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loop-mediated isothermal amplification

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https://www.readbyqxmd.com/read/27924549/identification-of-ochratoxin-a-producing-black-aspergilli-from-grapes-using-loop-mediated-isothermal-amplification-lamp-assays
#1
Michelangelo Storari, Giovanni A L Broggini
The loop-mediated isothermal amplification (LAMP) allows the rapid and specific amplification of target DNA under isothermal conditions without a prior DNA purification step. Moreover, successful amplifications can be directly evaluated through a color change of the reaction solutions. Here, we describe two LAMP assays for the detection of ochratoxin-A producing black aspergilli isolated from grapes. The two assays can detect DNA of OTA-producing black aspergilli following a very simple sample preparation and have the potential to significantly speed up the routine monitoring of these toxigenic molds in vineyards...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27916953/rapid-sensitive-detection-of-bartonella-quintana-by-loop-mediated-isothermal-amplification-of-the-groel-gene
#2
Shoukui Hu, Lina Niu, Lijuan Luo, Xiuping Song, Jimin Sun, Qiyong Liu
Trench fever, caused by Bartonella quintana, is recognized as a re-emerging and neglected disease. Rapid and sensitive detection approaches are urgently required to monitor and help control B. quintana infections. Here, loop-mediated isothermal amplification (LAMP), which amplifies target DNA at a fixed temperature with high sensitivity, specificity and rapidity, was employed to detect B. quintana. Thirty-six strains, including 10 B. quintana, 13 other Bartonella spp., and 13 other common pathogens, were applied to verify and evaluate the LAMP assay...
December 1, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27906100/an-isothermal-dna-amplification-method-for-detection-of-onchocerca-volvulus-infection-in-skin-biopsies
#3
Ole Lagatie, Michelle Merino, Linda Batsa Debrah, Alexander Y Debrah, Lieven J Stuyver
BACKGROUND: Diagnostic procedures for the diagnosis of infection with the nematode parasite Onchocerca volvulus are currently based on the microscopic detection of microfilariae in skin biopsies. Alternative approaches based on amplification of parasitic DNA in these skin biopsies are currently being explored. Mostly this is based on the detection of the O-150 repeat sequence using PCR based techniques. METHODS: An isothermal, loop-mediated amplification method has been designed using the mitochondrial O...
December 1, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27899288/one-step-reverse-transcription-loop-mediated-isothermal-amplification-for-the-detection-of-maize-chlorotic-mottle-virus-in-maize
#4
Ling Chen, Zhiyuan Jiao, Dongmei Liu, Xingliang Liu, Zihao Xia, Congliang Deng, Tao Zhou, Zaifeng Fan
Maize chlorotic mottle virus (MCMV) is spreading in many regions worldwide, causing maize lethal necrosis when co-infected with a potyvirid. In this study, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect MCMV in maize. A set of four specific primers was designed based on the conserved coat protein gene sequences of MCMV. The RT-LAMP could be completed within 60min under isothermal condition at 63°C. The sensitivity test showed that the RT-LAMP was about 10-fold more sensitive than RT-PCR and no cross-reactivity was detected with other viral pathogens infecting maize in China...
November 27, 2016: Journal of Virological Methods
https://www.readbyqxmd.com/read/27890084/comparison-of-molecular-and-conventional-methods-for-the-diagnosis-of-fasciola-hepatica-infection-in-the-field
#5
Maria Immaculata Arifin, Johan Höglund, Adam Novobilský
The liver fluke, Fasciola hepatica, is one of the major parasite threats to livestock industries world-wide. In sheep and cattle, F. hepatica infection is commonly diagnosed using a range of methods. Aside from conventional coprological and serological diagnostic methods, there are also several molecular methods available based on the detection of liver fluke DNA in faeces. In this study, the outcomes of faecal egg count (FEC), serology and coproantigen ELISA (cELISA) were compared with the performance of polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) in diagnosis of F...
