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at the interface of physics & neuroscience

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CNP Partnerships with industry

Scientifica Centre of Excellence
https://www.scientifica.uk.com/

Launched in June 2017, the Scientifica Centre of Excellence at the Neurophotonics Centre in Quebec City has provided Summer School students with on-site technical support from Scientifica experts, thereby ensuring all Scientifica multiphotonic microscopes used during this event work optimally.

Additionnally, the center is hosting visits for scientists interested in learning more about these systems and ​their capabilities.

Another objective of the Scientifica Centre of Excellence is to allow an unrestricted customization of the Scientifica equipment to match the needs of neuroscientists, who often cannot find the right tool for their investigation when relying solely on standard commercial equipment. This unparralleled customization capability offers neuroscientists of the Canadian Neurophotonics Platform the best of both worlds, giving them the type of flexibility they need, while maintaining the support of Scientifica’s engineering team.

Doric Lenses
http://doriclenses.com/

Involved in technological development of miniature portable instruments for imagery in mice (microendoscopes), photometry, and wireless devices for multisite measurement of neuronal electrical activity.

Doric Lenses is also involved with the CNP to train highly qualified personel through MITACS internships for graduate students, and during the Frontiers in Neurophotonics Summer School.

In addition, Doric Lenses has hired many students from the Biophotonics program at Université Laval at the end of their studies.

Bliq photonics
https://bliqphotonics.com/

Bliq photonics is a spin-off of the CNP, specialized in the development, production and marketing of new solution in optic microscopy. In collaboration with Yves De Koninck’s team, it works to deploy the technologies of the axicon and SLAM by using exclusive operating licenses for these patented technologies and incorporating them in microscopes it develops and produces.

Bliq photonics also employs researchers that have graduated from the Biophotonics Graduate Program.  These graduates possess the necessary experience to work efficiently on the advanced optical systems destined for research in biological sciences.

Zilia
https://ziliahealth.com/

In partnership with Professor Daniel Côté from the CNP, Zilia combines imagery, spectrometry and artificial intelligence to detect biomarkers involved in eye, neurological and systemic diseases.

LumiSTAR Biotechnology
http://www.lumistar.com.tw/

LumiSTAR has licensed red and near-infrared Ca2+ biosensors developed by the team of Robert E. Campbell. These biosensors are being used for characterization of induced pluripotent stem cells (iPSCs), high content all-optical phenotypic screening, drug discovery, and toxicity testing.

CNP International outreach

The CNP has increased the impact of the research performed by each site and produced innovative new tools that are in high demand from the broader neuroscience community. It has played an essential role to consolidate Canada’s position at the forefront in this extremely rapidly expanding field. Indeed, several of the facilities owe their value to innovation and increased competitiveness of their users by providing them access to rare, and often unique technologies on the international scene. Proper support for personnel and maintenance of the facilities is essential, allowing them to remain ahead of their worldwide competitors by providing them with the ability to continue to innovate.

International collaboration

Yves De Koninck - Picture by Prof. Mark HutchinsonThe Canadian Neurophotonics Platform has developed links with international partners, notably for the training of highly qualified personel.  These collaboration have facilitated the participation of members of these teams to the Frontiers in Neurophotonics Summer School.

Center for Nanoscale Biophotonics – Australia
http://cnbp.org.au/

Boston University Neurophotonics Centre – USA
https://www.bu.edu/neurophotonics/

 

The Frontiers in Neurophotonics International Symposium

The CNP has been strongly involved in the organization of the Frontiers in Neurophotonics International Symposium.  The CNP coordinator, Dr. Mario Méthot, is one of the main organizers of this event, which is co-organized by Canadian and French researchers.

The symposium brings together leading developers and users of advanced optical approaches to study brain functions, from receptor dynamics in synapses, to sensory processing in intact brains, to the development of innovative approaches that can lead to new clinical and therapeutic opportunities.

The next edition of the Frontiers in Neurophotonics International Symposium will take place in Quebec City, October 4-7, 2020.

More details: https://frontiersneurophotonics.org/

Neurotechnology International Symposium

Organised in collaboration with Bordeaux Neurocampus, the first edition of this international symposium took place October 6-8, 2019, in Quebec City. The main objective of this Symposium was to foster the creation of new high-performance international collaborations resulting in collaborative and interdisciplinary projects in the field of neurotechnologies, for example in the development and use of new sensors and analytical tools for understanding the functioning of the intact and pathological brain.

