Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)—5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)—by the TET/JBP family of dioxygenases prompted intensive studies of their functional roles in mammalian cells. However, the functional interplay of these less abundant modified nucleotides in other eukaryotic lineages remains poorly understood. We carried out a systematic study of the content and distribution of oxi-mCs in the DNA and RNA of the basidiomycetes Laccaria bicolor and Coprinopsis cinerea, which are established models to study DNA methylation and developmental and symbiotic processes. Quantitative liquid chromatography–tandem mass spectrometry revealed persistent but uneven occurrences of 5hmC, 5fC and 5caC in the DNA and RNA of the two organisms, which could be upregulated by vitamin C. 5caC in RNA (5carC) was predominantly found in non-ribosomal RNA, which potentially includes non-coding, messenger and small RNA species. Genome-wide mapping of 5hmC and 5fC using the single CG analysis techniques hmTOP-seq and foTOP-seq pointed at involvement of oxi-mCs in the regulation of gene expression and silencing of transposable elements. The implicated diverse roles of 5mC and oxi-mCs in the two fungi highlight the epigenetic importance of the latter modifications, which are often neglected in standard whole-genome bisulfite analyses.     

Revisiting santa rosalia to unfold a degeneracy of classic models of speciation

Abstract Many classic models of speciation incorporate assortative mating based on mating groups, such as plants with different flowering times, and they investigate whether an ecological trait under disruptive natural selection becomes genetically associated with the selectively neutral mating trait. It is well known that this genetic association is potently destroyed by recombination. In this note, we point out a more fundamental difficulty: if a "knife-edge" symmetry assumption of previous models is violated, then the mating trait is no longer neutral and sexual selection eliminates the polymorphism in the mating locus. This result strengthens the growing consensus that magic traits are the more likely route to nonallopatric speciation. We expand the model assuming also ecological selection on the mating trait and investigate the conditions for natural selection to overcome sexual selection and maintain mating polymorphism; we find that the combination of natural and sexual selection can cause also bistability of allele frequencies.     

Acute toxicity and quality of life in high risk prostate cancer patients: Updated results of randomized hypofractionation trial

Purpose

The aim of our study was to perform the final analysis of acute toxicity and quality of life data obtained from 221 consecutive patients who suffered from intermediate-to-high risk prostate cancer.

The Hydronium Tetrafluoroborate Dimer in Nonpolar Media and its Proton NMR Spectrum

Hydronium tetrafluoroborate ion pairs, H₃O⁺·BF₄ ^- have been shown computationally to be unstable toward decomposition, in the absence of solvation or electrostatic interactions existing in crystals. As the proton NMR spectrum of a hydronium salt with the octanesulfonate-antimony pentachloride complex anion was reported in freon solution, we investigated the hypothesis that larger ionic clusters were present in the nonpolar solvent. It was found that the dimer (H₃O⁺·BF₄ ^-)₂ was stable at the MP2/6-31G* level. GIAO-B3LYP chemical shift calculations with the same basis set and also with the 6-31G**, 6-31++G**, 6-311++G**, dzvp, tzp, tz2p, and qz2p basis sets conducted on the hydronium fluoroborate dimer reproduce the main features of the experimental spectrum: the existence of two signals with a two-to-one intensity ratio and the more intense resonance at higher frequency (more deshielded). The alternative structures, of hydronium tetrafluoroborate ion pairs with one and with two hydrogen bonds between anion and cation, give calculated chemical shifts which are farther from the experimental values.     

Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights

Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pK_a calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA.     

Cossidae of the socotra archipelago (yemen)

The faunistic composition of the family Cossidae (Lepidoptera) of the Socotra Archipelago is revised. Five species are recognized, including two new species (Mormogystia brandstetteri and Meharia hackeri), and dubious identifications and records are discussed. Adults and genitalia are illustrated and bionomic details, DNA barcodes and a synonymic checklist for Socotran cossids are provided. A review of their distribution reveals that at least 80 percent of Socotra's cossids are unique to the archipelago, which is renowned for its endemism. A checklist listing all the species from generas Meharia, Mormogystia, Aethalopteryx, Azygophleps, as well as the synonymy and distribution is provided.     

