Profile

I live with my partner close to the University of  York where I work in a structural biology research lab. Spring is my favourite season, when the snow drops and daffodils begin to flower after being cold over winter ( a process called vernalisation).  In my spare time, I enjoy reading (sci fi, fantasy, biographies and modern fiction) watching silly TV shows and movies, playing xbox games (like Diablo3, Fallout etc) eating food from different countries, as well as walking and cycling in the outdoors. I also enjoy travelling to other countries to meet new people and explore new landscapes, cultures, histories and food.  Another major interest of mine is using art and design to display information (such as scientific data; http://tabletopwhale.com/2016/04/11/virus-trading-cards.html) in beautiful and easy-to-understand images, like the poster of virus structures.https://cdn.rcsb.org/pdb101/learn/resources/200-viruses/200-viruses-poster-ids.pdf

I work with molecules that are too small to see.  They are measured in nanometers (10^-9 m), a size scale you could call the nanoverse.  To give you an idea of how small this is, a single sheet of ordinary paper is 100, 000 nanometers thick and the molecules I work with are 10,000 times smaller than that.  I farm bacteria, a special lab strain that is not dangerous, to make these proteins for me and I use genetic engineering as a recipe to tell the bacteria what the protein should look like.  One protein looks like a donut with a hole in the middle and we are have used this molecule as a nanopore sensor to “see” what other biological molecules (DNA and protein) look like.  We use an electron microscope to take pictures of these molecules (I’ve attached some below)

and then put them into tiny holes (nanopores) in very thin metal sheets (1 nm thick, also see below)

to make a ‘hybrid’ nanopore.  Using a special machine with electrodes on either side of this thin sheet, we can measure the tiny tiny changes in electrical current that happen as DNA moves through the nanopore.  The combination of these tiny changes gives us an identifying feature (a bit like your finger print) for a particular DNA.  We hope that we can use this new technology to track the changes in DNA and proteins that happen as cancer cells develop or when a virus infects a cell.  If we understand it, we can control it.  If we can control it, we can cure it.

Normally, my day usually begins before I even leave home with the boring things like reading and answering emails and checking my schedule for meetings.  To make this more enjoyable I do it on my couch with my laptop and a cup of coffee.

When I arrive at work around 9.30 am, I check the plan I made the day before for all the lab based things I need to do.  Growing bacteria and making protein takes several days and I need to be organised to do everything in the right order and at the right time.  Some steps like growing bacteria or clearing a protein solution by spinning it at really high speeds (like a washing machine on spin cycle), or purifying in on a special machine that removes all the extra proteins

can take 1-4 hours, so it is important to get these steps going asap otherwise I will still be in the lab at 10 pm at night (not fun).Once these steps are going I can take 20 minutes for morning tea (Strong Black coffee for me) and discuss experiment problems, data analysis and what to do next with my fellow scientists.

Back to the lab to set up more experiments (tests  to see if my protein works the way it should) before going to a talk from another scientist about their work.  This is important because it keeps me thinking about new ways to do things and gives me good ideas to use in my experiments.  Sometimes these talks are over lunchtime so I only have a few minutes to gobble my lunch before going into the lecture room.  Other times my experiments are going on without me and I can take a longer lunch and chat with my co-workers.

Back to the lab, check that my bacteria are growing happily (we measure the number of cells by seeing how much light can pass through the culture liquid in a spectrophotometer – less light = lots of cells = happy culture).  If so its time to tell them to start making protein (I do this by adding a special chemical to the media) and then leave them to it until the next day.

Time to start writing up the reports from the days work, back to the lab to check how pure my portal nanopore protein is.  I do this by separating them through a jelly like material (gel) using an electric field in a special buffer that makes them all charged.  Little proteins move fast and reach the bottom, big proteins move slow and stay higher up and I can see where they are by staining them with dye.

More report writing and planning for the next days work.  I need to make sure everything is ready for the next steps of the experiments.  Time to go home, hopefully its only around 6pm, more likely it is 7 or 8.

In the Coronaverse, I am working from home because all the labs that aren’t directly working towards tests, cures or vaccines for the coronavirus SARS-CoV2 (that causes COVID-19) have been closed down.  So my day begins as usual with emails and then continues with videoconference meetings and lectures.  The rest of my day is filled with reading academic papers to stay up to date with the latest advancements, followed by analysing data so that we can understand what proteins look like (like the one below)

and writing papers to tell other people about the work we have been doing.