A day in the life of a PhD student, Guest blog

Guest blog: A Day in the Life of a PhD student. Bri L.

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Bri’s blog posts were ones that inspired me to start my Day in the Life of a PhD student feature so you could get a taste of how varied my days in the lab could be. So there was no better place to start with the guest blogs to show how varied PhDs are by asking Bri to be a part of my blog.

Luckily she agreed.

So, I will hand you over to the second guest blogger this week 🙂 Enjoy 🙂

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Hello! My name is Bri and I am a second year PhD student from Australia. My research is within the field of conservation psychology and I focus on marine ecotourism and conservation. I have always been passionate about conservation, and I feel so privileged that my work is based on my passions.

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During my first year of my PhD, I created my blog www.drofwhat.com which focuses on my studies and adventures. I love to write about my PhD journey, provide general study tips, and inspire people to explore nature. I have met so many wonderful PhD students, scientists, students, and conservationists through my blogging journey and love the opportunity to be featured on other people’s blogs.

This day in the life of blog post follows one of my Tuesdays in April:

7:19am – I am starting my day with a coffee in bed. The weather has cooled down, so it is so lovely to snuggle under the quilts for a little longer.

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8:06am – All ready to leave for work and the long day ahead.

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8:39am – After a quick stop off at the food store I have arrived at work and I’m ready to eat breakfast (oats and blueberries this morning).

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10:07am – More emails, it has seriously felt as though my days are filled with emails lately. I have four email accounts which I have to keep on top of so it is super time consuming. I think I am completely up to date from the weekend now though!

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11:01am – Qualitative data analysis time. This analysis for my first study has been a serious slow burn, I have probably spent over 100 hours on it already and I am only roughly 3 quarters through my initial analysis.

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12:32pm – Enjoying lunch outside in the sunshine!

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2:42pm – I am having a break from data analysis to write down a quick training plan for netball training tonight (My best friend and I coach an under 15s team).

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3:38pm – I have arrived at home for a quick stop off before heading down to netball training.

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5:23pm – Netball training time- I normally am in more appropriate attire, but I have to leave early for an online meeting for another volunteer position, so boots it is today.

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6:24pm – I am all set up for my online monthly meeting for my state coordinator role.

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8:09pm – The meeting has just finished, so I can finally switch my brain off and enjoy dinner.

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9:49pm – I am finishing the night with some embroidering. I really enjoy doing some crafty activities a couple of nights a week as a way for me to wind down. I picked up a cheap shirt from the op-shop and am attempting to embroider a whale shark on the back of it. It is then off to bed to wake up early for another long day at work tomorrow.

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How  does your typical day studying for your PhD compare to this? Or one of my days here? Please do share in the comments below. Or if you want to share a typical day in the life of your PhD journey please get in contact to do a guest blog.

Keep up to date with Bri’s blog here.

Huge thanks to Bri for guest blogging for Soph talks science – don’t forget to keep up to date with all new blog posts, all the latest news and more! Find me and Soph talks science blog on Facebook, Twitter and Instagram.

A day in the life of a PhD student

A day in the life of a PhD student. Chapter 5.

As a PhD student, I often get asked the question ‘So what do you do?’

A simple enough question. A simple enough answer of ‘I research embryonic stem cells and how they use oxygen concentration and glycolysis, a type of metabolism, to stay as stem cells’.

But sometimes I then get asked ‘No! I mean what do you do in a typical day?’

Again, a simple enough question. But probably a little more complicated to answer. There is not typical day as a PhD student working in the lab – you just do whatever experiments need doing – or perhaps whatever experiments your cells allow you to do! Because of this variety coupled with my want to be able to explain a usual day for me, it resulted in this ‘A day in the life of a PhD student’ feature. A snippet into my days in the lab to show how varied by work is.

So I thought it was time to show another day – especially now I am starting to do some new experiments that I can introduce to you. So – welcome to Chapter 5 of ‘A Day in the Life of a PhD student’.

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8:03am – The worst time of day – the alarm call! But now that the clocks have gone back, it is making getting up in the mornings that little bit easier as it is brighter outside! But it’s only making it a little bit easier!

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9:27am – So I have been in work a good 20 minutes already and Windows is STILL configuring updates! With lab meeting starting in 3 minutes time, I gave up my quest to check emails this morning and just headed into the lab and started some experiments that could be running whilst I’m in meetings this morning.

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9:31am – So my new experiments are looking at the DNA of my embryonic stem cells. We want to find out if a certain protein is switching on the expression of my gene of interest in my stem cells and I am doing this using ChIP. Now I’m not eating crisps or fries depending on where you are in the world, but instead ChIP stands for chromatin immunoprecipitation assay. Basically what this experiment does is extract all the DNA from my cells in the form of chromatin – which is DNA with all of its associated proteins still attached. Feel free to ask me some more questions about chromatin but for this post we will leave it at that and delve into it deeper in another blog post at a later date. Anyway, once the chromatin is free from the cell we chop it up into smaller fragments and then add an antibody that will bind to our certain protein. We then move onto the precipitation step. We use magnetic beads that will bind to the antibody and bring with it anything that the antibody has bound to – so hopefully the protein and some DNA. After a few more steps, we want to see if our certain protein is bound to a specific DNA sequence which it would have pulled out of the solution with it when we added the magnetic beads.

