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https://www.readbyqxmd.com/read/28919163/multiplex-pcr-and-ngs-based-identification-of-mrna-splicing-variants-analysis-of-brca1-splicing-pattern-as-a-model
#1
Jan Hojny, Petra Zemankova, Filip Lhota, Jan Sevcik, Viktor Stranecky, Hana Hartmannova, Katerina Hodanova, Ondrej Mestak, David Pavlista, Marketa Janatova, Jana Soukupova, Michal Vocka, Zdenek Kleibl, Petra Kleiblova
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28906580/comparison-of-one-commercial-and-two-in-house-taqman-multiplex-real-time-pcr-assays-for-detection-of-enteropathogenic-enterotoxigenic-and-enteroaggregative-escherichia-coli
#2
Andreas Hahn, Marc Luetgehetmann, Olfert Landt, Norbert Georg Schwarz, Hagen Frickmann
OBJECTIVE: Enteropathogenic, enterotoxigenic, and enteroaggregative Escherichia coli (EPEC, ETEC, EAEC) are among the most frequent causes of diarrhea during travel or on military deployments. Cost efficient and reliable real-time multiplex PCR (mPCR) assays are desirable for surveillance or point prevalence studies in remote and resource-limited tropical settings. We compared one commercial PCR kit and two in-house assays without using a gold standard to estimate sensitivity and specificity of each assay...
September 14, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28888870/efficient-differentiation-of-corynebacterium-striatum-corynebacterium-amycolatum-and-corynebacterium-xerosis-clinical-isolates-by-multiplex-pcr-using-novel-species-specific-primers
#3
Carolina S Santos, Juliana N Ramos, Veronica V Vieira, Carina S Pinheiro, Roberto Meyer, Neuza M Alcantara-Neves, Rommel T Ramos, Artur Silva, Raphael Hirata, Liza Felicori, Carlos Ruiz de Alegría Puig, Jesús Navas, Vasco Azevedo, Ana L Mattos-Guaraldi, Luis G C Pacheco
A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.
September 6, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28888869/development-of-a-set-of-multiplex-pcrs-for-detection-of-genes-encoding-cell-wall-associated-proteins-in-staphylococcus-pseudintermedius-isolates-from-dogs-humans-and-the-environment
#4
Nathita Phumthanakorn, Pattrarat Chanchaithong, Nuvee Prapasarakul
Staphylococcus pseudintermedius commonly colonizes the skin of dogs, whilst nasal carriage may occur in humans who are in contact with dogs or the environment of veterinary hospitals. Genes encoding cell wall-associated (CWA) proteins have been described in Staphylococcus aureus but knowledge of their occurrence in S. pseudintermedius is still limited. The aim of the study was to develop a method to detect S. pseudintermedius surface protein genes (sps) encoding CWA proteins, and to examine the distribution of the genes in isolates from different sources...
September 6, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28877158/antibiotic-use-in-hospitalized-children-with-respiratory-viruses-detected-by-multiplex-polymerase-chain-reaction
#5
Pavel Goriacko, Lisa Saiman, Philip Zachariah
BACKGROUND: Multiplex polymerase chain reaction (mPCR) based methods are increasingly used to detect respiratory pathogens in children. While rapid identification of viruses has been shown to reduce antibiotic use, the impact of detecting specific viruses on antibiotic utilization has not been ascertained. This study compared antibiotic utilization among hospitalized children who tested positive for different respiratory viruses at admission. METHODS: A single-center study of hospitalized children under 21 years of age who tested positive at admission for at least one respiratory virus by mPCR from October 1 2012 to October 1 2015 was performed...
September 5, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28799826/multiplex-assay-for-identifying-animal-species-found-in-the-tibetan-area-using-the-mitochondrial-12s-rrna-gene
#6
Jung Nam Lee, MingFeng Jiang, YongLi Wen, ShiLin Li, GuoRong Yuan
Southwestern China has an area with unique natural conditions located in alpine regions at altitudes from 2000 to 5000 m; this area is referred to as the Qinghai-Tibetan plateau (QTP). Unique animals, such as yaks (Bos grunniens), are found extensively on the plateau of Southwestern China due to its unique environment. In recent years, the prevalence of fake meat products such as fake jerky has increased in this area. This research was conducted as an attempt to develop a reliable multiplex polymerase chain reaction (mPCR) detection method for identifying nine animal species found in QTP...