December 15, 2016: Veterinary Parasitology
https://www.readbyqxmd.com/read/27882242/development-of-a-loop-mediated-isothermal-amplification-for-diagnosis-of-ascaris-lumbricoides-in-fecal-samples
#6
Esther A Shiraho, Agola L Eric, Ibrahim N Mwangi, Geoffrey M Maina, Joseph M Kinuthia, Martin W Mutuku, Robert M Mugambi, Jackson M Mwandi, Gerald M Mkoji
Ascaris lumbricoides is a nematode parasite that causes the common tropical infection ascariasis in humans. It is also considered among the neglected tropical diseases. Diagnosis relies mainly on microscopy-based methods which are laborious, are limited by low sensitivity, and require high expertise. We have developed a loop mediated isothermal amplification (LAMP) for diagnosis of ascariasis in fecal samples, based on the first internal transcribed (ITS-1) spacer region of the ribosomal DNA. We used Primer Explorer V4 software to design primers...
2016: Journal of Parasitology Research
https://www.readbyqxmd.com/read/27873004/use-of-a-novel-metal-indicator-to-judge-loop-mediated-isothermal-amplification-for-detecting-the-35s-promoter
#7
Xiaofu Wang, Zhenfang Fu, Xiaoyun Chen, Cheng Peng, Xiaoli Xu, Wei Wei, Feiwu Li, Junfeng Xu
Loop-mediated isothermal amplification (LAMP) is a widely used isothermal nucleic acid amplification method. Here we developed a new closed-tube colorimetric method for judging LAMP with a novel metal indicator. First, the metal indicator, acid chrome blue K (ACBK), was evaluated in the LAMP reaction with various combinations of reaction reagents, such as reaction buffer, dNTP mixtures, primer mixtures, or Mg(2+). We found that the solution color of the LAMP reaction with ACBK changed from red to blue based on a decrease in the Mg(2+) concentration in the reaction solution...
November 21, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27864860/evaluation-of-a-loop-mediated-isothermal-amplification-assay-based-on-hrpz-gene-for-rapid-detection-and-identification-of-pseudomonas-syringae-pv-lachrymans-in-cucumber-leaves
#8
Xiang-Long Meng, Xue-Wen Xie, Yan-Xia Shi, A-Li Chai, Zhan-Hong Ma, Bao-Ju Li
AIMS: Cucumber angular leaf spot caused by Pseudomonas syringae pv. lachrymans (Psl) is an important and destructive disease worldwide, and no effective technique has been developed for the control of the pathogen. Detection of infection or latent in cucumber plants is critical to evaluate disease progress and strengthening management to avoid a serious epidemic in the fields. In this paper, we developed a rapid and sensitive method for detection of Psl using a isothermal method known as loop-mediated amplification (LAMP)...
November 19, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27856278/most-probable-number-loop-mediated-isothermal-amplification-mpn-lamp-for-quantifying-waterborne-pathogens-in-25min
#9
Farhan Ahmad, Robert D Stedtfeld, Hassan Waseem, Maggie R Williams, Alison M Cupples, James M Tiedje, Syed A Hashsham
We are reporting a most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction. LAMP assays for uidA from E. coli and gelE from E. faecalis were successfully performed directly on cells up to single digit concentration using a commercial real time PCR instrument. Threshold time values of LAMP assays of bacterial cells, heat treated bacterial cells (95°C for 5min), and their purified genomic DNA templates were similar, implying that amplification could be achieved directly from bacterial cells at 63°C...
November 14, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27845796/paper-microchip-with-a-graphene-modified-silver-nano-composite-electrode-for-electrical-sensing-of-microbial-pathogens
#10
Mohammadali Safavieh, Vivasvat Kaul, Sultan Khetani, Anupriya Singh, Karan Dhingra, Manoj Kumar Kanakasabapathy, Mohamed Shehata Draz, Adnan Memic, Daniel R Kuritzkes, Hadi Shafiee
Rapid and sensitive point-of-care diagnostics are of paramount importance for early detection of infectious diseases and timely initiation of treatment. Here, we present cellulose paper and flexible plastic chips with printed graphene-modified silver electrodes as universal point-of-care diagnostic tools for the rapid and sensitive detection of microbial pathogens or nucleic acids through utilizing electrical sensing modality and loop-mediated isothermal amplification (LAMP). We evaluated the ability of the developed paper-based assay to detect (i) viruses on cellulose-based paper microchips without implementing amplification in samples with viral loads between 10(6) and 10(8) copies per ml, and (ii) amplified HIV-1 nucleic acids in samples with viral loads between 10 fg μl(-1) and 10(8) fg μl(-1)...