This procedure though needs several days work just to get one result and today is the second day so probably won’t make much sense, But what I am starting this morning is the steps to check if my chromatin has been chopped up enough – which we will see later.

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11:27am – On to the second meeting of the morning. The first one was the whole lab meeting. We have these usually once a week just so we can all catch up on what everyone is doing, see if anyone needs any help with any issues they may be having and discussing any problems or things that need to be dealt with.

For my second meeting of the morning, I had booked in my supervisor to discuss more specifically what I have been up to in the lab and what other experiments needed to be done. The result was that I need one more result before I can submit a manuscript for my first paper which hopefully can be submitted by the end of the summer. Fingers crossed all goes well. So apart from discussing what experiments I need to do ASAP, we also divulged into what I would be starting after that to hopefully get paper number 2 (and number 3 hopefully!) before I graduate with my PhD. As I have never published in a journal before, discussions lead on to where I even begin to look for where to submit to and all this complicated business so if anyone has any advice it would be greatly appreciated!

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1:14pm – In the window I had between meetings, I started the steps to develop my Western blot which I have discussed in more detail in Chapter 4 of this feature. So now it was time to add my developer fluid and run over to my second home – the dark room – to see if my western blot had worked or not.

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2:40pm – So, this morning I started preparing my ChIP samples to analyse whether I had chopped up my chromatin enough. And we analyse this by running the samples on a gel! Now – if you have read my other blogs in this feature, this might seem a little familiar to you! Back in Chapter 1 I showed you how I start a Western blot and run a gel to separate proteins. Well, this is what I am doing here but with a different type of gel. Proteins are much, much bigger in size compared to DNA so this gel is thicker and has smaller ‘holes’ so even something as small as DNA can be separated by how long it is. But much like the gels I use for Western blotting, I still have to make the gels which is what I am doing here.

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2:42pm – This particular gel is made by adding some powder called agarose to a buffer and then heating it in a microwave to help the powder to dissolve.

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2:46pm – Once the agarose was dissolved and the solution had been cooled slightly, the liquid was poured into the mould, a comb added so there was spaces to add my samples later on and it was allowed to set.

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2:53pm – While I am waiting for my gel to set, my Western blot had worked so it was time to probe it for beta actin expression. This protein’s expression stays the same no matter what conditions you inflict on your cells because it makes up part of your cell’s skeleton – called the cytoskeleton – and it helps to stop your cell caving it on itself. So it’s expression never changes because your cell always needs the same amount of actin. But we probe for it’s expression in a Western blot as it is our housekeeping gene. It checks that we have loaded the same amount of protein per sample and so any changes we see in the expression of our protein of interest is sue to some biological reason and not just because I accidentally loaded more protein into one well compared to another.

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3:07pm – Gel is all set. Samples were loaded in the well left by removing the comb which you can see with the green rectangles in the gel. And we are ready to click GO and let the DNA separate by size just like the proteins do in a Western blot.
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3:16pm – While that is running it is time to grab a (very) late lunch! Didn’t bring any lunch with me from home so popped across to the shop! Followed by the obligatory daily Facebook browse whilst munching away at my desk and stopping my stomach from rumbling anymore!

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4:15pm – Gel has finished running so now it is time to image my gel and see whether my DNA has been chopped up enough. So when I was making the gel I added in a dye that binds to DNA and then glows under UV light to reveal where my DNA is in the gel. Here, I’ve put my gel on a UV light box which will show me those all important results.

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4:18pm – One good result and one bad result! So the two columns on the left hand side are my size markers. So I need to run these alongside my samples to know what size the DNA is otherwise it would have been pointless running my gel. The two columns on the right are my samples. They both have basically appeared as smears because when I chop up my DNA for the ChIP assay it is totally random so in theory there is all different sizes of all different sequences shown here. But you can see the right hand sample shows a bigger smear which goes higher up the gel. The higher up the gel, the bigger the pieces of DNA. So unfortunately this sample has not chopped up my DNA into small enough pieces compared to the sample on the left.

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4:27pm – So although one of my samples hasn’t been chopped up enough, I thought it was probably best to measure the DNA concentration in both samples in case I can use it, or I can chop up the DNA some more. So we do this using a spectrophotometer called the Nanodrop. This tells you how much DNA is in the sample by measuring how much UV light is absorbed at certain wavelengths.

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5:06pm – So today I am running very behind schedule due to both meetings over running this morning – but I’ll soldier on as science never stops! Spending a few minutes writing up my lab book, catching up on emails, ordering reagents and labelling my Western blots ready for analysis.

