Research Plan
At the long term the envisaged research and method development aims at providing both an understanding of system level adaptation processes of plants to environmental challenges and the means for a targeted improvement of crop plants.
Great value is set on the establishment of a strong research and teaching infrastructure in Systems Biology at the Potsdam-Golm Science Centre, with a particular focus on plants.
The research programme in GoFORSYS will be organised in six work packages (WP), each of which will managed by one of the Partners as indicated:
WP 1: General bioinformatics and computational methods
WP 2: Development of new analytic tools for systems analysis
WP 3: Multilevel systems analysis of responses in Chlamydomonas
WP 4: Testing of the applicability of models developed in Chlamydomonas
by comparison with the response of model higher plants
WP E: Implementation of the educational concept
WP M: Management of the project
Each work package consists of a number of sub-work packages.
WP 1 General bioinformatics and computational methods
managed by Prof. Dr. Joachim Selbig, Institute of Biochemistry and Biology and Institute of Computer Science / Bioinformatics, University of Potsdam
Systems Biology means integrating experimental data with computational and theoretical approaches to build an understanding of pathways, cells, organs, and complete organisms. It combines concepts from different scientific disciplines to obtain an integral understanding of biological systems in terms of their components and their interactions. Systems Biology is characterized by a diversity of heterogeneous data including discrete sequence information, continuous gene expression data, functional annotations of genes, networks of interacting molecules, sets of differential equations describing the dynamics of the underlying system, localizations of proteins within a cell, phylogenetic trees relating species, and numerous other data types. Therefore, the seamless integration of such disparate data sets is an essential prerequisite for any Systems Biology approach and poses formidable challenges to the Bioinformatics infrastructure development work. Sub-work packages WP1.1 and WP1.2 focus more on traditional Bioinformatics whereas sub-work packages WP1.3 and WP1.4 focus more on Systems Biology.
WP 1.1 Data warehousing
WP 1.2 Genome analysis and comparison
WP 1.3 Integrated data analysis
WP 1.4 Modelling and simulation methods
WP 2. Development of new analytic tools for
systems analysis
managed by Prof. Dr. Bernd Müller-Röber, Institute of Biochemistry and Biology / Molecular Biology, University of Potsdam
Many analytic platforms required are already established or can be rapidly adapted including commercial expression arrays for Chlamydomonas, Arabidopsis and tomato, robotized enzyme assays for >45 enzymes, rapid robotised assays for total protein, chlorophyll a, chlorophyll b, and starch, GC-TOF and LC-MS metabolite profiling, nuclear transformation of the species used and plastid transformation.
However, in some cases further development will be required, and these are listed as specific work packages.
WP 2.1 Quantification of proteins
WP 2.2 Analysis of protein turnover
WP 2.3 Elaboration of metabolite profiling
WP 2.4 Analysis of fluxes into specific products
WP 3. Multilevel systems analysis of responses
in Chlamydomonas
managed by Dr. Ralph Bock, Director, Department 3,Max Planck Institute of
Molecular Plant Physiology
WP 3.1 Different steady state conditions
WP 3.2 Genetic manipulations
WP 3.3 Time resolution of responses in transients
WP 4. Testing of the applicability of models developed
in Chlamydomonas by comparison with the
response of model higher plants
managed by Prof. Dr. Mark Stitt, Director, Department 2, at the Max Planck Institute
of Molecular Plant Physiology
In general, two different sorts of experimental systems will be used to test the applicability of the models developed in Chlamydomonas to higher plants. The first (WP4.1 and 4.2) will involve analysis of the response in higher plants to the same environmental challenges that are analysed in Chlamydomonas (light intensity, light quality, temperature, nitrogen). The second (WP4.3 and 4.4) will be based on natural variation in the rate of photosynthesis and growth found in a model plant species (Arabidopsis) and a model crop (tomato). Natural diversity is used because this is an unbiased source of variation, which has been selected for, and in which it can be asked if changes in the composition of the photosynthetic apparatus lead to a predictable phenotype, i.e. predicable changes in the rate of photosynthesis and the response to different environmental conditions.
WP 4.1 Responses to environmental changes
WP 4.2 Similarity of the regulatory networks
WP 4.3 Identification of genotypes differing in photosynthesis and growth
WP 4.4 Systems analysis to identify the molecular basis of genotype-
related differences in photosynthesis and growth
WP M: Management of the project
This WP comprises all activities related to the management of the IRC.
WP M.1 Coordination of activities
WP M.2 Communication
WP M.3 Development of new initiatives
WP E: Implementation of the educational concept
for the implementation of a high-quality international PhD Programme on Systems
Biology.
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