Dr Jamie Flynn

Dr Jamie Flynn

Project Management

Office - DVC (Research and Innovation) (Anatomy)

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.

Read more

Career Summary

Biography

Dr Jamie Flynn

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 [link to bios] 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.”

“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.”


Qualifications

  • Bachelor of Biomedical Sciences (Hons), University of Newcastle
  • Doctor of Philosophy, University of Newcastle

Keywords

  • Anatomy
  • Lightsheet Microscopy
  • Microscopy
  • Neurophysiology

Languages

  • English (Mother)

Fields of Research

Code Description Percentage
111699 Medical Physiology not elsewhere classified 50
110999 Neurosciences not elsewhere classified 50

Professional Experience

UON Appointment

Title Organisation / Department
Casual Lecturer University of Newcastle
School of Biomedical Sciences and Pharmacy
Australia

Professional appointment

Dates Title Organisation / Department
1/07/2016 -  Project Leader - 3D Tissue Clearing and Lightsheet Microscopy Facility

The newly founded 3D Tissue Clearing and Lightsheet Microscopy Facility, based at the Hunter Medical Research Institute (HMRI), has combined 3D tissue clearing methods with lightsheet microscopy technology to allow rapid 3D interrogation of biological systems and disease processes. This world-first facility is now being used by HMRI and UoN researchers to shed new light on diseases such as cancer, spinal cord injury, chronic pain, asthma, osteoarthritis, infertility, and kidney disease.

Hunter Medical Research Institute
3D Tissue Clearing and Lightsheet Microscopy Facility

Teaching appointment

Dates Title Organisation / Department
18/07/2008 - 12/12/2014 Tutor (Musculoskeletal Anatomy) Faculty of Health
Australia

Awards

Award

Year Award
2011 National Finalist - Three Minute Thesis Competition
Three Minute Thesis
2010 SfN Graduate Student Travel Award
Society for Neuroscience

Prize

Year Award
2010 University Medal
Faculty of Health, University of Newcastle

Research Award

Year Award
2011 Spinal Cord Injury Travel Award
Spinal Cord Injury Network

Scholarship

Year Award
2012 HMRI Jennie Thomas Exchange Scholarship
Hunter Medical Research Institute
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Journal article (13 outputs)

Year Citation Altmetrics Link
2017 Battistuzzo CR, Rank MM, Flynn JR, Morgan DL, Callister R, Callister RJ, Galea MP, 'Effects Of treadmill training on hindlimb muscles of spinal cord¿injured mice', Muscle and Nerve, 55 232-242 (2017) [C1]
DOI 10.1002/mus.25211
Citations Scopus - 1Web of Science - 1
Co-authors Robert Callister, Robin Callister, Michelle Rank
2017 Flynn JR, Conn VL, Boyle KA, Hughes DI, Watanabe M, Velasquez T, et al., 'Anatomical and Molecular Properties of Long Descending Propriospinal Neurons in Mice', FRONTIERS IN NEUROANATOMY, 11 (2017) [C1]
DOI 10.3389/fnana.2017.00005
Citations Scopus - 1Web of Science - 1
Co-authors Brett Graham, Robert Callister
2016 Battistuzzo CR, Rank MM, Flynn JR, Morgan DL, Callister R, Callister RJ, Galea MP, 'Gait recovery following spinal cord injury in mice: Limited effect of treadmill training', Journal of Spinal Cord Medicine, 39 335-343 (2016) [C1]

© 2016, © The Academy of Spinal Cord Injury Professionals, Inc. 2016. Several studies in rodents with complete spinal cord transections have demonstrated that treadmill training... [more]

© 2016, © The Academy of Spinal Cord Injury Professionals, Inc. 2016. Several studies in rodents with complete spinal cord transections have demonstrated that treadmill training improves stepping movements. However, results from studies in incomplete spinal cord injured animals have been conflicting and questions regarding the training dosage after injury remain unresolved. Objectives: To assess the effects of treadmill-training regimen (20 minutes daily, 5 days a week) for 3, 6 or 9 weeks on the recovery of locomotion in hemisected SCI mice. Methods: A randomized and blinded controlled experimental trial used a mouse model of incomplete spinal cord injury (SCI). After a left hemisection at T10, adult male mice were randomized to trained or untrained groups. The trained group commenced treadmill training one week after surgery and continued for 3, 6 or 9 weeks. Quantitative kinematic gait analysis was used to assess the spatiotemporal characteristics of the left hindlimb prior to injury and at 1, 4, 7 and 10 weeks post-injury. Results: One week after injury there was no movement of the left hindlimb and some animals dragged their foot. Treadmill training led to significant improvements in step duration, but had limited effect on the hindlimb movement pattern. Locomotor improvements in trained animals were most evident at the hip and knee joints whereas recovery of ankle movement was limited, even after 9 weeks of treadmill training. Conclusion: These results demonstrate that treadmill training may lead to only modest improvement in recovery of hindlimb movement after incomplete spinal cord injury in mice.

