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https://www.readbyqxmd.com/read/28542573/development-of-real-time-pcr-and-loop-mediated-isothermal-amplification-lamp-assays-for-the-differential-detection-of-digital-dermatitis-associated-treponemes
#1
Kelly Anklam, Megan Kulow, Wataru Yamazaki, Dörte Döpfer
Bovine digital dermatitis (DD) is a severe infectious cause of lameness in cattle worldwide, with important economic and welfare consequences. There are three treponeme phylogroups (T. pedis, T. phagedenis, and T. medium) that are implicated in playing an important causative role in DD. This study was conducted to develop real-time PCR and loop-mediated isothermal amplification (LAMP) assays for the detection and differentiation of the three treponeme phylogroups associated with DD. The real-time PCR treponeme phylogroup assays targeted the 16S-23S rDNA intergenic space (ITS) for T...
2017: PloS One
https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#2
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28534230/trueperella-pyogenes-isolated-from-a-brain-abscess-of-an-adult-roebuck-capreolus-capreolus
#3
Jörn-Peter Wickhorst, Abdulwahed Ahmed Hassan, Omar Hashim Sheet, Tobias Eisenberg, Osama Sammra, Mazen Alssahen, Christoph Lämmler, Ellen Prenger-Berninghoff, Michael Zschöck, Markus Timke, Amir Abdulmawjood
The present study was designed to characterize phenotypically and genotypically a Trueperella pyogenes strain isolated from a brain abscess of an adult roebuck (Capreolus capreolus). The species identity could be confirmed by phenotypical investigations, by MALDI-TOF MS analysis, and by sequencing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rRNA intergenic spacer region (ISR); by sequencing the target genes rpoB, gap, and tuf; and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay...
May 23, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28527390/on-filter-direct-amplification-of-legionella-pneumophila-for-rapid-assessment-of-its-abundance-and-viability
#4
Farag A Samhan, Tiffany M Stedtfeld, Hassan Waseem, Maggie R Williams, Robert D Stedtfeld, Syed A Hashsham
Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory...
May 13, 2017: Water Research
https://www.readbyqxmd.com/read/28514671/evaluation-of-improved-is6110-lamp-assay-for-diagnosis-of-pulmonary-and-extra-pulmonary-tuberculosis
#5
Deepali Joon, Manoj Nimesh, Mandira Varma-Basil, Daman Saluja
In the present study, IS6110 loop mediated isothermal amplification (LAMP) assay was modified using dUTP-UNG (uracil-DNA N-glycosylase) strategy to prevent carryover contamination, and was evaluated using clinical specimens. The clinical specimens were collected from 236 suspected patients of pulmonary tuberculosis and 315 specimens of suspected patients of extra pulmonary tuberculosis. DNA was extracted from specimens and used as template for nucleic acid amplification. The results were evaluated with culture method as gold standard...
May 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28512232/loop-mediated-isothermal-amplification-for-extended-spectrum-%C3%AE-lactamase-gene-detection-in-poultry-carcase
#6
M Kirchner, F Lemma, L Randall, M F Anjum
No abstract text is available yet for this article.
May 16, 2017: Veterinary Record
https://www.readbyqxmd.com/read/28493052/development-of-a-colorimetric-reverse-transcription-loop-mediated-isothermal-amplification-assay-for-the-detection-of-mirafiori-lettuce-big-vein-virus
#7
Mohammad Amin Almasi
An RT-LAMP assay was developed to detect Mirafiori lettuce big vein virus (MiLBVV) and was compared with DAS-ELISA and RT-PCR. All primers were designed on the basis of the coat protein gene of the virus. In addition, a novel immunocapture (IC) RT-LAMP assay for rapid and easy detection of MiLBVV was developed, and factors such as safety, simplicity, cost, user-friendliness and safety were compared with those of DAS-ELISA, RT-PCR and RT-LAMP assays. Compared with DAS-ELISA and RT-PCR, RT-LAMP and IC-RT-LAMP had higher sensitivity (100-fold) but similar specificity, with the advantage of a shorter assay time and no need for RNA extraction (in IC-RT-LAMP)...
May 10, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28484128/characterizing-the-temporal-patterns-of-avian-influenza-virus-introduction-into-japan-by-migratory-birds
#8
Manabu Onuma, Masayoshi Kakogawa, Masae Yanagisawa, Atsushi Haga, Tomomi Okano, Yasuko Neagari, Tsukasa Okano, Koichi Goka, Mitsuhiko Asakawa
The objectives of the present study were to observe the temporal pattern of avian influenza virus (AIV) introduction into Japan and to determine which migratory birds play an important role in introducing AIV. In total, 19,407 fecal samples from migratory birds were collected at 52 sites between October 2008 and May 2015. Total nucleic acids extracted from the fecal samples were subjected to reverse transcription loop-mediated isothermal amplification to detect viral RNA. Species identification of host migratory birds was conducted by DNA barcoding for positive fecal samples...
