Biomedical subjects

Claudia Preininger

Publications and source records attributed to Claudia Preininger.

3 recordsLinked to original sources

PubMed2004

Quick and simple: quality control of microarray data.

MOTIVATION: Microarrays are high-throughput tools for parallel miniaturized detection of biomolecules. In contrast to experiments using ratios of signals in two channels, experiments with only one fluorescent dye cause special problems for data analysis. The present work compares algorithms for quality filtering on spot level as well as array/slide level. RESULTS: Methods for quantitative spot filtering are discussed and new sets of quality scores for data preprocessing are designed. As measures of spot quality also reflect the quality of protocols, they were employed to find the optimal print buffer in an optimization experiment. In order to determine problematic arrays within a set of replicates we tested methods of outlier detection which can suitably replace the visual inspection of slides. CONTACT: Ursula.Sauer@arcs.ac.at.

Algorithms↗

PubMed2004

Photoactivatable copolymers of vinylbenzyl thiocyanate as immobilization matrix for biochips.

Biochip surfaces for immobilization of DNA and proteins require reactive polymers with high immobilization capacity and low nonspecific binding. Most reactive surfaces consist of matrixes that provide epoxy, aldehyde, or amino functions for biomolecule binding. The most widely used oligonucleotide modification is a C6-amino link. The high reactivity of isothiocyanate groups (NCS) toward amines was therefore the motivation to employ photogenerated NCS groups as binding sites for NH(2)-terminated oligonucleotides. Photosensitive poly(styrene-co-4-vinylbenzyl thiocyanate) (PST-co-VBT) was synthesized and applied as novel material for DNA and protein immobilization. The immobilization capacity of PST-co-VBT was a function of UV energy density used for photoactivation and was approximately 80% at 450 mJ cm(-)(2) (lambda(ex) = 254 nm). This surface was superior to tested commercial chip surfaces in signal-to-noise-ratio and reproducibility. Print buffer and spacer length were optimized for maximum fluorescence signal with DNA and proteins. UV exposure conditions and oligonucleotide modification were correlated, showing that this photochemical approach can be successfully applied for surface patterning of biochips.

Base Sequence↗

PubMed2004

ARChip epoxy and ARChip UV for covalent on-chip immobilization of pmoA gene-specific oligonucleotides.

ARChip Epoxy and ARChip UV are presented as novel chip platforms for oligonucleotide immobilization. ARChip Epoxy is made of reactive epoxy resin available commercially. ARChip UV consists of photoactivatable poly(styrene-co-4-vinylbenzylthiocyanate). Both ARChip surfaces are tested in a model assay based on oligonucleotide probes from a real-life genotyping project and are evaluated in comparison with five commercial chip surfaces based on nitrocellulose, epoxy, and aldehyde polymer, and two different aminosilanes. Optimum print buffer, spotter compatibility, and data normalization are discussed.

Bacteria↗