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5:21pm – It’s that time of day again – feeding time! For any newbies to my blog I work on embryonic stem cells and they are proper divas of the cell world! We try and keep them happy by feeding them every single day so they don’t differentiate! I have written a post before about feeding my cells so check that out here if you want to know some more about that!

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5:43pm – All lab work is done for the day! But now for the paperwork! I’ve got to write up everything in my lab book and also put any new data into my data file so I can make graphs and test for significance! But I am also quite a visual learner so after all the discussion I had with my supervisor in our meeting this morning, I wanted to put that into more of a diagram for both the cell types I am working on to compare similarities and differences. I also wanted to map out the gaps I have and think about the experiments I need to finish that or at least start finding out what is going on in these pesky cells!

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5:50pm – Home time! Very glad for my 30 second walk home right now! Really tired today!

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6:46pm – So after a bit of a binge watching crap on TV, dinner is prepped and in the oven so I thought I would try and be a little productive this evening. I’m going on holiday next week 🙂 so thought it was about time to check out what clothes I had, and more importantly which of those fit me, and started to make piles of shoes, toiletries and other things I might need to bring. I finished with starting to prepare my hand luggage pile which is going to go in my this new backpack I bought and am actually in love with!

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8:22pm – Dinner eaten! Putting off doing the washing up by watching the Masters! Chilling for the rest of the evening before heading back into the lab tomorrow 🙂

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What is a typical day like for you and your science research?Please share your stories so anyone who reads this blog can see how varied a scientist’s day can be! It is not lab 9am-5pm Monday to Friday.

I hope you enjoyed another insight into my life as a PhD student. Please feel free to ask my any questions you might have about what I’ve written about today or my work in general if you like.

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Please don’t forget to keep up to date on all my new blog posts, all the latest news and more! Find me and Soph talks Science on Facebook, Twitter and Instagram.

A day in the life of a PhD student

A day in the life of a PhD student. Chapter 4.

Hello and welcome to yet another insight into my daily life as a PhD student in a stem cell lab!

After a slow January with cells and experiments, February is here and the incubator is overflowing with cells – mainly for my experiments actually :/ so I thought it was time to update you with another day in the life of a PhD student post!

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7:42 am – Alarm goes! Time to wake up and get to it! Today I wasn’t heading straight into the lab. I had some ‘admin’ to sort out at home first and actually having breakfast – which is basically unheard of for me!

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10:14 am – Finally made it to work! The joys of working in academia – means I can roll into work at this time if I need to! So, to start off my working day, it was the usual checking emails, labelling any experiments I had finished the previous day etc. I’m also trying to write a guest blog post so I had that open ready to write during all the incubation steps I had during my experiments for the day – watch this space for that guest blog post being published soon!

But it was time to actually face the lab and doing experiments. So today I embark on the second day of our Western blotting protocol. I’ve shown you the first day way back in Chapter 1 of this series but now you can get a flavour of what the next steps after that were. So my membranes have been in primary antibody overnight so we wash our membranes first thing in the morning to remove any unbound antibody and then add a secondary antibody. These antibodies recognise the primary antibody so increase the intensity of our protein band.

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11:28am – I get an hour long break now from the Western blot! But I’m starting my second experiment of the day. I want to do an immunostaining on my cancer stem cells to see whether they are expressing my protein of interest and it’s the method of how I get the blue and green images I have shown in my previous ‘Cellfie’ of the month blog posts. And if you want to learn more about the cancer stem cells I’m researching check out February’s ‘Cellfie’ of the month. I won’t go into the details of what I have done for this technique as I’ve gone through it before – but if you’re new to my blog or missed it just follow this here but it’s basically another technique I use to see where my protein of interest is expressed in my cells using antibodies. It uses the same principle as Western blotting!

12:36pm – I seem to be doing too many experiments for the one shaker we have in the lab. I’ll just hope noone else needs to use it :/ But the primary antibodies have been added to my immunocytochemistry plates and they are now binding to the proteins in my cells in the dark. And the secondary antibody has been washed off the membrane now and it’s time to develop the blot!

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12:52pm – The set up for Western blot development in our lab is old school! We use X-ray films and the set up takes up a lot of space! So basically – on our membranes are a series of protein bands that are all separated by size by they are invisible at the moment! The development stage is where we make these bands visible but hopefully we will only get the one or two bands appear that are specific to the protein we are interested in. Fingers crossed that the protein band that contains our protein of interest has been bound by the primary antibody and now all of those primary antibodies have been bound by a secondary antibody.

On the end of our secondary antibody though is a tag or a label and when we add our detector fluid this is going to switch on that tag which will show us where on our membrane the antibodies have bound – which should be where our protein is!

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1:02pm – Detector fluid added and the clock has started! The tag on the end of the secondary antibody will only be switched on for a short while so we need to use the X-ray film to see where they are bound before it turns off again!

