Center of Biotechnology (CeBiTec), Department of Genetics
Brief description of the participant organisation
The Center of Biotechnology (CeBiTec) is the central scientific institution at Bielefeld University dedicated to interdisciplinary research in life sciences. It consolidates research activities in the fields of biotechnology, molecular biology, genome research, systems biology, biochemistry, nano- and biophysics, bioinformatics and computer science. In addition, the CeBiTec is equipped with the Technology Platform Genomics supporting high-throughput technologies in genome research and the Bioinformatics Resource Facility (BRF).
Main tasks in the project
Partner UB is involved in 454-pyrosequencing of total metagenomic and mobilome DNA preparations and in establishment of a bioinformatics platform for metagenomic data storage, annotation and analysis. In addition, a web-based database environment for project management purposes will be developed.
Previous experience relevant to the tasks
Several microbial genomes were established at the Department of Genetics (CeBiTec). Genome and post-genome research on some of these microorganisms was done in the framework of the GenoMik-Plus network that is coordinated at Bielefeld University. Different plasmids encoding antibiotic resistance and degradative capabilities were isolated from bacteria residing in the activated sludge compartments of wastewater treatment plants. These plasmids were analysed at the genomic as well as at the functional level. Very recently, a pilot study accessing the plasmid metagenome (mobilome) of wastewater treatment plant bacteria was conducted. The Department of Genetics runs and has access to state-of-the-art sequencing technologies. Very recently, the Genome Sequencer FLX System (Roche) was installed at the CeBiTec. Computer scientists of the Bioinformatics Resource Facility (BRF) at the CeBiTec are working in applied bioinformatics. They provide the complete bioinformatics infrastructure and software solutions for genome and post-genome projects such as for example a high-performance compute cluster with more than 500 CPUs, the annotation software tool GenDB and the Sequence Analysis and Management System SAMS. In addition, a wide range of standard bioinformatics tools and bio-databases are made available.
Tauch, A., Trost, E., Bekel, T., Goesmann, A., Ludewig, U. & Pühler, A. (2006) Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System. Biochemica 4: 4-6
Krause, L., Diaz, N., Bartels, D., Edwards, R., Pühler, A., Rohwer, F., Meyer, F. & Stoye, J. (2006). Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22(14): 281-289
Schlüter, A., Szczepanowski, R., Pühler, A. & Top, E. M. (2007). Genomics of IncP-1 antibiotic resistance plasmids from wastewater treatment plants provides evidence for a widely accessible drug resistance pool. FEMS Microbiol Rev, 31 (4): 449-477.
Schlüter, A., Krahn, I., Kollin, F., Bönemann, G., Stiens, M., Szczepanowski, R., Schneiker-Bekel, S. & Pühler, A. (2007). IncP-1 b plasmid pGNB1 isolated from a bacterial community of a wastewater treatment plant mediates decolorization of triphenylmethane dyes. Appl Environ Microbiol 73(20), 6345-6350.
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