The SWAN biomedical discourse ontology.

Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies community. In this paper, we present and discuss the SWAN ontology of biomedical discourse. We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies.

Increased seizure threshold and severity in young transgenic CRND8 mice.

Reports suggest that Alzheimer's disease (AD) patients show a high life-time prevalence of seizure-like disorders. The transgenic CRND8 (TgCRDN8) is a mouse model of AD-like amyloid pathogenesis that expresses a double-mutant form of human amyloid precursor protein 695 (K670N/M671L and V717F). We have previously reported that post-plaque TgCRND8 mice exhibited a lower threshold to seizure with a more severe seizure type when challenged with pentylenetetrazole (PTZ) intravenously. Here, we now report that pre-plaque TgCRND8 mice also demonstrate an increased sensitivity to PTZ-induced seizures with a more severe seizure type over age-matched littermate controls. A lower threshold and more severe seizure type in TgCRND8 mice prior to and after plaque deposition suggest that this genotype difference may be due to beta-amyloid (Abeta) toxicity rather than plaque formation. Thus, the TgCRND8 mice are not only a model for Abeta production and plaque deposition, but may also be useful for AD associated seizure.

Measuring human beta-secretase (BACE1) activity using homogeneous time-resolved fluorescence.

The human beta-secretase enzyme, BACE1, mediates a critical step in the production of A beta(40) and A beta(42) peptides which are responsible for the severe neuronal cell death and insoluble amyloid plaques of Alzheimer's disease (AD). Several lines of evidence suggest that potent BACE1 inhibitors represent an attractive A beta-lowering strategy for AD. We designed a simple homogeneous time-resolved fluorescence (HTRF) assay which utilizes the fluorescence resonance energy transfer (FRET) pair europium and allophycocyanin for measuring BACE1 enzymatic activity in a high-throughput manner. Robust FRET was observed when an 18-amino-acid APP Swedish-synthetic peptide that was N-terminally labeled with europium cryptate and C-terminally biotinylated was incubated with streptavidin-coupled cross-linked allophycocyanin (SA-XL665). Purified BACE1 enzyme caused a time- and concentration-dependent linear change in FRET at low nanomolar enzyme concentrations. This assay was used to compare the autoprocessed "mature" BACE1 enzyme (sautoBACe1) and the soluble proBACE1 for activity and inhibition by selected peptidic BACE inhibitors. sautoBACE1 displayed only a modest increase in activity compared to sproBACE1 and this activity was uninhibited by the BACE1 prodomain peptide. Interestingly, the BACE1 prodomain peptide was able to partially inhibit sproBACE1 activity. IC(50s) for a P10-P4' statine BACE1 inhibitor, OM99-2, and OM-003 determined using the HTRF assay were in good agreement with those reported in the literature. The primary advantages of the HTRF-formatted BACE1 protease assay include appropriate reflection of native BACE1 activity, high sensitivity, low variability, and intrinsic quench correction afforded by ratiometric measurements made between EuK and SA-XL665 fluorophores.