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Rapid PCR

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https://www.readbyqxmd.com/read/28350876/mipe-a-metagenome-based-community-structure-explorer-and-ssu-primer-evaluation-tool
#1
Bin Zou, JieFu Li, Quan Zhou, Zhe-Xue Quan
An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers...
2017: PloS One
https://www.readbyqxmd.com/read/28350870/bacterial-clonal-diagnostics-as-a-tool-for-evidence-based-empiric-antibiotic-selection
#2
Veronika Tchesnokova, Hovhannes Avagyan, Elena Rechkina, Diana Chan, Mariya Muradova, Helen Ghirmai Haile, Matthew Radey, Scott Weissman, Kim Riddell, Delia Scholes, James R Johnson, Evgeni V Sokurenko
Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E...
2017: PloS One
https://www.readbyqxmd.com/read/28346841/rapid-and-reliable-genotyping-of-hla-b-57-01-in-four-chinese-populations-using-a-single-tube-duplex-real-time-polymerase-chain-reaction-assay
#3
Min Han, Xing Kang, Zhengbin Liu, Tingting Zhang, Yanwei Li, Chao Chen, Huijuan Wang
HLA-B*57:01 is strongly associated with severe adverse drug reaction induced by the anti-HIV drug abacavir (ABC) and antibiotic flucloxacillin. This study was dedicated to establishing a new method for HLA-B*57:01 genotyping and investigating the HLA-B*57:01 distribution pattern in four Chinese populations. A single-tube duplex real-time polymerase chain reaction (PCR) system was established by combining the amplification refractory mutation system and TaqMan probe. The reliability of this assay was validated by comparing the genotyping results with those by sequence-based typing...
March 27, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28343161/fulminant-invasive-meningococcal-disease-due-to-serogroup-y-infection-a-highly-unusual-case-reflecting-worrying-increases-in-carriage-and-incidence
#4
Akash Maniam, Sriram Ravichandran
A young man presented to accident and emergency with a short history of diarrhoea and vomiting, with no medical history. He deteriorated rapidly during triage and never regained consciousness. He was pronounced dead after hours of attempted resuscitation. He was found to have organisms suggestive of diplococci on his blood film and subsequently had MenY found via PCR testing. This case illustrates a highly unusual presentation of invasive meningococcal disease caused by MenY which is quietly and dangerously increasing in incidence in the UK, particularly in young healthy patients...
March 25, 2017: BMJ Case Reports
https://www.readbyqxmd.com/read/28343091/rapid-detection-and-ruling-out-of-neonatal-sepsis-by-pcr-coupled-with-electrospray-ionization-mass-spectrometry-pcr-esi-ms
#5
Cristina Delcò, Oliver Karam, Riccardo Pfister, Alain Gervaix, Gesuele Renzi, Stéphane Emonet, Jacques Schrenzel, Klara M Posfay-Barbe
BACKGROUND: Sepsis is an important cause of morbidity and mortality in neonates and clinicians are typically required to administer empiric antibiotics while waiting for blood culture results. However, prolonged and inappropriate use of antibiotics is associated with various complications and adverse events. Better tools to rapidly rule out bacterial infections are therefore needed. AIMS: We aimed to assess the negative predictive value of PCR coupled with Electrospray Ionization Mass Spectrometry (PCR/ESI-MS) compared to conventional blood cultures in neonatal sepsis...
March 23, 2017: Early Human Development
https://www.readbyqxmd.com/read/28342740/the-development-of-a-real-time-reverse-transcription-polymerase-chain-reaction-rrt-pcr-assay-using-taqman-technology-for-the-pan-detection-of-bluetongue-virus-btv
#6
Catherine Mulholland, Michael J McMenamy, Bernd Hoffmann, Bernadette Earley, Bryan Markey, Joseph Cassidy, Gordon Allan, Michael D Welsh, John McKillen
Bluetongue virus (BTV) is an infectious, non-contagious viral disease of domestic and wild ruminants that is transmitted by adult females of certain Culicoides species. Since 2006, several serotypes including BTV-1, 2, 4, 6, 8, 9 and 16, have spread from the Mediterranean basin into Northern Europe for the first time. BTV-8 in particular, caused a major epidemic in northern Europe. As a result, it is evident that most European countries are at risk of BTV infection. The objective of this study was to develop and validate a real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assay based on TaqMan technology for the detection of representative strains of all BTV serotypes...