Partnership with the Sentinel North Program at Université Laval to develop internatlonal outreach with

  • Université Côte d’Azur,
  • The Arctic University of Norway
  • Creation of International Mixed Unit on research in Neurodevelopment and child psychiatry with the Université de Lausanne, Switzerland.

 

 

 

 

CNP Collaborations

The Canadian Neurophotonics platform is unique in its collaborative nature.

Collaboration within Canada and between platform members

CNP Schema

Although the fields of optogenetics and connectomics are already well established, they are far from mature. The potential for new knowledge derived from these tools is immense. However, a recurring theme within the field is the need to optimize and advance current technology and directions. To fully apply this technology requires a collaborative community such as the one brought together under this platform.

The three Core Facilities have worked closely to maximize compatibility between new light-based tools produced by this facility, viral vectors produced by the Viral Vector Facility, and optical devices produced by the Photonics Technology Development Facility. Accordingly, this platform has been uniquely positioned to simultaneously optimize hardware (i.e., devices), wetware (i.e., proteins and viral delivery methods), and software (i.e., image processing tools) for maximum performance. To the best of our knowledge, there are no other technology development platforms that offer comparable levels of synergy between hardware, wetware, and software development.

Funding under the Canadian Neurophotonics platform has further enabled development and application in this rapidly evolving field. CNP researchers have decided to pool their efforts with the goal of using the experimental and operational leverage afforded by the team. The scale of the project ranges from probe development to animal models of disease, highlighting the importance of the collaborative nature of the CNP’s work.

Some examples of collaboration within platform members; Sarah Aufmkolk and Zahraa Chorghay from Ed Ruthazer’s lab at McGill (cosupervised by Paul Wiseman) have done third-harmonic generation signal imaging of myelin in Xenopus. Sarah Aufmkolk from Ed Ruthazer’s lab (together with Paul Wiseman) has also collaborated with Robert Campbell to do light sheet imaging of Nir-GECO2.

Organization of two Canadian Network of Scientific Platform meetings

The Canadian Network of Scientific Platforms – Réseau canadien des plateformes scientifiques (CNSP-RCPS cnsp-rcps.ca) is a pan-Canadian network of professional/staff working in any aspect of research scientific platforms (i.e. technology resources, core facilities) at the technical, managerial or administrative level. The aim of the network is to represent diverse technologies and institution types from regions all across the country.

As the Central Canada representative on the executive committee of the CNSP-RCPS, Marie-Ève Paquet, Coordinator of the Viral Vector production core, participated in the organisation of two Canadian Network of Scientific Platform meetings,

June 18-19, 2018, Edmonton

June 9 – 11, 2020 Toronto

CNP-Driven Technological Advancements

Production of new fluorescent proteins

Dr. Robert Campbell and his team, as the Optogenetic Protein Engineering Node of the Canadian Neurophotonics Platform, have been very active in the development of new fluorescent proteins that can be used as tools to for imaging dynamic biochemical events in live cells and tissues. The Campbell lab distribute these tools to cell biologists and neuroscientists who apply them to address questions ranging from fundamental mechanisms in cell biology, to the underlying causes of mental illness, to the development of novel therapeutics.

Lists of fluorescent proteins developed by Robert Campbell, Canadian Neurophotonics Platform Core member

Development of improved genetically encoded contrast agents for photoacoustic microscopy (Robert E. Campbell’s team)

Development of a new series of genetically encoded voltage indicators for imaging of neuronal activity (Robert E. Campbell’s team)

Invention of a new system of optogenetic control based on photcleavage of a genetically encoded protein (Robert E. Campbell’s team)

  • W. Zhang (equal contribution), A.W. Lohman (equal contribution), Y. Zhuravlova, X. Lu, M.D. Wiens, H. Hoi, S. Yaganoglu, M.A. Mohr, E.N. Kitova, J.S. Klassen, P. Pantazis, R.J. Thompson, and R.E. Campbell*, “Optogenetic Control with a Photocleavable Protein, PhoCl”, Nat. Methods, 2017, 14, 391-394.

Development of  improved green, yellow, red, and near-infrared fluorescent genetically encoded Ca2+ indicators for imaging of neuronal activity (Robert E. Campbell’s team)

Development of a bright and high-performance bioluminescent Ca2+ indicator (Robert E. Campbell’s team)

Development of first-generation genetically encoded K+ sensors (Robert E. Campbell’s team)

Development of red fluorescent glutamate indicators for visualization of excitatory neurotransmission (Robert E. Campbell’s team)

Developing use of optical approaches to study functional features of central synapses function and plasticity

The uOttawa node has developed experimental and computational expertise to meaningfully use optical approaches to study functional features of central synapses function and plasticity.  The group uses multiphoton imaging and uncaging of caged molecules to activate and monitor the electrical activity (Lee et al., Neuron 2016), the trafficking of receptors (George et al., eLife, 2015) and neurotransmitter release at single synapses (Soares et al., 2017).

