Max Planck Institute for Marine Microbiology (MPI)

The Max Planck Institute (MPI) for Marine Microbiology in Bremen was founded in 1992 and investigates the role, diversity and features of microorganisms, especially of bacteria, and their interaction with physical and chemical processes in marine and other aquatic habitats.

The Department of Molecular Ecology was established in 1997, starting as an independent junior research group. It currently directs its work towards understanding the structure and function of microbial communities of different complexity and their dynamics with regard to biotic and abiotic changes in the environment. Emerging approaches include extraction of genomic fragments directly from the environment (metagenomics).

The Microbial Genomics Group was established in 2003 in the Department of Molecular Ecology. The main research areas are genomic techniques to study the molecular adaptations of environmental bacteria when exposed to changing environmental conditions. Main areas of work are functional genome analysis with bioinformatics techniques; transcriptomics on microarrays for expression profiling; phylogenetic reconstructions and software development for gene-finding, (meta)genome analysis and data integration.

To approach complex questions in microbial ecology, currently competencies in the following fields are maintained:

• Identification and quantification of organisms with fluorescence in situ hybridization (FISH). This includes besides conventional microscopy, confocal laser scanning microscopy and flow-cytometry.
• Identification of organisms based on the microarray technology.
• Analysis of diversity and phylogeny of marine microorganisms by comparative sequence analysis using the bioinformatic software package ARB (http://www.arb-home.de).
• Whole genome sequencing and functional analysis of environmentally relevant microorganisms (REGX-Project, http://www.regx.de ).
• Integration of heterogeneous data from marine systems as a member of the bioinformatics platform of the NoE “Marine Genomics”.
• NoE “Marine Genomics”: MPI has the lead functions of the Microbial Node and of the work package on Environmental Genomics; it is member of the steering and training committee as well as of the bioinformatics and technological platforms as a medium throughput facility and for the integration of heterogeneous data from marine systems.
• NoE “Marine Biodiversity and Ecosystem Functioning (MARBEF)”: MPI is member of the steering and executive committee, with responsibilities for training and data management as well as for the coordination of microbiology and molecular ecology work packages

Role within the project:
The Microbial Genomics Group is the lead party of the METAFUNCTIONS Consortium. Preliminary work has resulted in the first proof of principle that the planned approach can be successfully utilised. A first version of a database and mapserver has been developed, details of which have recently been published in the article “Megx.net—database resources for marine ecological genomics” (Nucleic Acids Research, 2006, Vol. 34, D390–D393 Database issue). Further details are accessible under www.megx.net

Key Personal:

- Prof. Frank Oliver Glöckner

- Dr. Johanna Wesnigk

- Dr. Thierry Lombardot

- Dr. Christine Klockow

- Ph D student Renzo Kottmann (M. Sc.)

The Global Resource Information Database (GRID)

GRID is a worldwide network of 15 environmental data centers. It is part of the Division of Early Warning and Assessment (DEWA) of the United Nations Environment Program (UNEP). The GRID network was first launched in 1985 with centers in Geneva (http://www.grid.unep.ch) and Nairobi.

GRID-Geneva's principal activity is to provide high-quality environmental data and information, to underpin UNEP's review of the state of the environment and provide early warning on emerging environmental threats. At the same time, GRID-Geneva offers technical services and develops value-added environmental products to support the work of other entities on a case-by-case basis. Over the years, the office has compiled an extensive archive of geo-spatial and tabular databases, and is currently using state-of-the-art information technology to make them accessible to the global community through Internet-based applications.

GRID-Geneva as partnership between UNEP and University of Geneva

GRID-Geneva in Europe is indeed part of UNEP, but it is also a member of a partnership with University of Geneva (UNIGE). GRID’s research projects are conducted under this partnership, and personnel taking part in these activities are paid through the services of UNIGE.


Role within the project:

To advance the development of a Geographic Information System (GIS) combining genomic and ecological data, we offer competencies in the following specific domains:

• Geographic information systems (GIS), remote sensing, and modeling to provide: better insights to decision-makers, sustainable use of natural resources, analysis of emerging environmental problems and threats. Recent applications in this domain include: satellite imagery analysis to map chlorophyll concentration of Lebanon's coastal water as a response to land-derived pollution; evolution of the Mesopotamian marshlands ecosystem, and modeling of asymmetric wind speed profiles of global cyclones.
• Integration, dissemination and communication of geographic information visually on the World Wide Web through a GIS (webmapping). GRID-Geneva is responsible for the complete design, data gathering and formatting, and on-line interface of several data portals and map servers such as:
  • The GEO Data Portal, the authoritative source for data sets used by UNEP and its partners in the Global Environment Outlook (GEO) report; the portal allows easy display of data interactively and as dynamically generated maps, graphs and tables (http://geodata.grid.unep.ch/).
  • PreView - InternetMapServer Project: this has been recognized by the international scientific community as a powerful and innovative modeling tool to identify risk and human vulnerability to natural hazards in relation to socio-economic and physical factors (Link).

Other web-based GIS services include the European Internet Map Server, and Africa GIS-Web portal, which permit to create dynamic maps and related GIS databases on Africa’s physical environment.

