Developing an integrative approach to phenomics for industrial biomedical and environmental applications

Advances in understanding complex biological responses have never been so urgent given the unprecedented rates of local and global environmental change, and the increasing pressures on biological systems. Embryos are extremely sensitive to environmental change and exhibit incredible diversity and dynamism in spatial, functional and temporal phenotypic change. They therefore present a unique system for pushing the boundaries of how we measure complex biological responses to an increasingly complex and anthropogenically impacted natural world. The first four years of my FLF supported the development of entirely new technologies and approaches for measuring environmental sensitivity during the earliest stages of life, in marine and freshwaters. The Fellowship supported moving research away from traditional manual phenotypic approaches to measuring the biology of developing animals at their most dynamic, and moving towards integrative, data-rich and scalable methods of measuring whole-organismal biological responses.

I will use a three year extension to my FLF, broadly in line with my initial Fellowship, to drive impact from the innovation to date by: i) Establishing the capability for predictive phenomics in developing organisms, to enable biological responses to be predicted via timeseries models trained using deep learning on the basis of the previous developmental phenotype. This will have broad relevance for predicting sensitivity, artificially selecting for particular outcomes in later life and enabling dynamic feedback loops within experiments to assess the time-specific effects of different environmental drivers. ii) Creating digital twinning between laboratory and field instruments to enable dynamic environmental synchronisation of field conditions in the laboratory to assess the real-time biological impacts of simulated environmental events in the field. iii) Extending the user base of the EmbryoPhenomics instrumentation and research approaches to different research areas, continents and sectors. Working with local user groups and the open-source hardware community we will extend the applicability of these approaches to the challenges of different stakeholders.

Establishing a global community of users will support environmental sensitivity experiments being run in parallel globally, but will also enable a concerted effort to document the visible physiological diversity of organisms during their early life, via timelapse bioimaging. The resulting video will be maintained in the first open-source repository of developing organisms and will be invaluable to both researchers, but also as a resource for shining a light on the hidden world of biological development, within the context of global environmental change.