Establishing The Edinburgh Super-Resolution Imaging Consortium (ESRIC)

Lead Research Organisation: Heriot-Watt University
Department Name: Sch of Engineering and Physical Science

Abstract

Recently, the detail with which biologists can examine microscopic samples has increased dramatically. Improvements in this microscopic 'resolution' can be split into; temporal (the speed with which biologists can look at fast changing things) and spatial (the size of objects, or spacing between them). Recent advancements in technology, combined with some clever biology, means that we can, for the first time, determine the precise positions of many 10000s of single molecules, their interactions, movements and formation into structures within living cells, with millisecond (1000s of frames of a 'movie' per second) rates. As molecules are the fundamental units of cells, and cells are the minimal units of life, increases in resolution are starting to revolutionise our understanding of cell biology by examining directly the molecular workings of cells.

The technological improvements that make this possible have come from the physical sciences: mathematics, physics, chemistry as well as engineering. To continue with this progress, the UK scientific community needs to bring the best cell biologists with the most appropriate biological tools and questions, together with researchers at the cutting edge of the physical sciences. Work at the so-called 'Life Science Interface' is not straightforward; it requires extra time for the various researchers involved to speak to each other, specialised infrastructure, a genuine desire to work across traditional scientific boundaries, as well as committed support from both the funders and the institutional management to ensure that these ambitious collaborations can work. To date, few institutions in the UK can claim success in this.

Heriot Watt University is well known internationally for its work in the physical sciences particularly. Taking advantage of this, the University established the 'Life Science Interface Laboratory (LSI)' in 2010 with a large investment in both equipment and staff recruitment. Recruiting biologists with a proven track record of working at the interfaces with mathematics, physics and chemistry, a new Research Institute was established, led by cell biologists, to accelerate the interactions between disciplines. This Institute established a close collaboration with the nearby Institute of Genetics and Molecular Medicine (IGMM), known for its advanced biology aimed at addressing the molecular mechanisms that underly human disorders and diseases. This collaboration is proving very productive, with many small-scale pilot projects under-way investigating the use of the new 'super-resolution' imaging techniques described above, applied to cutting-edge biological questions in human healthcare.

Here, we are requesting support for new equipment and technical support to bolster this collaboration. Three new microscopes are requested, which will allow more cell biologists to 'see' structures and molecules in their samples in unprecedented detail. Combined with the facilities at the LSI at Heriot Watt, the 'Edinburgh Super-Resolution Imaging Consortium' (ESRIC) will bring together every single currently available live cell super-resolution imaging approach, together with world-leading cell biologists and physical scientists and engineers with a proven track record of cross-disciplinary successes; something unique in the UK. We are also requesting funding to pursue research across ESRIC, which will in addition be made openly available to a large number of cell biologists across Edinburgh. Importantly, simply purchasing new commercially available microscopes is not the limit of our ambition; the engineers and physicists in our consortium, directed and informed by cell biologists, are already developing the 'next generation' of imaging approaches that will be necessary to continue progress in biological discovery: of equal importance, the senior management of all the Institutes in ESRIC are demonstrably committed to this activity.

Technical Summary

We are requesting funding to establish the 'Edinburgh super-resolution consortium' (ESRIC), bringing together a large cohort of high-profile cell biologists with engineers, mathematicians, physicists and chemists. We request funds for 3 imaging platforms: a gSTED and white-light-laser (WLL) upgrade to an already UK-unique Leica SMD (single molecule detection) FLIM and FCS system, and Nikon SIM and STORM systems: all platforms will be openly accessible to optical physicists for add-on modification and data analysis development. The WLL upgrade will permit the use of any fluorohore in the visible range in STED, FLIM and FCS experiments. With these additions, ESRIC will contain every current super-resolution imaging and spectroscopic approach in a managed facility able to be accessed by a wide audience of biologists with internationally recognised research programmes, providing platforms to quantify cell biology over a range of scales from single molecules to the intra-vital, matched by expert signal processing, mathematical and physics input to create the 'next generation' of imaging approaches and analyses. No single imaging technique can address the various questions asked by modern biology and additionally, comparing data across imaging approaches is important. For example, PALM is (currently) limited to TIRFM-illuminated-sections at the base of cells, whilst gSTED can be used anywhere in 3-D at high frame rates. Super-resolution imaging cannot quantify protein interactions but combined with FLIM and FCS here, users will be able to do this. PALM and STORM require software reconstructions; comparing such data with gSTED and SIM can confirm that molecule localisation maps correlate with true sub-diffraction-sized structures. Also importantly, we have assembled an inter-disciplinary team who will work closely with the biologists in ESRIC to refine and deliver the next generation of imaging technologies, instrumentation and analytical approaches.

Planned Impact

Beneficiaries from the research of the ESRIC consortium will be academic, clinical, patient groups and non-academic communities.

