Final papers from my PhD

I am happy to report that the last two papers from my PhD are now available for everyone to read!

Two Is Better Than One: Studying Ustilago bromivora–Brachypodium Compatibility by Using a Hybrid Pathogen

This, along with the U. bromivora genome paper,  is probably the most important paper from my PhD. Those two papers formed the basis of my thesis. Although I did not manage to fully answer the question I set out to answer, this is a paper where most of the experiments, most of the analysis and most of the writing was done by me, so it is special to me. It’s also quite interesting! If you want to know exactly what we learned, you can read the paper itself but I will give you a brief summary of what we were trying to learn.

We knew there were two very closely-related fungal species which could infect different host plants. This told us that although they were very similar, there was something important about them that was different; we wanted to know what that was. Even more exciting, we could create a hybrid between the two fungi that was still able to infect one of the host plants. What I was trying to do was take the hybrid and breed it over and over again with the parent that couldn’t infect while making sure that the hybrid could infect. After enough generations, we should then find the hybrid would be genetically almost identical to the non-infecting parent but with just a tiny bit of the infecting parent inside it. That would tell us what the difference between them was and we could then try to figure out how that part of the genome led to interactions with the plant. Continue reading

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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

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