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Multiplex PCR

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https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#1
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28726194/association-between-the-prevalence-of-somatic-mutations-in-pik3ca-gene-in-tumors-and-clinical-and-morphological-characteristics-of-breast-cancer-patients
#2
M L Filipenko, N A Os'kina, I A Oskorbin, O V Mishukova, L K Ovchinnikova, E S Gershtein, N E Kushlinskii
The presence of activating somatic mutations in codons 542 and 545 of exon 9 (p.E542K c.1624G>A and p.E545K c.1633G>A) and in codon 1047 of exon 20 (p.H1047R c.3140A>G and p.H1047L c.3140A>T) of PIK3CA gene encoding catalytic p110α-subunit of phosphatidylinositol-3-kinase was studied in tumors of 473 breast cancer patients by multiplex allele-specific real-time PCR. Fifty-eight (12.3%) different mutations were found. An increase in the frequency of PIK3CA gene mutations with disease progression (from 2...
July 18, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28721852/effective-identification-of-lactobacillus-casei-group-species-genome-based-selection-of-the-gene-mutl-as-the-target-of-a-novel-multiplex-pcr-assay
#3
Benedetta Bottari, Giovanna E Felis, Elisa Salvetti, Anna Castioni, Ilenia Campedelli, Sandra Torriani, Valentina Bernini, Monica Gatti
Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. The close genetic relationship among those species, as well as the similarity of biochemical properties of the strains, hinders the development of an adequate selective method to identify these bacteria...
July 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28720458/prevalence-of-cutaneous-beta-and-gamma-human-papillomaviruses-in-the-anal-canal-of-men-who-have-sex-with-women
#4
Vitaly Smelov, Rachel Hanisch, Sandrine McKay-Chopin, Olga Sokolova, Carina Eklund, Boris Komyakov, Tarik Gheit, Massimo Tommasino
BACKGROUND: Data regarding anal cutaneous HPV detection among HIV-positive and HIV-negative persons largely relies on studies among men who have sex with men in limited geographical settings. Understanding the distribution, determinants, and potential human health effects of anal cutaneous HPV types among men who have sex with women (MSW) is important. METHODS: Anal canal swab samples from 415 Russian MSW (384 HIV-negative and 31 HIV-positive) were tested for 43 β-HPVs and 29 γ-HPVs, using a multiplex PCR combined with Luminex technology...
June 2017: Papillomavirus Research
https://www.readbyqxmd.com/read/28720292/serotypes-and-spa-types-of-erysipelothrix-rhusiopathiae-isolates-from-british-pigs-1987-to-2015
#5
Mark McNeil, Priscilla F Gerber, Jill Thomson, Susanna Williamson, Tanja Opriessnig
Erysipelothrix spp. cause a range of clinical signs in pigs and at least 28 different Erysipelothrix spp. serotypes have been identified. In this study, 128 isolates of Erysipelothrix spp. from pigs in Great Britain from 1987 to 2015 were characterised by serotyping and multiplex real time PCR assays targeting the surface protective antigen (Spa) and the main genotypes (Erysipelothrix rhusiopathiae, Erysipelothrix tonsillarum and Erysipelothrix spp. strain 2). All 128 British isolates were characterised as E...
July 2017: Veterinary Journal
https://www.readbyqxmd.com/read/28719834/the-exon3-deleted-growth-hormone-receptor-gene-polymorphism-d3-ghr-is-associated-with-insulin-and-spontaneous-growth-in-short-sga-children-nesgas
#6
Mathilde Gersel Wegmann, Ajay Thankamony, Edna Roche, Hilary Hoey, Jeremy Kirk, Guftar Shaikh, Sten-A Ivarsson, Olle Söder, David B Dunger, Anders Juul, Rikke Beck Jensen
OBJECTIVE: The effect of a common polymorphism in the Growth Hormone (GH) receptor (d3-GHR) gene on growth, metabolism and body composition was examined in short children born small for gestational age (SGA) on GH treatment. DESIGN: In 96 prepubertal, short SGA children treated with high-dose GH (67μg/kg/day) in the NESGAS study, insulin sensitivity (IS), insulin secretion and disposition index (DI) were determined during the first year of treatment. Body composition was analysed by DXA...