And we do this in the dark room! And it is where I spend about 99.99% of my lab time – or at least it feels like I spend that amount of time in here! Now this might remind you of films where characters are sat under some red light developing photographs? That is basically what I try to achieve every time I go in here except I’m developing a picture of my protein bands using the Xray film! There are lots of more high tech ways to develop Western  blots now – maybe some of you reading this do it a different way, if you do please comment below so others can learn about the way you do it 🙂 – but we stick to this method as it is the best for the stem cells we are researching!

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1:37pm – After a host of different exposure times and quite possible different membranes if I’m looking at different proteins – this is what I get! A small piece of blue xray film which has black bands on it! These are those invisible protein bands I’ve been telling you about but you can now see them!

For this particular experiment I was looking at four different samples, hence you can see four bands horizontally – one for each sample. The same amount of protein has been added to the gel for each sample so some bands appear darker than others because there is more of that protein in that sample compared to the other ones!

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2:02pm – Back in the main lab now and time to add the secondary antibody to my immunostaining plates. The plates are inside the boxes – I promise I’m not eating my lunch in the lab!

But also, we need to check that the differences in the band intensity from my Western blot are due to a biological reason and not just because I loaded the wrong amount. So I’ve now added my membranes to an antibody which will bind to what we call a ‘housekeeping gene’. What this means is that it recognises a protein that doesn’t change expression between cells no matter what conditions we change! So if the bands from this protein are the same, then we know the differences in the bands we saw before are due to a biolgical reason!

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2:38pm – I told you! No lunch in the lab, instead I have a break in my Western blot and my immunostaining now which means I can actually get some food! Thank goodness as my stomach was starting to rumble quite loudly by this point!

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3:18pm – Secondary antibody step is now complete for the  immunostaining. Now we need to stain the nuclei of our cells using the DAPI stain I explained in my first ever Cellfie of the month post! Once that is done, the plates are stored in the fridge until I have some time to take some images!

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3:43pm – Back to the dark room I go! Time to see if our ‘housekeeping gene’ bands look about the same level. 5 minutes later – I have more pieces of film to add to my ever growing collection! And the bands look good! We have a biological effect 🙂

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4:02pm – Time to label my pieces of Xray film up so I know what samples these bands are from and what protein I was looking at so I can quantify the expression between my samples later! I also spent a bit of time writing a section of this guest blog post I have been drafting.

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4:43pm – Feeding time in the lab again! So my stem cells have been fed in a different lab but now I’m looking after my cancer stem cells. If we kept feeding and feeding our cells they would keep growing and growing and eventually they would run out of space in the tissue culture flasks or plates that they are in and more than likely die. So in order to keep them growing, we split them every few days. This basically means that I unstick them from the bottom of their flasks and only move half of them into a new flask which means there are less cells in the flask but they have more space now to keep growing!

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5:20pm – This time is for my end of day admin! I have done the quantification of my Western blot which has shown me some exciting results 🙂 which I would love to share but you’ll have to wait for my publication to see 🙂 And then everything I’ve done in the lab today gets written up into my lab book, followed by a quick check of my emails before turning the computer off and heading home!

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6:56pm – I wasn’t home for long though! In the door, quick change and back out the door as I need to get a gym session in! I’ve tried to be a lot better this year with the health and exercise malarkey! So far it seems to be going quite well. I’ve also found that I actually quite enjoy it when I’m there – the problem is getting me there! I’ve also found it’s a good stress reliever! As a very busy PhD student, it is a good way for me to release some excess energy before heading back home and can actually chill for the night!

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7:56pm – Workout done! Walk home to burn those extra few calories! Time to eat! And probably do a bit more work on my guest blog post, or maybe I’ll just chill and watch some TV.

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My days are definitely getting busier now and they are definitely getting longer with all my lab work and other scicomm commitments I’m starting! But hopefully I will be organised and manage it all! But I would much prefer to be busy than not have anything to do for days on end.

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What is a typical day like for you and your science research? Please share your stories so anyone who reads this blog can see how varied a scientist’s day can be! It is not lab 9am-5pm Monday to Friday.

I hope you enjoyed another insight into my life as a PhD student. Please feel free to ask my any questions you might have about what I’ve written about today or my work in general if you like.

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Please don’t forget to keep up to date on all my new blog posts, all the latest news and more! Find me and Soph talks Science on Facebook, Twitter and Instagram.

A day in the life of a PhD student, Science & me

My first steps to inspiring the new generation of scientists.

PhDs are full of amazing opportunities and memorable moments – but this one I didnt expect to have. The opportunity to teach high school students about me, my lab life and my research!

I have always said that I could NEVER be a teacher – but after today I feel like maybe I could. So Ive also shown you as part of my blog certain ‘days in the life of a PhD’ which so far have only shown different days in the lab – so although this post isnt the same format I wanted to show that some of my days can be soent at training courses – so today I spent my day at a ‘Meet the Scientist’ training day with the LifeLab at the Univeristy of Southampton and started my journey to become a STEM ambassador.

