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; 
Yuko, Lennart, and LZ1

Short Visit from Yuko Sato

Our collaborator Yuko Sato paid us a short visit from Japan. Yuko is a Kimura Lab Members at the Tokyo Institute of Technology, who develop innovative in vivo imaging approaches targeting post-translational modifications.

During the visit, Yuko and Lennart executed pilot experiments for light sheet-based in vivo imaging. We hope the photo conveys our joy at the last, successful attempt at our experiments. Thank you for the visit!

Shai giving Friday Seminar

MPI-CBG Internal Seminar with Shai & Lennart

The MPI of Cell Biology and Genetics (CBG) traditionally has an internal seminar, weekly on Fridays. It used to showcase achievements of students and PostDocs after 2-3 years of work, thus keeping the whole CBG community informed of the different types of research being done at the institute. The format was now changed to two presentations: 30 minutes + questions for a speaker with 2-3 years of research behind them, and 10 minutes without questions for a student or PostDoc in their first year of research. On Friday, October 2nd, Shai and Lennart were the first members of the Vastenhouwlab to present in the new format. While the hour from 16:00-17:00 was rather packed, it was good to present a very accomplished work alongside new ideas and first experimental results.


Pavel Vopalensky

Pavel comes from a small village close to Jihlava, Czech Republic and grew up surrounded by the mild hills of the Bohemian-Moravian highlands frisking in pine scented forests, golden fields and blossoming meadows. To better comprehend the beauty of nature, he went to study biochemistry and biotechnology at the Institute of Chemical Technology in Prague. Afterwards, he continued with PhD studies at the Institute of Molecular Genetics in Prague elucidating the evolutionary origin of the vertebrate eye. He decided to stay in evo-devo for his first postdoc and joined the group of Prof. Detlev Arendt at EMBL Heidelberg. Here, while analyzing the developmental cell lineage and the dynamic gene expression in the marine worm Platynereis dumeriliiPavelgot interested how is differential gene expression orchestrated at the molecular level. Therefore, he joined Dr. Nadine Vastenhouw’s lab in fall 2015 to investigate transcriptional regulation underlying the first lineage decisions in zebrafish development. In his free time, Pavel likes singing in a choir or playing drums and exploring countryside hiking or biking together with his family.

Best PostDoc Speaker & Future PhD Position

Lots to celebrate! Vania has found a new PhD position at the CRTD in Dresden, which she will start in October. Good luck on the way! Krishnendu was voted for as best oral PostDoc presenter at the MPI-CBG PostDoc retreat. Cake + Champagne, and the weather played along 🙂

Hint for Vania's cake: it relates to her new position in neural development...

Vania Tsata

Vania* comes from Athens, Greece, where she also did her undergrad studies in the Biology Department. She absolutely loves coffee and finds it necessary to start the experimental or any other day with a cappuccino. Vania discovered her passion for science during her undergrad thesis, in the lab of Dr. Poulopoulou in Athens Medical School. There, she investigated the role of neuroligins in the glutamatergic signaling of T-lymphocytes of healthy and autistic children. Vania moved to Dresden in November 2012 to join the group of Dr. Stephan Speier as a research assistant, focusing on β-cell physiology. In October 2013, Vania joined the Master’s Program in Regenerative Biology and Medicine offered by the TU and the Center for Regenerative Therapies Dresden. After joining the Vastenhouw lab for a 3-months rotation and fascinated by the developmental transitions of the vertebrate embryo and also zebrafish as a model organism, she decided to stay a bit more and complete her master thesis in the lab. Now she is working on the role of histone level in setting the timing for zygotic genome activation.

*Or “Vasiliki Tsata”, which is her formal name, and also crucial info for her photo to make sense. LH