July 12, 2017: Growth Hormone & IGF Research
https://www.readbyqxmd.com/read/28719323/burden-and-seasonality-of-viral-acute-respiratory-tract-infections-among-outpatients-in-southern-sri-lanka
#7
David Shapiro, Champica K Bodinayake, Ajith Nagahawatte, Vasantha Devasiri, Ruvini Kurukulasooriya, Jeremy Hsiang, Bradley Nicholson, Aruna Dharshan De Silva, Truls Østbye, Megan E Reller, Christopher W Woods, L Gayani Tillekeratne
In tropical and subtropical settings, the epidemiology of viral acute respiratory tract infections varies widely between countries. We determined the etiology, seasonality, and clinical presentation of viral acute respiratory tract infections among outpatients in southern Sri Lanka. From March 2013 to January 2015, we enrolled outpatients presenting with influenza-like illness (ILI). Nasal/nasopharyngeal samples were tested in duplicate using antigen-based rapid influenza testing and multiplex polymerase chain reaction (PCR) for respiratory viruses...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719310/severity-of-pneumonia-in-under-5-year-old-children-from-developing-countries-a-multicenter-prospective-observational-study
#8
Thomas Bénet, Valentina Sanchez Picot, Shally Awasthi, Nitin Pandey, Ashish Bavdekar, Anand Kawade, Annick Robinson, Mala Rakoto-Andrianarivelo, Maryam Sylla, Souleymane Diallo, Graciela Russomando, Wilma Basualdo, Florence Komurian-Pradel, Hubert Endtz, Philippe Vanhems, Gláucia Paranhos-Baccalà, For The Gabriel Network
Pneumonia is the leading cause of death in children. The objectives were to evaluate the microbiological agents linked with hypoxemia in hospitalized children with pneumonia from developing countries, to identify predictors of hypoxemia, and to characterize factors associated with in-hospital mortality. A multicenter, observational study was conducted in five hospitals, from India (Lucknow, Vadu), Madagascar (Antananarivo), Mali (Bamako), and Paraguay (San Lorenzo). Children aged 2-60 months with radiologically confirmed pneumonia were enrolled prospectively...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28718958/multiplex-pcr-scheme-for-variant-plasmid-mediated-class-c-%C3%AE-lactamase-typing
#9
Le Van Chuong, Virapong Prachayasittikul, Chartchalerm Isarankura Na Ayudhya, Ratana Lawung
BACKGROUND: An increasing of prevalence and diversification of plasmid-mediated AmpC (pAmpC) has been emerged worldwide. The incidence of pAmpC resulted in increasing β-lactamase production and conferred resistance to almost all β-lactam antibiotics excluding carbapenems. The lack of standard method for pAmpC identification and classification exert a challenge in epidemiological surveillance and infection control practices. METHODS: A robust, single tube multiplex PCR has been developed to classify six different pAmpC groups including CIT (CMY-2 like, LAT and CFE), ECB (ACT, MIR), MOX & CMY-1 like, DHA, ACC, and FOX...
July 18, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28717662/clinical-and-molecular-characterization-of-cystinuria-in-a-french-cohort-relevance-of-assessing-large-scale-rearrangements-and-splicing-variants
#10
Pascaline Gaildrat, Said Lebbah, Abdellah Tebani, Bénédicte Sudrié-Arnaud, Isabelle Tostivint, Guillaume Bollee, Hélène Tubeuf, Thomas Charles, Aurelia Bertholet-Thomas, Alice Goldenberg, Frederic Barbey, Alexandra Martins, Pascale Saugier-Veber, Thierry Frébourg, Bertrand Knebelmann, Soumeya Bekri
BACKGROUND: Cystinuria is an autosomal recessive disorder of dibasic amino acid transport in the kidney and the intestine leading to increased urinary cystine excretion and nephrolithiasis. Two genes, SLC3A1 and SLC7A9, coding respectively for rBAT and b0,+AT, account for the genetic basis of cystinuria. METHODS: This study reports the clinical and molecular characterization of a French cohort including 112 cystinuria patients and 25 relatives from 99 families. Molecular screening was performed using sequencing and Quantitative Multiplex PCR of Short Fluorescent Fragments analyses...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717325/tetracycline-resistance-phenotypes-and-genotypes-of-coagulase-negative-staphylococcal-isolates-from-bubaline-mastitis-in-egypt
#11
K A Abd El-Razik, A A Arafa, R H Hedia, E S Ibrahim
AIM: This study was devoted to elucidate the tetracycline resistance of coagulase-negative staphylococci (CNS) derived from normal and subclinical mastitic (SCM) buffaloes' milk in Egypt. MATERIALS AND METHODS: A total of 81 milk samples from 46 normal buffalo milk samples and 35 SCM buffalo milk samples at private dairy farms of Egypt were used in this study. CNS were identified using phenotypic and molecular methods (polymerase chain reaction [PCR]). CNS isolates were tested for tetracycline resistance using routine methods and multiplex PCR targeting tetracycline (tet) resistance genes followed by sequencing of positive PCR products and phylogenetic analysis...