The collaboration already established by GRID-Geneva with other institutions specialized in GIS will provide access to extended data sources. GRID-Geneva is the perfect candidate to provide GIS concepts and tools to this project, as well as environmental geographic data.


Key Personnel:

Dr. Jean Michel Jaquet

He will be the Metafunctions project manager for the GRID-Geneva and the scientific focus point concerning GIS and oceanic-environmental parameters.

Key words: Management, GIS analysis, oceanography

jaquet(at)grid.unep.ch

0041 22 917 82 89

Dr. Andrea de Bono

He will be mainly focused on collecting and processing oceanic environmental parameters, performing GIS analysis for retrieve the missing data, management of data storage in the ecological database, and in the development of the Metagenome map server

Key words: Data processing, GIS analysis, database management, web mapping

debono(at)grid.unep.ch

0041 22 917 82 40

Gregory Giuliani

He will be mainly focused on the development of the web mapping application and the administration of the metafunctions server at GRID-Geneva. He will also perform GIS analysis and data processing.

Key words: Web mapping, system administrator, database management, GIS analysis and data processing.

giuliani(at)grid.unep.ch

0041 22 917 84 17

Poznan University of Technology (PUT)

Poznan University of Technology is one of the biggest Universities of Technology in Poland. It is divided into eight faculties one of them being Faculty of Computing Science and Management. The Institute of Computing Science is one of the three institutes in the Faculty of Computing Science and Management. Its predecessor, the Institute of Control Engineering, was established in 1970, in 1988 changed the name for the Institute of Computer Science, Automatics and Robotics. Finally, in 1990, after extraction of a new chair, the Institute got its present shape. The staff of the Institute consists of over 100 people, including over 80 persons occupying academic positions. The Institute of Computing Science at Poznan University of Technology is one of the leading institutes in Poland in the areas of computing science, operational research, combinatorial optimization, artificial intelligence, and computational biology.

Role within the project:

PUT is responsible for the development of a system for an automated retrieval and extraction of environmental and metagenomic data. Based on the Institute of Computing Science staff broad knowledge and experience concerning many areas of computer science, the methods of finding information about marine microorganisms in the papers available in Internet will be developed. In practice, in order to identify organisms of this kind, geographic information will be analyzed. The analyzis of this information will allow to distinguish between marine and other organisms. It will be the basis for extracting the corresponding nucleotide sequences from data banks and environmental information provided in the papers describing the analyzed sample. All the data will be stored in the database combining sequence, environmental and geographic information. The development of the system which will enable automatic extraction of information of these types is a unique undertaking. Moreover, the system to be developed is crucial for other parts of the project since the extracted data will be the basis for the analysis being the purpose of the project.

Contact person: Prof. Jacek Blazewicz

Key Personal:

- Prof. Jacek Blazewicz

- Dr. Piotr Formanowicz

- Dr. Marta Szachniuk

- Marcin Radom, M.Sc.

- Agnieszka Rybarczyk, M.Sc.

Supporting Team:

- Dr. Marta Kasprzak

- Dr. Piotr Łukasiak

Bremerhaven Institute for Biological Information Systems at the Technology Transfer Centre Bremerhaven (TTZ)

The Technology Transfer Centre Bremerhaven (TTZ) was established in 1987 and comprises six institutes for applied research and development (R&D). More than 80 highly qualified employees (scientists and engineers) are working on application-oriented projects in the fields of bioinformatics, biotechnology, environmental technology, food and bioprocess engineering, and energy and process engineering on a national and international level. Since its foundation, the TTZ Bremerhaven has successfully completed more than 4000 projects, most of them carried out in close cooperation with European partners and founded by the EC.


The Bremerhaven Institute for Biological Information Systems (BIBIS) was founded in autumn 2002. The goal of BIBIS is the development and maintenance of bioinformatics software to support biologists addressing problems like genome analysis of microorganisms, which play an important role in quality control in the food industry, in global matter cycles in marine ecosystems or as pathogens in medicine. BIBIS works in close cooperation with several biological groups from the MPI for Marine Microbiology, the Alfred-Wegener-Institute for Polar- and Marine Research (AWI), the Centre of Applied Gensensors (CAG) and others.


From the technological point of view BIBIS has competencies in the following fields:

• Methods and algorithms for extensive sequence comparison, for instance generalised suffix trees, alignments, pattern discovery for genome analysis and orthology detection,
• Propositional and relational data mining methods for classification and clustering problems,
• Knowledge-based information systems including knowledge representation and reasoning, ontologies for automated genome annotation and data integration problems.

Role within the project:

TTZ is the leader of work package 4, Analysis. Together with MPI different scenarios will be specified in order to infer a formal definition of the gene patterns. After this specification phase the main task consists in the software development for the new data mining methods. Application of the new tools developed as well as evaluation of the gene patterns found will be done together with the experts from MPI.

Contact:

Dr. Uta Bohnebeck

TTZ-Bremerhaven

An der Karlstadt 10

D-27568 Bremerhaven


Phone: +49 471 9448 609

Mail: bohnebeck(at)ttz-bremerhaven.de