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Synthetic Biology
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Synthetic biology represents the rising field of integrating large-scale genetic engineering strategies in the life sciences, with the aim to create novel functions or combinations of functions in biological machines.
There are numerous ways of working in the field of synthetic biology; generating synthetic organisms, standardizing genetic parts for customized implementation, creating novel chassis-organisms for à la carte use. At SSB in Wageningen we focus on a limited number of topics, depicted below.
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Summary of research activities
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Exploring regulatory logics
All organisms regulate their gene expression by a variety of dynamic mechanisms, such as different promoters, a range of transcription factors, but also through the regulatory power of small RNAs (sRNAs).
In our group, we analyze mobile (and hence, promiscuous) promoters in prokaryotes, as well as the potential of sRNAs in regulating gene clusters acquired via horizontal gene transfer.
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Key Publication: van Passel MW, Marri PR, Ochman H.
The emergence and fate of horizontally acquired genes in Escherichia coli.
PLoS Comput Biol. 2008 PMID 18404206
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Single cell fungi
Filamentous fungi are notable secretors of hydrolytic enzymes as well as a range of industrially relevant metabolites, giving them the nickname ‘the versatile cell factory’.
We investigate the possibility to render these organisms to a permanent single cell state.
This could benefit the industrial processing of the strains, and potentially increase the yield of secretory processes.
Furthermore, this may shed light on the processes that are involved in the multicellularity and cell-to-cell communication of these industrially interesting strains.
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Standardization of genetic parts
For many bacteria, the Registry of Standardized Parts has genetic building blocks available for modular tinkering. For Aspergillus, this does not yet exist. In combination with the Fungal Systems Biology group, we aim to construct a range of standardized parts that will enable a cleaner engineering approach in fungal synthetic biology.
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Genome streamlining of Pseudomonas putida
Audrey Leprince (post-doctoral researcher)
Large-scale genome streamlining is at the heart of synthetic biology by generating specialized organisms for a range of applications. Using customized transposons, large genomic regions can be easily removed, and the resulting organisms can be tested for a optimal performance for a range of conditions. Simultaneously, by using a known and sequenced genome, fundamental questions concerning metabolism can be studied.
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Modes of biological adaptation
Synthetic biology represents an amalgamation of different disciplines, amongst which molecular biology, systems biology, biological engineering. Still, it is striking that there is still a need for a descriptive approach. The integration of entire genetic circuits into new hosts is not unknown to biology, and numerous examples exist in which entire pathways are transferred between organisms. Therefore, we set out to uncover unifying principles in adaptative strategies, be it by targeting single genes or by reshuffling entire pathways.
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