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!

Mykola Markadeiev

Mykola was born in Ukraine and has a passion for trekking, skydiving and (suddenly) table-tennis. He studied Molecular Biology and Genetics in Taras Shevchenko University of Kyiv, where he took part in projects on liver regeneration and gerontology. Willing to explore Europe, the spirit of scientific adventure brought him to Dresden, doing his Masters in Regenerative Biology and Medicine. There he participated in research on murine neurogenesis, zebrafish regeneration and stem cell niches of Drosophila. He joined the Vastenhouw lab to help the project of Carine Stapel on single molecule RNA imaging.

Lucia Selfa

Lucia was born in Madrid and started her studies in Biomedical Sciences in Alcalá de Henares. By the end of her degree, her interest to discover the world dragged her to join the Erasmus program and move to Amsterdam, where she had her first contact with epigenetics during her Bachelor Thesis at the Netherlands Cancer Institute, participating in a haploid genetic screen of inhibitors targeting epigenetic modifiers.  Willing to explore other fields in science, as well as other countries and cultures, she joined the Master’s Program in Regenerative Biology and Medicine in Dresden. After looking into adult neurogenesis and planarian regeneration, she has now joined the lab to help understanding the role of histones in transcriptional regulation.

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.

 

Lennart at MBL Zebrafish Course

Lennart just came back from the 2015 Zebrafish Development and Genetics course at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, USA. The panoramic shot below shows the idyllic location of the MBL campus: student housing on the left, a research buildings on the right, and the magnificent view of Eel Pond in the middle of Woods Hole.

The two week course covers an eclectic overview of backgrounds, concepts, and experimental approaches. The MBL and Woods Hole environment, the small course size of 22 participants, and the commitment of organizers and instructors allow for very hands-on training sessions and a very communal atmosphere. Check out the photos to get an impression of the training sessions and great social atmosphere that make this course so unique.