May 7, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28469259/multiplex-detection-of-bacteria-on-an-integrated-centrifugal-disk-using-bead-beating-lysis-and-loop-mediated-amplification
#9
He Yan, Yunzeng Zhu, Yan Zhang, Lei Wang, Junge Chen, Ying Lu, Youchun Xu, Wanli Xing
Although culture-based identification of bacteria is the gold-standard for the diagnosis of infectious diseases, it is time consuming. Recent advances in molecular diagnostics and microfluidic technologies have opened up new avenues for rapid detection of bacteria. Here, we describe a centrifugal-microfluidic chip for the detection of bacteria by integrating the cell lysis, clarification, and loop-mediated amplification (LAMP). The major advantages of this chip are as follows. Firstly, bacteria lysis was innovatively achieved by rotating a pair of magnets to generate bead-beating while the chip was kept stationary during lysis, which simplified the chip design because no additional valve was needed...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28469032/rapid-and-specific-detection-of-asian-and-african-lineage-zika-viruses
#10
Nunya Chotiwan, Connie D Brewster, Tereza Magalhaes, James Weger-Lucarelli, Nisha K Duggal, Claudia Rückert, Chilinh Nguyen, Selene M Garcia Luna, Joseph R Fauver, Barb Andre, Meg Gray, William C Black, Rebekah C Kading, Gregory D Ebel, Guillermina Kuan, Angel Balmaseda, Thomas Jaenisch, Ernesto T A Marques, Aaron C Brault, Eva Harris, Brian D Foy, Sandra L Quackenbush, Rushika Perera, Joel Rovnak
Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription...
May 3, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28460328/isothermal-assay-targeting-class-1-integrase-gene-for-environmental-surveillance-of-antibiotic-resistance-markers
#11
Robert D Stedtfeld, Tiffany M Stedtfeld, Hassen Waseem, Meridith Fitschen-Brown, Xueping Guo, Benli Chai, Maggie R Williams, Trevor Shook, Amanda Logan, Ally Graham, Jong-Chan Chae, Woo-Jun Sul, Jacob VanHouten, James R Cole, Gerben J Zylstra, James M Tiedje, Brad L Upham, Syed A Hashsham
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP)...
April 28, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28457896/accelerated-isothermal-nucleic-acid-amplification-in-betaine-free-reaction
#12
Cuiping Ma, Yifan Wang, Pansong Zhang, Chao Shi
Betaine was used as a common additive to isothermal nucleic acid amplification reactions because of lowering the melting temperature (Tm) of DNA. Herein, we reported a novel finding that betaine was inhibiting the reaction efficiency of isothermal amplification reactions. In this work, we have verified this finding by classical loop-mediated isothermal amplification that the addition of 0.8 M betaine inhibited the efficiency of reaction dropping to approximately 1%. Additionally, we clarified the mechanism of betaine hindering isothermal amplification reactions with a molecular barrier to lower associate rate constant K1 for intermolecular hybridization...
April 27, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28450195/evaluation-of-the-eazyplex-mrsa-assay-for-the-rapid-detection-of-staphylococcus-aureus-in-pleural-and-synovial-fluid
#13
D Henares, P Brotons, X Buyse, I Latorre, H D de Paz, C Muñoz-Almagro
OBJECTIVE: Loop-mediated isothermal amplification (LAMP) is a simple and sensitive technique for rapid microbiological diagnosis. The aim of this study was to evaluate the analytical and diagnostic performance of the LAMP eazyplex MRSA test for the direct detection and differentiation of methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) in synovial/pleural fluid. METHODS: Analytical validation included the determination of the limit of detection (LoD) and analytical specificity of the eazyplex MRSA test...
April 24, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28438685/genotypic-detection-of-the-blactx-m-1-gene-among-extended-spectrum-%C3%AE-lactamase-producing-enterobacteriaceae
#14
Amornrat Thuengern, Surakit Nathisuwan, Mullika T Chomnawang, Chanpen Wiwat, Krit Thirapanmethee
OBJECTIVES: Extended-spectrum β-lactamases (ESBLs), a group of β-lactamase enzymes produced by bacteria in the family Enterobacteriaceae, are becoming a major problem in the healthcare community worldwide. Although many attempts have been made in the detection of ESBL-producing bacteria, the cost and speed of detection remains an important challenge. Therefore, this study aimed to develop a rapid, effective and affordable method for detection of the blaCTX-M-1 ESBL gene by a loop-mediated isothermal amplification (LAMP) technique...
