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Wheat domestication accelerated evolution and triggered positive selection in the beta-xylosidase enzyme of Mycosphaerella graminicola
(2009)PLoS ONEPlant cell wall degrading enzymes (PCWDEs) of plant pathogens are receiving increasing interest for their potential to trigger plant defense reactions. In an antagonistic co-evolutionary arms race between host and pathogen, PCWDEs could be under strong selection. Here, we tested the hypothesis that PCWDEs in the fungal wheat pathogen Mycosphaerella graminicola have been positively selected by analyzing ratios of non-synonymous and synonymous ...Journal Article -
Ground-state statistics from annealing algorithms
(2009)New Journal of PhysicsWe study the performance of quantum annealing for systems with ground-state degeneracy by directly solving the Schrödinger equation for small systems and quantum Monte Carlo simulations for larger systems. The results indicate that naive quantum annealing using a transverse field may not be well suited to identify all degenerate ground-state configurations, although the value of the ground-state energy is often efficiently estimated. An ...Journal Article -
Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism
(2009)PLoS GeneticsTrf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene ...Journal Article -
Muon spin rotation study of magnetism and superconductivity in BaFe2−xCoxAs2 and Pr1−xSrxFeAsO
(2009)New Journal of PhysicsWe present a muon spin rotation (μSR) study of the magnetic and superconducting properties of single crystals of electron-doped BaFe2−xCoxAs2 with x = 0.08, 0.20 and 0.25 (Tc = 9, 25 and 20 K) and of polycrystalline hole-doped Pr1−xSrxFeAsO with x = 0 and 0.2 (Tc = 15 K). In the former series, we observe some interesting parallels with the electron-doped SmFeAsO1−xFx 1111-type system (Drew et al 2009 Nat. Mater. 8 310). In particular, we ...Journal Article -
Optical properties of TiN thin films close to the superconductor–insulator transition
(2009)New Journal of PhysicsWe present the intrinsic optical properties over a broad spectral range of TiN thin films deposited on an Si/SiO2 substrate. We analyze the measured reflectivity spectra of the film-substrate multilayer structure within a well-establish procedure based on the Fresnel equation and extract the real part of the optical conductivity of TiN. We identify the metallic contribution as well as the finite energy excitations and disentangle the ...Journal Article -
Momentum-resolved superconducting gap in the bulk of Ba1−xKxFe2As2 from combined ARPES and μSR measurements
(2009)New Journal of PhysicsHere we present a calculation of the temperature-dependent London penetration depth, λ(T), in Ba1-xKxFe2As2 (BKFA) on the basis of the electronic band structure (Zabolotnyy et al 2009 Nature 457 569, Zabolotnyy et al 2009 Physica C 469 448) and momentum-dependent superconducting gap (Evtushinsky et al 2009 Phys. Rev. B 79 054517) extracted from angle-resolved photoemission spectroscopy (ARPES) data. The results are compared to the direct ...Journal Article -
Imprinting of the polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis
(2009)PLoS GeneticsBalanced maternal and paternal genome contributions are a requirement for successful seed development. Unbalanced contributions often cause seed abortion, a phenomenon that has been termed “triploid block.” Misregulation of imprinted regulatory genes has been proposed to be the underlying cause for abnormalities in growth and structure of the endosperm in seeds with deviating parental contributions. We identified a mutant forming unreduced ...Journal Article -
The Drosophila SH2B family adaptor Lnk acts in parallel to chico in the insulin signaling pathway
(2009)PLoS GeneticsInsulin/insulin-like growth factor signaling (IIS) plays a pivotal role in the regulation of growth at the cellular and the organismal level during animal development. Flies with impaired IIS are developmentally delayed and small due to fewer and smaller cells. In the search for new growth-promoting genes, we identified mutations in the gene encoding Lnk, the single fly member of the SH2B family of adaptor molecules. Flies lacking lnk ...Journal Article -
Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: Methodology and performance
(2009)International Journal of Molecular SciencesWe review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the ...Journal Article -
Rupture Pathway of Phosphatidylcholine Liposomes on Silicon Dioxide
(2009)International Journal of Molecular SciencesWe have investigated the pathway by which unilamellar POPC liposomes upon adsorption undergo rupture and form a supported lipid bilayer (SLB) on a SiO2 surface. Biotinylated lipids were selectively incorporated in the outer monolayer of POPC liposomes to create liposomes with asymmetric lipid compositions in the outer and inner leaflets. The specific binding of neutravidin and anti-biotin to SLBs formed by liposome fusion, prior to and ...Journal Article