Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

A genetic algorithm for the automated generation of molecules within constraints

Summary A genetic algorithm has been designed which generates molecular structures within constraints. The constraints may be any useful function, for example an enzyme active site, a pharmacophore or molecular properties from pattern recognition or rule-induction analyses. The starting point may be random or may utilise known molecules. These are modified to grow into families of structures which, using the evolutionary operators of selection, crossover and mutation evolve to better fit the constraints. The basis of the algorithm is described together with some applications in lead generation, 3D database construction and drug design. Genetic algorithms of this type may have wider applications in chemistry, for example in the design and optimisation of new polymers, materials (e.g. superconducting materials) or synthetic enzymes.     

The Astrochemical Observatory: Molecules in the Laboratory and in the Cosmos

Astrochemistry is a discipline consolidated recently, although its roots extend back to the dawn of early civilization with the observation and mapping of the sky. The way to the understanding of the common natural laws on earth and in space paved by Galilei's observations by the telescope, has been extended in the last decades, by new technologies such as radioastronomy and space missions. Plenty of new chemistry was surprisingly discovered. Extreme rich information on the chemical “composition” of the universe is being obtained, either from the other planets and satellites in the Solar System, from meteorites and comets, or from the interstellar space. In this article we will present selected topics regarding the chemical structures and reactions being discovered. Particular attention will be devoted to aspects considered as relevant for the prebiotic processes on earth, such as those involving chirality and its role played in the origin and evolution of life.     

Evolution of Er^3＋ Distribution in the Oxyfluoride Glass Ceramics with Heating

The distribution characteristics of Er3+ ions doped in the oxyfluoride glass ceramics containing LaF3 nanocrystals heat-treated at 650 ℃ for different durations were investigated. The results of the integral absorption cross-section analysis demonstrated that the partition fraction of Er3+ in LaF3 nanocrystals increases with prolonging of heating time. The anomalous phenomena of Er3+ emissions in the up-and the down-conversion fluorescence spectra are well explained based on the calculated results.     

用氨基酸加和法计算多肽的脂水分配系数

Based on amino acid addition model, a set of hydrophobicity contributions of amino acids was obtained from the multivariate linear regression analysis of peptides' octanol/water partition coefficients. Multivariate regression was performed on a training set of 219 peptides including dipeptides to pentapeptides which we compose 21 natural amino acids. The correlation coefficients for the whole set fitting are 0. 978 and 0- 974, for log P and log D respectively. In addition, a new test method -evolution test-for regression analysis was discussed. The result of evolution test for amino acid addition model shows the advantage of this new test method.     

Synthesis of Layered Carbonitrides from Biotic Molecules for Photoredox Transformations

The construction of layered covalent carbon nitride polymers based on tri-s-triazine units has been achieved by using nucleobases (adenine, guanine, cytosine, thymine and uracil) and urea to establish a two-dimensional semiconducting structure that allows band-gap engineering applications. This biomolecule-derived binary carbon nitride polymer enables the generation of energized charge carrier with light-irradiation to induce photoredox reactions for stable hydrogen production and heterogeneous organosynthesis of C−O, C−C, C−N and N−N bonds, which may enrich discussion on chemical reactions in prebiotic conditions by taking account of the photoredox function of conjugated carbonitride semiconductors that have long been considered to be stable HCN-derived organic macromolecules in space.