Category Archives: General

Lab Retreat 2017

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Tis that time of the year again! This year’s Vastenhouw Lab retreat took place in Technische Universität (TU) Dresden’s Computer Science green building. Together with Vasily Zaburdaev (MPI-PKS) and Thomas Quail (Jan Brugues lab, MPI-CBG), we had a matinee of stimulating and fruitful discussions.

In the evening, we all gathered around a kitchen and bar – where we got to cook our dinner and shake our cocktails (with some help from the professionals). A festive night for the Vastenhouw Lab! There were also hellos and goodbyes. We welcomed new lab members and said farewell to the veterans, as they transition to the next chapter of their career.

        

 

eLife Paper on Refractive Index Matching in Live Imaging

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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.

Edlyn at MPI-CBG Postdoc Retreat

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Edlyn attended the 7th Annual MPI-CBG Postdoc Retreat, which took place in the beautiful and picturesque Tisá, Czech Republic, from 19th to 21st of June, 2017.

The three-day retreat included talks (and elevator pitches) from fellow postdocs at the institute & invited external speakers:

  • Dr. Simon Reber (Humboldt-Universität, Berlin),
  • Dr. Elvan Boke (Centre for Genomic Regulation, Barcelona),
  • Dr. Selina Wray (University College London),
  • Dr. Adrian Raga (Katholieke Universiteit Leuven),
  • Dr. Olof Idevall-Hagren (Uppsala University);

and talks from our very own: Dr. Jacqueline Tabler and Dr. Christoph Zechner.

The retreat was scientifically enriching and also featured a hiking trip in Bohemian Switzerland, through the sandstone rocks of the Tisá Walls.

2017-06-20 15.48.04     

Science outreach – for juniors and seniors

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Last month Pavel, Lennart, and Máté shared their enthusiasm for science as part of the “Junior Doktor” and “Seniorenakademie” series at our institute.

Pavel taught highly motivated pupils from primary school about the evolution of the eye. This was followed up by a microscopy session where the ‘scientists of the future’ got to look at zebrafish pineal glands and stained nuclei of zebrafish embryos.

Máté gave a seminar about transcription factors to an excited elder audience. He talked about general concepts of how transcription factors can orchestrate gene expression programs with some examples from his own research in zebrafish.

Amy Dowdle’s visit

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At the beginning of May we had the pleasure of welcoming Amy Dowdle from the lab of Julia Horsfield, University of Otago, New Zealand. It was an exciting one week visit as part of a working collaboration between our two labs. The week involved developmentally staging zebrafish embryos to testing morpholinos on the timing of genome activation. We look forward to many more exchanges of knowledge and skills in the future!

EMBO Workshop@MPI-CBG: Maternal-Zygotic Transition

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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

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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.

 

BioRxiv: Histone and transcription factor binding competition

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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