March 22, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28341587/impact-of-rapid-molecular-respiratory-virus-testing-on-real-time-decision-making-in-a-pediatric-emergency-department
#7
Daniel T Rogan, Mohit S Kochar, Samuel Yang, James V Quinn
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory respiratory PCR testing is accurate albeit slow for ED management, whereas rapid antigen testing is inaccurate. We determined the impact of bedside influenza/RSV PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28340585/analytical-sensitivity-of-current-best-in-class-malaria-rapid-diagnostic-tests
#8
Alfons Jimenez, Roxanne R Rees-Channer, Rushini Perera, Dionicia Gamboa, Peter L Chiodini, Iveth J González, Alfredo Mayor, Xavier C Ding
BACKGROUND: Rapid diagnostic tests (RDTs) are today the most widely used method for malaria diagnosis and are recommended, alongside microscopy, for the confirmation of suspected cases before the administration of anti-malarial treatment. The diagnostic performance of RDTs, as compared to microscopy or PCR is well described but the actual analytical sensitivity of current best-in-class tests is poorly documented. This value is however a key performance indicator and a benchmark value needed to developed new RDTs of improved sensitivity...
March 24, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28340181/different-expression-patterns-of-sperm-motility-related-genes-in-testis-of-diploid-and-tetraploid-cyprinid-fish1
#9
Fangzhou Hu, Kang Xu, Yunfan Zhou, Chang Wu, Shi Wang, Jun Xiao, Min Wen, Rurong Zhao, Kaikun Luo, Min Tao, Wei Duan, Shaojun Liu
Sperm motility is an important standard to measure the fertility of male. In our previous study, we found that the diploid spermatozoa from allotetraploid hybrid (4nAT) had longer durations of rapid and slow progressive motility than haploid spermatozoa from common carp (COC). In this study, to explore sperm motility-related molecular mechanisms, we compared the testis tissues transcriptomes from two years old male COC and 4nAT. The RNA-seq data revealed that 2985 genes were differentially expressed between COC and 4nAT, including 2216 up-regulated and 769 down-regulated genes in 4nAT...
March 7, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28339688/an-activity-staining-method-on-filtration-paper-enables-high-throughput-screening-of-temperature-sensitive-and-inactive-mutations-of-rice-%C3%AE-amylase-for-improvement-of-rice-grain-quality
#10
Hiromoto Yamakawa, Rieko Hirai-Kimura, Yuriko Nakata, Masaru Nakata, Masaharu Kuroda, Takeshi Yamaguchi
α-Amylase is a starch-hydrolyzing enzyme (EC 3.2.1.1) indispensable for germination of cereal seeds, but it is also expressed during the ripening stage. Previous studies demonstrated that the enzyme is activated in developing rice seeds under extremely hot weather and triggers a loss of grain quality by hindering the accumulation of storage starch in the endosperm. Since inactive or, preferably, heat-labile α-amylases are preferable for breeding premium rice, we developed a method for rapid screening of inactive and temperature-sensitive mutants of the enzyme by combining the random mutagenesis by error-prone PCR and an on-filter activity test of the recombinant enzyme expressed by Escherichia coli...
February 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28339458/rapid-surveillance-for-vector-presence-rsvp-development-of-a-novel-system-for-detecting-aedes-aegypti-and-aedes-albopictus
#11
Brian L Montgomery, Martin A Shivas, Sonja Hall-Mendelin, Jim Edwards, Nicholas A Hamilton, Cassie C Jansen, Jamie L McMahon, David Warrilow, Andrew F van den Hurk
BACKGROUND: The globally important Zika, dengue and chikungunya viruses are primarily transmitted by the invasive mosquitoes, Aedes aegypti and Aedes albopictus. In Australia, there is an increasing risk that these species may invade highly urbanized regions and trigger outbreaks. We describe the development of a Rapid Surveillance for Vector Presence (RSVP) system to expedite presence- absence surveys for both species. METHODOLOGY/PRINCIPAL FINDINGS: We developed a methodology that uses molecular assays to efficiently screen pooled ovitrap (egg trap) samples for traces of target species ribosomal RNA...
