Isolation of Ustilago bromivora strains

I published a new article in Bio-Protocol¬†this week describing how to isolate strains of Ustilago bromivora from the spore material that forms on infected plants. It’s certainly not all my work; the protocol is a modification of a published protocol and has been worked on by many people in the Djamei lab, as indicated in the acknowledgements. I just happened to be the one who chose to write it up.

After the publication of our previous paper on the U. bromivora/Brachypodium pathosystem, we were approached by Bio-Protocol to publish certain protocols in full in their journal. You would think that people would be eager. It’s a lab protocol and writing it up takes very little work yet you get an article published. I was the only one that expressed an interest in writing this up. I imagine it’s because it’s not a “sexy” paper but that mindset neglects something very important. Science is not just about findings; it’s a way of discovering how the world works which can be applied to any situation. At the foundation of that is the idea of sharing one’s methods so that, at least in principle, anyone with sufficient skill can repeat what you have done. Continue reading

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My paper on a new plant pathogen system

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Different accessions of Brachypodium infected with Ustilago bromivora. The fungus is the black material in the spikelet. (Source: My new paper!)

I finally have the first publication from my PhD out! It’s quite a nice paper too which took a lot longer than expected. And it’s also open access so everyone can read it! If you do, you’ll learn about a new system we have set up for understanding plant pathogen interactions with the fungus Ustilago bromivora and the grass Brachypodium distachyon.

My contribution to this is almost entirely in bioinformatics. The genome assembly had been performed before I joined the group, but I did the genome analysis and comparative genomics, starting off visiting some collaborators in Munich. This was quite nice; going in a direction which is becoming more and more important and taking things further than I had before. Continue reading