DOI 10.1080/10790268.2015.1133017
Citations Scopus - 1Web of Science - 1
Co-authors Robert Callister, Michelle Rank, Robin Callister
2015 Rank MM, Flynn JR, Battistuzzo CR, Galea MP, Callister R, Callister RJ, 'Functional changes in deep dorsal horn interneurons following spinal cord injury are enhanced with different durations of exercise training', JOURNAL OF PHYSIOLOGY-LONDON, 593 331-345 (2015) [C1]
DOI 10.1113/jphysiol.2014.282640
Citations Scopus - 12Web of Science - 10
Co-authors Michelle Rank, Robert Callister, Robin Callister
2015 Rank MM, Flynn JR, Galea MP, Callister R, Callister RJ, 'Electrophysiological characterization of spontaneous recovery in deep dorsal horn interneurons after incomplete spinal cord injury', Experimental Neurology, 271 468-478 (2015) [C1]

© 2015 Elsevier Inc. In the weeks and months following an incomplete spinal cord injury (SCI) significant spontaneous recovery of function occurs in the absence of any applied th... [more]

© 2015 Elsevier Inc. In the weeks and months following an incomplete spinal cord injury (SCI) significant spontaneous recovery of function occurs in the absence of any applied therapeutic intervention. The anatomical correlates of this spontaneous plasticity are well characterized, however, the functional changes that occur in spinal cord interneurons after injury are poorly understood. Here we use a T10 hemisection model of SCI in adult mice (9-10 wks old) combined with whole-cell patch clamp electrophysiology and a horizontal spinal cord slice preparation to examine changes in intrinsic membrane and synaptic properties of deep dorsal horn (DDH) interneurons. We made these measurements during short-term (4 wks) and long-term (10 wks) spontaneous recovery after SCI. Several important intrinsic membrane properties are altered in the short-term, but recover to values resembling those of uninjured controls in the longer term. AP discharge patterns are reorganized at both short-term and long-term recovery time points. This is matched by reorganization in the expression of voltage-activated potassium and calcium subthreshold-currents that shape AP discharge. Excitatory synaptic inputs onto DDH interneurons are significantly restructured in long-term SCI mice. Plots of sEPSC peak amplitude vs. rise times suggest considerable dendritic expansion or synaptic reorganization occurs especially during long-term recovery from SCI. Connectivity between descending dorsal column pathways and DDH interneurons is reduced in the short-term, but amplified in long-term recovery. Our results suggest considerable plasticity in both intrinsic and synaptic mechanisms occurs spontaneously in DDH interneurons following SCI and takes a minimum of 10 wks after the initial injury to stabilize.

DOI 10.1016/j.expneurol.2015.07.002
Citations Scopus - 4Web of Science - 3
Co-authors Robert Callister, Michelle Rank, Robin Callister
2015 Palmer WM, Martin AP, Flynn JR, Reed SL, White RG, Furbank RT, Grof CPL, 'PEA-CLARITY: 3D molecular imaging of whole plant organs', SCIENTIFIC REPORTS, 5 (2015) [C1]
DOI 10.1038/srep13492
Citations Scopus - 13Web of Science - 11
Co-authors Antony Martin, Chris Grof
2013 Flynn JR, Dunn LR, Galea MP, Callister R, Callister RJ, Rank MM, 'Exercise Training after Spinal Cord Injury Selectively Alters Synaptic Properties in Neurons in Adult Mouse Spinal Cord', JOURNAL OF NEUROTRAUMA, 30 891-896 (2013) [C1]
DOI 10.1089/neu.2012.2714
Citations Scopus - 11Web of Science - 10
Co-authors Michelle Rank, Robin Callister, Robert Callister
2011 Flynn JR, Graham BA, Galea MP, Callister RJ, 'The role of propriospinal interneurons in recovery from spinal cord injury', Neuropharmacology, 60 809-822 (2011) [C1]
DOI 10.1016/j.neuropharm.2011.01.016
Citations Scopus - 54Web of Science - 48
Co-authors Robert Callister, Brett Graham
2011 Flynn JR, Brichta AM, Galea MP, Callister RJ, Graham BA, 'A horizontal slice preparation for examining the functional connectivity of dorsal column fibres in mouse spinal cord', Journal of Neuroscience Methods, 200 113-120 (2011) [C1]
DOI 10.1016/j.jneumeth.2011.06.017
Citations Scopus - 7Web of Science - 7
Co-authors Alan Brichta, Robert Callister, Brett Graham
2011 James MH, Charnley JL, Flynn JR, Smith DW, Dayas CV, 'Propensity to 'relapse' following exposure to cocaine cues is associated with the recruitment of specific thalamic and epithalamic nuclei', Neuroscience, 199 235-242 (2011) [C1]
Citations Scopus - 31Web of Science - 29
Co-authors Douglas Smith, Christopher Dayas
2011 Brown AL, Flynn JR, Smith DW, Dayas CV, 'Down-regulated striatal gene expression for synaptic plasticity-associated proteins in addiction and relapse vulnerable animals', International Journal of Neuropsychopharmacology, 14 1099-1110 (2011) [C1]
Citations Scopus - 17Web of Science - 14
Co-authors Christopher Dayas, Douglas Smith
2010 James MH, Charnley JL, Jones E, Levi E, Yeoh JW, Flynn JR, et al., 'Cocaine- and amphetamine-regulated transcript (CART) signaling within the paraventricular thalamus modulates cocaine-seeking behaviour', Plos One, 5 e12980 (2010) [C1]
DOI 10.1371/journal.pone.0012980
Citations Scopus - 44Web of Science - 38
Co-authors Douglas Smith, Christopher Dayas
2007 Flynn JR, Bolton PS, 'Measurement of the vertebral canal dimensions of the neck of the rat with a comparison to the human', Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 290 893-899 (2007) [C1]
DOI 10.1002/ar.20523
Citations Scopus - 13Web of Science - 11
Co-authors Philip Bolton
Show 10 more journal articles

