Cerebrospinal fluid amyloid beta peptide patterns in Alzheimer's disease patients and nondemented controls depend on sample pretreatment: indication of carrier-mediated epitope masking of amyloid beta peptides

A quantitative urea-based amyloid beta (Abeta)-sodium dodecyl sulfate-polyacrylamide gel electrophoresis with Western immunoblot (Abeta-SDS-PAGE/immunoblot) reveals highly conserved and disease-specific Abeta peptide patterns (Abeta 1-37, 1-38, 1-39, 1-40, 1-42) in Alzheimer's disease (AD) patients and nondemented controls. For further standardization of this method, we analyzed cerebrospinal fluid (CSF) of eight probable AD patients and seven nondemented controls using different preanalytical procedures for Abeta-SDS-PAGE/immunoblot and Abeta1-42-enzyme linked immunosorbent assay (ELISA). Both diagnostic groups were discriminated significantly by absolute levels of Abeta1-42 and ratios of Abeta1-42/40, 1-42/38, 1-42/39. Preanalytical freezing of CSF led to a highly significant loss of all Abeta peptide species. This effect was most pronounced for Abeta1-42 and completely prevented by SDS-heat denaturation prior to freezing. Prolonged storage of SDS-heat denatured CSF led to a selective loss of Abeta1-42 and impaired the discrimination of diagnostic groups as measured by Abeta-SDS-PAGE/immunoblot. Neither freezing nor storage significantly affected absolute Abeta1-42 levels as determined by Abeta1-42-ELISA, but both impaired the discrimination of diagnostic groups. Hence, we suggest immediate analysis of samples for Abeta1-42-ELISA, analysis after a short freezing interval for Abeta-SDS-PAGE/immunoblot, and avoidance of prolonged storage intervals. Remarkably, Abeta-SDS-PAGE/immunoblot measured threefold higher levels of Abeta1-42 in CSF than Abeta1-42-ELISA. In summary, our results indicate carrier-mediated epitope masking of Abeta1-42.     

A scoring function for docking ligands to low-resolution protein structures

We present a docking method that uses a scoring function for protein-ligand docking that is designed to maximize the docking success rate for low-resolution protein structures. We find that the resulting scoring function parameters are very different depending on whether they were optimized for high- or low-resolution protein structures. We show that this docking method can be successfully applied to predict the ligand-binding site of low-resolution structures. For a set of 25 protein-ligand complexes, in 76% of the cases, more than 50% of ligand-contacting residues are correctly predicted (using receptor crystal structures where the binding site is unspecified). Using decoys of the receptor structures having a 4 A RMSD from the native structure, for the same set of complexes, in 72% of the cases, we obtain at least one correctly predicted ligand-contacting residue. Furthermore, using an 81-protein-ligand set described by Jain, in 76 (93.8%) cases, the algorithm correctly predicts more than 50% of the ligand-contacting residues when native protein structures are used. Using 3 A RMSD from native decoys, in all but two cases (97.5%), the algorithm predicts at least one ligand-binding residue correctly. Finally, compared to the previously published Dolores method, for 298 protein-ligand pairs, the number of cases in which at least half of the specific contacts are correctly predicted is more than four times greater.     

On the stability of backward differentiation methods

Summary The approximation of linear systemsy=–A(t)y+b(t) by backward differentiation methods up to order 5 is considered. It is proved that the error does not increase if the real symmetric matrixA(t) is positive definite andA(t) is negative semi-definite.     

Optimal centered forms

A simple expression for an optimal center of a centered form is presented. Among all possible centers within a given interval this center yields the greatest lower bound or the lowest upper bound of a centered form, respectively. It is also shown that one-sided isotonicity holds for such centered forms.     

Photofragmentation of closo-carboranes part 1: Energetics of decomposition

The ionic fragmentation following B 1s and C 1s excitation of three isomeric carborane cage compounds [closo-dicarbadodecaboranes: orthocarborane (1,2-C2B10H12), metacarborane (1,7-C2B10H12), and paracarborane (1,12-C2B10H12)] is compared with the energetics of decomposition. The fragmentation yields for all three molecules are quite similar. Thermodynamic cycles are constructed for neutral and ionic species in an attempt to systemically characterize single-ion closo-carborane creation and fragmentation processes. Lower energy decomposition processes are favored. Among the ionic species, the photon-induced decomposition is dominated by BH+ and BH2(+) fragment loss. Changes in ion yield associated with core to bound excitations are observed.     

Photoionization of atmospheric aerosol constituents and precursors in the 7-15 eV energy region: experimental and theoretical study

Photoionization mass spectrometry (PIMS) has been used to study the dissociative ionization of three anthropogenic atmospheric aerosol precursors (o-xylene, 2-methylstyrene, indene) and five of their main atmospheric degradation products (o-tolualdehyde, 2-methylphenol, o-toluic acid, phthalic acid, and phthaldialdehyde). Ionization and fragment appearance energies have been experimentally determined in the 7-15 eV photon energy regime. Moreover, intensive ab inito quantum chemical calculations have been performed to compute the first ionization energies and heats of formation of these compounds (including also phthalic anhydride). Several methods have been used, and the theoretical results are compared to the experimental values with the aim to find the best method to predict thermochemical data for similar molecules. The vacuum-UV fragmentation pathways following photoionization are discussed. The results of this work are important with respect to the analytical chemistry of these compounds since their basic gas phase ion energetics data are mostly unknown. They will help in interpreting real-time mass spectrometric measurements used for the study of organic aerosol formation in smog chambers and in the real atmosphere.     

On the pointwise matrix product and the mean value theorem

Bounds for the pointwise or Schur product of two matrices are derived with respect to the spectral norm 6·6. For real symmetric and positive semidefinite matrices Q=(q_ij) one of them gives a bound of 6|Q6, |Q|=(|q_ij|). Two of these bounds are applied to obtain a mean value theorem for g: t→f(A(t)) where A(t) is a matrix depending on a parameter t and f is a function on the spectrum of A(t).     

Energetic modelling for carbon fibre reinforced carbon

In this contribution an energetic model for multi-phase materials is developed describing the influence of microstructure on different length scales as well as the evolution of phase changes. Restrictions on the energy functional are discussed. In such a non-convex framework, interfacial contributions serve for relaxing the total energy. Such models can be applied to describe the macroscopic material properties of carbon fibre reinforced carbon where phase transitions between regions of different texture of the carbon matrix are observed on nanoscale as well as columnar microstructures on microscale [2]. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)