The group recently developed experimental and modern computational approaches to calibrate the properties of the glutamate optical reporter iGluSNFR and established its potential for the characterization of synaptic properties. This combined optical, electrophysiological and computational approach showed that this sensor is a reliable and linear encoder of glutamate concentration at individual synapses, with sufficient potency to detect single endogenous vesicle release events. A model-based statistical toolbox was developed to extract physiological properties (vesicle number, size and release probability) from the optical signal (Soares et al. 2019).

The group is also using modern computational approaches to model synaptic, cellular, network and behavioural dynamics from electrophysiological and optogenetic approaches.

Viral Vector Production Core Growth

The fluorescent proteins created by the Optogenetic Protein Engineering Node of the Canadian Neurophotonics Platform are produced by the viral vector production core, to be tested by the testing nodes of the CNP.  These tools are also shared with the scientific community.

Viral vector core growth graphThe Viral Vector production core has grown significantly over the last years, both in terms of number of viral vectors distributed, and in the number of clients.

The viral vector core has also developed and implemented new approaches and systems to improve services, including

  • Rabies viruses (self inactivating and G-deleted, G or EnvA peudotyped)
  • New capsids for systemic injection
  • Purification from culture medium
  • qPCR Titration protocols optimization and ddPCR implementation
  • Development of serotype testing kits
  • EM characterization of AAV particles
  • Online ordering via tools.neurophotonics.ca

 

Other technologies developed by the Neurophotonics Platform include

  • Wireless technologies with Benoît Gosselin and Doric Lenses
  • Axicon-based volumetric microscopy (patent obtained by Yves De Koninck’s team to  protect intellectual property)
  • SLAM superresolution microscopy (patent obtained by Yves De Koninck’s team to  protect intellectual property)
  • Development & improvements of new epidural probes (in conjunction with optogenetics)

 

 

CNP Discoveries

Discovery on memory encoding in the brain

 

Testing of various viral vectors in vivo

  • AAV2/8-CAG-Flex-ChR2-TdTomato
  • AAVDj-EF1a-DIO-MU6-TdTomato-DIO-a5KD
  • AAVDj-EF1a-DIO-MU6-TdTomato-DIO-a5neg
  • AAV9-CAG-Flex-frwd-ChR2-tdTomato
  • AAV9-EF1a-DIO-IC++-eYFP
  • AAV9-CAG-Flex-WGA-eGFP
  • AAV9.CAG.GCaMP6s.WPRE.SV40
  • AAVPHP.eB-Syn-HA-KCC2
  • AAV1237small AAV2/1-Syn-HA-KCC2
  • GFAP-LCK-tdTomato-V5-jGCaMP7f
  • pAAV-hDlx-GqDREADD-dTomato-Fishell-4 – AAV2/5
  • AAV2/9 CAG-DIO-superCLOM-NRN1
  • AAV2/9 Flex CAG-GCaMP6f + m-Ruby2
  • AAV2/9 miniHCRT-ChR2-EYFP
  • AAV9-CAG-FlicR
  • AAV9-Syn-FlicR1
  • AAV8-CAG-FlicR
  • AAV2/1-GFAP-Cyto-iGluSnFr-L
  • AAV2/1-GFAP-Cyto-iGluSnFr-V
  • AAV1-GFAP-Cyto-iGluSnFr-L-CNP-CRIUSMQ
  • AAV1-GFAP-Cyto-iGluSnFr-V-CNP-CRIUSMQ
  • AAV2/1 GFAP-Cyto-iGluSnFr eGFP-Y
  • AAV2/1 GFAP-Cyto-iGluSnFr Suer Y
  • hSyn-NlucNG6S
  • AAV2/1 hSyn-NlucNG6S
  • AAV2/5 GFAP-Cyto-iGluSnFr eGFP-Y
  • AAV5 GFAP-Cyto-iGluSnFr eGFP-Y
  • AAV2/9 CGA-NirGECO1 (lot 657)
  • AAVPHP-B CAG-Gcamp6s
  • AAV2/9 hSyn Nir GECO (lot 717)
  • AAV2/PHP-B-AAV CAG-Gcamp6s (lot 396)
  • AAV2/9 CGA-jrGECO1 (lot 421)
  • AAV2/9 CGA-Flex0jrGECO1 (lot 536)
  • AAV9.Syn.NES-jRGECO1a.WPRE.SV40
  • AAV2/PHP.eB-hSyn-GCaMP6s-WPRE
  • AAV2/PHP.eB-Syn.NES-jRGECO1a.WPRE.SV40 (lot 1100)
  • AAV2/php.b-hSyn-FRGeco1a (lot 1209)
  • AAV2/php.b-hSyn-FRGeco1b (lot 1210)
  • AAV2/php.b-hSyn-FRGeco1c (lot 1211)
  • AAV2/php.b-hSyn-FRGeco1d (lot 1212)
  • AAV2/PHP.eB-Syn-Flex-Gcamp6s (lot 1381)

