keyword
MENU ▼
Read by QxMD icon Read
search

Multiplex PCR

keyword
https://www.readbyqxmd.com/read/28441441/a-novel-multiplexed-probe-based-quantitative-pcr-assay-for-the-soybean-root-and-stem-rot-pathogen-phytophthora-sojae-utilizes-its-transposable-element
#1
James S Haudenshield, Jeong Y Song, Glen L Hartman
Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields...
2017: PloS One
https://www.readbyqxmd.com/read/28439839/a-robust-protocol-to-quantify-circulating-cancer-biomarker-micrornas
#2
Emma Bell, Hannah L Watson, Shivani Bailey, Matthew J Murray, Nicholas Coleman
Reverse-transcriptase quantitative PCR (RT-qPCR) is a widely used method for quantifying microRNAs (miRNAs) in cells and tissues. However, the quantification of miRNAs in the circulation presents specific challenges. Here, we describe an optimized protocol using a small amount of input material to assess serum sample quality and quantify levels of a panel of up to 20 miRNAs. This is achieved by multiplexing Taqman miRNA stem-loop primers in the reverse transcription step. An additional multiplexed pre-amplification step is used to increase the sensitivity of the final quantification step, which is carried out using standard Taqman qPCR methodology...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439828/interrogation-of-functional-mirna-target-interactions-by-crispr-cas9-genome-engineering
#3
Yale S Michaels, Qianxin Wu, Tudor A Fulga
Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439479/simple-sequence-repeat-markers-for-k%C3%A4-nuka-kunzea-spp-myrtaceae-present-in-new-zealand
#4
Dagmar F Goeke, Caroline M Mitchell, Claudia Lange, Gary J Houliston
PREMISE OF THE STUDY: We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on kānuka (Kunzea spp.; Myrtaceae). METHODS AND RESULTS: A shotgun sequencing library was constructed from leaf material of K. robusta using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand Kunzea species. Each of these loci cross-amplified in all tested species...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28438642/diagnostic-microarray-for-14-water-and-foodborne-pathogens-using-a-flatbed-scanner
#5
Vidya Srinivasan, Robert D Stedtfeld, Dieter M Tourlousse, Samuel W Baushke, Yu Xin, Sarah M Miller, Trinh Pham, Jean-Marie Rouillard, Erdogan Gulari, James M Tiedje, Syed A Hashsham
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology...
April 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28438568/a-novel-mutation-in-pmrb-mediates-colistin-resistance-during-therapy-of-acinetobacter-baumannii
#6
Elias Dahdouh, Rosa Gómez-Gil, Sonia Sanz, Bruno González-Zorn, Ziad Daoud, Jesús Mingorance, Monica Suárez
Acinetobacter baumannii is a highly versatile nosocomial pathogen. Multidrug resistance among A. baumannii isolates led to the use of colistin, subsequently giving rise to colistin-resistant strains. In this study, the genetic and phenotypic profiles of two colistin-resistant A. baumannii isolates were investigated. Two A. baumannii isolates were obtained from Patient 1 (C071 and C440) and three isolates were obtained from Patient 2 (C080, C314 and C428). Susceptibility profiles were determined by VITEK(®)2 and Etest...
April 21, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28438442/molecular-identification-of-enterocytozoon-bieneusi-and-encephalitozoon-spp-in-immunodeficient-patients-in-ahvaz-southwest-of-iran
#7
Mehdi Tavalla, Masoumeh Mardani-Kateki, Rahman Abdizadeh, Roohangiz Nashibi, Abdollah Rafie, Shahram Khademvatan
Microsporidia are often considered as an opportunistic infection in patients with impaired immune systems such as transplant recipients and patients with acquired immune deficiency syndrome (AIDS). Due to the increasing prevalence of parasitic infections and immunodeficiency diseases; the aim of the study is to evaluate molecular identification of Enterocytozoon bieneusi and Encephalitozoon spp. in immunodeficient patients in Ahvaz, southwest of Iran. At first, 310 stool samples were collected from patients with immunodeficiency...
