Press Releases

International Workshop “Marine Genomics meets Marine Diversity” in Bremen, 8 – 9 June 2006


On the road to integration
 

A bundle of new technologies has emerged over the last years. Fast DNA sequencing (Pyrosequencing), DNA chips, proteomics and geographic information systems (GIS) to integrate oceanography, diversity and genomics are ready for application. The central question is now how to combine these tools to solve burning ecological questions like: Who is out there and what are they doing?
Last week an international workshop was held at the Bremen Max Planck Institute for Marine Microbiology. From 8 – 9 June 2006 sixty participants from eleven countries, including the USA presented state of the art results on marine microbial diversity and genome research and held lively discussions.The sessions covered the issues diversity, genomics, ecology, technology, and bioinformatics, including databases and portals. The workshop was funded by the European Commission as part of the activities of a large Network of Excellence called “Marine Genomics Europe”

(www.marine-genomics-europe.org).

It has been underlined by the participants that biology has moved on from a single experiment endeavour to a high throughput science with the amount of data produced every day exceeding the ability of a single researcher to intellectually ingest this rich harvest. Only a tight connection between experts in biology and ecology with technology and bioinformatics will make it possible to identify the key players as well as the basic structural and functional elements of ecosystems, in which microorganisms play an important role. A better understanding of the forces driving marine ecosystems is the ultimate goal of marine microbial ecology and will help to manage protection and exploitation of natural resources and services in a sustainable way.

 
The organiser of the workshop Prof. Dr. Frank Oliver Gloeckner summarises “These kind of meetings are very important to establish interdisciplinary connections in order to join forces and intensify interdisciplinary research. We want to reach a better understanding of the cycles of matter with the help of classical ecology, genomics and information technology. This is dearly needed for predicting global change effects and modeling ocean ecosystems, which are earth support systems.”

For more information contact:

Prof. Dr. Frank Oliver Gloeckner

eu-workshops(at)mpi-bremen.de

More Information can be found at www.metafunctions.org and www.microbial-genomics.de

Press Information: Metafunctions Project

Mapping Environmental Clues to Decipher the Function of Genes

Scientists are becoming increasingly interested in metagenomes – the collection of genes from organisms in particular environments.

The METAFUNCTIONS project*, which started on 1 October 2005 is pooling expertise in bioinformatics, computer science, geographical information systems and marine sciences to develop a data-mining system that correlates genetic patterns in genomes and metagenomes with contextual environmental data. This innovative tool may enable scientists to infer functions and activities for sequenced hypothetical genes, thus providing a wealth of information about niche adaptations as well as new enzymes and proteins for medical and industrial use.

The development of the METAFUNCTIONS approach is only possible through the integration of the diverse range of expertise from four European institutions from Germany, Switzerland and Poland. The innovative combination has the potential to produce a technology with broad application and high potential pay-off.

In the last seven years, more than 260 microbial genomes have been successfully sequenced while over 600 are currently in progress. So far, researchers have largely focused on bacteria that are medically important; ‘environmentally important’ organisms (e.g. those involved in methane production and consumption) have not received the same attention.

As it is difficult to culture ecologically relevant bacteria for genomic sequencing under laboratory conditions scientists often take DNA samples directly from the environment instead. Sequences of these samples are known as metagenomes – not the genome of an organism, but the genetic make-up of a particular environment.

Exploring new territory

A wealth of metagenome information is emerging– but the tools to analyse it are seriously lacking. Consequently, METAFUNCTIONS will develop a novel data-mining system that can identify relationships between sequenced genes and their environmental and ecological context. The ultimate aim is to determine the function of as yet unknown genes, known as hypothetical genes.

For this purpose, a ‘Genomes MapServer’ is under construction, soon allowing scientists around the world to access integrated genomic and ecological data and clearly visualise the results of their analyses.

Drawing on expertise

Techniques used are natural language processing to collate literature data and convert them into a structured, database format. METAFUNCTIONS also relies heavily on data-mining techniques to identify novel or interesting patterns in genomic data. Another innovative aspect of this project is the use of geographic information systems (GIS). GIS tools provide for the simulation and analysis of events from a geographical or spatial perspective.

Novel patterns – for example, the physical clustering of genes within a genome – will be correlated to the contextual habitat data. For instance, a particular cluster of genes may be found in a number of genomes and metagenomes all taken from high-temperature environments. It would be reasonable to infer that the gene must play some role in enabling survival in extreme heat.

In particular, the Metafunctions project will help to break through the current backlog in assigning function to the vast number of conserved hypothetical genes that high-throughput genomic sequencing has produced. Marine ecology, biotechnology, medicine and many industrial sectors could all benefit from the mapping that METAFUNCTIONS will give to ecological genomics.

*Official title: Environmental- and metagenomics – a bioinformatics system to detect and assign functions to habitat-specific gene patterns. A research project funded by the European Commission within Framework Programme 6 under the NEST – Newly Emerging Science and Technology Adventure initiative.


The Coordinator is the Max Planck Institute for Marine Microbiology, Bremen, Germany

Partners are:

  • United Nations Environment Programme, Global Resource Information Database – Europe jointly with University of Geneva
  • Poland: Institute of Computing Science, Poznan University of Technology
  • Germany: Technology Transfer Centre, BIBIS, Bremerhaven

Further information

Prof. Frank Oliver Glöckner

Max Planck Institute for Marine Microbiology

Microbial Genomics Group

Celsiusstrasse 1

28359 Bremen, Germany

Tel: +49 (0)42 12028 - 970, or 0421-200 3167

Fax: +49 (0)421 2028 -580

E-mail: fog(at)mpi-bremen.de

Website: www.microbial-genomics.de, http://www.megx.net, www.metafunctions.org

V.i.S.d.P. Prof. Frank Oliver Glöckner