SHeffield IMAging (SHIMA)

Lead Research Organisation: University of Sheffield
Department Name: Krebs Institute for Biomolecular Researc

Abstract

Imaging has been at the heart of huge leaps in understanding in biology and medicine, from the discovery of bacteria using the first microscopes to neuroimaging to determine brain function. All the advances have been totally dependent on the development of new technologies. This is particularly so for the study of objects too small to be seen by the naked eye, where microscopes are essential. Elucidating how cells function, whether they be from humans, plants, fungi or bacteria requires the ability to be able to see the components that make up the cell, determine their localisation and establish how they move relative to each other. In particular this has been driven by developments in microscopy coupled with the use of probes to fluorescently label molecules inside cells and so be able to localise and track them, giving key insights into processes such as cell division, growth and differentiation. However traditional optical microscopy approaches are limited in resolution to about 200 nm, which prevents the nanoscale visualisation of the myriad smaller structures and processes within the cell. Only very recently have new super-resolution (SR) microscopy approaches been invented to allow resolution down to single molecules. Thus we are at a tipping point, where existing methods and levels of understanding will become rapidly superseded by new approaches. In Sheffield we have been quick to recognise the potential of this opportunity and we are at the forefront of the development of new methods in SR microscopy. This includes building our own microscopes, coupling fluorescence microscopy with other high-resolution approaches and applying these advances to important biological and biomedical questions. We are thus ideally placed to optimally exploit the new SR technology as part of a programme of development integrated with application. The University of Sheffield (UoS) is a well-established centre with great strengths in many aspects of biomedical and biological research that are poised to reap the benefits from the new SR technologies.
We propose to establish a world-class centre in SR imaging, entitled Sheffield Imaging (SHIMA), based on our current strengths, the proposed project and a large strategic investment by the University of Sheffield. We will purchase commercial SR systems for both Structured Illumination Microscopy (SIM) and Stochastic Optical Reconstruction Microscopy (STORM) as complementary systems allowing single molecule resolution and live cell imaging. The equipment will be housed in our Light Microscopy Facility (LMF) to allow multiple user access from the outset. SR is an emerging field and so an imaging, development centre will be established to drive forward technological advances, for transfer to the LMF. To enhance technology development we will conduct specific seed projects to produce novel probes for both SIM and STORM, to increase the versatility of the techniques and to increase the speed of STORM to allow live cell imaging in 3D. With commercial partners we will ensure the rapid translation of our developments for the community. An interdisciplinary team will manage SHIMA, ensuring optimal technology development within the context of its direct application. Two SHIMA senior experimental officers (SEOs) will be responsible for interdisciplinary technology development, production of novel probes and establishment of widespread biomedical applications. The SEOs will be responsible for training of users, both internal and external creating a vibrant atmosphere of expert researchers across the University (and beyond) with a seamless interface between technology development and application via the LMF. The UoS is committed to SHIMA not only by a substantial direct investment in the project but also via a wider initiative in imaging to establish Sheffield as a key international centre in SR imaging.

Technical Summary

Super-resolution (SR) microscopy is beginning to allow exciting new discoveries to be made across biomedical and biological disciplines. Rapid and widespread application of the new technology has been hampered by the lack of robust, affordable commercial systems and the dearth of compatible probes. We aim to establish a world-class centre in SR imaging based on our existing strengths in technology development and its biomedical application, the proposed project and a significant investment by the University of Sheffield. We will utilise commercial Structured Illumination Microscopy (SIM) and Stochastic Optical Reconstruction Microscopy (STORM) systems in a range of applications but, crucially, also embed the commercial instrumentation within a culture of technology development via a new centre for biophysical imaging. This will ensure that emerging technologies are quickly translated into wide usage by the biomedical community, further enhanced by our close association with industry, ensuring translation of our developments. At the outset we have identified probe development and increasing the image acquisition speed of STORM as key goals for our programme. The University of Sheffield will make a direct investment in the project by funding a senior experimental officer, refit of a new microscopy development facility, PhD studentships and a contribution towards the large equipment costs. The 5-year duration of the funded programme will ensure the optimal development and application of SR microscopy across the University, with greatest impact. Our ambitious project will be significantly enhanced as imaging is a flagship initiative for the University of Sheffield, creating a vibrant interface of technology to fully exploit the potential of the technologies within the context of their application to generate new levels of biomedical understanding.

Planned Impact

The proposed programme will develop a sustainable, integrated platform of super-resolution microscopy development and its widespread application. There will be a variety of impacts over a range of timescales and arenas.

