With just a week to go until Christmas, everyone in the lab is either in a ‘gotta get these experiments done ASAP’ mood, or just already in holiday mode (there is also the third option, which is, ‘what holiday?’- but we’ll leave those guys alone).
It’s also feeling a lot like summer, because the country is heating up! These are the times I’m glad I don’t work outside (RIP Tradies). Aircon is life.
But while I’ll be working on my Thesis throughout this upcoming break (just one more results chapter at least), it’s nice to take this opportunity to reflect on the year that’s been. I could also reflect on the decade, but… that’s just too hard.
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Being in the final year of my Ph. D, this year just whizzed by. I’m still in denial about it being mid December. My supervisor did warn me that the latter half will disappear quite quickly (and that I need to seriously keep on top of things), and, like with most things, she was right!
This year started with picking up the pieces after my first, first author manuscript was rejected (I think the rejection email came this time last year). Thankfully the journal still sent through reviewer comments, so we came up with a strategy to address the issues raised and planned a massive re-attempt at what was quite a large proportion of the experiments.
So, February was a bit of a blur. I had a large number of big experiments to do, it had to be done ASAP so there was quite a bit of pressure, but… I did it. Sometimes you just have to knuckle down and get shit done. By March the samples were run on the machines and data was ready to be processed and analysed, and by April I had some early drafts of what became my big metabolic pathway maps (hello Adobe Illustrator). I was also writing the new version of this manuscript for resubmission elsewhere, so while there were experiments to do and data to analyse, I also had to write alongside. Oooh- And teach, because I always need money. #studentlife
During that time I had my three year review meeting (see my previous post on this topic), which I was very nervous about because the previous meeting hadn’t gone so well. Objectively speaking it might not have been that bad, but I realised that some previous incidents in my life meant I was essentially getting triggered and having panic attacks during these professional meetings. Meetings shouldn’t elicit a fight/flight/freeze response. It meant that while I knew stuff, I couldn’t articulate them when asked about my data, and I came across as someone who didn’t know what they were doing/talking about. It wasn’t really the case, but I just couldn’t communicate my ideas because I was so stressed. It made me feel quite depressed (although at the time I didn’t recognise it) and very anxious, which lead to a drop in overall productivity.
So- in the year that followed, I went to see a psychologist, worked on myself, and learned how to deal with those situations a little better. It was definitely baby steps, but I noticed a huge difference when I could walk into the room and not freak out. It was probably the first time my mind didn’t freeze or blank out in a meeting. I left feeling very accomplished, which was a huge (and refreshing) step. I do highly recommend seeking professional help if you feel like you’re struggling. You shouldn’t leave that stuff to fester, because it never really goes away.
Also in February I was chosen to give a short talk, as part of the Australian Society for Microbiology’s Nancy Millis Student Award competition. Essentially you submit an abstract, and if chosen to present, give a 10 minute talk on your research. A panel of judges decides on the best presenter, who are all Ph. D students. Each state branch holds the event, and the winner from each state gets free registration and some $$$ to go toward accommodation and travel to attend the annual national conference. I hadn’t actually given a proper oral presentation during my Ph. D (well- aside from our Institute Student Retreat, but, that’s a bit different), so I thought I’d challenge myself this year and just try it out. Either way I gave it a go, and while it was terrifying, I ended up getting a bit of money toward attending the conference, so it was actually very nice in the end.
During this time I also had to generate a particular strain of my bug. If you’re familiar with how Bacteriology experiments work, you can have a normal, unaltered strain (typically referred to as ‘wild type’), then a mutant which lacks a specific gene of interest (which prevents said strain from making your protein of interest, because genes are essentially instructions for the organism to make specific proteins), then a ‘complemented strain’, which is essentially the mutant which has had the gene of interest artificially re-introduced. Either way you have bugs that are ‘unaltered’, bugs which have one specific thing missing, and then another set of bugs which have had said missing thing reintroduced. In the unaltered one, everything should be ‘normal’, but the mutant which lacks specific thing/protein may behave differently, which then tells you what the specific protein may be doing for the bacteria. The complement, which should have that missing item returned (albeit artificially), should behave more or less like the wild type/unaltered… although sometimes this may not be the case (because bacteria are complicated).
ANYWAY- I had to isolate a mutant strain (which my supervisor had already made), make the complemented strain, then do the relevant experiments.
I then ran away to the conference, which was my first semi-solo trip interstate (usually I had conference buddies to get a sharehouse with), where I gave another talk, which was even more terrifying than the first one (the room was quite packed and had lots of very big name researchers in it).
As soon as I got back from the conference, my housemate gave her Ph. D Oration, and I then had to knuckle down again as we got ready to submit our revised and re-vamped manuscript. So that was my July (I think I had a birthday in there somewhere). August was the student retreat, where I gave another talk (talk count #3), followed by my own Ph. D Oration (talk count #4), followed immediately by my 3.5 year review meeting. I sucessfully got an extension of my candidature to four years, and also got some experiments and figures done in preparation for reviewer comments for the resubmitted manuscript. #Refresh This worked out really well because by the time we got the comments back, the experiments outlined in the major revisions had already been done, so all we had to do was write some rebuttals and say, ‘here’s the data you wanted’, rather than spend an additional month doing said experiments. I also gave another talk (talk count #5) as part our research institute’s 5 year anniversary celebrations as I’d won the host-pathogen category with my submitted abstract. Such talks. Much adrenaline.
Now at this stage I was getting pretty obsessed with my #refresh routine. Thankfully I was put out of my misery mid September when we found out the paper had finally been accepted. While we did do lab paper lunch to celebrate, I had also already moved on to finalising experiments in preparation for my second manuscript (because that’s how life works here). September to early October was more hectic than February- I seriously can’t recall what happened. I was also teaching at the time so my poor students had to deal with a stressed out demonstrator (I’m so sorry).
But then I went on leave (which is kinda why September-October was so crazy- I had to finish stuff before I left), which was really nice. I was supposed to write this second manuscript but I actually ended up not doing much work (I did write a blog post about the first manuscript, though). It was a good break, and it did make me feel more refreshed and ready to work by the time I got back. A system reboot, if you will.
I ended up writing the full draft of this second manuscript in time to send it to co-authors late last month, and then finally submitted it early this month. Submission was great, but then dawned the realisation (well- in reality I knew it already) that I had to write my Ph. D thesis and start seriously applying for work. While we wait to hear back about this second manuscript (will we hear back before Christmas, or after? Who knows??), I’m writing, doing some experiments to add to my thesis, prepping some strains to do some experiments in anticipation of reviewer comments, and generally returning to my night owl routine.
It’s been a massive year (I’m sure I’ve missed some stuff), full of ups and downs (but I think mostly ups) and tonnes of new experiences. It’ll be nice to unwind a bit during Christmas, but bloody hell it’s been a rollercoaster year. I may or may not post before the holidays, but if not- I hope you, wherever you are, have a wonderful break.
Categories: Ph D posts
ABugsLife
A Ph. D graduate in Microbiology, residing in Victoria, Australia. Currently working in multiple locations but still in the STEM field. 👀 🦠 🧫 🧬
A Bug's Life 
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