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!

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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! 

What I have learned so far v3.0

The Fringe is finally over! I must say that I have out-Fringed myself this year, I went to 9 shows! 9 shows! Little old me who vowed to avoid the Fringe! In my defense it is hard to avoid it when they are set up right outside the office window and the smell of the food trucks waft through the open windows.

This year again, I wanted to impart my wisdom to you dear blog readers. I am officially at the end of my PhD (how did that even happen? Where have 3 years gone?), I am a little older and a little wiser and a lot more resilient, so it is time for round 3 of Katherine’s kernels of wisdom. If you missed the first two versions you can read them here and here.

Time is your enemy
Time is sneaky, it’ll lull you into a false sense of safety, because hey, you have 3 whole years to work in the lab, it’ll be a breeze. Let me tell you, it is definitely not a breeze. It is a full fledged hurricane-force wind. Time management is essential! There will be some quieter times in your PhD, for instance when you first start in the lab, when you are waiting for cells, flies, worms, etc. Although it is tempting to take it easy during this time, take advantage of it to get ahead. Maybe start writing a literature review or format your figures. I know that a break is well-deserved especially after particularly hectic weeks, but trust me, future you will be eternally grateful for any little bit of work that you do now that will help them in the future. Regular meetings with your supervisor will also help you keep on schedule.

There are very high highs and very low lows
Science and research in general is wonderful. There are so many novel things out there to observe and discover. When somethings goes right (like when I finally saw a phenotype after working on the same model for 3 years) you are elated. Absolutely nothing can bring you down. It is important to remember these highs when things stop working. Because inevitably, things will stop working… The phenotype that you were basing a whole chapter on could turn out to just be an artefact of one experiment on one day, the whole day you set aside for electrophysiological recordings could go down the drain because your cells were unhealthy… As a PI once grumbled to me on a Friday night as we were sat passing cells: “Science is 1% joy and 99% sheer devastation”. This is why all little wins should be celebrated.

Have a good support system
Whether these are other PhD students who understand what you are going through, old friends who try their best to make you forget about science when you are with them, parents, siblings or the barista at your favourite coffee shop, it is important to have a social life outside of the lab. I mean, who else are you going to celebrate all your little victories with?

Get out of the lab
I know I say this every year, but I can not emphasise how important it is to have a life outside of work. PhDs take over your life. It is good to have an outlet outside of the lab to put your energy into. Anything that is able to push your research out of the foreground of your mind for a wee bit. It could be yoga, cooking, building a flux capacitor, baking, going to the gym, playing Klingon boggle, knitting, teaching or learning a new skill like how to read Elvish.

Get as much experience as possible
Despite microscopes and stimulators not working, I still think that going to India was a high point of my PhD. Not only did it teach me how the internal components of a stimulator and microscope power supply box work, but it gave me the chance to play the role of expert. Although this can be terrifying, it is such a good exercise. You learn to troubleshoot, you learn the references of all the key papers in the field off by heart and it ensures that you fully understand why specific standards are used in the field.
Any type of work experience in a different lab is a huge asset as it allows you to learn new techniques and new ways of doing things. As I’ve already said, labs everywhere can be very different from each other. The more exposure to different labs you get the more ready you’ll feel when the day finally comes to leave your little PhD lab nest and fly into the world of postdoc-hood.

Post-PhD life
Speaking of postdoc-hood, if at the end of your PhD, you decide academia or even science isn’t for you, that is okay, don’t let anyone say differently. Sure a subset of skills acquired during your PhD won’t be particularly relevant outside a lab (I don’t know many government officials who do daily transfections or data analysts who do regular genotyping), but there are so many transferable skills that you gain from doing a PhD: time management, attention to detail, perseverance, data management, ability to synthesise information,  resilience, problem-solving, good written and oral skills, just to name a few. The years spent on your PhD will not be in vain, in fact, just the opposite, they make you a strong candidate for any job for which you wish to apply.

