DNA strand displacement, strand annealing and strand swapping by the Drosophila Bloom's syndrome helicase

Genetic analysis of the Drosophila Bloom's syndrome helicase homolog (mus309/DmBLM) indicates that DmBLM is required for the synthesis-dependent strand annealing (SDSA) pathway of homologous recombination. Here we report the first biochemical study of DmBLM. Recombinant, epitope-tagged DmBLM was expressed in Drosophila cell culture and highly purified protein was prepared from nuclear extracts. Purified DmBLM exists exclusively as a high molecular weight (∼1.17 MDa) species, is a DNA-dependent ATPase, has 3′→5′ DNA helicase activity, prefers forked substrate DNAs and anneals complementary DNAs. High-affinity DNA binding is ATP-dependent and low-affinity ATP-independent interactions contribute to forked substrate DNA binding and drive strand annealing. DmBLM combines DNA strand displacement with DNA strand annealing to catalyze the displacement of one DNA strand while annealing a second complementary DNA strand

On high-speed turning of a third-generation gamma titanium aluminide

Gamma titanium aluminides are heat-resistant intermetallic alloys predestined to be employed in components suffering from high mechanical stresses and thermal loads. These materials are regarded as difficult to cut, so this makes process adaptation essential in order to obtain high-quality and defect-free surfaces suitable for aerospace and automotive parts. In this paper, an innovative approach for longitudinal external high-speed turning of a third-generation Ti-45Al-8Nb- 0.2C-0.2B gamma titanium aluminide is presented. The experimental campaign has been executed with different process parameters, tool geometries and lubrication conditions. The results are discussed in terms of surface roughness/integrity, chip morphology, cutting forces and tool wear. Experimental evidence showed that, due to the high cutting speed, the high temperatures reached in the shear zone improve chip formation, so a crack-free surface can be obtained. Furthermore, the use of a cryogenic lubrication system has been identified in order to reduce the huge tool wear, which represents the main drawback when machining gamma titanium aluminides under the chosen process condition

Exhaustive generation of kk-critical H\mathcal H-free graphs

We describe an algorithm for generating all $k$-critical $\mathcal H$-free graphs, based on a method of Ho\`{a}ng et al. Using this algorithm, we prove that there are only finitely many $4$-critical $(P_7,C_k)$-free graphs, for both $k=4$ and $k=5$. We also show that there are only finitely many $4$-critical graphs $(P_8,C_4)$-free graphs. For each case of these cases we also give the complete lists of critical graphs and vertex-critical graphs. These results generalize previous work by Hell and Huang, and yield certifying algorithms for the $3$-colorability problem in the respective classes. Moreover, we prove that for every $t$, the class of 4-critical planar $P_t$-free graphs is finite. We also determine all 27 4-critical planar $(P_7,C_6)$-free graphs. We also prove that every $P_{10}$-free graph of girth at least five is 3-colorable, and determine the smallest 4-chromatic $P_{12}$-free graph of girth five. Moreover, we show that every $P_{13}$-free graph of girth at least six and every $P_{16}$-free graph of girth at least seven is 3-colorable. This strengthens results of Golovach et al.Comment: 17 pages, improved girth results. arXiv admin note: text overlap with arXiv:1504.0697

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae

OBJECTIVES: The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. METHODS: Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. RESULTS: A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. CONCLUSIONS: This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial

Magnetic and electronic structures of superconducting RuSr2_2GdCu2_2O8_8

The coexistence of ferromagnetism and superconductivity in RuSr$_2$GdCu$_2$O$_8$ was reported both from experiments (by Tallon et. al.) and first-principles calculations (by Pickett et. al.). Here we report that our first-principles full-potential linearized augmented plane wave (FLAPW) calculations, employing the precise crystal structure with structural distortions (i.e., RuO$_6$ rotations) determined by neutron diffraction, demonstrate that antiferromagnetic ordering of the Ru moments is energetically favored over the previously proposed ferromagnetic ordering. Our results are consistent with recently performed magnetic neutron diffraction experiments (Lynn et. al). Ru $t_{2g}$ states, which are responsible for the magnetism, have only a very small interaction with Cu $e_g$ states, which results in a small exchange splitting of these states. The Fermi surface, characterized by strongly hybridized $dp\sigma$ orbitals, has nesting features similar to those in the two-dimensional high $T_c$ cuprate superconductors.Comment: 6 pages,6 figures, accepted for publication in Phys. Rev.

Benchmarking common quantification strategies for large-scale phosphoproteomics

Quantitative phosphoproteomics has become a standard method in molecular and cell biology. Here, the authors compare performance and parameters of phosphoproteome quantification by LFQ, SILAC, and MS2-/MS3-based TMT and introduce a TMT-adapted algorithm for calculating phosphorylation site stoichiometry

Analysis of OPM potentials for multiplet states of 3d transition metal atoms

We apply the optimized effective potential method (OPM) to the multiplet energies of the 3d$^n$ transition metal atoms, where the orbital dependence of the energy functional with respect to orbital wave function is the single-configuration HF form. We find that the calculated OPM exchange potential can be represented by the following two forms. Firstly, the difference between OPM exchange potentials of the multiplet states can be approximated by the linear combination of the potentials derived from the Slater integrals $F^2({\rm 3d,3d})$ and $F^4({\rm 3d,3d})$ for the average energy of the configuration. Secondly, the OPM exchange potential can be expressed as the linear combination of the OPM exchange potentials of the single determinants.Comment: 15 pages, 6 figures, to be published in J. Phys.

First-principles calculations of the self-trapped exciton in crystalline NaCl

The atomic and electronic structure of the lowest triplet state of the off-center (C2v symmetry) self-trapped exciton (STE) in crystalline NaCl is calculated using the local-spin-density (LSDA) approximation. In addition, the Franck-Condon broadening of the luminescence peak and the a1g -> b3u absorption peak are calculated and compared to experiment. LSDA accurately predicts transition energies if the initial and final states are both localized or delocalized, but 1 eV discrepancies with experiment occur if one state is localized and the other is delocalized.Comment: 4 pages with 4 embeddded figure