Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

Abstract

Background Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value fluctuations from video. They offer significant potential in addressing the phenotyping bottleneck in biology and are effective at identifying lethal endpoints and measuring specific functional traits, but the extent to which they might contribute additional understanding of the phenotype remains unknown. Consequently, here we test the biological significance of EPTs and their responses relative to fundamental thermodynamic principles. We achieve this using the entire embryonic development of Radix balthica, a freshwater pond snail, at different temperatures (20, 25 & 30 °C) and comparing responses against predictions from Arrhenius’ equation (Q10 = 2). Results We find that EPTs are thermally sensitive and their spectra of frequency response enable effective high-dimensional treatment clustering throughout organismal development. Temperature-specific deviation in EPTs from thermodynamic predictions were evident and indicative of physiological mitigation, although they differed markedly in their responses from manual measures. The EPT spectrum was effective in capturing aspects of the phenotype predictive of biological outcomes, and suggest that EPTs themselves may reflect levels of energy turnover. Conclusions Whole-organismal biology is incredibly complex, and this contributes to the challenge of developing universal phenotyping approaches. Here, we demonstrate the biological relevance of a new holistic approach to phenotyping that is not constrained by preconceived notions of biological importance. Furthermore, we find that EPTs are an effective approach to measuring even the most dynamic life history stages.

LabEmbryoCam: An opensource phenotyping system for developing aquatic animals

“…Aquatic embryos are emerging as natural models for phenomics.They are scalable in both size and taxonomic diversity, and are also the most dynamic stage of life, during which organisms' typically have heightened sensitivity to their environment [4]. Repeated video observation of individual embryos has proven a powerful method for assessing long term changes in growth and movement, via visualization of embryonic development as a timelapse, and as an approach to measuring real-time physiological responses such as heart rate, behaviour and machine proxy traits [5,6,7,8,9,10]. The LabEmbryoCam is optimized towards efficiently achieving repeated video image acquisition of embryos in a multiwell plate format for the duration of development, or an experiment.…”

“…To assess the capability of video produced using the LabEmbryoCam for automated image analysis, it was analysed using the open-source Python package EmbryoCV [7]. EmbryoCV produced effective measures of change to size, movement, and also energy proxy traits -energy in the spectrum of fluctuating pixel values, an emerging transferrable phenotyping approach [8,11] (Figure 14). The LabEmbryoCam was effective in generating video of a quality that enabled the extraction of continuous individual-level physiological data, including growth, movement and energy proxy traits.…”

Phenomics as an approach to Comparative Developmental Physiology

“…Now, phenomics is regularly utilised in characterising the genetic basis of complex traits, for tackling disease ( Denny et al, 2010 ; Pendergrass et al, 2011 ; 2013 ; Hebbring, 2014 ; Özdemir, 2020 ), selective breeding ( Crossa et al, 2021 ) and in the characterisation of responses to toxicants ( Audira et al, 2020 ; 2021 ; Hussain et al, 2020 ). Phenomics is also becoming increasingly utilised in the assessment of responses to environmental change, particularly within the crop sciences (e.g., Warringer et al, 2003 ; Schnaubelt et al, 2013 ; Singh et al, 2018 ; Adhikari et al, 2019 ; Li et al, 2019 ; Marsh et al, 2021 ; Tills et al, 2021 ; 2022 ).…”

“…Due to the disjunct between the amount of phenotypic information acquired, and what could be feasibly analysed manually by a user, we began considering holistic and non-supervised approaches to measuring development–moving away from trait-specific approaches ( Tills et al, 2013 ; Tills et al, 2022 ). Most recently, in an attempt to integrate as broad a range of a developing organism’s physiology and behaviour, this has taken the form of an approach termed ‘energy proxy traits’ ( Tills et al, 2021 ). EPTs measure all observable movement-based characteristics of an individual in a video as a spectrum of energy associated with frame-to-frame signals in the brightness of fluctuating mean pixel values.…”

A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures

“…Phenomics has enabled the tackling of key challenges including the production of drought-resistant crops in plant sciences, and identifying disease phenotypes in biomedicine ( Furbank and Tester, 2011 ; Großkinsky et al, 2015 ; Neto and Borém, 2015 ; Alexandrov et al, 2016 ; Tardieu et al, 2017 ; Davatzikos et al, 2018 ). Despite the pressing need to assess phenotypic sensitivity to global climate change, the use of phenomics in environmental physiology and developmental biology remains comparatively scarce ( Tills et al, 2018 , 2021 , 2023 ). However, ‘energy proxy traits’ (EPTs) have emerged as a tractable approach to phenomics when using early life stages as objects of study ( Tills et al, 2018 , 2021 ).…”