Mg²⁺ Enhances the Formation of 2′,3′-cGMP, an Intermediate of RNA Cleavage by Binase

© 2016, Springer Science+Business Media New York.Binase, the ribonuclease secreted by Bacillus pumilus, is an endonuclease that cleaves the phosphodiester bond between the 3′-guanyl residue and 5′-OH residue of an adjacent nucleotide, with the formation of a corresponding intermediate, 2′,3′-cGMP on the first stage of a catalytic reaction. Binase possesses selective antitumor effect and induces apoptosis of lung carcinoma A549 cells. It was shown that the 2′,3′-cGMP messenger could exist in the reaction mixture over an hour. Furthermore, the addition of divalent non-transition metal Mg2+ increases the level of 2′,3′-cGMP formed by binase and that could be associated with the stabilization of RNA tertiary structure by this metal. It has been shown that exogenous 2′,3′-cGMP does not induce apoptosis of A549 cells, which are sensitive to binase. However, taking into account the cell-penetrating ability of binase, it can be concluded that 2′,3′-cGMP contributes to apoptogenic binase action only when it is formed intracellularly

Effect of nitrogen ion irradiation parameters on properties of nitrogen-containing carbon coatings prepared by pulsed vacuum arc deposition method

Studies of the effect of nitrogen ion irradiation on the structure and properties of nitrogenated amorphous carbon coatings prepared on polished sitall and silicon substrates by the pulsed vacuum arc deposition method are presented. The techniques used in the investigations were electron energy loss spectroscopy, Raman spectroscopy, and atomic force microscop

Palindromic Decompositions with Gaps and Errors

Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient algorithms for the factorization of sequences into palindromes and maximal palindromes have been devised in recent years. We extend these studies by allowing gaps in decompositions and errors in palindromes, and also imposing a lower bound to the length of acceptable palindromes. We first present an algorithm for obtaining a palindromic decomposition of a string of length n with the minimal total gap length in time O(n log n * g) and space O(n g), where g is the number of allowed gaps in the decomposition. We then consider a decomposition of the string in maximal \delta-palindromes (i.e. palindromes with \delta errors under the edit or Hamming distance) and g allowed gaps. We present an algorithm to obtain such a decomposition with the minimal total gap length in time O(n (g + \delta)) and space O(n g).Comment: accepted to CSR 201

Influence of formation conditions, subsequent annealing and ion irradiation on the properties of nanostructured coatings based on amorphous carbon with gold, silver and nitrogen additives

Nanostructured coatings based on amorphous carbon and carbon-doped with gold, silver, and nitrogen were obtained by the pulsed vacuum-arc method. Carbon coatings have been annealed in a vacuum as well as treated with argon ion

Identification of 2′,3′-cGMP as an intermediate of RNA catalytic cleavage by binase and evaluation of its biological action

© 2015 Pleiades Publishing, Ltd. Binase, the RNAse from Bacillus pumilus, is an endonuclease that cleaves the phosphodiester bond between the 3′-guanyl residue and 5′-OH residue of an adjacent nucleotide, with the formation of a corresponding intermediate, 2′,3′-cGMP. Subsequent hydrolysis of 2′,3′-cGMP into a 3′-phosphate is highly specific and proceeds slowly. Thus, a question arises in respect to the time interval that this positional isomer exists during catalytic cleavage of RNA by binase, and whether it may contribute to antitumor activity of the enzyme. In this study, we found, by implementing an enzyme-linked immunosorbent assay, that during catalytic cleavage of RNA by binase, 2′,3′-cGMP is maintained in the reaction mixture for about one hour. Activation of phosphodiesterases did not lead to a complete elimination of 2′,3′-cGMP. The highest amount of 2′,3′-cGMP was detected at pH 8.5, underat which conditions, it reached nanomolar levels. The Iinitial RNA concentration in the reactions was in the range of 100-1000 μg/mL. We found that exogenous 2′,3′-cGMP, as well as its positional isomer, 3′,5′-cGMP, do not induce apoptosis of human lung adenocarcinoma A549 cells, which are sensitive to binase apoptogenic activity. Taking into consideration the data on binase internalization, and on the role of 2′,3′-cGMP in the activation of opening of mitochondrial pores, we propose that 2′,3′-cyclic guanosine phosphates contributes to apoptotic processes, induced by binase, only when generated intracellularly

Polarization Dependence of Anomalous X-ray Scattering in Orbital Ordered Manganites

