Science Diaries: Three months to go

Science Diaries: Three months to go

Two months later and it’s time for another Science Diaries post. Since my last one, I’ve learnt how to create a multilevel regression statistical model  (I won’t bore you with the details!) in order to analyse my animal data sets which was a massive hurdle. As of yesterday I’ve now run all of my data (I think) through the model, so I’m a very happy girl. Here’s another snapshot of my day as a PhD student.

Onto the next phase…

0621 yoga

6:21am: The constant desk work is really starting to feel detrimental to my body despite being a very active person outside of PhD work. It’s easy for a few hours to pass whilst just sitting running the statistics model on data set after data set.  So I’ve decided to start 20 minute morning yoga sessions to improve mobility. This morning was the first one!

.

0702 breakfast7:02am: Protein porridge is my favourite way to start the day. Genuinely makes me so happy early in the morning! Sets me up for a productive day of work. A lot of science communication Twitter chitchat happens US time, so I normally combine breakfast with catching up on conversations I’ve missed overnight.

.

0836 Nipper check

8:36am: Today was another NiPPeR study on-call day. I briefly explained what this study is all about and how I’m involved in my last Science Diaries post. No deliveries over night and no women in labour ward meant it was a placenta processing-free day for me.

.

0950 meeting prep

9:50am: Every Wednesday at 10am I have a meeting with my primary supervisor. The first part of my morning was gathering all the data I had analysed over the past week so we could discus the results. We also have a kids day organised by my supervisor in a couple of weeks which I’m helping out with, so I thought I should probably swat up on what I’m supposed to be doing for it!

.

1133 supervisor meeting

11:33am: My PhD meeting is over which was really productive! We discussed my data and a few extra things I could do with it. I’m now at the point where I’ve done all the data analysis I can do for now, so it’s onto the thesis writing. This was a pretty daunting realisation! We also discussed viva dates following a conversation my supervisor had with my internal and external examiners. SCARY! It all feels a lot more real now.

.

1357 plan IG post

1:57pm: Lunch eaten and my lunchtime walk done to properly stretch those desk-bound legs! I finished my lunch break with planning my Instagram post which was all about making daily goals to stay on track, and how that helps us to feel more motivated and positive about work.

 

.   1526 amazeing placenta

3:26pm: Time for my friend Emma and I to have some filming fun! I’m currently doing an engagement and science communication internship with my department. We have various research themes and I’m filming interviews with researchers from each one. Today I was making the most of Emma having her a-MAZE-ing placenta game at work so managed to get some good footage of her for the public engagement theme. Totally love this girl, she’s mad.

.

1640 deadlines

4:40pm: Now that it’s time to write this thesis, a plan is definitely required. I’m giving myself until Christmas to hand it in, I don’t want to go into 2018 with this still looming over me. So it’s T minus three months and deadlines are getting set. It’s going to be tough but it’s the final phase now, just got to power on through and stay focussed.

.

1804 Bright Club

6:04pm: I’ve finished PhD work for the day and walked the extremely long 7 minute walk back home. So for some strange reason I’ve agreed to perform at Bright Club this Friday in my PhD city of Southampton, UK. It’s an event where researchers become comedians for the evening so I did a little bit of practice before my housemate came home. I’ve never done anything like this before so I’m a little nervous, but very excited! All the comedy sets will be going up on YouTube so I’ll hopefully be blogging about it next week and sharing the footage… if it goes well of course!

.

1943 dinner

7:43pm: Dinner time. This evening was chilli with a little bit of mushroom rice and green veg. I was trying to be healthy today but then my housemate decided to make cake, which of course I was not going to say no to. I’m looked after so well! I may never move out.

.

2013 blogging and film

8:13pm: Normally I CrossFit in the weekday evenings but I’ve started being more organised in order to push my blog further, whilst having a good balance between PhD work/blogging/fitness/social life. I always publish my blog posts on a Thursday so I’m now setting aside Wednesday evenings to write a blog post or finish bits off if I started it at the weekend. I wrote this blog post whilst watching a film on the sofa… and of course eating cake. Perfect way to blog!

.

If you want to get a good feel of what my science life is like then head over and follow my Instagram account. This is where I share my journey as a scientist and PhD student through photography and daily Instagram stories!

.

***

.

What stage are you at in your PhD/science career?

Is there anything about life in science/academia you’d like to know more about? As always I love to here from you in the comments below…

.

blog-signature

.

♥ Follow my blog to get notified on fresh content! Just enter your email above.

Connect with me on Facebook, Twitter, Instagram & LinkedIn to follow my science life.

♥ Follow my blog with Bloglovin.

Advertisements

Science Diaries: The inbetweeny stage

Science Diaries: The inbetweeny stage

.

For those of you who have read my previous blog posts or follow me on social media, you’ll know that I’m a PhD student and I finished all my lab work in December 2016. In my final week of running around like crazy getting everything finished up, I published a blog post called LabLife: the final week showcasing what a day in the life of a science PhD student was like.

.

With being out of the laboratory setting I thought why would people want to see a day in the life post without all the exciting experiments? But in actual fact the lab part is only one chapter of the PhD process, admittedly a very big one, but there is so much more to research than running experiments! There’s a lot of data handling, image processing, statistics and thesis/publication writing to do as well before we get awarded that Dr title! So I feel that this side of PhD life is important to show to those thinking of going into research, or for current researchers who like to have a nose at what others get up to!

.

So where am I at with my PhD?

Little bit of background: my research is all to do with Are you what your mother ate? I investigate how maternal diets (high-fat and vitamin D deficient) during pregnancy alter the baby’s muscle function in later life. In terms of experiments I carried out long contractile studies to test the peak force generated by the muscles, and I’ve carried out staining techniques to visualise the different types of muscle fibres and also the amount of fat accumulated in the muscle samples (changes can alter muscle function). This all means a lot of files, a lot of microscope images… and a lot of time sitting analysing all of these. I call this the inbetweeny phase – lab work is over but thesis writing isn’t quite on the radar!

It took me ages to analyse the different types of muscle fibres in all my samples as this involved counting and drawing around 1000s and 1000s of cells. That finally got done (yay!) and then I moved onto quantifying the amount of lipid accumulation in the samples. Admittedly I struggled for a while with focus and motivation (useful tips here!) as for a very active person sitting all day every day and doing the same thing day-in day-out is hard! I was also juggling other exciting science communication opportunities so it took a little longer than planned. BUT that analysis has now been completed and here is another post in the Science Diaries…

.

.

FullSizeRender 13

Alarm goes off at 6:15am. Surprisingly I was pretty good on the snooze front! I have a little scroll through Instagram and Twitter to wake myself up properly and to see what’s going on in the science world. I’m so much more productive in the mornings so I’ve been trying to shift my working day earlier. Top tip: playing to your strengths makes working so much more effective!

.

FullSizeRender 17

6:32am: Breakfast time, my favourite meal. My good ol’ trusty protein porridge to give those brain cells their much needed energy for a day in front of the computer clicking some buttons.

.

FullSizeRender 11

8:10am: Today was an on-call day for me. For a little extra cash now my PhD funding is over (super sad, I know), I process placentas when women give birth who are consented to the NiPPeR study. The study is all about nutritional intervention before and during pregnancy to maintain healthy glucose levels and offspring health. I do my 10 minute round route to check for any deliveries throughout the day. If there is a placenta my job is super simple, cut some chunks of placenta and umbilical cord, and freeze them for another scientist to analyse in the future.

.

FullSizeRender 15

9:04am: Getting through more oil red O analysis. This was the technique I used to stain my muscle samples so any fat/lipid in the tissue was stained red. I previously took multiple photos of each sample with a fancy microscope and I’m now using a programme called Fiji Image J to get the images ready for lipid area quantification. I want to know the total muscle tissue area and how much of that is made up by lipid. It’s a pretty long process, and not the most exciting!

.

FullSizeRender 18

11:00am: Tea break. Like I mentioned in my top 10 PhD survival tips, caffeine is an important necessity when it comes to doing a PhD.

.

img_1603

11:34am: Tea break over and time to check Twitter and emails before carrying on with the oil red O image analysis. Got a lot of work on and need to keep focussed? Top tip: don’t open up your emails first thing in the morning, this can put you onto a different path than you were planning on for your days work. Limit those distractions. Is it really that important that the email can’t wait until a few hours in?

.

FullSizeRender 16

1:15pm: Super duper happy as my image processing is done and now it’s time to run my macro to generate my oil red O data. I select all my files, I press “run” on the macro (piece of code I wrote telling the computer programme what to do) and I sit and wait for the computer to do its thing. How wonderful!

.

img_1610

4:43pm: After the computer gave me the numbers I wanted, I compiled all the data into a spreadsheet… and voila graphs! Science is funny, after many weeks of lab work and many days of analysis I get four graphs (each row showing the same data, just a different format). Annoyingly some of the results aren’t what I hoped for (that’s science for you) but some data (third row down in particular) is really intriguing when considering some of my other data, so that’s pretty cool!

.

img_1612

6:31pm: The daily CrossFit workout done – heavy deadlifts and some running. Time for drinks and food with friends. Accomplishing my work goal means guilt-free treats! Exercising and socialising is so important for that work-life balance, it means your life isn’t all about work and gives your body and mind that much needed time out.

.

***

 

What stage are you at in your PhD/science career?

Is there anything about life in science/academia you’d like to know more about?

Comment below!

.

blog-signature

.

Follow my blog! Just click the link in the side bar above.

Connect with me on Facebook, Twitter, Instagram and LinkedIn

Science Diaries: The final lab week

Science Diaries: The final lab week

f

Since my first blog post “Are you what your mother ate?” I’ve been working like crazy in the lab to finish my final experiments for my entire PhD (absolute madness!), and after over three years of PhD life and hard work the final lab week is here!

