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Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven
Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot...
March 14, 2018: Bioinformatics
Jay K Bhattarai, Dharmendra Neupane, Bishal Nepal, Vasilii Mikhaylov, Alexei V Demchenko, Keith J Stine
Nanoporous gold (np-Au), because of its high surface area-to-volume ratio, excellent conductivity, chemical inertness, physical stability, biocompatibility, easily tunable pores, and plasmonic properties, has attracted much interested in the field of nanotechnology. It has promising applications in the fields of catalysis, bio/chemical sensing, drug delivery, biomolecules separation and purification, fuel cell development, surface-chemistry-driven actuation, and supercapacitor design. Many chemical and electrochemical procedures are known for the preparation of np-Au...
March 16, 2018: Nanomaterials
Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt
Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing...
March 16, 2018: Microbial Genomics
Varun Vohra, Francesco Galeotti, Umberto Giovanella, Wojciech Mroz, Mariacecilia Pasini, Chiara Botta
Push-coating is a green and extremely low-cost process in which only few microliters of conjugated polymer solutions are used to produce thin films using capillary forces. Here, we adapt this fabrication technique to replicate self-assembled nanoporous structures on green and red light-emitting conjugated polymer thin films. These films display ring-like photoluminescence and are successfully integrated into polymer light-emitting devices as emitting layers. At low applied voltages, the green-emitting devices exhibit electroluminescence from hexagonally arranged nanopixel arrays resulting from a stronger electric field in the thinner areas inside the pores...
March 16, 2018: ACS Applied Materials & Interfaces
Cheryl Suwen Law, Siew Yee Lim, Abel Santos
This study presents a nanofabrication approach that enables the production of nanoporous anodic alumina distributed Bragg reflectors (NAA-DBRs) with finely engineered light filtering features across the spectral regions. The photonic stopband (PSB) of these NAA-based photonic crystal (PC) structures is precisely tuned by an apodization strategy applied during stepwise pulse anodization with the aim of engineering the effective medium of NAA-DBRs in depth. We systematically assess the effect of different fabrication parameters such as apodization function (i...
March 15, 2018: Scientific Reports
István Prazsák, Dóra Tombácz, Attila Szűcs, Béla Dénes, Michael Snyder, Zsolt Boldogkői
The vaccinia virus is a large, complex virus belonging to the Poxviridae family. Here, we report the complete, annotated genome sequence of the neurovirulent Western Reserve laboratory strain of this virus, which was sequenced on the Pacific Biosciences RS II and Oxford Nanopore MinION platforms.
March 15, 2018: Genome Announcements
Angus McMullen, Hendrick W de Haan, Jay X Tang, Derek Stein
Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force...
February 16, 2018: Physical Review Letters
Pradipta Kr Das
An analytical model for the electrophoretic speed of DNA translocating through nanopore functionalized with polyelectrolyte brush is developed for the first time. The electrophoretic speed depends on DNA surface potential, applied electric field, viscosity and permittivity of solution along with velocity and electrostatic potential at liquid/ polyelectrolyte layer interface where the interface seemed to behave similar to that of a solid state nanopore wall. Under the limit of Debye-Hückel linearization, the electrostatic potential at liquid/ polyelectrolyte layer interface and at DNA surface have been calculated...
March 15, 2018: Electrophoresis
Cosimo Cumbo, Luciana Impera, Crescenzio Francesco Minervini, Paola Orsini, Luisa Anelli, Antonella Zagaria, Nicoletta Coccaro, Giuseppina Tota, Angela Minervini, Paola Casieri, Claudia Brunetti, Antonella Russo Rossi, Elisa Parciante, Giorgina Specchia, Francesco Albano
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology...
February 16, 2018: Oncotarget
Shan Wei, Zachary R Weiss, Zev Williams
Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples' genomic DNA in under three hours, including library preparation and sequencing...
March 14, 2018: G3: Genes—Genomes—Genetics
Ganhua Xie, Pei Li, Zhiju Zhao, Zhongpeng Zhu, Xiang-Yu Kong, Zhen Zhang, Kai Xiao, Liping Wen, Lei Jiang
Water wetting behavior in nano-confined environments plays an important role in mass transport and signal trans-mission of organisms. It is valuable and challengeable to investigate how water behaves in such a nanometer-scale with external stimuli, in particular with electric field and light. Unfortunately, the mechanism of hydrophobic reaction inside the nano-spaces is still obscure and lacks of experimental supporting for the current electric-field- or photo-responsive nanochannels which suffer from fragility or monofunctionality...
March 15, 2018: Journal of the American Chemical Society
Roshan Kumar, Raniki Kumari, Sanjay Kumar, Deepak Kumar Jangir, Tushar Kanti Maiti
α-Synuclein, a major constituent of proteinaceous inclusions named Lewy body, has been shown to be released and taken up by cells, which may facilitate its progressive pathological spreading and neuronal cell death in Parkinson's disease. However, the pathophysiological effect and signalling cascade initiated by extracellular α-synuclein in cellular milieu are not well understood. Herein we have investigated the perturbations induced by low molecular weight α-synuclein and different types of α-synuclein oligomers in the neuroblastoma SH-SY5Y cells...
