Genome Architecture Meeting at ICTP, Trieste

Lennart participated in the meeting “Genome Architecture in Space and Time”, which took place at the International Center for Theoretical Physics in Trieste from June 20th to 24th. The venue would suggest a Physics and Theory heavy meeting – and certainly there was some of that – but the conference covered various aspects of genome architecture. From newest biophysical and imaging approaches, via medical relevance of aberrations in genomic structural elements, to polymer folding models, a truly eclectic mix of questions and approaches was presented. Unusual for an international meeting, the invited speakers had about 45 minutes each. Throughout, this time was put to good use, allowing comprehensive introductions, sometimes reaching back decades to lead up to the most up-to-date questions.

Carine Stapel attends the MBL Embryology Course 2016

From June 4 to July 17 Carine joined the MBL Embryology course in Woods Hole. This course has a longstanding tradition (since 1893) in teaching students, postdocs and faculty the nuts and bolts of developmental biology. From C. elegans, chick and ctenophore to sea urchin, snails and squid (and zebrafish of course!), the morning lectures and experiments that lasted until the wee hours of the night covered them all. Now let’s see if she can convince the Vastenhouw lab to add some new species to its repertoire! 

Pavel visits the lab of Prof. Tatjana Sauka-Spengler in Oxford

In mid-March 2016, Pavel visited the lab of our collaborator Prof. Tatjana Sauka-Spengler in Oxford, UK. Tatjana’s lab established a genetically encoded system for biotinylation of specific targets in fish cells, allowing, among other applications, tissue-specific isolation of nuclei.

Supervised by a cheerfully enthusiastic PhD student Vanessa Chong, Pavel performed several rounds of nuclei isolation and is looking forward to introduce this method to Vastenhouw lab. 

Apart from having great time in Tatjana’s lab, Pavel also explored the charming campus of the Oxford University.

Thanks the entire Sauka-Spengler lab for a great time!

Setting up the experiment

Pavel’s Birthday

The Vastenhouw Lab celebrated Pavel's birthday with delicious bakery goods from the Czech Republic.  Gastrulating zebrafish embryos made from Play-Doh were an absolute must for the celebration.

Segmented Cells

FISHing fish, explained on thenode

Our recent publication is covered in a piece on FISHing fish. Check out the description and a bit of a behind-the-scenes insight into of the paper!

Link to post on thenode

Paper reference:

Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W.; Vastenhouw, Nadine L.
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
Development, 143, no. 3, pp. 540-546, (2016)

New Years Dinner

To celebrate the beginning of the New Year, the Vastenhouw lab had a delicious meal at Fischhaus Dresden. This idyllic restaurant is situated at the edge of the forest and with freshly fallen snow, the atmosphere was magical.

Methods Article in ‘Development’

We are happy to post about our lab’s recent publication in Development. The article describes how to label and analyze single mRNA molecules, within single cells, at different stages of the zebrafish embryo’s development. With this technique, we hope to open new avenues into gene expression patterns and cellular differentiation programs.

The project was chiefly driven Carine Stapel, currently a PhD student in the Vastenhouw Lab. Carine developed the experimental protocol. The associated, freely available image analysis and quantification pipeline was developed in collaboration with Gene Myer’s research group as well as the Scientific Computing Facility. In fact, all work was done in-house at the MPI-CBG, demonstrating the institute’s wide array of qualifications as well as its collaborative spirit.

The article and protocol are available from Development, and the article also contains the analysis pipeline in its Supplementary Information. Article Page at Development

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

L. Carine StapelBenoit LombardotColeman BroaddusDagmar KainmuellerFlorian JugEugene W. MyersNadine L. Vastenhouw;