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New International Research Training Group at LMU

The Regulation and Evolution of Cellular Systems

Munich, 11/17/2008

The Deutsche Forschungsgemeinschaft (German Research Foundation) has approved the new research training group “Regulation and Evolution of Cellular Systems (RECESS)” at LMU and TU München, which will be carried out in cooperation with the nationally leading Lomonosov Moscow State University (MSU) as an “international research training group” (IRTG). Research groups from bioinformatics, informatics, proteomics, biology, biochemistry and bioengineering will come together in this interdisciplinary program for particularly qualified postgraduates. The program starts on 1 April 2009 and will be funded initially for 4.5 years with 2.25 million euros. “Among other things, we will be focusing on modeling regulation networks of genes and proteins and comparing the models in different organisms,” reports LMU computer scientist Professor Ralf Zimmer, a spokesperson for the project. “Genes provide the blueprints for proteins over several intermediate steps. We intend to study the regulation of these steps, as well as cellular activities at the protein level – in order to ultimately understand complex biological systems better.” The spokesman at TUM is Professor Dmitrij Frishman.

Genes are sections of DNA, the molecule governing our heredity, and provide the blueprints for proteins, the most important functional elements in the cell. Between a gene and a protein, however, are several steps that are still far from being understood, and yet they are essential for cellular activity. In an initial step, the information in a gene is transferred to messenger RNA, a nucleic acid closely related to DNA. This RNA molecule, however, can still be modified to yield the final template for the associated protein. Proteins synthesized on the basis of this RNA are often modified subsequently.

One particularly important and frequent chemical modification is the attachment of phosphate groups. According to estimates, every third protein in the cell is phosphorylated at least once. The small phosphate group can have an enormous effect. In some cases, it acts as an on-off switch. That means its presence decides whether a protein is active or inactive. Phosphorylation also influences whether proteins are degraded again or not.

The research within the new research training group will be organized into several areas: Comparative genomics of metabolic and regulatory systems, network-based interpretation of transcriptome and proteome data, and posttranscriptional regulation mechanisms will be investigated to reveal when and under what circumstances which genes and which proteins are active. Together with internationally renowned expert Professor Mikhail Gelfand of the MSU, Zimmer intends to study the regulation of alternative splicing of RNA, which is a crucial type of RNA processing in order to generate a wide variety of structurally and functionally diverse proteins.

“Given modern, experimental methods such as microarrays and next generation, ‘deep’ sequencing methods ,we also want to take a look at the complement of all RNAs produced as genes are transcribed, as well as the regulation mechanisms of their modification,” reports Zimmer. “We will focus on the proteins built on the basis of these RNA molecules and their  subsequent chemical modifications, primarily in the phosphorylation of proteins, which can be measured for different organisms using quantitative mass spectrometry. We are glad to have the leading expert Professor Matthias Mann from the Max Planck Institute for Biochemistry as a partner in the training group to help us in phosphoproteomics.”

Whether the focus is on the genes, on the RNA, or on the proteins, the interactions and interdependent effects of the molecules will always lead to tremendous amounts of data, which will have to be interpreted and modeled as biological systems using powerful computers. It is the only way to detect similarities and differences that will point towards any underlying patterns. “Our research contributes to the new, currently developing and extremely complex field of systems biology,” says Zimmer. “Research groups at LMU, TUM, and MSU as well as the MPI for Biochemistry and the HelmholtzZentrum Munich (HZM)  with expertise and an international reputation in this field are among the partners of the training group. That will hopefully allow us to make progress in relatively short time.”

The second important pillar of the postgraduate training group, alongside research, is the teaching and training program, which is coordinated by LMU researcher Professor Volker Heun. It shall prepare the postgraduates for their research into understanding complex biological systems. It will be based on the very successful bachelor/master/diploma programs in bioinformatics established by the two Munich universities in 2000 and the University of Moscow in 2002. The new IRTG will form a network of postgraduates who will be investigating scientific questions together in an interdisciplinary approach. The postgraduates will be trained theoretically and practically. They can then get specialized education and training at all three universities involved in Munich and Moscow as well as at te HZM and the MPI for Biochemistry.

“This way, our postgraduate training will go far beyond of what is possible in the usual doctoral projects within an individual faculty, department or workgroup,” Zimmer tells us. “In addition to the research results, the fruits of our international research training group will be a new generation of scientists competent in methods from different research groups and with experience from international cooperative efforts. The alumni will have learned to interpret new genetic, genomic and proteomic data: for new insights and models for the regulation and evolution of cellular processes.”

 

Contact:
Professor Dr. Ralf Zimmer
Chair of Computer Science at LMU Munich
Tel.: +49 (0) 89 / 2180 – 4052
Fax: + 49 (0) 89 / 2180 – 4054
E-Mail: zimmer@bio.ifi.lmu.de
Web: www.bio.ifi.lmu.de

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