Conjoint Associate Professor John Flynn

Conjoint Associate Professor

School of Medicine and Public Health

Complementary collaboration leads to commercialisation

Jamie’s research career started with a bachelor of Biomedical Science at the University of Newcastle back in 2005. Undertaking a PhD in Brett Graham and Bob Callister’s lab, Jamie learned electrophysiology and a technique called ‘patch-clamp electrophysiology’ to record electrical signals from individual neurons.

“My whole PhD was examining spinal cord injury and looking at how neurons can rewire after damage, and making electrical recordings to show how the spinal cord recovers over time, forming new circuits along the way.”
“During this time, I spent about nine months over at The Salk Institute of Biological Studies in San Diego, working in Professor Martyn Goulding’s lab. That’s where I delved into the genetics and anatomy behind basic types of spinal cord neurons, which gives you a wealth of information.

I came back here with some new techniques and became heavily invested in anatomy. What do these cells look like? Where do they go? Who do they talk to? These are questions that have got to be answered. After delving into this research, I found these questions were extremely difficult to  – answer with traditional 2D histology, which is where 3D clearing techniques (e.g. CLARITY) could help. Here was a way to actually study these neurons, all intact. That’s when I went boots and all into new 3D histology methods, such as CLARITY.”

That’s how Jamie, William Palmer and Antony Martin started talking. “Will and Ant were working on plant biology and had a lot of similar issues regarding structure/function relationships. After coming back from San Diego, the guys said ‘let’s try it in plants’. This is a big challenge because plants are so different from mammalian tissues, so they developed Plant Enzyme Assisted-CLARITY (PEA-CLARITY). Their big breakthrough was converting CLARITY into something that could be used in plants as well.”

Building a $1 million microscope for $70 000

“That’s crossing big boundaries there, because plant sciences and medical sciences – they rarely talk to each other. Yet here’s a technique that jumped from one, over to the other and the benefits are absolutely enormous.”
After refining several 3D clearing techniques, we hit a roadblock. You can’t use standard microscopes to image this, it takes days if not weeks to do it properly, and you can’t block up a microscope like that – other people need to use it. So we decided we needed a lightsheet microscope. There’s only a few commercial options right now, and they’re all very expensive. So that’s why we decided to build our own.”

"That’s when HMRI came on board with Jennie Thomas AM, HMRI Life Governor and the Newcastle Permanent Charitable Foundation. They gave us lab space and the money to buy the parts, and over six months we got it working. The team now run the lab as a communal facility to ensure all labs at HMRI and UON have access to the technology."

Jamie laughs that he, Will and Antony just about live in each other’s’ pockets. “We all have unique skill sets, and that’s why we’re so lucky to have a team like this. So few people have the opportunity to work with people who complement each other so well.”

Read more about the CLARITY light-sheet microscope project.

Jamie Flynn

Complementary collaboration leads to commercialisation

Joint Project Leader for 3D Tissue Clearing and Lightsheet Microscopy Facility at HMRI.

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Conjoint Associate Professor John Flynn


Conjoint Associate Professor
School of Medicine and Public Health
College of Health, Medicine and Wellbeing

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