Conference (3 outputs)

Year Citation Altmetrics Link
2015 Rank M, Flynn J, Galea M, Callister R, Callister R, 'The spinal cord that changes itself: spontaneous recovery of interneurons after incomplete spinal cord injury', JOURNAL OF NEUROCHEMISTRY (2015) [E3]
Co-authors Michelle Rank, Robin Callister, Robert Callister
2012 Flynn JR, Callister RJ, Graham BA, 'Electrophysiological properties of identified long descending propriospinal neurons in mice', Abstracts. Australian Neuroscience Society 32nd Annual Meeting (2012) [E3]
Co-authors Robert Callister, Brett Graham
2012 Brown AL, Flynn JR, Dayas CV, Smith DW, 'Altered gene expression in cell signalling pathways of midbrain dopamine neurons from addiction and relapse vulnerable animals', Drug and Alcohol Review: Abstracts of the Australasian Professional Society on Alcohol and other Drugs Conference 2012 (2012) [E3]
Co-authors Douglas Smith, Christopher Dayas
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Grants and Funding

Summary

Number of grants 4
Total funding $193,049

Click on a grant title below to expand the full details for that specific grant.


20171 grants / $20,000

Three-dimensional characterisation of a potential neuropathic pain$20,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor Jamie Flynn, Associate Professor Brett Graham
Scheme Project Grant
Role Lead
Funding Start 2017
Funding Finish 2017
GNo G1700090
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

20162 grants / $163,049

Virtual Biobank$160,000

Funding body: Australian National Data Service

Funding body Australian National Data Service
Project Team Doctor Jamie Flynn, Doctor Antony Martin, Mr Will Palmer
Scheme Research Grant
Role Lead
Funding Start 2016
Funding Finish 2016
GNo G1601108
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

Bringing CLARITY to Brain Cancer$3,049

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor Jamie Flynn, Doctor Craig Gedye
Scheme Project Grant
Role Lead
Funding Start 2016
Funding Finish 2016
GNo G1600967
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

20121 grants / $10,000

Intrinsic and synaptic properties of propriospinal neurons$10,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Doctor Jamie Flynn
Scheme Research Grant
Role Lead
Funding Start 2012
Funding Finish 2012
GNo G1200566
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y
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Research Projects

3D Tissue Clearing and Lightsheet Microscopy Facility 2015 - 2019

The newly founded 3D Tissue Clearing and Lightsheet Microscopy Facility, based at the Hunter Medical Research Institute (HMRI), has combined 3D tissue clearing methods with lightsheet microscopy technology to allow rapid 3D interrogation of biological systems and disease processes. This world-first facility is now being used by HMRI and UoN researchers to shed new light on diseases such as cancer, spinal cord injury, chronic pain, asthma, osteoarthritis, infertility, and kidney disease.


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News

UON researchers shine in a glittering field of finalists

September 7, 2016

The University of Newcastle (UON) Alumni Awards Finalists have been announced, and we are delighted to see a broad range of UON researchers represented in the outstanding field.

Hand-built microscope gives greater clarity

March 2, 2016

Three young University of Newcastle (UON) biologists have hand-built a state-of-the-art laser microscope at HMRI that delivers clear three-dimensional cellular images with unparalleled speed and precision.

Dr Jamie Flynn

Positions

Project Management
Office - DVC (Research and Innovation)
Research and Innovation Division

Casual Lecturer
School of Biomedical Sciences and Pharmacy
Faculty of Health and Medicine

Focus area

Anatomy

Contact Details

Email jamie.flynn@newcastle.edu.au
Phone (02) 4921 8771
Mobile 0416003787
Fax (02) 4921 7905
Link Personal webpage

Office

Room MS312
Building Medical Sciences
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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