 

I hope that my kernels of wisdom throughout these 3 years have been helpful. Doing a PhD is a lot of work, so hopefully my advice can help make it all go smoother. Now, I have used up my self-allocated productive procrastination time for today, back to thesis-writing…

 

 

Fifth Fringe in Edinburgh

In true Edinburgh Fringe Festival fashion, the weather has turned very grey and rainy. George Square Gardens have been transformed into Fringe venues. Tourists are out in full force with soggy maps trying to soak up Edinburgh, before all-things Fringe engulf the city (I think it may be too late).

 

Lab stuff
I try to be as on top of my data as possible, but somehow some data had slipped through the cracks. I just found 5 days-worth of imaging experiments I’d forgotten doing in the mad dash leading up to Christmas/India. When I say just found, I mean just found, literally an hour ago! 5 folders from December are just sitting on my hard drive waiting to be analysed. The more data, the better, right? I’ve been doing lots of imaging recently to try to finish up the last few experiments I need for my thesis. A thesis does not have to tell a full story (papers do), but I have the cells and I may or may not be putting off actually writing up. Productive procrastination at its finest! I’m hoping to be done all my experiments by mid September at the absolute latest (and now that I’ve written it down it has to happen 😀 ).

 

More Edinburgh adventures
Of course everyone chooses the final crunch of my PhD to come visit. I like it though, it is a welcome distraction. Since one of my best friends from home came to visit at the end of June, I have also had one of my close friends from school come visit for a weekend and a childhood friend come up from London. I have explored Edinburgh, all the closes and the bridges and the haunted vaults (again). I’ve been all over New Town and Old Town and had my fair share of haggis. It has been very good way to keep my mind off the panic*.

*Yes, the fear has become the panic. I try not to let it overwhelm me (deep yoga breaths). I do have plenty of time and more than enough data. I try not to dwell on it. The panic can be kept at bay by lots of yoga, making my way through my analysis and weekly meetings with my supervisor. I’ve also made lists of what is done and what I have yet to do. The panic is curled up in a corner right now, I feel on top of things, but a simple “how’s you’re writing going?” could set it off again!

Back again

I hear that while I was enjoying rooftop terrasses in Montreal, the weather in Edinburgh was just as nice (I saw proof in the form of sunburns when I got back!). Unfortunately, I missed it. In fact, the weather since I’ve gotten back here has been quite grey and rainy as seen in this month’s photo- grey skies and green trees. Let’s hope there are still a few days of summer left!

Lab work
I’ve been back for 2 weeks now and I am officially back in Edinburgh until I submit my thesis *audible gulp*. While waiting for my experiments to start up when I was in India, I made lists (one of my favourite things to do) of what I have left to do in terms of experiments for each chapter. I haven’t quite started any of those yet. I’ve actually added more onto the list! I know that at some point I am going to have to draw the line and stop doing experiments so I can focus on writing up otherwise I’ll never write my thesis. There are just so many cool experiments left to do! I can definitely see how North American PhDs last 5+ years. There are just so many unanswered questions that are left to explore! Right now the important thing is figuring out which experiments are needed for my thesis and which ones I can do after submission to enhance a potential paper. It is exciting and scary. Although I’ve written up my MScRes thesis, this one seems different, more formal perhaps. I was flipping through an old PhD student’s thesis today and I was overwhelmed by “the Fear“*. I just have to get on with these experiments. The sooner I start, the sooner I finish. I’m hoping to finish all my experiments by September to submit before Christmas!

Visiting Edinburgh
Although I’ve been in Edinburgh almost 4 years now (how time flies!) there are so many hidden gems around the city that I haven’t fully explored yet. One of my best friends from home was visiting last week and together we explored all the different alleys and closes in the Old Town. We walked along the waters of Leith and explored New Town as well. We also went on a haunted walk that explored some of Europe’s most haunted locations which lucky for us are a stone’s throw away from  the George Square campus! Whether or not you believe in the paranormal, these tours are pretty freaky (the tour guide kind of looked like a goth vampire in a long leather trench coat), but also really interesting historically. It provides a new perspective on Edinburgh and points out some of the darker moments in its history that have made the city what it is today. I come from Montreal which just celebrated its 375th birthday; Canada celebrated its 150th this weekend (my friend and I celebrated with some good maple syrup). It always impresses me so much that there are buildings in Edinburgh that are so much older than that. The history here is incredible!

