Atomic and electronic structure of graphene oxide/Cu interface

The results of X-ray photoemission (XPS) and valence bands spectroscopy, optically stimulated electron emission (OSEE) measurements and density functional theory based modeling of graphene oxide (GO) placed on Cu via an electrophoretic deposition (EPD) are reported. The comparison of XPS spectra of EPD prepared GO/Cu composites with those of as prepared GO, strongly reduced GO, pure and oxidized copper demonstrate the partial (until C/O ratio about two) removal of oxygen-containing functional groups from GO simultaneously with the formation of copper oxide-like layers over the metallic substrate. OSEE measurements evidence the presence of copper oxide phase in the systems simultaneously with the absence of contributions from GO with corresponding energy gap. All measurements demonstrate the similarity of the results for different thickness of GO cover of the copper surface. Theoretical modeling demonstrates favorability of migration of oxygen-containing functional groups from GO to the copper substrate only for the case of C/O ratio below two and formation of Cu-O-C bonds between substrate and GO simultaneously with the vanishing of the energy gap in GO layer. Basing on results of experimental measurements and theoretical calculations we suggest the model of atomic structure for Cu/GO interface as Cu/CuO/GO with C/O ratio in gapless GO about two.Comment: 22 pages, 14 figures, accepted to Thin Solid Films journa

7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli

14 pags., 9 figs.This work investigated the structural and biological properties of DNA containing 7,8-dihydro-8-oxo-1,N6-ethenoadenine (oxo-ϵA), a non-natural synthetic base that combines structural features of two naturally occurring DNA lesions (7,8-dihydro-8-oxoadenine and 1,N6-ethenoadenine). UV-, CD-, NMR spectroscopies and molecular modeling of DNA duplexes revealed that oxo-ϵA adopts the non-canonical syn conformation (χ = 65º) and fits very well among surrounding residues without inducing major distortions in local helical architecture. The adduct remarkably mimics the natural base thymine. When considered as an adenine-derived DNA lesion, oxo-ϵA was >99% mutagenic in living cells, causing predominantly A→T transversion mutations in Escherichia coli. The adduct in a single-stranded vector was not repaired by base excision repair enzymes (MutM and MutY glycosylases) or the AlkB dioxygenase and did not detectably affect the efficacy of DNA replication in vivo. When the biological and structural data are viewed together, it is likely that the nearly exclusive syn conformation and thymine mimicry of oxo-ϵA defines the selectivity of base pairing in vitro and in vivo, resulting in lesion pairing with A during replication. The base pairing properties of oxo-ϵA, its strong fluorescence and its invisibility to enzymatic repair systems in vivo are features that are sought in novel DNA-based probes and modulators of gene expression.MIT Skoltech Next Generation Program Pilot Grant (to J.M.E.); National Institutes of Health (NIH) [R01-CA080024 to J.M.E.]; NIEHS Center Grant [P30-ES002109 (to Center for Environmental Health Sciences, which provided access to NGS facilities)]; Skoltech (to T.S.Z.); MICINN [PID2020-116620GB-I00 to C.G.]; Ministry of Science and Higher Education Russian Federation [07515-2021-1049 to A.V.A. – synthesis and UV/CD studies]. Funding for open access charge: Skoltech.Peer reviewe

A MSFD complementary approach for the assessment of pressures, knowledge and data gaps in Southern European Seas : the PERSEUS experience

PERSEUS project aims to identify the most relevant pressures exerted on the ecosystems of the Southern European Seas (SES), highlighting knowledge and data gaps that endanger the achievement of SES Good Environmental Status (GES) as mandated by the Marine Strategy Framework Directive (MSFD). A complementary approach has been adopted, by a meta-analysis of existing literature on pressure/impact/knowledge gaps summarized in tables related to the MSFD descriptors, discriminating open waters from coastal areas. A comparative assessment of the Initial Assessments (IAs) for five SES countries has been also independently performed. The comparison between meta-analysis results and IAs shows similarities for coastal areas only. Major knowledge gaps have been detected for the biodiversity, marine food web, marine litter and underwater noise descriptors. The meta-analysis also allowed the identification of additional research themes targeting research topics that are requested to the achievement of GES. 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license.peer-reviewe

Laboratory Study of Turbulent Mass Exchange in a Stratified Fluid

In this study, a laboratory experiment was conducted to investigate quantitatively turbulent exchange between two quasi-homogeneous layers of equal thickness and different density (salinity), as well as the fine structure of the density transition zone (interface) between the layers. The fluid was continuously stirred by a system of horizontally oscillating vertical rods, piercing through both layers and producing vertically homogeneous turbulent impact in a two-layered fluid. In every experimental run, the stirring process was carried out continuously from certain initial state up to the complete mixing of the layers. The buoyancy flux between the layers was estimated using the data on time changes of the salinity in both upper and lower layers. The fine structure of density interface was measured by vertically profiling conductivity microprobe. The results were presented in a dimensionless form and analyzed depending on two dimensionless parameters as follows: the Richardson number, Ri, and Reynolds number, Re. It was found that if Ri>Ri∗Re where Ri∗ is the critical Richardson number, the interface exists in “sharpening” mode and in “eroding” (diffusive) mode if RiRi∗Re. The maximum mixing efficiency was achieved at critical Richardson number, when the density interface was in a transition state between the sharpening and diffusive modes

Glycosylation of Receptor Binding Domain of SARS-CoV-2 S-Protein Influences on Binding to Immobilized DNA Aptamers

Nucleic acid aptamers specific to S-protein and its receptor binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus 2) virions are of high interest as potential inhibitors of viral infection and recognizing elements in biosensors. Development of specific therapy and biosensors is complicated by an emergence of new viral strains bearing amino acid substitutions and probable differences in glycosylation sites. Here, we studied affinity of a set of aptamers to two Wuhan-type RBD of S-protein expressed in Chinese hamster ovary cell line and Pichia pastoris that differ in glycosylation patterns. The expression system for the RBD protein has significant effects, both on values of dissociation constants and relative efficacy of the aptamer binding. We propose glycosylation of the RBD as the main force for observed differences. Moreover, affinity of a several aptamers was affected by a site of biotinylation. Thus, the robustness of modified aptamers toward new virus variants should be carefully tested

Anticyclonic eddies in the deep eastern Black Sea in summer-autumn 1999 (satellite and ship-borne observations

peer reviewe

Frontal currents in the rotating fluid over sloping bottom: influence of canyons

4 pages, 3 figuresPeer reviewe

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (<i>R</i>)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(−)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475–510 nm; Stokes shifts 125–160 nm or 7520–8960 cm^–1) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold