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https://www.readbyqxmd.com/read/29781618/field-detection-of-citrus-huanglongbing-associated-with-candidatus-liberibacter-asiaticus-by-recombinese-polymerase-amplification-within-15-min
#1
Wenjuan Qian, Ying Lu, Youqing Meng, Zunzhong Ye, Liu Wang, Rui Wang, Qiqi Zheng, Jian Wu
Candidatus Liberibacter asiaticus(Las)is the most prevalent bacterium associated with Huanglongbing which is one of the most destructive diseases of citrus. In this paper, an extremely rapid and simple method for field detection of Las from leaf samples based on recombinase polymerase amplification (RPA) is developed. Three RPA primer pairs were designed and evaluated. RPA amplification was optimized so that it could be accomplished within 10 min. In combination with DNA crude extraction by 50-fold diluting after 1 min of grinding in 0...
May 21, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29781033/microarray-analysis-of-circular-rna-expression-profiles-associated-with-gemcitabine-resistance-in-pancreatic-cancer-cells
#2
Chao Xu, Yue Yu, Fei Ding
Pancreatic cancer (PC) is one of the most malignant tumors of the digestive system due to its rapid progression, metastasis and resistance to chemotherapy. Gemcitabine (GEM) chemotherapy is the first‑choice treatment for advanced PC. However, the effect of GEM‑based chemotherapy on PC is limited due to the development of chemoresistance, and the molecular mechanisms underlying this resistance have yet to be investigated. Circular RNAs (circRNAs), which can function as microRNA sponges, have been found to be involved in the development of several types of cancer...
May 17, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29780399/oxidative-stress-and-aberrant-programmed-cell-death-are-associated-with-pollen-abortion-in-isonuclear-alloplasmic-male-sterile-wheat
#3
Zihan Liu, Xiaoyi Shi, Sha Li, Lingli Zhang, Xiyue Song
Cytoplasmic male sterility is crucial for the utilization of hybrid heterosis and it possibly occurs in parallel with tapetal programmed cell death (PCD) and oxidative metabolism responses. However, little is known about the mechanisms that underlie pollen abortion in wheat. Therefore, we obtained two isonuclear alloplasmic male sterile lines (IAMSLs) with Aegilops kotschyi and Ae. juvenalis cytoplasm. Compared with the maintainer line, cytochemical analyses of the anthers demonstrated that the IAMSLs exhibited anomalous tapetal PCD and organelles, with premature PCD in K87B1-706A and delayed PCD in Ju87B1-706A...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29780175/rapid-identification-of-a-cooling-tower-associated-legionnaires-disease-outbreak-supported-by-polymerase-chain-reaction-testing-of-environmental-samples-new-york-city-2014-2015
#4
Isaac Benowitz, Robert Fitzhenry, Christopher Boyd, Michelle Dickinson, Michael Levy, Ying Lin, Elizabeth Nazarian, Belinda Ostrowsky, Teresa Passaretti, Jennifer Rakeman, Amy Saylors, Elena Shamoonian, Terry-Ann Smith, Sharon Balter
We investigated an outbreak of eight Legionnaires' disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings) <1 km from patient residences, a market misting system, a community-wide water system used for heating and cooling, and potable water. To support a timely public health response, we used real-time polymerase chain reaction (PCR) to identify Legionella DNA in environmental samples within hours of specimen collection...
April 2018: Journal of Environmental Health
https://www.readbyqxmd.com/read/29778881/polymerase-chain-reaction-pcr-based-methods-promising-molecular-tools-in-dentistry
#5
REVIEW
Shahriar Shahi, Sepideh Zununi Vahed, Nazanin Fathi, Simin Sharifi
Polymerase chain reaction (PCR) has become a popular diagnosis and research technique in dentistry. Several studies show that its high sensitivity and specificity allow it as a precise, efficient, and rapid method for detection, identification, and quantification of microorganism. Several genetic polymorphisms can be determined along with detection of immune and inflammatory markers, therefore providing the more accurate perception into the mechanisms underlying the dental and periodontal disease. This review paper discusses the application of PCR as a diagnostic technique in periodontology, endodontic infections, implant-related, and peri-implantitis infection, immune and inflammatory markers identification and genetic polymorphism as well as application of next generation sequencing and gene microarray technology in dentistry mentioned...