In order to determine types of the orbital ordering in manganites, we study theoretically the polarization dependence of the anomalous X-ray scattering which is caused by the anisotropy of the scattering factor. The general formulae of the scattering intensity in the experimental optical system is derived and the atomic scattering factor is calculated in the microscopic electronic model. By using the results, the X-ray scattering intensity in several types of the orbital ordering is numerically calculated as a function of azimuthal and analyzer angles.Comment: 9 pages, 7 figure

Resonant X-ray Scattering in Manganites - Study of Orbital Degree of Freedom -

Orbital degree of freedom of electrons and its interplay with spin, charge and lattice degrees of freedom are one of the central issues in colossal magnetoresistive manganites. The orbital degree of freedom has until recently remained hidden, since it does not couple directly to most of experimental probes. Development of synchrotron light sources has changed the situation; by the resonant x-ray scattering (RXS) technique the orbital ordering has successfully been observed . In this article, we review progress in the recent studies of RXS in manganites. We start with a detailed review of the RXS experiments applied to the orbital ordered manganites and other correlated electron systems. We derive the scattering cross section of RXS where the tensor character of the atomic scattering factor (ASF) with respect to the x-ray polarization is stressed. Microscopic mechanisms of the anisotropic tensor character of ASF is introduced and numerical results of ASF and the scattering intensity are presented. The azimuthal angle scan is a unique experimental method to identify RXS from the orbital degree of freedom. A theory of the azimuthal angle and polarization dependence of the RXS intensity is presented. The theoretical results show good agreement with the experiments in manganites. Apart from the microscopic description of ASF, a theoretical framework of RXS to relate directly to the 3d orbital is presented. The scattering cross section is represented by the correlation function of the pseudo-spin operator for the orbital degree of freedom. A theory is extended to the resonant inelastic x-ray scattering and methods to observe excitations of the orbital degree of freedom are proposed.Comment: 47 pages, 24 figures, submitted to Rep. Prog. Phy

Volume formula for a Z2\mathbb{Z}_2-symmetric spherical tetrahedron through its edge lengths

The present paper considers volume formulae, as well as trigonometric identities, that hold for a tetrahedron in 3-dimensional spherical space of constant sectional curvature +1. The tetrahedron possesses a certain symmetry: namely rotation through angle $\pi$ in the middle points of a certain pair of its skew edges.Comment: 27 pages, 2 figures; enhanced and improved exposition, typos corrected; Arkiv foer Matematik, 201

Ribonucleolytic activity of mycoplasmas

Mycoplasmas are incapable of de novo synthesis of nucleotides and must therefore secrete nucleases in order to replenish the pool of nucleic acid precursors. The nucleolytic activity of mycoplasmas is an important factor in their pathogenicity. Bacterial ribonucleases (RNases) may produce a broad spectrum of biological effects, including antiviral and antitumor activity. Mycoplasma RNases are therefore of interest. In the present work, the capacity of Acholeplasma laidlawii and Mycoplasma hominis for RNase synthesis and secretion was studied. During the stationary growth phase, these organisms were found to synthesize Mg2+-dependent RNases, with their highest activity detected outside the cells. Localization of A. laidlawii RNases was determined: almost 90% of the RNase activity was found to be associated with the membrane vesicles. Bioinformational analysis revealed homology between the nucleotide sequences of 14 Bacillus subtilis genes encoding the products with RNase activity and the genes of the mycoplasmas under study. Amino acid sequences of 4 A. laidlawii proteins with ribonuclease activity and the Bsn RNase were also established. © 2014 Pleiades Publishing, Ltd

Patterns of calcium oxalate monohydrate crystallization in complex biological systems

The paper presents the features of calcium oxalate crystallization in the presence of additives revealed through experimental modeling. The patterns of phase formation are shown for the Ca{2+} – C[2]O[4]{ 2–} – H[2]O and Ca{2+} – C[2]O[4]{2–} – PO[4]{3–} – H[2]O systems with the components and pH of the saline varying over a wide concentrations range. The effect of additives on crystallization of calcium oxalate monohydrate was investigated. It was found that the ionic strength and magnesium ions are inhibitors, and calcium oxalate and hydroxyapatite crystals are catalysts of calcium oxalate monohydrate crystallization. The basic calcium phosphate (apatite) was found to be most thermodynamically stable, which indicates its special role in kidney stone formation since it is found in virtually all stones