1. P ATHO G ENO M ICS PORTUGAL Partner 9 P ATHO G ENO M ICS PORTUGAL Partner 9

2. Summary Examples of available Infrastructures Examples of available Infrastructures Projects in Pathogenomics before 2004 Projects in Pathogenomics before 2004 Projects in Pathogenomics > 2004 Projects in Pathogenomics > 2004 Research Fields for the future Research Fields for the future

3. Instituto Gulbenkian Ciência Platform from Affimetrix This Unit provides services in DNA Sequencing and Genotyping, as well as in Affymetrix DNA Chip Analysis. The latest Affimetrix Gene Chip Hybridisation and Scanning Station is available. ICG also have a bioinformatics unit. Responsibility: Dr. Joerg Becker. National Institute of Health Dr. Ricardo Jorge The NIH is equipped with a core facility, providing services of High-throuphput DNA Sequencing, Genotyping, Molecular Biology, and DNA expression Responsibility: Dr. Maria de Fátima G.C. Bacharel Proteomics: Core facility is also equipped with a Biacore system for studying biomolecular interactions in real time by Label-free surface plasmon resonance (SPR) based technology. Responsibility: Dr. Deborah Penque. Examples of available Infrastructures

4. Projects in Pathogenomics before 2004 Screening for new Candida albicans virulence factors associated with morphogenesis using proteomics methodologies. - Universidade de Aveiro Isolation of molecules involved in high-affinity iron uptake systems of Leishmania infantum - Instituto de Biologia Molecular e Celular – IBMC The glyoxalase pathway in Leishmania: Potential therapeutical applications - Universidade de Lisboa - Fundação da Faculdade de Ciências

5. Host-Parasite Interactions during the Hepatic Stages of Malaria Infections - Instituto Gulbenkian de Ciencia The effect of chloroquine on the modulation of mosquito response to Plasmodium infection - Universidade Nova de Lisboa - Instituto de Higiene e Medicina Tropical – IHMT Structural characterization of MrkD protein from Klebsiella pneumoniae : implications in the epithelial adhesion properties of the microorganism. - Universidade Nova de Lisboa - Instituto de Tecnologia Química e Biológica – ITQB Projects in Pathogenomics before 2004

6. Functional genomics in malaria – an unbias RNAi screen to determine the required host cell molecules and pathways for Plasmodium sporozoite fully development inside hepatocytes - Instituto de Medicina Molecular Projects in Pathogenomics > 2004

7. DBYeast: Infrastructures and algorithms for analysis and identification of gene regulatory networks - Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa Identification of Glycosylation-associated genes induced by Helicobacter pylori in gastric cells: a glycomic approach - Instituto de Patologia e Imunologia Molecular Insights into the complex regulatory networks acting in yeast cells challenged with drugs/chemical stresses: genome-wide expression approaches supported by bioinformatics - Instituto Superior Técnico Projects in Pathogenomics > 2004

8. Diagnostic - Screening techniques and bioinfoirmatics: Development of a hybrid neural network search engine to provide a database of medically important microorganisms Metagenomic technologies to examine the DNA of nonculturable bacteria and microbial consortia without any sub-culturing, thereby allowing to understand the interplay of genes and functions in an ecosystem, regardless of the specific microbial hosts. How the genes of all members of a community relate to the functions carried out by that particular community? Research Fields for the future

9. Diagnostic - Screening techniques and bioinfoirmatics: Methods of detecting and identifying novel microbial products are likely to be scrutinized and improved upon, expanding the ability to exploit the metabolic versatility of microbes in providing powerful antibiotics, therapeutics, and other materials. Development of rapid diagnostic methods to identify resistant bacteria with application on international surveillance systems. Research Fields for the future

10. Microbes: Yeasts: Analysis and identification of gene regulatory networks Helicobacter pylori: Identification of the gluconeogenic pathway enzymes used for anabolic biosynthesis in H. pylori. Neisseria meningitidis: Antibiotic resistant markers, adhesion markers and markers as potential vaccines against meningococci. Research Fields for the future

11. Host-microbe interaction: Cell-cell communication: Klebsiella pneumoniae Nosocomial infection: Klebsiella pneumoniae: identification of extended-spectrum beta-lactamases by genomic approach Pseudomonas aeruginosa: identification of mettalo-beta- lactamases by genomic approach Research Fields for the future

12. Host-microbe interaction: Antimicrobial resistance mechanisms (also Public health needs): Neisseria meningitidis Mycobacterium tuberculosis Research Fields for the future