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…

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;