Now I must start on those experiments and make a plan for writing my thesis *another audible gulp*.

 

* The Fear arises in final year PhD students when they realise that the end is near and everything needs to come together. It can be exacerbated by things going wrong (which will happen), papers getting rejected (again, it will happen) and seeing blissful and completely unaware earlier year students (their turn will come).

Here we go again

The weather in Edinburgh was gorgeous last week! I was so mesmerised by the sun that I completely forgot to take a picture of George Square Gardens before leaving! Thankfully my friend took one for me from our office when I was already on board a plane to Montreal! (Thank you Amy!)

Lab stuff
Getting back from India was rough… The jetlag was unpleasant and the weather-which was cold and rainy (I brought the monsoon back with me you see) was unbearable. Luckily it started to clear up right before I had to pick up and leave again.

I got back from India and spent 2 weeks in Edinburgh before jetting off again to go to a conference (more on that later). I was back in Edinburgh just enough time to have a barbecue in the Meadows and repeat an experiment that hadn’t worked. I had stained and imaged a few cells right before going to India in January. Unfortunately, something went wrong with my staining and I couldn’t see my protein of interest. I repeated the experiment when I got back and I think it has worked this time. At least I could see the staining with the microscope, so that’s a good start. I’ll start on the analysis this week. I spent the rest of my 2 weeks analysing the data I had collected in India. Despite the little hiccups, the data look good. I met with my supervisors to show them my results and they are pleased with the work that I managed to do. It was a bumpy road, but all in all it was a great experience and it is a bonus that data actually did come out of it.

CAN meeting
I only spent 2 weeks in Edinburgh, because then I had to rush back to Montreal for the Canadian Association of Neuroscience (CAN) annual meeting. I’ve been away from Canada for almost 4 years, so it was good to see what research is being done and catch up with some old professors. I presented a poster that was very similar to what I presented at SfN. Although there were no synaptic vesicle recycling experts who came to my poster (there aren’t really any in Canada), I got the chance to explain my work to lots of people who weren’t familiar with my protein of interest or my imaging technique. It was really good to get a new fresh perspective on my work. People would ask questions that may have seemed naive but they made me question things and change my perspective on my research. Overall it was a really great conference. I want to thank CAN and IBRO for awarding me with a travel grant to attend the conference.

I now have 2.5 weeks off at home to relax, get over my latest bout of jetlag, analyse some images, start writing a paper, start thinking about my thesis and apply for another travel grant. A week in the life of a PhD student…

Three months have come and gone

This is my last week in India! The past 3.5 months have really flown by! I am definitely going to miss the weather and the beautiful campus views. This is the view from the colonnade by the front of the building.

Lab work
It is fascinating how everything can go wrong in so little time. My last post was full of optimism, everything had started to work, unfortunately that did not last long (that is the reason why this post is coming so late). Let’s go by chronological order, shall we?

•First, the stimulator which I use to stimulate my cells during my live cell imaging stopped working correctly. It took us two weeks, (a few electric shocks) and multiple discussions with the Instrumentation department and Electronics department and even getting a Warner engineer out to take a look at it before we figured out what was wrong. Unfortunately one of the components had broken and cannot be fixed. A new stimulator was ordered, but it will take at least three months to arrive. Luckily my supervisor in Edinburgh could lend us one for the rest of my stay here. He promptly shipped us one which worked perfectly (for a little while…)
•Everything was working again, my cells were healthy and responding to stimulation, it was all going swimmingly until there was some kind of power surge that fried major components of the microscope, including the power supply and lamp box. No one is quite sure how this happened. The microscope engineer came in to have a look and will try to fix the components or get us new ones as they were plugged into the electrical line that should be infallible to surges.
•A fuse blew in the new stimulator from Edinburgh! Luckily it was just a fuse and once I changed it, it all worked perfectly again.