November 15, 2016: Nanoscale
https://www.readbyqxmd.com/read/27836764/direct-detection-of-various-pathogens-by-loop-mediated-isothermal-amplification-assays-on-bacterial-culture-and-bacterial-colony
#11
Muxia Yan, Weidong Li, Zhenwen Zhou, Hongxia Peng, Ziyan Luo, Ling Xu
In this work, loop-mediated isothermal amplification based detection assay using bacterial culture and bacterial colony for various common pathogens direct detection had been established, evaluated and further applied. A total of five species of common pathogens and nine detection targets (tlh, tdh and trh for V. Parahaemolyticus, rfbE, stx1 and stx2 for E. coli, oprI for P. aeruginosa, invA for Salmonella and hylA for L. monocytogenes) were performed on bacterial culture and bacterial colony LAMP. To evaluate and optimize this assay, a total of 116 standard strains were included...
November 9, 2016: Microbial Pathogenesis
https://www.readbyqxmd.com/read/27833616/coconut-lethal-yellowing-diseases-a-phytoplasma-threat-to-palms-of-global-economic-and-social-significance
#12
REVIEW
Geoff M Gurr, Anne C Johnson, Gavin J Ash, Bree A L Wilson, Mark M Ero, Carmel A Pilotti, Charles F Dewhurst, Minsheng S You
The recent discovery of Bogia coconut syndrome in Papua New Guinea (PNG) is the first report of a lethal yellowing disease (LYD) in Oceania. Numerous outbreaks of LYDs of coconut have been recorded in the Caribbean and Africa since the late Nineteenth century and have caused the death of millions of palms across several continents during the Twentieth century. Despite the severity of economic losses, it was only in the 1970s that the causes of LYDs were identified as phytoplasmas, a group of insect-transmitted bacteria associated with diseases in many other economically important crop species...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27833606/surveillance-of-dihydropteroate-synthase-genes-in-stenotrophomonas-maltophilia-by-lamp-implications-for-infection-control-and-initial-therapy
#13
Jin Zhao, Yubin Xing, Wei Liu, Wentao Ni, Chuanqi Wei, Rui Wang, Yunxi Liu, Youning Liu
Stenotrophomonas maltophilia is a common nosocomial pathogen that causes high morbidity and mortality. Because of its inherent extended antibiotic resistance, therapeutic options for S. maltophilia are limited, and sulfamethoxazole/trimethoprim (SXT) is the only first-line antimicrobial recommended. However, with the spread of dihydropteroate synthase (sul1 and sul2) genes, global emergence of SXT resistance has been reported. There is an urgent need to develop a rapid and sensitive but cost-efficient method to monitor the dissemination of sul genes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27829667/novel-ph-sensing-semiconductor-for-point-of-care-detection-of-hiv-1-viremia
#14
R Gurrala, Z Lang, L Shepherd, D Davidson, E Harrison, M McClure, S Kaye, C Toumazou, G S Cooke
The timely detection of viremia in HIV-infected patients receiving antiviral treatment is key to ensuring effective therapy and preventing the emergence of drug resistance. In high HIV burden settings, the cost and complexity of diagnostics limit their availability. We have developed a novel complementary metal-oxide semiconductor (CMOS) chip based, pH-mediated, point-of-care HIV-1 viral load monitoring assay that simultaneously amplifies and detects HIV-1 RNA. A novel low-buffer HIV-1 pH-LAMP (loop-mediated isothermal amplification) assay was optimised and incorporated into a pH sensitive CMOS chip...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27827432/evaluation-of-the-illumigene-malaria-lamp-a-robust-molecular-diagnostic-tool-for-malaria-parasites
#15
Naomi W Lucchi, Marie Gaye, Mammadou Alpha Diallo, Ira F Goldman, Dragan Ljolje, Awa Bineta Deme, Aida Badiane, Yaye Die Ndiaye, John W Barnwell, Venkatachalam Udhayakumar, Daouda Ndiaye
Isothermal nucleic acid amplification assays such as the loop mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to amplify the DNA. To further facilitate the use of LAMP assays in remote settings, simpler sample preparation methods and lyophilized reagents are required. The performance of a commercial malaria LAMP assay (Illumigene Malaria LAMP) was evaluated using two sample preparation workflows (simple filtration prep (SFP)) and gravity-driven filtration prep (GFP)) and pre-dispensed lyophilized reagents...
