TissueDistributionDBs: a repository of organism-specific tissue-distribution profiles

Tissue-distribution profiles are crucial for understanding the characteristics of cells and tissues in terms of their differential expression of genes. Most of the currently available resources for tissue-distribution profiles are either specialized for a few particular organisms, tissue types and disease stages or do not consider the “tissue ontology” levels for the calculation of the tissue-distribution profiles. Therefore, we have developed “TissueDistributionDBs”, a repository of tissue-distribution profiles based on the expressed sequence tags (ESTs) data extracted from the UniGene database by employing “Tissue Ontology” available at BRENDA. To overcome the occurrence of the natural language variations in the EST’s source tissue-type terms, we have generated a “tissue synonym library” and standardized these tissue-type terms by cross-referencing to the controlled vocabulary for tissue-type terms available at BRENDA “Tissue Ontology”. Furthermore, we have provided a quantitative expression for genes among the tissue types at various anatomical levels by constructing “tissue slims”. Concurrently, the expression among tissue types is used for tissue-distribution calculations. The resulting output profiles can be queried by the Sequence Retrieval System (SRS) and are currently available for 20 different model organisms. We benchmarked our database system against the Swissprot database using a set of 40 different tissue types. This database system is useful for the understanding of the tissue-specific expression patterns of genes, which have implications for the identification of possible new therapeutic drug targets, in gene discovery, and in the design and analysis of micro-arrays. TissueDistributionDBs can be accessed via the World Wide Web (www) at http://genius.embnet.dkfz-heidelberg.de/menu/tissue_db/.     

Electrokinetic investigations of charged porous membranes

Asymmetric ultrafiltration membranes were prepared from fully aromatic polyamides differing in the diamine monomers of the polymeric backbone and from polysulfone. Nanofiltration membranes were made from polysulfone and polyethersulfone. The polysulfone as well as the polyethersulfone were chemically modified to change the surface charges of the membranes that were made from these polymers. This means neutral, positively as well as negatively charged membranes could be employed for the measurements. The surface properties of the membranes as a function of pH were determined by measuring the streaming potential in a perpendicular and horizontal mode. Applying proteins the values of the streaming potential changed depending on the original charges of the membranes as well as on the pH of the solution. The values shifted to either higher or lower absolute values. Thus, characterization of unused and used membranes can be carried out by electrokinetic measurements. This was also demonstrated using a membrane fitted out with invertase. The zeta potential of nanofiltration membranes, however, was only evaluated from the results obtained with the horizontally run cell.     

Use of solid-phase microextraction-capillary-gas chromatography (SPME-CGC) for the varietal characterization of wines by means of chemometrical methods

The extraction of wine aroma compounds was studied by direct-SPME (DI/SPME), headspace-SPME (HS/SPME) and multiple-headspace-extraction-SPME (MHE/SPME). The aromagrams obtained by HS/SPME-CGC were evaluated with chemometrical methods for the varietal classification of wines. Received: 25 July 1997 / Revised: 24 September 1997 / Accepted: 7 October 1997     

Noniterative biexponential fluorescence lifetime imaging in the investigation of cellular metabolism by means of NAD(P)H autofluorescence.

The cofactors NADH and NADPH, hereafter NAD(P)H [NAD(P)= nicotinamide adenine dinucleotide (phosphate)], belong to the principal endogenous indicators of energetic cellular metabolism. Since the metabolic activity of cells is given by the ratio between the concentrations of free and protein-bound NAD(P)H, the development of autofluorescence techniques which accurately measure the modifications to this ratio is particularly significant. Hitherto the methods applied in the monitoring of cellular metabolism have provided either imprecise results, due to interference of the NAD(P)H signal by perturbing factors, or they have required a complicated internal calibration. We employ biexponential fluorescence lifetime imaging (FLIM) in order to discriminate between the free and protein-bound NAD(P)H without any previous calibration. Thus, we have obtained directly, and for the first time, a high-resolution map of cellular metabolism, that is, an image of the contribution of the protein-bound NAD(P)H to the cumulative NAD(P)H fluorescence signal. Moreover, we demonstrate that protein-NAD(P)H complexes characterised by different fluorescence lifetimes are not uniformly distributed all over the cell, as assumed until now, but are concentrated in certain cellular regions. The different fluorescence lifetimes indicate either different protein-NAD(P)H complexes or different bond strengths between NAD(P)H and the protein in these complexes. Since an important aspect in biological applications is to monitor the dynamics of the relevant processes (such as cellular metabolism), rapid dynamical techniques, for example, rapid biexponential fluorescence lifetime imaging, are needed. Furthermore, it is necessary to reduce the evaluation effort as much as possible. Most of the evaluation techniques in multiexponential FLIM are time-expensive iterative methods. The few exceptions are connected with a loss of information, for example, global analysis; or a loss in accuracy, for example, the rapid evaluation technique (RLD). We implement for the first time in FLIM a noniterative, nonrestrictive method originally developed by Prony for approximations of multiexponential decays. The accuracy of this method is verified in biexponential FLIM experiments in time-domain on mixtures of two chromophores both in homogenous and in heterogeneous media. The resulting fluorescence lifetimes agree (within error margins) with the lifetimes of the pure substances determined in monoexponential FLIM experiments. The rapidity of our evaluation method as compared to iterative pixel-by-pixel methods is evidenced by a reduction of the evaluation time by more than one order of magnitude. Furthermore, the applicability of this method for the biosciences is demonstrated in the investigation of cellular metabolism by means of NAD(P)H endogenous fluorescence.     

A fluorescence-based synthetic LPS sensor

For the detection of bioanalytes, there is an ongoing search for synthetic sensors to replace enzyme-based assays which are sensitive to contaminants or suboptimal storage conditions. Lipopolysaccharide (LPS), a bacteria-borne endotoxin that may lead to life-threatening conditions such as septic shock, is one such case. Fluorescently labeled analogues of two peptide variants derived from the putative ligand-binding domain of the LPS-binding protein CD14 were developed that detect and discriminate LPS and lipids down to the submicromolar concentration range. Peptides are terminally labeled with carboxyfluorescein and tetramethylrhodamine. For one given peptide, sensitivity and specificity for the detection of LPS and discrimination from other lipids are achieved by spectral signatures that combine changes in the fluorescence resonance energy transfer (FRET) between both dyes and the total emission of tetramethylrhodamine. Alternatively, specificity is obtained by combining the FRET efficiencies of both peptide variants. In comparison to published synthetic LPS sensors, the CD14-derived sensors yield an increase in sensitivity by about 3 orders of magnitude and exhibit specificity for analytes for which the design of synthetic recognition elements is a challenging task. Moreover, one of the sensors enabled the detection of LPS in the presence of up to 50% fetal calf serum, thereby demonstrating the feasibility of this peptide-based approach for clinically relevant samples.