Lab retreat 2017 was a great success

We all moved for three days to Groesbeek for our yearly lab retreat, this year organised by three new PhD students, Eunice, Daan and Sieze. They did a wonderful job: many people introduced a problem in the morning, from technical (how to model complex communities) to more evolutionary (why do lactic acid bacteria make flavours?), which led to group discussions, model making and literature search – which was slightly compromised by shitty wifi, but G4 worked wonderfully too. In the evening or morning the results were presented, and we can conclude that many issues are not solved yet (some were!), but alliances have been formed in the group to solve them back in Amsterdam. And we learned a lot!

Here is Frank discussing with Johan and Daan, … and beer. Meanwhile, other were preparing food – no thinking without enough energy.

here Esther, Bas and Eunice organise the dinner: we had chilli one day, spinach lasagna the other day. Always fun to cook for 20 in a kitchen without sharp knives…

and of course, getting to know each other in different ways. “Cow trade” is a wonderful card game that requires bluff, wit and a bit of luck. Paul fooled all of us by playing ignorance of the game, and buying in too high, but in the end he took us to the cleaners.

Finally, Jurgen organised a pub quiz, with impossible questions about long forgotten music, but since he was making most of the pictures, we have no picture. Sorry Jurgen, but thanks for a wonderful evening, and everybody else for a great retreat!


paper by Johan got three stars recommendation at F1000

Herbert Sauro, systems and synthetic biologist from University of Washington, Seattle, recommended the 2015 BioEssays review that Johan wrote together with Frank and Bas, saying it is an essential read for biochemistry textbook writers. The review is about the regulation of glycolysis, explained from a functional supply-demand perspective. See Access the recommendation on F1000Prime for the recommendation text.
Thanks for the warm words Herbert!

Iraes Rabbers wins the AIMMS PhD competition

On the 13th of April, our institute, the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), organised its annual symposium with a PhD student contest for best talk of the day. Iraes Rabbers presented her thesis work on the optimality of protein expression in E coli, and won! Congrats Iraes, well done!

Our master in Bioinformatics and Systems Biology is TOP!

In the latest results from the National Student Enquete (Inquiry) NSE our master got an 8.2 out of 10, and this makes it officially a TOP master, one of only 6 TOP masters at the VU. The master is a joined effort of Systems Bioinformatics and Bioinformatics from the VU, and the Life Science groups from the University of Amsterdam. For more information about the TOP master, go here.

First recommendation for F1000 published

Bas was asked to contribute recommendations to the Faculty of 1000, and group members can nominate papers, and help write the recommendation – and get the credits. This month’s recommendation can be seen here.

Article details:
Dynamic control of gene regulatory logic by seemingly redundant transcription factors.
Z AkhavanAghdam, J Sinha, OP Tabbaa and N Hao
elife 2016 Sep 30; 5
DOI: 10.7554/eLife.18458

When the yeast genome was first sequenced in 1996, scientists were puzzled by the seeming redundancy of genes; in fact, the whole genome of Saccharomyces cerevisiae was duplicated during its evolution. Many – not necessarily conflicting – explanations were provided, such as enhancing flux {1}, acting (or not) as backup systems {2}, or leading to differential sensitivity to external cues {3}. This paper by the Hao lab extends work done in the O’Shea lab {4,5} on the dynamics of Msn2/Msn4-mediated transcriptional regulation to provide another functionality – to act as dynamic logical gates. From the paper: “Either Msn2 or Msn4 alone is sufficient to induce the expression of target genes with fast kinetics promoters, constituting what is essentially a biological ‘OR’ logic gate. In contrast, the induction of target genes with slow kinetics promoters requires activation of both factors, forming an ‘AND’ gate.” The work emphasizes the role of time scales in regulation logic, and adds a beautiful example to the collection of functional network motifs {6}.

I would like to thank Dr Johan van Heerden for assistance in the preparation of this recommendation.

{1} Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Conant GC, Wolfe KH. Mol Syst Biol. 2007; 3:129 PMID: 17667951 DOI: 10.1038/msb4100170
{2} The cellular robustness by genetic redundancy in budding yeast. Li J, Yuan Z, Zhang Z.
PLoS Genet. 2010 Nov; 6(11):e1001187 PMID: 21079672 DOI: 10.1371/journal.pgen.1001187
{3} The competitive advantage of a dual-transporter system. Levy S, Kafri M, Carmi M, Barkai N. Science. 2011 Dec 9; 334(6061):1408-12 PMID: 22158820 DOI: 10.1126/science.1207154
{4} Tunable signal processing through modular control of transcription factor translocation. Hao N, Budnik BA, Gunawardena J, O’Shea EK. Science. 2013 Jan 25; 339(6118):460-4 PMID: 23349292 DOI: 10.1126/science.1227299
{5} Signal-dependent dynamics of transcription factor translocation controls gene expression. Hao N, O’Shea EK. Nat Struct Mol Biol. 2011 Dec 18; 19(1):31-9 PMID: 22179789 DOI: 10.1038/nsmb.2192
{6} Network motifs in the transcriptional regulation network of Escherichia coli. Shen-Orr SS, Milo R, Mangan S, Alon U. Nat Genet. 2002 May; 31(1):64-8 PMID: 11967538 DOI: 10.1038/ng881


it happened again: a dry PhD student turns wet

Chrats is a computer scientist specialised in machine learning, which he applies to metagenomics data of wine fermentations. He could not resist to test some of his predictions in the lab. One of the great advantages of having both dry and wet people in the same lab. We are all very proud…


Philipp Savakis got his PhD

Philipp -postdoc in the group- defended his PhD at the University of Amsterdam, with prof Klaas Hellingwerf as promoter. He did very well and with his direct and very correct answers, it appeared harder for the committee members than for him! Well done Philipp!


Mark Hanemaaijer got his PhD

Mark defended his PhD thesis on the modelling of microbial ecosystems on November the 22nd 2016. Ines Thiele, Hans Westerhoff, Gerard Muyzer, Fons Stam and Herwig Bachmann were in the thesis committee. Thanks to them for their efforts and congrats to Mark!


Housewarming party in Arnhem

Bas moved to a new house with a view over the Rhine and gave a housewarming party for the group. “Good food, good wine, good company and a great venue” summarizes the party, according to Brett.