Sarah Bowman was a PhD student with Jürgen Knoblich between 2003 and 2007. She now works at Harvard University - and reflected on her experience at IMP and IMBA.
I was at the IMP and IMBA from October 2003 to December 2007. What brought me to the German-speaking world in the first place was a Fulbright Fellowship to Germany. This gave me the opportunity to spend the academic year 2002-2003 working with Suzanne Eaton in Dresden, at the Max Planck Institute for Cell Biology and Genetics.
While I was there, I learned about various international PhD programs throughout Europe, and since they’re significantly shorter than American PhDs, I thought it sounded like a good deal. So I applied to the VBC PhD Program and was accepted into Jürgen Knoblich’s lab when he was still a junior group leader at the IMP.
Those five years were an interesting time to be an American in Europe, and I learned as much about myself, my nationality, and politics in general as I did about how to do science. As the four years allotted to complete my degree drew to a close, I looked back to the US for postdoc positions. I leaned towards working in the Boston area to be closer to my family.
When choosing a postdoc position, one often hears the advice to change the model system and keep studying the same topic you learned in your PhD, or change the topic and keep the model. I chose the second option: to work with flies like I did in Jürgen’s lab but change the topic from cell biology and genetics to chromatin and transcription. In the Kingston lab at Harvard Medical School (our academic home) and Massachusetts General Hospital (our physical and financial home), we study the non-covalent modification of chromatin structure.
That’s about as broad as it sounds. Bob Kingston’s students and fellow postdocs tackle everything from analysing the enzymology of nucleosome re-modellers, to determining the crystal structure of protein complexes that interact with nucleosomes, to describing the position of nucleosomes on the DNA sequence and how this affects transcriptional regulation.
This last subject is how my project fits into the Kingston lab. After learning about Polycomb proteins and all the open questions about their function from Leonie Ringrose, I went to the Kingston lab to study how Polycomb proteins interact with nucleosomes to silence gene transcription. It’s been an interesting transition. Thinking of all the genetic experiments I could do in developing flies to test the relationship between nucleosome positioning and Polycomb-dependent gene silencing seems super interesting to me, but technically it’s quite challenging. Most chromatin and transcription research is done in cultured cells, not model organisms.
One reason for this is many of the assays that describe chromatin structure – like chromatin IP, or nuclease sensitivity mapping – typically require hundreds of millions to billions of identical cells. It’s difficult to harvest that kind of material from a multicellular organism, because they’re often small and by definition contain a mixture of cell types. So I dedicated the first two years of my postdoc to developing techniques that harvest pure populations of cells from Drosophila embryos, and performing chromatin assays in the relatively small number of cells I’m able to harvest. This third year I’ve been learning how to work with the genome-wide deep sequencing data I’ve produced. Hopefully the upcoming year will be when I finally translate all of this into new manuscripts.
Progress comes slower than I expected, but this is part of the challenge when changing topics in a postdoc. I now have technical experience in areas I never had before, like flow cytometry, purification of nucleic acids, fractionation of chromatin, RT-qPCR, microarray design and analysis, second generation sequencing, and analysis of genomic data. As my postdoc progresses, I’m looking forward to applying what I learned in Vienna – hypothesis-driven genotype-phenotype experiments in Drosophila – to nucleosome positioning and Polycomb-dependent gene regulation.
By Sarah Bowman, first published in 2010
Alumni Stories: quick links
Angelika Amon - Jörg Betschinger - Sarah Bowman - Rafal Ciosk - Greg Emery - Silke Hauf - Christian Häring - Konrad Hochedlinger - Andrea Hutterer - Claudine Kraft - Christoph Lengauer - Marieke von Lindern - Mark Petronczki - Walter Schmidt - Camilla Sjögren - Andrew Straw - Attila Toth - Giulio Superti-Furga - Frank Uhlmann - Hartmut Vodermaier