Starting up in science – Nature.com
When Ali talks about the brain, her eyes widen and sparkle with child-like glee. “All cells are special, but I love neurons the most,” she says. “And they have to function your whole life. It’s crazy. It kind of gives you vertigo, thinking about all this stuff going on in your own cells.”
In every one of these vertigo-inducing neurons, a fleet of motor proteins ensures the safe passage of cargo from the cell’s main body down its axon, or nerve fibre, and back again. That cellular shuttle system is crucial because it supplies materials to the ends of the axon, where electrical signals jump from one neuron to another.
Inside neurons, the motor proteins travel along tracks called microtubules. For some long neurons in the spinal cord, the journey from end to end could take two weeks. When motor proteins fail to do their work, as they do in motor neuron disease, the effects on the network can be devastating.
Ali wants to know how these proteins load and lug their precious cargo. They can carry freight many times their size — large organelles such as mitochondria, or proteins contained in bubbles called vesicles. One class of motor protein called kinesins look like upside-down Ys, and their two ‘legs’ plod along the microtubules in eight-nanometre steps, shuttling newly made components to the ends of the axon.
Ali knows that different cargos can travel to the ends of axons at very different rates. But the kinesin that does the hauling moves forwards at an almost constant speed. Ali wants to understand how kinesin activates — or loads its cargo — and how that sets the pace of the journey. If she can do that, she can take a stab at working out how the process breaks down in disease.
She can just about see these proteins at work in single neurons in a dish, but it’s hard to observe them properly. Ali’s dream microscope, which would allow her to track motor proteins as they carry cargo in live neurons, is a big part of her grant application and costs a quarter of a million pounds. “£250k is a lot of money, but it’s a lot of microscope,” she says. “I always think of the money as science tokens — ‘I can buy this much science’.”
For now, she is having to settle for putting the proteins under a shared microscope and watching them float freely in fluid, spying on them as they open and close like the legs of synchronized swimmers.
Ali describes all of this to the judges in her pitch for the Sir Henry Dale Fellowship at Wellcome in June 2018, outlining how she plans to study kinesin and what she needs to make it happen. Afterwards, Ali recalls, there wasn’t much time to take stock of how it had gone because Dan had a deadline a few days later. “I had to finish my interview, and then sort of drop everything to make sure that I was covering everything at home while Dan was finishing his grant application,” she says.
A few weeks after her interview, Ali checks her phone after a lab meeting: “And literally the first thing I saw was this e-mail in my inbox. And I just knew, even though I hadn’t seen the content of it, that it was negative.”
She forces herself to read the e-mail, which is brief and confirms her fear: she hasn’t got the fellowship. Then she calls Dan. “And then I ran away and had some lunch. And a big piece of chocolate brownie and a small cry and got back to work again.”
Ali is immediately pragmatic about what to do next. She knows she can apply to other funding bodies, and probably to the same fellowship programme, which she is most familiar with. She knows her weak spots. “Even though I can do all this stuff, I don’t necessarily project impermeable confidence. When you’re trying to essentially give a pitch and get people on board with your vision … you kind of have to be bullet-proof in the confidence department.”
But it’s hard to project that confidence when you know your job is at stake. Ali joined SITraN on a three-year, fixed-term contract and must pass her probation to convert it to an open-ended job. The main way to pass is to win a grant that can support the lab, and she fears she’ll be let go if she doesn’t get a cash infusion.
At lunch, Dan had suggested cocktails, but they’d decided to hold off until the evening. “He’s probably more upset than I am,” Ali says. “His phrase is that we win together and we lose together, and I think we get so tied up with wanting each other to succeed.”
The couple had lost together before, in 2017, when Dan applied for a Sir Henry Dale Fellowship in a previous round and didn’t get it. Dan is reworking his presentation for a second application this year, hoping that he can convince the judges to fund his work on a molecular mystery.
The enhancers that he studies reside in poorly understood regions of the genome that do not serve as templates for proteins, but instead encode snippets of RNA called enhancer RNAs.
