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Institute of Bio- and Geosciences

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Research

Regulatory mechanisms allow for adaptation of living cells not only to a changing environment, but also to intracellular states. In the fields of Metabolic Engineering and Synthetic Biology, detailed knowledge of the host’s regulatory mechanisms is pivotal for rational strain development.
Synthetic biology can be considered as "... the design and construction of new biological components, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. Synthetic biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components (parts of enzymes, genetic circuits, metabolic pathways, etc.) that can be modeled, understood, and tuned to meet specific performance criteria, and the assembly of these smaller components into larger integrated systems that solve specific problems." (Taken from Keasling, JD; ACS Chem. Biol. 2008; 3 (1): 64–76)
Our research on global regulation and on Metabolic Engineering of Corynebacterium glutamicum and Escherichia coli focuses on the production of amino acids, other primary metabolites as well as new products and thus belongs to the field of White Biotechnology.

Methodology

Strains are constructed by molecular biological methods and characterized by functional genomic tools combined with classical analytical and biochemical methods.
For monitoring of global gene expression we are using whole-genome oligonucleotide microarrays.

Methodology Figure 1

DNA microarrays experiments are performed with the MAUI hybridization system (BioMicro Systems) and microarrays are scanned with a GenePix 4000B device (Molecular Devices).
All microarray expression data and the detailed experimental information are collectively stored for further analysis in the IBT microarray database in MIAME compliant format (MGED).





For data handling freely available R-packages (Bioconductor) as well as self-made Windows-based tools are used (Result-Handling, Summarize Expression Data, Cluster & TreeView).

Methodology Figure 2

Methodology Figure 3

Methodology Figure 4

Proteome analysis and protein identification is performed by 2D-gel electrophoresis and MALDI-ToF/ToF-MS (Ultraflex III, Bruker).

For the analysis of metabolites the institute is equipped with a GC/ToF system.


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