Mission: possible

At first glance, the Crick’s Making Lab looks similar to the other 200 labs in the building. But look closer, and unexpected items reveal themselves: on one side of the lab, a board of tools, wires and circuit boards; on the other, scientific cupboards called ‘fume hoods’ that contain miniature plumbing, or microfluidics; at the back, 3D printers that pump out collagen instead of plastic. 

The seven-strong team, led by former industrial engineer Albane Imbert, encompass a huge range of technical skills – from bioengineering to robotics – united by a keen interest in applying these skills to biological questions. 

Together, they form one of the Crick’s 19 ‘Science Technology Platforms', teams of specialists who provide the Crick’s wider research labs with expertise and support in everything from genomics to structural biology. 

“Researchers come to us with very specific problems that are halting their ability to progress,” says Albane. “We help them tackle these challenges by applying existing technologies in new ways or by building innovative, bespoke devices. Often, this means asking the scientists to think about their experiments a bit more holistically to open doors for creativity.” 

As well as inventing bespoke solutions to current research challenges, Albane’s team run their own projects, aiming to pre-empt the kinds of questions scientists might have in the future. “We’re constantly thinking of new ways to use the state-of-the-art kit in the lab, so we can offer alternative approaches, enabling researchers to overcome limitations and even tackle questions from a completely new perspective,” she says. 

From recreated mini organ systems to 3D-printed ‘behavioural arenas’ for fruit fly larvae, the following three snapshots take a deep dive into how the Making Lab’s bespoke designs answer challenging biological questions or democratise existing technologies. 

Making Lab member Federico Nebuloni is an expert in microfluidics, which he describes as ‘mini plumbing’: manipulating tiny amounts of fluid in small channels.

He applies this principle to an emerging technology called an ‘organ-on-a-chip’, a miniature model that recreates an organ function. “The recapitulated organ system fills an area on a slide roughly the size of a pound coin,” he describes. “And it can be developed from cells taken from a specific patient to see how their genetics influences organ function.”

This technique caught the attention of researchers Paola Bonfanti and Julia Rodrigues, who work in the Crick’s Epithelial Stem Cell Biology and Regenerative Medicine lab, where they study the lining cells, or epithelia, that coat organs such as our oesophagus or airways. These are often the first line of defence against infectious bugs trying to get inside.

They are particularly interested in the genetic condition cystic fibrosis, where people can’t clear mucus in the airways, leading to repeated infections.  Although gene therapy, replacing the faulty genes causing the disease, holds promise for long-term treatment, the biggest hurdle lies in how to deliver a therapy to specific cells.

“Ideally, gene therapy for the lungs would be inhalable,” says Paola. “But there are huge challenges in delivering a drug via the airways, which act as a physical barrier to stop things getting into the lungs. There are strong immune defences against pathogens, and thick mucus that could prevent medication from being absorbed.”

Traditionally, drug development involves work with animals, but as their airways can differ from our own, including during disease processes, Paola and Julia took advantage of Federico’s expertise, working together to develop an airway-on-a-chip device.

The organ on a chip device made by the Making Lab at the Crick. Credit: Dave Guttridge. 

“The device contains two compartments separated by a thin membrane, one with epithelial cells that line the outside of the airways and one with cells that line the blood vessels surrounding the airways, called endothelial cells,” explains Federico.

Epithelial stem cells are added to the top chamber; upon exposure to instructive signals, these cells can then become any of the diverse cell types of the airways. “In the epithelial layer, this includes mucus producing cells and cilia, hair-like projections that beat to trap and move mucus,” adds Julia.

The organ-on-a-chip is also integrated into a circuit of channels that continuously supply nutrients to the cells, mimicking the way the bloodstream feeds tissues. The chip’s meticulous design allows cells to be monitored in real time using high resolution microscopy.

“We can create the chips using healthy cells or cells with cystic fibrosis mutations, which end up producing a lot more mucus,” explains Julia. “Then we can see whether further genetic editing has an effect on mucus production or cilia beating.”

For Paola, the new device opens doors for studying a whole range of diseases affecting barriers like the airways, from lung cancer to asthma to respiratory infections, especially as the models can be generated with patient derived cells that contain specific mutations.

“We could even flow through particulates found in the air to see how pollution impacts our airways, and if certain mutations make this better or worse,” she says.

Aiming to work closely with the pharmaceutical industry to produce the chips at scale, Paola and Julia believe it’s a prime example of the exciting new technologies coming online that could help reproduce human diseases in an accessible way, and reduce the number of animal studies needed before drugs enter clinical trials.

Lab lead Petr Znamenskiy is interested in brain circuitry to understand how animals perceive and navigate their environment, especially through vision.

Brain circuits in the visual cortex are made up of tens, if not hundreds, of cell types, and Petr is interested in where exactly each cell type is found in the circuit. Using a technique called ‘spatial transcriptomics’, his team can record gene expression in brain cells in a 3D tissue sample. By studying these patterns directly from the tissue, the location of cells and genes is preserved like coordinates on a map.