November 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27824866/a-field-tailored-reverse-transcription-loop-mediated-isothermal-assay-for-high-sensitivity-detection-of-plasmodium-falciparum-infections
#16
Sylvie Kemleu, Dylan Guelig, Carole Eboumbou Moukoko, Estelle Essangui, Steven Diesburg, Abas Mouliom, Bernard Melingui, Jeanne Manga, Christiane Donkeu, Annie Epote, Gaëtan Texier, Paul LaBarre, Robert Burton, Lawrence Ayong
Highly sensitive and field deployable molecular diagnostic tools are critically needed for detecting submicroscopic, yet transmissible levels of malaria parasites prevalent in malaria endemic countries worldwide. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated in comparison with thick blood smear microscopy, an antigen-based rapid diagnostic test (RDT), and an in-house RT-PCR targeting the same RT-LAMP transcript. The optimized assay detected Plasmodium falciparum infections in as little as 0...
2016: PloS One
https://www.readbyqxmd.com/read/27814391/characterization-of-snp-and-structural-variations-in-the-mitochondrial-genomes-of-tilletia-indica-and-its-closely-related-species-formed-basis-for-a-simple-diagnostic-assay
#17
Mui-Keng Tan, Harsh Raman, Grant Chambers, Indu Sharma, Zhiliang Chen, Nandan Deshpande, Marc R Wilkins
Tilletia indica causes the disease Karnal bunt in wheat. The disease is under international quarantine regulations. Comparative mitochondrial (mt) genome analysis of T. indica (KX394364 and DQ993184) and T. walkeri (EF536375) has found 325 to 328 SNPs, 57 to 60 short InDels (from 1 to 13 nt), two InDels (30 and 61 nt) and five (>200 nt) presence/absence variations (PAVs) between the two species. The mt genomes of both species have identical gene order. The numbers of SNPs and InDels between the mt genomes of the two species are approximately nine times of the corresponding numbers between the two T...
2016: PloS One
https://www.readbyqxmd.com/read/27812041/strand-exchange-nucleic-acid-circuitry-with-enhanced-thermo-and-structure-buffering-abilities-turns-gene-diagnostics-ultra-reliable-and-environmental-compatible
#18
Zhentong Zhu, Yidan Tang, Yu Sherry Jiang, Sanchita Bhadra, Yan Du, Andrew D Ellington, Bingling Li
Catalytic hairpin assembly (CHA) is one of the most promising nucleic acid amplification circuits based on toehold-mediated strand exchange reactions. But its performance is usually ruined by fluctuated environmental temperatures or unexpected self-structures existing in most real-world targets. Here we present an amide-assistant mechanism that successfully reduces the prevalence of these problems for CHA and maximizes its thermo- and structure- buffering abilities. Such an organic amide-promoted CHA (shortened as OHT-CHA) can unprecedentedly amplify through 4 °C to 60 °C without rebuilding sequences or concerning target complexity...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27809497/improved-performance-of-loop-mediated-isothermal-amplification-assays-via-swarm-priming
#19
Rhett L Martineau, Sarah Anne Murray, Shufang Ci, Weimin Gao, Shih-Hui Chao, Deirdre R Meldrum
This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed 'Swarm primers' based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites...
November 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27793644/rapid-and-sensitive-detection-of-zika-virus-by-reverse-transcription-loop-mediated-isothermal-amplification
#20
Xuan Wang, Fenggui Yin, Yuhai Bi, Gong Cheng, Jing Li, Lidan Hou, Yunlong Li, Baozhi Yang, Wenjun Liu, Limin Yang
BACKGROUND: Zika virus (ZIKV) is an arbovirus that recently emerged and has expanded worldwide, causing a global threat and raising international concerns. Current molecular diagnostics, e.g., real-time PCR and reverse transcription PCR (RT-PCR), are time consuming, expensive, and can only be deployed in a laboratory instead of for field diagnostics. OBJECTIVES: This study aimed to develop a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform showing sensitivity, specificity, and more convenience than previous methods, being easily distributed and implemented...
October 25, 2016: Journal of Virological Methods
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