The LifeLab in Southampton opens their doors to Year 9 students (13-14 years old) and is a fully functional lab that allows the students to carry out a variety of experiments from taking their own blood pressure to gel electrophoresis!! But the part of their day they find the most interesting is the ‘Meet the Scientist’ session where they have an opportunity to meet two scientists and discuss their research with them.

So as part of my blog is to try and inspire the younger generation and future generation of scientists I jumped at the chance to sign up to these opportunities and complete this training to boost my confidence about carrying out a ‘Meet the Scientist’ session by myself with a bunch of teenagers – a thought that at the start of the day made me feel incredibly anxious.

It was a training day I thoroughly enjoyed – not something you often hear from someones who has spent their whole day on a course – but it was great!

But there was one aspect I want to share with you! We were challenged to perform a 2 minute elevator pitch to tell the students who we all were, why we got into science, what we actually do and why they should be interested! Luckily I managed to pull on my 3 minute thesis training for this so I felt quietly confident. But next we had to condense that into just 30 seconds for a competition! Everyone in the session stood up and shared their 39 second introduction and everyone else in the session wrote down on sticky notes a question they would ask from that 3o second intro! Here are some of the questions I got:

I loved doing the 3 minute thesis challenge but really enjoyed doing it in 30 seconds so I thought I would extend the challenge to you my readers. I will write what my 30 second intro was and I want you to ask questions that you would ask from that. I want to say at this point thay there are NO stupid questions. Just get involved and ask a question!

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‘Hi. Im Sophie and Im a PhD student here in Southampton. I work with some cells called embryonic stem cells. These cells are really really special and unique because they can make any cell type that you find in your body! Think of them like the blank tiles you use in scrabble – you can use them as any letter of the alphabet. This makes these stem cells incredibly powerful for future medicine because we could make skin cells to treat burns patients or even brain cells to treat Alzheimers and dementia. In fact, we could make any type of cell that we want or are missing’.

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Above are some of the more interesting questions I received back from the rest of the group to help you with your questions. But now its over to you – what would you ask me??

So Ive taken the first steps towards doing some teaching and getting hands on with inspiring younger students to choose science. All I need to do now is wait for a session with a school and prepare all the crazy prop ideas I thought up today to help with my session. Im talking paper mache blastocysts and outfits for stem cells!!

S.x

A day in the life of a PhD student

A day in the life of a PhD student. Chapter 3.

Christmas is over and now it’s time to head back to studying, researching and working! That daunting early morning alarm that you haven’t heard for weeks, cold and wet mornings combined with spending too much time on my first day back in the freezers is not something I want to be doing to try and get back into the swing of things – but how should I go about it? Ease myself back in? Or throw myself back in? Definitely slow and steady this year. So, I thought I would show you a slow day in the life of a PhD student – the first day back after Christmas.

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8:20am – Definitely did not want to get up this morning! So it was a much later start than usual, plus it’s always that little bit easier getting out of bed if there is light coming in through the window.

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8:55am – Packing time! Making sure I have all my new stationary supplies, diary, laptop, thesis and most importantly, lunch!

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9:15am – Sitting at my desk which seems like quite a surreal feeling considering I’ve had nearly a month off with Christmas and hospital etc. But I do like a routine, so I will be glad to be back doing something productive rather than not being able to move a lot like I was before Christmas. First job – unpack, organise desk and check emails! Luckily I have been checking them on odd days over the holidays so I didn’t have as many to deal with this morning as I would have done.

10:00am – Due to my sickness before Christmas, I was way behind on my lab book. Luckily I had made quick notes of what I did on each day and what my fellow lab mates had done for me, so next job was to decipher them and get my lab book up to date with all the experiments I did and the samples I collected. Then the more tricky job was to find where the samples were that others had collected for me.

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11:34am – FOUND THEM! It was much easier than I was anticipating thanks to an organised past me and helpful lab mates who had left me notes saying where they had left my samples. So, I popped them on some ice to thaw so I could extract the protein from them and do a Bradford assay which I have shown you on a previous day in the life of a PhD student chapter.

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12:31pm – Another main priority I had today was to get some cells out of the freezer and get them growing so I could start doing some experiments again. Our lab tech was preparing the stem cell stocks that the whole lab use, so today I took some of the cancer stem cells out that I and a few others use. So after running round the lab turning everything back on again and letting it warm up, I got some cancer stem cells out of the liquid nitrogen stores and transported on some dry ice just before thawing. I took it upon myself to pour some water over the dry ice (after my cells had been taken out!) to take a much cooler picture rather than just a vial in a box full of ice! Yawn! This looks so much more exciting!

