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Nanopore

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https://www.readbyqxmd.com/read/29352158/fabrication-of-multiple-nanopores-in-a-sinx-membrane-via-controlled-breakdown
#1
Yunlong Wang, Cuifeng Ying, Wenyuan Zhou, Lennart de Vreede, Zhibo Liu, Jianguo Tian
This paper reports a controlled breakdown (CBD) method to fabricate multiple nanopores in a silicon nitride (SiNx) membrane with control over both nanopore count and nanopore diameter. Despite the stochastic process of the breakdown, we found that the nanopores created via CBD, tend to be of the same diameter. We propose a membrane resistance model to explain and control the multiple nanopores forming in the membrane. We prove that the membrane resistance can reflect the number of nanopores in the membrane and that the diameter of the nanopores is controlled by the exposure time and strength of the electric field...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351868/an-aptamer-nanopore-enabled-microsensor-for-detection-of-theophylline
#2
Silu Feng, Changtian Chen, Wei Wang, Long Que
This paper reports an aptamer-based nanopore thin film sensor for detecting theophylline in the buffer solution and complex fluids including plant extracts and serum samples. Compared to antibody-based detection, aptamer-based detection offers many advantages such as low cost and high stability at elevated temperatures. Experiments found that this type of sensor can readily detect theophylline at a concentration as low as 0.05µM, which is much lower than the detection limit of current lab-based equipment such as liquid chromatography (LC)...
January 10, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29351296/hybrid-genome-assembly-and-annotation-of-paenibacillus-pasadenensis-strain-r16-reveals-insights-on-endophytic-life-style-and-antifungal-activity
#3
Alessandro Passera, Luca Marcolungo, Paola Casati, Milena Brasca, Fabio Quaglino, Chiara Cantaloni, Massimo Delledonne
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one...
2018: PloS One
https://www.readbyqxmd.com/read/29350911/a-programmable-dna-origami-platform-for-organizing-intrinsically-disordered-nucleoporins-within-nanopore-confinement
#4
Patrick D Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K Davis, Kenny Kwok Hin Chung, David Baddeley, Andela Saric, Thomas J Melia, Bart W Hoogenboom, Chenxiang Lin, C Patrick Lusk
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated, but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ~40 nm diameter transport channel contributes to their collective properties and function...
January 19, 2018: ACS Nano
https://www.readbyqxmd.com/read/29350527/shuttle-suppression-by-polymer-sealed-graphene-coated-polypropylene-separator
#5
Xuewu Ou, Yanzi Yu, Ruizhe Wu, Abhishek Tyagi, Minghao Zhuang, Yao Ding, Irfan Haider Abidi, Heng-An Wu, Feng-Chao Wang, Zhengtang Luo
"Shuttle effect" of lithium polysulfides (LiPS) leads to poor performance and short cycle life of Li-S battery, thus limiting their practical application. We demonstrate here that after coating polypropylene (PP) separator with a continuous monolayer graphene, the "shuttle effect" can be significantly suppressed by limiting the passage of long chain LiPS. The graphene/PP separator can be further modified by sealing the big holes or pores on graphene with in situ polymerized nylon-66, via an interfacial polymerization reaction between diamine and adipoyl chloride supplied by the aqueous and oil phase, respectively from each side of the membrane...
