On Wednesday, June 29, Frank gave his inaugural speech for this University Research Chair in Interdisciplinary Life Sciences. The speech was in Dutch and with it came a written text. The day ended with a party where Frank received two wonderful gifts from the department and other colleagues: a glider (sailplane) flight and a picture of Frank explaining his Fabulous Fundamental Formula of Fitness, printed on wood.
You can download the written text (in Dutch) by clicking: inaugurele rede.
Theoretical work from two former PhD students in the lab, Meike Wortel and Evert Bosdriesz is now published in Nature Scientific Reports (link to paper). It provides a theory that links molecular networks -using metabolic control analysis- and selection pressure in the chemostat. It is also shown that co-existence of fermenters and respirers can occur in population dynamical simulations of chemostat evolution, when product inhibition is taken into account.
Bas gave a 1 hour tutorial on stoichiometric modelling and flux balance analysis at the Whole Cell Modelling Course in Barcelona. The lecture was taped. It is really basic, but one of the students from the US told Bas that his talk alone was worth the trip over the ocean. Well, that must have been slightly exaggerated, but you can find the talk here.
We are just back from our yearly retreat, this year in Bakkeveen, a village in Friesland. We made a list of problems that we tried to solve in teams. Since we have many new experimental people in the team, focus was on concepts and small toy models. Here Bas explains model making to two of the experimental yeastie boys, Rick and Dennis.
A recent paper in Nature Systems Biology and Applications, with Bas as co-author, reports on international workshops held within the ISBE initiative (Infrastructure Europe of Systems Biology) to discuss the curriculum for a Master Program in Systems Biology. Our master program fits these recommendations very well!
C2W is a biweekly magazine published by the KNCV (Royal Netherlands Chemical Society). Bas was interviewed for the latest edition. He talks about his scientific career and discusses current and future goals of the lab’s research. The interview is only available in Dutch.
A pdf version of the interview can be viewed here.
Image courtesy of Kevin Kosterman.
Jurgen co-authored a paper in BMC genomics that uses mathematical modelling to understand the gene expression cascade in Trypanosoma brucei. You can read it here.
The current analysis is a follow-up of two previous publications from Jurgen that describe the contruction of a model of the gene expression cascade in T. brucei (Haanstra et al., 2008) and the extension of this model to the entire genome (Fadda et al., 2014). Here, using genome-scale quantitative data on various levels of the gene expression cascade, we compared model-simulated mRNA abundances to the actual in vivo mRNA abundances on a per-gene basis.
This analyses revealed that levels of mRNAs in procyclic form trypanosomes (the life-stage inside the tsetse fly) are determined mainly by transcript length and mRNA decay, with some control of precursor processing. In bloodstream forms (when the parasite lives in the mammalian bloodstream) variations in nuclear events play a larger role in transcriptome regulation, suggesting aquisition of new control mechanisms during adaptation to mammalian parasitism.
Susanne will defend her thesis on May 24 and today we received copies of it! This work is a successful collaboration with the Joachim Goedhart and Dorus Gadella, both from the University of Amsterdam.
You can find it here: Our new Current Opinion in Microbiology Review
It discusses how different cultivation methods can be used to select mutant bacteria with improved macroscopic growth parameters and our current understanding of whether such parameters trade off.
For more information see: O2 building information
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