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Femtosecond transient absorption measurements powered by 40 fs laser pulses reveal that ultrafast isomerization takes place upon S1 excitation of both CH2I2 and CHBr3 in the gas phase. The photochemical conversion process is direct and intramolecular, i.e., it proceeds without caging media that have long been implicated in the photo-induced isomerization of polyhalogenated alkanes in condensed phases. Using multistate complete active space second order perturbation theory (MS-CASPT2) calculations, we investigate the structure of the photochemical reaction paths connecting the photoexcited species to their corresponding isomeric forms. Unconstrained minimum energy paths computed starting from the S1 Franck–Condon points lead to S1/S0 conical intersections, which directly connect the parent CHBr3 and CH2I2 molecules to their isomeric forms. Changes in the chemical bonding picture along the S1/S0 isomerization reaction path are described using multireference average coupled pair functional (MRACPF) calculations in conjunction with natural resonance theory (NRT) analysis. These calculations reveal a complex interplay between covalent, radical, ylidic, and ion-pair dominant resonance structures throughout the nonadiabatic photochemical isomerization processes described in this work. [ABSTRACT FROM AUTHOR]

Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5′ ends of housekeeping genes. As a rule, interbands display preferential “head-to-head” orientation of genes. They are enriched for “broad” class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5′-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called “grey” bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date. [ABSTRACT FROM AUTHOR]

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed. [ABSTRACT FROM AUTHOR]

Lygus (Insecta: Heteroptera: Miridae) is a Holarctic genus, and some of its representatives are important pests. Determining the Lygus species identity and their interrelationships is challenging. Our study aimed to delimit five trans-Palearctic species of this group: L. gemellatus, L. pratensis, L. punctatus, L. rugulipennis and L. wagneri. We implemented analyses of morphological characters, morphometrics, cytochrome c oxidase subunit I (COI) and 16S rRNA sequences. The results showed that those species could be delimited using morphology and most species pairs were different in morphometrics. Both COI and 16S rRNA were useful for species identification. Resulting phylogenetic trees contained two highly supported clades. One clade included species known from the Palearctic only, the other clade contained species with Nearctic and Holarctic distribution. Species were mostly poorly supported or non-monophyletic. Molecular species delineation approaches yielded results that generally did not correspond to the morphologically delimited species. [ABSTRACT FROM AUTHOR]

Postoperative Tibial chronic osteomyelitis is one of the most challenging orthopaedic conditions especially when extensive, the anatomy of subcutaneous anteromedial part of the tibia with less soft tissue coverage complicates the situation. The extent of infected tibial part varies in size and duration from one patient to another. We report our experience using Bifocal and Monofocal bone transport techniques with regard to clinical outcome, recurrence of infection and re-fracture rate. This is a retrospective observational review of 49 patients with postoperative Tibial chronic osteomyelitis which were treated using either Bifocal distraction compression BFDCO technique group I (31 patients) or Monofocal compression osteosynthesis MFCO technique Group II (18 patients). The average age of the patients was (41.6 ± 13.1 years), (range: 17–67 years). Leg length discrepancy was measured in 33 (58.9%) patients with an average of (1.4 ± 1.7 cm). Contracture of the ankle joint and equinus deformity were detected in 36 (64.3%) patients. Pre and Post-operative radiography together with Modified Irzhansky A.A et al. leg functional assessment system were used to assess the functional outcome. The time spent in the Ilizarov fixator (External Fixation Index) in the first group was (142 ± 72 days) and in the second group was (75 ± 54 days). The infection recurred in 2 patients (6%) in group I and in 5 patients (28%) in group II. Lack of consolidation or re-fracture within 6 months after the dismantling of the apparatus was detected in 6 patients (19.5%) in group I and in 5 patients (27.8%) in group II. Lack of consolidation or re-fracture within 6 months after dismantling of the apparatus in group I was detected in 6 patients (19.5%) in group I and in 5 patients (27.8%) in Group II. The average functional state score (AFSS) in the first group was (12.45 ± 2.41) on admission and increased to (16.16 ± 2.99) on the final follow-up which corresponded to a "good" result. In the second group II the AFSS was (12.11 ± 2.22) on admission and increased to (15.06 ± 2.88) at the final follow-up which corresponded to a "satisfactory" result. Treatment of Tibial chronic osteomyelitis using either Bifocal or Monofocal bone transport is an effective method. However our results have demonstrated better functional outcome and less infection recurrence and re-fracture rates when using the Bifocal distraction compression technique (BFDCO). [ABSTRACT FROM AUTHOR]

R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation by cleaving the RNA strand within a hybrid RNA–DNA duplex. In this study, the kinetic features of the interaction of RH1 from Escherichia coli with R-loops of various structures were investigated. It was found that the values of the dissociation constants Kd were minimal for complexes of RH1 with model R-loops containing a 10–11-nt RNA–DNA hybrid part, indicating effective binding. Analysis of the kinetics of RNA degradation in the R-loops by RH1 revealed that the rate-limiting step of the process was catalytic-complex formation. In the presence of RNA polymerase, the R-loops containing a ≤16-nt RNA–DNA hybrid part were efficiently protected from cleavage by RH1. In contrast, R-loops containing longer RNA–DNA hybrid parts, as a model of an abnormal transcription process, were not protected by RNA polymerase and were effectively digested by RH1. [ABSTRACT FROM AUTHOR]