August 11, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28781945/profiling-of-virulence-associated-factors-in-shigella-species-isolated-from-acute-pediatric-diarrheal-samples-in-tehran-iran
#7
Sajad Yaghoubi, Reza Ranjbar, Mohammad Mehdi Soltan Dallal, Somayeh Yasliani Fard, Mohammad Hasan Shirazi, Mahmood Mahmoudi
OBJECTIVES: The genus Shigella comprises the most infectious and diarrheagenic bacteria causing severe diseases, mostly in children under five years of age. This study aimed to detect nine virulence genes (ipaBCD, VirA, sen, set1A, set1B, ial, ipaH, stx, and sat) in Shigella species (spp.) using multiplex polymerase chain reaction (MPCR) and to determine the relation of Shigella spp. from pediatric diarrheal samples with hospitalization and bloody diarrhea in Tehran, Iran. METHODS: Shigella spp...
June 2017: Osong Public Health and Research Perspectives
https://www.readbyqxmd.com/read/28755939/multiplex-pcr-coupled-with-propidium-monoazide-for-the-detection-of-viable-cronobacter-sakazakii-bacillus-cereus-and-salmonella-spp-in-milk-and-milk-products
#8
Shuang Yu, Leina Yan, Xin Wu, Fan Li, Dong Wang, Hengyi Xu
Cronobacter sakazakii, Bacillus cereus, and Salmonella spp. are common food-borne pathogens. The aim of this study was to develop a sensitive, specific, and rapid method for the simultaneous detection of these 3 pathogens in milk and milk products. Three specific primers were designed based on ompA, invA, and cesB of C. sakazakii, Salmonella spp. and B. cereus, respectively, for use in a multiplex PCR (mPCR). To eliminate false-positive results, cells were pretreated with propidium monoazide (PMA) for the selective elimination of the genomic DNA of dead cells...
July 26, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28755449/population-structure-and-attribution-of-human-clinical-campylobacter-jejuni-isolates-from-central-europe-to-livestock-and-environmental-sources
#9
J Kovac, B Stessl, N Čadež, I Gruntar, M Cimerman, K Stingl, M Lušicky, M Ocepek, M Wagner, S Smole Možina
Campylobacter jejuni is among the most prevalent causes of human bacterial gastroenteritis worldwide. Domesticated animals and, especially, chicken meat are considered to be the main sources of infections. However, the contribution of surface waters and wildlife in C. jejuni transmission to humans is not well understood. We have evaluated the source attribution potential of a six-gene multiplex PCR (mPCR) method coupled with STRUCTURE analysis on a set of 410 C. jejuni strains isolated from environment, livestock, food and humans in central Europe...
July 28, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/28729548/multiplex-polymerase-chain-reaction-for-pathogen-detection-in-donor-recipient-corneal-transplant-tissue-and-donor-storage-solution
#10
Takehiro Hariya, Kazuichi Maruyama, Sunao Sugita, Masayo Takahashi, Shunji Yokokura, Kota Sato, Yasuhiro Tomaru, Norio Shimizu, Toru Nakazawa
Corneal transplantation is a safe, reliable method of restoring visual acuity in patients with corneal disorders. Although it has a very high success rate, rejection can still occur, especially if the site is infected. Therefore, seeking to find better ways to manage infection risk, this study investigated a new technique, based on multiplex polymerase chain reaction (mPCR), to identify pathogens, including viruses, bacteria, and fungi, in corneal transplantation recipient sites, donor corneas and the donor cornea storage solution...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28666619/development-of-a-multiplex-pcr-for-identification-of-%C3%AE-hemolytic-streptococci-relevant-to-human-infections-and-serotype-distribution-of-invasive-streptococcus-agalactiae-in-thailand
#11
Anusak Kerdsin, Rujirat Hatrongjit, Shigeyuki Hamada, Yukihiro Akeda, Marcelo Gottschalk
A multiplex polymerase chain reaction (mPCR) was developed for simultaneous detection (single reaction) of genes specific to five frequent clinically relevant β-hemolytic streptococcal species: Streptococcus pyogenes (Spy1258), Streptococcus agalactiae (cfb and cpn60), Streptococcus dysgalactiae subsp. equisimilis (16S-23S intergenic spacer) , S. equi subsp. zooepidemicus (esaA and sorD), and Streptococcus anginosus group (moaC). No cross-reaction was observed with other bacterial species. This test was validated and successfully used with 725 clinical isolates involved in pathological conditions in Thailand and collected between March 2014 and December 2015...
