time polymerase chain reaction (PCR) coamplification of 18S ribosomal RNA with several genes of interest was used in this study with MGB Eclipse (Nanogen, San Diego, CA) hybridization probes. The results may be useful for high throughput gene expression studies as they simplify validation experiments.
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Lin CK, Lin JC. Development of PCR primers based on a fragment from randomly amplified polymorphic DNA for the detection of Escherichia coli O157:H7/NM. Mol Cell Probes 2006; 21:182-9. [PMID: 17178212 DOI: 10.1016/j.mcp.2006.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 11/06/2006] [Accepted: 11/09/2006] [Indexed: 11/20/2022]
Abstract
Serotype O157:H7 of EHEC is by far the most prevalent serotype associated with haemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS). Although PCR methods aimed on the detection of genes associated with the pathogenicity of Escherichia coli O157:H7 have been reported, tests allowing the direct identification of this serotype are rare. In this study, we used RAPD-PCR tests to analyze strains of E. coli O157:H7 serotype, strains of non-pathogenic E. coli, and strains of other pathotypes, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), and enteroaggregation E. coli (EAggEC). One RAPD fragment co-shared by serotype O157:H7 strains was observed when 10-mer primer termed as OPQ3 was used. After sequencing this fragment, three primers were designed and combined to form two PCR primer pairs. These two primer pairs were highly specific to the strains belonging to E. coli O157:H7/NM (non-motile).
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Affiliation(s)
- Chien-Ku Lin
- Department of Food Science and Nutrition, Hungkuang University, Shalu, Taichung County, Taiwan 43302, ROC.
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Abstract
The Grueneberg ganglion (GG) is a cluster of neurones present in the vestibule of the anterior nasal cavity. Although its function is still elusive, recent studies have shown that cells of the GG transcribe the gene encoding the olfactory marker protein (OMP) and project their axons to glomeruli of the olfactory bulb, suggesting that they may have a chemosensory function. Chemosensory responsiveness of olfactory neurones in the main olfactory epithelium (MOE) and the vomeronasal organ (VNO) is based on the expression of either odorant receptors or vomeronasal putative pheromone receptors. To scrutinize its presumptive olfactory nature, the GG was assessed for receptor expression by extensive RT-PCR analyses, leading to the identification of a distinct vomeronasal receptor which was expressed in the majority of OMP-positive GG neurones. Along with this receptor, these cells expressed the G proteins Go and Gi, both of which are also present in sensory neurones of the vomeronasal organ. Odorant receptors were expressed by very few cells during prenatal and perinatal stages; a similar number of cells expressed adenylyl cyclase type III and G(olf/s), characteristic signalling elements of the main olfactory system. The findings of the study support the notion that the GG is in fact a subunit of the complex olfactory system, comprising cells with either a VNO-like or a MOE-like phenotype. Moreover, expression of a vomeronasal receptor indicates that the GG might serve to detect pheromones.
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Affiliation(s)
- Jörg Fleischer
- University of Hohenheim, Institute of Physiology, Stuttgart, Germany.
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Aoi Y, Hosogai M, Tsuneda S. Real-time quantitative LAMP (loop-mediated isothermal amplification of DNA) as a simple method for monitoring ammonia-oxidizing bacteria. J Biotechnol 2006; 125:484-91. [PMID: 16790287 DOI: 10.1016/j.jbiotec.2006.04.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 04/01/2006] [Accepted: 04/10/2006] [Indexed: 11/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) of DNA is a novel technique for the amplification of DNA under isothermal conditions. For the first time, we applied this method to develop a simple and quantitative monitoring method for environmental microorganisms targeting amoA gene in ammonia-oxidizing bacteria. Quantitative analysis was performed first by measuring fluorescence derived from an intercalation dye using a real-time thermal cycler, and then by measuring the turbidity of the reaction solution using a real-time turbidimeter. As a result, it was possible to quantify the initial amoA DNA concentration from an environment with a sensitivity down to 10(2) DNA copies of target DNA and a dynamic range of 7-9 orders in magnitude. Background DNA from nontargeted bacteria (Pseudomonas denitrificans) that does not encode amoA gene did not affect the quantitative capability of LAMP. Over results suggested that the real-time LAMP is effective for monitoring microorganisms and their gene expression in environments.
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Affiliation(s)
- Yoshiteru Aoi
- Department of Chemical Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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Abstract
A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly degenerate primers for a set of genomic sequences. We report on the success of the program in several applications, one of which is an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.
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Affiliation(s)
- Chaim Linhart
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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50
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Abstract
Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles.
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Affiliation(s)
- Kai Müller
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany.
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