Development of an automated analytical system for measurement of whole-organism environmental sensitivity of aquatic embryos

Lead Research Organisation: University of Plymouth
Department Name: Sch of Biological and Marine Sciences

Abstract

Our planet is undergoing unprecedented environmental change and there is an urgent need to understand how species respond to altered abiotic conditions. Development of new technologies has recently seen a revolution in Biology with the advent of tools that enable us to quantify how organisms respond to environmental change at the level of molecules and genes in extremely fine detail. This technological approach to measuring how an organism responds to changes in their environment has become a central theme across Biology. However, technologies for measuring whole-organism level responses have not kept pace, leading to a disconnect between our understanding at these two levels of biological organization. This disconnect is due, in large part, to the challenge of quantifying, in a meaningful way, the complexity and diversity of form and function that is observed at the whole-organism level.

The task of quantifying form and function at the whole-organism level is most challenging for organisms during their early development when both form and function are undergoing dynamic transitions. Yet it is at this time when organisms may be most sensitive to environmental stress. Furthermore, the experience of embryos to such stress can have impacts that persist into later life stages, including reproduction. It is therefore important that the effects of environmental stress on early life stages are incorporated into monitoring and prediction of how organisms will respond to forecasted global environmental change.

A major objective in our laboratory is to gain a better understanding of how environmental stressors affect the physiology of early life stages of aquatic invertebrates. We have developed a unique bio-imaging capability that allows us to produce high-resolution (temporal and spatial) time lapse video of developing embryos, exposed to tightly controlled environmental conditions. We then extract data from these videos to quantify their physiological function using manual video analysis. Such manual data extraction is time consuming and can be an error-prone and subjective process. Consequently, the process of image analysis forms a major bottleneck in the efficacy and application of this approach to quantification of the responses of large numbers of organisms to environmental change.

The main aim of this project is to develop an analytical platform encompassing image analysis pipelines that automate the measurement of a wide range of embryonic features from video. To achieve this we will build image analysis pipelines for measuring functionally relevant traits including growth, gross movement, muscle contraction, heart function, developmental stage and developmental rates. Image analysis pipelines will be embedded within an analytical platform creating a system for organism-wide measurement of different functional traits in individual embryos. Short- and long-term responses of two species (a marine shrimp and freshwater snail) to contrasting temperatures will be used to develop, optimize and validate the analytical framework. The resultant data will enable unrivalled measurement of the responses of developing organisms to factors including environmental stress. This analytical platform would be a powerful tool to any field with an interest in measuring phenotypes in organisms developing in transparent egg capsules e.g. environmental sensitivity measurement, ecotoxicology and drug discovery.

Increasing mean global temperatures are threatening both freshwater and marine ecosystems and the use of contrasting temperature will enable assessment of the efficacy of the automated analytical platform in quantifying the sensitivity of early life stages to a current global threat. The analytical resource being developed in this project will facilitate the development of a fully automated capability for measuring the responses and sensitivities of embryonic stages to environmental stress across different aquatic species.

Planned Impact

The main non-academic beneficiaries of the technology developed during this project will be organisations that could benefit from automated high-throughput systems for phenome-wide measurements. Such organisations include, but are not limited to those that have set agendas focused on prediction and mitigation of the effects of climate change on the world's ecosystems and that quantify the responses of aquatic organisms to environmental pollutants. Phenome-wide physiological measurements in non-model organisms would enable more robust predictions of biological sensitivity to environmental change that would be of considerable interest to the Intergovernmental Panel on Climate Change (IPCC), the United Nations Framework Convention on Climate Change (UNFCCC) and the Convention on Biodiversity (CBD). Within Europe the EU Commissions White paper Adapting to Climate Change, encouraged the development of "measures that address biodiversity loss and climate change in an integrated manner". At the European level, the project outcomes will be of interest to the European Environment Agency (EEA) and its agenda to "...help the Community and member countries make informed decisions about improving the environment".

At the National level, the analytical platform developed in this project relates directly to NERC's overall goal of "delivering world-leading environmental research at the frontiers of knowledge enabling society to respond urgently to global climate change and the increasing pressure on natural resources, contributing to UK leadership in predicting the regional and local impacts of environmental change and creating, and supporting vibrant, integrated, research communities". The technology and its results will also be of relevance to the 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. We will also make results and the technology developed during this project available to DEFRA's Climate Change Risk Assessment 2017.

Research from this project will be disseminated through engagement via educational resources. An educational resource is currently being built by the PI and PDRA, based on videos and data generated using our bio-imaging hardware. This resource provides Virtual Experiments for secondary and undergraduate level educators, offering schools, colleges and universities a cost-effective way of giving pupils important experience in biological observation and experimentation. Video generated during the course of this project will be made available within this educational framework and form a range of educational resources made available to both local schools and undergraduate level Marine Biology students at Plymouth University. Furthermore, during the course of this project the research team will disseminate the aims and technological developments of the project to the public via a public lecture, facilitating dissemination to a wide audience.

The analytical platform developed during the course of this project could have socio-economic impact within the eco-toxicology industry by making viable a broader range of organisms than the traditional model organisms. This could lead to both Reductions in the volume of (protected) animal research, but also Refinements of the end points being employed. These are two of the three principle aims of the 3Rs.

