Our theoretical work on rate maximisation in metabolism has
been published in Plos Computational Biology. In this work, we took a very
general approach to ask a very specific question: we included genome-scale
metabolic networks, complicated enzyme kinetics, and arbitrary constraints on
enzyme expression, and then asked what metabolism looks like for a
microorganism that maximises its biomass production. The answer: it looks quite
simple. Only a few independent pathways are used by the microbe, giving rise to
the linear relations and growth laws that are found across microbiology. With
this result, we can not only model important phenomena such as overflow
metabolism and co-consumption, but we can even understand them.
Over the past years, we have worked on this project a lot
and we are very proud of the result. Daan: “Personally, I got the best
introduction to academics and systems biology that I could have hoped for: from
mathematical optimisation approaches (taught by Bob), doing lab work and coping
with the corresponding disappointments (taught by Coco), to thinking,
theorizing, writing and picking colours for your figures (taught by Bas and
Frank).” We hope that our general, theoretical approach, will lead to more
results and a better overall understanding in the near future.
Dennis’ work on the behaviour of fluorescent proteins (FPs) in baker’s yeast has been published! With the help of Daan de Groot and Phillipp Schmidt, a variety of fluorescent proteins were characterised for various properties, including brightness, photobleaching, photochromism, day-to-day variation andmonomerism. Many FPs showed different performance in yeast compared to previous characterisations done in vitro, in bacteria or in mammalian cells. To improve expression of good performing FPs in yeast, Dennis codon optimized them. Surprisingly, codon-optimization affected the FP traits, either positively or negatively. Still, this new set of FPs outperforms conventional FPs, with improved experimental signal readout, opening new experimental possibilities.
Niclas defended his PhD thesis, titled “Balance on many scales: Growth and gene expression in Bacillus subtilis” on January the 18th 2018. James Locke, Frank Schreiber, Rutger Hermsen, Sander Tans, Leendert Hamoen and Bas Teusink were in the thesis committee. A big thanks to the committee for their efforts, and congrats to you Dr. Niclas!
On January 11th Johan van Heerden defended his PhD entitled: “Dynamic regulation of yeast glycolysis through trehalose cycling: a probabilistic view of metabolic transitions”, of which Bas was the promoter. The committee comprised of prof Stefan Hohmann, prof Hans Westerhoff, prof Barbara Bakker, prof Frank Bruggeman and Dr Aljoscha Wahl. Previous group members, Jan Berkhout and Filipe Santos were the paranymphs.
Dan Fraenkel and Jens Nielsen recently undertook an in-depth review and extended analysis of our Science paper (van Heerden et al., 2014), and we are excited to see that their story has been published!
We have been hard at work developing an automated segmentation and tracking tool to analyse microscopic time-lapse movies of growing bacteria. After a few minor adjustments and additions we can now also segment and track fission yeast (Schizosaccharomyces pombe) growing on an agarose pad.
Our algorithm is now in its final stages of development and testing, and should be ready for release early next year.