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Multiplex PCR

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https://www.readbyqxmd.com/read/27929456/high-throughput-detection-of-respiratory-pathogens-in-animal-specimens-by-nanoscale-pcr
#1
Laura B Goodman, Renee R Anderson, Marcia Slater, Elen Ortenberg, Randall W Renshaw, Brittany D Chilson, Melissa A Laverack, John S Beeby, Edward J Dubovi, Amy L Glaser
Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27928486/phylogenetic-background-of-enterotoxigenic-and-enteroinvasive-escherichia-coli-from-patients-with-diarrhea-in-sirjan-iran
#2
Taifeh Hoseinzadeh, Reza Ghanbarpour, Farokh Rokhbakhsh-Zamin
BACKGROUND AND OBJECTIVES: Diarrheagenic Escherichia coli (DEC) strains are a major cause of intestinal syndromes in the developing countries. The aim of this study was to determine the prevalence of enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC) in relation to phylogenetic background from patients with diarrhea. MATERIALS AND METHODS: A total of 110 E. coli isolates were obtained from diarrhea patients in Sirjan, southeast of Iran. The E. coli isolates were confirmed using biochemical and bacteriological tests...
June 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/27928482/frequency-of-genes-encoding-erythromycin-ribosomal-methylases-among-staphylococcus-aureus-clinical-isolates-with-different-d-phenotypes-in-tehran-iran
#3
Sareh Sadat Hosseini, Mohammad Niakan, Horieh Saderi, Mitra Motallebi, Morovat Taherikalani, Khairollah Asadollahi, Mohammad Emaneini
BACKGROUND AND OBJECTIVES: Macrolide, lincosamide and streptogramin type B (MLSB) antibiotics are important in the treatment of Staphylococcus aureus infections and existence of isolates with ability to resist against MLSB antibiotics is worrisome. MATERIALS AND METHODS: In this cross sectional study, 101 S. aureus isolates were collected from patients of five selected hospitals in Tehran over a period of five months. Disk diffusion tests and differentiation between constitutive and inducible resistances were carried out by D-test...
June 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/27928081/multiplex-polymerase-chain-reaction-for-detection-of-gastrointestinal-pathogens-in-migrant-workers-in-qatar
#4
John M Humphrey, Sanjay Ranbhise, Emad Ibrahim, Hamad E Al-Romaihi, Elmoubasher Farag, Laith J Abu-Raddad, Marshall J Glesby
The causes of infectious diarrhea among the migrant worker population in Qatar are not well understood. We conducted a prospective observational study to understand the demographic and clinical characteristics and infectious causes of diarrhea among migrant workers in Doha, Qatar. A total of 126 male workers presenting to the Qatar Red Crescent Worker's Health Center outpatient clinic or emergency department were studied over a 5-month period in 2015-2016. Epidemiologic surveys were administered to all subjects and the prevalence of 22 different stool pathogens was determined using multiplex polymerase chain reaction (PCR) (FilmArray(®) Gastrointestinal PCR)...
December 7, 2016: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/27924595/quantitative-analysis-of-periodontal-pathogens-using-real-time-polymerase-chain-reaction-pcr
#5
Mª José Marin, Elena Figuero, David Herrera, Mariano Sanz
The quantitative polymerase chain reaction (qPCR) is a variant of PCR aimed to detect and quantify a targeted DNA molecule through the addition of probes labeled with fluorescent molecules that emit fluorescence within each amplification cycle, what results in fluorescence values proportional to the amount of accumulated PCR product. This chapter presents the detailed procedures for quantification of different periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, and Fusobacterium spp...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924546/multiplex-detection-of-toxigenic-penicillium-species
#6
Alicia Rodríguez, Juan J Córdoba, Mar Rodríguez, María J Andrade
Multiplex PCR-based methods for simultaneous detection and quantification of different mycotoxin-producing Penicillia are useful tools to be used in food safety programs. These rapid and sensitive techniques allow taking corrective actions during food processing or storage for avoiding accumulation of mycotoxins in them. In this chapter, three multiplex PCR-based methods to detect at least patulin- and ochratoxin A-producing Penicillia are detailed. Two of them are different multiplex real-time PCR suitable for monitoring and quantifying toxigenic Penicillium using the nonspecific dye SYBR Green and specific hydrolysis probes (TaqMan)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924545/multiplex-detection-of-fusarium-species
#7
Tapani Yli-Mattila, Siddaiah Chandra Nayaka, Mudili Venkataramana, Emre Yörük
Multiplex PCR is a powerful method to detect, identify, and quantify the mycotoxigenic fungus by targeting the amplification of genes associated with mycotoxin production and detection, identification, and quantification of Fusarium species. As compared with uniplex PCR, it has several advantages such as low cost, shortened time, and simultaneous amplification of more than two genes (in only one reaction tube). Here, we describe multiplex PCR-based detection and identification of trichothecene-, zearalenone-, fumonisin-, and enniatin-producing Fusarium species, the use of multiplex PCR in multiplex genotype assay and the use of multiplex TaqMan real-time qPCR...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924544/multiplex-detection-of-aspergillus-species
#8
Pedro Martínez-Culebras, María Victoria Selma, Rosa Aznar
Multiplex real-time polymerase chain reaction (PCR) provides a fast and accurate DNA-based tool for the simultaneous amplification of more than one target sequence in a single reaction. Here a duplex real-time PCR assay is described for the simultaneous detection of Aspergillus carbonarius and members of the Aspergillus niger aggregate, which are the main responsible species for ochratoxin A (OTA) contamination in grapes. This single tube reaction targets the beta-ketosynthase and the acyl transferase domains of the polyketide synthase of A...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27923785/genetic-determination-of-the-vascular-reactions-in-humans-in-response-to-the-diving-reflex
#9
Tatiana I Baranova, Dmitrii N Berlov, Oleg S Glotov, Ekaterina A Korf, Alexey D Minigalin, Alla V Mitrofanova, Ildus I Ahmetov, Andrey S Glotov
The purpose of this study was to investigate the genetic mechanisms of the defense vascular reactions in response to the diving reflex in humans with polymorphisms in the genes ADBR2, ACE, AGTR1, BDKRB2, and REN. We hypothesized that protective vascular reactions, in response to the diving reflex, are genetically determined and are distinguished in humans with gene polymorphisms of the renin-angiotensin and kinin-bradykinin system. A total of 80 subjects (19±1.4 years) participated in the study. The intensity of the vascular response was estimated using photopletismogram...
