A platform for environmental phenomics

The planet is undergoing an unprecedented environmental alterations and there is an urgent need to understand how species will respond to altered conditions associated with climate change (global warming, sea level rise, ocean acidification) and pollutants. Development of new technologies has recently seen a revolution in Biology with the advent of tools that enable us to quantify, in extremely fine detail, how organisms respond to environmental change at the level of molecules and genes. Such environmental -omics approaches to measuring how an organism responds to changes in their environment have become a major theme in Biology, particularly for molecular level -omics. These approaches rely on technologies to automate the generation of large quantities of data in a high-throughput manner.
A major objective in our laboratory is to gain a better understanding of how environmental stressors affect the physiology (i.e. the function) and morphology (i.e. the form) of early life stages in aquatic invertebrates. These observable characteristics, the phenome, provide important information on responses at the level of the whole-organism. We have developed a unique bioimaging technology for quantifying the phenome in aquatic embryos. This platform, produces high-resolution (temporal and spatial) time lapse video of large numbers of developing embryos, exposed to tightly controlled environmental conditions. This video is used to quantify aspects of embryonic growth, morphology and physiology. Initially this data extraction was primarily via manual observation, which creates a bottleneck in the application of this technology. Consequently, we have recently developed analytical software that works complimentary to the bioimaging technology and which automates the quantification of the phenome in large numbers of embryos. The analytical software enables the quantification of the phenome from hundreds of millions of images with a resolution and scale that is not possible via manual analysis and consequently it significantly increases the power and high throughput nature of this technology.

This pathfinder award would facilitatate market research to determine whether our platform for measuring phenomic responses of aquatic invertebrate embryos has the potential to be extended for use as a general tool in environmental phenomics research, including applications in ecotoxicology and other environmental impact studies. Potential users such as NGOs, water authorities, environmental consultancies and companies in the chemical, pharmaceutical, dyestuffs, plastics and laboratory equipment sectors will be identified and canvassed; and phenomics activities at institutions in UK and elsewhere will be identified. The aim is to use this research to direct and drive a NERC follow-on fund proposal to carry our research targeting phenomic measurements that are of relevance to potential markets.

Our current POC grant is focused on developing automated analytical pipelines to facilitate phenome-wide physiological measurements in non-model organisms would enable more robust predictions of biological sensitivity to environmental change. Such a capability would be of potential interest to bodies such as the Intergovernmental Panel on Climate Change (IPCC), the United Nations Framework Convention on Climate Change (UNFCCC), the Convention on Biodiversity (CBD), the European Environment Agency (EEA) and the UK Environment Agency (EA) in their obligations under the Water Framework Directive to improve and maintain water quality, in this case the biological quality and adaptive potential of freshwater species. The research that would be undertaken through a Pathfinder award would allow us to evaluate and adapt (through a follow on fund) our phenomics capability within regulatory, Environmental Impact Assessment (EIA) contexts, such as those required for chemicals, animal health products, nanotechnology products and human health products. Within the eco-toxicology industry a broader range of test organisms and more efficient way of identifying early warning biomarkers of environmental effects could lead to both Reductions in the volume of (protected) animal research, but also Refinements of the end points being employed; two of the three principle aims of the 3Rs.