Search results for "Nanopore"

Positron annihilation characterization of free volume in microand macro-modified Cu0.4Co0.4Ni0.4Mn1.8O4ceramics

2016

Free volume and pore size distribution size in functional micro and macro-micro-modified Cu0.4Co0.4Ni0.4Mn1.8O4 ceramics are characterized by positron annihilation lifetime spectroscopy in comparison with Hg-porosimetry and scanning electron microscopy technique. Positron annihilation results are interpreted in terms of model implication positron trapping and ortho-positronium decaying. It is shown that free volume of positron traps are the same type for macro and micro modified Cu0.4Co0.4Ni0.4Mn1.8O4 ceramics. Classic Tao-Eldrup model in spherical approximation is used to calculation of the size of nanopores smaller than 2 nm using the ortho-positronium lifetime.

Positron Annihilation Lifetime Spectroscopy Insight on Free Volume Conversion of Nanostructured MgAl2O4 Ceramics

2021

H.K. and A.I.P. are grateful for the support from the COST Action CA17126. H.K. was also supported by the Ministry of Education and Science of Ukraine (project for young researchers No. 0119U100435). In addition, I.K. and H.K. were also supported by the National Research Foundation of Ukraine via project 2020.02/0217, while the research of A.I.P. was funded by the Latvian research council via the Latvian National Research Program under the topic ?High-Energy Physics and Accelerator Technologies?, Agreement No: VPP-IZM-CERN-2020/1-0002. In addition, the research of A.I.P. has been supported by the Latvian-Ukrainian Grant LV-UA/2021/5. The Institute of Solid State Physics, University of Latvi…

Negative differential resistance and threshold-switching in conical nanopores with KF solutions

2021

Negative differential resistance (NDR) phenomena are under-explored in nanostructures operating in the liquid state. We characterize experimentally the NDR and threshold switching phenomena observed when conical nanopores are immersed in two identical KF solutions at low concentration. Sharp current drops in the nA range are obtained for applied voltages exceeding thresholds close to 1 V and a wide frequency window, which suggests that the threshold switching can be used to amplify small electrical perturbations because a small change in voltage typically results in a large change in current. While we have not given a detailed physical mechanism here, a phenomenological model is also includ…

Repair of a Bacterial Small β-Barrel Toxin Pore Depends on Channel Width

2017

ABSTRACT Membrane repair emerges as an innate defense protecting target cells against bacterial pore-forming toxins. Here, we report the first paradigm of Ca2+-dependent repair following attack by a small β-pore-forming toxin, namely, plasmid-encoded phobalysin of Photobacterium damselae subsp. damselae. In striking contrast, Vibrio cholerae cytolysin, the closest ortholog of phobalysin, subverted repair. Mutational analysis uncovered a role of channel width in toxicity and repair. Thus, the replacement of serine at phobalysin´s presumed channel narrow point with the bulkier tryptophan, the corresponding residue in Vibrio cholerae cytolysin (W318), modulated Ca2+ influx, lysosomal exocytosi…

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

2017

Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results f…

HPG pore: an efficient and scalable framework for nanopore sequencing data.

2016

The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable. Here we present HPG Pore, a toolkit for …

2016

We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …

High-throughput sequencing (HTS) for the analysis of viral populations

2020

The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely appli…

Chromosome-scale assembly of the yellow mealworm genome

2022

Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% an…

Label-Free Pyrophosphate Recognition with Functionalized Asymmetric Nanopores

2016

[EN] The label¿free detection of pyrophosphate (PPi) anions with a nanofluidic sensing device based on asymmetric nanopores is demonstrated. The pore surface is functionalized with zinc complexes based on two di(2¿picolyl)amine [bis(DPA)] moieties using carbodiimide coupling chemistry. The complexation of zinc (Zn2+) ion is achieved by exposing the modified pore to a solution of zinc chloride to form bis(Zn2+¿DPA) complexes. The chemical functionalization is demonstrated by recording the changes in the observed current¿voltage (I¿V) curves before and after pore modification. The bis(Zn2+¿DPA) complexes on the pore walls serve as recognition sites for pyrophosphate anion. The experimental re…