April 21, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28435891/detection-of-anaplasma-phagocytophilum-babesia-microti-borrelia-burgdorferi-borrelia-miyamotoi-and-powassan-virus-in-ticks-by-a-multiplex-real-time-reverse-transcription-pcr-assay
#8
Rafal Tokarz, Teresa Tagliafierro, D Moses Cucura, Ilia Rochlin, Stephen Sameroff, W Ian Lipkin
Ixodes scapularis ticks are implicated in transmission of Anaplasma phagocytophilum, Borrelia burgdorferi, Borrelia miyamotoi, Babesia microti, and Powassan virus. We describe the establishment and implementation of the first multiplex real-time PCR assay with the capability to simultaneously detect and differentiate all five pathogens in a single reaction. The application of this assay for analysis of ticks at sites in New York and Connecticut revealed a high prevalence of B. microti in ticks from Suffolk County, NY...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435108/molecular-characterization-and-antimicrobial-susceptibility-of-the-ca-mrsa-isolated-from-healthcare-workers-tehran-iran
#9
Solmaz Ohadian Moghadam, Mohammad Modoodi Yaghooti, Nasrin Pourramezan, Mohammad Reza Pourmand
INTRODUCTION: Methicillin resistant Staphylococcus aureus (MRSA) has become as a nosocomial pathogen worldwide. Considering the importance of MRSA typing for understanding the evolution and dissemination of these strains, we studied the molecular characteristics of MRSA colonized healthcare workers (HCWs). METHODOLOGY: All MRSA isolated from HCWs, were genotyped using staphylococcal cassette chromosome mec (SCCmec) with multiplex PCR assay, multilocus sequence typing (MLST) and spa typing...
April 20, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28434824/multiple-pathogen-biomarker-detection-using-an-encoded-bead-array-in-droplet-pcr
#10
Prem Kumar Periyannan Rajeswari, Lovisa M Soderberg, Alia Yacoub, Mikael Leijon, Helene Andersson Svahn, Haakan N Joensson
We present a droplet PCR workflow for detection of multiple pathogen DNA biomarkers using fluorescent color-coded Luminex® beads. This strategy enables encoding of multiple singleplex droplet PCRs using a commercially available bead set of several hundred distinguishable fluorescence codes. This workflow provides scalability beyond the limited number offered by fluorescent detection probes such as TaqMan probes, commonly used in current multiplex droplet PCRs. The workflow was validated for three different Luminex bead sets coupled to target specific capture oligos to detect hybridization of three microorganisms infecting poultry: avian influenza, infectious laryngotracheitis virus and Campylobacter jejuni...
April 20, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28433894/a-functional-snp-mcp-1-2518a-g-predispose-to-renal-disorder-in-indian-systemic-lupus-erythematosus-patients
#11
Vinod D Umare, Vandana D Pradhan, Anjali G Rajadhyaksha, Kanjaksha Ghosh, Anita H Nadkarni
Systemic Lupus Erythematosus (SLE) is a clinically heterogeneous chronic, inflammatory autoimmune disorder that affects multiple organs where exact etiology of the disease is not yet clearly understood. Various evidences suggest that genetic polymorphisms in inflammatory mediators like cytokines and chemokines may influence development of the disease. Here, we investigated whether functional polymorphism at the Monocyte Chemoattractant Protein-1 (MCP-1) regulatory region associates with disease phenotype in Indian SLE patients...