ESRIC will be established as a Centre of Excellence in super-resolution imaging and spectroscopies, providing local (Edinburgh), national (UK) and trans-national (European) access to the highest-quality and widest range of equipment, expertise and infrastructure for a large number of the best biologists.

In the immediate term, the research and technolgical developments and innovations, disseminated though peer-reviewed publications and though conference presentations, will benefit researchers in both the life and physical sciences.

Using super-resolution and dynamic imaging to study intra-cellular trafficking and sub-cellular compartmentalisation of mutant proteins associated with Mendelian human diseases, such as the ciliopathies, which are characterised by an apparently bewildering array of clinical symptoms associated with different mutations within the same genes, will make an important impact towards understanding the aetiology of these disorders, stratifying them according to cilia dysfunction rather than just gene mutation, and therefore providing affected patients, their families, and the clinicians who care for them, with much better information.

The development, through ESRIC, of novel signal processing approaches directed towards intravital imaging of proteins, drugs, and protein-protein interactions in cancer cells in the vivo environment hold the promise of providing powerful pre-clinical in vivo models of cancer within which to test and assay novel therapeutic anti-cancer compounds.

A vast amount of money, effort, samples and research time has been invested both nationally and internationally in genome-wide association studies (GWAS) to identify genomic variants that track with complex and common human disease. Whereas variants identified as associated with disease traits that are within genes immediately lend themselves to further functional analysis, half of the variants map a long way from any recognised gene. Our proposals to investigate genome nanostructure by super-resolution microscopy, with an especial focus on long-range gene regulatory landscapes, will have immediate impact in addressing the current lack of mechanistic understanding of human genome regulation and will therefore allow for better exploitation of the current and future investments in GWAS leading to improvements in human health and quality of life.

The development and utilisation of new and innovative methodologies, equipment, techniques, technologies, and tools within this proposal, all associated with addressing real biological problems and physiological cell systems, will create a vibrant cross-disciplinary research environment. This will enhance the research capacity, knowledge and skills of the Edinburgh scientists directly involved, and will train a new generation of highly-skilled researchers who can cut across traditional discipline boundaries.

The engagement of equipment manufacturers, the established links of Heriot-Watt with companies in the areas of photonics, optics, and software, together with the proven ability of ESRIC members to take their innovations in microscopy through to commercialisation means that this proposal has the potential to attract future R&D investment in these areas and to make contributions toward wealth creation and economic prosperity. We have a proven track record of commercialisation in these areas; the IGMM developed and commercialised optical projection tomography, now adopted world wide as a high resolution imaging technique. Heriot Watt spun-out Edinburgh Instruments Ltd, a highly successful laser, TCSPC and FLIM technology company, which has created >£110M of business, with 80% exported to 50 countries. Professor Des Smith, the founder and CSO, is a member of IB3. We will draw on these experiences to develop technologies developed in ESRIC.

Publications

10 25 50
 
Description Wellcome trust multi-user equipment award
Amount £779,000 (GBP)
Funding ID 208345/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2017 
End 11/2022
 
Description Collaboration on Early Careers Grants with John Mullins 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration to provide support and access to super-resolution microscopy and live cell imaging expertise and systems.
Collaborator Contribution Society of Endocrinology Early Careers Research Funding providing £2400 for equipment access
Impact None yet
Start Year 2014
 
Description Collaboration on new MRC project with Prof Peter Brophy 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration to provide super-resolution imaging expertise to project
Collaborator Contribution MRC funding of £12000 for equipment facility access
Impact None yet
Start Year 2014
 
Description Collaboration with Seth Grant Centre for Clinical Sciences Grant 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration to provide access and expertise in super-resolution microscopy
Collaborator Contribution Funding from the Centre for Clinical Sciences, The University of Edinburgh with £2400 for equipment access
Impact None yet
Start Year 2014
 
Description PhD sponsorship 
Organisation Baillie Gifford
Country United Kingdom 
Sector Private 
PI Contribution Expertise.
Collaborator Contribution £50K charitable donation for 50% of a 4-year PhD studentship
Impact none yet
Start Year 2014
 
Description Public exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Poster Presentation
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact 200 members of the public attended a workshop organised by the ESRC entitled 'The revolution will be bio'. We provided a mid-sized exhibit in collaboration with Leica Microsystems, showcasing fluorescence imaging and multi-disciplinary research.

This led to several requests from various members of the public for lab visits, which we are arranging. In addition we had a University press release and wrote an entry on the ESRC blog.
Year(s) Of Engagement Activity 2012
 
Description Public lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public talk and discussion afterwards. Led to discussion and further invitations.

This led to further public engagement invitations to speak at schools and other science festivals. 2 school children came to visit the lab.
Year(s) Of Engagement Activity 2014
 
Description public exhibitions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact We have participated in 25 science festivals this year, reaching several 1000 members of the public.

Several new invitations, schools talks, outreach activities
Year(s) Of Engagement Activity 2014