June 27, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28638437/a-multiplex-pcr-for-rapid-identification-of-brassica-species-in-the-triangle-of-u
#12
Joshua C O Koh, Denise M Barbulescu, Sally Norton, Bob Redden, Phil A Salisbury, Sukhjiwan Kaur, Noel Cogan, Anthony T Slater
BACKGROUND: Within the Brassicaceae, six species from the genus Brassica are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six Brassica species are described by U's triangle model. Extensive shared traits and diverse morphotypes among Brassica species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species...
2017: Plant Methods
https://www.readbyqxmd.com/read/28629316/a-multiplex-primer-design-algorithm-for-target-amplification-of-continuous-genomic-regions
#13
Ahmet Rasit Ozturk, Tolga Can
BACKGROUND: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor...
June 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28624018/difference-in-the-craniocaudal-gradient-of-the-maximum-pixel-value-change-rate-between-chronic-obstructive-pulmonary-disease-patients-and-normal-subjects-using-sub-mgy-dynamic-chest-radiography-with-a-flat-panel-detector-system
#14
Yoshitake Yamada, Masako Ueyama, Takehiko Abe, Tetsuro Araki, Takayuki Abe, Mizuki Nishino, Masahiro Jinzaki, Hiroto Hatabu, Shoji Kudoh
OBJECTIVES: To compare the craniocaudal gradients of the maximum pixel value change rate (MPCR) during tidal breathing between chronic obstructive pulmonary disease (COPD) patients and normal subjects using dynamic chest radiography. MATERIALS AND METHODS: This prospective study was approved by the institutional review board and all participants provided written informed consent. Forty-three COPD patients (mean age, 71.6±8.7 years) and 47 normal subjects (non-smoker healthy volunteers) (mean age, 54...
July 2017: European Journal of Radiology
https://www.readbyqxmd.com/read/28615466/-pathotyping-multiplex-pcr-assay-for-haemophilus-parasuis-a-tool-for-prediction-of-virulence
#15
Kate J Howell, Lucy A Weinert, Sarah E Peters, Jinhong Wang, Juan Hernandez-Garcia, Roy R Chaudhuri, Shi-Lu Luan, Øystein Angen, Virginia Aragon, Susanna M Williamson, Paul R Langford, Andrew N Rycroft, Brendan W Wren, Duncan J Maskell, Alexander W Tucker
Haemophilus parasuis is a diverse bacterial species that is found in the upper respiratory tracts of pigs and can also cause Glässer's disease and pneumonia. A previous pangenome study of H. parasuis identified 48 genes that were associated with clinical disease. Here, we describe the development of a generalized linear model (termed a pathotyping model) to predict the potential virulence of isolates of H. parasuis based on a subset of 10 genes from the pangenome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence...
