Isolation of Escherichia coli inner membranes by metal affinity two-phase partitioning

As reduction of sample complexity is a central issue in membrane proteomic research, the need for new pre-fractionation methods is significant. Here we present a method for fast and efficient enrichment of Escherichia coli inner membranes expressing a His-tagged integral membrane L-fucose-proton symporter (FucP). An enriched inner membrane fraction was obtained from a crude membrane mixture using affinity two-phase partitioning in combination with nickel-nitrilotriacetic acid (Ni-NTA) immobilized on agarose beads. Due to interaction between the beads and FucP, inner membranes were selectively partitioned to the bottom phase of a polymer/polymer aqueous two-phase system consisting of poly(ethylene glycol) (PEG) and dextran. The partitioning of membranes was monitored by assaying the activity of an inner membrane marker protein and measuring the total protein content in both phases. The enrichment of inner membrane proteins in the dextran phase was also investigated by proteomic methodology, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), trypsin digestion and liquid chromatography in combination with tandem mass spectrometry (LC-MS/MS). Using a high level of significance (99.95%) in the subsequent database search, 36 proteins assigned to the inner membrane were identified in the bottom phase, compared to 29 when using the standard sucrose gradient centrifugation method for inner membrane isolation. Furthermore, metal affinity two-phase partitioning was up to 10 times faster than sucrose gradient centrifugation. The separation conditions in these model experiments provide a basis for the selective isolation of E. coli membranes expressing His-tagged proteins and can therefore facilitate research on such membrane proteomes.     

Preparation and characterization of terraced surfaces of low-index faces of anatase, rutile, and brookite

Simple polishing and relatively low temperature annealing procedures for preparing atomically flat terraced surfaces of various single-crystal TiO2 polymorphs are described. Anatase (101), anatase (001), rutile (100), rutile (110), and brookite (111) surfaces could all be prepared with a terraced surface structure as revealed in AFM images. The rutile (100) and (110) and anatase (101) surfaces were also shown to produce acceptable LEED patterns immediately upon insertion into a UHV system without the usual sputter and anneal cycles.     

Validation of the extended Tanaka column characterization protocol by multivariate analysis of chromatographic retention of low‐molecular‐weight analytes on reversed phase columns using methanol and acetonitrile as organic modifiers

The validity of the extended Tanaka column characterization procedure against the retention behavior of 101 analytes of widely differing properties chromatographed on five differing stationary phase chemistries has been established using a chemometric technique called principal component analysis (PCA). It was concluded that the simple and conveniently determined column characterization parameters covered the same space in the PCA loading plot as the retention times for the 101 differing analytes. This confirms that the ten column characterization parameters of the extended Tanaka protocol encode the same information as the retention times of the 101 analytes. Significant selectivity differences were observed between stationary phases and the mobile‐phase modifiers – MeOH and MeCN. PCA contribution plots served as a convenient way to highlight specific selectivity differences between stationary phases. logD values exhibited a poor correlation with retention indicating that retention in RP‐LC is not solely dictated by the analyte's hydrophobicity. The use of MeOH was found to generate greater selectivity differences with the five stationary phases than when MeCN is used.     

Enantiospecific kinking of DNA by a partially intercalating metal complex

Opposite enantiomers of [Ru(phenanthroline)(3)](2+) affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced by wedge-intercalation of one but not the other enantiomer. This effect is exploited by several classes of DNA operative proteins.     

Analysis of parameter effects on chemical reaction coupled transport phenomena in SOFC anodes

Mass, heat and momentum transport processes are strongly coupled by internal chemical reforming reactions in planar design solid oxide fuel cell (SOFC) anodes. In this paper, a three-dimensional computational fluid dynamics approach is applied to simulate and analyze reforming reactions of methane and various transport processes in a duct relevant for SOFC anodes. The results show that the anode duct design and operating parameters, grouped as three characteristic ratios, are significant for the chemical reactions and further for multi-species distribution, fuel gas transport and heat transfer in the sub-domains of the anode.     

Some remarks on the perturbation and variation–perturbation calculations of the free energy for quantum systems

A generalization of the Gibbs–Bogoliubov inequality F ? F₀ + 〈H ? H₀〉₀ for the free energy F is studied which leads to a variation principle for this quantity that may be of importance in certain computational applications to quantum systems. This approach is coupled with a study of the perturbation expansion of the free energy for a canonical ensemble with H = H₀ + λV in the general case when H₀ and V do not commute. The second- and high-order derivatives of the free energy with respect to the perturbation parameter λ are calculated. From the second-order term is finally obtained a second-order correction to the previous variational minimum for the free energy.     

Nucleic acid-metal interactions. IV. Complexes of Ag(I) with thymine and cytosine from studies of UV and IR dichroic spectra

The linear dichroism of the complexes of thymine and cytosine with silver(I) ions dispersed in stretched polyvinylalcohol films was measured in the infrared and in the near ultraviolet regions of the spectrum. The infrared results were helpful in establishing the orientation of the complexes in the films; they also confirmed that the site of silver binding in the case of cytosine involves the carbonyl oxygen. The ultraviolet spectra were deconvoluted into separate electronic transitions and the corresponding transition moments of silver complexes were determined.     

Accuracy of radial basis function interpolation and derivative approximations on 1-D infinite grids

Radial basis function (RBF) interpolation can be very effective for scattered data in any number of dimensions. As one of their many applications, RBFs can provide highly accurate collocation-type numerical solutions to several classes of PDEs. To better understand the accuracy that can be obtained, we survey here derivative approximations based on RBFs using a similar Fourier analysis approach that has become the standard way for assessing the accuracy of finite difference schemes. We find that the accuracy is directly linked to the decay rate, at large arguments, of the (generalized) Fourier transform of the radial function. Three different types of convergence rates can be distinguished as the node density increases – polynomial, spectral, and superspectral, as exemplified, for example, by thin plate splines, multiquadrics, and Gaussians respectively. Bengt Fornberg: The work was supported by NSF grants DMS-9810751 (VIGRE), DMS-0073048 and DMS-0309803.Natasha Flyer: The work was supported by the NSF grant DMS-9810751 (VIGRE).