Parallelised live microscopy for high-throughput behavioural phenotyping in malaria research

Many smaller, simpler microscopes can often see more than one large, expensive machine. We propose to innovate a research-quality, fully automated microscope design that can be tailored to a particular experiment and easily replicated to perform many experiments in parallel. With computer vision to control and analyse these experiments, the bottlenecks of equipment and staff time are removed, and it becomes possible to keep pace with new genetic technologies - even for previously time-consuming studies, for example measuring the invasion of red blood cells by plasmodium parasites. We will develop the microscopy and computer vision technologies, demonstrate their efficacy in our malaria lab and those of our collaborators, and release open-source designs that allow others to replicate our progress. The ability to screen hundreds of different mutant strains efficiently will lead to a deeper understanding of many diseases, ultimately creating new drug discovery targets and potentially leading to new vaccines for conditions like malaria.

Gene editing is in the midst of a revolution thanks to CRISPR-Cas9 protocols, and cell phenotyping needs to keep pace. Specifically in malaria, our collaborators are now scaling up knockouts in P. falciparum using CRISPR, and expect to make 200 knockout lines this year, and 1000 in the next five years . While strain generation is scaling so dramatically , phenotyping is not, i.e. we cannot determine the function of these genes - we need robust and cheap scalable phenotyping assays, which involve live cell imaging, and specifically of host/pathogen invasions. It is not conceivable to perform these assays through current methods and technologies. New, much more automated and affordable approaches to imaging have to be developed and deployed. This would then allow us to systematically screen GM lines for several phenotypes, including merozoite number, cytokinesis, egress and invasion. We address here the case of malaria, but point out that very similar challenges and objectives can be identified in many other infectious diseases.

Societal Impact
Half of the world's population is currently at risk of malaria with an estimated 214 million cases in 2015. There is considerable global effort to eliminate infectious diseases, with research targeted at meeting the sustainable development goal of ending epidemics related to malaria by 2030. To achieve these ambitious targets, and have significant impact on health and well-being on a global scale, the research at medical centres can be supported significantly by efforts in the physical sciences. This project aims to make use of the recent developments in low cost electronics, sensors and optics with advances in data analysis technique to produce a step change in how experiments can be performed to study host/pathogen interactions. Through automation of data collection and analysis results can be produced in days instead of months. The technique applied to the study of invasion phenotyping for malaria can aid the acceleration of vaccine development with the prospect of applying the know-how from the project to other infectious diseases.


Scientific dissemination
The results of the project will be disseminated through usual scientific channels with publication in high impact journals and presentations at international conferences. In addition there will be on-going collaboration with malaria groups in the UK, in particular Julian Rayner at the Wellcome Sanger Institute and Jake Baum in the Life Science Department at Imperial College who will have input on the scientific programme as well as being beta testers of the automated systems. The partners also have considerable experience with outreach projects with the microscope demonstrated at numerous events in Cambridge and further afield, with microscopes for education taken to countries including India, Gambia and Tanzania. The project partners will continue to support outreach activities with inclusion of results from the project.

Economic Impact
The ability to produce a system that can produce results at least an order of magnitude faster than current methods offers opportunities for a range of medical applications. The scaling up of the system within the project will be supported by the commercialisation partner, WaterScope, who will be involved with the project from the onset by offering free consultancy. WaterScope are a spin out from the University of Cambridge which is developing microscopy based products including rapid bacteria testing for drinking water and low-cost malaria testing systems. The project partners including WaterScope have experience working together and also with Cambridge Enterprise, the University's Technology Transfer Office and so are well placed to capture and exploit any IP generated by the project. In addition funding is requested for attendance for one of the post-doctoral researchers on the Impulse Entrepreneurship programme which will be an opportunity to evaluate commercial viability of outputs from the project under the mentorship of successful serial entrepreneurs from the Cambridge community.