First-principles calculations of phonon and thermodynamic properties of AlRE (RE= Y, Gd, Pr, Yb) intermetallic compounds

The phonon and thermodynamic properties of rare-earth-aluminum intermetallics AlRE (RE=Y, Gd, Pr, Yb) with B2-type structure are investigated by performing density functional theory and density functional perturbation theory within the quasiharmonic approximation. The phonon spectra and phonon density of states, including the phonon partial density of states and total density of states, have been discussed. Our results demonstrate that the density of states is mostly composed of Al states at the high frequency. The temperature dependence of various quantities such as the thermal expansions, the heat capacities at constant volume and constant pressure, the isothermal bulk modulus, and the entropy are obtained. The electronic contribution to the specific heat is discussed, and the presented results show that the thermal electronic excitation affecting the thermal properties is inessential.Comment: 17 pages,8 figure

Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?

<p>Abstract</p> <p>Background</p> <p>Array-based Comparative Genomic Hybridization (CGH) data have been used to infer phylogenetic relationships. However, the reliability of array CGH analysis to determine evolutionary relationships has not been well established. In most CGH work, all species and strains are compared to a single reference species, whose genome was used to design the array. In the accompanying work, we critically evaluated CGH-based phylogeny using simulated competitive hybridization data. This work showed that a limited number of conditions, principally the tree topology and placement of the reference taxon in the tree, had a strong effect on the ability to recover the correct tree topology. Here, we add to our simulation study by testing the use of CGH as a phylogenetic tool with experimental CGH data from competitive hybridizations between <it>N. crassa </it>and other <it>Neurospora </it>species. In the discussion, we add to our empirical study of <it>Neurospora </it>by reanalyzing of data from a previous CGH phylogenetic analysis of the yeast <it>sensu stricto </it>complex.</p> <p>Results</p> <p>Array ratio data for <it>Neurospora </it>and related species were normalized with loess, robust spline, and linear ratio based methods, and then used to construct Neighbor-Joining and parsimony trees. These trees were compared to published phylogenetic analyses for <it>Neurospora </it>based on multilocus sequence analysis (MLSA). For the <it>Neurospora </it>dataset, the best combination of methods resulted in recovery of the MLSA tree topology less than half the time. Our reanalysis of a yeast dataset found that trees identical to established phylogeny were recovered only by pruning taxa - including the reference taxon - from the analysis.</p> <p>Conclusion</p> <p>Our results indicate that CGH data can be problematic for phylogenetic analysis. Success fluctuates based on the methods utilized to construct the tree and the taxa included. Selective pruning of the taxa improves the results - an impractical approach for normal phylogenetic analysis. From the more successful methods we make suggestions on the normalization and post-normalization methods that work best in estimating genetic distance between taxa.</p

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

Background Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group. Results Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes, genes present in not all, but more than one strain, was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant 13 evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence. Conclusion Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan genome guarantees the species a quick and economical response to diverse environments

Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.

Pneumococcal serotypes are represented by a varying number of clonal lineages with different genetic contents, potentially affecting invasiveness. However, genetic variation within the same genetic lineage may be larger than anticipated