March 24, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28338200/glioma-cells-promote-angiogenesis-through-the-release-of-exosomes-containing-long-non-coding-rna-pou3f3
#12
H-L Lang, G-W Hu, Y Chen, Y Liu, W Tu, Y-M Lu, L Wu, G-H Xu
OBJECTIVE: Angiogenesis is a key event in the progression of gliomas, and emerging evidence suggests that exosomes are signaling extracellular organelles that modulate the tumor microenvironment and promote angiogenesis and tumor progression. This study aimed to explore the mechanism by which glioma-derived exosomes affect angiogenesis. MATERIALS AND METHODS: qRT-PCR was used to determine the expression level of linc-POU3F3 in glioma tissue as well as glioma cell lines...
March 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28338022/alizarin-red-s-for-online-pyrophosphate-detection-identified-by-a-rapid-screening-method
#13
Jens Fischbach, Qiuting Loh, Frank F Bier, Theam Soon Lim, Marcus Frohme, Jörn Glökler
We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337426/pathogen-identification-in-suspected-cases-of-pyogenic-spondylodiscitis
#14
Ahmad Farajzadeh Sheikh, Azar D Khosravi, Hamed Goodarzi, Roohangiz Nashibi, Alireaza Teimouri, Azim Motamedfar, Reza Ranjbar, Sara Afzalzadeh, Mehrandokht Cyrus, Mohammad Hashemzadeh
Pyogenic spinal infection continues to represent a worldwide problem. In approximately one-third of patients with pyogenic spondylodiscitis, the infectious agent is never identified. Of the cases that lead to organismal identification, bacteria are more commonly isolated from the spine rather than fungi and parasites. This study applied universal prokaryotic 16S rRNA PCR as a rapid diagnostic tool for the detection of bacterial agents in specimens from patients suspected of pyogenic spondylodiscitis. Gram and Ziehl-Neelsen staining were used as a preliminary screening measure for microbiologic evaluation of patient samples...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28336361/a-novel-multiplex-pcr-assay-for-simultaneous-detection-of-nine-clinically-significant-bacterial-pathogens-associated-with-bovine-mastitis
#15
Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Wasim Shehzad, Peter C Thomson
For rapid and simultaneous detection of nine bovine mastitic pathogens, a sensitive and specific multiplex PCR assay was developed. The assay was standardized using reference strains and validated on mastitic milk cultures which were identified to species level based on 16S rRNA sequencing. Multiplex PCR assay also efficiently detected the target bacterial strains directly from milk. Detection limit of the assay was up to 50 pg for DNA isolated from pure cultures and 10(4) CFU/ml for spiked milk samples. As estimated by latent class analysis, the assay was sensitive up to 88% and specific up to 98% for targeted mastitic pathogens, compared with the bacterial culture method and the 16S rRNA sequence analysis...
March 20, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28335696/development-and-initial-evaluation-of-a-lateral-flow-dipstick-test-for-antigen-detection-of-entamoeba-histolytica-in-stool-sample
#16
Syazwan Saidin, Muhammad Hafiznur Yunus, Nurulhasanah Othman, Yvonne Ai-Lian Lim, Zeehaida Mohamed, Nik Zairi Zakaria, Rahmah Noordin
Entamoeba histolytica infection remains a public health concern in developing countries. Early diagnosis of amoebiasis can avoid disease complications, thus this study was aimed at developing a test that can rapidly detect the parasite antigens in stool samples. Rabbits were individually immunized with recombinant pyruvate phosphate dikinase (rPPDK) and E. histolytica excretory-secretory antigens to produce polyclonal antibodies. A rapid dipstick test was produced using anti-rPPDK PAb lined on the dipstick as capture reagent and anti-EhESA PAb conjugated to colloidal gold as the detector reagent...
