Biomedical subjects

Beate Sick

Publications and source records attributed to Beate Sick.

5 recordsLinked to original sources

PubMed2006

Quality assessment of Affymetrix GeneChip data.

Affymetrix GeneChips are one of the best established microarray platforms. This powerful technique allows users to measure the expression of thousands of genes simultaneously. However, a microarray experiment is a sophisticated and time consuming endeavor with many potential sources of unwanted variation that could compromise the results if left uncontrolled. Increasing data volume and data complexity have triggered growing concern and awareness of the importance of assessing the quality of generated microarray data. In this review, we give an overview of current methods and software tools for quality assessment of Affymetrix GeneChip data. We focus on quality metrics, diagnostic plots, probe-level methods, pseudo-images, and classification methods to identify corrupted chips. We also describe RNA quality assessment methods which play an important role in challenging RNA sources like formalin embedded biopsies, laser-micro dissected samples, or single cells. No wet-lab methods are discussed in this paper.

Animals↗

PubMed2005

RACE: Remote Analysis Computation for gene Expression data.

The Remote Analysis Computation for gene Expression data (RACE) suite is a collection of bioinformatics web tools designed for the analysis of DNA microarray data. RACE performs probe-level data preprocessing, extensive quality checks, data visualization and data normalization for Affymetrix GeneChips. In addition, it offers differential expression analysis on normalized expression levels from any array platform. RACE estimates the false discovery rates of lists of potentially regulated genes and provides a Gene Ontology-term analysis tool for GeneChip data to support the biological interpretation and annotation of results. The analysis is fully automated but can be customized by flexible parameter settings. To offer a convenient starting point for subsequent analyses, and to provide maximum transparency, the R scripts used to generate the results can be downloaded along with the output files. RACE is freely available for use at http://race.unil.ch.

Computational Biology↗

PubMed2004

Multiparameter microscopy and spectroscopy for single-molecule analytics.

The ability to monitor several parameters simultaneously from distinct individual fluorescent reporter molecules facilitates the disentanglement of complex and interacting systems and opens new perspectives in areas from basic science to biopharmaceutical technology. By combining annular illumination microscopy, time-correlated single-photon counting, and multichannel detection, we were able to determine 14 independent parameters from one individual fluorophore. The whole set of parameters was deduced from the few properties of the fluorescence photons, i.e., arrival time, wavelength, and polarization. With this approach, the intensity, the polarization, and the spectral dynamics can be analyzed on a nanosecond time scale and the mean values can be monitored with submillisecond time resolution. Nanosecond spectral dynamics of single molecules has been observed, to the best of our knowledge, for the first time. From our experience, we can determine all parameters for more than 30% of the illuminated fluorophores in biological samples and for more than 80% in doped polymeric films.

Journal Article↗

PubMed2003

The citrate carrier CitS probed by single-molecule fluorescence spectroscopy.

A prominent region of the Na(+)-dependent citrate carrier (CitS) from Klebsiella pneumoniae is the highly conserved loop X-XI, which contains a putative citrate binding site. To monitor potential conformational changes within this region by single-molecule fluorescence spectroscopy, the target cysteines C398 and C414 of the single-Cys mutants (CitS-sC398, CitS-sC414) were selectively labeled with the thiol-reactive fluorophores AlexaFluor 546/568 C(5) maleimide (AF(546), AF(568)). While both single-cysteine mutants were catalytically active citrate carriers, labeling with the fluorophore was only tolerated at C398. Upon citrate addition to the functional protein fluorophore conjugate CitS-sC398-AF(546), complete fluorescence quenching of the majority of molecules was observed, indicating a citrate-induced conformational change of the fluorophore-containing domain of CitS. This quenching was specific for the physiological substrate citrate and therefore most likely reflecting a conformational change in the citrate transport mechanism. Single-molecule studies with dual-labeled CitS-sC398-AF(546/568) and dual-color detection provided strong evidence for a homodimeric association of CitS.

Bacterial Proteins↗

PubMed2002

Coupled rotation within single F0F1 enzyme complexes during ATP synthesis or hydrolysis.

F0F1 ATP synthases are the smallest rotary motors in nature and work as ATP factories in bacteria, plants and animals. Here we report on the first observation of intersubunit rotation in fully coupled single F0F1 molecules during ATP synthesis or hydrolysis. We investigate the Na+-translocating ATP synthase of Propionigenium modestum specifically labeled by a single fluorophore at one c subunit using polarization-resolved confocal microscopy. Rotation during ATP synthesis was observed with the immobilized enzyme reconstituted into proteoliposomes after applying a diffusion potential, but not with a Na+ concentration gradient alone. During ATP hydrolysis, stepwise rotation of the labeled c subunit was found in the presence of 2 mM NaCl, but not without the addition of Na+ ions. Moreover, upon the incubation with the F0-specific inhibitor dicyclohexylcarbodiimide the rotation was severely inhibited.

Adenosine Triphosphate↗