Review of the Eospilarctia yuennanica group (Lepidoptera, Erebidae, Arctiinae) from the Indo - Himalayan region, with description of two new species and one subspecies

Twonew Eospilarctia species and one new subspecies from China, Myanmar and Vietnam, respectively, are described. Superficially the new species Eospilarctia maciaisp. n., Eospilarctia naumannisp. n. and Eospilarctia yuennanica fansipanassp. n. resemble related congeners but they can be distinguished by the differences in wing pattern, genitalia and distribution provided. Eospilarctia yuennanica guangdonga Dubatolov, Kishida & Wang, 2008 is upgraded to species level. A checklist of the genus Eospilarctia and a key to the Eospilarctia yuennanica (Daniel, 1943) species-group, based on external characters and male genitalia, is presented.     

Cuttlebone as a Marine-Derived Material for Preparing Bone Grafts

The use of synthetic materials for biomedical applications still presents issues owing to the potential for unfavourable safety characteristics. Currently, there is increasing interest in using natural, marine-derived raw materials for bone tissue engineering. In our study, the endoskeleton of the mollusc Sepia, i.e. cuttlebone (CB), was used with regenerated cellulose (RC) to prepare three-dimensional composite bone grafts. CB microparticles were mechanically immobilised within a cellulose gel, resulting in a macroporous structure upon lyophilisation. The interconnected porous structure of the regenerated cellulose/cuttlebone (RC/CB) composite was evaluated by micro-computed tomography. The porosity of the composite was 80%, and the pore size predominantly ranged from 200 to 500 μm. The addition of CB microparticles increased the specific scaffold surface by almost threefold and was found to be approximately 40 mm^?1. The modulus of elasticity and compressive strength of the RC/CB composite were 4.0?±?0.6 and 22.0?±?0.9 MPa, respectively. The biocompatibility of the prepared RC/CB composite with rat hepatocytes and extensor digitorum longus muscle tissue was evaluated. The obtained data demonstrated that both the composite and cellulose matrix samples were non-cytotoxic and had no damaging effects. These results indicate that this RC/CB composite is a novel material suitable for bone tissue-engineering applications.     

External electric control of the proton pumping in bacteriorhodopsin

Comparative analysis of the photoelectric response of dried films of purple membranes (PM) depending on their degree of orientation is presented. Time dependence of the photo-induced protein electric response signal (PERS) of oriented and non-oriented films to a single laser pulse in the presence of the external electric field (EEF) was experimentally determined. The signal does not appear in the non-oriented films when the EEF is absent, whereas the PERS of the oriented PM films demonstrates the variable polarity on the microsecond time scale. In the presence of the EEF the PERS of the non-oriented film rises exponentially preserving the same polarization. The polarization of the PERS changes by changing the polarity of the EEF with no influence on the time constant of the PERS kinetics. The EEF effect on the PERS of the oriented films is more complicated. By subtracting the PERS when EEF ≠ 0 from the PERS when EEF = 0 the resulting signal is comparable to that of the non-oriented films. Generalizing the experimental data we conclude that the EEF influence is of the same origin for the films of any orientation. To explain the experimental results the two-state model is suggested. It assumes that the EEF directionally changes the pK_a values of the Schiff base (SB) and of the proton acceptor aspartic acid D85 in bacteriorhodopsin. Because of that the SB→D85 proton transfer might be blocked and consequently the L→M intermediate transition should vanish. Thus, on the characteristic time scale τ _{L → M} ≈ 30 μs; both intermediates, the M intermediate, appearing under normal conditions, and the L intermediate as persisting under the blocked conditions when D85 is protonated, should coexist in the film. The total PERS is a result of the potentials corresponding to the electrogenic products of intermediates L and M that are of the opposite polarity. It is concluded that the ratio of bacteriorhodopsin concentrations corresponding to the L and M intermediates is driven by the EEF and, consequently, it should define the PERS of the non-oriented films. According to this model the orientation degree of the film could be evaluated by describing the PERS.