This paper presents the results of computational analysis of unsteady natural convection of a non-Newtonian fluid in an enclosure, taking into account the time sinusoidal dependence of the wall temperature. The analysis has been carried out to reveal the dependence of the emerging streamlines, isotherms, average Nusselt number and flow intensity on the controlling parameters such as Rayleigh number (Ra = 104–106), power-law index (n = 0.6–1.4), and side wall temperature oscillation frequency (f = 0.01π–0.05π). The problem has been worked out by the finite difference technique including the successive under-relaxation procedure, the locally one-dimensional Samarskii scheme, and the Thomas algorithm. The results show that a pseudoplastic fluid with high Rayleigh numbers and high oscillation frequencies is more suitable for intensifying the convective heat and mass transfer. • Unsteady natural convection of a non-Newtonian fluid in an enclosure under the time sinusoidal wall temperature is studied. • The effects of Rayleigh number, power-law index, and side wall temperature oscillation frequency are examined. • A growth of the oscillation frequency shortens the oscillation period and enhances the convective flow in the cavity. • A pseudoplastic fluid with high Rayleigh numbers and high oscillation frequencies is more suitable for heat transfer. [ABSTRACT FROM AUTHOR]

Oligonucleotide conjugates with boron clusters have found applications in different fields of molecular biology, biotechnology, and biomedicine as potential agents for boron neutron capture therapy, siRNA components, and antisense agents. Particularly, the closo-dodecaborate anion represents a high-boron-containing residue with remarkable chemical stability and low toxicity, and is suitable for the engineering of different constructs for biomedicine and molecular biology. In the present work, we synthesized novel oligonucleotide conjugates of closo-dodecaborate attached to the 5′-, 3′-, or both terminal positions of DNA, RNA, 2′-O-Me RNA, and 2′-F-Py RNA oligomers. For their synthesis, we employed click reaction with the azido derivative of closo-dodecaborate. The key physicochemical characteristics of the conjugates have been investigated using high-performance liquid chromatography, gel electrophoresis, UV thermal melting, and circular dichroism spectroscopy. Incorporation of closo-dodecaborate residues at the 3′-end of all oligomers stabilized their complementary complexes, whereas analogous 5′-modification decreased duplex stability. Two boron clusters attached to the opposite ends of the oligomer only slightly influence the stability of complementary complexes of RNA oligonucleotide and its 2′-O-methyl and 2′-fluoro analogs. On the contrary, the same modification of DNA oligonucleotides significantly destabilized the DNA/DNA duplex but gave a strong stabilization of the duplex with an RNA target. According to circular dichroism spectroscopy results, two terminal closo-dodecaborate residues cause a prominent structural rearrangement of complementary complexes with a substantial shift from the B-form to the A-form of the double helix. The revealed changes of key characteristics of oligonucleotides caused by incorporation of terminal boron clusters, such as the increase of hydrophobicity, change of duplex stability, and prominent structural changes for DNA conjugates, should be taken into account for the development of antisense oligonucleotides, siRNAs, or aptamers bearing boron clusters. These features may also be used for engineering of developing NA constructs with pre-defined properties. [ABSTRACT FROM AUTHOR]

Antiarrhythmic effects of melatonin have been demonstrated ex vivo and in rodent models, but its action in a clinically relevant large mammalian model remains largely unknown. Objectives of the present study were to evaluate electrophysiological and antiarrhythmic effects of melatonin in a porcine model of acute myocardial infarction. Myocardial ischemia was induced by 40-min coronary occlusion in 25 anesthetized pigs. After ischemia onset, 12 animals received melatonin (4 mg/kg). 48 intramyocardial electrograms were recorded from left ventricular wall and interventricular septum (IVS). In each lead, activation time (AT) and repolarization time (RT) were determined. During ischemia, ATs and dispersion of repolarization (DOR = RTmax − RTmin) increased reaching maximal values by 3–5 and 20–25 min, respectively. Ventricular fibrillation (VF) incidence demonstrated no relations to redox state markers and was associated with increased DOR and delayed ATs (specifically, in an IVS base, an area adjacent to the ischemic zone) (p = 0.031). Melatonin prevented AT increase in the IVS base, (p < 0.001) precluding development of early VF (1–5 min, p = 0.016). VF occurrence in the delayed phase (17–40 min) where DOR was maximal was not modified by melatonin. Thus, melatonin-related enhancement of activation prevented development of early VF in the myocardial infarction model. [ABSTRACT FROM AUTHOR]

