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Nanopore sequencing

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https://www.readbyqxmd.com/read/29156123/a-nanopore-based-label-free-and-real-time-monitoring-assay-for-dna-methyltransferase-activity-and-inhibition
#1
Sana Rauf, Ling Zhang, Asghar Ali, Jalal Ahmad, Yang Liu, Jinghong Li
DNA methylation catalyzed by DNA methyltransferase plays an important role in many biological processes. However, conventional assays proposed for DNA methyltransferase activity are laborious and discontinuous. We describe a novel method for real-time monitoring of the activity and kinetics of Escherichia coli DNA adenine methyltransferase (Dam), using nanopore technique coupled with enzyme-linkage reactions. A double-stranded DNA probe AB having a recognition sequence 5'-GATC-3' for both Dam and MboI restriction endonuclease was prepared...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155823/development-and-preliminary-evaluation-of-a-multiplexed-amplification-and-next-generation-sequencing-method-for-viral-hemorrhagic-fever-diagnostics
#2
Annika Brinkmann, Koray Ergünay, Aleksandar Radonić, Zeliha Kocak Tufan, Cristina Domingo, Andreas Nitsche
BACKGROUND: We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. METHODOLOGY: An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform...
November 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29146902/single-molecule-multiplexed-nanopore-protein-screening-in-human-serum-using-aptamer-modified-dna-carriers
#3
Jasmine Y Y Sze, Aleksandar P Ivanov, Anthony E G Cass, Joshua B Edel
The capability to screen a range of proteins at the single-molecule level with enhanced selectivity in biological fluids has been in part a driving force in developing future diagnostic and therapeutic strategies. The combination of nanopore sensing and nucleic acid aptamer recognition comes close to this ideal due to the ease of multiplexing, without the need for expensive labelling methods or extensive sample pre-treatment. Here, we demonstrate a fully flexible, scalable and low-cost detection platform to sense multiple protein targets simultaneously by grafting specific sequences along the backbone of a double-stranded DNA carrier...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29144014/translocation-of-precision-polymers-through-biological-nanopores
#4
Mordjane Boukhet, Niklas Felix König, Abdelaziz Al Ouahabi, Gerhard Baaken, Jean-François Lutz, Jan C Behrends
Nanopore analysis, which is, currently, chiefly used for DNA sequencing, is also an appealing technique for characterizing abiotic polymers. As a first step toward this goal, nanopore detection of non-natural monodispersed poly(phosphodiester)s as candidate backbone structures is reported herein. Two model homopolymers containing phosphopropyl repeat units (i.e., 56 or 104 r.u.) and a short thymidine nucleotide sequence are analyzed in the present work. They are tested in two different biological nanopores, α-hemolysin from Staphylococcus aureus, and aerolysin from Aeromonas hydrophila...
November 16, 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29131223/enhancing-the-sensitivity-of-dna-detection-by-structurally-modified-solid-state-nanopore
#5
Kidan Lee, Hyomin Lee, Seung-Hyun Lee, Hyun-Mi Kim, Ki-Bum Kim, Sung Jae Kim
Solid-state nanopore is an ionic current-based biosensing platform, which would be a top candidate for next-generation DNA sequencing and a high-throughput drug-screening tool at single-molecular-scale resolution. There have been several approaches to enhance the sensitivity and reliability of biomolecule detection using the nanopores particularly in two aspects: signal-to-noise ratio (SNR) and translocation dwell time. In this study, an additional nano-well of 100-150 nm diameter and the aspect ratio of ∼5 called 'guide structure' was inserted in conventional silicon-substrate nanopore device to increase both SNR and dwell time...
November 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/29126224/dbtss-dbkero-for-integrated-analysis-of-transcriptional-regulation
#6
Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki
DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29123646/first-de-novo-draft-genome-sequence-of-oryza-coarctata-the-only-halophytic-species-in-the-genus-oryza
#7
Tapan Kumar Mondal, Hukam Chand Rawal, Kishor Gaikwad, Tilak Raj Sharma, Nagendra Kumar Singh
Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time that more than 85.71 % of the genome coverage and the data have been deposited in NCBI SRA, with BioProject ID PRJNA396417.
2017: F1000Research
https://www.readbyqxmd.com/read/29122881/whole-genome-sequencing-of-a-human-clinical-isolate-of-emm28-streptococcus-pyogenes-causing-necrotizing-fasciitis-acquired-contemporaneously-with-hurricane-harvey
#8
S Wesley Long, Priyanka Kachroo, James M Musser, Randall J Olsen
We discovered an emm28 Streptococcus pyogenes isolate causing necrotizing fasciitis in a patient exposed to the floodwaters of Hurricane Harvey in the Houston, TX, metropolitan area in August 2017. The Oxford Nanopore MinION instrument provided sufficient genome sequence data within 1 h of beginning sequencing to close the genome.
November 9, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29122092/rapid-and-accurate-sequencing-of-enterovirus-genomes-using-minion-nanopore-sequencer
#9
Ji Wang, Yue Hua Ke, Yong Zhang, Ke Qiang Huang, Lei Wang, Xin Xin Shen, Xiao Ping Dong, Wen Bo Xu, Xue Jun Ma
OBJECTIVE: Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. METHODS: In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION...
