The Fairy tale of Academia

Sang to the tune of The Pogues Fairytale of New York

It was Christmas eve eve
At the lab bench
A post doc said to me
Won’t see another one
And then he hit submit,
A Nature manuscript,
I turned my face away
And dreamed of first authorship.

This labworks nearly done
Screw you, reviewer one.
I’ve got a feeling
This year’s when we’ll publish.
So Happy Christmas
I love you science.
I can see a better time
When my h-index is high.

They’ve got funding that’s stunning,
They’ve got grants to behold
But the work is just constant
And this we were told.

When I first joined the lab,
On a cold weekday eve
I wondered if Nature was waiting for me.

There’ll be data
There’ll be graphs
Therell be plenty of cash
When the labs finished working
Theyll go back for more.
The PI will be grinning
Fellowships we’ll be winning
We submit on a weekend,
Accepted next day!

The students of the PhD cohort
Will be pipetting happily
And the paper will be out
For all to see.

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Jingle Cells

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Jingle Cells, Jingle Cells

Jingle through the lab

Oh what fun it is to stain

and visualise with DAB

 

My friend Sarah is very talented at knitting and made these festive cells as decorations for the lab and I LOVE them. From left to right: astrocyte, endothelial cell, red blood cell, neuron and stem cell. The Santa hats are an excellent flourish.

Christmas is nearly here and the lab is emptying out as everyone heads home. My last day is tomorrow and I’ve been trying to wrap up experiments like I wrap up Christmas presents… bad joke.

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Something I’ve managed to do is a podcast episode with a few others from our SCRM science communications group Team RegeneratED. We recorded it in a tiny little room in the lab which none of us had noticed before. Very Room of Requirement. You can listen to our podcast here! Hope you enjoy it and if there’s any advice, we’re looking to make more podcasts in the new year.

The first half of the podcast is a SCRM scientist talking about their work. I had a great interview with Elaine Emmerson who is a new group leader at the SCRM. I really enjoyed learning about her reserach and I also found it interesting to hear about her career progression. What she said about realising that your own ideas were valid and interesting has actually really stuck with me since the interview and I think it’s something I need to work on too!

The second half of the podcast is a very serious discussion about the Science of Santa and his liver health. No, really. I made some questionable calculations about how much alcohol Santa is consuming on Christmas eve and we got a liver expert, Phil Starkey Lewis from the Forbes group, in to tell us how much cirrhosis we could expect in Santa…

 

Merry Christmas everyone!

Pinterest-Perfect

A counterbalance post about the first year of my PhD

20171205_120112If you work in a lab you’ll know the occasional necessity for zoning out in tissue culture when you’re doing mundane tasks, and then you’ll probably also know the horror of kneeling down to get something out of the fridge, your trailing wire getting caught and ripping your earphones right out of your head. Ouch.

So, I bought a set of wireless headphones for the lab to avoid this disaster in the future because I’m always plugged in. Recently I was listening to a podcast called Stuff Mom Never Told You, which discusses “the business of being women from every imaginable angle” and they have an episode about not living a ‘Pinterest-Perfect life’ which made me think about my online presence. While I rarely post on Twitter and mostly post shots of my dog on Facebook, it occurred to me that perhaps people interested in doing a PhD, particularly those for the Tissue Repair programme, might end up reading some of this blog in the hope of finding more about my experiences and whether they would want to end up doing one too. I write generally all the cool stuff and am generally pretty upbeat but, as a counterbalance, here are some potentially brutal things about PhD life.

It’s often thankless. Getting a PhD is competitive, (even though once you’re in academia it seems like everyone has one) so to get there you need to have had a fair amount of successes. However, science can be a cruel mistress as anyone who’s worked in it would agree. Experiments don’t work and you’re not always sure why, you have very little measure of your achievements and it can often feel unrewarding. Nature recently conducted a survey and found that mental health distress is more likely for PhD students than other highly educated individuals. I’ve been thinking about this and on top of all the usual reasons cited (long hours, pressures, lack of support systems) I reckon that when you take high achieving people and put them in an environment where a lot of stuff just literally does not work they will inevitably experience issues.

20171205_124304It’s isolating. I don’t really tell anyone what I’ve done all day. One of the coolest and most terrifying things about a PhD is that you are in charge of what you do day-to-day. This means you have to be self-motivated to get things done but it also means you sort of report to no-one. My husband asks about my day but he’s not working in science so the details of my hilarious escapades and resounding failures at the bench don’t make a lot of sense. I tell my supervisor the overview pretty regularly but not the boring details and certainly not every day. The people that I work with probably bear the brunt of it (you know who you are) but even then I spend a lot of time in my own head. Maybe the headphones don’t help with this!