September 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28612135/comparative-study-of-genexpert-mtb-rif-assay-and-multiplex-pcr-assay-for-direct-detection-of-mycobacterium-tuberculosis-in-suspected-pulmonary-tuberculosis-patients
#16
Anil Kumar Sah, Bishnu Joshi, Dhruba Kumar Khadka, Birendra Prasad Gupta, Anurag Adhikari, Subodh Kant Singh, Ganesh Rai, Geeta Shrestha Vaidya, Reema Rajbhandari, Basant Pant, Shiba Kumar Rai
Pulmonary tuberculosis (PTB) is one of the major infectious diseases in developing countries. The objective of this study was to compare rapid diagnostics technique, GeneXpert MTB/RIF (GeneXpert) and Multiplex PCR assay (MPCR) targeting IS6110 segment and mpb64 gene for direct detection of Mycobacterium tuberculosis (MTB) in suspected PTB patients. A cross sectional study was carried among 105 sputum samples from suspected PTB patients to evaluate GeneXpert and Multiplex PCR who visited National Tuberculosis Center, Nepal...
September 2017: Current Microbiology
https://www.readbyqxmd.com/read/28584712/prevalence-and-seroepidemiology-of-haemophilus-parasuis-in-sichuan-province-china
#17
Zhenghao Wang, Qin Zhao, Hailin Wei, Xintian Wen, Sanjie Cao, Xiaobo Huang, Rui Wu, Qigui Yan, Yong Huang, Yiping Wen
Haemophilus parasuis, the causative agent of Glässer's disease, has been reported as widespread, but little is known about its epidemiology in the Sichuan province of China. The goal of our research is to reveal the prevalence and distribution of H. parasuis in this area. Sampling and isolation were performed across Sichuan; isolates were processed using serotyping multiplex PCR (serotyping-mPCR) and agar gel diffusion (AGD) for confirmation of serovar identity. This study was carried out from January 2014 to May 2016 and 254 H...
2017: PeerJ
https://www.readbyqxmd.com/read/28574617/confirmed-identification-and-toxin-profiling-of-campylobacter-jejuni-using-a-thermostabilized-multiplex-pcr-formulation
#18
Nitya Ramachandran, Shylaja Ramlal, Harsh Vardhan Batra
Cytolethal distending toxin (CDT) producing Campylobacter jejuni species are one of the leading causes of human gastroenteritis worldwide. The main intent of the study was to develop a multiplex PCR assay for the confirmed identification and toxin profiling of C. jejuni. The genes targeted were rpo B as genus specific, hip O for species; cdt A, cdt B, cdt C encoding respective subunit proteins of CDT with Internal Amplification Control (IAC). To enhance its application as a pre-mixed ready-to-use format, the master mix of developed mPCR was dried by lyophilization and stability was assessed...
July 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28571452/miniaturized-thermocycler-based-on-thermoelectric-heating-for-diagnosis-of-sexually-transmitted-disease-by-dna-amplification
#19
Hyunjung Lim, Ga Eun Jo, Kyong Soo Kim, Seung Min Back, Hyuk Choi
Sexually transmitted disease (STD) is among the most common infectious diseases; therefore, it is necessary to develop sensitive early diagnostic techniques. As the gold standard, polymerase chain reaction (PCR) has been most widely employed for STD diagnosis; however, PCR requires large and expensive instruments. In this study, miniaturized thermal cycler using Peltier modules was developed for the PCR analysis. In comparison with the conventional PCR instrument, the Peltier-based micro-PCR (P-mPCR) device developed in this study enables one to amplify and successfully distinguish between DNA of different sizes...
May 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28559002/assessment-of-the-automated-multiplex-pcr-unyvero-i60-iti-%C3%A2-cartridge-system-to-diagnose-prosthetic-joint-infection-a-multicenter-study
#20
D Malandain, P Bémer, A G Leroy, J Léger, C Plouzeau, A S Valentin, A Jolivet-Gougeon, D Tandé, G Héry-Arnaud, C Lemarié, M Kempf, L Bret, C Burucoa, S Corvec
OBJECTIVES: Prosthetic joint infections (PJI) are responsible for significant morbidity and mortality and their number continues to rise. Their management remains complex, especially the microbiological diagnosis. Besides "homemade" tests developed by several teams, new molecular biology methods are now available with different analytical performance and usability. METHODS: We studied the performances of one of these tests: ITI(®) multiplex PCR (mPCR) by the Curetis(®) company and compared it either to "optimized" culture or to 16S rRNA PCR...
May 27, 2017: Clinical Microbiology and Infection
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