Search Results
Automated and rapid identification of multidrug resistant Escherichia coli against the lead drugs of acylureidopenicillins, cephalosporins, and fluoroquinolones using specific Raman marker bands
A Raman-based, strain-independent, semi-automated method is presented that allows the rapid (<3 hours) determination of antibiotic susceptibility of bacterial pathogens isolated from clinical samples. Applying a priori knowledge about the mode of action of the respective antibiotic, we identified characteristic Raman marker bands in the spectrum and calculated batch-wise weighted sum scores from standardized Raman intensity differences between spectra of antibiotic exposed and nonexposed samples of the same strains. The lead substances for three relevant antibiotic classes (fluoroquinolone ciprofloxacin, third-generation cephalosporin cefotaxime, ureidopenicillin piperacillin) against multidrug-resistant Gram-negative bacteria (MRGN) revealed a high sensitivity and specificity for the susceptibility testing of two Escherichia coli laboratory strains and 12 clinical isolates. The method benefits from the parallel incubation of control and treated samples, which reduces the variance due to alterations in cultivation conditions and the standardization of differences between batches leading to long-term comparability of Raman measurements. © 2020 The Authors. Journal of Biophotonics published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Electrochemical growth mechanism of nanoporous platinum layers
Porous platinum is a frequently used catalyst material in electrosynthesis and a robust broadband absorber in thermoelectrics. Pore size distribution and localization determine its properties by a large extent. However, the pore formation mechanism during the growth of the material remains unclear. In this work we elucidate the mechanism underlying electrochemical growth of nanoporous platinum layers and its control by ionic concentration and current density during electrolysis. The electrode kinetics and reduction steps of PtCl4 on platinum electrodes are investigated by cyclic voltammetry and impedance measurements. Cyclic voltammograms show three reduction steps: two steps relate to the platinum cation reduction, and one step relates to the hydrogen reduction. Hydrogen is not involved in the reduction of PtCl4, however it enables the formation of nanopores in the layers. These findings contribute to the understanding of electrochemical growth of nanoporous platinum layers in isopropanol with thickness of 100 nm to 500 nm.
Correlations between the structure and superconducting properties of MT-YBaCuO
Comprehensive experimental results of fully oxidized (up to YBa2Cu3O6,9-7) melt-Textured YBaCuO materials with different microstructures are presented. These microstructures are built respectively: (1) with a high dislocations density but almost without twins (after high temperature treatment at 2 GPa) and (2) with a high twin density, but practically free from dislocations and stacking faults (after high temperature oxygenation at 10-16 MPa). It is shown that for attaining high critical current densities and fields of irreversibility (jc(H-c, 0 T)=9•104 A/cm2, H irr=9.7 T at 77 K), a high twin density in YBa2Cu3O6.9-7 matrix of MT-YBCO is required. The density of twins in fully oxidized materials depends on the distances between Y2BaCuO5 inclusions, larger twin densities are related to shorter distances between inclusions. The influence of phase composition of the initial powder mixtures on the distances between Y2BaCuO5 inclusions have been characterized and discussed. © Published under licence by IOP Publishing Ltd.
Disturbing-free determination of yeast concentration in DI water and in glucose using impedance biochips
Deionized water and glucose without yeast and with yeast (Saccharomyces cerevisiae) of optical density OD600 that ranges from 4 to 16 has been put in the ring electrode region of six different types of impedance biochips and impedance has been measured in dependence on the added volume (20, 21, 22, 23, 24, 25 µL). The measured impedance of two out of the six types of biochips is strongly sensitive to the addition of both liquid without yeast and liquid with yeast and modelled impedance reveals a linear relationship between the impedance model parameters and yeast concentration. The presented biochips allow for continuous impedance measurements without interrupting the cultivation of the yeast. A multiparameter fit of the impedance model parameters allows for determining the concentration of yeast (cy) in the range from cy = 3.3 × 107 to cy = 17 × 107 cells/mL. This work shows that independent on the liquid, i.e., DI water or glucose, the impedance model parameters of the two most sensitive types of biochips with liquid without yeast and with liquid with yeast are clearly distinguishable for the two most sensitive types of biochips.
Numerical and Experimental Demonstration of Intermodal Dispersive Wave Generation
Evidence of intermodal dispersive wave generation mediated by intermodal cross-phase modulation (iXPM) between different transverse modes during supercontinuum generation in silicon nitride waveguides is presented. The formation of a higher-order soliton in one strong transverse mode leads to phase modulation of a second, weak transverse mode by iXPM. The phase modulation enables not only supercontinuum generation but also dispersive wave generation within the weak mode, that otherwise has insufficient power to facilitate dispersive wave formation. The nonlinear frequency conversion scheme presented here suggests phase-matching conditions beyond what is currently known, which can be exploited for extending the spectral bandwidth within supercontinuum generation.
Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80
A PVL-positive, methicillin-susceptible Staphylococcus aureus was cultured from pus from cervical lymphadenitis of a patient of East-African origin. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence of etD and edinB. The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain´s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from other S. aureus lineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended from walJ to sirB. It comprised ORF-CM14 and the ACME-III element. A homologous but larger fragment was also found in an atypical S. aureus CC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other deviating region comprised the region from htsB to ecfA2, i.e., another 3% of the genome. It was very similar to CC1 sequences. Either this suggests an incorporation of CC1 DNA into the study strain, or alternatively a recombination event affecting “canonical” CC80. Thus, the study strain bears witness of several recombination events affecting supposedly core genomic genes. Although the exact mechanism is not yet clear, such chimerism seems to be an additional pathway in the evolution of S. aureus. This could facilitate also a transmission of virulence and resistance factors and therefore offer an additional evolutionary advantage.
Background Reduction in STED-FCS Using a Bivortex Phase Mask
Fluorescence correlation spectroscopy (FCS) is a valuable tool to study the molecular dynamics in living cells. When used together with a super-resolution stimulated emission depletion (STED) microscope, STED-FCS can measure diffusion processes on the nanoscale in living cells. In two-dimensional (2D) systems like the cellular plasma membrane, a ring-shaped depletion focus is most commonly used to increase the lateral resolution, leading to more than 25-fold decrease in the observation volume, reaching the relevant scale of supramolecular arrangements. However, STED-FCS faces severe limitations when measuring diffusion in three dimensions (3D), largely due to the spurious background contributions from undepleted areas of the excitation focus that reduce the signal quality and ultimately limit the resolution. In this paper, we investigate how different STED confinement modes can mitigate this issue. By simulations as well as experiments with fluorescent probes in solution and in cells, we demonstrate that the coherent-hybrid (CH) depletion pattern created by a bivortex phase mask reduces background most efficiently and thus provides superior signal quality under comparable reduction of the observation volume. Featuring also the highest robustness to common optical aberrations, CH-STED can be considered the method of choice for reliable STED-FCS-based investigations of 3D diffusion on the subdiffraction scale. Copyright © 2020 American Chemical Society.
Genotyping of methicillin resistant Staphylococcus aureus from the United Arab Emirates
Reports from Arabian Gulf countries have demonstrated emergence of novel methicillin resistant Staphylococcus aureus (MRSA) strains. To address the lack of data from the United Arab Emirates (UAE), genetic characterisation of MRSA identified between December 2017 and August 2019 was conducted using DNA microarray-based assays. The 625 MRSA isolates studied were grouped into 23 clonal complexes (CCs) and assigned to 103 strains. CC5, CC6, CC22 and CC30 represented 54.2% (n/N = 339/625) of isolates with other common CCs being CC1, CC8, CC772, CC361, CC80, CC88. Emergence of CC398 MRSA, CC5-MRSA-IV Sri Lanka Clone and ST5/ST225-MRSA-II, Rhine-Hesse EMRSA/New York-Japan Clone in our setting was detected. Variants of pandemic CC8-MRSA-[IVa + ACME I] (PVL+) USA300 were detected and majority of CC772 strains were CC772-MRSA-V (PVL+), “Bengal- Bay Clone”. Novel MRSA strains identified include CC5-MRSA-V (edinA+), CC5-MRSA-[VT + fusC], CC5-MRSA-IVa (tst1+), CC5-MRSA-[V/VT + cas + fusC + ccrA/B-1], CC8-MRSA-V/VT, CC22-MRSA-[IV + fusC + ccrAA/(C)], CC45-MRSA-[IV + fusC + tir], CC80-MRSA-IVa, CC121-MRSA-V/VT, CC152-MRSA-[V + fusC] (PVL+). Although several strains harboured SCC-borne fusidic acid resistance (fusC) (n = 181), erythromycin/clindamycin resistance (ermC) (n = 132) and gentamicin resistance (aacA-aphD) (n = 179) genes, none harboured vancomycin resistance genes while mupirocin resistance gene mupR (n = 2) and cfr gene (n = 1) were rare. An extensive MRSA repertoire including CCs previously unreported in the region and novel strains which probably arose locally suggest an evolving MRSA landscape. © 2020, The Author(s).
Charged domains in ferroelectric, polycrystalline yttrium manganite thin films resolved with scanning electron microscopy
We have investigated ferroelectric charged domains in polycrystalline hexagonal yttrium manganite thin films (Y1Mn1O3, Y0.95Mn1.05O3, Y1Mn0.99Ti0.01O3, and Y0.94Mn1.05Ti0.01O3) by scanning electron microscopy (SEM) in secondary electron emission mode with a small acceleration voltage. Using SEM at an acceleration voltage of 1.0 kV otherwise homogenous surface charging effects are reduced, polarization charges can be observed and polarization directions (±Pz) of the ferroelectric domains in the polycrystalline thin films can be identified. Thin films of different chemical composition have been deposited by pulsed laser deposition on Pt/SiO2/Si structures under otherwise same growth conditions. Using SEM it has been shown that different charged domain density networks are existing in polycrystalline yttrium manganite thin films. © 2020 IOP Publishing Ltd.
What the Phage: a scalable workflow for the identification and analysis of phage sequences
Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).