idw – Informationsdienst Wissenschaft
Nachrichten, Termine, Experten
Nachrichten, Termine, Experten
idw - Informationsdienst
Wissenschaft
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 -938, or 0421-200 3167
Fax: +49 (0)421 2028 -580
E-mail: fogmpi-bremen.de
http://www.mpi-bremen.de Website Max Planck Institute for Marine Microbiology
http://www.regx.de Website Real Environmental Genomics
14 scientists from several European countries met for the first time at the Max-Planck-Institute for ...
MPI Bremen
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Criteria of this press release:
Biology, Chemistry, Environment / ecology, Geosciences, Information technology, Oceanology / climate
transregional, national
Research projects
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