Development & testing of the ‘CLP’ molecule series for normalizing inhibition in different disorders (chronic pain, autism, epilepsy, etc)

Mapplebeck JCS, Lorenzo LE, Lee KY, Gauthier C, Muley MM, De Koninck Y, Prescott SA, Salter MW. Chloride Dysregulation through Downregulation of KCC2 Mediates Neuropathic Pain in Both Sexes. Cell Rep. 2019 Jul 16;28(3):590-596.e4.

Ferrini F, Lorenzo LE, Godin AG, Quang ML, De Koninck Y. Enhancing KCC2 function counteracts morphine-induced hyperalgesia. Sci Rep. 2017 Jun 20;7(1):3870.

It can also be noted that a partnership was developed with Hofmann-La Roche (2013-2015) to improve potency and bioavailability of the best CLP molecules candidates for indications such as autism and pain.

The CNP has also initated discussions with SOVAR (https://www.sovar.com/) for the promotion of CLP molecules (November 2019).

Articles using the tools developed by the Molecular Tools Platform

The authors of the following articles have reported back to us that they used tools developed by the Molecular Tools Platform. This list is non-exhaustive.

  1. Barrett, K. T., Roy, A., Rivard, K. B., Wilson, R. J. A. & Scantlebury, M. H. Vagal TRPV1 activation exacerbates thermal hyperpnea and increases susceptibility to experimental febrile seizures in immature rats. Neurobiology of Disease 119, 172–189 (2018).
  2. Beaudry, H., Daou, I., Ase, A. R., Ribeiro-da-Silva, A. & Séguéla, P. Distinct behavioral responses evoked by selective optogenetic stimulation of the major TRPV1+ and MrgD+ subsets of C-fibers. Pain 158, 2329–2339 (2017).
  3. Chabrat, A. et al. Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation. Nature Communications 8, 933 (2017).
  4. Chapdelaine, P. et al. Development of an AAV9 coding for a 3XFLAG-TALEfrat#8-VP64 able to increase in vivo the human frataxin in YG8R mice. Gene Ther. 23, 606–614 (2016)
  5. Doucet-Beaupré, H. et al. Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons. Proc. Natl. Acad. Sci. U.S.A. 113, E4387–96 (2016).
  6. Josset, N. et al. Distinct Contributions of Mesencephalic Locomotor Region Nuclei to Locomotor Control in the Freely Behaving Mouse. Current Biology 28, 884–901.e3 (2018).
  7. Petitjean, H. et al. Recruitment of Spinoparabrachial Neurons by Dorsal Horn Calretinin Neurons. CellReports 28, 1429–1438.e4 (2019).
  8. Petitjean, H. et al. Dorsal Horn Parvalbumin Neurons Are Gate-Keepers of Touch-Evoked Pain after Nerve Injury. CellReports 13, 1246–1257 (2015).
  9. Qian, Y. et al. A genetically encoded near-infrared fluorescent calcium ion indicator. Nature Publishing Group 16, 1–12 (2019).

 

 

 

Training

The Canadian Neurophotonics Platform has been contributing to training the next generation of neurophotonics experts through a series of training events that have been held since its inception.

CNP Meetings and Data Blitzes

CNP members and their teams have participated in yearly data blitzes in which trainees present their research results to all members of the platform, to get valuable feedback and insight from colleagues that have complementary expertise.

Neurophotonics satellite meetings at CAN

The CNP also organizes a yearly neurophotonics workshop for the scientific community at large, to introduce the tools and technologies using light that can be used to study the brain and nervous system. These introductory workshops have been held as satellite symposia of the Canadian Neuroscience Meeting.

