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Multiplex PCR

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https://www.readbyqxmd.com/read/28813625/detection-of-first-line-drug-resistance-mutations-and-drug-protein-interaction-dynamics-from-tuberculosis-patients-in-south-india
#1
Somanna Ajjamada Nachappa, Sumana M Neelambike, Chokkanna Amruthavalli, Nallur B Ramachandra
Diagnosis of drug-resistant tuberculosis predominantly relies on culture-based drug susceptibility testing, which take weeks to produce a result and a more time-efficient alternative method is multiplex allele-specific PCR (MAS-PCR). Also, understanding the role of mutations in causing resistance helps better drug designing. AIMS: To evaluate the ability of MAS-PCR in the detection of drug resistance and to understand the mechanism of interaction of drugs with mutant proteins in Mycobacterium tuberculosis...
August 16, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28812131/dna-degrades-during-storage-in-formalin-fixed-and-paraffin-embedded-tissue-blocks
#2
Alice Guyard, Alice Boyez, Anaïs Pujals, Cyrielle Robe, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch, Odette Georges, Jean-Christophe Fournet, Elie-Serge Zafrani, Karen Leroy
Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5...
August 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28809773/a-macaque-model-for-rectal-lymphogranuloma-venereum-and-non-lymphogranuloma-venereum-chlamydia-trachomatis-impact-on-rectal-simian-human-immunodeficiency-virus-acquisition
#3
Sundaram Ajay Vishwanathan, Rachael D Aubert, Monica R Morris, Chunxia Zhao, Christi Philips, George M Khalil, Frank Deyounks, Kristen Kelley, Jana M Ritter, C Y Chen, Ellen N Kersh, Janet M McNicholl
BACKGROUND: Sustained genital tract inflammation caused by sexually transmitted infections (STIs) is known to increase risk of vaginal human immunodeficiency virus (HIV) infections but, to our knowledge, there are no nonhuman primate studies that have evaluated its link to rectal HIV acquisition. METHODS: Rhesus macaques inoculated with Chlamydia trachomatis (CT) (serovars LGV-L2 and CT-E; n = 7) or saline (n = 7) received up to 20 rectal challenges twice a week of simian/HIV immunodeficiency virus (SHIVSF162p3)...
September 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28807338/molecular-pathology-diagnosis-of-diffuse-large-b-cell-lymphoma-using-biomed-2-clonal-gene-rearrangements
#4
Saeid Ghorbian
BACKGROUND: Clonality testing for immunoglobulin gene rearrangement analysis could be implemented effectively as a useful technique for conventional diagnosis of lymphoma. The European Biomedicine and Health Concerted Action Project BMH4-CT98-3936 (BIOMED-2) have been suggested a gold standard method to clonality detection. OBJECTIVES: We tested empirically clonality rearrangements of IGH and incomplete IGH D-J, on formalin-fixed, paraffin embedded (FFPE) tissue of patients with diffuse large B cell lymphoma (DLBCL)...
August 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28807095/simultaneous-detection-of-13-key-bacterial-respiratory-pathogens-by-combination-of-multiplex-pcr-and-capillary-electrophoresis
#5
Lu Xi Jiang, Hong Yu Ren, Hai Jian Zhou, Si Hong Zhao, Bo Yan Hou, Jian Ping Yan, Tian Qin, Yu Chen
OBJECTIVE: Lower respiratory tract infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory bacteria. To compensate for the limits of current respiratory bacteria detection methods, we developed a combination of multiplex polymerase chain reaction (PCR) and capillary electrophoresis (MPCE) assay to detect thirteen bacterial pathogens responsible for lower respiratory tract infections, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Mycoplasma pneumoniae, Legionella spp...
August 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28803391/mutational-analysis-of-the-rb1-gene-and-the-inheritance-patterns-of-retinoblastoma-in-jordan
#6
Yacoub A Yousef, Abdelghani Tbakhi, Maysa Al-Hussaini, Ibrahim AlNawaiseh, Ala Saab, Amal Afifi, Maysa Naji, Mona Mohammad, Rasha Deebajah, Imad Jaradat, Iyad Sultan, Mustafa Mehyar
Retinoblastoma (RB) is a childhood cancer developing in the retina due to RB1 pathologic variant. Herein we are evaluating the oncogenic mutations in the RB1 gene and the inheritance patterns of RB in the Jordanian patients. In this prospective study, the peripheral blood of 50 retinoblastoma patients was collected, genomic DNA was extracted, mutations were identified using Quantitative multiplex PCR (QM-PCR), Allele-specific PCR, Next Generation Sequencing analysis, and Sanger sequencing. In this cohort of 50 patients, 20(40%) patients had unilateral RB and 30(60%) were males...