April 20, 2017: Cytokine
https://www.readbyqxmd.com/read/28433078/haplotype-counting-for-sensitive-chimerism-testing-potential-for-early-leukemia-relapse-detection
#12
Marija Debeljak, Evelina Mocci, Max C Morrison, Aparna Pallavajjalla, Katie Beierl, Marie Amiel, Michaël Noë, Laura D Wood, Ming-Tseh Lin, Christopher D Gocke, Alison P Klein, Ephraim J Fuchs, Richard J Jones, James R Eshleman
Fields of forensics, transplantation, and paternity rely on human identity testing. Currently, this is accomplished through amplification of microsatellites followed by capillary electrophoresis. An alternative and theoretically better approach uses multiple single-nucleotide polymorphisms located within a small region of DNA, a method we initially developed using HLA-A and called haplotype counting. Herein, we validated seven additional polymorphic loci, sequenced a total of 45 individuals from three of the 1000 Genomes populations (15 from each), and determined the number of haplotypes, heterozygosity, and polymorphic information content for each locus...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28433076/identification-of-ntrk3-fusions-in-childhood-melanocytic-neoplasms
#13
Lu Wang, Klaus J Busam, Ryma Benayed, Robert Cimera, Jiajing Wang, Ryan Denley, Mamta Rao, Ruth Aryeequaye, Kerry Mullaney, Long Cao, Marc Ladanyi, Meera Hameed
Spitzoid neoplasms are a distinct group of melanocytic tumors. Genetically, they lack mutations in common melanoma-associated oncogenes. Recent studies have shown that spitzoid tumors may contain a variety of kinase fusions, including ROS1, NTRK1, ALK, BRAF, and RET fusions. We report herein the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms with spitzoid and/or atypical features, based on genome-wide copy number analysis by single-nucleotide polymorphism array, which showed intragenic copy number changes in NTRK3...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28431057/quantitative-analysis-of-pkp2-and-neighbouring-genes-in-a-patient-with-arrhythmogenic-right-ventricular-cardiomyopathy-caused-by-heterozygous-pkp2-deletion
#14
Keiko Sonoda, Seiko Ohno, Sou Otuki, Koichi Kato, Nobue Yagihara, Hiroshi Watanabe, Takeru Makiyama, Tohru Minamino, Minoru Horie
Aims: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a disease mainly caused by desmosome gene mutations. The genetic culprit, however, remains elusive in ∼50% of ARVC patients. One of the reasons for missing genetic abnormalities is the difficulty in detecting large deletions/duplications, which are called as copy number variation (CNV) by the Sanger sequencing method. This study aimed to identify CNVs in PKP2 and a part of other desmosome genes in ARVC patients. Methods and Results: The study cohort consisted of 71 ARVC probands who were diagnosed as definite or borderline cases based on 2010 Task Force Criteria...
April 1, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28430157/development-of-user-friendly-method-to-distinguish-subspecies-of-the-korean-medicinal-herb-perilla-frutescens-using-multiplex-pcr
#15
Yonguk Kim, Ah-Young Kim, Ara Jo, Hakjoon Choi, Seung-Sik Cho, Chulyung Choi
Perilla (Perilla frutescens) is an economically and culturally important plant in East Asia. Plant breeding between cultivars has enhanced the genetic diversity of perilla overall, but means that functionally diverse subspecies are more difficult to identify and distinguish. In this study, we developed gene-based DNA markers to distinguish between the Korean herbal medicinal perilla varieties. We identified informative simple sequence repeat (SSR) regions on the promoter regions of the Myb-P1 and dihydroflavonol 4-reductase (DFR) genes, as well as a large insertion-deletion (indel) region in the limonene synthase (LS) gene, and developed markers to characterize the distinct subspecies differences (PfMyb-P1pro, PfDFRpro, and PfLS, respectively)...