January 19, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29348401/three-dimensional-bicontinuous-nanoporous-materials-by-vapor-phase-dealloying
#6
Zhen Lu, Cheng Li, Jiuhui Han, Fan Zhang, Pan Liu, Hao Wang, Zhili Wang, Chun Cheng, Linghan Chen, Akihiko Hirata, Takeshi Fujita, Jonah Erlebacher, Mingwei Chen
Three-dimensional bicontinuous open (3DBO) nanoporosity has been recognized as an important nanoarchitecture for catalysis, sensing, and energy storage. Dealloying, i.e., selectively removing a component from an alloy, is an efficient way to fabricate nanoporous materials. However, current electrochemical and liquid-metal dealloying methods can only be applied to a limited number of alloys and usually require an etching process with chemical waste. Here, we report a green and universal approach, vapor-phase dealloying, to fabricate nanoporous materials by utilizing the vapor pressure difference between constituent elements in an alloy to selectively remove a component with a high partial vapor pressure for 3DBO nanoporosity...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29347730/rigidity-induced-scale-invariance-in-polymer-ejection-from-capsid
#7
R P Linna, P M Suhonen, J Piili
While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids. Ejections start from strongly confined polymer conformations of constant initial monomer density. We find that, unlike for fully flexible polymers, for semiflexible polymers the force measured at the pore does not show a direct relation to the instantaneous ejection velocity...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347452/incorporating-born-solvation-energy-into-the-three-dimensional-poisson-nernst-planck-model-to-study-ion-selectivity-in-kcsa-k-channels
#8
Xuejiao Liu, Benzhuo Lu
Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#9
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29343861/sensing-native-protein-solution-structures-using-a-solid-state-nanopore-unraveling-the-states-of-vegf
#10
Nitinun Varongchayakul, Diana Huttner, Mark W Grinstaff, Amit Meller
Monitoring individual proteins in solution while simultaneously obtaining tertiary and quaternary structural information is challenging. In this study, translocation of the vascular endothelial growth factor (VEGF) protein through a solid-state nanopore (ssNP) produces distinct ion-current blockade amplitude levels and durations likely corresponding to monomer, dimer, and higher oligomeric states. Upon changing from a non-reducing to a reducing condition, ion-current blockage events from the monomeric state dominate, consistent with the expected reduction of the two inter-chain VEGF disulfide bonds...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29342277/finding-nemo-hybrid-assembly-with-oxford-nanopore-and-illumina-reads-greatly-improves-the-clownfish-amphiprion-ocellaris-genome-assembly
#11
Mun Hua Tan, Christopher M Austin, Michael P Hammer, Yin Peng Lee, Laurence J Croft, Han Ming Gan
Background: Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes which warrant investigation...
January 12, 2018: GigaScience
https://www.readbyqxmd.com/read/29341378/halloysite-nanotubes-green-nanomaterial-for-functional-organic-inorganic-nanohybrids
#12
REVIEW
Wei Ma, Hui Wu, Yuji Higaki, Atsushi Takahara
The unique one-dimensional nanoporous structure and the reactive external and internal surfaces make halloysite nanotube (HNT) an interesting nanomaterial for various applications. HNT is a green nanomaterial because it is easily available from abundant deposits in nature and is biocompatible with low cytotoxicity. After a brief introduction on the structure of HNT, recent advances in surface modification of HNT and its functional organic-inorganic nanohybrids including hybrid nanocontainers, flame retardant nanocomposites, dye removal adsorbents, liquid marbles, and superamphiphobic coatings are introduced...
January 17, 2018: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/29340588/antimicrobial-resistant-klebsiella-pneumoniae-carriage-and-infection-in-specialized-geriatric-care-wards-linked-to-acquisition-in-the-referring-hospital
#13
Claire L Gorrie, Mirjana Mirceta, Ryan R Wick, Louise M Judd, Kelly L Wyres, Nicholas R Thomson, Richard A Strugnell, Nigel F Pratt, Jill S Garlick, Kerrie M Watson, Peter C Hunter, Steve A McGloughlin, Denis W Spelman, Adam W J Jenney, Kathryn E Holt
Background: Klebsiella pneumoniae is a leading cause of extended-spectrum beta-lactamase (ESBL) producing hospital-associated infections, for which elderly patients are at increased risk. Methods: We conducted a 1-year prospective cohort study, in which a third of patients admitted to two geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory...
January 11, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29338842/real-time-nanopore-based-recognition-of-protein-translocation-success
#14
David P Hoogerheide, Philip A Gurnev, Tatiana K Rostovtseva, Sergey M Bezrukov
A growing number of new technologies are supported by a single- or multi-nanopore architecture for capture, sensing, and delivery of polymeric biomolecules. Nanopore-based single-molecule DNA sequencing is the premier example. This method relies on the uniform linear charge density of DNA, so that each DNA strand is overwhelmingly likely to pass through the nanopore and across the separating membrane. For disordered peptides, folded proteins, or block copolymers with heterogeneous charge densities, by contrast, translocation is not assured, and additional strategies to monitor the progress of the polymer molecule through a nanopore are required...
