Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes

Biased usage of amino acids near exon-intron boundaries is phylogenetically widespread and characteristic of species for which there are expected to be problems defining exons

The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast

Coding sequence evolution was once thought to be the result of selection on optimal protein function alone. Selection can, however, also act at the RNA level, for example, to facilitate rapid translation or ensure correct splicing. Here, we ask whether the way DNA works also imposes constraints on coding sequence evolution. We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. Controlling for gene expression and intra-gene location, we find a nucleosome-free “linker” sequence to evolve on average 5–6% slower at synonymous sites. A reduced rate of evolution in linker is especially evident at the 5′ end of genes, where the effect extends to non-synonymous substitution rates. This is consistent with regular nucleosome architecture in this region being important in the context of gene expression control. As predicted, codons likely to generate a sequence unfavourable to nucleosome formation are enriched in linker sequence. Amino acid content is likewise skewed as a function of nucleosome occupancy. We conclude that selection operating on DNA to maintain correct positioning of nucleosomes impacts codon choice, amino acid choice, and synonymous and non-synonymous rates of evolution in coding sequence. The results support the exclusion model for nucleosome positioning and provide an alternative interpretation for runs of rare codons. As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread

Рекомендации по ограничению динамических перенапряжений в обмотке ротора асинхронизированного турбогенератора

In this paper, a Volume-of-Fluid (VOF)-based approach for the Direct Numerical Simulation (DNS) of reactive mass transfer in gas–liquid flows is described. At the interface, local thermodynamic equilibrium is assumed and modelled by Henry's law. First numerical simulation results are presented for non-reactive and reactive mass transfer from rising gas bubbles to a surrounding liquid. For the evaluation of reactive mass transfer simulations with a consecutive, competitive reaction system in the liquid, a local selectivity is employed

Dynamo generated field emergence through recurrent plasmoid ejections

Magnetic buoyancy is believed to drive the transport of magnetic flux tubes from the convection zone to the surface of the Sun. The magnetic fields form twisted loop-like structures in the solar atmosphere. In this paper we use helical forcing to produce a large-scale dynamo-generated magnetic field, which rises even without magnetic buoyancy. A two layer system is used as computational domain where the upper part represents the solar atmosphere. Here, the evolution of the magnetic field is solved with the stress--and--relax method. Below this region a magnetic field is produced by a helical forcing function in the momentum equation, which leads to dynamo action. We find twisted magnetic fields emerging frequently to the outer layer, forming arch-like structures. In addition, recurrent plasmoid ejections can be found by looking at space--time diagrams of the magnetic field. Recent simulations in spherical coordinates show similar results.Comment: 4 pages, 8 figures, To appear in the proceedings of the IAU273 "Physics of Sun and Star Spots

GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

Integrating genome-scale sequence, expression, structural and protein interaction data from E. coli we establish an interaction between chaperone (GroEL) dependency and optimal codon usage.Highly expressed sporadic substrates of GroEL employ more optimal codons than expected, show enrichment for optimal codons at structurally sensitive sites and greater conservation of codon optimality under conditions of relaxed purifying selection.We suggest that highly expressed genes cannot routinely utilize GroEL for error control so that codon usage has evolved to provide complementary error limitation, whereas obligate GroEL substrates experience relaxed selection on codon usage.Our results support a critical role of misfolding prevention in gene evolution

Исследование спектральных свойств когерентного дифракционного излучения от периодических структур

При пролете электрона вблизи периодической структуры генерируется поляризационное излучение, называемое дифракционным излучением от периодических структур (grating diffraction radiation). При пролете электрона параллельно решетке возникает хорошо изученное излучение Смита-Парселла. Однако при непараллельном пролёте также может возникать излучение. В данной работе проводится анализ спектральных характеристик когерентного дифракционного излучения от решеток, экспериментально полученных на ускорителе KEK-LUCX (г. Цукуба, Япония). Представлены спектры излучения, получаемые при разных углах ориентации решетки. Полученные спектральные характеристики сравниваются с теоретически рассчитанными.When an electron passes close to the periodic structure polarization radiation is generated, called diffraction radiation from periodic structures (grating diffraction radiation). When an electron passes parallel to the grating, well-studied Smith-Purcell radiation arises. However, in the case of a nonparallel flight, radiation can also occur. In this work, we analyze the spectral characteristics of coherent diffraction radiation from gratings, experimentally obtained at the accelerator KEK-LUCX (Tsukuba, Japan). Radiation spectrums obtained at different angles of grating orientation are presented. The obtained spectral characteristics are compared with theoretically calculated

Electro-extractive fermentation for efficient biohydrogen production

Electrodialysis, an electrochemical membrane technique, was found to prolong and enhance the production of biohydrogen and purified organic acids via the anaerobic fermentation of glucose by Escherichia coli. Through the design of a model electrodialysis medium using cationic buffer, pH was precisely controlled electrokinetically, i.e. by the regulated extraction of acidic products with coulombic efficiencies of organic acid recovery in the range 50–70% maintained over continuous 30-day experiments. Contrary to\ud previous reports, E. coli produced H2 after aerobic growth in minimal medium without inducers and with a mixture of organic acids dominated by butyrate. The selective separation of organic acids from fermentation provides a potential nitrogen-free carbon source for further biohydrogen production in a parallel photofermentation. A parallel study incorporated this fermentation system into an integrated biohydrogen refinery (IBR) for the conversion of organic waste to hydrogen and energy