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https://www.readbyqxmd.com/read/28811193/a-novel-detection-procedure-for-mutations-in-the-23s-rrna-gene-of-mycoplasma-pneumoniae-with-peptide-nucleic-acid-mediated-loop-mediated-isothermal-amplification-assay
#1
Jun Sakai, Takuya Maeda, Norihito Tarumoto, Kazuhisa Misawa, Shinsuke Tamura, Kazuo Imai, Toshiyuki Yamaguchi, Satoshi Iwata, Takashi Murakami, Shigefumi Maesaki
Rapid and easy detection of a single nucleotide point mutation of bacterial genes, which is directly linked to drug susceptibility, is essential for the proper use of antimicrobial agents. Here, we established a detection method using a peptide nucleic acid mediated loop-mediated amplification (LAMP) assay for macrolide (ML)-susceptible Mycoplasma pneumoniae. This assay specifically detected the absence of missense mutations encoding the central loop of domain V in the gene encoding 23S rRNA, which can reduce the affinity for MLs and subsequently generate ML-resistant strains of M...
August 12, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28807759/development-of-a-highly-resolved-loop-mediated-isothermal-amplification-method-to-detect-the-n526k-ftsi-mutation-of-%C3%AE-lactamase-negative-ampicillin-resistant-haemophilus-influenzae
#2
Shinsuke Tamura, Takuya Maeda, Kazuhisa Misawa, Morichika Osa, Takaaki Hamamoto, Atsushi Yuki, Kazuo Imai, Kei Mikita, Kyoko Morichika, Akihiko Kawana, Hiroshi Matsumoto, Shigeaki Nonoyama
Rapid and easy detection of sequence polymorphisms, including nucleotide point mutations of bacterial pathogens responsible for amino acid substitutions linked to drug resistance, is essential for the proper use of antimicrobial agents. Here, a detection method using loop-mediated amplification (LAMP) combined with amplification refractory mutation system (ARMS) to accurately distinguish a different single nucleotide in the target sequence was established, named ARMS-SNP LAMP. This procedure is capable of species-specific detection of a nucleotide (1578T) in the ftsI gene on Haemophilus influenzae without amplifying the sequence carrying the point mutations (T1578G/A) in β-lactamase-negative ampicillin resistant (BLNAR) strains...
August 11, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28803792/rapid-and-visual-detection-of-leptospira-in-urine-by-ligb-lamp-assay-with-pre-addition-of-dye
#3
Syed Atif Ali, Gurpreet Kaur, Nongthombam Boby, T Sabarinath, Khushal Solanki, Dheeraj Pal, Pallab Chaudhuri
Leptospirosis is considered to be the most widespread zoonotic disease caused by pathogenic species of Leptospira. The present study reports a novel set of primers targeting LigB gene for visual detection of pathogenic Leptospira in urine samples through Loop-mediated isothermal amplification (LAMP). The results were recorded by using Hydroxyl napthol blue (HNB), SYBR GREEN I and calcein. Analytical sensitivity of LAMP was as few as 10 leptospiral organisms in spiked urine samples from cattle and dog. LigB gene based LAMP, termed as LigB-LAMP, was found 10 times more sensitive than conventional PCR...
August 10, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28803416/rapid-screening-method-for-male-dna-by-using-the-loop-mediated-isothermal-amplification-assay
#4
Masashi Kitamura, Seiji Kubo, Jin Tanaka, Tatsushi Adachi
Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min...
August 12, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28799069/rae1-mediated-nuclear-export-of-rnc1-is-an-important-determinant-in-controlling-mapk-signaling
#5
REVIEW
Ryosuke Satoh, Kanako Hagihara, Reiko Sugiura
In eukaryotic cells, RNA binding proteins (RBPs) play critical roles in regulating almost every aspect of gene expression, often shuttling between the nucleus and the cytoplasm. They are also key determinants in cell fate via controlling the target mRNAs under the regulation of various signaling pathways in response to environmental stresses. Therefore, understanding the mechanisms that couple the location of mRNA and RBPs is a major challenge in the field of gene expression and signal responses. In fission yeast, a KH-type RBP Rnc1 negatively regulates MAPK signaling activation via mRNA stabilization of the dual-specificity MAPK phosphatase Pmp1, which dephosphorylates MAPK Pmk1...
