Community Research and Development Information Service - CORDIS

Final Report Summary - PHOQUS (PHOtonic tools for Quantitative imaging in tissUeS)

Life science research is dedicated to understanding the structure and function of living systems, bridging scales from the molecular, cellular, tissue and organ to the organism level. Imaging is one of the key investigative technologies in the study of living systems. Light microscopy based imaging especially has become one of the major research tools in both life and medical sciences since it can span dimensions from the molecular to cellular organelles, cells, tissues and even whole organisms on time scales from milliseconds to days. Furthermore light can be used efficiently to manipulate molecules and organelles with high precision in-vitro and in-vivo. The discovery and use of genetically encoded fluorescent proteins in combination with the rapid development of genetic modification techniques now allows direct labeling of many biological molecules in living cells, organs and organisms. This enables functional studies of these molecules in complex processes in living systems using fluorescence microscopy based imaging techniques. Live imaging technologies are now used in all leading life and medical sciences institutes in academia and pharmaceutical industries worldwide. The challenges to be met are manifold; there is a great desire and need to image processes at increasingly higher spatial and temporal resolution deeper into tissues and organisms. This requires the continuous development of state of the art imaging modalities, techniques and instrumentation, as well as the development improved sample preparation and labelling techniques.

To stay at the forefront of these developments it is necessary to invest in the acquisition and development of state-of-the-art equipment of ever increasing complexity and cost but, more importantly, it requires many more researchers to be trained to work at the interface between the traditional disciplines of life sciences and photonics. This is one of the primary goals of PHOQUS.

To this end 13 Early Stage Researchers (ESRs), from backgrounds in physics, photonics, molecular biology, biotechnology and biomedical engineering, were recruited from across the Europe via a Marie-Curie Initial Training Network (Innovative PhD Doctoral Training Programme) to train them in the development and application of novel imaging modalities at the interface between Life and Photonic Sciences. The programme made use of the world-class strengths in Life and Photonic Sciences established at the University of Dundee and its 20 associated partners from both from academia and industry and in Finland, Germany, Italy, Ireland, Lithuania, Switzerland and the UK.

Training was delivered around specific research projects addressing complex processes in living organisms, linking events from the molecular and cellular to the tissue and organismal scale in basic research, medicine and drug discovery. Each research project was jointly supervised by life and physical scientists and linked to specific academic and industrial partners for specific skill building.

During the course of their studies:

• All of the 13 ESRs undertook at least one longer secondment to an Associated Partner
• 19 scientific deliverables were completed and 19 milestones (specific project targets) were achieved
• All projects have achieved exciting new and publishable results, 8 papers were already published in peer-reviewed, scientific journals
• 4 conference proceedings and one book chapter was published
• 47 papers or posters were presented at national and international Scientific Conferences and Symposiums
• All ESRs attended 2 PHOQUS Summer Schools in Edinburgh and Dundee respectively; Associate Staff, Industrial Partners and a number of external speakers also attended
• All of the ESRs attended a wide range of training programmes including two 3-day events specific to the PHOQUS Programme (Microscopy Workshop, August 2014 and a Photonics Workshop, September 2014)
• All ESR’s took part in national and international scientific conferences and presented their work in oral presentations and posters
• All of the ESRs trained in communication and engagement skills and undertook a wide range of outreach activities enabling them to engage with the public to convey the significance and importance of their work
• Some of the ESRs assisted in the establishment of a Marie Curie Alumni Association (MCAA) Chapter in Scotland and were awarded €1000 from them to fund their outreach activities

The highly interdisciplinary training provided the ESRs with expert knowledge and a broad skills set at the cutting edge interface of Life and Photonic Sciences and placed them in an excellent position to further their career in academia and/or the industrial sector. The research outputs from the projects not only led to the development of novel and compact advanced imaging tools and protocols, but also generated novel and important insights in the control of cell division, cell migration and tissue dynamics and mechanics in development, health and disease, especially cancer and cardiovascular disease. State-of-the-art equipment and systems have been built or customised under PHOQUS’ guidance, including:

• A dedicated CARS microscope that allows monitor drug metabolism in cells and tissue samples.
• A state-of-the-art Stimulated Emission Depletion (STED) microscope used to study the organization of the mitotic spindle in normal and transformed cells.
• A custom designed optical tweezer used to study the role of microtubule end binding proteins during mitosis in yeast.
• A high resolution total internal reflection (TIRF) system with an integrated tweezer used to manipulate high strength photonics beads as well as organelles in cells such as cell junctions.
• A custom high speed lightsheet microscope able to record cell behaviour of hundreds of thousands of cells in living chick embryos for up to several days.
• A systems for high resolution endoscopic fluorescent imaging and optical manipulation through a very thin high resolution single mode optical fibre was designed and established. This system is now being developed for imaging neurons deep in the brains of living free moving mice.
• Novel ultrasound based methods for high resolution imaging of tissue structure of gut and gut organoid cultures as well as measuring some of the key parameters were developed
• Photometric methods to measure blood oxygenation, primary metabolites and blood flow and their use in the assessment of cardiac risks in heathy and ‘at risk’ volunteers were developed.
• Novel semiconductor based low cost pulsed femto second infrared red lasers were developed and validated for their use in multi photon microscopy.

The outputs from the challenging projects undertaken by the ESRs are driving fundamental research around the world and will undoubtedly have direct applications in medicine, especially diagnosis, and in the pharmaceutical industry now and in the longer term.

All of the ESRs are currently involved in the arduous process of writing up their theses for examination. Two of the ESRs have already completed their studies and will graduate with a PhD from the University of Dundee in November 2017.

For more details see -

Contact details: Mrs Janette Moore, Project Manager
Phone: 44 1382 384049

Contact details: Cornelis J Weijer, Project Coordinator
Phone: 44 1382 385191

Reported by

United Kingdom


Life Sciences
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