One of my reasons in making this blog is to give others an insight into the life of a PhD student. When I applied for my PhD I was currently doing my masters project but knew a PhD was going to be a big step up. I wanted to understand more about what it was like to do one, but couldn’t find many people’s experiences documented online. So here is is, one day in the life of one PhD student…

f

no1_img_3347-edit
Wakey wakey

After pressing snooze on my alarm a good few times and being too cosy to jump out of bed, a typical day for me starts at 6:45am. I get up, and as it’s December I go and find my advent chocolate which makes getting up that little bit easier! Porridge is always my staple breakfast as it gives me a good amount of energy to start a day in the lab. My walk into work is about 20 minutes which is great – not too far away but enough time to get fresh air and clear my mind before I’m deep in antibody calculations, immunofluorescence staining, PCR analysis and microscopy. A LOT to do!

f

no2_img_3227-edit
Work begins

Works starts nice and early at 8am (got to be productive before the necessary tea break)! First things first, check my to-do list that I made at the start of the week. Top tip – being organised and planning your week is a massive help to keeping on track and being productive amongst the craziness of a PhD. The last couple of months I’ve been doing a lot of immunofluorescence staining so I check my plan and grab the right set of samples out of the freezer and let them air dry before I start the experiment.

f

no3_img_3229-edit
Getting prepped

Whilst waiting for the samples to dry I check emails, calculate antibody dilutions and prepare the necessary buffers to use for my immunofluorescence staining.

What is immunofluorescence staining?

So my project is all about looking at how the offspring’s skeletal muscle development and function is affected by a maternal high-fat (first study) or vitamin D deficient (second study) diet. Research shows that diet can alter the type of muscle fibres that make up an individual’s muscle, so this is what this experiment is for. As a brief insight, I have cross sections of muscle samples previously cut and put onto glass slides (as you can see in the previous picture). Different muscle fibres express different types of the protein myosin heavy chain (MHC). Adding antibodies specific for these proteins and then adding a fluorescent tag to each one allows me to see which fibres are what type under the microscope, and ultimately see how the number of each type of muscle fibre changes with a normal or altered diet.

f

no4_img_3232-edit
Primary antibodies on and two hours to wait!

These primary antibodies are what attach to the specific types of MHC protein. I make two different cocktails of antibodies which are mixed with either of the two different buffers made above. One muscle sample will be incubated in three out of five primary antibodies, and another section of the same muscle will be incubated with the other two antibodies. I also have to include ‘negative controls’, these are sections of the same sample which are incubated in just the buffer without any antibodies. As there are no antibodies applied to these samples, in theory they should not fluoresce when I image the samples, and it shows that any fluorescence is due to the primary antibody attaching to the correct molecule.

f

no5_img_3274-edit
Tea break o’clock

The 11am tea break is a fundamental part of my day! My friends in the lab and I pretty much always have this without fail. Bit of caffeine and a catch up means a boost of energy and ready to go… until lunch break!

f

no6_img_3409-edit
Catch up take one: PCR analysis

Whilst waiting for my two-hour incubation to finish I catch up on other bits of work. Here I’m analysing a PCR I did a couple days before. PCR (polymerase chain reaction) is a technique that allows me to quantify how much of a specific gene is expressed in my tissue samples. Here I was looking at the gene troponin 1 – a gene important for the expression of a protein involved in muscle contraction regulation. I’m seeing a few significant differences (yay!), a point where all PhD students have a feeling of relief!

f

no7_img_3236-edit
Primary antibodies off, secondary antibodies on

After two hours, the primary antibodies are washed off with the buffers and the secondary antibodies are applied for one hour. The different secondary antibodies recognise their corresponding primary antibody and bind to them. They have a fluorophore attached and this is what makes the muscle fibres a fluorescent colour when I look at the samples down the microscope. It’s important that these are incubated with a non-see through lid as exposure of the fluorophore to light will ruin the fluorescent signal. Too much exposure to light = experiment fail.

f

no8_img_3294-edit
Catch up take two. Making pretty pictures

After my secondary antibodies have been applied, washed off after an hour and stored away ready for image analysis the next day, I catch up on some remaining image analysis from the previous day. This is all done in a dark room – how wonderful! This picture shows a typical muscle cell stained for the fibre type IIa. Using the fluorescent microscope, I change the filters to view the other fluorophores applied to the sample and therefore see the other fibre types which fluoresce in different colours. I use green, red and blue, which means pretty looking pictures!

f

no9_img_3351-edit
Me time = crossfit time

Lab work for the day done and off to crossfit I go.

A work/life balance is extremely important to me, and exercise is essential. If possible I go every weekday evening. Working out helps me stay healthy and gives me that time away from the lab to focus on something else, and relax.

After crossfit, it’s time to meet up with friends or go home and chill with some food. Day done!

******

There it is, a snapshot of one day in the lab. Admittedly I am in my last week but this has been a pretty typical day for me over the last couple months in between other experiments going on. Of course a day in the lab can be completely different to this. I had days where I’d be doing long 18-hour days due to animal studies, or shorter days in my first year when there wasn’t as many bits and pieces to do. But for those who don’t know what kind of thing us PhD students get up to, I hope this gives you a bit more of an idea!

So my lab time is up, and off I go to enjoy my Christmas holidays before I start the mammoth task of writing my thesis.

Merry Christmas everyone!

blog-signature