May 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29778563/development-and-evaluation-of-a-rapid-nucleic-acid-amplification-method-to-detect-influenza-a-and-b-viruses-in-human-respiratory-specimens
#6
Sonja Elf, Pauliina Auvinen, Lisa Jahn, Karoliina Liikonen, Solveig Sjöblom, Päivi Saavalainen, Minna Mäki, Kevin E Eboigbodin
Isothermal nucleic acid amplification methods can potentially shorten the amount of time required to diagnose influenza. We developed and evaluated a novel isothermal nucleic acid amplification method, RT-SIBA to rapidly detect and differentiate between influenza A and B viruses in a single reaction tube. The performance of the RT-SIBA Influenza assay was compared with two established RT-PCR methods. The sensitivities of the RT-SIBA, RealStar RT-PCR, and CDC RT-PCR assays for the detection of influenza A and B viruses in the clinical specimens were 98...
April 18, 2018: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29777679/development-of-dnazyme-based-pcr-signal-cascade-amplification-for-visual-detection-of-listeria-monocytogenes-in-food
#7
Zhanmin Liu, Chenhui Yao, Cuiyun Yang, Yanming Wang, Sibao Wan, Junyi Huang
Listeria monocytogenes is an important food-borne pathogen, and it can cause severe diseases. Rapid detection of L. monocytogenes is crucial to control this pathogen. A simple and robust strategy based on the cascade of PCR and G-quadruplex DNAzyme catalyzed reaction was used to detect L. monocytogenes. In the presence of hemin and the aptamer formed during PCR, the catalytic horseradish peroxidase-mimicking G-quadruplex DNAzymes allow the colorimetric responses of target DNA from L. monocytogenes. This assay can detect genomic DNA of L...
May 16, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29777597/microdevice-based-solid-phase-polymerase-chain-reaction-for-rapid-detection-of-pathogenic-microorganisms
#8
Quang Nghia Pham, Kieu The Loan Trinh, Seung Won Jung, Nae Yoon Lee
We demonstrate the integration of DNA amplification and detection functionalities developed on a lab-on-a-chip microdevice utilizing solid-phase polymerase chain reaction (SP-PCR) for point-of-need (PON) DNA analyses. First, the polycarbonate microdevice was fabricated by thermal bonding to contain microchambers as reservoirs for performing SP-PCR. Next, the microchambers were subsequently modified with polyethyleneimine and glutaraldehyde for immobilizing amine-modified forward primers. During SP-PCR, the immobilized forward primers and freely diffusing fluorescence-labeled reverse primers cooperated to generate target amplicons, which remained covalently attached to the microchambers for the fluorescence detection...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777376/comprehensive-molecular-diagnosis-of-epstein-barr-virus-associated-lymphoproliferative-diseases-using-next-generation-sequencing
#9
Shintaro Ono, Manabu Nakayama, Hirokazu Kanegane, Akihiro Hoshino, Saeko Shimodera, Hirofumi Shibata, Hisanori Fujino, Takahiro Fujino, Yuta Yunomae, Tsubasa Okano, Motoi Yamashita, Takahiro Yasumi, Kazushi Izawa, Masatoshi Takagi, Kohsuke Imai, Kejian Zhang, Rebecca Marsh, Capucine Picard, Sylvain Latour, Osamu Ohara, Tomohiro Morio
Epstein-Barr virus (EBV) is associated with several life-threatening diseases, such as lymphoproliferative disease (LPD), particularly in immunocompromised hosts. Some categories of primary immunodeficiency diseases (PIDs) including X-linked lymphoproliferative syndrome (XLP), are characterized by susceptibility and vulnerability to EBV infection. The number of genetically defined PIDs is rapidly increasing, and clinical genetic testing plays an important role in establishing a definitive diagnosis. Whole-exome sequencing is performed for diagnosing rare genetic diseases, but is both expensive and time-consuming...
