Limiting the Extent of the RDN1 Heterochromatin Domain by a Silencing Barrier and Sir2 Protein Levels in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, transcriptional silencing occurs at the cryptic mating-type loci (HML and HMR), telomeres, and ribosomal DNA ( rDNA; RDN1). Silencing in the rDNA is unusual in that polymerase II (Pol II) promoters within RDN1 are repressed by Sir2 but not Sir3 or Sir4. rDNA silencing unidirectionally spreads leftward, but the mechanism of limiting its spreading is unclear. We searched for silencing barriers flanking the left end of RDN1 by using an established assay for detecting barriers to HMR silencing. Unexpectedly, the unique sequence immediately adjacent to RDN1, which overlaps a prominent cohesin binding site (CARL2), did not have appreciable barrier activity. Instead, a fragment located 2.4 kb to the left, containing a tRNA(Gln) gene and the Ty1 long terminal repeat, had robust barrier activity. The barrier activity was dependent on Pol III transcription of tRNA(Gln), the cohesin protein Smc1, and the SAS1 and Gcn5 histone acetyltransferases. The location of the barrier correlates with the detectable limit of rDNA silencing when SIR2 is overexpressed, where it blocks the spreading of rDNA heterochromatin. We propose a model in which normal Sir2 activity results in termination of silencing near the physical rDNA boundary, while tRNA(Gln) blocks silencing from spreading too far when nucleolar Sir2 pools become elevated.

Avian diversification patterns across the K-Pg boundary: Influence of calibrations, datasets, and model misspecification

Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.

Pressure and thermally induced stages of wear in dry sliding of a steel ball against an aluminium-silicon alloy flat

Wear of etched near-eutectic aluminium silicon alloy slid against a steel ball under ambient is explored. The sliding velocity is kept low (0.01 m/s) and the nominal contact pressure is varied in a 15-40 MPa range. Four stages of wear are identified; ultra mild wear, mild wear, severe wear and post severe oxidative wear. The first transition is controlled by the protrusions of silicon particles, projecting out of the aluminium alloy matrix. Once these protrusions disappear under pressure and sliding, oxidation and bulk energy dissipation mechanisms take over to institute transitions to other stages of wear. The phenomenological characteristics of wear stages are explored using a variety of techniques including nanoindentation, focused ion beam milling, electron microscopy, X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDS) and optical interferometry. (c) 2010 Elsevier B.V. All rights reserved.

Local structure of Sr(2)FeMoxW1-xO(6) double perovskites studied by EXAFS

Sr2FeMoO6 double perovskits display low field MR at a relatively high temperature and unusual ferromagnetic properties. These compounds depicts metal to insulator transition increasing x above x(c) similar to 0.25. A comparative analysis of the near edge regions (XANES) suggests that iron is Fe3+ in the metallic range. Checking the end compounds, we found that the doped samples can be viewn as inhomogeneous distributions of the end compounds. This could help to distinguish between the two scenarios proposed to explain the metal to insulator transition. Moreover, the local atomic structure of Sr2FeMoxW1-xO6 as a function of composition (0 <= x <= 1) has been investigated by Extended X-ray absorption spectroscopy (EXAFS) a the Fe, Mo, Sr K-edges andW L-III-edge.

Growth of ionization currents in dry air at high values of E/N

Uniform field steady-state ionization currents were measured in dry air as a function of N at constant E/N (E is the electric field strength and N the gas number density) and constant electrode separation d for 14·13 × 10-16 less-than-or-eq, slant E/N less-than-or-eq, slant 282·5 × 10-16 V cm2. Uniform field sparking potentials were also measured for Nd range 1·24 × 1016 less-than-or-eq, slant Nd less-than-or-eq, slant 245 × 1016 cm-2. The ratio of the Townsend primary ionization coefficient α to N, α/N, was found to depend on E/N only. The secondary coefficients were also evaluated for aluminium and gold-plated electrodes for the above range of E/N. Measurements of the sparking potentials showed that Paschen's law is not obeyed in air at values of Nd near and below the Paschen minimum.

An investigation of the PrBa2Cu3O7-δ system

Members of the PrBa2Cu3O7–delta system possessing the orthorhombic structure over a wide range of oxygen stoichiometry (delta=–0.5 to +0.5) have been prepared and characterized. Similar compositions with a tetragonal structure have also been prepared. None of the oxides is superconducting, independent of the structure or stoichiometry. Praseodymium seems to be present to a small extent in the 4+ state in oxygen-excess (negative delta) samples. Orthorhombic PrBa2Cu3O7–delta samples show the presence of twins suggesting that twins arise from orthorhombicity and have no relation to the superconductivity. A neutron diffraction study of a near-stoichiometric sample has shown a disordered orthorhombic structure with 72% occupancy of the 01 (chain) sites and with no interchange between Pr and Ba sites.