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12:41pm – The key to thawing cells is to do it as quickly as possible! My cancer stem cells were frozen down in a freezing solution before Christmas before storage – but if the cells are in that solution and not frozen, they don’t like it and it will start to kill them off. So, I have a few minutes to get my cells from -80C to 37C and get them out of the freezing solution! The vial of cells is put into the water bath until the cells have thawed. We then mix them with some more media and spin that mixture in a centrifuge that spins it 1500 times per minute!! After a few minutes, there is a pellet of cells at the bottom of my tube and the liquid sat on top. That liquid contains the freezing solution so we pour that off and then mix the cell pellet with some more media before putting it into one of our flask to let them grow. Hopefully I did it quick enough! I will find out tomorrow when I check on my cells – if they are all stuck down in the flask it means I did a good job at freezing them and unfreezing them quickly. If there are lots of cells floating – it means a lot of cells have died and maybe I was too slow in the freezing or thawing. But the good news is that these are cancer stem cells and in comparison to the embryonic stem cells, they are really easy to grow!

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1:10pm – Time to extract my protein from my samples! Feels very weird holding a pipette in my hand for after so long! Luckily I haven’t forgotten how! We lyse the cells or break them up using a process called sonication. As we do this in the water bath, there are high frequency vibrations that agitate the cells and cause them to break up releasing the protein locked inside! Much like my cells were mixed in with the freezing solution, my protein is mixed in here too – so I need to spin my samples in the centrifuge again but this time they need to be spun about 10,000 times per minute!! However, this time I do still get a pellet at the bottom of my tube surrounded by some liquid, but this time we want to get rid of the pellet and keep the surrounding solution. It is different this time compared to using my cells is because of the speed the centrifuge and the size of the thing we are interested in. So, our cells are quite big in the grand scheme of things and so will pellet at the bottom of the tube even at slower speeds. Cell debris, which is what we are getting here when we isolate the protein from our samples, is smaller than whole cells, so you need to spin the centrifuge even faster. However, proteins are very small! So the speed we have been spinning at is not fast enough to force the proteins to the bottom of the tube to make a pellet, so they float around in the liquid still. We would need speeds much much faster than 10,000 a minute to force the proteins into a pellet!

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1:52pm – time for another Bradford assay, but my first Bradford assay of 2017 🙂 I’ve talked you through this technique before in a previous chapter here, but in short I have just extracted the protein from my samples, so this allows me to estimate how much protein is in my samples. And from the dark blue colour in all the wells on the right, it means there is lots of protein in my samples 🙂

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2:09pm – Need to get back into the habit of keeping my lab book up to date now. So I have got all the data from today and processed it, so making sure I write about my Bradford assay and cells in detail!! and before I forget what I did!

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2:22pm – One of my science New Years resolutions was a challenge to read 230 papers this year – one for each working day. So – the first day back and the first paper. I work on embryonic stem cells and am about to start looking at chromatin state and methylation so I thought this would be useful for me and the new stage I’m about to start (as soon as the cells are up and running! :/)

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3:01pm – After neglecting my thesis all Christmas and my transfer viva on Friday, it is probably time that I give this a read. I’ve got some more data since submitting my thesis so I have all my new figures ready, just need to read through and get prepared for any questions I may get asked. Very anxious about this – so need to get more prepared!

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5:07pm – 2 hours of viva prep done but still don’t feel like I have achieved much and don’t know enough. So I’m off home to continue reading and hopefully some of the information will be retained. Fingers crossed! But should probably get back to it! Head down and prep, prep, prep!

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Definitely a nice, slow and easy day to get back into the swing of things after the holidays. How was everyone’s first day back at work? Did you achieve much? I imagine everyone is back at work by now, but what are your tips for easing back into your routine after the festive period?

S.x

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A day in the life of a PhD student

A day in the life of a PhD student. Chapter 2.

It’s most definitely been a while since I showed you what a typical day for me as a PhD student is like. So, since Chapter 1. I have finished all the experiments I needed for my transfer thesis, written that in full and had my transfer viva date set. Scary!

One of the main reasons behind this mini series was to show you the variation of my days – so the day I picked to share with you in Chapter 2 could not have been more different to Chapter 1. I’ve not been in the lab much recently due to my writing commitments and I also need to prepare for the next stage of my research – which at the moment is involving A LOT of waiting!

As I’ve said previously, these blogs are going to be personal to me and are not reflective of every single PhD in every single field. It’s all about the variation!

7:45am – Far too dark and far too early to be getting out of bed! But obviously I need to drag myself out of bed to get all those ‘morning jobs’ done before heading to work just like anybody else 🙂
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9:15am – Arrived back at my desk for another day of staring at screens! Checking emails, grabbing some tea (as our office is freezing!) and a standard morning natter with the lab gals! To be honest, I was probably just delaying getting on with any work!
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9:52am – Couldn’t delay any longer – so time to get down to some work! The next stage of my experiments is going to include some chromatin immunoprecipitation experiments or more affectionately known as ChIP. I’ve never done this technique before so I’m quite excited to learn something new – but it does come with a lot of planning, ordering and then waiting! This morning kicked off with getting quotes for reagents, ordering reagents, and then designing the probes and primers that are specific to the region of DNA that I’m interested in.
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11:33am – And I am still going! All the reagents I need have been ordered by now and primers designed! The rest of the morning involved writing a new ChIP protocol for me 🙂 and all the boring but necessary risk assessments that come with that! But this has been helpful to actually go through the protocol in full before I give it a go, so I at least sort of know what I’m supposed to be doing.

