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Forschungsstelle
EU FRP
Projektnummer
00.0422-2
Projekttitel
EBP: Comparative analysis of proteome modulation in human pathogenic bacteria for the identification of new vaccines, diagnostics and antibacterial drug targets.
Projekttitel Englisch
EBP: Comparative analysis of proteome modulation in human pathogenic bacteria for the identification of new vaccines, diagnostics and antibacterial drug targets.

Texte zu diesem Projekt

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Forschungsprogramme
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Kurzbeschreibung
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Partner und Internationale Organisationen
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Abstract
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Datenbankreferenzen
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Erfasste Texte


KategorieText
Schlüsselwörter
(Englisch)
Database; proteomics; bacterial pathogens; bioinfomatics; software development;
Life Sciences; Medicine; Health; Safety; Scientific Research; Social Aspects
Alternative Projektnummern
(Englisch)
EU project number: QLK2-2000-01536
Forschungsprogramme
(Englisch)
EU-programme: 5. Frame Research Programme - 1.1.2 Control of infectious diseases
Kurzbeschreibung
(Englisch)
See abstract
Partner und Internationale Organisationen
(Englisch)
Coordinator: Chiron SpA, Siena (I)
Abstract
(Englisch)
Within the EU LIFE/INFECTIOUS DISEASES Programme, the thematic network entitled ' Comparative analysis of proteome modulation in human pathogenic bacteria for the identification of new candidate vaccines, diagnostics and antibacterial drug targets ' is a two years project formed by 12 European Research Institutions and Universities from 8 European countries, and coordinated by an industrial partner.
The consortium performs pilot studies on comparative analyses of proteome modulation of bacterial pathogens in physiologically relevant conditions, with the scope of exploring if the implementation of state-of-the-art proteomics technologies can lead to a rapid identification of eligible protein candidates for future health-care product development.
Six pathogenic bacteria have been selected, that are all relevant for human health, as they are still causing outstanding problems for either treatment or protection against the disease they cause. At least one full genome sequence is available for each of them.
Partners are using and developing various technological approaches including non-exhaustively bidimensional electrophoresis, mass spectrometry, immunoblotting, or parallel transcript analyses with whole genome DNA microarrays. They are using dedicated bioinformatics tools to perform protein identification, characterization. As they generate heterogeneous data, the integration of those data are requiring the creation of a database system that enable the storing and handling of these valuable information
Ten workpackages are dividing the tasks and activities of the consortium. The Geneva team is constituted by people from the Medical Faculty of the Geneva University and from the Swiss Institute of Bioinformatics (SIB) well known in the proteomics field, such as Denis F. Hochstrasser, Pierre-Alain Binz, Christine Hoogland, Khaled Mostaguir. The multidisciplinary tasks of the Geneva group are included in 3 workpackages, named ' a bacterial proteomics database ', ' Integration of transcriptomics data ' and ' standards and sensitivity issues '.
Our contribution includes both drylab and wetlab aspects. After the first year in this project, we have significantly improved the functionality of make2ddb, a software package allowing individual labs to handle, treat and publish their proteomics data on their own web. Make2ddb is freely available from ExPASy (http://www.expasy.org/ch2d/make2ddb.html). New functionality recently added concern for example a NiceView of the protein data available in the database, and possibility to retrieve lists of proteins identified on a particular map
The standardization proposed by the world-wide known SWISS-2DPAGE database, developed at the SIB, has been used to establish a relational schema to allow easier management of proteomics data in the network. This includes the development of a syntax checker of the data in the previous format to be pushed in the new system, the physical implementation of the relational tables, and the automatically insertion of the proteomics data. Perl language and Apache web server (freeware) have been used as implementation of the scripts. Frequent queries have been built to have faster and more intuitive access to the data. The main index for protein sequences, namely the SWISS-PROT knowledgebase, maintains itself cross-references to these proteomics databases, thus forming a network of interconnected databases
The wetlab contribution is focused on the continuous improvement of proteomics related experimental protocols that are made available to the network partners. This include protocols for sample preparation, 2-D electrophoresis, peptide mass fingerprining, tandem mass spectrometry and other protein identification methods.
Datenbankreferenzen
(Englisch)
Swiss Database: Euro-DB of the
State Secretariat for Education and Research
Hallwylstrasse 4
CH-3003 Berne, Switzerland
Tel. +41 31 322 74 82
Swiss Project-Number: 00.0422-2