August 12, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28803013/short-communication-detection-of-stx2-and-elt-genes-in-bovine-milk-by-using-a-multiplex-pcr-system
#7
R D S Nandi, A C Campos, J J Puño-Sarmiento, R P Maluta, S P D Rocha, R K T Kobayashi, G Nakazato
The aim of this study was to detect 2 important toxin genes from diarrheagenic Escherichia coli (DEC) in bovine milk using a new multiplex PCR. To standardize the multiplex PCR, the stx2 and elt genes were investigated for the detection of Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC), respectively. The DNA template was prepared with a thermal procedure (boiling) and a commercial kit. Samples consisted of UHT and pasteurized milk, both skimmed, and STEC and ETEC were tested in concentrations between 10(1) and 10(9) cfu/mL...
August 9, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28802185/diagnostic-yield-and-clinical-impact-of-routine-cell-culture-for-respiratory-viruses-among-children-with-a-negative-multiplex-rt-pcr-result
#8
M AlGhounaim, Y Xiao, C Caya, J Papenburg
BACKGROUND: Polymerase chain reaction (PCR) is the reference standard for respiratory virus testing. However, cell culture may still have added value in identifying viruses not detected by PCR. OBJECTIVES: We aimed to estimate the yield and clinical impact of routine respiratory virus culture among children with a negative PCR result. STUDY DESIGN: A retrospective cohort study was performed from Jan. 2013 to Sept. 2015. Respiratory samples from hospitalized or immunocompromised patients <18years old were routinely inoculated on traditional tube cell culture monolayers if they tested negative by a PCR assay for 12 respiratory viruses...
July 29, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28801345/molecular-basis-for-increased-susceptibility-of-indigenous-north-americans-to-seropositive-rheumatoid-arthritis
#9
Stephen W Scally, Soi-Cheng Law, Yi Tian Ting, Jurgen van Heemst, Jeremy Sokolove, Aaron J Deutsch, E Bridie Clemens, Antonis K Moustakas, George K Papadopoulos, Diane van der Woude, Irene Smolik, Carol A Hitchon, David B Robinson, Elizabeth D Ferucci, Charles N Bernstein, Xiaobo Meng, Vidyanand Anaparti, Tom Huizinga, Katherine Kedzierska, Hugh H Reid, Soumya Raychaudhuri, René E Toes, Jamie Rossjohn, Hani El-Gabalawy, Ranjeny Thomas
OBJECTIVE: The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the 'shared susceptibility epitope (SE)'. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection...
August 11, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28801089/clinical-and-microbiological-characteristics-of-patients-with-bacteremia-caused-by-campylobacter-species-with-an-emphasis-on-the-subspecies-of-c-fetus
#10
Yen-Hung Liu, Wataru Yamazaki, Yu-Tsung Huang, Chun-Hsing Liao, Wang-Hui Sheng, Po-Ren Hsueh
OBJECTIVES: This study was intended to investigate the clinical and microbiological characteristics of patients with bacteremia caused by Campylobacter species. METHODS: From April 1998 to May 2014, 56 adults with bacteremia caused by Campylobacter species were evaluated. These Campylobacter species isolates were confirmed to the species level using 16S rRNA gene sequencing (all isolates) and multiplex PCR analysis (for C. fetus only). The performance of identification for Campylobacter species by the Bruker Biotyper MALDI-TOF MS was evaluated...
July 25, 2017: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
https://www.readbyqxmd.com/read/28801087/cause-of-acute-encephalitis-encephalopathy-in-japanese-children-diagnosed-by-a-rapid-and-comprehensive-virological-detection-system-and-differences-in-their-clinical-presentations
#11
Kei Takasawa, Ryuichi Nakagawa, Shigeru Takishima, Kengo Moriyama, Ken Watanabe, Koji Kiyohara, Takeshi Hasegawa, Masahiro Shimohira, Kenichi Kashimada, Norio Shimizu, Tomohiro Morio
BACKGROUND: Acute encephalitis/encephalopathy (AE/E) is a rare and severe complication of common childhood infections; however, a treatment strategy based on clinical and pathological evidence has not been established. METHODS: The clinical data and aetiological results using a rapid and comprehensive virological detection system of 62 Japanese children diagnosed with AE/E from 2010 to 2014 were collected. We assessed clinical differences between causes and effectiveness of our multiplex PCR system to establish a pathogen-based treatment strategy for AE/E...