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12:59pm – Time to do something in the lab today I think! So, as well as starting the new set of experiments for my PhD, I want to do a few more experiments to support the results I already have. Today I’m trying to optimise the conditions for a lactate assay as I’m interested in stem cell metabolism. The main aim for this metabolic assay is to see if the amount of lactate that is produced through glycolysis changes in my stem cells in response to the different conditions I subject them to.
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1:50pm – Reading the numbers from my assay and realising that the conditions I have tried are not good enough 😦 But as I have all the reagents thawed on ice already, I thought I’d try it again using slightly different conditions.
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3:43pm – Second repeat done! Reading of the numbers looked good! So, I tried to analyse the experiment in full. It is the first time I’ve done this particular experiment so apart from adjusting conditions in the lab, I have had to optimise the best way to calculate the data from that. The trend is definitely the result I wanted to see which is a bonus, but I know there were steps in the method that I could do better to improve these results, so as it was a trial – these results won’t be used but it has taught me some valuable tips and tricks for when I start the next repeat.
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3:49pm – You can probably guess what time of the day comes next – CELL CULTURE 🙂 So, as you might know by now, as well as stem cells, I do a bit of work on cancer stem cells – but these don’t need feeding every day. Today was one of those days where they didn’t need feeding and didn’t need splitting! So, after a quick look under the microscope, I didn’t need to do anything else with these today!
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3:51pm – A quick hop across to our stem cell lab revealed I had a bit of a problem 😦 Looking at my stem cells under the microscope showed they had an infection 😦 which means they have to be thrown away and I have to go scrounging around my lab mates to see if they have some spare wells that I can split myself a new plate of cells from! Luckily there was, but not today – so experiments were not delayed too much!

As I had no cells to feed, I spent some time setting up the feeder-free plates and anything else I may need to start the ‘proper’ lactate assays that I talked about before!
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5:13pm – After writing everything up in my lab book and writing tomorrow’s ‘To Do’ list, I headed back home. A quick change into some slouchy joggers and making hot chocolate topped with cream and marshmallows because it is that time of year and it’s cold outside, and its time to sit down and do some editing to an article I’m writing (watch this space!).
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6:37pm – Just over an hour of editing done so think it’s time to call it a day on that! Time now to get some food and sit down for a long over-due TV binge of the Walking Dead! I am seriously behind so no spoilers please!
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So, as I hope you can see even being a lab based PhD student doesn’t mean I am in the lab 24 hours a day, 7 days a week! There is a fair bit of ‘paperwork’ that comes with it! Now is just a matter of waiting for my orders to arrive to start new experiments and in the meantime practice my writing through blogging and my articles and do any helpful experiments for my thesis 🙂

Hopefully this has given you another idea about what I might get up to in a working day! Or maybe it’s got you intrigued, so I hope you are looking forward to the next post in this series but feel free to ask me any questions in the mean time. I’d be more than happy to chat to you about it ☺️

But that’s another day done, and another step closer to finishing my PhD 😛

S.x

Find me and Soph talks Science on Facebook, Twitter and Instagram.

A day in the life of a PhD student

A day in the life of a PhD student. Chapter 1.

Since my I won my first science prize!!! …. well sort of! blog post all the way back in February, I’ve actually won a science prize! It was another three minute thesis competition – but it was the actual university- wide competition where I won the audience prize within my Faculty’s heat- so I must have some sort of talent for trying to explain my research to a general audience as they liked it 🙂

I do try and explain what I do, but every time I visit home there is ALWAYS someone who wants to know the details. Now most people I know back home already know that I’m doing a PhD in stem cell research, so that’s not the question they ask me. They are more interested in what I actually do in a typical day – which is generally quite hard to describe as it is so varied! I imagine most of my friends and family think I’m leading this glamorous lab lifestyle where I’m constantly doing more and more experiments with no issues, and that each and every day I’m one step closer to finding a cure for cancer or that big discovery that is going to change the world. But unfortunately, it is quite the opposite! A day in the life of a PhD student is typically a long, drawn out fight with cells and equipment to get experiments to work. And this is repeated over and over again until you finally get that one day where everything fits into place! Everything works, you have your EUREKA! moment and it makes up for all those other days!

Now I’m probably painting what I do in a really bad light! It is not that bad, I promise! It’s frustrating, yes! But I do love it!

