EmbryoPhenomics: A New Technology For Capturing The Dynamic Process Of Embryonic Development

Genomics is the study of the molecular basis of life and has boomed as a result of new technologies. Genomics adopts a reductionist approach to understanding life – studying how the smallest components of an organism work or respond to the environment. There is no doubt that this approach is now central to every area of biological and medical research and has driven significant advances in our understanding.

In contrast, technologies for studying the whole-organism are less-well developed, particularly when it comes to the scale and quality of data that researchers can produce (Kültz 2013). Phenomics is the acquisition of high-dimensional data on an organism-wide scale – and is the natural complement to genomics. Put simply, it is the application of technology to quantify the phenotype — the observable characteristics of whole organisms — thoroughly and with high precision. Phenomics is already being used in plant science and medicine, but it remains a relatively unexplored approach in biology, perhaps due to a lack of appropriate technologies (Houle et al 2010).

Fig. 1. The EmbryoPhenomics facility at the University of Plymouth. Image courtesy Oliver Tills.

EmbryoPhenomics

Embryonic development is the most dynamic life stage with significant changes happening temporally, spatially, and functionally. Manual approaches to quantifying development will always be suboptimal, not surprising, given the mind-boggling complexity of the biological processes involved. So, scientists at the University of Plymouth have developed EmbryoPhenomics, new phenomics technology for studying aquatic embryos. This technology consists of custom bioimaging hardware (OpenVIM) and analytical software (EmbryoCV). OpenVIM records the entire development (days, weeks, or even months) of hundreds of microscopic embryos while simultaneously controlling the embryonic environment. EmbryoCV uses autonomous image analysis to analyze the hundreds of thousands of images of each developing embryo acquired by OpenVIM in order to quantify biological responses including changes in growth, behavior, cardiac activity, and overall health. The key strengths of this approach are that it captures biological responses that would not be noticed using traditional manual observation and it can analyze large numbers of embryos simultaneously.

The embryonic development of a pond snail from Oli Tills on Vimeo.

Fig. 2. The 10-day development of a freshwater snail in just 30 seconds. Video courtesy Oliver Tills.

EmbryoPhenomics technology appears in a new study published in PLoS Biology. Here, it is applied to assessing the vulnerability of early life stages of a marine shrimp and a freshwater snail to climate change-related drivers. The researchers used the technology to measure the response of > 350 aquatic embryos of two quite different species, in a range of experiments that consisted of > 30 M images. They discovered that animals had fundamentally different developmental trajectories under increased temperatures, including those that embryos are already experiencing in their environments. Furthermore, a combination of temperature and salinity stress had even greater effects on growth and behavior, which is particularly worrying given that climate change is leading to changes in a broad range of environmental parameters.

EmbryoPhenomics – a novel technology from Oli Tills on Vimeo.

Fig. 3. The developmental trajectories of 140 freshwater snails in different temperatures. Video courtesy Oliver Tills.

While providing important insights into the potential effects of climate change, the high-dimensional data produced by EmbryoPhenomics also helps us to understand better the complex process of development. The team are currently streamlining the technology and developing more advanced analytics with the help of artificial intelligence to further enhance the capability of this cutting-edge approach.

These findings are described in the article entitled A high-throughput and open-source platform for embryo phenomics, recently published in the journal PLOS Biology.

Video produced using OpenVIM: www.vimeo.com/channels/embryonicdevelopment. Information about the EmbryoPhenomics technology: www.embryophenomics.org

References:

  1. Houle, D., Govindaraju, D.R. & Omholt, S., 2010. Phenomics: the next challenge. Nature Reviews Genetics, 11: 855–866.
  2. Kültz, D. et al., 2013. New Frontiers for Organismal Biology. BioScience, 63: 464–471.

About The Author

Oliver Tills

Oliver Tills is a Teaching and Research Associate (Marine Biology) at the School of Biological & Marine Sciences (Faculty of Science & Engineering), University of Plymouth.

I am fascinated by the dynamic process of embryonic development in aquatic organisms. During this process there are complex and interconnected changes happen on a second, minute, hour and daily timescale and this includes changes in morphology, physiology and behaviour.

My research focusses on understanding the implications of this variation for ecological and evolutionary processes. This has required the development of new technologies and approaches for capturing the dynamic process of embryonic development in unprecedented temporal, spatial and functional resolution. EmbryoPhenomics http://www.embryophenomics.org is a high-throughput technology that incorporates bioimaging hardware and software and which quantifies the process of embryonic development in new ways. While I am a biologist by training, I have spent a significant portion of my time developing new bioimaging technologies and writing software for high-throughput image- and data-analysis in Python and R.

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