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

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

4 pages, 3 figuresPeer reviewe

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

peer reviewe

Automated Tethered Profiler for Hydrophysical and Bio-Optical Measurements in the Black Sea Carbon Observational Site

Special Issue Technological Oceanography.-- 17 pages, 13 figurese.g., daily thermocline, variation in solar irradiance, thermohaline convection, and intermittent mixing. These processes should be regularly observed with sufficient time resolution at fixed geographical locations. This study provides a brief overview of the carbon observational site in the Northeastern Black Sea. The focus is on the design of a new tethered profiler Winchi for the inner continental shelf part of the site. The profiler hull and two outriggers comprise an open trimaran platform that is positively buoyant and tends to maintain a horizontal position in the water. The lower end of the winch wire is secured to the bottom anchor. By unwinding/winding the wire, the profiler ascends/descends while measuring the depth profiles of marine environment parameters ranging from the seafloor to air–sea interface. After surfacing, the profiler determines its location using the Global Positioning System (GPS) and transmits data to (and from) a server on land through the Global System for Mobile Communications (GSM). Initial field tests with the Winchi profiler at the Northeastern Black Sea shelf exhibited promising results. We report these early tests to demonstrate the use of WinchiThe research and development of the new tethered profiler Winchi was carried out within the framework of the assignment of the Ministry of Science and Higher Education of Russia No 0128-2021-0018 and supported in part by the Russian Fund for Basic Research via grant No 19-05-00459With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe