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Nanopore sequencing

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https://www.readbyqxmd.com/read/28100585/fast-and-accurate-de-novo-genome-assembly-from-long-uncorrected-reads
#1
Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic
The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28088017/co-delivery-of-ibuprofen-and-gentamicin-from-nanoporous-anodic-titanium-dioxide-layers
#2
Anna Pawlik, Magdalena Jarosz, Karolina Syrek, Grzegorz D Sulka
Although single-drug therapy may prove insufficient in treating bacterial infections or inflammation after orthopaedic surgeries, complex therapy (using both an antibiotic and an anti-inflammatory drug) is thought to address the problem. Among drug delivery systems (DDSs) with prolonged drug release profiles, nanoporous anodic titanium dioxide (ATO) layers on Ti foil are very promising. In the discussed research, ATO samples were synthesized via a three-step anodization process in an ethylene glycol-based electrolyte with fluoride ions...
January 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28077442/miniaturized-nanopore-dna-sequencing-accelerating-the-path-to-precision-medicine
#3
Linnea M Baudhuin, Matthew J Ferber
No abstract text is available yet for this article.
January 11, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28062856/rapid-resistome-mapping-using-nanopore-sequencing
#4
Eric van der Helm, Lejla Imamovic, Mostafa M Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten O A Sommer
The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping...
January 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28062043/subangstrom-measurements-of-enzyme-function-using-a-biological-nanopore-sprnt
#5
A H Laszlo, I M Derrrington, J H Gundlach
Nanopores are emerging as new single-molecule tools in the study of enzymes. Based on the progress in nanopore sequencing of DNA, a tool called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT) was developed to measure the movement of enzymes along DNA in real time. In this new method, an enzyme is loaded onto a DNA (or RNA) molecule. A single-stranded DNA end of this complex is drawn into a nanopore by an electrostatic potential that is applied across the pore. The single-stranded DNA passes through the pore's constriction until the enzyme comes into contact with the pore...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28043580/application-of-highly-portable-minion-nanopore-sequencing-technology-for-the-monitoring-of-nosocomial-tuberculosis-infection
#6
Matthew Bates, Pascal Polepole, Nathan Kapata, Matt Loose, Justin O'Grady
Referral hospitals in sub-Saharan Africa concentrate large numbers of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) patients, failed by community TB services. We have previously shown, from enhanced screening and through autopsy studies, a significant burden of missed TB infections at the University Teaching Hospital, Lusaka, Zambia, with many patients dying or being discharged without treatment. With minimal TB isolation facilities and minimal political will to invest in broader screening and isolation, the risk of nosocomial transmission is likely to be extremely high...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28039163/training-alignment-parameters-for-arbitrary-sequencers-with-last-train
#7
Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C Frith
: LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. AVAILABILITY AND IMPLEMENTATION: the source code is freely available at http://last.cbrc.jp/ CONTACT: mhamada@waseda.jp or mcfrith@edu.k.u-tokyo...
December 30, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28004567/dna-origami-graphene-hybrid-nanopore-for-dna-detection
#8
Amir Barati Farimani, Payam Dibaeinia, Narayana R Aluru
DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases...
December 22, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28003261/innovations-and-challenges-in-detecting-long-read-overlaps-an-evaluation-of-the-state-of-the-art
#9
REVIEW
Justin Chu, Hamid Mohamadi, René L Warren, Chen Yang, Inanc Birol
: Identifying overlaps between error-prone long reads, specifically those from Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB), is essential for certain downstream applications, including error correction and de novo assembly. Though akin to the read-to-reference alignment problem, read-to-read overlap detection is a distinct problem that can benefit from specialized algorithms that perform efficiently and robustly on high error rate long reads. Here, we review the current state-of-the-art read-to-read overlap tools for error-prone long reads, including BLASR, DALIGNER, MHAP, GraphMap, and Minimap...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28000682/electronic-single-molecule-identification-of-carbohydrate-isomers-by-recognition-tunnelling
#10
JongOne Im, Sovan Biswas, Hao Liu, Yanan Zhao, Suman Sen, Sudipta Biswas, Brian Ashcroft, Chad Borges, Xu Wang, Stuart Lindsay, Peiming Zhang
Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization...
December 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27964738/erratum-to-the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#11
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
No abstract text is available yet for this article.
December 13, 2016: Genome Biology
https://www.readbyqxmd.com/read/27960493/mechanical-trapping-of-dna-in-a-double-nanopore-system
#12
Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, Aleksei Aksimentiev
Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude...
