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! 

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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!

The first month in India

Isn’t the view incredible? This is the view from the colonnade at the front of the building where the lab is. The architecture is very open concept like in other warm and tropical countries. This lets in lots of natural light, a nice cool breeze and obviously the heat! It is 34C here (and it isn’t even summer yet)!

Lab work
I’ve been here 24 days and I haven’t really started any of my own experiments yet. I have helped and supervised other students’ experiments. I have also made up all the solutions that I need. There are so many things that need setting up when you move to a new place. It gives me newfound appreciation for our technician in Edinburgh who makes up all of our solutions and aliquots out reagents for us so we can focus on our experiments. The good news is that now everything is ready to go for my experiments and I should be able to jump on the microscope here in a few weeks! This may be the longest I will have been away from a microscope since starting my MSc. I think I am starting to experience symptoms of withdrawal!

A lab is a lab is a lab (maybe not)
So it turns out this lab is different from the ones I’ve worked in in Montreal and Edinburgh. Sure there are pipettes, beakers and nitrile gloves, but the way the lab is run is different. The lab is open concept and there are people doing electrophysiology on one side and on the other side are student benches. The lab is huge! There are 50 people! I’m sure I haven’t even met half of them yet! It is a multidisciplinary lab with different members doing electrophysiology, imaging and molecular biology. I think that the fact that there are so many people doing so many different things is what is so different.

Out and about
The campus is at the North of Bangalore and there is not much around. I have ventured into the city centre a few times (a 30-minute drive away). My second supervisor was here with his family last weekend and I joined them on a visit to the modern art gallery. I have also been to Commercial Street which is a street lined with shops and vendors and thousands of people both locals and tourists. You can find saree shops, traditional craft shops, shoe shops, pharmacies, jewellery shops…

Now, I’m off to take advantage of the sun! (I’ll try to send some of the sun Edinburgh’s way as the weather there is quite rainy currently.)

Here goes nothing

Hmmm it seems like George Square Gardens has undergone a major transformation this month…The reason this picture is taken at the airport is because I am off to India for a few months! (More on that follows.)

Lab work
January has been a very short month. I’ve only spent 3 weeks in the lab but they were arguably the most productive 3 weeks of my PhD. I’ve finished all the experiments for one of my thesis chapters. This was particularly important as I can now start writing up the chapter and paper to accompany it while I am waiting for my experiments to start in India.

Prepping for India
I am moving to India for a few months as part of a collaboration. We had an Indian PhD student and postdoc come to Edinburgh for 3 months this spring to learn the techniques that we routinely do in our lab. Now I am going over there to do those same experiments on their models and foster new collaborations. This is a fantastic albeit slightly scary experience. I’ve always said that the University of Edinburgh’s collaborative research is a huge asset. I am truly glad that I can take full advantage of it during my PhD.

I already moved from Canada to the UK, so I should be used to travelling across the Commonwealth countries, but this move feels different. Of course some things are the same: visa applications, the mad dash to get everything sorted out/finished before leaving… Other things are completely different. I had already been to the UK prior to moving here; I’ve never been to India, it is all new and unknown. I’ve had to get loads of immunisations (better safe than sorry) and load up on allergy medication (it is quite unfortunate that I am allergic to major components of Indian cuisine).

I suppose that a lab is a lab is a lab. Once you’ve seen one you’ve seen them all, right? That should be an element of consistency to ease my nerves, because as everyone in the Hugh Robson Building can testify, I have been quite nervous leading up to this trip. I would like to thank everyone for keeping me calm and sane, for all the comforting hugs I’ve gotten and for the lovely guidebook of Bangalore.

Now I must be off to my gate. I will keep you all posted about how it is all going in India once I get there and get settled in!