Summertime science

Look no more construction in George Square! Look at all the glorious sunshine! The weather since coming back from Tuscany has been remarkably gorgeous. The temperature even reached 27C in Edinburgh this week (twice!). It is so distracting and lovely…

Gordon Research Conference
I had an incredible time at the conference. To start off, my talk went really well. I had practiced it once in front of the lab in Edinburgh. I also had the chance to practice it in front of a few members of my second supervisor’s lab a few days before the conference. This practice was very important as I was practicing in front of people who although very knowledgeable about Fragile X, didn’t know much about vesicle recycling. This practice helped me figure out which slides to spend more time explaining and whether my vocabulary was too full of jargon and strange abbreviations. I really want to thank everyone who looked at my slides and sat through my presentation. I was lucky that my presentation was the third of the day and the first one about Fragile X. People were still captivated and jet-lag had not kicked in yet! It was also a very friendly and non-intimidating environment as there were no PIs present, only postgraduate students and early career researchers. I had great questions (that I could answer!) and feedback following my talk. It was a very positive experience and I am looking forward to giving more talks in the future.

As for the actual conference itself, it was so amazing to put a face to the names of all the leaders in the Fragile X field and also get the chance to have breakfast with them in the morning! The atmosphere was very convivial. I think this was due to the small size of the conference. There were 160 attendees. The hotel where the conference was held was beautiful as well, up in the mountains overlooking Barga. All the talks were inspiring and really interesting. The conference really provided a snapshot of all the work being done in the Fragile X and autism field. I cannot wait for the next one!

Lab stuff
After the conference, I went on holiday in Italy for a few days to let everything sink in (okay, mostly because I love Italy and Italian food). I have now been back in the lab for a week and I am more motivated than ever to finish all of my experiments and submit a paper. As I don’t have any cells for the time being, I am busying myself making lists (my favourite thing to do), lists of experiments left to do for each project, lists of what I need to do every day to ensure I can get everything done in a reasonable time frame and within the 22 months I have left on the contract, lists of all the reagents I need to complete said work… Since I have scheduled in some free time on my lists, I am now trying to collaborate with other labs to teach them some new skills and help them publish some exciting new work. It’s always good to collaborate with other labs and share knowledge. It provides an opportunity to gain invaluable skills and gather new insight. It also allows you to work with new people and see different ways that people do science. I’m really enjoying it and it gives me a break from my microscope.

More exciting news: I am graduating in a few days! I cannot believe it. After almost 4 years, it is finally here. I think it’ll all finally sink in once I get tapped on the head and change my title on everything from “Miss” to “Dr” or Katherine Bonnycastle, PhD. I may or may not intend to do that immediately after the ceremony.

Now I will go enjoy the sunshine while it is still here!

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Something old, something new

The weather in Edinburgh has been absolutely lovely as of late. It’s almost a shame that I am leaving the glorious sunshine in Edinburgh for the beautifully warm Italy (more on that later).

Lab stuff
I’ve been settling in to my postdoc position quite nicely. It’s not really very different from my PhD. I’m still coming in, imaging my cells, analysing the images and playing around with GraphPad to try to interpret all of my results. In fact, I spent so much time doing analysis last week that images of cells are now burnt into my retina. In the last month, I have had a meeting with my supervisor to discuss the next 2 years and what needs to be accomplished. We discussed plans for publishing papers and which key experiments would be required to complete the various different stories that I have going on. Because I did both my MSc and PhD in the same lab, I told my supervisor that I wanted to learn additional skills and gain proficiency in different experimental techniques. I don’t think I will be able to master a new technique in the 23 months I have left, but even a little bit of knowledge and experience goes a long way in helping with my « hire-ability » as a more senior postdoc down the line.

All in all, I would definitely say that the transition was quite smooth and I am excited to get everying started and start working towards my first first-author paper (ideally in Nature, but I’ll settle for Nature Neuroscience in a pinch- just kidding, my aim is just to produce very sound reproducible data).

Gordon Research Conference
So why is it that I am writing yet another blog post from the airport you ask? Why is it that I am leaving Edinburgh once again? Is it just because I really like what they’ve done with the Edinburgh airport? Alas, I am off to a Gordon Research Conference in Tuscany. This conference is different to the other conferences I’ve attended in a few different ways. Firstly, it is a much smaller conference with only about 200 attendees. Secondly, it is quite a specialised conference with the specific theme of Fragile X and Autism-related disorders which is one of the models that I work on. This conference is preceded by a seminar for early career researchers which allows us to showcase our research in a less intimidating environment without more established PIs present. I have been asked by the organisers to present my data in a 15 minute talk! A talk! Not just a poster presentation! A talk in front of 43 people (yes I counted the number of attendees for the seminar). This is a really exciting albeit perhaps a bit nerve-wracking experience. I’ve spent all week analysing data, making figures and working on my slides. My presentation is on Saturday, wish me luck!

Now I must be off to board my flight! See you soon Edinburgh! Italia ci vediamo pronto!

Done, done and done

I’m not sure what has happened to spring in Edinburgh… The daffodils came up and subsequently dried out on the one sunny day we had a week and a half ago, then they shriveled up and died this week with the temperature hovering around 6C in the mornings. George Square is a huge construction site, but at least the grass in the garden is growing

Viva: check
I had my viva on Friday 13th April. I’m not sure where to start in my description of it. It lasted a full 4 hours! It was not a particularly good experience. The best way to describe it is overwhelming and exhausting. It is all a blur now. As soon as my examiners asked me the first question, I got quite nervous, I wasn’t too nervous before this point. In fairness to me, it was a difficult question (this has since been confirmed by others in my field). Although I felt I had annotated and hi-lighted my thesis to an inch of its life, I don’t know if any of that came in handy. That said, I probably would not have been able to cope with the examiners questions as well as I did (or at least as well as the examiners said I did) had a not spent hours scribbling away. My examiners were incredibly knowledgeable about lots of different things, so their questions and our discussions sometimes veered off topic, but I suppose that is what a viva is. I was asked to give a quick elevator pitch of my work, which most people are asked. That was the easy bit, that part, I had rehearsed. The rest was a wee bit more unpleasant. I was asked lots of questions about the existing literature in the field, we spent at least half of the 4 hours on my introduction. There wasn’t that much emphasis on my actual results, which is the part that I knew best! Luckily when all was said and done, I was greeted in the common room by all my friends and a nice glass of bubbly. I’m glad that it is done and that I never have to do it again.

Note: I don’t want anyone who has an upcoming viva date to feel uneasy now. It is important that I reiterate that this was how I felt. My examiners thought I did brilliantly and congratulated me on being able to answer all their questions well. So I suppose that all the preparation did come in handy.

DarfyejWAAAgaQF
With my lovely PhD cap that my lab mates made me, complete with ependorfs, cells in a dish, cupcakes and little figures doing yoga

Corrections: check
Luckily, I didn’t really have any corrections. I corrected my typos during my viva prep and I noticed some mistakes in figure legends which I printed out and provided to my examiners at the beginning of my viva. Therefore, I had already completed all of my corrections and was ready to submit my thesis for a final read-through by the examiners on the Monday. I can now print my final hard copy and apply for graduation this summer!

Visa: check
During all of my viva preparations, I was also busy with visa applications. I applied for a visa to work as a postdoc in the UK, in the same lab. That got granted a few days before my viva! My contract is for 2 years and this should allow me to finish up all of the experiments needed to submit my papers. This is particularly important, as I would like to go back to North America where having a few papers out of your PhD allows you to compete with North American grads who did their PhDs in 5+ years and had the time to publish before leaving the lab. My focus is now on publishing my little heart out so I can start to think about applying for fellowships next year. (I know next year already! Science never stops!)

Okay, I said my focus is on publishing, but actually, it is currently in vacation mode as I am off on a tropical post-viva holiday next week. After that, right back to imaging.

