Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.

The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3', 5'-bis pyrophosphate (ppGpp) is increased. This increase allows ppGpp to bind to BipA and switch its binding specificity from ribosomes to small ribosomal subunits. A conformational change of BipA upon ppGpp binding could explain the ppGpp regulation of the binding specificity of BipA. Here, we present the structures of the full-length BipA from Escherichia coli in apo, GDP-, and ppGpp-bound forms. The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form. This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present. This molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response

Combination of automated solid-phase and enzymatic oligosaccharide synthesis provides access to α(2,3)-sialylated glycans

A synthetic strategy combining automated solid-phase chemical synthesis and enzymatic sialylation was developed to access α(2,3)-sialylated glycans.</p

Fully electromagnetic nonlinear gyrokinetic equations for tokamak edge turbulence

An energy conserving set of the fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to both L-mode turbulence with large amplitude and H-mode turbulence in the presence of high E Χ B shear has been derived. The phase-space action variational Lie perturbation method ensures the preservation of the conservation laws of the underlying Vlasov-Maxwell system. Our generalized ordering takes ρ[sub ]i [\sub]<< ρϑ¡ ~ LE ~ Lp << R (here ρ[sub ]i [\sub] is the thermal ion Larmor radius and ρϑ¡ = [B over Bϑ] ρ[sub ]i [\sub]), as typically observed in the tokamak H-mode edge, with LE and Lp being the radial electric field and pressure gradient lengths. We take κ[sub ] perpendicular to[/sub] ρ[sub ]i [\sub] ~ 1 for generality, and keep the relative fluctuation amplitudes eδφ ⁄ Τ[sub ]i [\sub]~ δΒ ⁄ Β up to the second order. Extending the electrostatic theory in the presence of high E Χ B shear [Hahm, Phys. Plasmas 3, 4658 (1996)], contributions of electromagnetic fluctuations to the particle charge density and current are explicitly evaluated via pull-back transformation from the gyrocenter distribution function in the gyrokinetic Maxwell's equation

A Procedure for Determination of Degradation Acceptance Criteria for Structures and Passive Components in Nuclear Power Plants

The Korea Atomic Energy Research Institute (KAERI) has been collaborating with Brookhaven National Laboratory since 2007 to develop a realistic seismic risk evaluation system which includes the consideration of aging of structures and components in nuclear power plants (NPPs). This collaboration program aims at providing technical support to a five-year KAERI research project, which includes three specific areas that are essential to seismic probabilistic risk assessment: (1) probabilistic seismic hazard analysis, (2) seismic fragility analysis including the effects of aging, and (3) a plant seismic risk analysis. The understanding and assessment of age-related degradations of structures, systems, and components and their impact on plant safety is the major goal of this KAERI-BNL collaboration. Four annual reports have been published before this report as a result of the collaboration research

Electronic structure of crystalline binary and ternary Cd-Te-O compounds

The electronic structure of crystalline CdTe, CdO, $\alpha$-TeO$_2$, CdTeO$_3$ and Cd$_3$TeO$_6$ is studied by means of first principles calculations. The band structure, total and partial density of states, and charge densities are presented. For $\alpha$-TeO$_2$ and CdTeO$_3$, Density Functional Theory within the Local Density Approximation (LDA) correctly describes the insulating character of these compounds. In the first four compounds, LDA underestimates the optical bandgap by roughly 1 eV. Based on this trend, we predict an optical bandgap of 1.7 eV for Cd$_3$TeO$_6$. This material shows an isolated conduction band with a low effective mass, thus explaining its semiconducting character observed recently. In all these oxides, the top valence bands are formed mainly from the O 2p electrons. On the other hand, the binding energy of the Cd 4d band, relative to the valence band maximum, in the ternary compounds is smaller than in CdTe and CdO.Comment: 13 pages, 15 figures, 2 tables. Accepted in Phys Rev

ELM triggering conditions for the integrated modeling of H-mode plasmas

Recent advances in the integrated modeling of ELMy H-mode plasmas are presented. A model for the H-mode pedestal and for the triggering of ELMs predicts the height, width, and shape of the H-mode pedestal and the frequency and width of ELMs. Formation of the pedestal and the L-H transition is the direct result of ExB flow shear suppression of anomalous transport. The periodic ELM crashes are triggered by either the ballooning or peeling MHD instabilities. The BALOO, DCON, and ELITE ideal MHD stability codes are used to derive a new parametric expression for the peeling-ballooning threshold. The new dependence for the peeling-ballooning threshold is implemented in the ASTRA transport code. Results of integrated modeling of DIII-D like discharges are presented and compared with experimental observations. The results from the ideal MHD stability codes are compared with results from the resistive MHD stability code NIMROD.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

GaN and InN nanowires grown by MBE: a comparison

Morphological, optical and transport properties of GaN and InN nanowires grown by molecular beam epitaxy (MBE) have been studied. The differences between the two materials in respect to growth parameters and optimization procedure was stressed. The nanowires crystalline quality has been investigated by means of their optical properties. A comparison of the transport characteristics was given. For each material a band schema was shown, which takes into account transport and optical features and is based on Fermi level pinning at the surface.Comment: 5 pages, 5 figure

Composite Skyrme Model with Vector Mesons

We study the composite Skyrme model, proposed by Cheung and G\"{u}rsey, introducing vector mesons in a chiral Lagrangian. We calculate the static properties of baryons and compare with results obtained from models without vector mesons.Comment: LaTeX, 9 pages, 3 figures, to be published in Phys. Rev.