August 10, 2017: Current Genetics
https://www.readbyqxmd.com/read/28798845/vancomycin-resistant-gene-identification-from-live-bacteria-on-an-integrated-microfluidic-system-by-using-low-temperature-lysis-and-loop-mediated-isothermal-amplification
#6
Wen-Hsin Chang, Ju-Ching Yu, Sung-Yi Yang, Yi-Cheng Lin, Chih-Hung Wang, Huey-Ling You, Jiunn-Jong Wu, Mel S Lee, Gwo-Bin Lee
Vancomycin-resistant Enterococcus (VRE) is a kind of enterococci, which shows resistance toward antibiotics. It may last for a long period of time and meanwhile transmit the vancomycin-resistant gene (vanA) to other bacteria. In the United States alone, the resistant rate of Enterococcus to vancomycin increased from a mere 0.3% to a whopping 40% in the past two decades. Therefore, timely diagnosis and control of VRE is of great need so that clinicians can prevent patients from becoming infected. Nowadays, VRE is diagnosed by antibiotic susceptibility test or molecular diagnosis assays such as matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and polymerase chain reaction...
March 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28790157/sirt7-and-the-dead-box-helicase-ddx21-cooperate-to-resolve-genomic-r-loops-and-safeguard-genome-stability
#7
Chenlin Song, Agnes Hotz-Wagenblatt, Renate Voit, Ingrid Grummt
R loops are three-stranded nucleic acid structures consisting of an RNA:DNA heteroduplex and a "looped-out" nontemplate strand. As aberrant formation and persistence of R loops block transcription elongation and cause DNA damage, mechanisms that resolve R loops are essential for genome stability. Here we show that the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase DDX21 efficiently unwinds R loops and that depletion of DDX21 leads to accumulation of cellular R loops and DNA damage. Significantly, the activity of DDX21 is regulated by acetylation...
August 8, 2017: Genes & Development
https://www.readbyqxmd.com/read/28780114/development-of-a-novel-loop-mediated-isothermal-amplification-assay-for-the-detection-of-lipolytic-pseudomonas-fluorescens-in-raw-cow-milk-from-north-china
#8
Liang Xin, Lanwei Zhang, Zhaoxu Meng, Kai Lin, Shuang Zhang, Xue Han, HuaXi Yi, Yanhua Cui
Lipases secreted by psychrotrophic bacteria are known to be heat resistant and can remain active even after the thermal processing of milk products. Such enzymes are able to destabilize the quality of milk products by causing a rancid flavor. Rapid detection of a small amount of heat-resistant lipase-producing psychrotrophic bacteria is crucial for reducing their adverse effects on milk quality. In this study, we established and optimized a novel loop-mediated isothermal amplification (LAMP) assay for the detection of Pseudomonas fluorescens in raw cow milk, as the most frequently reported heat-resistant lipase-producing bacterial species...
August 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28776530/rapid-laboratory-diagnosis-of-pulmonary-tuberculosis
#9
Prasanna Bhirud, Ameeta Joshi, Nilma Hirani, Abhay Chowdhary
BACKGROUND: Tuberculosis (TB) ranks as the second leading cause of death from an infectious disease worldwide. Early diagnosis of Mycobacterium tuberculosis in clinical samples becomes important in the control of TB both for the treatment of patients and for curbing of disease transmission to the others in the community. The study objective was to perform Ziehl-Neelsen (ZN) staining, fluorochrome staining, line probe assay (LPA), and loop-mediated isothermal amplification (LAMP) assay for rapid detection of pulmonary TB (PTB) and to compare the results of LPA and LAMP in terms of sensitivity, specificity, and turnaround time...
