User:Kirti

Kirti Prakash is a participant of the EMBO practical course Light sheet microscopy 2014.

About me
I am a Phd student in Christoph Cremer’s group at Institute of Molecular Biology, Mainz and Heidelberg University. I did my master’s from Aalto University at Department of Information and Computer Science. During my master’s, I worked extensively with ChIP-Seq, RNA-Seq and recently, with HiC data. After my master’s, I spend about a year at University of Helsinki working on genome annotation and characterisation of Birch. At Helsinki, I learnt a lot, but also, sort of got tired of Bioinformatics and decided to switch to a field where I could start from zero. Also, the stay at Helsinki made me realise that chromatin and histone modifications is one area that I really want to explore. So after several rounds of blind deconvolution, I found myself doing super-resolution microscopy to understand nuclear architecture. What a divine coincidence !

About my Phd project
The main focus of my Phd project in understanding how chromatin organises itself inside nucleus, and for this we need to develop new tools and methods. We already have made first steps in this direction, and I am really excited to see how this fields develops. On microscopy side, I am aiming to integrate a technique of single molecule localisation microscopy (SPDM, Spectral Precision Distance Microscopy) with a method of structured illumination microscopy (SMI, Spatially Modulated Illumination) in a single setup. Briefly, the underlying principle of SPDM is to label proteins with fluorescent molecules that can reversibly switch between fluorescent state and a metastable dark state. Since only a fraction of molecules will switch back to the fluorescent state at a given time, their location can be determined. The underlying principle behind SMI is to create interference in axial direction between two laser beams propagating in opposite directions such that structured illumination takes form of a standing wave. The object is moved through this wave field in highly precise steps. Thereby, the fluorescence emission is modulated by the interference pattern, allowing high frequency structured information passed through the detecting objective lens.

Course project
The main experiment that I will carry out during the course is PhD work of Elke Roovers in Rene Ketting’s lab at IMB, Mainz. Elke is investigating the function of Tdrd6a in zebrafish. She crossed mutant fish with the transgenic line with the EGFP under the askopos promoter and would like to follow the induction of PGCs, as marked by EGFP ideally up to ±24hpf. I must confess that I have very modest background and knowledge both in development biology and light sheet microscopy. But, I hope that I am able to learn a bit about these two exciting fields, and also make my little contributions to the projects of others.