Petr uses a spatial transcriptomic technique called BARseq , which involves tagging transcripts – the molecular message from the gene being expressed – with a coloured dye, one letter at a time. Each transcript eventually receives its own colour barcode, which can connect its identity and location.

Alex Becalick, a member of Petr’s team, started using BARseq during his PhD to map how neurons carrying visual and other sensory information communicate.

“It’s an incredible technique, but it’s a very manual process,” he explains. “We have to image the tissue using a microscope, take it off to add chemicals to stain an individual ‘letter’, image again, add more chemicals… and so on.”

Partly to speed up their own work, and also to make the technique accessible to other labs at the Crick, Petr and Alex knew they needed to automate this arduous process so that barcodes could be read quickly and cheaply.  They reached out to bioengineer Simon Tupin in the Making Lab.

“We designed an automated system where the tissue slide stays put on the microscope, and a syringe pump dispenses chemicals before the tissue is imaged, and that step is then repeated over and over again,” Simon describes. “One of the main benefits is that the slide doesn’t leave its spot, so the images don’t get misaligned, which was an issue with doing this manually.” 

An automated system from the Making Lab at the Crick. Credit: Dave Guttridge.

Press ‘go’ and the system runs overnight, controlling temperature with a heated plate. Just eight chemicals are used to sequence barcodes for all cell types in the tissue.

“It’s been a game changer, giving time back to analyse the results,” says Petr. “It also democratises spatial transcriptomics by lowering costs and technical barriers. It’s 50 times cheaper than commercially available systems, allowing us to ask questions and do experiments that wouldn’t have been possible otherwise.”

The automated BARseq equipment now sits in the Crick’s Light Microscopy facility. “We make a lot of our developments open access,” says Simon. “So, in theory, anyone should be able to set this up. We’re hoping that research teams in other institutions could now consider using a technique often seen as too time intensive or complex.”

“I knew when I started at the Crick, I needed something bespoke,” reflects neuroscientist Michael Winding, describing his ambitious goal to map the millions of nerve connections inside fruit fly larvae brains as they work together to access food. 

Before setting up his Social Circuits and Connectomics Lab at the Crick, Michael worked on a decade-long project to map the fruit fly larvae brain – a huge feat of engineering in a field known as connectomics. At the Crick, he’s continuing to use larvae to study brain circuits behind social behaviour.

“Larvae forage together, digging into the food to eat as much as possible,” he says. “They have to come up for air, or they’ll suffocate in the food, so working together to dig a bigger hole allows them to access more. We’re interested in the brain networks behind this learnt behaviour, and what situations cause it to fail.”

Studying this cooperative behaviour meant finding a way to watch and record larval behaviour continuously. Michael originally used a smartphone to record larvae sandwiched between two microscope slides, which worked, but wasn’t very easy to repeat. So, he approached Xavi Cano Ferrer, an engineer in the Making Lab, with some drawings in a notebook to see if he could make something unique.

“I used 3D printing to build Michael a behavioural arena, known as a ‘rig’, which contains larvae in a flat environment, limiting the probability of larvae overlapping and making tracking them much easier,” explains Xavi. “The camera sits on top of transparent panels, constantly recording and storing the data so Michael and team can analyse the larvae’s behaviour.” 

But Michael didn’t just need one rig; he needed dozens. By design, Xavi’s blueprint could be printed again and again, each rig with the same dimensions. 

Michael holding a dish of fruit fry larvae, ready to be placed in a behavioural arena, known as a ‘rig' that keeps the larvae in an environment where they can be filmed. Credit: Dave Guttridge.

In his lab now, about 350 rigs sit in a customised incubator or in a tailored shelving unit also designed by Xavi. Everything has been thought through, down to a signalling system using different coloured LEDs, a temperature control system which takes into account heat from the cameras, and a clever cable-management system.

“The rigs even need their own Wi Fi network,” says Xavi. “That’s probably a situation our IT team weren’t expecting.”

The rigs’ adaptability allows Michael’s lab to explore many different research questions. “One line of work involves inactivating specific neurons in a larva’s brain using genetic tools, to investigate the impact on individual digging behaviour and group dynamics,” he explains. 

“Another involves social isolation – if you isolate a larva from birth, it can’t dig cooperatively in groups anymore. We’re interested to see how this changes brain circuitry.”

In the isolated larvae, Michael is exploring activating neurons in the brain with light, in a technique called optogenetics, to see if he can restore the digging behaviour.

“We know that people display both cooperative and competitive behaviour, but the underlying brain circuitry behind sometimes quite intricate behaviour isn’t well known,” Michael says. “We can’t investigate this directly in humans, but we’re hoping to learn the underlying principles from a simpler, but still interesting, animal.”