August 8, 2017: Brain & Development
https://www.readbyqxmd.com/read/28797659/a-preliminary-evaluation-study-of-new-generation-multiplex-str-kits-comprising-of-the-codis-core-loci-and-the-european-standard-set-loci
#12
Jolena Ying Ying Tan, Yuen Peng Tan, Shilen Ng, Annabel Suan Tay, Yong Han Phua, Wei Jie Tan, Terenze Yao Rui Ong, Li Min Chua, Christopher Kiu Choong Syn
The GlobalFiler™ (Life Technologies), Investigator(®) 24plex QS (Qiagen), and PowerPlex(®) Fusion 6C (Promega) kits are the latest generation 6-dye fluorescent chemistry STR-PCR amplification kits. These kits allow for the simultaneous amplification of the CODIS core loci and the European Standard Set loci, as well as a few Y-STR loci in addition to the standard sex-determining marker Amelogenin. The present study was designed to be a preliminary evaluation of the three STR-PCR kits in terms of sensitivity, profile recovery from degraded DNA samples, tolerance to PCR inhibitors, and detection of minor components in DNA mixtures...
July 25, 2017: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/28795619/hematological-and-molecular-characterization-of-a-novel-hb-a2-variant-with-homozygous-%C3%AE-thalassemia-2-in-a-southern-thai-individual
#13
Manit Nuinoon, Nutjaree Jeenduang, Aumpika Kesornsit, Dararat Horpet, Thunyaluk Plyduang
We report here the hematological and molecular features of a novel δ-globin chain variant found in a Southern Thai woman. Her complete blood count was as follows: red blood cell (RBC) count 5.90 × 10(12)/L, hemoglobin concentration (Hb) 12.6 g/dL, packed cell volume (PCV) 0.41 L/L, mean corpuscular volume (MCV) 69.5 fL, mean corpuscular Hb (MCH) 21.4 pg, mean corpuscular Hb concentration (MCHC) 30.7 g/dL and RBC distribution width (RDW) 13.1%. The blood smear demonstrated microcytic hypochromic RBCs suggestive of thalassemia trait...
August 10, 2017: Hemoglobin
https://www.readbyqxmd.com/read/28795230/improved-multiplex-pcr-primers-for-rapid-identification-of-coagulase-negative-staphylococci
#14
Jonguk Kim, Jisoo Hong, Jeong-A Lim, Sunggi Heu, Eunjung Roh
Coagulase-negative staphylococci (CNS) are opportunistic pathogens that are currently emerging as causative agents of human disease. Though CNS are widespread in the clinic and food, their precise identification at species level is important. Here, using 16S rRNA sequencing, 55 staphylococcal isolates were identified as S. capitis, S. caprae, S. epidermidis, S. haemolyticus, S. pasteuri, S. saprophyticus, S. warneri, and S. xylosus. Although 16S rRNA sequencing is universally accepted as a standard for bacterial identification, the method did not effectively discriminate closely related species, and additional DNA sequencing was required...
August 9, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28795223/high-resolution-melting-pcr-assay-applicable-for-diagnostics-and-screening-studies-allowing-detection-and-differentiation-of-several-babesia-spp-infecting-humans-and-animals
#15
Wioletta Rozej-Bielicka, Aleksander Masny, Elzbieta Golab
The goal of the study was to design a single tube PCR test for detection and differentiation of Babesia species in DNA samples obtained from diverse biological materials. A multiplex, single tube PCR test was designed for amplification of approximately 400 bp region of the Babesia 18S rRNA gene. Universal primers were designed to match DNA of multiple Babesia spp. and to have low levels of similarity to DNA sequences of other intracellular protozoa and Babesia hosts. The PCR products amplified from Babesia DNA isolated from human, dog, rodent, deer, and tick samples were subjected to high-resolution melting analysis for Babesia species identification...
