Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Resolution optimisation in micellar electrokinetic chromatography using empirical models

Theoretical and empirical models can be used to model the migration or separation characteristics in micellar electrokinetic chromatography in order to optimise the resolution. In this paper only empirical models were used, because it is easier and more straightforward to obtain these models. Several empirical approaches for the optimisation of the resolution were compared in order to determine which response should be modelled preferably. The use of models of the effective mobility in combination with average plate numbers proved to be the most suitable approach to optimisation of the resolution, because the relative prediction errors of the models of the effective mobility were a factor of 2-4 smaller than the relative prediction errors of the models of the apparent mobility. Moreover for the least separated peak pair the resolutions based on the models of the apparent and effective mobility showed relative prediction errors that were approximately a factor of 2 smaller than the relative prediction errors of the resolutions based on the models of the resolution and separation factor. The predictions of the separation factor based on the different models generally showed lower prediction errors than the predictions of the corresponding resolutions. Although the relative prediction errors were large, particularly for closely migrating compounds, the empirical approach will probably lead to the optimum separation buffer composition.     

End-point construction and systematic titration error in linear titration curves-precipitation reactions

The systematic titration error which is introduced by the intersection of tangents to hyperbolic titration curves is discussed for precipitation reactions. A simple expression for the systematic titration error is derived, and S/C_x² is proposed as a measure of the sharpness of the titration curve. The effects of the conditional solubility product (S), the concentration of the unknown component (C_x), and the ranges used for the construction of the end-point, are considered. A graphical method is presented for the selection of pairs of ranges which result in small systematic titration errors. For equal values of S/C_x² and 1/KC_x, the optimum combinations of ranges are different for precipitation and complexation titrations. The differences are not large for values smaller than about 0.002. For titration curves with a reversed L-shape, the error is calculated when the end-point is constructed by the intersection of the tangent to the second branch of the curve with volume axis; in this case equal ranges result in the same titration error for equal values of S/C_x² and 1/KC_x. The systematic titration error is equal to -S/C_x² when the tangent to the curve is taken at f_a = 3.0.     

Estimation of individual ultraviolet spectra in incomplete two-component separations by high-performance liquid chromatography

A method is described for the estimation of spectral features in a two-component chromatographic peak by means of a u.v. diode-array detector. The calculation relies on the assumption that the front of a fused chromatographic peak contains a single pure component. The spectrum of this component is used in calculating the concentration profile of the other component, thus allowing the determination of a solution band for the spectrum of the second component. The boundaries of the solution band are based on non-negativity restrictions of chromatographic and spectral features. The method does not require the use of principal components analysis.     

Studies on photoinduced effects in pulse-electrodeposited Ag/Hg-1212/CdSe hetero-nanostructures

Metal/superconductor/semiconductor (Ag/Hg-1212/CdSe) hetero-nanostructures have been fabricated using pulse-electrodeposition technique and are characterized by X-ray diffraction (XRD), full-width at half-maximum (FWHM) and scanning electron microscopy (SEM) studies. The junction capacitance of Ag/Hg-1212, Hg-1212/CdSe and Ag/Hg-1212/CdSe heterojunctions is measured in dark and under laser irradiation at room temperature. The nature of the junction formed and built-in-junction potentials were determined. The increase in carrier concentration across the junction due to photo-irradiation has been observed.     

Effect of laser irradiation of C-V characteristics of electrodeposited Ag/Tl-2223/CdSe hetero-nanostructures

One of the innovative technological directions for the high-temperature superconductors has been persued by fabricating the heteroepitaxial multilayer structures such as superconductor-semiconductor heterostructures. In the present investigation, metal/superconductor/semiconductor (Ag/Tl-2223/CdSe) hetero-nanostructures have successfully been fabricated using dc electrodeposition technique and were characterized by X-ray diffraction (XRD), full-width at half-maximum (FWHM) and scanning electron microscopy (SEM) studies. The measurement of junction capacitance as a function of biasing voltage was used for the estimation of junction built-in-potential (V _D) and to study the charge distribution in a heterojunction. The Mott-Schottky plots were measured for each junction in dark and under the photo-irradiation. The effect of laser irradiation on C-V characteristics of hetero-nanostructure has been studied.     

Glycopeptide and Oligosaccharide Libraries

Despite the burgeoning interest in the various biological functions and consequent therapeutic potential of the vast number of oligosaccharides found in nature on glycoproteins and cell surfaces, the development of combinatorial carbohydrate chemistry has not progressed as rapidly as expected. The reason for this imbalance is rooted in the difficulty of oligosaccharide assembly and analysis that renders synthesis a rather cumbersome endeavor. Parallel approaches that generate series of analogous compounds rather than real libraries have therefore typically been used. Since generally low affinity is obtained for interactions between carbohydrate receptors and modified oligosaccharides designed as mimetics of natural carbohydrate ligands, glycopeptides have been explored as alternative mimics. Glycopeptides have been proven in many cases to be superior ligands with higher affinity for a receptor than the natural carbohydrate ligand. High-affinity glycopeptide ligands have been found for several types of receptors including the E-, P-, and L-selectins, toxins, glycohydrolases, bacterial adhesins, and the mannose-6-phosphate receptor. Furthermore, the assembly of glycopeptides is considerably more facile than that of oligosaccharides and the process can be adapted to combinatorial synthesis with either glycosylated amino acid building blocks or by direct glycosylation of peptide templates. The application of the split and combine approach using ladder synthesis has allowed the generation of very large numbers of compounds which could be analyzed and screened for binding of receptors on solid phase. This powerful technique can be used generally for the identification and analysis of the complex interaction between the carbohydrates and their receptors.     

New probabilistic versions of the SIMCA and CLASSY Classification methods : Part 1. Theoretical description

The probabilistic SIMCA and CLASSY methods for multivariate classification are defined and explained in detail. The differences between the present algorithms and previous versions are described. Both probabilistic SIMCA and CLASSY methods construct principal-component class models and assume an ormal distribution for the residuals. The methods differ in the distributional assumptions for the object scores within the class model space. Details are given for the construction of probability density functions which conform to the model assumptions, and which can be substituted in Bayes' theorem to obtain posterior classification probabilities.     

New probabilistic version of the simca and classy classification methods : Part 2. Practical evaluation

The new probabilistic versions of SIMCA and CLASSY described in Part 1 are evaluated. Their classification performance is found to be generally better than those of the old versions. The results are also compared with those of the ALLOC and SLDA classification methods. General over-confident behaviour of the new SIMCA and CLASSY methods as well as ALLOC and SLDA is noted for two of the three data sets investigated (Iris and two wine data sets).