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

开发用于测量水生胚胎整个生物体环境敏感性的自动分析系统

• 批准号: NE/P003796/1
• 负责人: Simon Rundle
• 金额: $ 15.77万
• 依托单位: Plymouth University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FP003796%2F1
• 关键词: Development; automated; analytical; system; measurement

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.

我们的星球正在经历前所未有的环境变化，迫切需要了解物种如何应对改变的非生物条件。最近，随着新技术的发展，生物学发生了一场革命，工具的出现使我们能够在分子和基因的水平上以极其精细的细节量化生物体对环境变化的反应。这种测量生物体如何对环境变化做出反应的技术方法已经成为整个生物学的中心主题。然而，测量整个生物体水平反应的技术并没有跟上步伐，导致我们对这两个生物组织水平的理解脱节。这种脱节在很大程度上是由于以一种有意义的方式量化在整个生物体水平上观察到的形式和功能的复杂性和多样性的挑战。在整个有机体水平上量化形态和功能的任务对处于早期发育阶段的生物体来说是最具挑战性的，因为它们的形态和功能都经历着动态的转变。然而，正是在这个时候，生物体可能对环境压力最敏感。此外，胚胎在这种压力下的经历可能会影响到以后的生命阶段，包括生殖。因此，重要的是将环境压力对生命早期阶段的影响纳入监测和预测生物体将如何应对预测的全球环境变化。我们实验室的一个主要目标是更好地了解环境压力因素如何影响水生无脊椎动物早期生命阶段的生理。我们已经开发出一种独特的生物成像能力，使我们能够在严格控制的环境条件下制作高分辨率（时间和空间）的胚胎发育延时视频。然后，我们从这些视频中提取数据，使用人工视频分析来量化它们的生理功能。这种手动数据提取非常耗时，而且容易出错，而且是一个主观的过程。因此，图像分析过程构成了这种方法的有效性和应用的主要瓶颈，该方法用于量化大量生物体对环境变化的反应。该项目的主要目的是开发一个包含图像分析管道的分析平台，该平台可以自动测量视频中的各种胚胎特征。为了实现这一目标，我们将建立图像分析管道来测量功能相关特征，包括生长、粗大运动、肌肉收缩、心脏功能、发育阶段和发育速度。图像分析管道将嵌入到一个分析平台中，创建一个系统，用于测量个体胚胎的不同功能特征。两种物种（海洋虾和淡水蜗牛）对不同温度的短期和长期反应将用于开发、优化和验证分析框架。由此产生的数据将能够无与伦比地测量发育生物体对包括环境压力在内的因素的反应。这个分析平台将是一个强大的工具，任何有兴趣测量在透明卵胶囊中发育的生物体表型的领域，如环境敏感性测量，生态毒理学和药物发现。不断上升的全球平均温度正在威胁淡水和海洋生态系统，使用对比温度将能够评估自动化分析平台在量化早期生命阶段对当前全球威胁的敏感性方面的有效性。本项目正在开发的分析资源将有助于开发一种全自动能力，用于测量不同水生物种胚胎阶段对环境胁迫的反应和敏感性。

项目成果

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses.

• DOI: 10.1186/s12859-021-04152-1
• 发表时间: 2021-05-06
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Tills O;Spicer JI;Ibbini Z;Rundle SD
• 通讯作者: Rundle SD