July 2017: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28769894/a-historical-overview-of-research-on-babesia-orientalis-a-protozoan-parasite-infecting-water-buffalo
#10
REVIEW
Lan He, Qin Liu, Baoan Yao, Yanqin Zhou, Min Hu, Rui Fang, Junlong Zhao
Babesiosis is a globally important zoonotic disease caused by tick-borne intraerythrocytic protozoan of the genus Babesia (phylum apicomplexa). In China, there are five species that infect cattle buffalo and cause great economic loss, which include Babesia bigemina, B. bovis, B. major, B. ovata, and B. orientalis. Among them, B. orientalis is the most recently identified new Babesia species epidemic in China. This review summarized the work done in the past 33 years to give an overview of what learned about this parasite...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28768730/detection-of-plasmodium-spp-infection-by-the-illumigene%C3%A2-malaria-assay-compared-to-reference-microscopy-and-real-time-pcr
#11
Candace Rypien, Barbara Chow, Wilson Chan, Deirdre Church, Dylan R Pillai
Malaria is one of the leading causes of infectious disease in returning travelers from the tropics. Diagnosis of malaria is typically performed by examination of Giemsa-stained thick and thin peripheral blood smears, which is time-consuming, labor-intensive and requires high levels of proficiency. Alternatively, loop-mediated isothermal amplification (LAMP) is a new molecular method, which is rapid, sensitive, and requires less capital equipment and technological training. We conducted a retrospective study comparing two formats of a commercial LAMP assay (Meridian illumigene® Malaria [M] and Malaria Plus [MP]) versus reference microscopy on archived blood specimens (n=140) obtained from unique returning travelers suspected of having malaria...
August 2, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28759049/structural-basis-of-tir-domain-assembly-formation-in-mal-and-myd88-dependent-tlr4-signaling
#12
Thomas Ve, Parimala R Vajjhala, Andrew Hedger, Tristan Croll, Frank DiMaio, Shane Horsefield, Xiong Yu, Peter Lavrencic, Zahid Hassan, Garry P Morgan, Ashley Mansell, Mehdi Mobli, Ailis O'Carroll, Brieuc Chauvin, Yann Gambin, Emma Sierecki, Michael J Landsberg, Katryn J Stacey, Edward H Egelman, Bostjan Kobe
Toll-like receptor (TLR) signaling is a key innate immunity response to pathogens. Recruitment of signaling adapters such as MAL (TIRAP) and MyD88 to the TLRs requires Toll/interleukin-1 receptor (TIR)-domain interactions, which remain structurally elusive. Here we show that MAL TIR domains spontaneously and reversibly form filaments in vitro. They also form cofilaments with TLR4 TIR domains and induce formation of MyD88 assemblies. A 7-Å-resolution cryo-EM structure reveals a stable MAL protofilament consisting of two parallel strands of TIR-domain subunits in a BB-loop-mediated head-to-tail arrangement...
July 31, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28756184/development-and-validation-of-a-new-loop-mediated-isothermal-amplification-for-detection-of-pathogenic-leptospira-species-in-clinical-materials
#13
Yun-Hsiu Hsu, Shih-Jen Chou, Chih-Cheng Chang, Ming-Jeng Pan, Wei-Cheng Yang, Chuen-Fu Lin, Kun-Wei Chan
Leptospirosis, a global zoonotic disease, is often neglected but has a significant impact on human health. Here we reported a new loop mediated isothermal amplification (LAMP) assay targeting lipL32 gene of pathogenic Leptospira spp. Polymerase chain reaction (PCR), nested-PCR and real-time PCR assays were included in this study for the comparison of analytic and diagnostic sensitivity and specificity. LipL32 LAMP we designed enables detection of 10 copies of L. interrogans and has a higher diagnostic sensitivity (91...
July 26, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28740546/a-paper-based-device-for-performing-loop-mediated-isothermal-amplification-with-real-time-simultaneous-detection-of-multiple-dna-targets
#14
Youngung Seok, Hyou-Arm Joung, Ju-Young Byun, Hyo-Sung Jeon, Su Jeong Shin, Sanghyo Kim, Young-Beom Shin, Hyung Soo Han, Min-Gon Kim
Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device...
