Sq Evolution Vol 5 Mei Sawai ((FULL))

Andropin, which encodes an antibacterial protein, is closely linked to the Cecropin gene cluster of D. melanogaster. Andropin and Cecropins are considered to have originated from one common ancestor. However, the expression pattern of Andropin is distinct from that of Cecropins, being restricted to the adult male ejaculatory duct. To elucidate the evolutionary process of Andropin, we have sequenced Andropin genes from D. melanogaster and its closely related species. In D. melanogaster, the nucleotide diversity of Andropin is remarkably low compared to that of Cecropin. In contrast, nonsynonymous substitutions of Andropin are conspicuously frequent between species. From genomic Southern analysis, Andropin-like genes are present in at least the melanogaster species subgroup. The series of present results suggests that Andropin was born in the course of constructing the Drosophila Cecropin gene family and then started to evolve rapidly, in contrast to Cecropins.

Sterols, essential eukaryotic constituents, are biosynthesized through either cyclic triterpenes, lanosterol (fungi and animals) or cycloartenol (plants). The cDNA for OSC7 of Lotus japonicus was shown to encode lanosterol synthase (LAS) by the complementation of a LAS-deficient mutant yeast and structural identification of the accumulated lanosterol. A double site-directed mutant of OSC7, in which amino acid residues crucial for the reaction specificity were changed to the cycloartenol synthase (CAS) type, produced parkeol and cycloartenol. The multiple amino acid sequence alignment of a conserved region suggests that the LAS of different eukaryotic lineages emerged from the ancestral CAS by convergent evolution.

Sq Evolution Vol 5 Mei Sawai

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A new method of genetic programming, named chemical genetic programming (CGP), which enables evolutionary optimization of the mapping from genotypic strings to phenotypic trees is proposed. A cell is evolved which includes a DNA string that codes the fundamental mapping from the DNA code to computational functionality. Genetic modification of a cell's DNA allows the DNA code and the genotype-to-phenotype translation to coevolve. Building an optimal translation table enhances evolution within a population while maintaining the necessary diversity to explore the entire search space.

We carried out two-dimensional axisymmetric MHD simulations of core-collapse supernovae for rapidly rotating magnetized progenitors. By changing both the strength of the magnetic field and the spatial resolution, the evolution of the magnetorotational instability (MRI) and its impacts upon the dynamics are investigated. We found that the MRI greatly amplifies the seed magnetic fields in the regime where the buoyant mode, not the Alfvn mode, plays a primary role in the exponential growth phase. The MRI indeed has a powerful impact on the supernova dynamics. It makes the shock expansion faster and the explosion more energetic, with some models being accompanied by the collimated jet formations. These effects, however, are not made by the magnetic pressure except for the collimated jet formations. The angular momentum transfer induced by the MRI causes the expansion of the heating region, by which the accreting matter gain additional time to be heated by neutrinos. The MRI also drifts low-Yp matter from deep inside of the core to the heating region, which makes the net neutrino heating rate larger by the reduction of the cooling due to the electron capture. These two effects enhance the efficiency of the neutrino heating, which is found to be the key to boosting the explosion. Indeed, we found that our models explode far more weakly when the net neutrino heating is switched off. The contribution of the neutrino heating to the explosion energy could reach 60% even in the case of strongest magnetic field in the current simulations.

