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.

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!

December delights

I know this blog post is a few days late, we can just blame it on jet-lag or the weather. To make up for it, not only have I included a picture of George Square Gardens from December, but also a picture of the view from my bedroom here in Montreal. Isn’t the snow so fluffy and magical? I am definitely blaming it for delaying this post. 

Lab work

It has been a bit of a whirlwind since getting back from SfN. I had originally planned to get all of my imaging done before I went home for the holidays so that I could do data analysis during the break. So that didn’t happen… I was testing out a new imaging protocol and I just couldn’t quite get it to work properly. Although the live-cell fluorescence imaging assays that we do in our lab are relatively straightforward, there are so many little things that can ruin your timetrace acquisition. In my case, my cells were jumping in and out of focus during your 10-minute long experiment, making it practically impossible to track my fluorescent molecule. No one said science was easy. I did still manage to gather some data which I have yet to analyse. My biochemistry/ molecular biology experiments worked quite well however and all the analysis has been done for the experiments I’ve completed. Although the results weren’t what we had hypothesised (and will require tonnes of reading to make sense of them), the fact that I finally got the assay up and running and working with my different mutants definitely gives me that morale boost. You have to celebrate the small stuff in science! It doesn’t always work, but when it does, it is magical!

December delights

I have always loved the run-up to Christmas. Despite the lack of snow, Edinburgh definitely does its best to get everyone into the festive spirit. Between the Christmas Market on Princes St, office Christmas parties, turkey dinners, lab lunches, and departmental festive drinks in the Anatomy Museum, it is a wonder that anyone actually got anything done! The city is engulfed in Christmas lights and mulled wine spices. It is a lovely place to be! Currently, I am in Montreal. I get back to the warmer albeit wetter Edinburgh weather next week. I’ve taken advantage of my time off to do lots of yoga as to be more chilled and be able to start off this new year relaxed and peaceful (though that inner-peace will probably melt away as soon as something stops working or the lab fairy interferes). 

Happy 2017 everyone! May your year be filled with significant results! 

19 hours and 8 timezones later…

Winter is upon us, or rather it was last week, but the weather has been quite good this week, we are hitting double digits tomorrow! So it would be the absolute perfect time to head down to the Christmas Market or up Arthur’s Seat or even perhaps have a Meadows barbecue?

A few weeks ago, I went to the Society for Neuroscience (SfN) annual meeting in San Diego. As I mentioned last month, it is the biggest neuroscience meeting in the world! There were over 30000 attendees! That’s 1.5x bigger than the town I grew up in! It was so incredible to have so many neuroscientists all in one place! And the lovely San Diego Convention Centre managed to host all of us for 5 days. The conference itself was slightly overwhelming with dozens of overlapping symposia and mini-symposia and nano-symposia. It did take me a full day of preparation to figure out which talks I would attend, which posters I’d go see and which exhibitor booths I’d check out. I mostly stuck to presynaptic talks and talks about Fragile X syndrome and autism spectrum disorders. While the talks were very interesting, I thought that the poster sessions were most useful. It’s a way to see what other labs are doing, meet other people (and network) and actually ask questions and talk about your work and give advice and get feedback. I also attended the Canadian Association for Neuroscience (CAN) social and got the chance to catch up will some of my old undergrad professors from McGill (and jokingly/ maybe-not-so-jokingly ask them if they’d have any openings for postdocs in their labs in 12 months). I have managed to make several new connections which will benefit my ongoing research and potentially lead to me getting a postdoc position. I networked my little heart out. Going to this conference has whet my appetite for big international conferences. I am already preparing my abstract for the CAN meeting and looking for more travel grants to allow me to go back to SfN next year! I definitely have to acknowledge and thank the CMVM and Guarantors of Brain for providing me with the travel grants that made attending this conference possible.

On a side note: San Diego was gorgeous. It was definitely a long way to go and the jetlag was horrendous, but it was 100% worth it. It is an incredibly vibrant and welcoming city. I would highly recommend visiting! The palm-tree lined roads are so inviting and all the fresh seafood and Mexican-inspired dishes are delicious. I may have overdosed on fish tacos hehehe.