Full steam ahead

It snowed yesterday. Yes, you read right, it snowed… Just last year I was eating my body weight in delicious Indian mangoes and now I’ve had to trudge to work in the cold rain. How things change…

Viva date
Oyé oyé! I now have a viva date! April 13th 2018, Friday the 13th to be exact, is the day that I get to defend my thesis in front of an internal and external examiner. It’s a good thing scientists aren’t superstitious, right? (I say that as I gulp audibly only half for dramatic effect…) As the day approaches, I am getting more and more nervous. I’m re-reading my thesis and I can’t even remember writing it! I suppose that’s the side effect of writing it in November and having an April defense. I’ve already found a few mistakes, including a whole figure panel that was duplicated instead of having the actual figure put in! I’ll print that out and have it on hand for the examiners on that fateful Friday the 13th… My thesis is now colour-coded for background information, important references, rationales, key proteins and important results. I may have bought a new set of high-liters to annotate it all. I think I’ve got a good system going. I still have half my thesis to read and some key papers to re-read but I should have time to go through it all thoroughly before next week. (NEXT WEEK!!!!)

I’ve also been trying to keep on top of the latest literature in my field of research. I hear that a common question can relate to what has been published since submission. It’s good for me to keep on top of things anyway since I will be staying around the lab for a bit longer to finish up the experiments needed to submit papers. All in all, I think it’ll be fine. I still am nervous, but I suppose I can use that to my advantage. I’d rather be over-prepared than under prepared.

Lab stuff
I’ve been continuing working in the lab completing datasets to hopefully put a manuscript together in the next few months. In fact, two weeks ago, I imaged 34 cells in a day! A new personal best! I imaged 84 cells in 4 days that week. I think that may be a new lab record! I’m slowly getting through all that analysis. Healthy cells are always a joy to image and analyse. It would be great if experiments were always so enjoyable.

I’m also trying to set up some new collaborations with other groups. This will not only potentially lead to more co-authorships on papers, but it will give me the opportunity to work with other people and learn new techniques which I am quite excited about. As I have mentioned so many times in these past 3.5 years of blogging, I love how collaborative the University of Edinburgh is. I also think I lucked out by being affiliated to many big Centres (Centre for Discovery Brain Sciences, Patrick Wild Centre, Muir Maxwell Epilepsy Centre and the Simons Initiative for the Developing Brain) where researchers use different approaches to study the same models. This provides the perfect environment for collaboration and also allows us to leave no stone unturned in the search for future treatments. It truly is an inspiring environment.

Now time to get back to my pastel high-liters while I am still inspired and motivated! Wish me luck!

The waiting game

So Edinburgh has been under the siege of a major blizzard as you can see from this photo of George Square Gardens. In fact the University will be shut tomorrow. Snow day!

New year, new equipment, new student

After I submitted my thesis, I took a long break. I spent the holidays in Montreal followed by a trip to Australia. I only got back at the beginning of February. I flew around the world and thus returned to the lab a little under the weather but ready to get right back into the swing of things. But alas, I had been gone so long that there were a few new things in the lab, including a brand new microscope with focus control (no more z-drift!) and a brand new MSc student to supervise.

The microscope has proven to be somewhat problematic to use in its first month of action. Focus control refusing to run, neutral density filter not wanting to be controlled by the software and washers falling out of our filter wheel! After a few visits from Zeiss technicians, including one this morning, our beautiful new microscope and software are up and running ready for tomorrow’s snow day…

I also have an neuroscience MSc student working under my supervision. This is the first time I am teaching an MSc student. I have previously supervised PhD students who had past lab experience. This is a little different. What my student lacks in wet lab knowledge (though she is picking up the techniques quickly) she makes up for in ambition and motivation. And besides, with my viva pending it is probably good for me to go back to basics and explain the theory behind why we do what we do.

Viva date?

Speaking of vivas… I am still waiting for a viva date. I submitted in mid December. Whilst I am a bit disheartened (although mostly just impatient), I am using this time to prepare myself: combing over my thesis, re-reading articles, looking up various uses of different reagents… I am a bit nervous, but I think it will go well. As I have previously said, your thesis is your baby, it contains the past 3+ years of your life. I did all the experiments, I did background reading and I wrote the thesis. I should know most of the material pretty well. I still know that when I will be given a date, I will be frantically annotating my thesis and colour-coding key findings, important references and vital background information. I will be refreshing Pubmed to see if anyone has published anything related to my work. I know that each viva is different and there isn’t a universal question that everyone gets asked, aside from give an elevator pitch of your project. So it can be hard to know what to expect. From what I’ve gathered from speaking to other PhD students, I think that it is important to know the rationale behind why you did a specific experiment. I think you need to be able to justify your hypotheses especially if you haven’t clearly laid it out in your thesis. I’m sure it’ll all be fine. Apparently some people come out of their vivas saying that it was one of the most enjoyable experiences of their lives… I’ll keep you posted.

