By Jenny Shelton
After two and a half years in Mat Fisher’s group researching amphibian fungal pathogens Bd and Bsal it is now my time to bid farewell to the herpetology world. In October I started a PhD, with Mat as my primary supervisor, as part of the Science and Solutions for a Changing Planet (SSCP) Doctoral Training Program (DTP) funded by the Natural Environment Research Council (NERC) and Imperial’s Grantham Institute. (Now that is a lot of acronyms!) For my project I will be researching the human lung fungal pathogen Aspergillus fumigatus and whether its distribution in air and soil is linked to environmental factors and clinical disease. Same desk, group and lab, just a different fungus!
Particular highlights of the job have included the trip to the Pyrenees in September 2015 as Kieran’s field assistant, which was my first experience of fieldwork. We all had a good laugh at my lack of French-speaking ability (“Pour cidre?”) and I can’t shake the photo of me in my swimming costume catching tadpoles, but it was the perfect opportunity for me to practice catching frogs and to learn the standardized swabbing and toe-clipping protocols – all to the stunning backdrop of the Pyrenean lakes and mountains. Then in April 2016 I had the opportunity to undertake fieldwork in Taiwan on a trip organized by Dr Dirk Schmeller, in collaboration with Lin Chun-Fu and his team at Taiwan’s Endemic Species Research Institute (see my earlier blog post ‘Tracking Down Bd Taiwan’). This year I was awarded a National Geographic Young Explorer’s Grant to return to Taiwan and continue our research, and the trip in May was incredibly successful (see my previous blog post ‘Tracking Down Bd Taiwan- part 2!‘).
In the past few years I have had the pleasure of working with lots of fantastic people- microbiologists, herpetologists, infectious disease epidemiologists, bioinformaticians and students- who have sent us samples, visited us, hosted us and collaborated with us. In particular, I wish to thank Pria and Claudia who have taught me all the labwork I know and have been incredibly patient and supportive throughout. Also Simon for his infinite R and bioinformatics knowledge and Kieran for his microbiome advice and enthusiasm. I would also like to thank the groups in Estonia and at Brompton Hospital for kindly letting me shadow them in the lab and sharing with me their hints and tips for mycobiome analysis. When I started this job I knew virtually nothing about lab work, next-generation sequencing or bioinformatics so thank you to Mat for giving me the opportunity: it has been a steep learning curve but every day has been an adventure and I hope to have contributed as much to the project as I have gained from it! I feel incredibly fortunate to have undertaken fieldwork, lab work and analysis for this project and I know these skills will stand me in good stead for my PhD, and beyond.