Dinara Sharipova

Dinara is a Master student of Novosibirsk State University, which is located in the middle of Siberia in the scientific town called Akademgorodok. There, she is studying cell biology and genetics, and doing her research project in the laboratory of developmental epigenetics under the supervision of Prof. S.M. Zakian and S.P. Medvedev. Her research topic is related to cell modeling in neurodegenerative disorders on patient-specific induced pluripotent stem cells. During her Bachelor’s studies, she worked with Huntington’s disease cell model and now, for her Master’s, she is studying the molecular mechanisms involved in the progression of Parkinson’s disease. In spite of such neuroscientific direction in her research, she had always been fascinated by embryology and developmental biology – dating back to an embryology course in her university.

This summer, she is doing an internship in the Vastenhouw lab –  an opportunity to work with zebrafish embryos and to study the transcriptional landscape during early zebrafish development.

Apart from science, Dinara is interested in dancehall dancing, horseback riding, skating, and travelling.

Edlyn back from Postdoc Retreat

Edlyn returned from the 8th Annual MPI-CBG Postdoc Retreat, which took place in Lwowek Slaski, Poland, from 11-13th of June, 2018.

The three-day retreat featured talks from fellow postdocs at the institute & invited speakers, career panel session, and an afternoon of rafting along the Bóbr River.

Invited speakers:

  • Dr. Veronique Miron (University of Edinburgh)
  • Dr. Timothy Nott (University of Oxford)
  • Dr. Marc Güell (Pompeu Fabra University, Barcelona)
  • Dr. Sebastian van de Linde (University of Strathclyde, Glasgow)
  • Dr. Carl Modes (MPI-CBG, CSBD)

The postdocs also welcomed two postdocs from the Institute of Molecular Genetics of the ASCR (IMG), Prague as part of the ARIB “Teaming for Excellence” Program.

All hail Dr. Pálfy!

Congratulations Máté! No ATAC today. Instead, Máté successfully defended his PhD.

18 figurines gathered on Máté’s Doktorhut, making him the most connected member of the Vastenhouw lab!

We also bid Máté a fond farewell on this day. Best wishes for your next adventure!

Easter Egg-citement

We joined forces with members of Gaia Pigino’s lab for an artsy day of Easter Egg Painting!

So many artistic approaches to design our eggs, including lacquer/wax painting and onion peel/colouring dye.

Check out our Lab egg on the right, showing the different nationalities that make up the Vastenhouw Lab (Currywurst – Germany, Cornflower – Estonia, Tulip – the Netherlands, Hungarian Paprika – Hungary, Hamburger – USA, Maple Leaf – Canada)

Let’s get biophysical

Last week, the Vastenhouw lab was at the Biotechnology Center of TU Dresden (BIOTEC) for a symposium on the “Biophysics in the Nucleus”, with Nadine among the co-organizers. The meeting featured an excellent line up of speakers in the fields of chromatin remodeling, nuclear architecture, and transcription mechanisms.

Lots of fascinating talks and stimulating discussions covering many disciplines – biophysics, biochemistry, genetics, genomics, and single molecule microscopy!

Both Lennart and Máté were selected to give a talk, and Ksenia and David presented a poster of their projects.

 

 

Máté presenting his PhD work on the last day of the symposium.

Paper in Development about the loss of mesendodermal competence

We celebrated with cake and champagne the new paper from our lab published in Development.

The study, led by our former postdoc Pavel, determines the time during zebrafish development when the prospective ectoderm becomes unable to respond to mesendoderm-inducing Nodal signals. By activating the Nodal pathway with several different strategies, we showed that reduced expression of the Nodal coreceptor Oep causes loss of mesendodermal competence.

The champagne bottle was nicely decorated by Sabrina with the in situ hybridization protocol that was used in the paper.

Microenvironment preprint on bioRxiv

The manuscript for Lennart’s postdoc project “Transcription establishes microenvironments that organize euchromatin” is now up on bioRxiv.

We investigated how the process of accessing the information contained in DNA leads to its three-dimensional organization. By a combination of STED super-resolution imaging (thank you Alf Honigmann and lab!), Fab-based live imaging (thank you Yuko, and Hiroshi Kimura’s lab!), and physical modeling (thanks Vasily Zaburdaev and lab, and Frank Jülicher!), we concluded that the process is similar to the organization in a microemulsion. With the exception that ours contains not a conventional, but a catalytically active amphiphile.

Oh, and the twitter action’s here…

The One with the Goose

The legend goes that St. Martin once gave a homeless person half his coat, and saved them from the cold. With this good deed, the Church officials wanted to honour St. Martin by ordaining him as the next bishop. Being a modest man, he hid in a goose pen to avoid the Church officials. Well, the cackling of the geese betrayed him and the goose became the symbol of St. Martin’s day.

The lab celebrated the German tradition of Martinsgans (St. Martin’s goose) over a festive meal: roasted goose, Knudeln (German dumplings), Wurst (sausage), Flammkuchen (flame cake, German flatbread), and Kartoffeltasche (potato bag).

We also welcomed our guest for the week, Dr. Haruka Oda, a postdoctoral fellow from the lab of Dr. Hiroshi Kimura at Tokyo Institute of Technology.

Book chapter on how to smFISH in zebrafish embryos

Interested in detecting single transcripts from zebrafish embryos? or applying smFISH to your research?

Carine’s chapter in Methods in Molecular Biology is out!

The chapter provides a detailed protocol: from setting up the embryos to cryosection, to smFISH, to image analysis.

You’ll also find a description of the pipeline for membrane segmentation and transcription detection.

Visit Book Chapter at Methods in Molecular Biology