Lab stuff
Despite being in sunny California for a week, I have still managed to be productive in the lab this month (please don’t tell the lab fairy). It is currently the run-up to Christmas and everyone is trying to get stuff done- the mad dash has started. I think I have finally optimised an assay that I started working on in August! August! Yup, it has been a long process and there have been lots of different steps to work out. I am really hoping that now it works when I try it out with the mutants tomorrow. It’s all well and good that the WT works, but if the mutants don’t… back to square one. I’m not superstitious but please knock on all the wood, cross all your fingers (and toes) and send all of the positive vibes my way. Science is definitely a journey.

Happy Saint Andrew’s Day! If you are in Scotland you must go find yourself a ceilidh to go to! It is tradition after all.

Where are we? When are we? 

That is how one of the postdocs in the lab suggested I start off this blog post. Perhaps because I am a tad frazzled these days.

Time warp
I know that I have already mentioned that I do not know how time is going by so quickly, but I feel the need to reiterate this point. It feels like just yesterday I looked out the window and saw the multi-coloured Fringe posters and Underbelly tent. Then I blinked and entered some kind of time warp that has brought me to November. November! I really do not know where the time went.

I suppose that a lot of my time this term has been spent teaching. I am a facilitator in two new courses: Our Changing World (OCW) and Clinical Biochemistry and Endocrinology 3 (CBE3). The former is composed of a series of public talks on various issues that affect our global society including happiness, traffic and multiculturalism. After each lecture there is a group discussion which I facilitate. CBE3 is in a slightly different format: problem-based learning (PBL). The students are given an actual case report from a patient and go through it meticulously to try to understand all the components (from blood panel results to vague symptoms) and how they relate to the diagnosis. After the first session, they come up with questions they need to research to fully understand the case. During the second session, they get the opportunity to give comprehensive answers to all the questions raised. I facilitate these sessions and make sure that the students stay on track and discuss the relevant information.

Last May (which really doesn’t feel so far away now), I submitted an abstract for a poster at the Society for Neuroscience’s annual meeting in San Diego. My abstract was accepted, I was awarded travel grants and I will be on my merry way to the Pacific coast next Friday. The catch, my poster is still not made and the data is not yet fully analysed because of the little hiccough that I discussed last blog post (that base insertion knocking everything out of frame). This meeting is the largest neuroscience conference in the world with over 30000 people attending from more than 80 countries! This will be quite an interesting experience. It’ll give me the opportunity to present and defend my work in front of the leading experts in the field.

On that note, I am off to finish up my analysis and make my poster!

What I have learned so far v2.0

Things have seemed to settle down a bit in Edinburgh. The grass is staring to grow again in George Square Gardens, everyone is back from holidays and freshers are recovering from freshers flu.

As I did last year, I will once again provide you with Katherine’s kernels of wisdom (speaking about myself in the third person again). I am one year wiser and I am passing along all my wisdom to you, my lovely blog readers. These “what I have learned so far v2.0” should be taken along with what I learned from my first year to provide you with a sort of manual for “How to survive your PhD 101”.

You do not have much time
Three years may seem like ages, but let me tell you, if you blink, it’ll go right past. Three years is really not a long time to complete a PhD. In North America PhDs tend to last at least 5 years and usually even longer. The duration of PhDs here is both a blessing and a curse. If you decide midway through that science and academia is not for you, you will have only dedicated a small portion of your life to research. Nevertheless, you will have come out of your PhD with lots of other important transferable skills and a great work ethic. However, if you are incredibly passionate, three years may not be enough time to go down all the winding, twisting paths where your research question may drag you. You need to make sure to carefully plan your project. Although you may want to pursue every avenue, be sure to stay on course. I think that meeting often with your supervisor is the best way to stay on track. It is good to discuss your ideas and plans for other experiments.

Stay on top of your data analysis
I must admit that I am guilty of not quite being so timely with my data analysis. I must stress that it is really important (do as I say, not as I do, right?). If you don’t look at your data, how do you know that your experiments/ protocols are actually working? Analysing as you go along will save you time and effort in the long-run. You’ll be able to troubleshoot right away and won’t have to repeat experiments unnecessarily.

