Swammerdam Institute for Life Sciences

Science Research at UvA-VU: System microbiology

1 December 2015

‘We work together because we want to; together, we produce good science. This is not an institutionalised collaboration that was forced upon is, this really is bottom-up.’ Filipe Branco dos Santos was part of Bas Teusink’s Systems Bioinformatics group at the VU Amsterdam institute IBI, or Centre for Integrative Bioinformatics VU, between 2008 and 2013. In 2013, he launched his own group at Swammerdam Institute for Life Sciences (SILS).

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Strong relationship

Branco dos Santos explains that he maintained a strong relationship with Teusink and other colleagues and he still visits the VU every Friday. He is currently involved in several collaborations there with a few UvA colleagues. ‘We share a lot of research questions with each other, although the organisms subjected to this research are largely different. I study cyanobacteria and lactic acid bacteria. The latter slightly overlaps with Bas’ research, but other than that he studies very different microorganisms.’

Teusink and Branco dos Santos have a few outstanding research requests for new PhD projects. Their first joint PhD student has been studying regulatory networks and lactic acid bacteria since last year. ‘These bacteria either express proteins or don’t, depending on their immediate environment. We want to know how exactly this is regulated: which genes are expressed and when?’ Branco dos Santos explains that in order to study this, genes are characterised and, for instance, slightly modified, which in turn provides information on what these genes actually do. The researchers also compare strains with slightly different regulatory networks, under different circumstances. ‘The underlying theme is: how is life shaped by its environment?,’ he summarises.

Common denominator

This is also the biggest common denominator of all joint research carried out by both groups, Branco dos Santos continues. ‘In evolution, life is shaped by natural selection. A process exists, for instance, called optimisation, which allows only the best-adapted species to survive. If you were to carry this notion to the extreme, very little diversity would exist. But in actual fact nature is very diverse! And this is not only due to the fact that there are many different environments and different species are better adapted to each of these environments. That’s what we’re trying to find out.’

The expertise or techniques used are not strictly divided between both groups, according to Branco dos Santos. ‘Bas, for instance, has quite a lot of genome scale models, but I was partially responsible for creating those when I was still working there.’ The most important thing for him about this and other research projects is that he can collaborate with people who are good at what they do. ‘This sometimes leads you outside of your comfort zone, but it can also create a synergy that still works really well in our case.’

Text: Jeroen Scharroo

Published by  Faculty of Science