December 14, 2016: Nano Letters
https://www.readbyqxmd.com/read/27936625/self-assembly-of-an-%C3%AE-helical-peptide-into-a-crystalline-two-dimensional-nanoporous-framework
#13
Elizabeth L Magnotti, Spencer A Hughes, Rebecca S Dillard, Shengyuan Wang, Lillian Hough, Arshad Karumbamkandathil, Tianquan Lian, Joseph S Wall, Xiaobing Zuo, Elizabeth R Wright, Vincent P Conticello
Sequence-specific peptides have been demonstrated to self-assemble into structurally defined nanoscale objects including nanofibers, nanotubes, and nanosheets. The latter structures display significant promise for the construction of hybrid materials for functional devices due to their extended planar geometry. Realization of this objective necessitates the ability to control the structural features of the resultant assemblies through the peptide sequence. The design of a amphiphilic peptide, 3FD-IL, is described that comprises two repeats of a canonical 18 amino acid sequence associated with straight α-helical structures...
December 21, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27934066/nanopores-and-nanochannels-from-gene-sequencing-to-genome-mapping
#14
Stefan Howorka, Zuzanna Siwy
DNA strands can be analyzed at the single-molecule level by isolating them inside nanoscale holes. The strategy is used for the label-free and portable sequencing with nanopores. Nanochannels can also be applied to map genomes with high resolution, as shown by Jeffet et al. in this issue of ACS Nano. Here, we compare the two strategies in terms of biophysical similarities and differences and describe that both are complementary and can improve the DNA analysis for genomic research and diagnostics.
November 22, 2016: ACS Nano
https://www.readbyqxmd.com/read/27887629/the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#15
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27833119/streaming-current-magnetic-fields-in-a-charged-nanopore
#16
Abraham Mansouri, Peyman Taheri, Larry W Kostiuk
Magnetic fields induced by currents created in pressure driven flows inside a solid-state charged nanopore were modeled by numerically solving a system of steady state continuum partial differential equations, i.e., Poisson, Nernst-Planck, Ampere and Navier-Stokes equations (PNPANS). This analysis was based on non-dimensional transport governing equations that were scaled using Debye length as the characteristic length scale, and applied to a finite length cylindrical nano-channel. The comparison of numerical and analytical studies shows an excellent agreement and verified the magnetic fields density both inside and outside the nanopore...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27831497/improved-assembly-of-noisy-long-reads-by-k-mer-validation
#17
Antonio Bernardo Carvalho, Eduardo G Dupim, Gabriel Goldstein
Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads...
December 2016: Genome Research
https://www.readbyqxmd.com/read/27826518/false-positives-and-false-negatives-measure-less-than-0-001-in-labeling-ssdna-with-osmium-tetroxide-2-2-bipyridine
#18
Anastassia Kanavarioti
Osmium tetroxide 2,2'-bipyridine (OsBp) is known to react with pyrimidines in ssDNA and preferentially label deoxythymine (T) over deoxycytosine (C). The product, osmylated DNA, was proposed as a surrogate for nanopore-based DNA sequencing due to OsBp's "perfect" label attributes. Osmylated deoxyoligos translocate unassisted and measurably slow via sub-2 nm SiN solid-state nanopores, as well as via the alpha-hemolysin (α-HL) pore. Both nanopores discriminate clearly between osmylated and intact nucleobase; α-HL was also shown to discriminate between osmylated T and osmylated C...
2016: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/27784934/high-throughput-sequencing-an-overview-of-sequencing-chemistry
#19
REVIEW
Sheetal Ambardar, Rikita Gupta, Deepika Trakroo, Rup Lal, Jyoti Vakhlu
In the present century sequencing is to the DNA science, what gel electrophoresis was to it in the last century. From 1977 to 2016 three generation of the sequencing technologies of various types have been developed. Second and third generation sequencing technologies referred commonly to as next generation sequencing technology, has evolved significantly with increase in sequencing speed, decrease in sequencing cost, since its inception in 2004. GS FLX by 454 Life Sciences/Roche diagnostics, Genome Analyzer, HiSeq, MiSeq and NextSeq by Illumina, Inc...
December 2016: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/27752114/diversity-of-antibiotic-resistance-genes-in-canadian-isolates-of-aeromonas-salmonicida-subsp-salmonicida-dominance-of-psn254b-and-discovery-of-pasa8
#20
Mélanie V Trudel, Antony T Vincent, Sabrina A Attéré, Myriam Labbé, Nicolas Derome, Alexander I Culley, Steve J Charette
The bacterium Aeromonas salmonicida subsp. salmonicida is a common pathogen in fish farms worldwide. Since the antibiotic resistance of this bacterial species is on the increase, it is important to have a broader view on this issue. In the present study, we tested the presence of known plasmids conferring multi-drug resistance as well as antibiotic resistance genes by a PCR approach in 100 Canadian A. salmonicida subsp. salmonicida isolates. Our study highlighted the dominance of the conjugative pSN254b plasmid, which confers multi-drug resistance...
October 18, 2016: Scientific Reports
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