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Nanopore sequencing

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https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#1
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28430192/a-monodisperse-transmembrane-%C3%AE-helical-peptide-barrel
#2
Kozhinjampara R Mahendran, Ai Niitsu, Lingbing Kong, Andrew R Thomson, Richard B Sessions, Derek N Woolfson, Hagan Bayley
The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28422400/sequence-specific-covalent-capture-coupled-with-high-contrast-nanopore-detection-of-a-disease-derived-nucleic-acid-sequence
#3
Maryam Imani Nejad, Ruicheng Shi, Xinyue Zhang, Li-Qun Gu, Kent S Gates
Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but may not provide a durable signal. Sequence-specific covalent cross-link formation can anchor probes to target DNA and also may provide an additional layer of target selectivity. Here we develop a new cross-linking reaction for the covalent capture of specific nucleic acid sequences. This process involves reaction of an abasic site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence...
April 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28422265/nanoporous-poly-3-hexylthiophene-thin-film-structures-from-self-organization-of-a-tunable-molecular-bottlebrush-scaffold
#4
Suk-Kyun Ahn, Jan-Michael Y Carrillo, Jong K Keum, Jihua Chen, David Uhrig, Bradley S Lokitz, Bobby G Sumpter, S Michael Kilbey
The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(d,l-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28421749/design-of-multi-functional-nanogate-in-response-to-multiple-external-stimuli-using-amphiphilic-diblock-copolymer
#5
Kai Huang, Igal Szleifer
Nature uses the interplay between hydrophobic and electrostatic interactions of disordered proteins to orchestrate complicated molecular gate such as the nuclear pore complex to control the transport of biological masses. Inspired by nature, we here theoretically show that well-defined gate shape, sensitive response to pH and salt concentration, and selectivity in cargo transport can be simultaneously achieved by grafting amphiphilic diblock copolymers made of sequence-controlled hydrophobic and ionizable monomers on the inner surface of solid-state nanopore...
April 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28413619/picopore-a-tool-for-reducing-the-storage-size-of-oxford-nanopore-technologies-datasets-without-loss-of-functionality
#6
Scott Gigante
Oxford Nanopore Technologies' (ONT) MinION and PromethION long-read sequencing technologies are emerging as genuine alternatives to established Next-Generation Sequencing technologies. A combination of the highly redundant file format and a rapid increase in data generation have created a significant problem both for immediate data storage on MinION-capable laptops, and for long-term storage on lab data servers.  We developed Picopore, a software suite offering three methods of compression. Picopore's lossless and deep lossless methods provide a 25% and 44% average reduction in size, respectively, without removing any data from the files...
2017: F1000Research
https://www.readbyqxmd.com/read/28413259/materials-genome-in-action-identifying-the-performance-limits-of-physical-hydrogen-storage
#7
Aaron W Thornton, Cory M Simon, Jihan Kim, Ohmin Kwon, Kathryn S Deeg, Kristina Konstas, Steven J Pas, Matthew R Hill, David A Winkler, Maciej Haranczyk, Berend Smit
The Materials Genome is in action: the molecular codes for millions of materials have been sequenced, predictive models have been developed, and now the challenge of hydrogen storage is targeted. Renewably generated hydrogen is an attractive transportation fuel with zero carbon emissions, but its storage remains a significant challenge. Nanoporous adsorbents have shown promising physical adsorption of hydrogen approaching targeted capacities, but the scope of studies has remained limited. Here the Nanoporous Materials Genome, containing over 850 000 materials, is analyzed with a variety of computational tools to explore the limits of hydrogen storage...
April 11, 2017: Chemistry of Materials: a Publication of the American Chemical Society
https://www.readbyqxmd.com/read/28389823/chaperone-driven-polymer-translocation-through-nanopore-spatial-distribution-and-binding-energy
#8
Rouhollah Haji Abdolvahab
Chaperones are binding proteins working as a driving force in biopolymer translocation. They bind to the biopolymer near the pore and prevent its backsliding. Chaperones may have different spatial distributions. Recently, we showed the importance of their spatial distribution in translocation and its effects on the sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. Because of the exponential distribution of chaperones, the energy dependency of the translocation time will change...
April 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/28374130/dna-nanopore-functionalized-with-aptamer-and-cell-penetrating-peptide-for-tumor-cell-recognition
#9
Xi-Lin Guo, Dan-Dan Yuan, Ting Song, Xue-Mei Li
In the present work, DNA nanopore was composed of a bundle of six DNA duplexes folded from six DNA strands and functionalized with Ramos cell aptamer and cell-penetrating peptide (CPP). Herein, we present a unique dually conjugated molecule with an aptamer and cell-penetrating peptide for targeting and recognition of Ramos cells. The aptamer sequence was specific bound to Ramos cell, at the meanwhile the nanopore assembly was taken onto the surface of cell membrane and then got into the cells with the help of CPP...
April 3, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28369459/de-novo-assembly-and-population-genomic-survey-of-natural-yeast-isolates-with-the-oxford-nanopore-minion-sequencer
#10
Benjamin Istace, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury
BACKGROUND: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome...
February 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28362434/nanopore-sequencing-meets-epigenetics
#11
Michael C Schatz
No abstract text is available yet for this article.
March 31, 2017: Nature Methods
https://www.readbyqxmd.com/read/28348876/comparison-of-bacterial-genome-assembly-software-for-minion-data-and-their-applicability-to-medical-microbiology
#12
Kim Judge, Martin Hunt, Sandra Reuter, Alan Tracey, Michael A Quail, Julian Parkhill, Sharon J Peacock
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly...
September 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28337073/real-time-dna-sequencing-in-the-antarctic-dry-valleys-using-the-oxford-nanopore-sequencer
#13
Sarah S Johnson, Elena Zaikova, David S Goerlitz, Yu Bai, Scott W Tighe
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28335237/dna-sequencing-by-hexagonal-boron-nitride-nanopore-a-computational-study
#14
Liuyang Zhang, Xianqiao Wang
The single molecule detection associated with DNA sequencing has motivated intensive efforts to identify single DNA bases. However, little research has been reported utilizing single-layer hexagonal boron nitride (hBN) for DNA sequencing. Here we employ molecular dynamics simulations to explore pathways for single-strand DNA (ssDNA) sequencing by nanopore on the hBN sheet. We first investigate the adhesive strength between nucleobases and the hBN sheet, which provides the foundation for the hBN-base interaction and nanopore sequencing mechanism...
June 6, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334395/pore-guis-for-parallel-and-real-time-processing-of-minion-sequence-data
#15
Robert Stewart, Mick Watson
Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs. Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334071/on-the-design-and-prospects-of-direct-rna-sequencing
#16
Georgi K Marinov
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets...
February 17, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#17
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#18
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#19
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28298449/real-time-sequencing-of-mycobacterium-tuberculosis-are-we-there-yet
#20
Robyn S Lee, Madhukar Pai
Whole genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, the real-time, clinical utility has been low, in part due to the requirement for culture. In Votintseva et al (J Clin Microbiol https://doi.org/10.1128/JCM.02483-16), authors present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, generating drug resistance predictions and phylogenetic trees in 44 hours using the Illumina MiSeq. Authors also illustrate the potential for < 24 hour turnaround time from DNA extraction to clinically-relevant results, with Illumina MiniSeq and Oxford Nanopore Technologies' MinION...
March 15, 2017: Journal of Clinical Microbiology
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