2017: Theranostics
https://www.readbyqxmd.com/read/28729683/a-positive-feedback-loop-mediated-by-sigma-x-enhances-expression-of-the-streptococcal-regulator-comr
#15
Rabia Khan, Roger Junges, Heidi A Åmdal, Tsute Chen, Donald A Morrison, Fernanda C Petersen
Natural transformation is used by bacteria to take up DNA from their surroundings and incorporate it into their genomes. Streptococci do so during a transient period of competence, triggered by pheromones that they produce, secrete and sense under conditions influenced by the environment. In Streptococcus mutans, Streptococcus suis, and species of the bovis, salivarius and pyogenic groups of streptococci, the pheromone XIP is sensed by the intra-cellular regulator ComR, that in turn activates the transcription of comS, encoding the XIP precursor, and of sigX, encoding the only known alternative sigma factor in streptococci...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727723/analytical-sensitivity-and-specificity-of-a-loop-mediated-isothermal-amplification-lamp-kit-prototype-for-detection-of-trypanosoma-cruzi-dna-in-human-blood-samples
#16
Susana A Besuschio, Mónica Llano Murcia, Alejandro F Benatar, Severine Monnerat, Israel Cruz, Albert Picado, María de Los Ángeles Curto, Yutaka Kubota, Diana P Wehrendt, Paula Pavia, Yasuyoshi Mori, Concepción Puerta, Joseph M Ndung'u, Alejandro G Schijman
This study aimed to assess analytical parameters of a prototype LAMP kit that was designed for detection of Trypanosoma cruzi DNA in human blood. The prototype is based on the amplification of the highly repetitive satellite sequence of T.cruzi in microtubes containing dried reagents on the inside of the caps. The reaction is carried out at 65°C during 40 minutes. Calcein allows direct detection of amplified products with the naked eye. Inclusivity and selectivity were tested in purified DNA from Trypanosoma cruzi stocks belonging to the six discrete typing units (DTUs), in DNA from other protozoan parasites and in human DNA...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28720542/one-step-reverse-transcription-loop-mediated-isothermal-amplification-assay-for-detection-of-apple-chlorotic-leaf-spot-virus
#17
Dandan Peng, Jipeng Xie, Wei Qiang, Kai-Shu Ling, Liyun Guo, Zaifeng Fan, Tao Zhou
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV). In this method, a set of four primers was designed based on the conserved regions in the coat protein gene of ACLSV, and the primers were synthesized for the RT-LAMP assay using total RNA extracted from ACLSV-infected leaf tissues. The optimal reaction temperature and assay time were determined to be 64°C and 75min, respectively. The sensitivity of RT-LAMP reactions was reliable up to a maximum dilution of 1:3125, which was more sensitive than the RT-PCR assay...
July 15, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28716373/loop-mediated-isothermal-amplification-in-disposable-polyester-toner-microdevices
#18
Kezia Gomes de Oliveira, Juliane Cristina Borba, Alexandre Melo Bailão, Célia Maria de Almeida Soares, Emanuel Carrilho, Gabriela Rodrigues Mendes Duarte
In recent years, isothermal DNA amplification methods have emerged as an alternative in molecular diagnostics due to its ease of operation. The purpose of using isothermal amplification is to simplify the diagnostics work by i) eliminating heating cycles, ii) reducing equipment costs, and iii) providing rapid and accurate results in laboratories with limited resources. Here we show a simple and fast method for E. coli detection in disposable polyester-toner (PeT) microdevice. The amplification by LAMP of the malB gene from E...
July 14, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28712517/comparison-of-oropharyngeal-and-nasopharyngeal-swab-specimens-for-the-detection-of-mycoplasma-pneumoniae-in-children-with-lower-respiratory-tract-infection
#19
Fujio Kakuya, Takahiro Kinebuchi, Hitoshi Okubo, Kumihiro Matsuo
The oropharyngeal swab specimen was superior to the nasopharyngeal swab specimen for the detection of Mycoplasma pneumoniae in children with lower respiratory tract infection. The oropharyngeal loop-mediated isothermal amplification had 100% sensitivity and specificity compared with polymerase chain reaction testing, whereas the oropharyngeal rapid antigen detection test using immunochromatographic assay had relatively low sensitivity (66%) and reasonable specificity (90.7%).
July 13, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28702363/a-case-of-bacillus-calmette-gu%C3%A3-rin-cystitis-diagnosed-with-a-novel-loop-mediated-isothermal-amplification-method
#20
Kazuyoshi Tachi, Akinori Sato, Yuji Kouzaki, Takuya Maeda, Akihiko Kawana, Tomohiko Asano
Intravesical bacillus Calmette-Guérin (BCG) instillation is broadly used to prevent bladder cancer recurrence or to treat carcinoma in situ. BCG infection is rare but can cause serious problems because this strain has intrinsic resistance to pyrazinamide, a first-line anti-tuberculosis drug. Furthermore, there had been no specific and easy procedure accurately diagnosing BCG infection. In this case report we present the first case of BCG cystitis diagnosed with a newly developed easy-to-use diagnostic procedure using the loop-mediated isothermal amplification method...
September 2017: Urology Case Reports
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