December 6, 2016: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/27923589/comparative-detection-of-a-large-population-of-grapevine-viruses-by-taqman-%C3%A2-rt-qpcr-and-elisa
#10
Sébastien Bruisson, Sylvain Lebel, Bernard Walter, Laurent Prevotat, Sam Seddas, Paul Schellenbaum
Grapevine (Vitis spp) can be infected by numerous viruses that are often widespread and of great economic importance. Reliable detection methods are necessary for sanitary selection which is the only way to partly control grapevine virus diseases. Biological indexing and ELISA are currently the standard methods for screening propagation material, and PCR-methods are becoming increasingly popular. Due to the diversity of virus isolates, it is essential to verify that the tests allow the detection of the largest possible virus populations...
December 3, 2016: Journal of Virological Methods
https://www.readbyqxmd.com/read/27923522/development-of-a-multiplex-taqman-real-time-pcr-assay-for-typing-of-mycoplasma-pneumoniae-based-on-type-specific-indels-identified-through-whole-genome-sequencing
#11
Bernard J Wolff, Alvaro J Benitez, Heta P Desai, Shatavia S Morrison, Maureen H Diaz, Jonas M Winchell
We developed a multiplex real-time PCR assay for simultaneously detecting M. pneumoniae and typing into historically-defined P1 types. Typing was achieved based on the presence of short type-specific indels identified through whole genome sequencing. This assay was 100% specific compared to existing methods and may be useful during epidemiologic investigations.
November 25, 2016: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/27922429/multiplex-pcr-for-detection-of-helicobacter-pylori-infection-in-gastric-biopsies-with-lower-inflammatory-score
#12
Najmiyatul Fadilah, Alfizah Hanafiah, Hamizah Razlan, Zin Qin Wong, Isa Mohamed Rose, Md Mostafizur Rahman
BACKGROUND: No gold standard has yet been established for the diagnosis of H. pylori infection. A multiplex polymerase chain reaction (mPCR) was developed in this study for rapid, sensitive and specific detection of H. pylori from gastric biopsies. METHODS: H. pylori infections were determined by in-house rapid urease test (iRUT), culture, histology and multiplex PCR. RESULTS: A total of 140 (60.9%) from 230 patients were positive for H. pylori infection...
October 2016: British Journal of Biomedical Science
https://www.readbyqxmd.com/read/27919005/tracking-listeria-monocytogenes-contamination-and-virulence-associated-characteristics-in-the-ready-to-eat-meat-based-food-products-industry-according-to-the-hygiene-level
#13
A R Henriques, L T Gama, M J Fraqueza
Listeria monocytogenes isolates collected from final products and food contact surfaces of 10 ready-to-eat meat-based food products (RTEMP) producing industries were analyzed to relate their virulence-associated characteristics and genetic profiles with the hygiene assessment of those industries. Together with sample collection, an audit was performed to evaluate the implemented food safety management system and to investigate the specific audit requisites more associated to the occurrence of those L. monocytogenes serogroups frequently related with human disease...
November 21, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/27915107/association-between-the-agr-locus-and-the-presence-of-virulence-genes-and-pathogenesis-in-s-aureus-using-a-caenorhabditis-elegans-model
#14
Terissa A Thompson, Paul D Brown
BACKGROUND: S. aureus is a commensal pathogen with a virulon that is under agr control. agr dysfunction has been seen in clinical strains that do not respond positively to treatment. AIM: This study aimed to establish the association between the presence of genes in the virulon with agr present and to determine the relationship between agr presence or absence with pathogenicity. METHODS: PCR was used to identify the presence of the agr operon in 101 clinical S...
