My paper on a new plant pathogen system

elife-20522-fig4-v1

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.

Although the paradigm of lab work still seems dominant, it’s probably not going to stay that way; current advances and trends are just going to force change. The increase in automation and robotics, as well as the greater accuracy and reproducibility of such systems, will make lab work less like lab work and more how to use a robot. Further, there is a tendency to outsource to specialists. During my masters, I did all my sequencing myself. Now, we send the samples downstairs to a service which does the sequencing for us. These services cover many other aspects of research. Understanding techniques will still be important but the physical ability to do lab work will decrease in importance unless you are interested in being a technician.

The important part of being a scientist will be thinking up new experiments, guiding the research, analysing data and communicating results. The future in science will be far more computer based with the physical experiments carried out by technicians and companies that specialise in it.

This is one reason why I wanted to move to more computer work during my PhD, something which has partially happened. During my masters I had been introduced to the R statistical language and used it a bit but only to a small extent. Now, I feel that I have become quite competent in R as well as fairly good with using Bash scripting. I also briefly touched on Python and SQL but not for long. Most of what I did in this paper was using R, Bash and smaller programmes that others had written.

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One thought on “My paper on a new plant pathogen system

  1. Pingback: Isolation of Ustilago bromivora strains | Evidence & Reason

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