A Systems Biology Platform for Predictive Ecotoxicology in Daphnia magna

The monitoring of the environment for adverse effects of chemical pollution is of paramount importance in maintaining biodiversity and environmental health. This is particularly important for the aquatic environment into which a wide range of pollutants find their way, for example from pesticide run-off, industrial spills and excess nutrients from the release of untreated sewage. Pollution remains a major problem in the UK, with the Environment Agency estimating that up to 82% of rivers are 'at risk' from chemicals such as nitrate and phosphorus. Often adverse impacts to these pollutants can only be identified when they are sufficiently severe so as to affect survival of organisms and thus are identifiable at a late stage, after the damage is done. Attempts have been made to use more sensitive molecular indicators of early change ("biomarkers") but these generally inform only on the levels of chemical exposure and have limited diagnostic or predictive power in relation to toxicity. Therefore the application of molecular biomarkers to environmental monitoring has been very limited to date.
Inspired by the tremendous success of recent technologies in biomedicine, we propose to develop an equivalent system for biomarker discovery in an environmental context, i.e., to develop biomarkers for application to environmental monitoring and diagnostics. These technologies can measure many thousands of biochemicals (including gene products and metabolites) in exposed organisms and by using mathematical and computational tools we can identify the underlying pathways to toxicity. These computational models will enable us to discover a set of genes and metabolites that can be highly predictive of an adverse impact on living organisms and at the same time provide a characteristic fingerprint of the type of pollutant class(es) responsible for such impact. We will study these effects in the water flea (Daphnia magna) which is already commonly used in the testing of contaminated water samples for toxicity. A wide range of chemicals representing major pollutant classes will be assessed and the molecular signatures will be compared to physiological responses in the water fleas. This will allow us to discover molecular signatures that have high diagnostic value in an ecological context, specifically telling us about the health and reproductive fitness of the water fleas. Also, the computational methods will allow us to discover molecular signatures that causally relate to the water fleas' health. This represents a major advance over current molecular biomarkers.
Once these characteristic fingerprints of molecules that are predictive of different toxicities are established, we will test such fingerprints to be predictive of the chemical makeup of water samples taken from polluted environments and with proven environmental impact. Such sampling will be in collaboration with our project partner, the Environment Agency. We will be "blinded" to the nature of these samples, enabling a robust evaluation of our ability to (1) determine the "ecological status" of the water and (2) diagnose the underlying pollutant class, thus enhancing the regulators' ability to target remedial measures. Following this validation of the new predictive biomarkers we will convert them into simple, rapid and economic assays, resulting in the provision of a new generation of environmental monitoring tools. After the project, and through our collaborations with end-users in the UK, Europe and North America, we will seek to pilot our molecular biomarkers alongside conventional biological and chemical monitoring, e.g. as part of the Water Framework Directive. In summary, this exciting project is interdisciplinary, involving fundamental biochemistry and physiology, toxicology, molecular biology and bioinformatics, and promises a significant advance in the tools available to monitor the health of our environment.

The impact of this work relates to both the academic community and to a range of end users with interests in the maintenance of a healthy environment. Regarding the former, the provision of the first comprehensive integrated "molecular-physiology effects" dataset representing the response of an organism of relevance for environmental and toxicological assessment of chemicals will be an invaluable resource for academic researchers in ecotoxicology. The academic community within toxicology will benefit specifically from improved understanding of mechanisms of toxicity and by gaining a crucial knowledge for progressing the safety of chemicals such as pesticides and drugs. The pipeline we will develop and validate will represent an important reference for establishing a gold standard for 2nd generation biomarker discovery in the NERC and environmental biology international communities. Furthermore, the methodologies to be developed will help the progression of systems biology as an academic discipline well beyond the environmental biology area. The research will play a role in enhancing the integration of the disciplines of mathematics, computer science and biology. The early career researchers on the project will also benefit from expertise developed within a multidisciplinary research environment including interaction with end-users thus equipping them with skills appropriate for a future career at the interface between academia and industry or regulators in an environmental context.
The primary objective of this project is to develop, within the 3-year period, a proof-of-principle diagnostic approach for predictive ecotoxicology that is anticipated to have considerable value, in the future, within the context of the EU Water Framework Directive. Upon successfully demonstrating the value of this "2nd generation biomarker discovery" approach we plan to develop this into a practical and implementable tool for environmental monitoring and diagnostics. These tools will be directly relevant to "Good Environmental Status" (GES) defined as "Concentrations of contaminants at levels not giving rise to pollution effects". Hence the EA represents the major beneficiary within the UK. Other organisations involved in monitoring of the marine environment (Cefas and FRS within the UK and international organisations such as OECD, ICES and OSPAR will also benefit in the same way. Other organisations that would benefit from the novel diagnostic tools developed here are those associated with ecological risk assessment of chemicals not just confined to the aquatic environment, including industry (e.g. pharmaceutical companies such as AstraZeneca, Brixham Environmental Laboratory) and non-governmental organisations (e.g. Cefic, representing the European chemical industry) and the EC Joint Research Centre (JRC) for sustainable development. The novel biomarker sets will also be of value to international organisations beyond the EU such as the US Environmental Protection Agency and Environment Canada.

Ultimately there will be benefits to the wider public through improved and efficient monitoring of the environment for pollutant impact and thus maintenance of diversity in the countryside and enhancement of recreational sports such as fishing. Overall, the implementation of more efficient, more predictive and high-throughput assessment of the impact of pollutants in the environment, that should be achieved within 3 years of completion of the project, will be of benefit to regulators and policy makers, aiding more effective management of our water resources and the prioritisation of sites requiring remediation and thus offering benefits relating to health and wealth to society.