April 21, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28435249/detection-of-influenza-viruses-by-coupling-multiplex-reverse-transcription-loop-mediated-isothermal-amplification-with-cascade-invasive-reaction-using-nanoparticles-as-a-sensor
#15
Yiyue Ge, Qiang Zhou, Kangchen Zhao, Ying Chi, Bin Liu, Xiaoyan Min, Zhiyang Shi, Bingjie Zou, Lunbiao Cui
Influenza virus infections represent a worldwide public health and economic problem due to the significant morbidity and mortality caused by seasonal epidemics and pandemics. Sensitive and convenient methodologies for detection of influenza viruses are essential for further disease control. Loop-mediated isothermal amplification (LAMP) is the most commonly used method of nucleic acid isothermal amplification. However, with regard to multiplex LAMP, differentiating the ladder-like LAMP products derived from multiple targets is still challenging today...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28435073/evaluation-of-a-rapid-detection-for-coxsackievirus-b3-using-one-step-reverse-transcription-loop-mediated-isothermal-amplification-rt-lamp
#16
A Monazah, M Zeinoddini, A R Saeeidinia
Coxsackievirus B3 (CVB3) is a member of the genus Enterovirus within the family Picornaviridae and is an important pathogen of viral myocarditis, which accounts for more than 50% viral myocarditis cases. VP1 is major capsid protein that this region has a low homology in both amino acid and nucleotide sequences among Enteroviruses. Therefore we have chosen this region for designed a set of RT-LAMP primers for CVB3 detection. For this the total RNA was extracted from 24-h post infected-HeLa cells with complete cytopathic effect (CPE), and applied to a one-step reverse transcription loop-mediated isothermal amplification reaction (RT-LAMP) using CVB3-specific primers...
April 21, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28429714/pif1-family-dna-helicases-suppress-r-loop-mediated-genome-instability-at-trna-genes
#17
Phong Lan Thao Tran, Thomas J Pohl, Chi-Fu Chen, Angela Chan, Sebastian Pott, Virginia A Zakian
Saccharomyces cerevisiae encodes two Pif1 family DNA helicases, Pif1 and Rrm3. Rrm3 promotes DNA replication past stable protein complexes at tRNA genes (tDNAs). We identify a new role for the Pif1 helicase: promotion of replication and suppression of DNA damage at tDNAs. Pif1 binds multiple tDNAs, and this binding is higher in rrm3Δ cells. Accumulation of replication intermediates and DNA damage at tDNAs is higher in pif1Δ rrm3Δ than in rrm3Δ cells. DNA damage at tDNAs in the absence of these helicases is suppressed by destabilizing R-loops while Pif1 and Rrm3 binding to tDNAs is increased upon R-loop stabilization...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28427352/point-of-sampling-detection-of-zika-virus-within-a-multiplexed-kit-capable-of-detecting-dengue-and-chikungunya
#18
Ozlem Yaren, Barry W Alto, Priyanka V Gangodkar, Shatakshi R Ranade, Kunal N Patil, Kevin M Bradley, Zunyi Yang, Nikhil Phadke, Steven A Benner
BACKGROUND: Zika, dengue, and chikungunya are three mosquito-borne viruses having overlapping transmission vectors. They cause diseases having similar symptoms in human patients, but requiring different immediate management steps. Therefore, rapid (< one hour) discrimination of these three viruses in patient samples and trapped mosquitoes is needed. The need for speed precludes any assay that requires complex up-front sample preparation, such as extraction of nucleic acids from the sample...
April 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28427163/the-application-of-is6110-baced-loop-mediated-isothermal-amplification-lamp-in-the-early-diagnosis-of-tuberculous-meningitis
#19
Wen-Wen Sun, Qin Sun, Li-Ping Yan, Qing Zhang
Here, we evaluated the potential activity of rapid Mycobacterium tuberculosis detection with loop-mediated isothermal amplification (LAMP), for the early diagnosis of tuberculous meningitis (TBM). Patients with suspected TBM from January 2014 to December 2015 were reviewed retrospectively. The cerebrospinalfluid(CSF) was collected. Acid-fast bacillus (AFB) staining, MGIT 960 culture, real-time fluorescent quantitative polymerase chain reaction (RTFQ PCR) and LAMP were performed. A total of 200 patients were included in the study...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424530/molecular-diagnostic-assays-based-on-cpn60-ut-sequences-reveal-the-geographic-distribution-of-subgroup-16srxiii-a-i-i-phytoplasma-in-mexico
#20
Edel Pérez-López, Douglas Rodríguez-Martínez, Chrystel Y Olivier, Mauricio Luna-Rodríguez, Tim J Dumonceaux
Geographically diverse samples from strawberry exhibiting symptoms of Strawberry Green Petal (SbGP), periwinkle plants with virescence, and blackberry, blueberry, and raspberry plants displaying yellowing and inedible fruits, were assayed for the presence of phytoplasma DNA. PCR targeting the 16S rRNA-encoding gene and chaperonin-60 (cpn60) showed that the plants were infected with phytoplasma subgroup16SrXIII-(A/I)I (SbGP/MPV). To examine the geographic distribution of this pathogen in Mexico, we designed an array of cpn60-targeted molecular diagnostic assays for SbGP/MPV phytoplasma...
April 19, 2017: Scientific Reports
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