Interaction of 3-hydroxybenzoate-6-hydroxylase with cibacron blue

Cibacron blue is a potent inhibitor of 3-HBA-6-hydroxylase at a concentration < 1 mu M. Kinetic analyses revealed that at a concentration below 0.5 mu M the dye behaves as an uncompetitive inhibitor with respect to 3-HBA and competes with NADH for the same site on the enzyme. The alteration of the near-UV CD spectrum and quenching of the emission fluorescence of the enzyme by cibacron blue indicates a significant alteration in the environment of aromatic amino acid residues due to a stacking interaction and subtle conformatiodnal changes in the enzyme. The concentration-dependent quenching of the intrinsic fluorescence of the enzyme by cibacron blue was employed to determine the binding parameters such as association constant (K-a) and stoichiometry (r) for the enzyme-dye complex.

First-principles analysis of electron correlation, spin ordering and phonons in the normal state of FeSe1-x

We present first-principles density-functional-theory-based calculations to determine the effects of the strength of on-site electron correlation, magnetic ordering, pressure and Se vacancies on phonon frequencies and electronic structure of FeSe1-x. The theoretical equilibrium structure (lattice parameters) of FeSe depends sensitively on the value of the Hubbard parameter U of on-site correlation and magnetic ordering. Our results suggest that there is a competition between different antiferromagnetic states due to comparable magnetic exchange couplings between first- and second-neighbor Fe sites. As a result, a short range order of stripe antiferromagnetic type is shown to be relevant to the normal state of FeSe at low temperature. We show that there is a strong spin-phonon coupling in FeSe (comparable to its superconducting transition temperature) as reflected in large changes in the frequencies of certain phonons with different magnetic ordering, which is used to explain the observed hardening of a Raman-active phonon at temperatures (similar to 100 K) where magnetic ordering sets in. The symmetry of the stripe antiferromagnetic phase permits an induced stress with orthorhombic symmetry, leading to orthorhombic strain as a secondary order parameter at the temperature of magnetic ordering. The presence of Se vacancies in FeSe gives rise to a large peak in the density of states near the Fermi energy, which could enhance the superconducting transition temperature within the BCS-like picture.

Micromechanics Of Fatigue Crack-Growth At Low Stress Intensities In A High-Strength Steel

An attempt to systematically investigate the effects of microstructural parameters in influencing the resistance to fatigue crack growth (FCG) in the near-threshold region under three different temper levels has been made for a high strength low alloy steel to observe in general, widely different trends in the dependence of both the total threshold stress intensity range, DELTA-K(th) and the intrinsic or effective threshold stress intensity range, DELTA-K(eff-th) on the prior austenitic grain size (PAGS). While a low strain hardening microstructure obtained by tempering at high temperatures exhibited strong dependence of DELTA-K(th) on the PAGS by virtue of strong interactions of crack tip slip with the grain boundary, a high strength, high strain hardening microstructure as a result of tempering at low temperature exhibited a weak dependence. The lack of a systematic variation of the near-threshold parameters with respect to grain size in temper embrittled structures appears to be related to the wide variations in the amount of intergranular fracture near threshold. Crack closure, to some extent provides a basis on which the increases in DELTA-K(th) at larger grain sizes can be rationalised. This study, in addition, provides a wide perspective on the relative roles of slip behaviour embrittlement and environment that result in the different trends observed in the grain size dependence of near-threshold fatigue parameters, based on which the inconsistency in the results reported in the literature can be clearly understood. Assessment of fracture modes through extensive fractography revealed that prior austenitic grain boundaries are effective barriers to cyclic crack growth compared to martensitic packet boundaries, especially at low stress intensities. Fracture morphologies comprising of low energy flat transgranular fracture can occur close to threshold depending on the combinations of strain hardening behaviour, yield strength and embrittlement effects. A detailed consideration is given to the discussion of cyclic stress strain behaviour, embrittlement and environmental effects and the implications of these phenomena on the crack growth behaviour near threshold.

