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Partner 8 (IC-CSIC)

Partner 8 (IC-CSIC). Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) MANAGEMENT ACTIVITES Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es

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Partner 8 (IC-CSIC)

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  1. Partner 8 (IC-CSIC) Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) MANAGEMENT ACTIVITES Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es Chania, 3rd July 2011

  2. WP 5 & 6: Management activities WP 5: Metabolome analysis of the microbiome associated to polluted sites 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW WP 6: Microbial metagenomics and proteomics of the polluted sites

  3. WP 5 & 6: Management activities 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW

  4. WP 5 & 6: Management activities • ObjectivesWP5 • To provide a large-scale experimental pipeline for identifying metabolisms associated to polluted sites 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW • Task • 5.1. Metabolic reconstruction • 5.2. Construct the corresponding “metabolic atlas” of polluted sites • Deliverables • D5.1. Subset of biodeg-like KEEG database data available (M6) • D5.2. Protocols for protein and metabolite extraction (M12) • D5.3. Raw dataset generated (M24) • D5.4. Metabolic atlas produced (M28) • Partners • IC-CSIC (lead participant) • Bangor University and IAMC

  5. WP 5 & 6: Management activities 4 Metabolite sample Spectro. charact. Metabolite identification Metabolite atlas Biodeg metabolome 3 Protein sample 2D or shotgun Protein annotation Proteomic atlas Biodeg proteome 1 Clone library Screen method Clone selection Insert sequencing Gene annotation Marine sample DNA sample PCR and cloning 2 454 sequence Automatic annotation BLAST database Biodeg metagenome PCR and cloning 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW BLAST NCBI Selection of targets PCR and cloning SINGLE GENOMES OR METAGENOMES

  6. WP 5 & 6: Management activities 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW

  7. WP 5 & 6: Management activities Metabolite sample Spectro. charact. Metabolite identification Metabolite atlas Biodeg metabolome 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW

  8. WP 5 & 6: Management activities Protein sample 2D or shotgun Protein annotation Proteomic atlas Biodeg proteome 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW

  9. WP 5 & 6: Management activities * * Marine sample DNA sample 454 sequence Automatic annotation BLAST database Biodeg metagenome PCR and cloning DNA extraction and PCR amplification Sequencing and data analysis Selection Agarose gel 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW • Cloning, expression and characterization of enzymes for biodeg • Identification of positive PCRs • PCR amplification based on protein sequences

  10. WP 5 & 6: Management activities Clone library Screen method Clone selection Insert sequencing Gene annotation Marine sample DNA sample PCR and cloning 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW

  11. WP 5 & 6: Management activities ULIXES 1. WORKPACKAGES 2. NETWORK 3. TASKS 4. STRATEGY 5. ACTIVITIES 6. OVERVIEW Unique value to scientific community 1st Seawater genomic-proteomic-biochemical atlas BIODEG model established Functional BIODEG equivalence established New generation of BIODEG enzymes and networks Biodegradation strategies Unique value to ULISEX groups Reference labs in BIODEG analysis of (deep) seawater 1st complete Seawater BIODEG systems biology project • Ability or inability of (deep) seawater microbial communities to carry out its (basic or new) BIODEG functions • Recognize BIODEG uniqueness and link them to biodegradation strategies and microbial ecology

  12. Partner 8 (IC-CSIC) Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) MANAGEMENT ACTIVITES Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es Chania, 3rd July 2011

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