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https://www.readbyqxmd.com/read/27922678/a-novel-rapid-point-of-care-test-for-lung-cancer-patients-to-detect-epidermal-growth-factor-receptor-gene-mutations-by-using-real-time-droplet-pcr-and-fresh-liquid-cytology-specimens
#1
Shiho Asaka, Akihiko Yoshizawa, Kazuyuki Matsuda, Akemi Yamaguchi, Hiroshi Yamamoto, Takayuki Shiina, Rie Nakata, Kaoru Ogawa, Meng Zhang, Takayuki Honda
Epidermal growth factor receptor gene (EGFR) mutations are associated with response to tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). We developed a novel, rapid EGFR mutation assay using a real-time droplet-polymerase chain reaction machine (EGFR d-PCR assay). The purpose of this study was to validate the performance of the EGFR d-PCR assay using fresh liquid cytology specimens. We analyzed three major EGFR mutations (L858R in exon 21, E746_A750del in exon 19 and T790M in exon 20) in 80 fresh liquid cytology specimens of adenocarcinoma (ADC) or NSCLC-not otherwise specified (NOS) via the EGFR d-PCR assay and conventional real-time PCR assay using the therascreen® EGFR RGQ PCR kit (Therascreen assay)...
December 2, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27922429/multiplex-pcr-for-detection-of-helicobacter-pylori-infection-in-gastric-biopsies-with-lower-inflammatory-score
#2
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/27920888/development-of-a-high-resolution-melting-analysis-method-for-cyp2c19-17-genotyping-in-healthy-volunteers
#3
Zahra Ghasemi, Mehrdad Hashemi, Mahsa Ejabati, Seyyed Meisam Ebrahimi, Hamidreza Kheiri Manjili, Ali Sharafi, Ali Ramazani
BACKGROUND: Genetic polymorphisms of drug metabolisms by cytochrome P450 (P450s) could affect drug response, attracting particular interest in the pharmacogenetics. Due to the importance of CYP2C19* 17 allele and its capability of super- fast metabolism and also lack of information about distribution of the alleles in Iranian population, this research aimed to use High Resolution Melting (HRM) method compared to PCR-RFLP for genotyping healthy Iranian population. METHODS: Blood samples were collected from 100 healthy Iranian volunteers...
October 2016: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/27920764/one-step-pcr-detection-of-salmonella-pullorum-gallinarum-using-a-novel-target-the-flagellar-biosynthesis-gene-flhb
#4
Dan Xiong, Li Song, Shizhong Geng, Jing Tao, Shumin An, Zhiming Pan, Xinan Jiao
Salmonella enterica serovar Pullorum/Gallinarum is an important infectious pathogen that has caused widespread problems for chicken industry. Traditional Salmonella serotyping is an expensive and time-consuming process. In this study, we developed a rapid one-step polymerase chain reaction (PCR) method to identify S. Pullorum/Gallinarum. The PCR-based assay focuses on flhB, which shows a deficient region only in S. Pullorum/Gallinarum, compared with that of other serovars. The specificity and sensitivity of the PCR system were evaluated...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920757/advances-and-challenges-in-viability-detection-of-foodborne-pathogens
#5
REVIEW
Dexin Zeng, Zi Chen, Yuan Jiang, Feng Xue, Baoguang Li
Foodborne outbreaks are a serious public health and food safety concern worldwide. There is a great demand for rapid, sensitive, specific, and accurate methods to detect microbial pathogens in foods. Conventional methods based on cultivation of pathogens have been the gold standard protocols; however, they take up to a week to complete. Molecular assays such as polymerase chain reaction (PCR), sequencing, microarray technologies have been widely used in detection of foodborne pathogens. Among molecular assays, PCR technology [conventional and real-time PCR (qPCR)] is most commonly used in the foodborne pathogen detection because of its high sensitivity and specificity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920176/laboratory-diagnosis-of-chikungunya-virus-infections-and-commercial-sources-for-diagnostic-assays
#6
Barbara W Johnson, Brandy J Russell, Christin H Goodman
Detection of chikungunya virus (CHIKV) or viral RNA is the primary laboratory test used to diagnose infection in serum collected <6 days after onset of illness. Two real-time reverse transcription-polymerase chain reaction (RT-PCR) kits are available commercially, but validity data are limited. There are 2 commercial sources of inactivated positive-control CHIKV RNA to be used with purchased primers. The Centers for Disease Control and Prevention provides viral RNA-positive controls and primer and probe nucleotide sequences for real-time RT-PCR testing...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27917305/laboratory-diagnosis-for-outbreak-prone-infectious-diseases-after-typhoon-yolanda-haiyan-philippines
#7
Mariko Saito-Obata, Mayuko Saito, Titus C Tan, Inez Andrea P Medado, Clyde Dapat, Michiko Okamoto, Raita Tamaki, Rowena C Capistrano, Edelwisa Segubre-Mercado, Socorro P Lupisan, Hitoshi Oshitani
Typhoon Yolanda (Haiyan) hit the central part of the Philippines on November 8, 2013. To identify possible outbreaks of communicable diseases after the typhoon, nasopharyngeal swabs, stool and blood samples were collected from patients who visited the Eastern Visayas Regional Medical Center due to acute respiratory infection (ARI), acute gastroenteritis (AGE) or other febrile illness (OFI) including suspected dengue fever, between November 28, 2013 and February 5, 2014.   Methods: Samples were tested on-site for selected pathogens using rapid diagnostic tests...