Now off to sit in front of my window and be mesmerised by the wind blowing around the snow outside.

Thesis-writing freedom

The view of the construction site that is George Square. They have started some work behind our building, but luckily the trailers have not completely blocked out my view on George Square Gardens.

 

I’m free!
Well almost, not quite yet. I submitted my thesis on December 14th (yay!) and have been basking in freedom ever since! I have truly been taking advantage of my newfound free time to enjoy the festive season and do lots of yoga (I want to ensure that I have enough zen in reserve for when it comes time to prepare for my viva). I’m also using this time off to do a bit of travelling. When else am I going to have this much time off?

I spoke to so many fellow PhD students who submitted their theses. They all told me that submission was a bit of a let down. The last 3-4 years in the lab is boiled down to a 200-ish page document. You go to the College Postgrad Office to drop off your precious thesis, so it can be given to examiners. Then nothing. Actually nothing. Not a bad nothing, but a strange nothing. After so many years of early mornings, late nights, data analysis, successful experiments, somewhat less successful experiments, it can feel troubling to not really have anything to do. All of my friends who went through this described a feeling of emptiness, not quite happiness, maybe a wee bit of relief? They all expressed how they had just been fed up of proofreading their thesis and how they wanted it over and done with. Since I wrote my thesis in such a short time (see next section), I wasn’t yet fed up of it. I felt content when I left my thesis at the Postgrad Office, albeit perhaps a little tired and maybe verging on aimless. It is such a momentous occasion, however I feel like the emotion of it all only hits a bit later. I still haven’t fully realised that it is done. Perhaps this is because I haven’t had my viva yet? I’ll keep you posted. For now I am enjoying my free time away from the lab.

 

Thesis writing tips
Solely based on the time that it took the other PhD students in the lab (6 months-15 months), I’d say that I wrote my thesis quite quickly. I made all my figures in October. I wrote part time in October, while finishing up lab work (about 2 weeks). I spent another 3.5 weeks writing full time. I have to thank my supervisor for being so good at sending feedback for every chapter within less than 24 hours. I could not have powered through it without all of his comments, suggestions and support. Thank you Mike!

I do write quickly and luckily I had already written an MSc thesis, so I had a bit of practice for writing my PhD thesis. Here are my recommendations on how to power through writing a thesis. It probably won’t work for everyone, but it might be a useful stepping stone.

1-Make all your figures ahead of time
If all your figures are made, you have a good idea of your results so you can start to think about your discussion and tailor your reading for your introduction appropriately. Additionally if you show your supervisor your figures at the beginning, you won’t be stuck tweaking figure legends right before submission. If you make all of the figures for all of your chapters at the same time, it also helps with consistency.

2- Get out of the lab
Although it wasn’t hard to balance adjusting figures while running experiments, I found it difficult to find enough time to sit down and write during incubation periods. I was a lot more productive when I sat in the library and spent all day writing. I was lucky enough that I was still receiving my stipend and could afford to take time away just to write. This is not the case for everyone.

3-Read first
I found it easier to read 5-6 papers, related to what I was going to be writing when I started out my day. That way the literature was fresh in my mind and I didn’t have to stop writing when I was on a roll to find some more information (though this did inevitably still happen).

4-Just write
This part can be tricky. I know a lot of people who like to work on sentences until they are just right before moving on to the next one. I would recommend just sitting down and writing. I would sit down and write from 10h30 to 19h30 every day taking 15 minute breaks every 60-90 minutes depending on how it was going. You will write sentences that don’t make sense, but you can always fix those later. I think that starting is difficult, but once you get going, it is easy to continue writing and eventually everything will come into place. I personally started with my methods and results chapters. I then wrote the final discussion because everything was still fresh in my mind and I thought up an interesting model to explain my results. I then wrote my introduction which probably took the longest as there was lots of additional reading involved.

