Identification of novel biomarker candidates by differential peptidomics analysis of cerebrospinal fluid in Alzheimer's disease

The objective of this work was the application of peptidomics technologies for the detection and identification of reliable and robust biomarkers for Alzheimer's disease (AD) contributing to facilitate and further improve the diagnosis of AD. Using a new method for the comprehensive and comparative profiling of peptides, the differential peptide display (DPD), 312 cerebrospinal fluid (CSF) samples from AD patients, cognitively unimpaired subjects and from patients suffering from other primary dementia disorders were analysed as four independent analytical sets. By combination with a cross validation procedure, candidates were selected from a total of more than 6,000 different peptide signals based on their discriminating power. Twelve candidates were identified using mass-spectrometric techniques as fragments of the possibly neuroprotective neuroendocrine protein VGF and another one as the complement factor C3 descendent C3f. The combination of peptide profiling and cross validation resulted in the detection of novel potential biomarkers with remarkable robustness and a close relation to AD pathophysiology.     

Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase

Modelling of the first step of the deacylation reaction of benzylpenicillin in the E. coli TEM1 beta-lactamase (with B3LYP/6-31G + (d)//AM1-CHARMM22 quantum mechanics/molecular mechanics methods) shows that a mechanism in which Glu166 acts as the base to deprotonate a conserved water molecule is both energetically and structurally consistent with experimental data; the results may assist the design of new antibiotics and beta-lactamase inhibitors.     

Few-boson dynamics in double wells: from single-atom to correlated pair tunneling

We investigate few-boson tunneling in a one-dimensional double well, covering the full crossover from weak interactions to the fermionization limit of strong correlations. Based on exact quantum-dynamical calculations, it is found that the tunneling dynamics of two atoms evolves from Rabi oscillations to correlated pair tunneling as we increase the interaction strength. Near the fermionization limit, fragmented-pair tunneling is observed and analyzed in terms of the population imbalance and two-body correlations. For more atoms, the tunneling dynamics near fermionization is shown to be sensitive to both atom number and initial configuration.     

Electrochemical, morphological and microstructural characterization of carbon film resistor electrodes for application in electrochemical sensors

The electrochemical and microstructural properties of carbon film electrodes made from carbon film electrical resistors of 1.5, 15, 140 Ω and 2.0 kΩ nominal resistance have been investigated before and after electrochemical pre-treatment at +0.9 V vs SCE, in order to assess the potential use of these carbon film electrodes as electrochemical sensors and as substrates for sensors and biosensors. The results obtained are compared with those at electrodes made from previously investigated 2 Ω carbon film resistors. Cyclic voltammetry was performed in acetate buffer and phosphate buffer saline electrolytes and the kinetic parameters of the model redox system Fe(CN)₆^3−/4− obtained. The 1.5 Ω resistor electrodes show the best properties for sensor development with wide potential windows, similar electrochemical behaviour to those of 2 Ω and close-to-reversible kinetic parameters after electrochemical pre-treatment. The 15 and 140 Ω resistor electrodes show wide potential windows although with slower kinetics, whereas the 2.0 kΩ resistor electrodes show poor cyclic voltammetric profiles even after pre-treatment. Electrochemical impedance spectroscopy related these findings to the interfacial properties of the electrodes. Microstructural and morphological studies were carried out using contact mode Atomic Force Microscopy (AFM), Confocal Raman spectroscopy and X-ray diffraction. AFM showed more homogeneity of the films with lower nominal resistances, related to better electrochemical characteristics. X-ray diffraction and Confocal Raman spectroscopy indicate the existence of a graphitic structure in the carbon films.     

Binding sites of the viral RNA element TAR and of TAR mutants for various peptide ligands, probed with LILBID: A new laser mass spectrometry

A new laser-based mass spectrometry method, called laser induced liquid bead ion desorption (LILBID), was applied to investigate RNA:ligand interactions. As model system the HIV Tat:TAR transactivation complex and its binding behavior were analyzed. TARwt of HIV Type 1 and Type 2 and different artificial mutants were compared regarding their binding to Tat and different peptide ligands. Specific and nonspecific association to TAR was deduced, with the bulge being the well known specific binding site of TAR. In the case of triple arginine (RRR) as a nonspecific ligand, multiple electrostatic binding to TAR was found at higher concentration of RRR. This contrasted with the formation of only ternary complexes in competitive binding studies with TAR, Tat, and potential inhibitors. The fact that the stoichiometries of the complexes can be determined is a major advantage of MS methods over the widely applied fluorimetric methods. A quantitative evaluation of the spectra by a numeric model for ternary complex formation allows conclusions about the role and strength of the binding sites of the RNAs, the specificity and affinity of different ligands, the determination of apparent IC50 and KD values, and a comparison of the binding efficiencies of potential inhibitors.