Frontiers in Neurophotonics Summer School

Frontiers in Neurophotonics is an opportunity to meet fellow researchers and students from around the world, discuss and discover the latest advances in live cell optical imaging techniques put in perspective by experimental challenges in the field of neuroscience.

CNP platform members are actively involved in this Summer School, which is yearly opportunity to share the CNP’s expertise with students from around the world, and to showcase the CNP to an international audience.

The UBC node team have helped expand the Summer school program by providing raspberry pi workshops, in vivo imaging demos, and Matlab/python training.

Biophotonics Graduate Program

The Biophotonics graduate program at Université Laval is unique in Canada. It has become the official graduate program of the Sentinel North program, and thereby opens up to even broader themes in biophotonics (including, notably, environmental and cardio-metabolic dimensions)

Workshops on viral vectors

The Viral Vector core facility has presented and organised workshops for researchers and trainees.

  • workshop on viral vectors, Québec Pain Research Network, May 30th 2019
  • workshop on viral vectors for clinical applications, Québec Network of Junior Pain Investigators, Jan 24th 2020

Tissue Clearing and Expansion Microscopy workshop

Tissue Clearing and Expansion Microscopy are emerging tissue processing techniques with the potential to revolutionize histological investigation of brain circuits.  Tissue Clearing provides holostic data of entire brains with intact circuitry and Expasion Microscopy physically enlarges tissue, effectively turning every microscope into a super-resolution microscope – capable of revealing synaptic details.

The Dynamic Brain Circuits first organized a Tissue Clearing and Expansion Workshop at NeuroFutures 2017 in partnership with Leica and LifeCanvas.  This took place in the NeuroIamging and NeuroComputation Centre (NINC) at the DMCBH Keorner labs.  The morning session had speakers from MIT, UW and U Calgary discussing applications and protocols, home-built, DIY and commercial instruments.  The afternoon session was hands-on with examples of tissue expansion, imaging of cleared and expanded tissue and open source software tools.  Neurophotonics support was used to buy LifeCanvas instruments housed in the NINC so UBC labs could begin developing protocols.

More about the 2017 workshop: https://braincircuits.centreforbrainhealth.ca/news/2017/10/23/brain-clearing-workshops-july-12-2017

In 2019 the Dynamic Brain Circuits cluster partnered with the BC Regenerative Medicine Initiative to host a follow-up workshop.  The morning session had speakers from UW, U Calgary and Zeiss and emphasized expansion in multiple tissues, data collection and avenues for data processing and analysis.  The hands-on session emphasized data handling and demoed open source and commercial packages for processing and analysis in the NINC Data Analysis/Computation lab.

More about the 2019 workshop: https://bcregmed.ca/workshops/tissue-clearing-and-expansion/

With the initial investment from the platform, Expansion Microscopy is now in use in multiple UBC labs.  It was a focus for our recent CFI IF 2020 proposal, generated a proposal for DMCBH Innovation fund Kick Start grant, and has been extended to paraffin embedded tissue to allow scientists to work closely with pathologists and surgeons in DMCBH and at VGH.

NeuroFutures 2017, 2018, 2019

NeuroFutures brings together thought leaders in neuroscience and technology with representatives from academic, industry, clinical, and government to explore new frontiers in neuroscience and neurotechnology, including their clinical and commercial application. Major themes include neural circuit structure and dynamic function, brain mapping, decision making and control systems, healthy and disease states, neurocomputation, and neurotechnology innovations.

NeuroFutures2017 University of British Columbia July 9-11th – http://www.neuroscience.ubc.ca/Neurofutures/index.html

Neurofutures 2018, Seattle – https://riveraz.wixsite.com/neurofutures

Neurofutures 2019, http://neurofutures.org/2019/

Data management, coding and open science

Tools developed by the Neurophotonics platform are used to do experiments that produce enormous amounts of data.  Coding and data analysis evenings are part of the Frontiers in Neurophotonics Summer School, but CNP nodes also make this kind of training available to their groups.  For example, this training is available as part of the ecosystem at UBC through the Brain Circuits Cluster and NINC.  In 2020 we the UBC node will have 3 “Neurodata tutors”, which are graduate student top up awards for peer tutoring in data management, coding and open science.

Weekly Matlab training sessions, and drop-in Matlab and Python help sessions are available for neuroscience trainees at UBC, provided by CNP members Jeff LeDue and Alejo, who also provide an introduction to both Matlab and Python as part of the first year graduate introduction to neuroscience class at UBC.