October 21, 2016: PLoS Currents
https://www.readbyqxmd.com/read/27917160/development-of-multiple-cross-displacement-amplification-label-based-gold-nanoparticles-lateral-flow-biosensor-for-detection-of-shigella-spp
#8
Yi Wang, Yan Wang, Jianguo Xu, Changyun Ye
Shigella spp., the etiological agent of shigellosis or "bacillary dysentery," are responsible for considerable morbidity and mortality in excess of a million deaths globally per year. Although PCR-based techniques (such as PCR-based dipstick biosensors) have been used for the molecular diagnosis of infectious disease, these assays were restricted due to the need for a sophisticated thermal cycling apparatus to denature target templates. To facilitate simple and rapid detection of target pathogens, we successfully devised an inexpensive, reliable and nearly instrument-free molecular technique, which incorporates multiple cross displacement amplification (MCDA) combined with a newly designed lateral flow biosensor (LFB) for visual, sensitive and specific detection of Shigella...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916668/development-of-a-novel-real-time-rt-pcr-assay-to-detect-seneca-valley-virus-1-associated-with-emerging-cases-of-vesicular-disease-in-pigs
#9
Veronica L Fowler, Russell H Ransburgh, Elizabeth G Poulsen, Jemma Wadsworth, Donald P King, Valerie Mioulet, Nick J Knowles, Susanna Williamson, Xuming Liu, Gary A Anderson, Ying Fang, Jianfa Bai
Seneca Valley virus 1 (SVV-1) can cause vesicular disease that is clinically indistinguishable from foot-and-mouth disease, vesicular stomatitis and swine vesicular disease. SVV-1-associated disease has been identified in pigs in several countries, namely USA, Canada, Brazil and China. Diagnostic tests are required to reliably detect this emerging virus, and this report describes the development and evaluation of a novel real-time (r) reverse-transcription (RT) PCR assay (rRT-PCR), targeting the viral polymerase gene (3D) of SVV-1...
January 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/27915986/molecular-analysis-of-pseudomonas-aeruginosa-metallo-beta-lactamase-a-first-report-of-an-iranian-referral-pediatric-hospital
#10
Shima Mahmoudi, Babak Pourakbari, Mansoure Hosseini, Amir Esmaeil Alyari, Mohammad Taghi Haghi Ashtiani, Setareh Mamishi
INTRODUCTION: Pseudomonas aerouginosa is an important opportunistic pathogen causes clinical infections among ill patients. Metallo- Beta- lactamases (MBLs) are important mechanisms of carbapenem (drug of choice) resistance among Pseudomonas aerouginosa isolates. The aim of this study was to determine B- lactamases genes (bla-genes) in P. aerouginosa isolates and to detect percentage of MBLs among P. aerouginosa isolates in different wards. MATERIAL AND METHODS: Clinical isolates of P...
December 2, 2016: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/27915212/rapid-detection-and-evolutionary-analysis-of-legionella-pneumophila-serogroup-1-sequence-type-47
#11
M Mentasti, P Cassier, S David, C Ginevra, L Gomez-Valero, A Underwood, B Afshar, J Etienne, J Parkhill, V Chalker, C Buchrieser, T G Harrison, S Jarraud
OBJECTIVES: Legionella pneumophia serogroup 1 (Lp1) sequence type 47 is the leading cause of legionellosis in North-Western Europe but surprisingly it is rarely isolated from environmental samples. Comparative genomics was applied to develop a PCR assay and to better understand the evolution of this strain. METHODS: Comparative analysis of 36 genomes representative of the Lp species was used to identify specific PCR targets which were then evaluated in silico on 545 sequenced genomes, and in vitro on 436 Legionella strains, 106 respiratory samples and three environmental samples from proven ST47 sources...
November 30, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27915176/mining-identification-and-function-analysis-of-micrornas-and-target-genes-in-peanut-arachis-hypogaea-l
#12
Tingting Zhang, Shuhao Hu, Caixia Yan, Chunjuan Li, Xiaobo Zhao, Shubo Wan, Shihua Shan
In the present investigation, a total of 60 conserved peanut (Arachis hypogaea L.) microRNA (miRNA) sequences, belonging to 16 families, were identified using bioinformatics methods. There were 392 target gene sequences, identified from 58 miRNAs with Target-align software and BLASTx analyses. Gene Ontology (GO) functional analysis suggested that these target genes were involved in mediating peanut growth and development, signal transduction and stress resistance. There were 55 miRNA sequences, verified employing a poly (A) tailing test, with a success rate of up to 91...
