An open source protein gel documentation system for proteome analyses

Data organization and data mining represents one of the main challenges for modern high throughput technologies in pharmaceutical chemistry and medical chemistry. The presented open source documentation and analysis system provides an integrated solution (tutorial, setup protocol, sources, executables) aimed at substituting the traditionally used lab-book. The data management solution provided incorporates detailed information about the processing of the gels and the experimental conditions used and includes basic data analysis facilities which can be easily extended. The sample database and User-Interface are available free of charge under the GNU license from http://webber.physik.uni-freiburg.de/~fallerd/tutorial.htm.     

On the nature of the BOLD fMRI contrast mechanism

Since its development about 15 years ago, functional magnetic resonance imaging (fMRI) has become the leading research tool for mapping brain activity. The technique works by detecting the levels of oxygen in the blood, point by point, throughout the brain. In other words, it relies on a surrogate signal, resulting from changes in oxygenation, blood volume and flow, and does not directly measure neural activity. Although a relationship between changes in brain activity and blood flow has long been speculated, indirectly examined and suggested and surely anticipated and expected, the neural basis of the fMRI signal was only recently demonstrated directly in experiments using combined imaging and intracortical recordings. In the present paper, we discuss the results obtained from such combined experiments. We also discuss our current knowledge of the extracellularly measured signals of the neural processes that they represent and of the structural and functional neurovascular coupling, which links such processes with the hemodynamic changes that offer the surrogate signal that we use to map brain activity. We conclude by considering applications of invasive MRI, including injections of paramagnetic tracers for the study of connectivity in the living animal and simultaneous imaging and electrical microstimulation.     

Analysis of relative isotopologue abundances for quantitative profiling of complex protein mixtures labelled with the acrylamide/D3-acrylamide alkylation tag system

The new method of analysis of relative isotopologue abundances (ARIA) applied here is based on the evaluation of total isotope patterns of tryptic protein fragments measured by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) to calculate the mixing ratios of composites consisting of stable isotope labelled and isotopically natural (unlabelled) proteins, as described in an accompanying paper in this issue. Recently, Sechi (Rapid Commun. Mass Spectrom. 2002; 16: 1416-1424) and Gehanne et al. (Rapid Commun. Mass Spectrom. 2002; 16: 1692-1698) introduced the use of differential quantitative mass analysis by MALDI-TOFMS using mixtures of standard proteins alkylated prior to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with either acrylamide (AA) or deuterium-labelled [2,3,3'-D(3)]-acrylamide (D3AA). In the present study we validate the AA/D3AA system, firstly by measuring the yield of proteins alkylated with AA, and secondly by using differential radioactive labels ((125)I and (131)I) to quantitatively establish that non-comigration in 2D-PAGE is negligible. ARIA is then applied to quantitatively estimate the relative proportions of peptides labelled with AA or D3AA in the validated system, using typical silver-stained 2D-PAGE protein spots from 2D gels loaded with 150 microg of total liver protein. The precision and limitations of ARIA quantification of peptides differentially alkylated with isotopomeric reagents are discussed.     

Structure of 1-Thia-closo-dodecaborane(11), 1-SB11H11, as determined by microwave spectroscopy complemented by quantum chemical calculations

The microwave spectrum of 1-thia-closo-dodecaborane(11), 1-SB(11)H(11), has been investigated in the 23-62 GHz spectral region. The molecule is found to have C(5v) symmetry. The spectra of several isotopomers have been assigned and a precise substitution structure of the non-hydrogen atoms has been determined. The structure is in quite good agreement with the one determined previously by electron diffraction. Density functional theory calculations at the B3LYP/cc-pVTZ level were found to predict a structure that is in good agreement with the substitution structure.     

Direct continuous supercritical fluid extraction as a novel method of wine analysis. Comparison with conventional indirect extraction and implications for wine variety identification

Direct supercritical fluid extraction (SFE) of wines with carbon dioxide was compared to SFE of the sorbent used for solid-phase extraction of the same wine samples (SPE-SFE). Compared to SPE-SFE, the direct SFE results in amore specific and representative gas chromatographic fingerprint of the wine sample. The multivariate statistical processing of the direct SFE-GC data provides a clear-cut and sharp discrimination among the individual wine varieties while the discrimination based on the SPE-SFE-GC data is relatively poor. This finding reflects the adverse effects of additional analyte-sorbent interactions and sorption/desorption steps involved in SPE-SFE.     

Contents of Volume 24 (2003)

Volume Contents

Contents of Volume 23 (2003)     

Facility Update: The Center for Advanced Microstructures and Devices: A Status Report

The progress in the field of high resolution X-ray microscopy is caused in particular by the rapid developments of synchrotron radiation sources and X-ray optical elements, by the extension of the energy range, improved designs of X-ray microscopes and scanning X-ray microscopes, the use of CCD detectors with high detective quantum efficiency, the introduction of new imaging techniques, and the development of new fields of application.     

On line shape analysis in X-ray photoelectron spectroscopy

Any solid state X-ray photoelectron spectrum (XPS) contains contributions due to multiple inelastic scattering in the bulk, surface excitations, energy losses originating from the screening of the final state hole (intrinsic losses), and, for non-monochromatized incident radiation, ghost lines originating from the X-ray satellites. In the present paper it is shown how all these contributions can be consecutively removed from an experimental spectrum employing a single general deconvolution procedure. Application of this method is possible whenever the contributions mentioned above are uncorrelated. It is shown that this is usually true in XPS to a good approximation. The method is illustrated on experimental non-monochromatized MgK spectra of Au acquired at different detection angles but for the same angle of incidence of the X-rays.