Get out of the lab!
Even if your sole ambition in life is to win a Nobel Prize in Physiology or Medicine, there is no need to be in the lab 24/7. Find yourself a hobby, go to the gym, travel, paint, join a society or a committee or just go hang out at a pub or a coffee shop to wind down. Meet people from outside of your research area -if nothing else it’ll give you the chance to practice explaining your research to a lay audience and improve your science communication skills. If what you are studying truly is your one passion in life (in that case, congratulations on landing the best PhD project ever!) then go to talks and lectures on related topics. Try to do some teaching in your field as well, there are so many opportunities for demonstrating and facilitating undergraduate courses here. Just do not spend all your time in the lab, it’ll drive you crazy!

The best laid schemes of mice and men often go awry
I think last year I was being optimistic when I said that things don’t always go well. I’m being slightly more realistic this year and I am firmly stating: things will go wrong. In fact, a few weeks ago, I found out that one of the constructs that I had been working with had a single base insertion that knocked everything out of frame. Although it was devastating to find out that what I had been working on for a long time had to be repeated, it did explain why I was struggling to see my protein of interest! I have since fixed my construct and I am merrily on my way to repeat my experiments.

Take care of yourself
I know I said this last year, but it is worth repeating again. PhDs are stressful and they do completely take over your life. Try to follow some kind of routine. Do not forget to take care of yourself and eat and sleep.

I hope that these latest kernels of wisdom prove to be useful and helpful!

12 more months…

The Fringe is officially over. The giant purple cow has been deflated, the posters have been taken down and there is no longer anyone handing out flyers. Between the tourists who have left and the students who have not yet arrived for Freshers, George Square is quiet and peaceful.

Fringe-y fun
I have a confession, I may or may not have been converted to a Fringe fan! I cannot believe I am saying this, much less writing it here for everyone to see! Although I had only bought tickets to 3 shows as of my last blog post, I ended up going to 5 shows, that’s right, 5 shows! I enjoyed all of them. I saw magic and comedy and illusions and circus and hypnosis and improv oh my! I also did enjoy having both the Assembly and Underbelly bars a stone’s throw away from the lab. All the food trucks did also make for good lunch and supper options. I immersed myself in all things Fringe this year and I did enjoy it, although I am very happy to get some peace and quiet back.

Lab work
The good new is that I had caught up on my data analysis. The bad news is that I have fallen behind again. I must just be that productive at taking images on the microscope hehehe. The problem is, if I don’t do this analysis, I don’t know whether or not my experiments are finished! I am also attempting to pioneer a new protocol in the lab, so I have been going around the building asking everyone I know for tips on various steps of this elaborate protocol. I have read and re-read papers to try to figure out the best protocols to use. Ultimately I have opted to use the manufacturer’s protocol for each step to date and let me tell you, they really work. Those manufacturers do know their stuff.

2nd-year meeting
This post has been delayed a few days because I have been getting ready for my 2nd year progress meeting which was today. This meeting is with my supervisors and the chair of my committee. There is not really a fixed format for this meeting (not like for our 1st-year meeting. In my case, I opted to do a short data presentation to show everyone (specifically my second supervisor and chair) what I had been up to since I became a real PhD student. My 15 slides turned into an hour long presentation… but overall it was extremely productive. I got some good feedback and great ideas for other experiments that would compliment what I have already done. It was also incredibly scary! I AM GOING INTO MY FINAL YEAR! The end of this meeting was spent discussing staying on-track, finishing all my experiments and writing up my thesis. It was also a chance to discuss my future plans and what I intend to do with myself after I submit. Apparently I have until Christmas to mull it over and then I should start contacting prospective supervisors (*giant apprehensive gulp*). I know I have already been in Edinburgh for 3 years, but I really feel like the end of my PhD has crept up on me. So my plan for the next 12 months is to work hard and produce the best and loveliest thesis that there ever was.

Now I will leave you, as I go ponder my future and make a detailed list (my favourite thing to do) of what needs to be done before September 2017…