November 30, 2016: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/27910939/real-time-pcr-based-serotyping-of-streptococcus-agalactiae
#15
Kathleen M Breeding, Bhavana Ragipani, Kun-Uk David Lee, Martin Malik, Tara M Randis, Adam J Ratner
Group B Streptococcus (GBS) is an encapsulated, gram-positive pathogen that is an important cause of neonatal invasive infections, including sepsis and meningitis. There are ten known GBS serotypes based on distinct capsule compositions (Ia, Ib, II-IX), and current candidate capsular polysaccharide conjugate vaccines target only a subset of these. Serotyping of GBS isolates is important for understanding local epidemiology and for monitoring for serotype replacement or capsular switching. However, serotyping generally requires either latex agglutination, multiplex PCR with analysis of band sizes, or analysis of whole genome sequences-all techniques that are either expensive or not widely available...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910166/anchored-multiplex-pcr-for-targeted-next-generation-sequencing-reveals-recurrent-and-novel-usp6-fusions-and-upregulation-of-usp6-expression-in-aneurysmal-bone-cyst
#16
Natalya V Guseva, Omar Jaber, Munir R Tanas, Aaron A Stence, Ramakrishna Sompallae, Jenna Schade, Allison N Fillman, Benjamin J Miller, Aaron D Bossler, Deqin Ma
Primary aneurysmal bone cyst (ABC) is a neoplastic process due to recurrent translocations involving the USP6 gene. By fluorescence in situ hybridization, up to 69% of primary ABCs harbored USP6 translocations; no USP6 translocation was found in secondary ABC or giant cell tumor of bone (GCT). GCT can recur locally, metastasize to the lungs in some cases, and rarely undergo malignant transformation. Differentiating primary ABC from its mimics is important for treatment and prognosis. We evaluated USP6 fusion and expression in 13 cases of primary and 1 case of secondary ABC, and 9 cases of GCT using nucleic acid extracted from formalin-fixed, paraffin-embedded tissue and a next generation sequencing (NGS)-based assay...
November 7, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27909867/developmental-validation-of-the-homygene19-14y-system
#17
Weian Du, Ling Chen, Hong Liu, Pingming Qiu, Fayuan Li, Jing Gao, Yu Zhou, Bangchao Wang, Chao Liu
The HomyGene19+14Y System (HG19+14Y) is a PCR-based amplification kit that enables typing of 18 autosomal short tandem repeat (STR) loci (i.e., CSF1PO, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, Penta E, TPOX, TH01, vWA), 14 widely used Y chromosome STR (Y-STR) loci (Y_GATA_H4, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS456, DYS458, DYS635), and amelogenin. This multiplex system was designed for the simultaneous analysis of amelogenin-Y allele mutation, single-source searches, kinship (including familial searching), mixture profiles, international data sharing, and other forensic applications...
December 1, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27909068/use-of-multiplex-pcr-to-rapidly-diagnose-febrile-patients-during-a-gastroenteritis-outbreak-among-ebola-virus-treatment-unit-workers
#18
Tom O Evans, T Fominyam, S W Matthews, M S Bailey, E J Hutley
Multiplex PCR can provide rapid diagnosis for patients presenting with an acute undifferentiated febrile illness. Such technology is useful in deployed settings, where access to conventional microbiological diagnosis is limited. It was used in Sierra Leone to guide management of febrile healthcare workers, in whom Ebola virus disease was a possible cause. In particular, it informed appropriate antibiotic treatment while minimising the risk to clinicians of exposure to the causative organism.
December 1, 2016: Journal of the Royal Army Medical Corps
https://www.readbyqxmd.com/read/27907225/informativeness-of-ngs-analysis-for-vaginal-fluid-identification
#19
Saverio Giampaoli, Elisabetta DeVittori, Federica Valeriani, Andrea Berti, Vincenzo Romano Spica
The identification of vaginal fluids in forensic examinations plays an important role in crime scene reconstruction. Molecular detection of vaginal bacterial communities can lead to the correct discrimination of body fluids. These kinds of studies can be performed through multiplex real-time PCR using primers for a specific selection of bacteria. The availability of next-generation sequencing (NGS) protocols provided for the extension of the analysis to evaluate the prokaryotes present in specimens. In this study, DNA was extracted from 18 samples (vaginal, oral, fecal, yoghurt) and analyzed by real-time PCR and NGS...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27907129/meningococcal-carriage-in-military-recruits-and-university-students-during-the-pre-menb-vaccination-era-in-greece-2014-2015
#20
Kyriaki Tryfinopoulou, Konstantinos Kesanopoulos, Athanasia Xirogianni, Nektarios Marmaras, Anastasia Papandreou, Vassiliki Papaevangelou, Maria Tsolia, Aftab Jasir, Georgina Tzanakaki
PURPOSE: The aim of the study was to estimate the meningococcal carriage rate and to identify the genotypic characteristics of the strains isolated from healthy military recruits and university students in order to provide data that might increase our understanding on the epidemiology of meningococcus and obtain information which helps to evaluate the potential effects on control programs such as vaccination. METHODS: A total of 1420 oropharyngeal single swab samples were collected from military recruits and university students on voluntary basis, aged 18-26 years...
2016: PloS One
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