Differential Inhibition of APOBEC3 DNA-Mutator Isozymes by Fluoro- and Non-Fluoro-Substituted 2′-Deoxyzebularine Embedded in Single-Stranded DNA

The APOBEC3 (APOBEC3A-H) enzyme family is part of the human innate immune system that restricts pathogens by scrambling pathogenic single-stranded (ss) DNA by deamination of cytosines to produce uracil residues. However, APOBEC3-mediated mutagenesis of viral and cancer DNA promotes its evolution, thus enabling disease progression and the development of drug resistance. Therefore, APOBEC3 inhibition offers a new strategy to complement existing antiviral and anticancer therapies by making such therapies effective for longer periods of time, thereby preventing the emergence of drug resistance. Here, we have synthesised 2′-deoxynucleoside forms of several known inhibitors of cytidine deaminase (CDA), incorporated them into oligodeoxynucleotides (oligos) in place of 2′-deoxycytidine in the preferred substrates of APOBEC3A, APOBEC3B, and APOBEC3G, and evaluated their inhibitory potential against these enzymes. An oligo containing a 5-fluoro-2′-deoxyzebularine (5FdZ) motif exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable 2′-deoxyzebularine-containing (dZ-containing) oligo. A similar inhibition trend was observed for wild-type APOBEC3A. In contrast, use of the 5FdZ motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ-containing oligo both in the case of APOBEC3G_CTD and in that of full-length wild-type APOBEC3G.     

Preparation of Duplex Sequencing Libraries for Archival Paraffin-Embedded Tissue Samples Using Single-Strand-Specific Nuclease P1

DNA from formalin-fixed paraffin-embedded (FFPE) tissues, which are frequently utilized in cancer research, is significantly affected by chemical degradation. It was suggested that approaches that are based on duplex sequencing can significantly improve the accuracy of mutation detection in FFPE-derived DNA. However, the original duplex sequencing method cannot be utilized for the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, as FFPE DNA contains an excessive number of damaged bases, and these lesions are converted to false double-strand nucleotide substitutions during polymerase-driven DNA end repair process. To resolve this drawback, we replaced DNA polymerase by a single strand-specific nuclease P1. Nuclease P1 was shown to efficiently remove RNA from DNA preparations, to fragment the FFPE-derived DNA and to remove 5′/3′-overhangs. To assess the performance of duplex sequencing-based methods in FFPE-derived DNA, we constructed the Bottleneck Sequencing System (BotSeqS) libraries from five colorectal carcinomas (CRCs) using either DNA polymerase or nuclease P1. As expected, the number of identified mutations was approximately an order of magnitude higher in libraries prepared with DNA polymerase vs. nuclease P1 (626 ± 167/Mb vs. 75 ± 37/Mb, paired t-test p-value 0.003). Furthermore, the use of nuclease P1 but not polymerase-driven DNA end repair allowed a reliable discrimination between CRC tumors with and without hypermutator phenotypes. The utility of newly developed modification was validated in the collection of 17 CRCs and 5 adjacent normal tissues. Nuclease P1 can be recommended for the use in duplex sequencing library preparation from FFPE-derived DNA.     

A new approach for the synthesis of monodisperse zirconia powders with controlled particle size

In this work, the synthesis of hydrous zirconia by controlled double-jet precipitation (CDJP) was carried out in the pH range from 3 to 8. The evolution of particle shape and size during precipitation was investigated. It was found that at pH 3, 7, and 8 during the precipitation process there is no significant change in particle size, the suspension was gel-like, particles actively aggregated during drying. A gradual increase in particle size and a decrease in particle size dispersion specific for layer-by-layer aggregation was observed during CDJP at pH 4 to 6. The resulting particles do not aggregate and retain a rounded globular shape with a narrow size distribution during drying. Samples obtained at a pH above 6 are characterized after drying by a high specific surface area and porosity, as well as a reduced content of NO₃^- ions. The effect of pH precipitation on the phase composition and crystallite size of calcined samples was discussed.     

Die Gasdurchlässigkeit von Vakuummaterialien

This work presents investigations on the gas permeability of materials for use in unmanned space vehicles. The measurement system for determining the gas permeation coefficients of composite materials is designed on the basis of a helium leak detector. Due to permeation through the Vi-ton sealing the smallest flow that can be correctly measured by the system is 10⁻¹⁰ Pa · m³/s. The system was assessed with a PTFE polymer sample with a known helium permeability value. Furthermore, the gas perme-abilities of three composite materials were studied. The steady-state helium permeation coefficient in [Pa · m³/s] · [m/(m² · bar)] for high molecular weight polyethylene (HM-WPE) with 100 nm copper coating is 3.1 · 10⁻⁸, for high density polyethy lene (HDPE 209-07) with 100 nm copper coating it is 1.9 · 10⁻⁷; for vacuum-tight ceramics VK94-1 with glue K400 layer it is 2.2 · 10⁻⁹. Authors will be glad to measure the gas permeability of new materials that can be provided by readers of this publication.     

Effect of temperature and load on three-body abrasion of cermets and steel

The effect of temperature and load on three-body abrasion resistance has been examined for stainless steel, Cr₃C₂-Ni cermet, plain WC-Co hardmetal and yttria stabilized zirconia doped WC-based composites. Series of tests at various tribo-conditions were performed on a recently developed device. Coefficient of friction and materials response to abrasive actions have been analyzed and positive effect of zirconia addition on materials wear resistance has been shown. The low wear rates of ZrO₂ containing cermets are due to lower susceptibility of zirconia to transgranular crack propagation, smaller mean free path between ceramic grains and formation of lubricating glazed silica-rich layer.     

Laser-induced damage of hafnia coatings as a function of pulse duration in the femtosecond to nanosecond range

Laser-damage thresholds and morphologies of hafnia single layers exposed under femtosecond, picosecond, and nanosecond single pulses (1030/1064 nm) are reported. The samples were made with different deposition parameters in order to study how the damage behavior of the samples evolves with the pulse duration and how it is linked to the deposition process. In the femtosecond to picosecond regime, the scaling law of the laser-induced damage threshold as a function of pulse duration is in good agreement with the models of photo and avalanche ionization based on the rate equation for free electron generation. However, differences in the damage morphologies between samples are shown. No correlation between the nanosecond and femtosecond/picosecond laser-damage resistance of hafnia coatings could be established. We also report evidence of the transition in damage mechanisms for hafnia, from an ablation process linked to intrinsic properties of the material to a defect-induced process, that exists between a few picoseconds and a few tens of picoseconds.     

Hydroprocessing of Aromatics Using Sulfide Catalysts Supported on Ordered Mesoporous Phenol–Formaldehyde Polymers

Ni–W sulfide catalysts for the hydroprocessing of aromatic hydrocarbons were synthesized by the in situ decomposition of tetrabutylammonium nickel thiotungstate complex supported on ordered mesoporous phenol–formaldehyde polymer. Catalysts obtained with and without additional sulfidation with dimethyl disulfide were characterized by X-ray photoelectron spectroscopy and transmission electron microscopy. The catalytic activity has been studied using naphthalene, 1-methylnaphthalene, 2-methylnaphthalene, and anthracene as examples. It is shown that the system used in this study proved to be active in hydrogenation and hydrocracking of polyaromatic hydrocarbons.