May 18, 2018: International Journal of Hematology
https://www.readbyqxmd.com/read/29776924/tools-for-rapid-genetic-engineering-of-vibrio-fischeri
#10
Karen L Visick, Kelsey M Hodge-Hanson, Alice H Tischler, Allison K Bennett, Vincent Mastrodomenico
Vibrio fischeri is used as a model for number of processes, including symbiosis, quorum sensing, bioluminescence, and biofilm formation. Many of these studies depend on generating deletion mutants and complementing them. Engineering such strains, however, is a time-consuming, multi-step process that relies on cloning and subcloning. Here, we describe a set of tools that can be used to rapidly engineer deletions and insertions in the V. fischeri chromosome without cloning. We developed a uniform approach for generating deletions using PCR SOEing (Splicing by Overlap Extension) with antibiotic cassettes flanked by standardized linker sequences...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29776709/rapid-real-time-pcr-for-the-detection-of-imp-ndm-vim-kpc-and-oxa-48-carbapenemase-genes-in-isolates-and-spiked-stool-samples
#11
Marianne Lund, Marianne Bøgild Petersen, Anders Lægaard Jørgensen, Dorte Paulmann, Mikala Wang
An in-house real-time PCR was developed to detect the carbapenemase genes IMP, NDM, VIM, KPC and OXA-48 from both bacterial colonies and directly from fecal material. The assay is a multiplex PCR performed in two tubes with NDM, VIM and IMP genes detected in one tube and OXA-48 and KPC genes in the other. Despite the large amount of primers and probes necessary to cover all variants of especially the VIM and IMP genes, the efficiency of the PCR reactions was from 95 to 100%. When tested on 170 clinical strains and compared to culture results from a reference laboratory, 100% correspondence was found...
April 13, 2018: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29776628/molecular-pathology-techniques-advances-in-2018
#12
REVIEW
Mark J Bluth, Martin H Bluth
Molecular pathology techniques continue to evolve. Although polymerase chain reaction (PCR) remains the cornerstone methodology for nucleic acid amplification, improvements in nucleic acid detection methodologies (i.e. PCR) have increased the detection sensitivity by using fluorescent and bead based array technologies. Single base pair lesions can be detected via sequencing and related techniques to discern point mutations in disease pathogenesis. Novel technologies, such as high- resolution melting analysis, provide fast high throughput post PCR analysis of genetic mutations or variance in nucleic acid sequences...
June 2018: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29776538/rapid-detection-of-calr-type-1-and-type-2-mutations-using-pna-lna-clamping-loop-mediated-isothermal-amplification-on-a-cd-like-microfluidic-chip
#13
Guojun Cao, Jilie Kong, Zhifang Xing, Yigui Tang, Xinju Zhang, Xiao Xu, Zhihua Kang, Xueen Fang, Ming Guan
Bleeding and thrombosis represent common complications in myeloproliferative neoplasms (MPN) and significantly contribute to morbidity and mortality. Molecular markers, including CALR mutations, were considered not only as diagnostic markers, but also as risk factors for bleeding and thrombosis associated with MPN, especially for patients in remote primary hospitals. We sought to develop an easy-to-use assay for the rapid detection of CALR type 1 (CALR-1) and type 2 (CALR-2) mutations in Philadelphia chromosome-negative MPN patients...
September 18, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29776379/development-of-a-rapid-field-applicable-molecular-diagnostic-for-knockdown-resistance-kdr-markers-in-an-gambiae
#14
Vera T Unwin, Shaun Ainsworth, Emily J Rippon, El Hadji Amadou Niang, Mark J I Paine, David Weetman, Emily R Adams
BACKGROUND: The spread of insecticide resistance (IR) is a major threat to vector control programmes for mosquito-borne diseases. Early detection of IR using diagnostic markers could help inform these programmes, especially in remote locations where gathering reliable bioassay data is challenging. Most current molecular tests for genetic IR markers are only suitable for use in well-equipped laboratory settings. There is an unmet need for field-applicable diagnostics. METHODS: A single-cartridge test was designed to detect key IR mutations in the major African vector of malaria, Anopheles gambiae...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29775092/a-prospective-multi-centre-us-clinical-trial-to-determine-accuracy-of-febridx-point-of-care-testing-for-acute-upper-respiratory-infections-with-and-without-a-confirmed-fever
#15
Nathan I Shapiro, Wesley H Self, Jeffrey Rosen, Stephan C Sharp, Michael R Filbin, Peter C Hou, Amisha D Parekh, Michael C Kurz, Robert Sambursky
BACKGROUND: FebriDx is a 10-minute disposable point-of-care test designed to identify clinically significant systemic host immune responses and aid in the differentiation of bacterial and viral respiratory infection by simultaneously detecting C-reactive protein (CRP) and myxovirus resistance protein A (MxA) from a fingerstick blood sample. FebriDx diagnostic accuracy was evaluated in the emergency room and urgent care setting. METHODS: A prospective, multicentre, observational cohort study of acute upper respiratory tract infections (URIs), with and without a confirmed fever at the time of enrolment, was performed to evaluate the diagnostic accuracy of FebriDx to identify clinically significant bacterial infection with host response and acute pathogenic viral infection...