I know that I’ve had quite a bit of bad luck, but it is not all bad. I still have a functional stimulator, perfusion system and suction pump, so I moved my imaging set-up to another microscope and continued to image. And I’ve had the chance to do most of my analysis and it looks beautiful! Despite the mishaps, it looks like I’ll still have complete datasets. It has been a bit challenging, but PhD students are nothing if not resilient.

Exploring Bangalore
When I was not imaging and talking to various equipment engineers, I did have time to explore Bangalore. We visited the castle which is built in line with European architecture and is almost out of place in India. It was very pretty. The garden was planted so that there would always be different flowers in bloom. Speaking of flowers, we also went to the bustling KR Flower Market. It was beautiful. It was incredibly colourful! I have never seen so many flowers all in one place!


Discovering Munnar
Last weekend, we took a weekend trip to Munnar in Kerala. Munnar is full of tea plantations. It is so green and lush. We trekked through the tea plantation and watched a glorious sunrise. We drank lots of tea and indulged in Kerala cuisine where everything is cooked in ghee, not peanut oil, so I could eat it all. We did go during monsoon season and we got rained upon, but it was an incredible trip and I highly recommend it.

 

Last but not least, I would like to thank everyone in the lab for welcoming me and helping me familiarise myself with the lab and Indian culture. I would like to thank the PIs who were very helpful during the whole process. I also need to thank Instrumentation and the Electronics workshop for dealing with all the broken equipment!

 

Now off to enjoy my last few days!

 

Always an adventure

It is so nice to be able to work with this view. As I mentioned, there are so many people in the lab, it does occasionally feel quite crowded. Luckily there is a mezzanine with work stations between each floor of the building. It is so refreshing to just be able to sit partially outside and work while feeling the lovely breeze.

Lab stuff
Experiments have finally started! There were a few set backs: reagents still being in the US, fluorescent dyes not being fluorescent anymore… but we got there in the end. It can be really trying (but rewarding) to set up a brand new protocol in a lab where you are the sole expert and everyone you look to for advice (your own experts) is 5.5 hours behind you. After a few panicked emails to my supervisor and labmates in Edinburgh, I think that everything has been set up. The cells look happy, the microscope works and the results are starting to come in- what they look like I have no idea, analysis is the next step.
In my last post, I mentioned that perhaps a lab is a lab is a lab is not true. Even if you were to replicate the exact same experiments here and in Edinburgh there would be some things out with your control. For instance, room temperature. Summer has arrived in Bangalore, it is 37C everyday. Despite the air conditioning, room temperature is definitely warmer than it is in Edinburgh. Although not all labs are the same, I firmly believe that a microscope is a microscope is a microscope (well at least the epifluorescence one I use). When I am in that dark imaging room, listening to my podcasts and staring intently at the computer screen trying to detect subtle changes in fluorescence, I completely forget where I am. I could be back in my imaging room in Edinburgh. It is nice to have some familiarity so far away from home.

Holi in Hampi
I’ve been taking advantage of being in India to explore some of the surrounding areas. My friend lent me Lonely Planet’s Short Escapes from Bengaluru and the other students from Edinburgh and I are making our way through them. At the beginning of March we went to Hampi. Hampi is a UNESCO World Heritage Site with tonnes of gorgeous temple ruins. We saw all the ruins, watched an elephant get bathed in the river, climbed 575 steps to the Monkey Temple and almost lost my phone to a particularly cheeky monkey. What was really nice was that we were in Hampi during Holi, the Hindu festival of colours/ the festival of love. Holi is celebrated by throwing powdered colours at one another. Lucky for us, the colour was permanent (I am still washing green and pink out of my hair 3 weeks later!). It was an incredible experience that brought locals and tourists together. Children were sitting on our shoulders and showering everyone in colour. It was quite spectacular.


Mysore
Last weekend, we headed to Mysore to rack up some #wildmiles and raise awareness for intellectual disabilities, autism and fragile X syndrome. We climbed 1000 steps to reach a temple, only to discover it was being renovated and was covered in scaffolding! Mysore is a beautiful city with an incredible palace that was lit up at night. We also visited their massive market where our senses were overwhelmed by the colours, sounds and smells, it was hectic but beautiful.


Enjoy the pictures!