March 24, 2017: Pathogens and Global Health
https://www.readbyqxmd.com/read/28334789/comparative-evaluation-of-norovirus-infection-in-children-with-acute-gastroenteritis-by-rapid-immunochromatographic-test-rt-pcr-and-real-time-rt-pcr
#17
Kattareeya Kumthip, Pattara Khamrin, Wilaiporn Saikruang, Kanittapon Supadej, Hiroshi Ushijima, Niwat Maneekarn
Immunochromatographic (IC) test for norovirus detection is a rapid and simple detection method. This study evaluated the sensitivity and specificity of a recent version of R-Biopharm RIDA®QUICK Norovirus IC assay for norovirus detection in fecal specimens from children hospitalized with acute gastroenteritis. Fecal specimens were tested by IC kit in comparison with gold standard reverse transcription polymerase chain reaction (RT-PCR) and real-time RT-PCR. The IC kit showed high sensitivity and specificity comparable with PCR-based methods...
March 2, 2017: Journal of Tropical Pediatrics
https://www.readbyqxmd.com/read/28334704/combining-real-time-cold-and-mama-pcr-taqman-techniques-to-detect-and-quantify-r201-gnas-mutations-in-the-mccune-albright-syndrome%C3%A2
#18
Luisa de Sanctis, Ilaria Galliano, Paola Montanari, Patrizia Matarazzo, Daniele Tessaris, Massimiliano Bergallo
BACKGROUND/AIM: The McCune-Albright syndrome (MAS) is a potentially severe disorder hallmarked by fibrous bone dysplasia, café-au-lait skin spots, and endocrine hyperfunction. It is caused by postzygotic activating mutations at the R201 codon of the GNAS gene, leading to a state of somatic mosaicism. Our aim was to improve the mutation detection rate and to quantify the presence of R201 GNAS mutations in different DNA samples from MAS patients. METHODS: Real-time COLD- and MAMA-PCR TaqMan techniques were combined to search for R201 mutations in the DNA of blood or affected tissues from 16 previously molecularly characterized MAS patients, from a further 84 subjects with MAS signs who were R201 negative at RFLP analysis, and from 36 controls...
March 23, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28333348/promoter-characterization-and-expression-of-the-blakpc-2-gene-in-escherichia-coli-pseudomonas-aeruginosa-and-acinetobacter-baumannii
#19
Delphine Girlich, Rémy A Bonnin, Agnes Jousset, Thierry Naas
Objectives: KPC-producing pathogens exhibit variable carbapenem susceptibility levels, which is probably the result of the genetic environment of the bla KPC genes. Here we determined the transcriptional start sites (TSSs) and the expression of the bla KPC-2 gene in various genetic contexts and in different hosts ( Escherichia coli , Pseudomonas aeruginosa and Acinetobacter baumannii ). Methods: The bla KPC-2 genes along with the upstream sequences derived from Tn 4401b (structure A), Tn 4401b interrupted by Tn 3 /IS 26 (structure B) and Tn 4401b interrupted by Tn 5563 (structure C) were cloned in two E...
March 5, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28332721/rapid-detection-and-quantification-of-ebola-zaire-virus-by-one-step-real-time-quantitative-reverse-transcription-polymerase-chain-reaction
#20
Young-Tae Ro, Anysha Ticer, Ricardo Carrion, Jean L Patterson
Since Ebola virus causes a severe hemorrhagic fever in humans with mortality rates as high as 90%, the rapid and accurate detection of the virus is essential both for controlling the infection and for preventing further transmission. Here, we introduce one-step real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays for the rapid and quantitative detection of an Ebola Zaire strain using GP, VP24 or VP40 gene as a target. Routine assay conditions for hydrolysis probe detection were established by the manufacturer's protocol used in the assays...
March 23, 2017: Microbiology and Immunology
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