5- Word processors are your friends
Did you know that you can insert figure legends in MS Word that can then link up to a table of figures? If you style your thesis correctly, MS Word can also create a table of contents complete with hyperlinks! I would highly recommend learning to use these features as they do really come in handy, especially when your table of contents is 7 pages long…

As I said there are so many different ways to write a thesis. This one worked for me. I hope that I have provided some useful information. Good luck to thesis writers everywhere!

 

Now back to enjoying my freedom with a cup of tea followed by a lovely yoga practice!

The home stretch

I have thesis brain! I actually started writing this post in French…
This is the view from the library I was writing from when I was back in Montreal.

Thesis-writing
This is the final stretch. The end is in sight. I’ve spent the better part of the last month in a library writing my thesis. Remember how last time I mentioned that I realised how little I actually knew? I feel like I’ve made a little dent in that now. But more importantly I’ve read theories upon theories trying to put together what little we do actually know. I’ve also put my hat into the ring and proposed my own theories and written them in my discussion. The discussion was an interesting section to write. This is the section where you can come up with wild (or very tame and plausible) theories about how your little bit of research fits into the bigger picture. Who knows, maybe one day, my theory will turn out to be right, or totally wrong.

Writing a thesis is such a strange thing. It is incredibly elaborate and involves a lot of research. It is the summary of the past 3+ years of your life. How can you summarise the countless hours of imaging and data analysis, the hours spent interpreting successful and sometimes not so successful experiments into a single cohesive document? It is mind-boggling that in less than two weeks (fingers and toes crossed) I will be submitting the culmination of the last 3 years of my life. Completely mind-boggling!

I’m not quite out of the woods yet, I have corrections to do, parts to add and all the little bits and pieces to put together.

Writing progress report:
Methods: done
Results chapter 1: done
Results chapter 2: done
Final discussion: done
Results chapter 3: 60% finished corrections
Introduction: 40% finished corrections

SfN 2017
I did take 6 days off writing to attend the Society for Neuroscience’s annual meeting. This year it was held in Washington DC. The weather wasn’t as nice as it was in San Diego last year, but that didn’t make me enjoy the conference any less. If anything, the cold weather provided incentive to actually go and sit in a dark windowless conference room to listen to talks. Just kidding… This year, I went to fewer talks. Instead, I spent my time at the poster sessions learning new things, having stimulating conversations and actually fostering collaborations! There is a group in the United States, working on different mutations in the same protein as me. I spoke to the PI in the lab and he was really keen to start a collaboration and was willing to send us their reagents so we could expand our battery of assays on our mutations. This is very promising and could enhance both of our teams’ research.

I also had some really interested people asking me questions about my research while I was presenting my own poster. The work I was presenting could, at a glance, be puzzling: a postsynaptic protein affecting presynaptic function. Once I explained my work and how I though this postsynaptic protein was having a presynaptic effect (based on experiments from other groups working on this protein) people understood and I think I perhaps I gave them a new less compartmentalised view of synapses (all part of my master plan to spread knowledge of the theory that I included in my discussion).

 

Now off to get some rest so I can be incredibly productive and get everything done before I am back off to Montreal for the holidays!

The more you know, the less you actually do

George Square is now dressed in its autumnal coat. The air has gotten much colder. In fact, I’ve been wearing a big scarf and hat all week! And, I actually heard my first Christmas song playing today! Again, I’m writing this post from the Edinburgh airport, I’m a regular you see. I am escaping the chilly weather here to go frolic in the freezing weather of North America. 
Writing

You know the old adage: “the more you know, the more you realise the less you know”? I have definitely hit that stage in my writing. The more I read, the more I have to read because I no longer understand what I am reading. I have entered the world of protein signalling cascades. Phosphorylation activating proteins or inhibiting them, sumoylation, palmytolation, ubiquitination! So many post-translational modifications that can completely alter the function of a protein. I’ve been studying neuroscience for years, yet I still find it mind-boggling how many vastly different roles certain molecules can have. Or how certain pathways can mediate so many various cellular processes. I have realised how little I know. I have spent the past few days reading reviews upon reviews to get a better grasp at how everything comes together and works especially at the molecular level. 
I must say in writing my thesis, I have also discovered how lucky I am that I have so many fellow PhD students at the University working on the same models as I am. They have all provided me with priceless knowledge and references that I might not have found on my own. They have also proven to be excellent sounding boards because although they may not be familiar with my approach to studying the models, we have had very enlightening discussions which have been incredibly helpful for writing my actual discussion. 
Writing is more demanding than I had originally appreciated. I’ve still been doing some odd experiments in the lab, so I think that it has been hard to get into the writing mindset. However I am officially out of the lab so time to buckle down and get this finished before Christmas. 
Writing progress report: Methods 95% finished first draft; Results chapter 1: 85% finished corrections; Results chapter 2 85% finished first draft

To do: Introduction, Results chapter 3, Final discussion

Conferences

As I mentioned, I am at the airport getting ready to leave Edinburgh once again. Once again this year, I am attending the Society for Neuroscience (SfN) conference. This year it is being held in Washington DC. This is the biggest neuroscience conference in the world with over 30000 researchers coming together to share their science, debate current neurological topics and come together to collaborate to deepen our understanding of the brain. As I am right near the end of my degree, this is the perfect time to scout out potential postdoc supervisors and network my little heart out.

I’m also taking advantage of being on that side of the Atlantic to go home and write. I am hoping the change of scenery and lack of lab distractions will be very favourable for my writing. 
Time to board. I’m off again! À bientôt Edimbourg! 

Where has the time gone? 

How is it the middle of October?! How are the leaves already turned various shades of yellow and orange? How is it already dark by 18h30? When did this all happen?

Time warp

I know I have spoken at length in my blog posts about how time somehow manages to speed up in your third year. I didn’t realise that this phenomenon is exponentially exaggerated in fourth year! I do not know where the last 2 weeks have gone. All I know is that writing this blog post has been on my to-do list for over 2 weeks. Between finishing up experiments, supervising a PhD rotation student and writing my thesis, this blog post has just been delayed. I have decided that with every year of your degree, time speeds up (note: I obviously know this isn’t a real phenomenon, but relatively speaking, I feel a lot more rushed as time goes on, probably because there is less of it left!). During your first year, it feels as though everything takes ages to start and you just spend so much time reading and waiting to begin experiments. When second year comes along, you have reached your cruising speed, you know what you’re doing, you still have loads of time ahead of you, life is good. Then, third year hits. Your thesis committee starts asking you what you are going to do after your degree and tell you to write a plan for your thesis, but you feel like you’ve just gotten the hang of this whole PhD thing, and now you have to think about the end and how everything fits together and how it’ll form a cohesive (semi-cohesive) thesis. Then fourth year, out of the lab, except for maybe some control experiments and writing should take priority. You suddenly realise that maybe you should have done your experiment differently, but too late now, you have to make do with what you have… I know I make it sound really daunting, but I promise that doing a PhD is feasible and at times very enjoyable. 
Writing up

My goal is to submit my thesis by December. I have already submitted my Notice of Intention to Submit notifying the College that my submission is eminent. This notice gets the ball rolling and examiners can begin to be selected. My external examiner has already been selected for my viva which will be tentatively held in February! I feel like everything just got more real. This is finally happening! In terms of actual thesis writing, I’m trudging along slowly. I have decided to start by writing my results chapters. This way all my data will be fresh in my mind when it comes time to write my introduction and final discussion. This is to ensure that I don’t go off on tangents that are only tenuously related to my data in these sections. I have analysed all my data, reformatted all my graphs (my advice would be to decide on all your formatting the first time you plot your data, learn from my mistakes), written my figure legends and I am slowly getting into writing the actual body of the text. It’s a bit slow, but I do feel like I’m making progress. I hope to have a first (or maybe even second) draft the methods (which I started working on in India) and results completed by the end of the month. Then I have November to write the introduction and discussion. I can do it! I must admit I have started going to yoga twice a week now to stay calm. It is working. It does help that I’m also on my way to Italy for a few days. Hopefully it’ll be a relaxing and semi-productive change of scenery. 

Ciao Edimburgo! Ci vediamo pronto!