NEIL1 excises 3′ end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1

Base excision repair is the major pathway for the repair of oxidative DNA damage in human cells that is initiated by a damage-specific DNA glycosylase. In human cells, the major DNA glycosylases for the excision of oxidative base damage are OGG1 and NTH1 that excise 8-oxoguanine and oxidative pyrimidines, respectively. We find that both enzymes have limited activity on DNA lesions located in the vicinity of the 3′ end of a DNA single-strand break, suggesting that other enzymes are involved in the processing of such lesions. In this study, we identify and characterize NEIL1 as a major DNA glycosylase that excises oxidative base damage located in close proximity to the 3′ end of a DNA single-strand break

Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L.

One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulation of development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologues of DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied. Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1), which contains all main structural domains required for catalytic activity. Using homologous modeling, we have constructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix– hairpin–helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA, and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand. The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower efficiency, showing minimal activity in the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted in a global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein and other homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the status of epigenetic methylation and to control gene activity

Supergroup approach to the Hubbard model

Based on the revealed hidden supergroup structure, we develop a new approach to the Hubbard model. We reveal a relation of even Hubbard operators to the spinor representation of the generators of the rotation group of four-dimensional spaces. We propose a procedure for constructing a matrix representation of translation generators, yielding a curved space on which dynamic superfields are defined. We construct a new deformed nonlinear superalgebra for the regime of spinless Hubbard model fermions in the case of large on-site repulsion and evaluate the effective functional for spinless fermions.Comment: 17 pages, Theoretical and Mathematical Physics, V.166, n.2, p.209-222,201

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei–DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 Å resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 Å) and Nei-R252A (2.05 Å). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a ∼50° rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme

Cohomology Groups of Deformations of Line Bundles on Complex Tori

The cohomology groups of line bundles over complex tori (or abelian varieties) are classically studied invariants of these spaces. In this article, we compute the cohomology groups of line bundles over various holomorphic, non-commutative deformations of complex tori. Our analysis interpolates between two extreme cases. The first case is a calculation of the space of (cohomological) theta functions for line bundles over constant, commutative deformations. The second case is a calculation of the cohomologies of non-commutative deformations of degree-zero line bundles.Comment: 24 pages, exposition improved, typos fixe

Absence of lattice strain anomalies at the electronic topological transition in zinc at high pressure

High pressure structural distortions of the hexagonal close packed (hcp) element zinc have been a subject of controversy. Earlier experimental results and theory showed a large anomaly in lattice strain with compression in zinc at about 10 GPa which was explained theoretically by a change in Fermi surface topology. Later hydrostatic experiments showed no such anomaly, resulting in a discrepancy between theory and experiment. We have computed the compression and lattice strain of hcp zinc over a wide range of compressions using the linearized augmented plane wave (LAPW) method paying special attention to k-point convergence. We find that the behavior of the lattice strain is strongly dependent on k-point sampling, and with large k-point sets the previously computed anomaly in lattice parameters under compression disappears, in agreement with recent experiments.Comment: 9 pages, 6 figures, Phys. Rev. B (in press

Relativistic theory of inverse beta-decay of polarized neutron in strong magnetic field

The relativistic theory of the inverse beta-decay of polarized neutron, $\nu _{e} + n \to p + e ^{-}$, in strong magnetic field is developed. For the proton wave function we use the exact solution of the Dirac equation in the magnetic filed that enables us to account exactly for effects of the proton momentum quantization in the magnetic field and also for the proton recoil motion. The effect of nucleons anomalous magnetic moments in strong magnetic fields is also discussed. We examine the cross section for different energies and directions of propagation of the initial neutrino accounting for neutrons polarization. It is shown that in the super-strong magnetic field the totally polarized neutron matter is transparent for neutrinos propagating antiparallel to the direction of polarization. The developed relativistic approach can be used for calculations of cross sections of the other URCA processes in strong magnetic fields.Comment: 41 pages in LaTex including 11 figures in PostScript, discussion on nucleons AMM interaction with magnetic field is adde

Quasi Harmonic Lattice Dynamics and Molecular Dynamics calculations for the Lennard-Jones solids

We present Molecular Dynamics (MD), Quasi Harmonic Lattice Dynamics (QHLD) and Energy Minimization (EM) calculations for the crystal structure of Ne, Ar, Kr and Xe as a function of pressure and temperature. New Lennard-Jones (LJ) parameters are obtained for Ne, Kr and Xe to reproduce the experimental pressure dependence of the density. We employ a simple method which combines results of QHLD and MD calculations to achieve densities in good agreement with experiment from 0 K to melting. Melting is discussed in connection with intrinsic instability of the solid as given by the QHLD approximation. (See http://www.fci.unibo.it/~valle for related papers)Comment: 7 pages, 5 figures, REVte

The Atmospheric Chemistry Suite (ACS) of Three Spectrometers for the ExoMars 2016 Trace Gas Orbiter

The Atmospheric Chemistry Suite (ACS) package is an element of the Russian contribution to the ESA-Roscosmos ExoMars 2016 Trace Gas Orbiter (TGO) mission. ACS consists of three separate infrared spectrometers, sharing common mechanical, electrical, and thermal interfaces. This ensemble of spectrometers has been designed and developed in response to the Trace Gas Orbiter mission objectives that specifically address the requirement of high sensitivity instruments to enable the unambiguous detection of trace gases of potential geophysical or biological interest. For this reason, ACS embarks a set of instruments achieving simultaneously very high accuracy (ppt level), very high resolving power (>10,000) and large spectral coverage (0.7 to 17 μm—the visible to thermal infrared range). The near-infrared (NIR) channel is a versatile spectrometer covering the 0.7–1.6 μm spectral range with a resolving power of ∼20,000. NIR employs the combination of an echelle grating with an AOTF (Acousto-Optical Tunable Filter) as diffraction order selector. This channel will be mainly operated in solar occultation and nadir, and can also perform limb observations. The scientific goals of NIR are the measurements of water vapor, aerosols, and dayside or night side airglows. The mid-infrared (MIR) channel is a cross-dispersion echelle instrument dedicated to solar occultation measurements in the 2.2–4.4 μm range. MIR achieves a resolving power of >50,000. It has been designed to accomplish the most sensitive measurements ever of the trace gases present in the Martian atmosphere. The thermal-infrared channel (TIRVIM) is a 2-inch double pendulum Fourier-transform spectrometer encompassing the spectral range of 1.7–17 μm with apodized resolution varying from 0.2 to 1.3 cm−1. TIRVIM is primarily dedicated to profiling temperature from the surface up to ∼60 km and to monitor aerosol abundance in nadir. TIRVIM also has a limb and solar occultation capability. The technical concept of the instrument, its accommodation on the spacecraft, the optical designs as well as some of the calibrations, and the expected performances for its three channels are described

Properties of the barium strontium titanate film on the silicon substrate

The reported study was supported of the Russian Foundation for Basic Research, research project No. 18-42-160005. The work is partially performed according to the Russian Government Program of Competitive Growth of Kazan Federal University. A.S. Elshin thanks the Russian Foundation for Basic Research for financial support, project No. 17-32-50047