These are molecular switchboard operators, controlling whether genes are turned on or off at just the right time and place. When the switchboard goes awry, disease can follow. Errant enhancers have been linked to conditions such as cancer and neurodegenerative diseases. This means that these RNAs could provide an attractive drug target — but to design such drugs, researchers need to know how enhancer RNAs do their job.
During his postdoc, Dan showed that some enhancer RNAs bind to a protein called CBP that turns genes on by loosening tightly packaged regions of DNA.
Now, he wants to use that as a jumping-off point to pick apart how those enhancer RNAs work. A key experiment will be to use Dan’s favourite technique — cryo-electron microscopy (cryo-EM) — to see how one particular enhancer RNA changes the structure of CBP when it binds to it. He has been hooked on cryo-EM since graduate school. “I was incredibly taken with the fact that you could look down the microscope and see individual molecules of RNA polymerase in front of you,” he says. “It’s stuff like that that really stirs your excitement in science.”
But to get to that point, there is a slew of molecular biology to be done. Dan and his team must first purify the CBP protein away from all other proteins and cellular gunk, then find the right conditions to coax it to bind to its enhancer RNAs outside the cell. All of that has to happen before Dan even touches the electron microscope and starts collecting data.
These are the crucial steps that molecular biologists sweat over — each represents an opportunity for a project to get hung up for months. The painstaking work to optimize lab conditions and troubleshoot failed experiments rarely makes it into a scientific publication, but it underlies every discovery.
It is also not captivating conversation for a three-year-old.
“Ada shouts at us now,” says Ali. “If she’s bored by the conversation, like if it’s too much work-based, she’s like, ‘What are you talking about? Stop talking.’”
“Which is a very important perspective,” says Dan.
“So we have an extra person to ensure that the work–life balance is enforced at the other end,” adds Ali.
It’s not just for Ada’s benefit that Ali and Dan avoid talking shop. “Scientifically, we’re pretty distant,” says Dan. “We’ve tried quite hard to maintain that distance so we don’t end up talking about science all the time at home.”
Both rely on high-resolution microscopy to peer into the molecular world. But that is where the similarity of their work ends. They both claim to lack the deep background to fully grasp what the other is doing.“The funny thing is, although I’m very familiar with Dan’s work, I have no context for it,” says Ali. “I keep having to ask what enhancers are.”
“Yeah, which probably means I’m not giving you a very good answer,” Dan says.
“What are enhancers again?” Ali laughs, half-serious.
“Outside the realm of the basic techniques, there’s a lot of stuff I really don’t understand about what she does,” says Dan.
They might not sell their science well to each other, but both must think hard about how best to market their work to the grant panel. Around 200 new PIs around the country submit a full application to the Sir Henry Dale scheme each year, and only about 40 will be offered a fellowship. For Dan and Ali, their best shot at keeping their fledgling labs open is to win two of those places.
Next: Good news and bad news
Read part 2 of Starting up in science.
Nature 597, 608-613 (2021)
How we found Ali and Dan: Nature journalists asked staff members across the journal for examples of scientists who were going through big changes, such as starting up new labs or institutions, moving a lab to another country or retiring. We wanted to know — in real time — what these experiences are like. We contacted several scientists to get a sense of their stories and, crucially, whether they would be open to multiple visits over years from our reporting team, based in London. This profile of Ali and Dan does not represent the journey of every new principal investigator, but many researchers will recognize aspects in their own path to independence — including moves to other countries to improve skills, having to attract funding to retain jobs, and the ‘two-body problem’, in which scientist couples seek jobs in the same location.
This article is also available as a pdf version.
Authors: Kerri Smith, Heidi Ledford, Richard Van Noorden
Additional Reporting: Benjamin Thompson
Design: Lizzy Brown, Wesley Fernandes, Kelly Krause
Original photography: Chris Maddaloni for Nature
Subeditors: Anne Haggart, Anna Callender
Podcast editors: Benjamin Thompson, Kerri Smith
Editor: Richard Monastersky
Project leader: Kerri Smith
Personal photos provided by Alison Twelvetrees and Daniel Bose.