January 12, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29337540/enhanced-degradation-of-pesticide-dichlorophen-by-laccase-immobilized-on-nanoporous-materials-a-cytotoxic-and-molecular-simulation-investigation
#15
Abraham Vidal, Patricia Concepción García-Suárez, Evarista Arellano-García, Oscar Edel Contreras, Sergio Aguila
Use of pesticides is usually related to over-production of crops in order to overcome worldwide demand of food and alimentary safety. Nevertheless, pesticides are environmental persistent molecules, such as the organochlorine pesticides, which are often found in undesired places. In this work, we show that a hybrid nanomaterial (laccase - MSU-F) readily oxidizes the pesticide dichlorophen, reducing its acute genotoxicity and apoptotic effects. In order to predict chronic alterations related to endocrine disruption, we compared the calculated affinity of dichlorophen oxidized sub-products to steroid hormone nuclear receptors (NRs), using molecular simulation methods...
January 16, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29336439/tailoring-a-nanostructured-plasmonic-absorber-for-high-efficiency-surface-assisted-laser-desorption-ionization
#16
Jing-Jing Zhu, Xiao Meng, Chi Zhang, Jie Bian, Zhenda Lu, Ying Liu, Weihua Zhang
The surface-assisted laser desorption/ionization (SALDI) effect is investigated on Au plated anodized aluminum oxide (Au/AAO) thin films, a new type of low-cost broadband plasmonic absorber, which has attracted a lot of attention recently. Mass spectrometry (MS) measurements show that the ionization efficiency of Au/AAO substrates can be significantly improved (×30 fold) by simply tuning the size of nanopores in Au/AAOs. This leads to a signal-to-noise ratio of 394, which is 4 times better than the result obtained using the conventional matrix-assisted laser desorption/ionization (MALDI)-MS technique...
January 16, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29336352/one-pot-synthesis-of-ptpd-dendritic-nano-cube-cage-superstructure-on-graphenes-as-advanced-catalysts-for-oxygen-reduction
#17
Yuanyuan Zheng, Junhua Qiao, Junhua Yuan, Jianfeng Shen, Ai-Jun Wang, Peijun Gong
How to use of Pt economically and efficiently in the oxygen reduction reaction (ORR) is of theoretical and practical significance for the industrialization of the proton-exchange membrane fuel cells (PEMFCs). In order to minimize Pt consumption and optimize the ORR performance, the ORR catalysts are recommended to be designed as a porous nanostructure. Herein, we report one-pot solvothermal strategy to prepare PtPd dendritic nanocube cages via a galvanic replacement mechanism triggered by I- ion. These PtPd alloy crystals are nanoporous, and uniformly dispersed on the reduced graphene oxides (RGOs)...
January 16, 2018: Nanotechnology
https://www.readbyqxmd.com/read/29335185/one-step-electrochemical-route-to-the-fabrication-of-highly-ordered-array-of-cylindrical-nano-porous-structure-and-its-electrocatalytic-performance-toward-efficient-hydrogen-evolution
#18
H Ashassi-Sorkhabi, S Abolghasemi-Fakhri, B Rezaei Moghadam, H Javan
An efficient and non-precious metal catalyst is a key factor for hydrogen evolution reaction (HER). Here we report that the fabrication of highly ordered porous arrays of Cu-Zn-Ni alloy has been carried out in a one-step electrochemical route at a constant apparent current density of -3 A·cm-2. The optimum film composition and reactivity of the electrodes for catalytic hydrogen evolution reaction were analyzed by using different current densities, deposition time and bath concentration. For this purpose, onset potentials in linear sweep voltammograms (LSV) were compared...
January 8, 2018: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/29334379/highly-parallel-direct-rna-sequencing-on-an-array-of-nanopores
#19
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland, Michael Jordan, Jonah Ciccone, Sabrina Serra, Jemma Keenan, Samuel Martin, Luke McNeill, E Jayne Wallace, Lakmal Jayasinghe, Chris Wright, Javier Blasco, Stephen Young, Denise Brocklebank, Sissel Juul, James Clarke, Andrew J Heron, Daniel J Turner
Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29331138/role-of-non-equilibrium-conformations-on-driven-polymer-translocation
#20
H H Katkar, M Muthukumar
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations...
January 14, 2018: Journal of Chemical Physics
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