June 2017: Veterinary World
https://www.readbyqxmd.com/read/28717324/investigation-of-avian-influenza-infection-in-wild-birds-in-ismailia-and-damietta-cities-egypt
#12
Hanaa Mohamed Fadel, Rabab Afifi
AIM: This study was carried out to monitor avian influenza (AI) infection in wild birds in Egypt. MATERIALS AND METHODS: A total of 135 wild birds were examined for the presence of H5, H7, and H9 hemagglutination inhibition antibodies. Organs and swab samples of 75 birds were screened by multiplex real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) to detect AI subtypes H5, H7, and H9 matrix genes. RESULTS: The highest seropositive result was recorded in cattle egrets (90...
June 2017: Veterinary World
https://www.readbyqxmd.com/read/28716092/the-role-of-microglial-p2x7-modulation-of-cell-death-and-cytokine-release
#13
Yingbo He, Natalie Taylor, Lawrence Fourgeaud, Anindya Bhattacharya
BACKGROUND: ATP-gated P2X7 is a non-selective cation channel, which participates in a wide range of cellular functions as well as pathophysiological processes including neuropathic pain, immune response, and neuroinflammation. Despite its abundant expression in microglia, the role of P2X7 in neuroinflammation still remains unclear. METHODS: Primary microglia were isolated from cortices of P0-2 C57BL/6 wild-type or P2X7 knockout (P2X7(-/-)) mouse pups. Lipopolysaccharide, lipopolysaccharide plus IFNγ, or IL4 plus IL13 were used to polarize microglia to pro-inflammatory or anti-inflammatory states...
July 17, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28711952/polymorphic-variants-of-antioxidative-defense-enzymes-and-their-gene-gene-epistatic-interactions-in-systemic-lupus-erythematode-patients
#14
Tatjana Jevtovic Stoimenov, Milena Despotovic, Sonja Stojanovic, Jelena Basic, Dušica Pavlovic
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease in which pathogenesis oxidative stress has an important role. Single nucleotide polymorphisms (SNPs) in the genes that code enzymes involved in the antioxidative defense are possible factors that are responsible for their decreased activity of antioxidative defense enzymes. Thus, the aim of the study was to examine association of SNPs in these genes with SLE. A total of176 subjects were involved in this study. CAT A-21T (rs7943316), CAT C-262T (rs1001139) and manganese SOD (MnSOD) Ala16Val (rs4880) SNPs were determined using PCR-RFLP method, while GSTT1 and GSTM1 were determined using multiplex PCR...
July 15, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28711510/serotyping-of-brunei-pneumococcal-clinical-strains-and-the-investigation-of-their-capability-to-adhere-and-invade-a-brain-endothelium-model
#15
Nurul Adhwa Rahman, Aishah Sharudin, Suwarni Diah, Siti Hanna Muharram
INTRODUCTION: Pneumococcal infections have caused morbidity and mortality globally. Streptococcus pneumoniae (pneumococci) are commensal bacteria that colonize the nasopharynx, asymptomatically. From there, pneumococci can spread in the lungs causing pneumonia and disseminate in the bloodstream causing bacteremia (sepsis) and reach the brain leading to meningitis. Endothelial cells are one of the most important components of the blood-brain barrier that separates the blood from the brain and plays the first protective role against pneumococcal entry...
July 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28711440/prevalence-of-cervical-colonization-by-ureaplasma-parvum-ureaplasma-urealyticum-mycoplasma-hominis-and-mycoplasma-genitalium-in-childbearing-age-women-by-a-commercially-available-multiplex-real-time-pcr-an-italian-observational-multicentre-study
#16
Christian Leli, Antonella Mencacci, Maria Agnese Latino, Pierangelo Clerici, Mario Rassu, Stefano Perito, Roberto Castronari, Eleonora Pistoni, Eugenio Luciano, Daniela De Maria, Cristina Morazzoni, Michela Pascarella, Silvia Bozza, Alessandra Sensini
BACKGROUND: Mycoplasmas are frequently isolated from the genital tract. New molecular PCR-based methods for the detection of mycoplasmas can better define the real epidemiology of these microorganisms. The aim of this study was to evaluate the prevalence of mycoplasmas in a population of childbearing age women by means of PCR. METHODS: This 21-month multicentre observational study was conducted at four Italian clinical microbiology laboratories. Women reporting symptoms of vaginitis/cervicitis, or with history of infertility, pregnancy, miscarriage or preterm birth were included...
