On an overcast morning in October 2018, Ali crosses a busy road holding a cooler full of test tubes. She transports this precious cargo once a week to the laboratory of her chief collaborator, biophysicist Tim Craggs, in the physics department at the University of Sheffield.
Their collaboration was born out of a chance meeting even before Dan and Ali started in Sheffield. During a visit to campus, Dan met Tim and learned that he had built a special type of microscope for imaging single molecules. Ali immediately saw the potential of his own work.
“I’m like ‘Yes. This is what I need,” she recalls.
So now she’s doing the ten-minute walk through town at a careful pace to bring her samples to Tim’s microscope. She is trying to develop a way to study proteins one by one that could form the basis of her career as a principal investigator (PI). Deep in the physics building, Ali enters a dimly lit room where a stainless steel table is fitted with lasers and lenses. “My son calls it an air hockey table,” Tim said, pointing to the experimental facility. It’s basically a way to spy on forms of motor proteins called kinesins.
Kinesins are shaped like long sticks that have a hinge in the middle and two feet at one end. They are too small to be seen directly. But Ali spent weeks creating kinesin proteins adorned with fluorescent labels on each end. Scientists shoot laser light through a dilute drop of cellular fluid from Ali’s test tubes. When an individual kinesin molecule drifts under the laser, its fluorescent markers absorb energy and light up. The frequency of fluorescence shows whether the motor protein is folded tightly at the hinge or stretched open in its active form. “The actual experience – don’t tell anyone – is incredibly easy,” says Tim. The hardest job, he says, is Ali’s: preparing high-quality protein samples with the right kinds of labels inside the cells.
The technique is called fluorescence resonance energy transfer microscopy (FRET) and, to Ali’s delight, it seems to work. She hopes to use it to see how individual kinesin molecules change shape when they enter cellular cargo, and then to ask what conditions inside a cell affect this process. This could be the key breakthrough that answers Ali’s burning questions about how cargo travels through neurons at different speeds and what causes this process to malfunction. But it will take months, if not years, to go from a “quick and dirty” experiment to a reproducible, high-quality protocol, Ali says.
For Ali, the collaboration with Tim and his team, which has lasted for about a year, is crucial. This means that she has access to a microscope although she has little money and other people to exchange ideas. “When you’re starting out, you’re a team of one. It’s a pretty lonely place, ”she says.
Now, 18 months later, Ali’s lab is a team of three. She has hired a doctoral student, Evie Smith, who will work full time on the FRET experiment. A final year undergraduate student Ashleigh Davey has also joined the group to work on a “neuron-on-a-chip” project, which will allow the team to observe motor proteins moving around in cells. Ali was able to negotiate a move to a larger lab space. But money is still incredibly tight. Evie is funded by a doctoral research grant, but if Ashleigh is to stay for a doctorate, Ali will need to secure a grant to support her.
Dan’s team has also grown. Several short-term students have come and gone, but doctoral student Petra Celadova is a central figure. Petra joined us in November 2017 with years of lab experience already under her belt, and quickly took charge of her own project while helping Dan set up the lab.
One of its first steps will be to use CRISPR-Cas9 gene editing technology to mutate an activator in leukemia cells, looking for mutations that alter the function of the activator RNA. Less than a year after starting her project, says Dan, Petra is already independent. “She’ll tell you what to do, which I think is a good sign in a student,” he says. “I take great pleasure when she says ‘no, that’s how we should do this’.”
Petra is also aware of the harsh realities of lab work: She hopes to have her cell lines ready by the end of the year, but she knows the research won’t necessarily fit her schedule. “In science you always think you’ll have done more than you can actually do in a year,” she says.
Hear Ali and Dan’s story in our 4-part podcast mini-series. Going through Apple podcasts | Going through Google Podcasts | Going through Spotify