Pathway Processor is a tool for integrating whole-genome expression results into metabolic networks.

In our work, we have experience in applying peptide-tetramer assays. Primary and secondary CTL response against the C8 T cell epitope SIINFEKL was monitored in a study for maturing myeloid DCs and plasmacytoid DCs.

We have developed, at the Curie Institute, a unique methodology dedicated to the identification of phagosome proteins in dendritic cells, under various experimental conditions. This methodoly incorporates a unique sample preparation procedure based on 96 well plate complex sample trypsinization, a nano-LC-based peptide separation coupled to MSMS analysis sequencing. This procedure led us to the identification of 600 phagosomal proteins from murine DC phagosomes. An integrated software solution has been developed to analyse these results and to perform comparative analy...

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.

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...

Using MAGE-A3 as a model antigen we established a functional read-out system by transfection of CD4 T cells with RNA encoding T cell receptors recognizing MHC DP4 restricted MAGE-A3 epitopes.

Real time and immunohistochemistry analysis was performed in a study to evaluate whether iNOS can serve as a prognostic factor in stage III melanoma survival. The analysis showed that both iNOS and COX-2 alone significantly predicted OS. The BRAF/NRAS mutation status did not significantly differ between patient groups, although iNOS significantly correlated with BRAF mutation frequency. Furthermore, iNOS and COX-2 were significantly linked to a number of metastatic lymph nodes. However, iNOS maintained its statistical significance together with a number of lymph node...

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...

In our lab we have experience in performing real time PCR analyses.

For quantitative proteomic studies, our group recently described the SILAC (Stable Isotope Labelling by Amino Acids in Cell Culture) approach. In this method, independent populations of cells are grown in medium containing different non-radioactive isotope forms of essential amino acids (e.g. arginine and lysine). Because the cells cannot synthesize these amino acids, after some generations all proteins are labelled and therefore can be distinguished and quantified by the mass spectrometer. To generate a proteomic map of DCs which includes quantitative information that...

This puromycin-based technology was developed in our laboratory to monitor translation by FACs in individual or cell populations. It is a non-invasive method to monitor protein synthesis and cellular activation in single cells or heterologous populations.

This spectrometer was, among other things, used for an analysis of the integral plasma membrane proteome of D1 cells.

We have know-how on TaqMan gene expression assays by Perkin-Elmer Applied Biosystems. They are used, for instance, for PCR analysis.

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

Our lab has expertise in performing thymidine-incorporation assays. The assay is used, for instance, for the monitoring of the vaccine induced specific anti-tumor T cell responses.

The method is about transfecting CD4(+) and CD8(+) T cells with mRNA encoding recombinant immunoreceptors for use in the adoptive immunotherapy of cancer. CD4(+) and CD8(+) T cells were efficiently transfected with immunoreceptors specific for ErbB2 and CEA. The immunoreceptor expression was transient with half-maximal expression at day 2 and no detectable immunoreceptor expression at day 9 after electroporation. Opposed to standard procedures using retroviral gene transduction to constitutively express immunoreceptors in T cells, transient immunoreceptor expressi...

There is a two-photon intravital microscope available in the laboratory. It was used, among other things, to analyze the infiltration and destruction of solid tumors by CTLs.

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.

We have expertise in western blotting. Western blot was used, for instance, for the demonstration of protein kinase R phosphorylation on transduction.

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