I’ve been a bit quiet on the Ecologist’s Diary front for the past few months. I found myself having a light summer field season, which consisted only of a pleasant day trip to collect the 1 year samples for TeaComposition H2O. While I enjoy fieldwork, as an early career researcher, I am noticing that my research is less field-based and is having more and more of a structured feel: field – lab – desk – repeat.
Instead of fieldwork, most of my time this summer and autumn was spent preparing ~90 samples for genetic sequencing. Deakin University recently acquired a few Illumina platforms, so now we will be able to do the entire sequencing pipeline ourselves, from extraction and library prep to sequencing and bioinformatics! Prior to this very cool kit arriving, we were sending extracted nucleic acids away for sequencing, so the process between the extraction and bioinformatics has always been a bit of a black box for me.
Not anymore! In retrospect, processing 90 samples for the first run within a two week deadline, was overly ambitious. Those weeks consisted of another type of structure: PCR – gel – qubit – optimise – repeat. It was mind numbing at times…A pipetting robot would have helped…I am crossing my fingers for a robot appear in the lab one day. But overall, it was invaluable to learn these new skills, as those opportunities become rarer after the PhD years.
All the late nights in an un-airconditioned lab, culminated in one pipette tip. It doesn’t look like much, but it contained many hours in the field and lab and equally as much in supplies, reagents, kits and tears (no, not really). The feeling was terrifying (I hope we did everything correctly!) and exhilarating. We ended the day with some celebratory beverages, musing how great our data was going to be. (Which reminds me – adding on to Geshe’s last blog, we need to remind ourselves to take time out and celebrate the wins, whether it be an accepted paper, a best talk or poster prize, or a big win in the lab!)
I am looking forward to time when the TeaComposition H2O microbe samples will be analysed. In the meantime, those 90 samples I’ve just run will be keeping me busy in script terminals for the next while. Peppered in between those desk sessions, we will also be launching a wetland citizen science program in Melbourne, Sydney and Auckland this winter. More on that next time!