It’s consuming. The hours can be long, you can work weekends – this is what everyone tells you. What they don’t really mention is that it’s not the hours you are at work that are the problem, it’s the hours that you’re not, but you feel that you should be. I have woken up in the night with the words siRNA swimming around in my head or spent an evening out worrying about whether the cells I seeded would survive the night. Talking about this with a friend we agreed that it’s not necessarily about how much work you have, it’s about where you put your work in your life – do you put it all in the office and stay ‘til late or do you put it on a Sunday afternoon so you can leave a bit early another day… There’s always, always, work to be done so you just have to figure out where to put it in your week.

It’s actually a lot of fun. Okay so that has all sounded super negative and like I’m having a terrible time – I’m not. I wouldn’t change the fact that I’m doing a PhD, I wouldn’t change where I’m doing it and I wouldn’t change who I work alongside. My first year has been a massive learning curve in lots of ways and I wanted to be up front about the negatives. In the past when I’ve written about all the good stuff I’ve been doing, that’s been totally honest. I just think we should all be honest about the bad stuff too and not worry so much about showing off that Pinterest-perfect life.

 

Necessary networking

Last week I attended the launch of the new Edinburgh Small Vessel Disease Network. This was a day designed to bring together all people working on this disease from a number of different aspects including clinical, pre-clinical and epidemiological, as well as exploring different techniques that people are using. It was great to feel part of something and really inspired me in my project, a feeling I’m hoping I can carry for a while as I’m struggling with a few experiments at the moment! Reminding yourself of the bigger picture can really do wonders for your motivation.

I wrote a blog post for them about my research and how it could potentially bring together different groups, read it here. The afternoon was particularly good as the ‘early career researchers’ stuck around to see small post-doc presentations with no questions but small-group discussions with those around you. This lessened the pressure on the presenter and questioners alike as it’s easier to talk to others than raise your hand to ask a potentially daft questions (okay for me anyway).

I also got chatting with a post-doc I’d met at EuroGlia a few months ago and how she had just published her paper about mutations in the TREX1 gene in small vessel disease in Wellcome Open Research. This is a platform to immediately publish your paper, making sure that your data gets out in a much timelier manner instead of waiting around for months. You request reviewers and all their comments are public. It’s such a transparent and efficient way of sharing information between researchers and while many people won’t be on board right now, I think that this will really be the future of publishing. It will lift all the secrecy, any unpleasant competition and should eventually lead to a much more open society of research. It will be interesting to see how this changes over the course of the next few years, perhaps more ‘early career researchers’ will persuade their PIs of the benefits to the whole scientific community of publishing in this way.

Winning and Women

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As one of the shortlisted fourteen for the MRC Max Perutz prize, I got to go a writing masterclass and an awards ceremony in London this month. I was one of the runners-up (yay!), which was amazing and meant a comedy-sized cheque I’m not sure I can take to Halifax. See the pictures, read all the entries and spot how well the three runners up and winner co-ordinated our outfits  (blue florals and plain red.) Here’s a great picture of me with some important people in my life! On the left is one of my supervisors Anna Williams, who made the trip from Edinburgh during the day just to support me, returning on the sleeper train to run her clinic in the morning! On my other side are my husband and mum who I couldn’t be doing any of this without.

 

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The whole day organised by the MRC was excellent, with an afternoon learning from Dr Claire Ainsworth, former features editor of Nature and New Scientist and co-founder of SciConnect Ltd . Here’s a snap of me and Karolina, the other SCRM PhD student who was also shortlisted; we had a cracking view over London during the session. The evening got us all back together for prizes and prosecco. It was pretty interesting to see how the majority of those shortlisted were female, a fact that was commented on by one of the speakers at the event. It was also interesting to see that all the speakers were older men, though it is true that other members of the judging panel were women. Discussing this with a couple of others we talked about how we were lucky to have role models like our supervisors, why we see an imbalance not at the lower levels of academia but we do at the upper levels and how things might change. It’s a really pertinent topic at the moment and one I’d probably need to write a whole piece about some other time.

20171106_103207The day after the ceremony, waiting for our train, I convinced my non-sciencey mum and husband to come into the Wellcome collection where I nerded out with the full printed human genome, the artwork made of pills carved into the organ which they are designed to treat and a fairly disturbing set of medical instruments. One of my favourite facts about Henry Wellcome is that his wife absolutely hated his mad collecting habit and after they got divorced she became famous for her minimalist interior design. With a couple of million weird things that currently fill warehouses around London, you can see why she went to the other extreme.

