NetSlim: high-confidence curated signaling maps.

We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is a new resource that contains this 'core' subset of reactions for each pathway for easy visualization and manipulation. The pathways in NetSlim are freely available at http://www.netpath.org/netslim.

Effect of curcumin on proliferation of human retinal endothelial cells under in vitro conditions.

PURPOSE: To investigate the effect of high glucose on the proliferation of human retinal endothelial cells (HRECs) and to elucidate the possible mechanisms of antiangiogenic activity of curcumin, a diferuloylmethane. METHODS: Human retinal endothelial cells were isolated from the retinal tissue obtained from human donors and the culture system was established. The effect of curcumin on the proliferation of primary HRECs in the presence of low and high glucose was measured by MTT and thymidine uptake assays. Apoptosis was assessed by TUNEL assay and other adjuvant tools. Effect of curcumin on phorbol ester stimulated intracellular reactive oxygen species (ROS) generation in high glucose conditions was assessed by fluorescence assay. Finally, semiquantitative RT-PCR and Western blot analysis was performed to measure VEGF mRNA production and VEGF induced PKC-betaII translocation, respectively in the presence and absence of curcumin. RESULTS: HREC culture was established successfully at passages 3 and 4 at 80% confluence. Curcumin effectively inhibited endothelial cell proliferation in a dose-dependent manner. At a concentration of 10 microM, curcumin significantly inhibited HREC proliferation in high-glucose-treated cells, as verified by both MTT and thymidine uptake assay. Curcumin also showed a significant (P = 0.03) reduction of intracellular ROS generation in HRECs. RNA expression studies showed that curcumin had an inhibitory effect on the glucose-induced VEGF mRNA expression. In addition, VEGF-mediated, membrane-associated changes in the PKC-betaII translocation in HRECs was inhibited by 31% on treatment with 10 microM curcumin. CONCLUSIONS: These data suggest an underlying mechanism whereby curcumin induces the apoptosis in HRECs by the regulation of intracellular ROS generation, VEGF expression and release, and VEGF-mediated PKC-betaII translocation.

Proteomic resources: integrating biomedical information in humans.

Recent improvements in high-throughput proteomic technologies have unleashed the potential for generating vast amounts of data. Managing and sharing proteomic data is not an easy task. In this article, we will discuss some of the high-throughput proteomic techniques that are commonly used today. We will also review the major issues in sharing and dissemination of proteomic data and the recent community initiatives to standardize data formats and ontologies. An overview of the web-based resources and databases for analysis of proteomic data is also provided. Integration of disparate proteomic data sources with genomic and transcriptomic data should make systems biology type of approaches feasible in the near future.