Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

La 0.7Ca 0.3MnO 3 / Mn 3O 4 composites: Does an insulating secondary phase always enhance the low field magnetoresistance of manganites

Composites of magnetoresistive La 0.7Ca 0.3MnO 3 (LCMO) with insulating Mn 3O 4 are useful as a model system because no foreign cation is introduced in the LCMO phase by interdiffusion during the heat treatment. Here we report the magnetotransport properties as a function of sintering temperature T sinter for a fixed LCMO/Mn 3O 4 ratio. Decreasing T sinter from 1250 °C to 800 °C causes an increase in low field magnetoresistance (LFMR) that correlates with the decrease in crystallite size (CS) of the LCMO phase. When plotting LFMR at (77 K, 0.5 T) versus 1/CS, we find that the data for the LCMO/Mn 3O 4 composites sintered between 800 °C and 1250 °C follow the same trend line as data from the literature for pure LCMO samples with crystallite size >∼25 nm. This differs from the LFMR enhancement observed by many authors in the usual manganite composites, i.e., composites where the insulating phase contains cations other than La, Ca or Mn. This difference suggests that diffusion of foreign cations into the grain boundary region is a necessary ingredient for the enhanced LFMR. © 2012 American Institute of Physics.

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Assessing effects of site characteristics on remediation secondary life cycle impact with a generalised framework

The 'sustainable remediation' concept has been broadly embraced by industry and governments in recent years in both the US and Europe. However, there is a strong need for more research to enhance its 'practicability'. In an attempt to fill this research gap, this study developed a generalised framework for selecting the most environmentally sustainable remedial technology under various site conditions. Four remediation technologies were evaluated: pump and treat (P&T), enhanced in situ bioremediation (EIB), permeable reactive barrier (PRB), and in situ chemical reduction (ISCR). Within the developed framework and examined site condition ranges, our results indicate that site characteristics have a profound effect on the life cycle impact of various remedial alternatives, thus providing insights and valuable information for determining what is considered the most desired remedy from an environmental sustainability perspective. © 2014 © 2014 University of Newcastle upon Tyne.

Effect of buffer layer growth conditions on the secondary hexagonal phase content in cubic GaN films on GaAs(001) substrates

In this letter, we investigated the effect of the buffer layer growth conditions on the secondary hexagonal phase content in cubic GaN films on GaAs(0 0 1) substrate. The reflection high-energy electron diffraction (RHEED) pattern of the low-temperature GaN buffer layers shows that both the deposition temperature and time are important in obtaining a smooth surface. Four-circle X-ray double-crystal diffraction (XRDCD) reciprocal space mapping was used to study the hexagonal phase inclusions in the cubic GaN (c-GaN) films grown on the buffer layers. The calculation of the volume contents of the hexagonal phase shows that higher temperature and longer time deposition of the buffer layer is not preferable for growing pure c-GaN film. Under optimized condition, 47 meV FWHM of near band gap emission of the c-GaN film was achieved. (C) 2000 Elsevier Science B.V. All rights reserved.