August 10, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28795077/sensitive-molecular-diagnostics-for-cutaneous-leishmaniasis
#16
Orli Sagi, Anat Berkowitz, Shlomi Codish, Victor Novack, Aviv Rashti, Fouad Akad, Yonat Shemer-Avni
BACKGROUND: Rapid diagnosis of cutaneous leishmaniasis (CL) and identification of Leishmania species is highly important for the disease management. In Israel, CL is caused mainly by Leishmania major and Leishmania tropica species. METHODS: We established an easy to handle point of care lesion-swabbing, combined with a highly sensitive multiplex real time PCR (multiplex qPCR) for accurate and rapid diagnosis of Leishmania species. RESULTS: Using three probes: one general for: Leishmania species, and two specific for L major, and L tropica, we screened 1783 clinical samples collected during two years...
2017: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/28792998/validation-of-qf-pcr-for-prenatal-diagnoses-in-a-brazilian-population
#17
Renata Wendel de Moraes, Mario Henrique Burlacchini de Carvalho, Antonio Gomes de Amorim-Filho, Rossana Pulcineli Vieira Francisco, Renata Moscolini Romão, José Eduardo Levi, Marcelo Zugaib
OBJECTIVES: Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory. METHOD: A ChromoQuant QF-PCR kit containing 24 primer pairs targeting loci on chromosomes 21, 13, 18, X and Y was employed to identify aneuploidies of the referred chromosomes...
July 2017: Clinics
https://www.readbyqxmd.com/read/28792716/a-3-month-old-child-with-acute-gastroenteritis-with-enterovirus-d68-detected-from-stool-specimen
#18
Ngan T K Pham, Aksara Thongprachum, Tsuneyoshi Baba, Shoko Okitsu, Quang D Trinh, Shihoko Komine-Aizawa, Hiroyuki Shimizu, Satoshi Hayakawa, Hiroshi Ushijima
Enterovirus D68 (EV-D68) is known to be causative agent of mild to severe upper and lower respiratory illnesses in sporadic cases and outbreaks. We present a case report of a 3-month-old child with acute gastroenteritis who visited a pediatric clinic in Kyushu area in Japan in 2015. A stool sample collected from the patient was screened for diarrheal viruses by multiplex RT-PCR. The result showed that the sample was positive only for enterovirus, and EV-D68 clade B3 was identified by sequence analysis of the viral protein 1 gene...
July 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28791439/metabolic-crosstalk-between-fatty-pancreas-and-fatty-liver-effects-on-local-inflammation-and-insulin-secretion
#19
Felicia Gerst, Robert Wagner, Gabriele Kaiser, Madhura Panse, Martin Heni, Jürgen Machann, Malte N Bongers, Tina Sartorius, Bence Sipos, Falko Fend, Christian Thiel, Silvio Nadalin, Alfred Königsrainer, Norbert Stefan, Andreas Fritsche, Hans-Ulrich Häring, Susanne Ullrich, Dorothea Siegel-Axel
AIMS/HYPOTHESIS: Obesity-linked ectopic fat accumulation is associated with the development of type 2 diabetes. Whether pancreatic and liver steatosis impairs insulin secretion is controversial. We examined the crosstalk of human pancreatic fat cells with islets and the role of diabetogenic factors, i.e. palmitate and fetuin-A, a hepatokine released from fatty liver. METHODS: Human pancreatic resections were immunohistochemically stained for insulin, glucagon, somatostatin and the macrophage/monocyte marker CD68...
August 8, 2017: Diabetologia
https://www.readbyqxmd.com/read/28791034/a-high-throughput-standard-pcr-based-genotyping-method-for-determining-transgene-zygosity-in-segregating-plant-populations
#20
Lige Geng, Dewayne D Deng, Martin J Wubben, Johnie N Jenkins, Jack C McCarty, Ibrokhim Abdurakhmonov
In crop research programs that implement transgene-based strategies for trait improvement it is necessary to distinguish between transgene homozygous and hemizygous individuals in segregating populations. Direct methods for determining transgene zygosity are technically challenging, expensive, and require specialized equipment. In this report, we describe a standard PCR-based protocol coupled with capillary electrophoresis that can identify transgene homozygous and hemizygous individuals in a segregating population without knowledge of transgene insertion site...
2017: Frontiers in Plant Science
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