The newly characterized compounds complement the series of analogous uranyl complexes which allows one to elaborate on the dependence of the ratio between the sizes of carboxylate ligands and countercations on the resulting crystal system, as well as to assume the crystal system of compounds which have not yet been studied. Voronoi–Dirichlet polyhedra were used to estimate the sizes of ligands and countercations, as well as for the overall crystal chemical analysis. [Display omitted] Syntheses, IR spectroscopic and X-ray diffraction studies of new uranyl iodoacetate complexes with divalent metals were carried out: R [UO 2 (CH 2 ICOO) 3 ] 2 ·6H 2 O (R = Mg2+ (I), Mn2+ (II), Ni2+ (III)). It was established that isostructural I–III crystallize in the cubic crystal system and contain octahedral aqua complexes [ R (H 2 O) 6 ]2+, which connect hexagonal-bipyramidal complexes [UO 2 (CH 2 ICOO) 3 ]– into a three-dimensional framework by hydrogen bonds. Using molecular Voronoi–Dirichlet polyhedra, it was found that bifurcate halogen bonds O⋅⋅⋅I−C are also involved in the interconnection of anionic complexes. On the example of two series of stoichiometrically similar compounds dependence of the ratio of sizes of carboxylate ligands and counter cations on crystal system was observed and crystal systems for the compounds that have not yet been structurally characterized were assumed. [ABSTRACT FROM AUTHOR]

The choice of biomarkers for establishment of exposure to organophosphorus compounds (OPs) is made based on the results of assessment of the real situation with account for such factors as the required timeframe for providing the results of expert examination, nature and volume of biosamples, available equipment, and the degree of confidence of information on the influencing factor (substance, dose, way of entry, use of antidote). We estimated the efficiency of express methods of diagnosis of exposure to OPs, specifically, Ellman's cholinesterase activity assay, as well as GC-MS/MS and HPLC/MS/MS determination of OPs fluoride-regenerated from protein adducts and low-molecular hydrolytic metabolites of OPs, respectively. The objects of study were blood and urine samples of rats exposed to VR in a dose of 2×0.4LD50 under conditions of antidotal therapy with Carboxim {5-[[[2-[benzyl(diemthyl)ammonio]ethyl]amino]carbonyl]-2-[(hydroxyimino)methyl]-1-methylpyridinium dichloride}. Carboxim therapy led to AChE reactivation 3 h after exposure to VR, while in the absence of the therapy the AChE activity recovered within 3 days. Fluoride regeneration of VR from its blood plasma protein adducts was possible within 7 days after poisoning irrespective of whether the therapy was applied or not. O-isobutyl methylphosphonate was detected in urine 24 h after exposure in the urine samples of animals both subjected and not subjected to antidotal therapy, whereas after 3 days it was detected exclusively in the urine samples of animals not given the antidote. It was also found that blood plasma levels of free and esterified fatty acids can serve as an additional toxicodynamic parameter of VR poisoning. [ABSTRACT FROM AUTHOR]

The title compound, [Ni(BMTT)2], where BMTT is 1,3-bis(2- methyltetrazol-5-yl)triazenide (C4H6N11), presents a molecular complex with tridentate ligands. The tridentate mode of the ligand is realised through the central N atom of the triazene group and two N atoms of the two tetrazole rings. The [Ni(BMTT)2] molecule is the meridional isomer, with crystallographic &4macr; symmetry in space group P42/n. The nickel centre has a distorted octahedral environment, with two axial Ni—N bonds of 2.041 (2) Å and four equatorial Ni—N bonds of 2.0739 (14) Å. The molecules are linked together by van der Waals interactions only. [ABSTRACT FROM AUTHOR]

Apurinic/apyrimidinic endonuclease 1 (APE1) is one of the most important enzymes in base excision repair. Studies on this enzyme have been conducted for a long time, but some aspects of its activity remain poorly understood. One such question concerns the mechanism of damaged-nucleotide recognition by the enzyme, and the answer could shed light on substrate specificity control in all enzymes of this class. In the present study, by pulsed electron–electron double resonance (DEER, also known as PELDOR) spectroscopy and pre–steady-state kinetic analysis along with wild-type (WT) APE1 from Danio rerio (zAPE1) or three mutants (carrying substitution N253G, A254G, or E260A), we aimed to elucidate the molecular events in the process of damage recognition. The data revealed that the zAPE1 mutant E260A has much higher activity toward DNA substrates containing 5,6-dihydro-2′-deoxyuridine (DHU), 2′-deoxyuridine (dU), alpha-2′-deoxyadenosine (αA), or 1,N6-ethenoadenosine (εA). Examination of conformational changes in DNA clearly revealed multistep DNA rearrangements during the formation of the catalytic complex. These structural rearrangements of DNA are directly associated with the capacity of damaged DNA for enzyme-induced bending and unwinding, which are required for eversion of the damaged nucleotide from the DNA duplex and for its placement into the active site of the enzyme. Taken together, the results experimentally prove the factors that control substrate specificity of the AP endonuclease zAPE1. [ABSTRACT FROM AUTHOR]