Bacterial human virulence genes across diverse habitats as assessed by <i>In silico</i> analysis of environmental metagenomes

The occurrence and distribution of clinically relevant bacterial virulence genes across natural (non-human) environments is not well understood. We aimed to investigate the occurrence of homologues to bacterial human virulence genes in a variety of ecological niches to better understand the role of natural environments in the evolution of bacterial virulence. Twentyfour bacterial virulence genes were analyzed in 47 diverse environmental metagenomic datasets, representing various soils, seawater, freshwater, marine sediments, hot springs, the deep-sea, hypersaline mats, microbialites, gutless worms and glacial ice. Homologues to 17 bacterial human virulence genes, involved in urinary tract infections, gastrointestinal diseases, skin diseases, and wound and systemic infections, showed global ubiquity. A principal component analysis did not demonstrate clear trends across the metagenomes with respect to occurrence and frequency of observed gene homologues. Full-length (>95%) homologues of several virulence genes were identified, and translated sequences of the environmental and clinical genes were up to 50-100% identical. Furthermore, phylogenetic analyses indicated deep branching positions of some of the environmental gene homologues, suggesting that they represent ancient lineages in the phylogeny of the clinical genes. Fifteen virulence gene homologues were detected in metagenomes based on metatranscriptomic data, providing evidence of environmental expression. The ubiquitous presence and transcription of the virulence gene homologues in non-human environments point to an important ecological role of the genes for the activity and survival of environmental bacteria. Furthermore, the high degree of sequence conservation between several of the environmental and clinical genes suggests common ancestral origins

Rotated stripe order and its competition with superconductivity in La1.88_{1.88}Sr0.12_{0.12}CuO4_4

We report the observation of a bulk charge modulation in La$_{1.88}$Sr$_{0.12}$CuO$_4$ (LSCO) with a characteristic in-plane wave-vector of (0.236, $\pm \delta$), with $\delta$=0.011 r.l.u. The transverse shift of the ordering wave-vector indicates the presence of rotated charge-stripe ordering, demonstrating that the charge ordering is not pinned to the Cu-O bond direction. On cooling through the superconducting transition, we find an abrupt change in the growth of the charge correlations and a suppression of the charge order parameter indicating competition between the two orderings. Orthorhombic LSCO thus helps bridge the apparent disparities between the behavior previously observed in the tetragonal "214" cuprates and the orthorhombic yttrium and bismuth-based cuprates and thus lends strong support to the idea that there is a common motif to charge order in all cuprate families.Comment: 6 pages, 4 figue

Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stress

<p>Abstract</p> <p>Background</p> <p>Mitochondrial proteins are central to various metabolic activities and are key regulators of apoptosis. Disturbance of mitochondrial proteins is therefore often associated with disease. Large scale protein data are required to capture the mitochondrial protein levels and mass spectrometry based proteomics is suitable for generating such data. To study the relative quantities of mitochondrial proteins in cells from cultivated human skin fibroblasts we applied a proteomic method based on nanoLC-MS/MS analysis of iTRAQ-labeled peptides.</p> <p>Results</p> <p>When fibroblast cultures were exposed to mild metabolic stress – by cultivation in galactose medium- the amount of mitochondria appeared to be maintained whereas the levels of individual proteins were altered. Proteins of respiratory chain complex I and IV were increased together with NAD⁺-dependent isocitrate dehydrogenase of the citric acid cycle illustrating cellular strategies to cope with altered energy metabolism. Furthermore, quantitative protein data, with a median standard error below 6%, were obtained for the following mitochondrial pathways: fatty acid oxidation, citric acid cycle, respiratory chain, antioxidant systems, amino acid metabolism, mitochondrial translation, protein quality control, mitochondrial morphology and apoptosis.</p> <p>Conclusion</p> <p>The robust analytical platform in combination with a well-defined compendium of mitochondrial proteins allowed quantification of single proteins as well as mapping of entire pathways. This enabled characterization of the interplay between metabolism and stress response in human cells exposed to mild stress.</p

Suppression of the structural phase transition and lattice softening in slightly underdoped Ba(1-x)K(x)Fe2As2 with electronic phase separation

We present x-ray powder diffraction (XRPD) and neutron diffraction measurements on the slightly underdoped iron pnictide superconductor Ba(1-x)K(x)Fe2As2, Tc = 32K. Below the magnetic transition temperature Tm = 70K, both techniques show an additional broadening of the nuclear Bragg peaks, suggesting a weak structural phase transition. However, macroscopically the system does not break its tetragonal symmetry down to 15 K. Instead, XRPD patterns at low temperature reveal an increase of the anisotropic microstrain proportionally in all directions. We associate this effect with the electronic phase separation, previously observed in the same material, and with the effect of lattice softening below the magnetic phase transition. We employ density functional theory to evaluate the distribution of atomic positions in the presence of dopant atoms both in the normal and magnetic states, and to quantify the lattice softening, showing that it can account for a major part of the observed increase of the microstrain.Comment: 7 pages, 4 figure

Single-order-parameter description of glass-forming liquids:A one-frequency test

Thermo-viscoelastic linear-response functions are calculated from the master equation describing viscous liquid inherent dynamics. From the imaginary parts of the frequency-dependent isobaric specific heat, isothermal compressibility, and isobaric thermal expansion coefficient, we define a "linear dynamic Prigogine-Defay ratio" with the property that if this quantity is unity atone frequency, then it is unity at all frequencies. This happens if and only if there is a single-order-parameter description of the thermo-viscoelastic linear responses via an order parameter (which may be non-exponential in time). Generalizations to other cases of thermodynamic control parameters than temperature and pressure are treated in an Appendix.Comment: Replaces arXiv:cond-mat/040570

Measurement of unique magnetic and superconducting phases in oxygen-doped high-temperature superconductors La_2-xSr_xCuO_4+y

We present a combined magnetic neutron scattering and muon spin rotation study of the nature of the magnetic and superconducting phases in electronically phase separated La(2-x)Sr(x)CuO(4+y), x = 0.04, 065, 0.09. For all samples, we find long-range modulated magnetic order below T_N ~ T_c = 39 K. In sharp contrast wit oxygen-stoichiometric La(2-x)Sr(x)CuO(4), we find that the magnetic propagation vector as well as the ordered magnetic moment is independent of Sr content and consistent with that of the 'striped' cuprates. Our study provides direct proof that superoxygenation in La(2-x)Sr(x)CuO(4+y) allows the spin stripe ordered phase to emerge and phase separate from superconducting regions with the hallmarks of optimally doped oxygen-stoichiometric La(2-x)Sr(x)CuO(4)