June 28, 2017: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
https://www.readbyqxmd.com/read/28711173/presymptomatic-diagnosis-of-spinal-muscular-atrophy-through-newborn-screening
#17
Yin-Hsiu Chien, Shu-Chuan Chiang, Wen-Chin Weng, Ni-Chung Lee, Ching-Jie Lin, Wu-Shiun Hsieh, Wang-Tso Lee, Yuh-Jyh Jong, Tsang-Ming Ko, Wuh-Liang Hwu
OBJECTIVE: To demonstrate the feasibility of presymptomatic diagnosis of spinal muscular atrophy (SMA) through newborn screening (NBS). STUDY DESIGN: We performed a screening trial to assess all newborns who underwent routine newborn metabolic screening at the National Taiwan University Hospital newborn screening center between November 2014 and September 2016. A real-time polymerase chain reaction (RT-PCR) genotyping assay for the SMN1/SMN2 intron 7 c.888+100A/G polymorphism was performed to detect homozygous SMN1 deletion using dried blood spot (DBS) samples...
July 12, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28710778/a-detection-method-for-the-rash-and-fever-illness-associated-viruses-using-multiplex-rt-pcr
#18
Yuki Matsushima, Tomomi Shimizu, Ikuko Doi, Fuminori Mizukoshi, Koo Nagasawa, Akihide Ryo, Hideaki Shimizu, Masae Kobayashi, Keiji Funatogawa, Noriko Nagata, Mariko Ishikawa, Ayako Komane, Nobuhiko Okabe, Yoshio Mori, Makoto Takeda, Hirokazu Kimura
To detect various viral genes in the patients with rash and fever illness (RFI), a new multiplex (reverse transcription) polymerase chain reaction [(RT)-PCR] method was constructed. New primer sets were designed for the detection of herpes simplex viruses 1 and 2 (HSV1 and 2), and Epstein-Barr virus (EBV). The newly designed and previously reported primer sets were used to detect 13 types of RFI-associated viruses by multiplex (RT)-PCR assay systems. Moreover, to eliminate non-specific PCR products, a double-stranded specific DNase was used for the digestion of double-stranded DNA derived from the templates in clinical specimens...
July 15, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28709460/semi-quantitative-influenza-a-population-averages-from-a-multiplex-respiratory-viral-panel-rvp-potential-for-reflecting-target-sequence-changes-affecting-the-assay
#19
Kenneth H Rand, Maura Pieretti, Rodney Arcenas, Stacy G Beal, Herbert Houck, Emma Boslet, John A Lednicky
BACKGROUND: Yearly influenza virus mutations potentially affect the performance of molecular assays, if nucleic acid changes involve the sequences in the assay. Because individual patient viral loads depend on variables such as duration of illness, specimen type, age, and immunosuppression, we examined seasonal population averages of positive tests to smooth inherent variability. METHODS: We studied the population seasonal averages of the semi-quantitative nAMPs for the influenza matrix and hemagglutinin genes in the GenMark (Carlsbad, CA) Respiratory Viral Panel assay between 3 institutions over 3 Influenza seasons...
July 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/28708843/prevalence-of-respiratory-viruses-among-adults-by-season-age-respiratory-tract-region-and-type-of-medical-unit-in-paris-france-from-2011-to-2016
#20
Benoit Visseaux, Charles Burdet, Guillaume Voiriot, François-Xavier Lescure, Taous Chougar, Olivier Brugière, Bruno Crestani, Enrique Casalino, Charlotte Charpentier, Diane Descamps, Jean-François Timsit, Yazdan Yazdanpanah, Nadhira Houhou-Fidouh
BACKGROUND: Multiplex PCR tests have improved our understanding of respiratory viruses' epidemiology by allowing their wide range detection. We describe here the burden of these viruses in hospital settings over a five-year period. METHODS: All respiratory samples from adult patients (>20 years old) tested by multiplex-PCR at the request of physicians, from May 1 2011 to April 30 2016, were included retrospectively. Viral findings are reported by season, patient age group, respiratory tract region (upper or lower) and type of clinical unit (intensive care unit, pneumology unit, lung transplantation unit and other medical units)...
2017: PloS One
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