- Industry: potential users (expected timescale: year 2 onwards): will benefit by (i) being able to input into the future direction of SHIMA (ii) being able to explore potential applications for their research. The project will create a centre for integrated development and application of novel microscopy technologies.
- Industry: microscope manufacturers (expected timescale : year 4 onwards): will benefit from the technological developments arising from the initiative with potential for commercial exploitation.
- Local communities (expected timescale: year 2 onwards): via outreach activities will benefit from greater knowledge of this scientific area
- UK PLC (expected timescale year 2 onwards): will benefit through the development of imaging technologies and the commercial exploitation thereof.
- Undergraduate/postgraduate/post docs (expected timescale: year 1 onwards): will benefit through development of skills in super-resolution imaging techniques, particularly as it applies to the applications at the interface between biological and physical sciences.
- Media (expected impact: year 2 onwards): will benefit through the applicants' participation in radio and newspapers interviews.

Publications

10 25 50
 
Title Giant Inflatable E. coli 
Description 30M long inflatable E. coli 
Type Of Art Artwork 
Year Produced 2015 
Impact 100000 people saw it 
URL http://krebsfest.group.shef.ac.uk/
 
Description ITN European Industrial Doctorate
Amount € 800,000 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 06/2015 
End 05/2019
 
Description BIOPOL EU ITN training network 
Organisation Curie Institute Paris (Institut Curie)
Country France 
Sector Academic/University 
PI Contribution Co-I on the successful award (Euro 3.9 million), supervisor of Early Stage Researcher and co-supervisor of second Early Stage Researcher. Expertise in endocytosis and signalling.
Collaborator Contribution BIOPOL is an interdisciplinary European training network at the interface of cell biology, physics and engineering. BIOPOL aims specifically to understand fundamental mechanochemical principles guiding cellular behaviour and function and their relevance to human disease. A new supra-disciplinary research field is emerging bringing together the fields of molecular cell biology, physics and engineering aiming at an in-depth understanding of fundamental cellular mechanochemical principles. BIOPOL combines exactly this required expertise in one joint training program for young researchers. BIOPOL has assembled a unique multidisciplinary consortium bringing together top scientists from the fields of molecular/developmental cell biology, membrane physics, engineering as well as specialists from the private sector.
Impact Maib, Smythe and Ayscough, 2017. Forty years on, clathrin coated pits continue to fascinate. Perspective for Molecular Biology of the Cell. In press.
Start Year 2015
 
Description Cell division in Staphylococcus aureus 
Organisation University of Copenhagen
Country Denmark 
Sector Academic/University 
PI Contribution We have used super resolution microscopy to analyse the role of SosA as an inhibitor pf cell division.
Collaborator Contribution Our partners have made the genetic constructs necessary for analysis.
Impact Manuscript in preparation
Start Year 2014
 
Description MIMIC EU ITN network 
Organisation Mimetas BV
Country Netherlands 
Sector Private 
PI Contribution Co-supervisor of Early stafge researcher. Co-I on successful award.
Collaborator Contribution Provision of access to organ-on-a-chip technology
Impact None yet
Start Year 2016
 
Title Super resolution Image Analysis 
Description Improvements to image analysis software 
Type Of Technology Software 
Year Produced 2017 
Impact Ability to analyse images from across modalities. 
 
Description KrebsFest 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact KrebsFest was a week long Festival celebrating the scientific life and legacy of Sir Hans Krebs. The Festival involved talks by Nobel Prize winners, a Schools Night, Public Exhibition, several arts commissions, a Public Night, a commissioned video game, national press involvement etc. A giant E. coli also went on public dispaly with over 100000 visitors. It was one of the largest Festival ever organised by the University of Sheffield.
Year(s) Of Engagement Activity 2015
URL http://krebsfest.group.shef.ac.uk/
 
Description Krebsfest, University of Sheffield 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Several hundred people attended a range of events established to celebrate the work of the nobel laureate Sir Hans Krebs. We provided a display showing fluorescence labelling of the cytoskeleton as well as providing the opportunity for small children to paint cells on cookies.
Year(s) Of Engagement Activity 2016
URL http://krebsfest.group.shef.ac.uk/
 
Description Microscopy demonstration at University of Sheffield Researchers' Night 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talks sparked questions from the public on the work on membrane traffic in Sheffield
1000 people attended the krebsfest where we had hands on demonstations

Enthusiastic feedback from visitors. Sparked an application to the Royal Society Summer Exhibition
Year(s) Of Engagement Activity 2014,2015,2016
URL http://krebsfest.group.shef.ac.uk/
 
Description Public seminar during Science Week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Public talk on infectious disease, control and the spread of resistance.
Year(s) Of Engagement Activity 2016
 
Description School visits in Sheffield and the surrounding region 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Schools
Results and Impact Hands-on workshop on chromatography with Years 1 and 2. Presentations on how fertilised cells develop into whole organisms.

Very positive feedback from teachers and students alike.
Year(s) Of Engagement Activity 2007,2008,2009
 
Description Shambala Festival August 2016 
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 Krebsfest went on tour to the Shambala Festival with series of talks and workshops.
Year(s) Of Engagement Activity 2016
 
Description Virtual reality E. coli 
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 developed a virtual reality E. coli experience that was used at Festival of the Mind in September 2016. Hugely successful.
Year(s) Of Engagement Activity 2016