May 18, 2018: Annals of Medicine
https://www.readbyqxmd.com/read/29773138/multiplex-hydrolysis-probe-assay-for-the-simultaneous-detection-of-theileria-equi-and-babesia-caballi-infections-in-equids
#16
Raksha V Bhoora, Ronel Pienaar, Frances Cornelius, Antoinette Josemans, Olivier Matthee, Ratselane Marumo, Christo Troskie, Ben J Mans
Quantitative real-time PCR assays previously developed for the detection of Theileria equi and Babesia caballi, were combined in a single multiplex TaqMan qPCR platform for the simultaneous detection of both heamoprotozoan parasites in equids. The multiplex equine piroplasmosis (M-EP) qPCR assay was shown to be efficient and specific. The detection limit was determined to be 1.4 × 10-4 % parasitized erythrocytes (PE) for T. equi and 2.8 × 10-4 % PE for B. caballi. The effect of differential DNA concentrations on the outcome of the M-EP qPCR for each target species was also investigated...
May 15, 2018: Veterinary Parasitology
https://www.readbyqxmd.com/read/29772717/a-rapid-screen-for-host-encoded-mirnas-with-inhibitory-effects-against-ebola-virus-using-a-transcription-and-replication-competent-virus-like-particle-system
#17
Zhongyi Wang, Jiaming Li, Yingying Fu, Zongzheng Zhao, Chunmao Zhang, Nan Li, Jingjing Li, Hongliang Cheng, Xiaojun Jin, Bing Lu, Zhendong Guo, Jun Qian, Linna Liu
MicroRNAs (miRNAs) may become efficient antiviral agents against the Ebola virus (EBOV) targeting viral genomic RNAs or transcripts. We previously conducted a genome-wide search for differentially expressed miRNAs during viral replication and transcription. In this study, we established a rapid screen for miRNAs with inhibitory effects against EBOV using a tetracistronic transcription- and replication-competent virus-like particle (trVLP) system. This system uses a minigenome comprising an EBOV leader region, luciferase reporter, VP40, GP, VP24, EBOV trailer region, and three noncoding regions from the EBOV genome and can be used to model the life cycle of EBOV under biosafety level (BSL) 2 conditions...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29772236/identification-and-characterization-of-circular-rnas-in-rapid-atrial-pacing-dog-atrial-tissue
#18
Wenfeng Shangguan, Xue Liang, Wen Shi, Tong Liu, Manman Wang, Guangping Li
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs, and participating in the process of many diseases. However, the expression and functions of circRNAs in Rapid atrial pacing (RAP) dog atrial tissue still unknown. 12 canines were randomly assigned to control and pacing group. RAP at 500 beats per minute was maintained 14 days in the pacing group. The expression characterization of circRNAs were revealed by high-throughput sequencing. We totally predicted 15,990 circRNAs in dog atrial tissues...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29771869/performance-of-the-atlas-rapid-test-for-chlamydia-trachomatis-and-women-s-attitudes-toward-point-of-care-testing
#19
Lea E Widdice, Yu-Hsiang Hsieh, Barbara Silver, Mathilda Barnes, Perry Barnes, Charlotte A Gaydos
PURPOSE: This study compared performance of Atlas io® diagnostic platform, a point-of-care (POC) PCR assay for Chlamydia trachomatis (CT), to Aptima Combo 2, a standard of care laboratory-based nucleic acid amplification assay (NAAT), and evaluated patient attitudes toward POC testing. METHODS: Women ≥14 years undergoing CT screening/testing were recruited from an urban adolescent primary care practice (Teen Health Center, THC) and a sexually transmitted disease (STD) clinic...
May 1, 2018: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/29770110/a-pcr-based-method-for-rna-probes-and-applications-in-neuroscience
#20
Ruifang Hua, Shanshan Yu, Mugen Liu, Haohong Li
In situ hybridization (ISH) is a powerful technique that is used to detect the localization of specific nucleic acid sequences for understanding the organization, regulation, and function of genes. However, in most cases, RNA probes are obtained by in vitro transcription from plasmids containing specific promoter elements and mRNA-specific cDNA. Probes originating from plasmid vectors are time-consuming and not suitable for the rapid gene mapping. Here, we introduce a simplified method to prepare digoxigenin (DIG)-labeled non-radioactive RNA probes based on polymerase chain reaction (PCR) amplification and applications in free-floating mouse brain sections...
2018: Frontiers in Neuroscience
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