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Nanopore sequencing

Oleg E Shklyaev, Milton W Cole, Vincent H Crespi
Atomically thin cylindrical nanopores can change shape in response to physically adsorbed gas inside. Coupled to a gas reservoir, an initially collapsed pore can expand to allow the adsorbed gas to form concentric shells on the inner part of the pore, driven by adsorption energetics, not gas pressure. A lattice gas model describes the evolution of the nanotube pore shape and absorbed gas as a function of gas chemical potential at zero temperature. We found that narrow-enough tubes are always expanded and gas inside adsorbs in sequences of concentric shells as the gas chemical potential increases...
January 2017: Physical Review. E
Thomas Hoenen
Sequencing of virus genomes during disease outbreaks can provide valuable information for diagnostics, epidemiology, and evaluation of potential countermeasures. However, particularly in remote areas logistical and technical challenges can be significant. Nanopore sequencing provides an alternative to classical Sanger and next-generation sequencing methods, and was successfully used under outbreak conditions (Hoenen et al., 2016; Quick et al., 2016). Here we describe a protocol used for sequencing of Ebola virus under outbreak conditions using Nanopore technology, which we successfully implemented at the CDC/NIH diagnostic laboratory (de Wit et al...
November 5, 2016: Bio-protocol
S Palantavida, B Peng, I Sokolov
We report on a novel approach to synthesize ultrabright fluorescent silica particles capable of producing a large number of complex spectra. The spectra can be excited using a single wavelength which is paramount in quantitative fluorescence imaging, flow cytometry and sensing applications. The approach employs the physical encapsulation of organic fluorescent molecules inside a nanoporous silica matrix with no dye leakage. As was recently demonstrated, such an encapsulation allowed for the encapsulation of very high concentrations of organic dyes without quenching their fluorescent efficiency...
February 8, 2017: Nanoscale
Bert Vanmechelen, Annabel Rector, Piet Maes
Many methods for the discovery of novel viruses are based on amplification of the virus using consensus or degenerate PCR primers. A downside of this approach is that it requires prior knowledge of the viral nucleotide sequence to be applicable. Presented in this unit is a method for the sequence-independent amplification of circular viral genomes that is based on the rolling-circle mechanism used by certain viruses in their natural replication cycle. The amplification of the virus of interest is coupled to the isolation of the viral genome by gel extraction following a restriction digestion...
February 6, 2017: Current Protocols in Microbiology
Hiral N Patel, Ian Carroll, Rodolfo Lopez, Sandeep Sankararaman, Charles Etienne, Subba Ramaiah Kodigala, Mark R Paul, Henk W Ch Postma
We study how double-stranded DNA translocates through graphene nanogaps. Nanogaps are fabricated with a novel capillary-force induced graphene nanogap formation technique. DNA translocation signatures for nanogaps are qualitatively different from those obtained with circular nanopores, owing to the distinct shape of the gaps discussed here. Translocation time and conductance values vary by ∼ 100%, which we suggest are caused by local gap width variations. We also observe exponentially relaxing current traces...
2017: PloS One
Senne Cornelis, Yannick Gansemans, Lieselot Deleye, Dieter Deforce, Filip Van Nieuwerburgh
One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies' (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies...
February 3, 2017: Scientific Reports
Anita C Schürch, Willem van Schaik
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore)...
January 2017: Annals of the New York Academy of Sciences
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
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
Linnea M Baudhuin, Matthew J Ferber
No abstract text is available yet for this article.
January 11, 2017: Clinical Chemistry
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
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
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
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 CONTACT: or mcfrith@edu.k.u-tokyo...
December 30, 2016: Bioinformatics
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
Justin Chu, Hamid Mohamadi, René L Warren, Chen Yang, Inanç 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
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
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
No abstract text is available yet for this article.
December 13, 2016: Genome Biology
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
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
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