A day in the life (second year PhD student and RA)

Hi, I am Tapan. I am in my second year of PhD and I also work as a research assistant here at KCL. I work in Simon Hughes’s lab and we are interested in understanding molecular mechanisms underlying embryonic muscle development, growth and regeneration.

We use zebrafish embryos to discover how striated muscle grows and gets repaired. We aim to apply the knowledge gained to enhance tissue repair and diminish age-related muscle weakening in the human population. My project is looking at how muscle stem cells behave during normal embryonic development. Below is an example of how my day looks like (they are not this long generally but here is how this one unfolded):

Written by Tapan Pipalia

The view ‘from my room’ is great though compared to ‘of my room’ with an allotment nearby and Wembley Stadium (red arrow) in the backdrop.

7:10 Time to get out of bed after few customary snoozes! After spending a couple of minutes reflecting on mistakes I made the previous day (:p), back to getting ready, having my breakfast and rushing out to get to work; expecting it to be a long day.

8:30
At the station, waiting for the tube (left below). Scene (right below) just before I could even take my phone out thanks to being stuffed in the carriage.

9:15 Managed to survive the peak hour rush once again! View of the Shard outside the station. The building is a prominent feature of London’s skyline and is close to our campus.

9:30 Making the classic ‘to do list’ before jumping into action.

9:40 Extracting DNA from the samples using alkali lysis method. Incubation for 20 minutes.

10:00 Preparing DNA samples from above for genotyping (figuring out if a sample carries genetic mutation of interest or not) using high resolution melt (HRM) analysis.

10:15 Setting up the run on the HRM machine. Run time 1hr 30 minutes.

Using PCR machine for DNA incubation!

HRM machine!

10:30 Back to my bench to prepare reagents/reactions for cloning which I am aiming to do tomorrow (cutting and pasting DNA sequences together) using Gibson method.

They say ‘My house is my castle’. Well, I can say the same about my bench!

12:30 Analysis of HRM results from the morning experiment.

13:00 Refuelling myself- Lunch time!

13:40 Analysis of some datasets from an experiment I did a while ago.

14:25 Confocal computer repair.

Some research assistant admin duties. We are currently having issues with a computer attached to our confocal microscope which we rely on heavily to perform high resolution imaging of zebrafish embryos. Attempted different things to get it to work normally but failed with initial attempts.

This lovely PCR machine is doing the work for me while I’m having a pizza with fellow PhD students!

16:30 PCR time. Amplifying my gene of interest to use it later for Gibson cloning mentioned above. Incubation for 3 hours.

17.30 Pizza night! Our once a month formal social event for all PhD students within the department when we get to feast on pizzas (fully paid for by the department!) and listen to a talk on wacky topics from fellow PhD students. This week’s topic: The science behind reality TV.

18.30 Analysing embryos which are two days old under a low mag microscope (left below) to screen for any gross morphological defects (right below). They were from fish pairs which were mutant for one of the genes thought to be important for muscle development. Captured a few images for reference.

9.30 Reading papers-getting hold of a protocol-requesting the paper from the interlibrary loan service

20:30 Running samples from earlier PCR on a gel. Whilst the gel was running, attempted once again to fix the confocal computer. Ugh! Close but not quite there, solved one problem but the original problem remains to be fixed.

21:50 Setting up fish crosses to get some embryos. The fish facility where we keep fish in tanks (blue coloured tanks arranged in stacks- Top left and right). A male and female fish are separated by a barrier in breeding tanks (transparent ones- bottom right and left). In the morning next day, the barrier is removed and if they mate, we get more samples to work with! Hoping these ones give me more embryos tomorrow.