 

So I thought it would be fun to start a new little series called ‘A day in the life of a PhD student’ and I will pick a few different days to try and demonstrate how varied my days can be whilst giving you a taste for it. Obviously, these blogs are going to be personal to me and are not reflective of every single PhD in every single field. It’s all about variation!

 

A typical day starts around 7:30-8am when I wake up usually depending on how much I have to do in the lab that day, and how long it takes me to actually get up 😛 I conveniently live (literally!) a one minute walk away from work so I don’t have to get up extra early to travel etc. I usually get into the office about 9am. First job – look at the ‘To Do’ list, go get some ice and start ‘defrosting’ the samples that I need for my first experiment of the day – a Western blot. The next half hour or so is spent waiting for samples to thaw, checking any emails, setting up the rest of the equipment I need for my Western blot and preparing anything else I might need for later experiments.

9:19am and we are ready to embark on day 1 of my two day Western blot protocol. Western blotting in simpler terms is a technique I use nearly every day which involves loading my samples into a gel and seperating them by size. Then, using antibodies, I can pick out my protein of interest to measure how much there is in each of my samples.

So the first step is to make my gels and allow them to set which comes with its own issues! While they are setting I usually prepare my samples ready to load. Before the gels have set, we add a comb into the top so after they have set, it gives us gaps in the gel to load my samples into.

Gels set. Check.

Samples prepared and loaded. Check.

GO! GO! GO!

So, by 10:49am my samples are slowly moving through the gel and starting to seperating by size, which you can see in the photo above. As well as loading my samples, I also load a marker into one of the wells to run alongside my samples. This helps me to determine when to stop the seperating, as it shows me where a protein of a certain size will be roughly on the gel. But this seperating stage could take anything from an hour to two and a half hours!!!!


So while I’m waiting for my samples, I need to make up new buffers and solutions I need for most of the experiments I do. This really isn’t an exciting task but it’s just one of those things that needs to be done. It involves just weighing out different combinations of chemicals, mixing them usually in water and then checking their pH, or their acidity, and adjusting that if necessary.


12:04pm and it’s time for stage two of day one of the Western blot 💪🏼 This is the transfer stage where we want to move the proteins from the gel onto a membrane – which just looks like a bit of paper! This also keeps the proteins in the same position on the membrane as the gel, so the bigger proteins will be at the top and the smaller ones towards the bottom! This stage needs to be left for at least two hours – which means it is lunchtime! ☺️

12:35pm means food! Good job really as my stomach had started to rumble! Alongside stuffing my face, I scrolled aimlessly through Facebook and started doing some research for an article I want to write for Signal to Noise magazine. Check them out here! Or on Twitter @Signal2NoiseMag


13:59pm and I’ve been back in the lab and finished my next task – the Bradford assay. The aim of this is to work out how much protein is in my samples. I mix some of the Bradford reagent with some of my sample and it turns from brown to blue – so the more protein there is in my sample, the stronger the blue colour. You can see this with the two columns on the left in the photo. These are my standards which increase in concentration hence you can see them getting bluer and bluer!


If you had read my previous post Feeding time in the lab then you will remember that I work with embryonic stem cells and they need feeding every single day! So 14:32 is cell culture time! This time is spent just feeding my cells, setting up siRNA experiments and just the general stuff we need to do to be able to keep out cells growing happily!

As well as my work on embryonic stem cells, I also do a bit of work on some cancer cells – called teratocarcinoma cells. As with all cells these still need feeding but only every 2-3 days, so they are a bit easier to look after as they don’t need as much care and attention! So at 15:28 these cells again needed feeding today and I collected some protein samples from them, which I will eventually test in a Bradford assay followed by another Western blot!!

16:04 and it’s time to finish day 1 of the Western blot! My membranes that I transferred my protein onto earlier in the day are put in these tubes that have my antibodies in. They are put on this roller overnight to allow the antibodies to stick to my protein of interest so I can detect them tomorrow! I have tried not to bore you with loads of details about the Western blot and all the different stages, but hopefully you have a feeling for some of the steps. If you want to learn more about the Western blot, please feel free to get in touch and ask questions! And hopefully I can show day 2 of the Western blot in another later blog post in this mini series!

16:27 and it’s probably a bit late to start anything else today, so it’s time to head back to the office and write up everything that I’ve done today in my lab book, check emails again and prepare a ‘To Do’ list for tomorrow.

For me this is a fairly busy day, but when I am busy the time flies away. There was so many other things on my ‘To Do’ list that I wanted to get done today but time ran away from me so they are on tomorrow’s ‘To Do’ list now!! But it’s home time for today at about 5.30pm!

Hopefully this has given you a bit of an idea about what I might get up to in a working day! And maybe it’s got you intrigued, so I hope you are looking forward to the next post in this series but feel free to ask me any questions in the mean time. I’d be more than happy to chat to you about it ☺️

But that’s another day done, and another step closer to finishing my PhD 😛

S.x