November 24, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27915036/a-rapid-assay-for-detection-of-rose-rosette-virus-using-reverse-transcription-recombinase-polymerase-amplification-using-multiple-gene-targets
#13
Binoy Babu, Brian K Washburn, Steven H Miller, Kristina Poduch, Tulin Sarigul, Gary W Knox, Francisco M Ochoa-Corona, Mathews L Paret
Rose rosette disease caused by Rose rosette virus (RRV; genus Emaravirus) is the most economically relevant disease of Knock Out(®) series roses in the U.S. As there are no effective chemical control options for the disease, the most critical disease management strategies include the use of virus free clean plants for propagation and early detection and destruction of infected plants. The current diagnostic techniques for RRV including end-point reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR (RT-qPCR) are highly sensitive, but limited to diagnostic labs with the equipment and expertise; and is time consuming...
November 30, 2016: Journal of Virological Methods
https://www.readbyqxmd.com/read/27913256/rapid-upregulation-of-the-hippocampal-connexins-36-and-45-mrna-levels-during-memory-consolidation
#14
Siamak Beheshti, Reyhaneh Zeinali, Abolghasem Esmaeili
Gap junction channels are implicated in learning and memory process. However, their role on each of the particular stages of memory formation have been studied less. In this study, the time profile of the expression levels of hippocampal connexins 36 and 45 (Cx36 and Cx45) mRNAs was measured during memory consolidation, in a passive avoidance paradigm. Totally 36 adult male rats were distributed into 5 groups of each 6. At different times profiles (30min, 3, 6 and 24h) following training, rats were decapitated and their hippocampi were immediately removed and frozen in liquid nitrogen...
November 29, 2016: Behavioural Brain Research
https://www.readbyqxmd.com/read/27911895/dna-microarray-detection-of-18-important-human-blood-protozoan-species
#15
Mu-Xin Chen, Lin Ai, Jun-Hu Chen, Xin-Yu Feng, Shao-Hong Chen, Yu-Chun Cai, Yan Lu, Xiao-Nong Zhou, Jia-Xu Chen, Wei Hu
BACKGROUND: Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need. METHODOLOGY/PRINCIPAL FINDINGS: The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes...
December 2016: PLoS Neglected Tropical Diseases
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
#16
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/27907129/meningococcal-carriage-in-military-recruits-and-university-students-during-the-pre-menb-vaccination-era-in-greece-2014-2015
#17
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
https://www.readbyqxmd.com/read/27906992/a-dual-filtration-based-multiplex-pcr-method-for-simultaneous-detection-of-viable-escherichia-coli-o157-h7-listeria-monocytogenes-and-staphylococcus-aureus-on-fresh-cut-cantaloupe
#18
Ke Feng, Wenzhong Hu, Aili Jiang, Sarengaowa, Yongping Xu, Yu Zou, Liu Yang, Xin Wang
Fresh-cut cantaloupe is particularly susceptible to contamination with pathogenic bacteria, such as Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus. Therefore, development of rapid, yet accurate detection techniques is necessary to ensure food safety. In this study, a multiplex PCR system and propidium monoazide (PMA) concentration were optimized to detect all viable pathogens in a single tube. A dual filtration system utilized a filtration membrane with different pore sizes to enrich pathogens found on fresh-cut cantaloupe...
2016: PloS One
https://www.readbyqxmd.com/read/27903645/upgrading-short-read-animal-genome-assemblies-to-chromosome-level-using-comparative-genomics-and-a-universal-probe-set
#19
Joana Damas, Rebecca O'Connor, Marta Farré, Vasileios Panagiotis E Lenis, Henry J Martell, Anjali Mandawala, Katie Fowler, Sunitha Joseph, Martin T Swain, Darren K Griffin, Denis M Larkin
Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes. Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27902755/the-utility-of-malaria-rapid-diagnostic-tests-as-a-tool-in-enhanced-surveillance-for-malaria-elimination-in-vanuatu
#20
Wesley Donald, Cielo Pasay, Jean-Olivier Guintran, Harry Iata, Karen Anderson, Johnny Nausien, Karryn J Gresty, Norman C Waters, Lasse S Vestergaard, George Taleo, Qin Cheng
BACKGROUND: As part of efforts to eliminate malaria, Vanuatu has piloted the implementation of enhanced malaria surveillance and response strategies since 2011. This involves passive case detection (PCD) in health facilities, proactive case detection (Pro-ACD) and reactive case detection (Re-ACD) in communities using malaria rapid diagnostic tests (RDTs). While RDTs improve case management, their utility for detection of malaria infections in ACDs in this setting is unclear. METHODS: The utility of malaria RDTs as diagnostic tools was evaluated in PCD, in five rounds of Pro-ACDs and five rounds of Re-ACDs conducted in Tafea and Torba Provinces between 2011 and 2014...
2016: PloS One
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