Analysis of difference spectra of protonated DNA: determination of degree of protonation of nitrogen bases and the fractions of disordered nucleotide pairs.

The titration curves of nitrogen bases and fractions of disordered nucleotide pairs are obtained during DNA protonation. It is shown that purine bases are the first sites of the DNA double helix protonation. The cytosine protonation is due to proton-induced conformational transition within GC pairs with the sequence proton transfer from (N-7) of guanine to (N-3) of cytosine. Within DNA with unwound regions the bases are protonated in the following order: cytosine, adenine, guanine. It is shown that GC pairs are the primary centres in which the unwinding of protonated DNAs occurs.     

Aculeate Hymenoptera (Hymenoptera,Aculeata) Inhabiting Trap Nests in Crimea

Entomological Review - Trap nests for aculeate Hymenoptera were exposed during 15 years (2002–2016) in 80 localities of Crimea. A total of more than 500 trap nests containing about 25 000...     

CHILD: a new tool for detecting low-abundance insertions and deletions in standard sequence traces

Several methods have been proposed for detecting insertion/deletions (indels) from chromatograms generated by Sanger sequencing. However, most such methods are unsuitable when the mutated and normal variants occur at unequal ratios, such as is expected to be the case in cancer, with organellar DNA or with alternatively spliced RNAs. In addition, the current methods do not provide robust estimates of the statistical confidence of their results, and the sensitivity of this approach has not been rigorously evaluated. Here, we present CHILD, a tool specifically designed for indel detection in mixtures where one variant is rare. CHILD makes use of standard sequence alignment statistics to evaluate the significance of the results. The sensitivity of CHILD was tested by sequencing controlled mixtures of deleted and undeleted plasmids at various ratios. Our results indicate that CHILD can identify deleted molecules present as just 5% of the mixture. Notably, the results were plasmid/primer-specific; for some primers and/or plasmids, the deleted molecule was only detected when it comprised 10% or more of the mixture. The false positive rate was estimated to be lower than 0.4%. CHILD was implemented as a user-oriented web site, providing a sensitive and experimentally validated method for the detection of rare indel-carrying molecules in common Sanger sequence reads.     

Dynamics of the cAMP and cGMP content of the heart in transient coronary insufficiency in rats

Experiments made on 127 white random-bred male rats weighing 200 +/- 10 g with transitory coronary insufficiency (TCI) with varying duration of myocardial ischemia (MI) have revealed consistent changes in the heart cAMP and cGMP. During MI, there was a biphasic variation in the concentration of cyclic nucleotides: an initial appreciable increase in the concentration was replaced by its lowering. At the same time the time course of cGMP content was more mobile in nature as compared to cAMP Reperfusion made at an early period (within the first 40 min) did not normally bring about the normalization of heart content of cyclic nucleotides whose concentration time course depended on the duration of the preceding MI. The pattern of changes in the concentration of cyclic nucleotides in the heart in TCI correlated to a significant degree with the previously described time course of the activity of the sympath- and cholinergic mechanisms by which heart work, contractile function and rhythm are controlled during TCI.     

The anticancer activity of 3- and 10-bromofascaplysins is mediated by caspase-8, -9, -3-dependent apoptosis

3- and 10-Bromofascaplysins was previously found to possess cytotoxic activity. In this study, we investigated their cancer preventive and proapoptotic properties. These effects were tested on mouse skin epidermal JB6 P⁺ Cl41 cell line, its stable transfectants, and human tumor HL-60, THP-1, SNU-C4, SK-MEL-28, DLD-1, MDA-MB-231, and HeLa cells using a variety of assessments, including a cell viability (MTS) assay, flow cytometry, anchorage-independent soft agar assay, luciferase assay, mitochondrial permeability assay, and Western blotting. 3- and 10-Bromofascaplysins were effective at submicromolar concentrations as the anticancer agents, which exerted their action, at least in part, through the induction of caspase-8, -9, -3-dependent apoptosis.     

MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences

The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming.     

Study of the glow dynamics in a laser-produced plasma jet expanding across the magnetic field

Results are presented from experimental studies of the glow dynamics of a plasma jet generated during the irradiation of a plane aluminum target by an iodine laser pulse with the wavelength 1.315 μm. The laser pulse energy was 330–480 J, the pulse duration was 0.5 ns, and the focal spot diameter was 3 mm, the laser intensity on the target surface being ∼10¹³ W/cm². The jet expanded across an external magnetic field with the strength ∼1 kOe. The residual air pressure in the vacuum chamber was ∼10⁻⁵ Torr. The spatiotemporal behavior of the jet glow was investigated using a nine-frame camera in two mutually perpendicular directions (along and across the magnetic field). The results of measurements indicate azimuthal asymmetry of the jet expansion.     

Evolution and disease converge in the mitochondrion

Mitochondrial DNA (mtDNA) mutations are long known to cause diseases but also underlie tremendous population divergence in humans. It was assumed that the two types of mutations differ in one major trait: functionality. However, evidence from disease association studies, cell culture and animal models support the functionality of common mtDNA genetic variants, leading to the hypothesis that disease-causing mutations and mtDNA genetic variants share considerable common features. Here we provide evidence showing that the two types of mutations obey the rules of evolution, including random genetic drift and natural selection. This similarity does not only converge at the principle level; rather, disease-causing mutations could recapitulate the ancestral DNA sequence state. Thus, the very same mutations could either mark ancient evolutionary changes or cause disease.     

Measurements of plasma temperature in indirect drive targets from the shock wave velocity in aluminum in the Iskra-5 facility

Results are presented from the development of a method for measuring plasma temperature in indirect (X-ray) drive targets by recording the shock wave velocity in the Iskra-5 facility. The samples under investigation were irradiated by X-rays in a converter box, and the shock wave velocity was determined from the time at which the wave reached the back surface of the sample and the surface began to emit visible radiation. This emission, in turn, was detected by a streak camera. The results of experiments on the interaction of X radiation with a hot dense plasma, as well as the accompanying gas-dynamic processes in aluminum samples, are analyzed both theoretically and numerically. In experiments with Al and Pb samples, the shock wave velocity was measured to vary in the range U = 8–35 km/s, and the range of variation of the temperature of the box walls was measured to be T _e = 140–170 eV.