October 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/29120602/porphyrin-assisted-docking-of-a-thermophage-portal-protein-into-lipid-bilayers-nanopore-engineering-and-characterization
#10
Benjamin Cressiot, Sandra J Greive, Wei Si, Tomas C Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A Antson, Meni Wanunu
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29118413/fabrication-of-subnanometer-precision-nanopores-in-hexagonal-boron-nitride
#11
S Matt Gilbert, Gabriel Dunn, Amin Azizi, Thang Pham, Brian Shevitski, Edgar Dimitrov, Stanley Liu, Shaul Aloni, Alex Zettl
We demonstrate the fabrication of individual nanopores in hexagonal boron nitride (h-BN) with atomically precise control of the pore shape and size. Previous methods of pore production in other 2D materials typically create pores with irregular geometry and imprecise diameters. In contrast, other studies have shown that with careful control of electron irradiation, defects in h-BN grow with pristine zig-zag edges at quantized triangular sizes, but they have failed to demonstrate production and control of isolated defects...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29114013/nanopore-sequencing-comes-to-plant-genomes
#12
Nancy Rosenbaum Hofmann
No abstract text is available yet for this article.
November 7, 2017: Plant Cell
https://www.readbyqxmd.com/read/29113982/nanopore-sequencing-of-complex-genomic-rearrangements-in-yeast-reveals-mechanisms-of-repeat-mediated-double-strand-break-repair
#13
Ryan J McGinty, Rachel G Rubinstein, Alexander J Neil, Margaret Dominska, Denis Kiktev, Thomas D Petes, Sergei M Mirkin
Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy and (CGG)n repeats in fragile X syndrome, are also subject to double strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects...
November 7, 2017: Genome Research
https://www.readbyqxmd.com/read/29109544/mapping-and-phasing-of-structural-variation-in-patient-genomes-using-nanopore-sequencing
#14
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E Talkowski, Tobias Marschall, Jeroen de Ridder, Wigard P Kloosterman
Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29109480/detection-of-subclonal-l1-transductions-in-colorectal-cancer-by-long-distance-inverse-pcr-and-nanopore-sequencing
#15
Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A Aaltonen, Liisa Kauppi, Kimmo Palin
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29100084/profiling-of-short-tandem-repeat-disease-alleles-in-12-632-human-whole-genomes
#16
Haibao Tang, Ewen F Kirkness, Christoph Lippert, William H Biggs, Martin Fabani, Ernesto Guzman, Smriti Ramakrishnan, Victor Lavrenko, Boyko Kakaradov, Claire Hou, Barry Hicks, David Heckerman, Franz J Och, C Thomas Caskey, J Craig Venter, Amalio Telenti
Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci...
November 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29099796/genome-analysis-and-genetic-stability-of-the-cryptophlebia-leucotreta-granulovirus-crlegv-sa-after-15-years-of-commercial-use-as-a-biopesticide
#17
Marcel van der Merwe, Michael D Jukes, Lukasz Rabalski, Caroline Knox, John K Opoku-Debrah, Sean D Moore, Martyna Krejmer-Rabalska, Boguslaw Szewczyk, Martin P Hill
Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is an indigenous pest in southern Africa which attacks citrus fruits and other crops. To control T. leucotreta in South Africa, an integrated pest management (IPM) programme incorporating the baculovirus Cryptophlebialeucotreta granulovirus (CrleGV-SA) as a biopesticide has been implemented. This study investigated the genetic stability of a commercially produced CrleGV-SA product that has been applied in the field since 2000. Seven representative full-genome sequences of the CrleGV-SA isolate spanning a 15-year period were generated and compared with one another...
November 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29098311/a-single-nucleotide-polymorphism-in-the-fra-gene-results-in-fractured-starch-granules-in-barley
#18
Mika Saito, Tsuyoshi Tanaka, Kazuhiro Sato, Patricia Vrinten, Toshiki Nakamura
We report here that the mutation causing fractured starch granules in the barley line "Franubet" results from a point mutation in the barley gene corresponding to the rice FLO6 gene. The "fra" mutation in barley, which was originally isolated and characterized over 30 years ago, results in fractured starch granules and an opaque phenotype. This mutation has been used in breeding programs, since it appears to be useful in the production of pearled barley for human consumption. However, selection for this phenotype is difficult, since wild-type and heterozygous kernels cannot be distinguished phenotypically, and until now, the gene involved in this mutation has not been determined...
November 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29093467/nanopore-based-single-molecule-sequencing-of-the-d4z4-array-responsible-for-facioscapulohumeral-muscular-dystrophy
#19
Satomi Mitsuhashi, So Nakagawa, Mahoko Takahashi Ueda, Tadashi Imanishi, Martin C Frith, Hiroaki Mitsuhashi
Subtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC content. Sequencing these repetitive regions is challenging, even with recent improvements in sequencing technologies. Among these repeats, a haplotype carrying a particular sequence and shortening of the D4Z4 array on human chromosome 4q35 causes one of the most prevalent forms of muscular dystrophy with autosomal-dominant inheritance, facioscapulohumeral muscular dystrophy (FSHD)...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089590/campylobacter-fetus-meningitis-confirmed-by-a-16s-rrna-gene-analysis-using-the-minion-nanopore-sequencer-south-korea-2016
#20
Jangsup Moon, Narae Kim, Han Sang Lee, Hye-Rim Shin, Soon-Tae Lee, Keun-Hwa Jung, Kyung-Il Park, Sang Kun Lee, Kon Chu
No abstract text is available yet for this article.
November 1, 2017: Emerging Microbes & Infections
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