Sharing is Caring

My good friend Rebecca who I studied with during our undergraduate degree is doing her PhD in microbiology at University of York and runs a really great blog called An Anxious Scientist. She certainly shouldn’t be anxious about her blog, it’s awesome.

This month she asked me to write a guest piece for it after I got shortlisted for the Max Perutz MRC writing prize (yay).

Also starring, my ever glamorous Nana

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Read my post here: Communicating with all the colours of the wind

 

Western Blots: The Good, The Bad and The Ugly

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Striding into the lab with a cowboy swagger, the scientist plants her feet and stares down the opponent. Tucking back her lab coat, she spins her pipette deftly in its low slung holster. She knows there can only be one winner in this fight. Her adversary returns the steely glare… it is the western blot apparatus.

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 “Howdy pardner” Meet The Western Blot

wbLooking at the beautiful neat bands in many papers you would perhaps assume that the western blot is a simple, fool-proof technique. You would be wrong. They are the snake in your boot.

After recent repeated skirmishes with them, I’m here to share my own failures in the hope of preventing yours. Though not the most challenging in terms of skills needed, the western blot has taken down scientists of greater ability than me, so let’s not be lone rangers in this – circle the wagons and share our hardships.

“There’s not enough room for the both of us in this gel” Planning your western blot.

planSwing open the saloon doors and take the challenge head on. Have your ammunition ready for the fight: What proteins do you need antibodies to? How much will you need to dilute your samples? What volume will each of your gel wells hold… no really how much? The box might say 50µL but like the sheriff who tells you he’s taken down ten bandits at once, ask around to see what the real deal is.

“Load the wagons” Running your gel.

loadHead to the bar and select your poison (buffer). There probably won’t be a bartender with a Southern drawl to make it for you but I don’t know your lab so maybe there is. Set up your gel in your bucket full of buffer and pipette in your samples.

Just as a cowboy wouldn’t leave a barrel of his gun unfilled, nor should you leave a gel lane unloaded. The proteins wont run down the gel evenly and the ‘smile’ it leaves will not be on your face I can assure you.

Plug in your voltage – you might find it good to get things going with a low voltage then move to a higher one. Check for bubbles so you know there’s actually some electricity flowing and head off to get some grits, whatever they are.

“Stick ‘em up!” Getting the proteins onto the membrane.

sandwich

If your loading buffer has hit the bottom of the gel then you’re ready for round two. If it hasn’t, well keep firing ‘til it does.

Slosh out the trough and refill with a whole new buffer, layer up a sandwich with the gel and a membrane as the delicious sciencey filling and absorbent papers and furry scotch pads as the bread. It is ridiculously essential to put the sandwich the right way round in the bucket so the proteins transfer in the right direction. This is literally the one mistake I have yet to make because I am so paranoid about it, but bandits can storm the convoy at any time so I have to remain vigilant.

“3…2…1… Draw!” Remove your membrane.

membraneThat dreaded moment when you peel the membrane from the gel and reveal whether the proteins have transferred successfully is pretty nerve-wracking no matter how sure you are it was set up right. If it’s on the absorbent whatman paper and not on the membrane, accept defeat and know you live to fight another day.

If it’s on the membrane, yee-haw! Giddy up partner. Wash it in yet another buffer then in a blocking solution.

“Wanted… dead or alive” specific antibody targeting.

milkSnip that membrane up so you can stain for the different proteins you’re interested in. Hopefully you’ve got a validated antibody but frankly that’s a whole other fight in a whole other town. Dilute the primary antibody in blocking solution and immerse your membrane in it. Strap the nosebag on your horse and head home. Next day, wash away and then add your secondary antibody… I’ve ended up with completely null results after using the wrong secondary but it’s not like poisoning the water hole, you can always wash it off and try again.
“You looking at me?” Developing your western blot.

developThis part is the killer shot. The two days of splashing about in various buffers may have been completely in vain if you mess something up here. No pressure.

I mean what could go wrong now? Take your membrane, add your substrate, saddle up your steed and dash to the dark room or the scanner depending on your chosen method of punishment.

Just… do not forget what went where. Do not forget to line up your sheet with the ladder and draw it on. Do not for goodness sake accidentally mix up your western developing substrate kit reagents A and B with your protein assay kit reagents A and B, pipette the wrong thing on and mess up the entire membrane…

“You’re my favourite deputy”

I truly hope your westerns are peaceful, you lasso the data you hoped for and you can return to the ranch triumphant.