April 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28430087/modification-of-two-capripoxvirus-quantitative-real-time-pcr-assays-to-improve-diagnostic-sensitivity-and-include-beta-actin-as-an-internal-positive-control
#16
Amaresh Das, Ming Y Deng, Shawn Babiuk, Michael T McIntosh
Capripoxviruses (CaPVs), consisting of Sheeppox virus (SPV), Goatpox virus (GPV), and Lumpy skin disease virus (LSDV) species, cause economically significant diseases in sheep, goats, and cattle, respectively. Quantitative real-time polymerase chain reaction (qPCR) assays are routinely used for rapid detection of CaPVs in surveillance and outbreak management programs. We further modified and optimized 2 previously published CaPV qPCR assays, referred to as the Balinsky and Bowden assays, by changing commercial PCR reagents used in the tests...
May 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28428361/single-tube-dodecaplex-pcr-panel-of-polymorphic-microsatellite-markers-closely-linked-to-the-dmpk-ctg-repeat-for-preimplantation-genetic-diagnosis-of-myotonic-dystrophy-type-1
#17
Mulias Lian, Mingjue Zhao, Caroline G Lee, Samuel S Chong
BACKGROUND: Preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1) currently uses conventional PCR to detect nonexpanded dystrophia myotonica protein kinase (DMPK) alleles or triplet-primed PCR to detect the CTG-expanded alleles, coupled with analysis of linked microsatellite markers to increase diagnostic accuracy. We aimed to simplify the process of identification and selection of informative linked markers for application to DM1 PGD. METHODS: An in silico search was performed to identify all markers within 1-1...
April 20, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28427842/predominance-of-international-clone-2-oxa-23-producing-acinetobacter-baumannii-clinical-isolates-in-greece-2015-results-of-a-nationwide-study
#18
Spyros Pournaras, Konstantina Dafopoulou, Mariateresa Del Franco, Olympia Zarkotou, Evangelia Dimitroulia, Efi Protonotariou, Aggeliki Poulou, Raffaele Zarrilli, Athanasios Tsakris
In a previous nationwide study in Greece, OXA-58 was the sole carbapenemase present among carbapenem-resistant Acinetobacter baumannii (CRAB) isolated between 2000 and 2009. In this study, the antibiotic resistances, carbapenemase gene content and clonal relatedness of 194 single-patient CRAB clinical isolates collected randomly during 2015 from 11 tertiary hospitals located throughout Greece were investigated. Antimicrobial susceptibility was determined using commercial and dilution methods. PCR for carbapenemase genes were performed...
April 18, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28427352/point-of-sampling-detection-of-zika-virus-within-a-multiplexed-kit-capable-of-detecting-dengue-and-chikungunya
#19
Ozlem Yaren, Barry W Alto, Priyanka V Gangodkar, Shatakshi R Ranade, Kunal N Patil, Kevin M Bradley, Zunyi Yang, Nikhil Phadke, Steven A Benner
BACKGROUND: Zika, dengue, and chikungunya are three mosquito-borne viruses having overlapping transmission vectors. They cause diseases having similar symptoms in human patients, but requiring different immediate management steps. Therefore, rapid (< one hour) discrimination of these three viruses in patient samples and trapped mosquitoes is needed. The need for speed precludes any assay that requires complex up-front sample preparation, such as extraction of nucleic acids from the sample...
April 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28426525/gstm1-and-gstt1-genes-are-associated-with-dna-damage-of-p53-gene-in-coke-oven-workers
#20
Yuefeng He, Jun Qi, Fang He, Yongchang Zhang, Youlian Wang, Ruobing Zhang, Gang Li
OBJECTIVES: This study investigated whether variations in GSTT1 and GSTM1 gene are associated with the DNA damage level of p53 gene. METHODS: We quantified urinary 1-hydroxypyrene using high-performance liquid chromatography, and examined the DNA damage level of p53 gene by real-time quantitative PCR in 756 coke-oven workers. Multiplex PCR was used to detect the presence or absence of genes. RESULTS: DNA damage levels of p53 gene in the high exposure group and intermediate exposure group were significantly higher than that of p53 gene in the low exposure group (P < 0...
April 19, 2017: Journal of Occupational and Environmental Medicine
keyword
keyword
61585
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"