Phase stability and dielectric properties of ceramics in the Pb(Zn1/3Nb2/3)O3-Pb(Ni1/3Nb2/3)O3-PbTio3 relaxor ferroelectric system

The perovskite structure in Pb(Zn1/3Nb2/3)O3 can be stabilized by the addition of Pb(Ni1/3Nb2/3)O3 and PbTiO3.Pb(Ni1/3Nb2/3)O3 assists in lowering the sintering temperature and shifting the Curie temperature of ceramics while PbTiO3 helps to optimize the dielectric properties. The phase stability and dielectric properties of several compositions in the Pb(Zn1/3Nb2/3)O3-Pb(Ni1/3Nb2/3)O3-PbTiO3 ternary relaxor ferroelectric system were investigated for possible capacitor applications. The effect of calcining and sintering temperature on the stability of perovskite phase in PZN rich compositions was studied extensively as a function of composition. The boundary line separating perovskite and mixed phases was determined for compositions near PZN. Several compositions can be sintered below 1050°C. The dielectric properties of compositions near the mixed phase boundary showed strong dependence on the percentage of pyrochlore phase. Compositions with a dielectric constant of 12.500 at room temperature have been identified which meet Z5T and Y5U specifications for dielectric constant and tan δ.

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a vertical heated plate

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a heated vertical plate is studied for high Rayleigh numbers. Similarity solutions are obtained within the frame work of boundary layer theory for a power law variation in surface temperature,T Wpropx lambda and surface injectionv Wpropx(lambda–1/2). The analysis incorporates the expression connecting porosity and permeability and also the expression connecting porosity and effective thermal diffusivity. The influence of thermal dispersion on the flow and heat transfer characteristics are also analysed in detail. The results of the present analysis document the fact that variable porosity enhances heat transfer rate and the magnitude of velocity near the wall. The governing equations are solved using an implicit finite difference scheme for both the Darcy flow model and Forchheimer flow model, the latter analysis being confined to an isothermal surface and an impermeable vertical plate. The influence of the intertial terms in the Forchheimer model is to decrease the heat transfer and flow rates and the influence of thermal dispersion is to increase the heat transfer rate.

Screw dynamo and the generation of nonaxisymmetric magnetic fields

A mechanism is presented here for the amplification of large-scale nonaxisymmetric magnetic fields as a manifestation of the dynamo effect. We generalize a result on restrictions of dynamo actions due to laminar flow originally derived by Zeldovich, Ruzmaikin, and Sokolov [Magnetic Fields in Astrophysics (Gordon and Breach, New York, 1983)]. We show how a screwlike motion having phi and z components of velocity can help to grow a magnetic field. This model postulates a large-scale flow having phi and z components with radial dependences (helical flow). Shear in the radial field, because of a near-flux-freezing condition, causes amplification of the phi component of the magnetic field. The radial and axial components grow due to the presence of turbulent diffusion. The shear in the large scale flow induces an indefinite growth of magnetic field without the a effect; nevertheless, turbulent diffusion forms an important part in the overall mechanism.

Turbulent near-wake development behind a flat plate

An asymptotic analysis of the two-dimensional turbulent near-wake flow behind a Rat plate with sharp trailing edge has been formulated, The feature that the near-wake, which is dominated by the mixing of the oncoming turbulent boundary layers retains, to a large extent, the memory of the turbulent structure of the upstream boundary layer has been exploited to develop the analysis. This analysis leads to two regions of the near-wake flow (the inner near-wake and the outer near-wake) for which the governing equations are derived. The matching conditions among these regions lead to a logarithmic variation in the normal direction in the overlapping region surrounding the inner near-wake. These features are validated by the available experimental data. Similarity solutions for the velocity distribution (which satisfy the required matching conditions) in the inner near-wake and outer near-wake regions have been obtained by making the appropriate eddy-viscosity assumptions, Uniformly valid solutions for velocity distribution have been constructed for the near-wake. The solutions show good agreement with available experimental data. (C) Elsevier, Paris.

Analysis of laminates with ply drops

Thickness tapered laminates obtained by terminating a certain number of plies contain resin-rich areas called ‘resin pockets’ near ply drops, where high stress concentrations exist. Study of the effects of ply drops and resin pockets on the tensile behaviour of tapered laminates considering certain important parameters like taper angle, the number of plies dropped, and the fiber orientation is reported here. Estimation of the tensile strength of tapered laminates necessitates accurate determination of the state of stress near the ply-drop region, which is, in general, three-dimensional (3-D) in nature. Recognising the fact that full 3-D finite-element analysis becomes computationally exorbitant, special layered 3-D finite-element analysis is carried out. Laminates with ply drops along only one direction are analysed to elicit the nature of the local bending effects occurring near the ply drops. Complete 3-D Tsai–Wu criterion considering all the six stress components is used to obtain a quick and comparative assessment of the tensile strength of these laminates. High stress concentration zones are identified and the effects of number of plies dropped at a station and resin pocket geometry are illustrated. The mechanism of load transfer near ply drops and the local bending that occurs are described. Susceptibility of ply drop zones to the onset and subsequent growth of delaminations is also brought out.

Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.