March 14, 2018: Biomacromolecules
Deepti Chaturvedi, Radhakrishnan Mahalakshmi
Transmembrane β-barrel proteins (OMPs) are highly robust structures for engineering and development of nanopore channels, surface biosensors, and display libraries. Expanding the applications of designed OMPs requires the identification of elements essential for β-barrel scaffold formation and stability. Here, we have designed chimeric 8-stranded OMPs composed of strand hybrids of Escherichia coli OmpX and Yersinia pestis Ail, and identified molecular motifs essential for β-barrel scaffold formation. For the OmpX/Ail chimeras, we find that the central hairpin strands β4-β5 in tandem are vital for β-barrel folding...
March 14, 2018: Biochemistry
Xiaohan Chen, Golbarg M Roozbahani, Zijing Ye, Youwen Zhang, Rui Ma, Jialing Xiang, Xiyun Guan
Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis, and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion...
March 14, 2018: ACS Applied Materials & Interfaces
Jiahui Kou, Lin-Bing Sun
Due to their diverse structure, high porosity, and tunable functionality, metal-organic frameworks (MOFs) are of great inter-est for diverse applications including catalysis. However, the poor hydrostability of most reported MOFs hinders their cata-lytic applications seriously. In addition, the development of an effective method to improve the catalytic activity of MOFs is another challenge. Here, we report for the first time the development of a double-solvent strategy to fabricate MOFs inside silica nanopores...
March 14, 2018: ACS Applied Materials & Interfaces
Andriy Yaroshchuk, Mykola P Bondarenko
Current-induced concentration polarization of nanoporous media is explored theoretically by using approach of local thermodynamic equilibrium within nanopore cross-sections. The problem is solved in quadratures in terms of irreversible thermodynamics. The phenomenological coefficients are further specified by using capillary space-charge model for straight slit-like and cylindrical capillaries. This analysis reveals several novel features of current-induced concentration polarization related to the (electro)osmotic volume transfer...
March 14, 2018: Small
Juan Zheng, Junlong Huang, Fei Xu, Chuyi Ni, Xintong Xie, Fang Zhu, Dingcai Wu, Gangfeng Ouyang
Hollow carbon nanospheres (HCNs) with numerous nanopores in their ultrathin carbon shells have been prepared and applied as SPME fiber coatings. Benefiting from its ultrahigh surface area, short diffusion distance, and nitrogen doping, the HCNs-coated fiber demonstrates excellent properties of fast mass transfer, broad-spectrum adsorption and high extraction efficiencies. These encouraging results could offer a benchmark for developing advanced SPME in environment analyses requiring high-performance enrichment of abundant analytes, especially for unknown compounds...
March 14, 2018: Nanoscale
Aldo Eugenio Rossini, Fabrizio Gala, Mauro Chinappi, Giuseppe Zollo
Solid-state nanopores and nanogaps are emerging as promising tools for single molecule analysis. 2D materials, such as graphene, can potentially reach the spatial resolution needed for nucleic acid and protein sequencing. In the context of the density functional theory, atomistic modeling and non-equilibrium Green's function calculation, we show that glycine based polypeptide chains translocating across a nano-gap between two semi-infinite graphene nano-ribbons leave a specific transverse current signature for each peptide bond...
March 14, 2018: Nanoscale
Wei Li, Zehua Liu, Flavia Fontana, Yaping Ding, Dongfei Liu, Jouni T Hirvonen, Hélder A Santos
In the past two decades, porous silicon (PSi) has attracted increasing attention for its potential biomedical applications. With its controllable geometry, tunable nanoporous structure, large pore volume/high specific surface area, and versatile surface chemistry, PSi shows significant advantages over conventional drug carriers. Here, an overview of recent progress in the use of PSi in drug delivery and cancer immunotherapy is presented. First, an overview of the fabrication of PSi with various geometric structures is provided, with particular focus on how the unique geometry of PSi facilitates its biomedical applications, especially for drug delivery...
March 13, 2018: Advanced Materials
Tetsuo Yamaguchi, Ayan Maity, Vivek Polshettiwar, Makoto Ogawa
A colored hybrid based on a merocyanine adsorbed in a nanoporous-silica-composed dendritic fibrous silica was prepared by adsorption onto the nanoporous silica from a spiropyran solution during UV irradiation (photoinduced adsorption). The obtained red hybrid thus exhibited negative photochromism by visible-light irradiation. The hybrid was further combined with an organophilic clay by a solid-state mixing without using solvent to achieve excellent reversibility of the color change, which was thought to be achieved by molecular diffusion through the two materials, where nanoporous silica and organophilic clay accommodated the colored (merocyanine) and colorless (photogenerated spiropyran) isomers, respectively...
March 13, 2018: Inorganic Chemistry
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