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).     

Electrostatic free energy of weakly charged macromolecules in solution and intermacromolecular complexes consisting of oppositely charged polymers

When oppositely charged polyelectrolytes are mixed in water, attraction between oppositely charged groups may lead to the formation of polyelectrolyte complexes (associative phase separation, complex coacervation, interpolymer complexes). Theory is presented to describe the electrostatic free energy change when ionizable (annealed) (macro-)molecules form a macroscopic polyelectrolyte complex. The electrostatic free energy includes an electric term as well as a chemical term that is related to the dissociation of the ionic groups in the polymer. An example calculation for complexation of polyacid with polybase uses a cylindrical diffuse double layer model for free polymer in solution and electroneutrality within the complex and calculates the free energy of the system when the polymer is in solution or in a polyelectrolyte complex. Combined with a term for the nonelectrostatic free energy change upon complexation, a theoretical stability diagram is constructed that relates pH, salt concentration, and mixing ratio, which is in qualitative agreement with an experimental diagram obtained by Bungenberg de Jong (1949) for complex coacervation of arabic gum and gelatin. The theory furthermore explains the increased tendency toward phase separation when the polymer becomes more strongly charged and suggests that complexation of polyacid or polybase with zwitterionic polymer (e.g., protein) of the same charge sign (at the "wrong side" of the iso-electric point) may be due (in part) to an induced charge reversal of the protein.     

NMR relaxation of rigid molecules in the nematic phase of a discotic liquid crystal

Abstract

Frequency and temperature dependent NMR relaxation measurements were performed on deuteriated benzene, pyrene and triphenylene dissolved in the nematic phase of a discotic liquid crystal. The results show a strong frequency dependence of the spectral densities. Based on the symmetries of the system and the usual model for director fluctuations this frequency dependence should be equal for J ₁ and J ₂. From fitting the commonly used model of rotational diffusion and director fluctuations to the data we see that this is not the case for benzene and triphenylene, even though the fits themselves are satisfactory. Values for the elastic constants, effective viscosity and translational diffusion in similar discotic liquid crystals do not account quantitatively for the frequency dependence of benzene. For both pyrene and triphenylene quantitative comparison was impossible due to lack of translational diffusion data. We also find that the so-called cut-off wave-length is of the order of the dimensions of the liquid crystal molecules, just as in ordinary nematics.     

Dispersion of Gas Bubbles in Large-Scale Homogeneous Isotropic Turbulence

An approximate analysis is given of the dispersion of gas bubbles that rise at large Reynolds number through large-scale homogeneous, isotropic turbulence, characterized by the Kraichnan energy-spectrum function. A fairly well-established equation of motion of the bubbles, originally proposed by Thomas et al. [16], is used to derive a closed set of equations for the components of the dispersion tensor of the bubbles in a manner analogous to that used by Saffman [12] for fluid particles and by Pismen and Nir [10, 11] for solid particles. The equations are then solved to obtain the diffusivities and the intensities of bubble velocity fluctuations. Analytical solutions are compared with results from simulations of the bubble motion in a Gaussian random velocity field.     

An experimental study of the regimes of motion of spheres falling or ascending freely in a Newtonian fluid

This paper presents the results of an experimental investigation aimed at verifying some of the interesting conclusions of the numerical study by Jenny et al. concerning the instability and the transition of the motion of solid spheres falling or ascending freely in a Newtonian fluid. The phenomenon is governed by two dimensionsless parameters: the Galileo number G, and the ratio of the density of the spheres to that of the surrounding fluid ρ_s/ρ. Jenny et al. showed that the (G, ρ_s/ρ) parameter space may be divided into regions with distinct features of the trajectories followed eventually by the spheres after their release from rest. The characteristics of these ‘regimes of motion’ as described by Jenny et al., agree well with what was observed in our experiments. However, flow visualizations of the wakes of the spheres using a Schlieren optics technique raise doubts about another conclusion of Jenny et al., namely the absence of a bifid wake structure.     

Two-fluid model for the simultaneous flow of colloids and fluids in porous media

To describe the velocities of particles such as ions, protein molecules and colloids dispersed or dissolved in a fluid, it is important to also describe the forces acting on the fluid, including pressure gradients and friction of the fluid with the particles and with the porous media through which the fluid flows. To account for this problem, the use of a two-fluid model is described, familiar in the field of fluid mechanics, extended to include osmotic effects. We show how familiar relationships follow in various situations and give examples of combined fluid/particle transport in neutral and charged membranes driven by a combination of electrostatic, diffusional and pressure forces. The analysis shows how the same modeling framework can be generally used both for multidimensional electrokinetic flow through macroscopic channels and around macroscopic objects, as well as for mean-field modeling of transport through porous media such as gels and membranes.     

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.