The kinetics of oligopeptides formation in the flow systems glycine - sodium trimetaphosphate - imidazole/N-methylimidazole at thermocyclic regime was investigated by liquid chromatography (HPLC) and 31P NMR methods in the ranges of temperature from 45 to 90C and pH from 8.5 to 11.5. Formation of significant amounts of glycylglycine (yield up to 52%) and diglycylglycine was revealed. Better results are obtained at 75C in slightly alkaline conditions (pH 9.5-10.5), and in the presence of imidazole yields of oligopeptides are bigger than without this heterocycle. It should be mentioned that the used non-equilibrium regime of the glycylglycine and diglycylglycine syntheses turns out to be one of the most effective among all prebiotic syntheses reported so far in the literature, both in the absence and in the presence of imidazole. Earlier, H. Sawai and L.E. Orgel discovered that heterocycles, such as imidazole, can increase yields of peptides in solid state (Sawai H., Orgel L.E. (1975) J. Mol. Evol. 6:185-197. doi:10.1007/bf01732355). However, the proposed explanation of the catalytic effect of imidazole due to initial formation of N-triphosphoryl imidazole as a key intermediate is not working in the reactions studied by us because in the imidazole - trimetaphosphate mixture signals of any imidazole N-phosphates are absent in 31P NMR spectra. In this situation, a new imidazole catalysis mechanism by which imidazole reacts with cyclic N,O-phosphoryl glycine giving N-imidazolyl-O-glycyl phosphate as a key intermediate was proposed and validated in the present investigation. Detailed reaction mechanisms were proposed and justified by quantum chemical calculations using density functional theory (DFT) method at the high level (CAM-B3LYP/TZVP) with accounting solvent effect by the polarized continuum model (?-PCM). It is emphasized that while in the absence of imidazoles, prebiotic activation of amino acids occurs at the N-terminus, and in the presence of imidazoles it shifts to the O-terminus. This means that in the peptide elongation N-imidazolyl-O-aminoacyl phosphates play in prebiotic systems the outstanding role similar to that of aminoacyl adenylates formed at the ATP and aminoacyl-tRNA synthetases presence in biosystems. This seems to be a key pathway for prebiotic evolution in terms of peptide synthesis. So, the new crucial role of imidazoles in prebiotic evolution was discovered. The systems used and modes of their conversion can be good models for prebiotic peptide syntheses in a flow thermocyclic regime, including prebiotic peptide syntheses under conditions of various hydrothermal systems, particulary in Kamchatka, where temperature and pressure fluctuations are detected and pH varies from 2.0 to 9.5 while temperature ranges from 55 to 98oC in hot springs.

Further research can pertain to the synthesis of oligopeptides containing other amino acids and the synthesis of other biopolymers, primarily sugars. Particular attention will be paid to experimental and theoretical studies of mechanisms of heterogeneous catalysis in prebiotic syntheses of biopolymers. The focus will be on the role of coordination and complexation with metals in prebiotic syntheses, since metal complexes could control the stereoselectivity and specificity of many vital processes at the first stages of biochemical evolution.

A chemical genetic algorithm (CGA) in which several types of molecules (information units) react with each other in a cell is proposed. Not only the information in DNA, but also smaller molecules responsible for the transcription and translation of DNA into amino acids, are adaptively changed during evolution, which optimizes the fundamental mapping from binary substrings in DNA (genotype) to real values for a parameter set (phenotype). Through the struggle between cells containing a DNA unit and small molecular units, the codes (DNA) and the interpreter (the small molecular units) coevolve, and a specific output function, from which a cell's fitness is evaluated, is optimized. To demonstrate the effectiveness of the CGA, it is applied to a set of variable-separable and variable-inseparable problems, and it is shown that the CGA can robustly solve a wide range of optimization problems regardless of their fitness characteristics. To ascertain the optimization of the genotype-to-phenotype mapping by the CGA, we also conduct analytical experiments for some problems while observing the basin size of a global optimum solution in the binary genotype space. The results show that the CGA effectively augments the basin size, makes it easier for evolution to find a path to the global optimum solution, and enhances the GA's evolvability during evolution.

Self-adaptation is an essential feature of natural evolution. However, in the context of function optimization, self-adaptation features of evolutionary search algorithms have been explored mainly with evolution strategy (ES) and evolutionary ...

Abstract:Meander dynamics has been the focus of river engineering for decades; however, it remains a challenge for researchers to precisely replicate natural evolution processes of meandering channels with numerical models due to the high nonlinearity of the governing equations. The present study puts forward a nonlinear model to simulate the flow pattern and evolution of meandering channels. The proposed meander model adopts the nonlinear hydrodynamic submodel developed by Blanckaert and de Vriend, which accounts for the nonlinear interactions between secondary flow and main flow and therefore has no curvature restriction. With the computational flow field, the evolution process of the channel centerline is simulated using the Bank Erosion and Retreat Model (BERM) developed by Chen and Duan. Verification against two laboratory flume experiments indicates the proposed meander model yields satisfactory agreement with the measured data. For comparison, the same experimental cases are also simulated with the linear version of the hydrodynamic submodel. Calculated results show that the flow pattern and meander evolution process predicted by the nonlinear and the linear models are similar for mildly curved channels, whereas they exhibit different characteristics when channel sinuosity becomes relatively high. It is indicated that the nonlinear interactions between main flow and secondary flow prevent the growth of the secondary flow and induce a more uniform transverse velocity profile in high-sinuosity channels, which slows down the evolution process of meandering channels.Keywords: numerical simulation; nonlinear model; meander evolution; bank erosion be457b7860