My solution to this was not just dumping the issue on someone else's table (because in the long run, that would solve nothing), so I did what I could for the poor instrument in terms of replacing parts, cleaning of electrodes (with a toothbrush - I felt particularly scientific doing that) and modifying system settings. Meanwhile, with some invaluable help from fellow researchers, I was able to move my RNA work to our neighbouring department, which also had a Bioanalyzer instrument (functional). This way, my project slowly progressed and I was able to finally identify the first 8 samples for the first microarray slide.
The slow progress also enabled me to dedicate some time on a side-project though, but I now realise that it has grown into something larger than that. My supervisor opted for me to have a private meeting with one of the cruise chief scientists from where I got the cool dataset I've been working on for this side-project. Basically I've expanded on my initial piecewise SEM modelling by increasing my model size from 9 mixed effect models (one response variable per model) to 24, effectively more than doubling the size. In the beginning I wasn't even sure I could incorporate that many variables and successfully get any useful information out of it, but as I progressed through my optimization routine everything slowly fell into place. Now it's just a matter of interpreting it and put it into an ecosystem and oceanographic context. The cool thing about this dataset is that I had access to, in addition to the classic abiotic factors and nutrients like temperature and nitrogen, both abundance measurements of all major diazotrophic cyanobacteria and a range of different pigments, which can be linked to different kinds of phytoplankton in the water column. For most people, I'm guessing, that doesn't sound too exciting, but even though the marine diazotrophs I'm mostly interested in were first discovered more than a century ago, we know precious little about most of them. One being the nature of their different symbioses with eukaryotic phytoplankton. Therefore, I was hoping that the SEM could shed some light, by use of the pigments, on which type of phytoplankton the cyanobacterial diazotrophs seem to be hanging out with (in addition to all other interesting hypotheses)..
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| Map with integrated surface particulate organic carbon in the region of sampling for the dataset I used for my side-project. Southern Vietnam and the South China Sea. Satellite image generated from https://giovanni.sci.gsfc.nasa.gov/giovanni/. |
Anyway, today I took the leap and delivered my samples to the microarray analysis facility, and I'm hoping that it will give me some good results soon enough. I packed them neatly in a styrofoam box together with lots of ice and ice packs. Ideally, you want to transport RNA samples on dry-ice, but since the trip to the analysis facility is only 35 minutes, I'm fine with regular ice.
The thing about this project though, is that I've no idea of knowing if anything actually work until I get the results back of this analysis. In that regard I kind of see it almost as a leap of faith, since I always have this "worst-case scenario"-thought in the back of my head.
I've been rewarded with a lot of freedom (based on previous success) regarding this project, which I thoroughly enjoy, since it makes the science even more exciting, but that also means that success and shortcomings alike will fall squarely on my shoulders.
I had a similar conversation with my supervisor today and her only response was: "if that turns out to be the case, then at least you've learned a lot".
I know she's right. I tell myself the same thing from time to time, but for obvious reasons it felt better coming from her (she pays for both my time and material after all).
I'm really excited about the possible results and I'm hoping that the wait won't be too long.
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