In the DC-THERA effort to create new dendritic cell-based therapies, a wide range of information arising from genomics, proteomics, molecular cell biology and pre-clinical models is gathered and applied to the conduction of clinical trials. The DC-THERA Directory is intended to collect and semantically organize this data and to serve as a tool for collaboration among researchers and as a reference point for the information contained. As such it is a directory that provides summarized information and relations between resources and people involved. In particular, we ...

RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented. A co...

Microarray and gene expression are fundamental tools of nowadays Biology research. While standard formats and software systems have been developed to represent and publicly share information about microarray experiments, existing computational solutions give limited support to the representation of the outcomes, experimental hypotheses or conclusions about biological questions that are dealt with in gene expression analysis. We propose an OWL-based model and a Semantic Web-based approach to address the issue. We show that the formalization of microarray-related knowle...

Our laboratory has an Amaxa electroporator at its disposal. The electroporator is used, among other things, for the transfection of immature DCs with different constructs encoding for the oncogene Her-2/neu and as control PSA.

In our lab we have a two-photon microscope. For instance, cell death was assessed in the viable epidermis by non-invasive near infrared two-photon microscopy following micro-particle bombardment of murine skin.

This FACS analyser that is available to us is used, e.g., for the analysis of dendritic cells.

This platform with its state-of-the-art mass spectrometry facilities is led by Mann (P33). To enhance the platform, two additional groups were recruited as Third Parties: P114 Edwin Lasonder in Nijmegen (NL), and P113 Juri Rappsilber in Edinburgh (GB). The mass spectrometer has been used, for instance, to identify and quantify chemokine dependent tyrosine phosphorylation events. Furthermore, the success of SILAC labelling was analysed using the mass spectrometer.

Our laboratory has an electroporator at its disposal. It is used for instance for RNA electroporation into DC.

In our institute, we have a 9-colour FACS cell sorter our disposal. It is used, e.g., for the analysis of various DC populations.

Genopolis hosts a microarray platform that uses the Affymetrix GeneChip® microarray technology for genome and transcriptome analyses. In 2008, this platform was enhanced by the incorporation of a new institute [the Wellcome Trust Centre for Human Genetics] to provide ‘Illumina’ microarray profiling. The following services are currently available: Whole genome genotyping applications, which include: 1. family-based association studies 2. cancer genetics 3. population genetics 4. chromosomal copy number analysis Whole genome gene expression profiling application...

For our work, we have a fluorescence microscope at our disposal. We use it, among other things, to analyse DC distribution in spleen and how this is affected during inflammation driven by stromal cells or hematopoietic cells.

Our lab has expertise in lipofection of tumor-antigen-encoding RNA into DC. The method was compared to RNA electroporation into DC.

We have experience in querying DAVID, the Database for Annotation, Visualization and Integrated Discovery (http://david.abcc.ncifcrf.gov/) . For instance, we used DAVID for functional annotation of upregulated and downregulated genes by gene ontology classification and pathway analysis by several bioinformatics approaches. Preliminary results obtained from querying DAVID and Ontologizer (http://www.charite.de/ch/medgen/ontologizer/) show statistically significant enrichment for immunological-relevant signaling pathways and immunology-related GO terms of the upregula...

We have access to and experience with using a linear ion trap / Fourier Transform (LTQ-FT) hybrid mass spectrometer. For example, we use it to analyse purified tryptic peptides.

A comprehensive protein inventory of clinical grade immature and cytokine cocktail matured (Il-6, IL-1 beta, TNF alpha, PGE2; 48 hours) monocyte derived human dendritic cells (DC) from a healthy donor has been established by using high accuracy, high sensitivity protein identification technology. We have identified 2794 proteins in DCs by liquid chromatography tandem mass spectrometry.

In our lab, we have know-how about performing MPLC assays, such as using it in the establishment of immunomonitoring vaccination trials with RNA transfected DC by using overlapping peptides.

In our laboratory we carry out multiplex assays. For instance, multiplex analysis was used to study the response of human MoDC to yeast, spheroplasts, pseudohyphae and spores.

We have expertise on an HSV-based technology for the delivery of antigens to dendritic cells.

This gene gun was used for the delivery of vectors engineered to express distinct chemokines at the local skin site of mice.

We have experience in western blotting, which we use for example for the assessment of the efficiency of gene silencing.