eLife Paper on Refractive Index Matching in Live Imaging

Microscopes are optimized to give the clearest images, taking great care of all optical components along the light path. This has lead to a situation where the transition between a live sample and the surrounding liquid becomes the biggest imperfection in the optical path.

In this MPI-CBG/MPI-PKS/CSBD collaboration, lead by Tobias Boothe from the Rink lab, we show a simple but highly effective procedure to minimize the optical imperfection at the sample/medium interface. The technique is based on OptiPrep (chemical name: iodixanol), which can be ordered and used in any biological laboratory without any unusual equipment. Our technique worked with no toxicity or other problems in whole animals, primary cells, cell lines, as well as organoids.

Find our paper online with eLife.

EMBO Workshop@MPI-CBG: Maternal-Zygotic Transition

From 23rd to 26th April, the MPI-CBG hosted the first international meeting exclusively dedicated to the Maternal-Zygotic Transition (MZT). Under the title "Awakening of the genome: The maternal-to-zygotic transition", a jam-packed meeting program was presented under the umbrella of the EMBO event series.

Focusing on genome activation allowed a first-ever platform for the MZT community. Participants from all over the world gathered to showcase an extensive range of techniques, approaches, and biological questions. Plenty of new and unpublished data made it exciting, a meeting size of ~150 participants meant that everyone could be easily approached, and the wish for a repeat meeting was voiced several times.

eLife paper on ZGA timing: activator-repressor competition

Our study demonstrating how repressors (histones) and activators (transcription factors) jointly control transcription in the zebrafish embryo is now available online: Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. Joseph et al. eLife (2016)

Competition Model

In this study, lead by Shai Joseph (Vastenhouw Lab) and carried out collaboratively with the Shevchenko and Zaburdaev lab, we could quantitatively address a long-standing question: how is the timing at which transcription starts in embryos controlled?

By a combination of quantitative, molecular, and functional techniques, we found that the two most prominent hypotheses, the "depleted repressor" and the "increasing activator" models, can be unified in a competition model. Here, repressing histones and activating transcription factors go head-to-head competing for access to DNA target sites.

Additionally, the nuclear-to-cytoplasmic ratio - often defined in the number of genomes in an embryo - resurfaced as a key concept, though in the form of a volume ratio between cell nuclei and overall cytoplasm. While the global concentration of not DNA-bound histones did not change at the time of transcription onset, we detected a marked decrease in the concentration of not DNA-bound histones specifically within cell nuclei.

 

Cindy Horenburg

Cindy was born and raised in the lovely city of Dresden. In her twenties she moved to Zittau where, besides studying molecular biotechnology, she started climbing and through it discovered the beautiful nature of the region as seen from the mountain peaks. During her Bachelor thesis research, she learned to appreciate the zebrafish as a model organism and jumped into the new era of genome editing with the world-changing CRISPR/Cas9 technology. Currently, Cindy is part of the Regenerative Biology and Medicine master program in the CRTD, which allows her to extend her practical skills and deepen the knowledge in rotations with different labs in Dresden. For the 2017 summer term, she joined the Vastenhouwlab, bringing her genome editing skills to our studies of nuclear architecture. In her free time, she loves outdoor activities andjam sessions with other musicians.

BioRxiv: Histone and transcription factor binding competition

A preprint for our latest work is now on BioRxiv: “Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos”. The lead author of this study is Shai, with lots of support from within the Vastenhouw lab as well as the Zaburdaev (MPI-PKS) and Shevchenko labs (MPI-CBG).

You can go and read the preprint here: http://biorxiv.org/content/early/2017/04/13/125716

Lab Photo Session 2017

Julia Eichhorn from the CBG Photolab braved the freezing cold with us for our lab photo. Look at the snow!

There's also a photo of Mate taking a photo of Julia taking a photo of Edlyn. To avoid overly frozen smiles during our individual headshots, we did head back inside after all. Thanks Julia, great photos!

Shai wins short talk prize “Epigenetics In Development”

On October 20-22, almost half of the Vastenhouwlab participated at the Epigenetics in Development conference held at the IMB in Mainz, Germany. This exciting meeting brought together scientist from all over the world to discuss their view how epigenetics and gene regulation shapes a developing embryo. The topic was covered a broad range of perspectives from point mutations through chromatin landscapes to evolution.
 
Excitingly, Shai was selected to give his short talk “Competition between histones and transcription factor binding regulates zebrafish genome activation”, for which he was awarded the short talk prize. Congratulations, Shai!
 
Apart from the scientific program, one entire afternoon was dedicated to the excursion to a beautiful monastery, Kloster Eberbach, including a guided tour with wine tasting and a grand finish having a wonderful gala dinner.
 
PV