Publications

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Title Noisy Embryos Exhibition (Cambridge Science Festival 
Description Video and data from the project were used to create the artwork and exhibition 'Noisy Embryos' by the art-science group RADIX, which was shown at the Ruskin Gallery in Cambridge as part of the Cambridge Science Festival 2017. This included a joint talk with Prof Nick Hopwood (Cambridge University) entitled 'Noisy embryos: from the bane of embryology to indicators of the Anthropocene', which was also part of the Cambridge Science Festival 2017. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact The art-science collaboration between the PI (Rundle) and artists Deborah Robinson and David Strang has continued and the RADIX collective are currently writing an AHRC proposal with Social Scientists and Philosophers of Science at the University of Exeter. 
 
Description Phenomics is the acquisition of high-dimensional data of the observable characteristics (morphology, behaviour, physiology) of organisms. It is analogous and complementary to genomic approaches that investigate organismal respones at the molecular level, and has a similar potential to facilitate advances in biology. Whereas genomics can benefit from an abundance of standardised tools and technologies that are readily applicable to different species and scales of study, phenomics requires the development and application of less generic approaches. Consequently the availability of tools for generating high-dimensional phenotypic data remains a constraint in the ability to apply phenomics in biology. We have developed a versatile, modular platform that allows the automated, concomitant production of phenotypic data from large numbers of embryos exposed to different environmental conditions. This platform comprises bio-imaging hardware for videoing replicate embryos under controllable conditions and analytical software that automatically extracts data from these videos. We validated this platform by comparing automated, phenomic measurements with those generated using standard (manual) measurements, showing that it successfully quantified traits including growth rates, movement rates, cardiac rates and lethal end points. We then applied our approach in experiments assessing chronic and acute stress responses in aquatic invertebrate embryos. These experiments have led to important, new biological findings. In response to chronic exposure to different temperature regimes, we identified different functional responses at the phenome level, with temperature-dependent effects on form (growth), function (cardiac output) and behaviour (cumulative movement). Exposure to extreme temperatures revealed differences in levels of sensitivity between developmental stages, with early stages showing decreased survival rates in response to chronic exposure. Short-term exposure to multiple stressors (elevated temperatures and salinity), revealed interactive effects on growth and movement. Together, these experiments have highlighted the importance of phenomic responses early in development for gauging the effects environmental stress and demonstrate the promise of this technology in providing novel insights into the biological effects of environmental change.
Exploitation Route We obtained a NERC Pathfinder award to investigate the commercial potential of our technology. We are now in discussions with potential end users in the Ecotoxicology and Water Quality sectors to identify key chemicals and endpoints for further testing in our platform. Our phenomic approach will also be of use to researchers interested in gauging stress responses in a range of organisms and in those interested in mapping responses at the molecular (e.g. transcriptomic) level with those at the level of the phenotype.
Sectors Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

 
Description Pathfinder
Amount £18,000 (GBP)
Funding ID NE/R002142/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2017 
End 08/2017
 
Title A technological platform for phenomics in aquatic embryos 
Description Embryo-phenomics is a fully automated platform comprising hardware and software for measuring phenomic responses of aquatic embryos. The embryo-phenomics hardware is modular and versatile and the Python based high-throughput software extracts data from large image datasets quantifying morphological and physiological traits in developing aquatic embryos. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2018 
Provided To Others? No  
Impact This research tool is facilitating a new approach to quantifying responses of aquatic embryos to environmental stress, with unparalleled scale and precision. It has been applied to a number of different species and experimental designs, incorporating the analysis of > 100 M images and a paper describing the research technique and technology is in preparation. 
 
Description Italian Institute for Marine Science (ISMAR) - Simone Marini 
Organisation Italian National Research Council
Country Italy 
Sector Public 
PI Contribution Expertise in developmental eco-physiology, bio-imaging hardware and software development.
Collaborator Contribution Expertise in machine vision analysis and programming in Python.
Impact Conference and workshop presentations. Papers in preparation. Software developed.
Start Year 2016
 
Description Universidad Andres Bello - Enrico Rezende 
Organisation Andrés Bello University
PI Contribution Expertise in developmental eco-physiology and in automated bio-imaging technologies.
Collaborator Contribution Expertise in thermal sensitivity modelling.
Impact Paper in press. Joint PhD studentship. NERC standard grant application.
Start Year 2016
 
Description Dialogue on Methods for Ecology 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Round table event organised by British Antarctic Survey as part of the initiative for dialogue between ecologists and modellers. Presentation entitled 'An approach towards phenomics in aquatic embryos' was given by the project team.
Year(s) Of Engagement Activity 2016
 
Description Innovate UK Regional Meeting (Exeter) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact This was industrial strategy event organised by Innovate UK. A talk entitled 'Embryo phenomics: technological innovation for visualising temporal, spatial and functional diversity in developing embryos' was given by the project team.
Year(s) Of Engagement Activity 2018
 
Description Society for Experimental Biology Annual Conference presentation (Gothenburg) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The presentation 'An approach towards phenomics in aquatic embryos' was given by the project team at the SEB Annual Meeting in Gothenburg. This was part of the thematic session 'Climate Change and Aquatic Life: Effects of Multiple Drivers, from Molecules to Populations'.
Year(s) Of Engagement Activity 2017
 
Description University of Plymouth Industrial Strategy Event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact This event aimed to forge links between industry and academia and to explore opportunities for alignment with the UK governments industrial strategy. The talk 'Embryo phenomics: technological innovation for the future' was given by the project team.
Year(s) Of Engagement Activity 2018