Structural analysis of Salmonella enterica effector protein SopD

Salmonella outer protein D (SopD) is a type III secreted virulence effector protein from Salmonella enterica. Full-length SopD and SopD lacking 16 amino acids at the N-terminus (SopDDeltaN) have been expressed as fusions with GST in Escherichia coli, purified with a typical yield of 20-30 mg per litre of cell culture and crystallized. Biophysical characterization has been carried out mainly on SopDDeltaN. Analytical size exclusion chromatography shows that SopDDeltaN is monomeric and probably globular in aqueous solution. The secondary structure composition, calculated from the CD spectrum, is mixed (38% alpha-helix and 26% beta-strand). Sequence analysis indicates that SopD contains a coiled coil motif, as found in numerous other type III secretion system-associated proteins. This suggests that SopD has the potential for one or more heterotypic protein-protein interactions. Limited trypsin digestion of SopDDeltaN, monitored by both one-dimensional proton NMR spectroscopy and SDS-PAGE, shows that the protein has a large, protease-resistant core domain of 286 amino acid residues. This single-domain architecture suggests that SopD lacks a cognate chaperone. In crystallization trials, SopDDeltaN produced better crystals than either full-length SopD or trypsin-digested SopDDeltaN. Diffraction to 3.0 Angstrom resolution has so far been obtained from crystals of SopDDeltaN

Intraerythrocytic pH variations during hemodialysis: A 31P NMR study

Intraerythrocytic pH variations during hemodialysis: A 31P NMR study. Before hemodialysis, patients have an intraerythrocytic pH (pHi) and an extracellular pH, measured in whole blood (pHo), which are lower than those of healthy controls. During bicarbonate hemodialysis, pHi values continuously increase, approaching a normal value at the end of the session. Concomitantly, pHo values follow similar variations. During acetate hemodialysis, pHi values exhibit a steep initial decrease, reaching a minimum after about 15 minutes. Concurrently, however, pHo values decrease only slightly. This phenomenon seems to originate in the intraerythrocytic medium and might be due to a shift in intracellular CO2/bicarbonate equilibrium. This drop in pHi exhibits interpatient variability, suggesting that the magnitude of pH decrease would be correlated with the degree of the problems observed in some patients undergoing acetate hemodialysis

Solving the Boltzmann Equation on GPU

We show how to accelerate the direct solution of the Boltzmann equation using Graphics Processing Units (GPUs). In order to fully exploit the computational power of the GPU, we choose a method of solution which combines a finite difference discretization of the free-streaming term with a Monte Carlo evaluation of the collision integral. The efficiency of the code is demonstrated by solving the two-dimensional driven cavity flow. Computational results show that it is possible to cut down the computing time of the sequential code of two order of magnitudes. This makes the proposed method of solution a viable alternative to particle simulations for studying unsteady low Mach number flows.Comment: 18 pages, 3 pseudo-codes, 6 figures, 1 tabl

Electroweak Physics at HERA: Introduction and Summary

A high luminosity upgrade of HERA will allow the measurement of standard model parameters and the neutral current couplings of quarks. These results will have to be consistent with other precision measurements or indicate traces of new physics. The analysis of $W$ production will complement future results of LEP 2 and the Tevatron. We summarize the main results and conclusions obtained by the working group on Electroweak Physics concerning the potential of future experimentation at HERA.Comment: 12 pages (Latex), 4 figures (Postscript), to appear in the Proceedings of the Workshop on Future Physics at HERA. The complete report by the working group on electroweak physics at HERA is available from http://www.desy.de/~heraws96/proceeding

Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs

Background: Most developments in quantitative genetics theory focus on the study of intra-breed/line concepts. With the availability of massive genomic information, it becomes necessary to revisit the theory for crossbred populations. We propose methods to construct genomic covariances with additive and non-additive (dominance) inheritance in the case of pure lines and crossbred populations. Results: We describe substitution effects and dominant deviations across two pure parental populations and the crossbred population. Gene effects are assumed to be independent of the origin of alleles and allelic frequencies can differ between parental populations. Based on these assumptions, the theoretical variance components (additive and dominant) are obtained as a function of marker effects and allelic frequencies. The additive genetic variance in the crossbred population includes the biological additive and dominant effects of a gene and a covariance term. Dominance variance in the crossbred population is proportional to the product of the heterozygosity coefficients of both parental populations. A genomic BLUP (best linear unbiased prediction) equivalent model is presented. We illustrate this approach by using pig data (two pure lines and their cross, including 8265 phenotyped and genotyped sows). For the total number of piglets born, the dominance variance in the crossbred population represented about 13 % of the total genetic variance. Dominance variation is only marginally important for litter size in the crossbred population. Conclusions: We present a coherent marker-based model that includes purebred and crossbred data and additive and dominant actions. Using this model, it is possible to estimate breeding values, dominant deviations and variance components in a dataset that comprises data on purebred and crossbred individuals. These methods can be exploited to plan assortative mating in pig, maize or other species, in order to generate superior crossbred individuals in terms of performance

Towards Zero-waste Mineral Carbon Sequestration Via Two-way Valorization of Ironmaking Slag

A three-stage process was developed to transform blast furnace slag (BFS) into two valuable products: precipitated calcium carbonate (PCC) and zeolitic materials. The conceptualized process aims to simultaneously achieve sustainable CO2 sequestration and solid waste elimination. Calcium is first selectively extracted by leaching with an organic acid, followed by carbonation of the leachate to precipitate CaCO3. In parallel, the hydrothermal conversion of the extracted solid residues in alkali solution induces the dissolution/precipitation mechanism that leads to the formation of micro- and meso-porous zeolitic materials. Leaching selectivity was identified as a key factor in the valorization potential of both products. Acetic acid satisfactorily limited the leaching of aluminium, required for the subsequent synthesis of zeolites, and carbonation of the acetic acid leachate resulted in the production of PCC of varied mineralogy and morphology, depending on processing conditions. In the hydrothermal conversion stage, the formation of zeolitic phases was observed, and their characteristics were found to vary depending on the calcium extraction efficiency in the previous stage, and the alkali (NaOH) concentration. The zeolitic phases produced, in order of increasing valorization potential, were: tobermorite, sodalite, lazurite, and analcime