Mechanisms of physiological plasticity in early stage marine invertebrates in response to multiple stressors - epigenomic perspective in a global change context

海洋通常被认为是辽阔而一成不变的，能够吸收环境变化。然而，我们越来越意识到，海洋为我们人类做了一些事情(例如，通过提供海鲜，甚至通过提供我们从数十亿海洋浮游植物活动中呼吸的氧气)，而且，由于大气中二氧化碳的增加，这些海洋服务受到海洋化学变化的威胁。为了扩大我们对海洋生态系统脆弱性的了解，该项目的目标是通过研究海洋生物早期阶段(胚胎和幼体)对海洋中压力的耐受性，如更高的温度和海洋化学变化，来研究海洋生物对环境变化的适应能力。该项目的研究生物是紫海胆，一种在加州海岸发现的常见海洋无脊椎动物。尽管这似乎是一个奇怪的选择，但紫色海胆一直是发育生物学的模型研究生物，科学家们对它们的胚胎发育了解很多。在该项目中，研究人员将使用分子生物学工具，其中一些工具是在人类癌症生物学中开发的，以确定基因表达的时机如何提高胚胎和幼虫在面临环境压力时的成功。这个项目的新见解可能会为海洋生物如何以及以多快的速度适应海洋环境的变化提供一些线索和希望。该项目的目标是研究“基因组到物候组”的概念，并研究促使生物体生理能力随着环境变化而迅速变化的机制，这些过程将在生态而不是进化的时间尺度上运行。模型系统是紫海胆的早期生活史阶段，PI将专注于两个过程：代内可塑性和跨代可塑性(TGP)，他们将专门询问可能在快速时间尺度上改变早期海胆基因表达的表观遗传机制。对于环境与生物的相互作用，PI将侧重于共同出现的多种非生物因素(二氧化碳、氧气和温度)，这些因素在生态上相关，在紫海胆近岸栖息地高度可变，并预计在未来的气候变化情景中将发生巨大变化。该项目将探索全球变化背景下的生态表观基因组学。在方法上，PI计划做以下工作：(1)在不同的二氧化碳浓度和温度条件下培养海胆，然后测试后代的生理耐受性(生长、代谢率和脂肪含量)，(2)使用两种DNA甲基化全球模式的筛选方法：基于ELISA的方法，测量基因组DNA样本中5-甲基胞嘧啶(5-MC)的水平，以及甲基化敏感扩增多态性(MSAP)分析，(4)使用RNA-Seq评估基因表达模式，以及(5)使用Illumina®测序技术同时分析幼虫转录组和甲基组RNA-Seq结合全基因组亚硫酸氢甲基化测序。

The ocean is often viewed as vast and immutable, capable of absorbing environmental change. However, we are increasingly aware that the ocean does things for us as humans (e.g. by providing seafood, and even the oxygen we breath that comes from the activity of billions of marine phytoplankton), and further, that these ocean services are threatened by changes in ocean chemistry because of increased carbon dioxide in the atmosphere. To expand our knowledge about the vulnerability of marine ecosystems, the goal of this project is to study the resilience of marine organisms to environmental change by examining the tolerance of their early stages (embryos and larvae) to stresses in the ocean such as higher temperatures and changes in ocean chemistry. The study organism of this project is the purple sea urchin, a common marine invertebrate found on the California coast. Although this might seem like an odd choice, purple urchins have been model study organisms in developmental biology and scientists know a great deal about their embryos' development. For the project, the researchers will use molecular biology tools, some that were developed in human cancer biology, to determine how the timing of gene expression can improve the success of embryos and larvae in the face of environmental stress. New insight from this project will likely shed some light, and some hope, on how, and how fast, marine organisms can adjust to changes in their marine environment. The goal of this project is to study the "genome to phenome" concept, and to investigate mechanisms that contribute to rapid shifts in organismal physiological capacities in response to environmental change, processes that would operate on ecological rather than evolutionary time scales. The model system is the early life-history stages of the purple sea urchin Strongylocentrotus purpuratus, and the PIs will focus on two processes: intragenerational plasticity and transgenerational plasticity (TGP) where they will specifically interrogate epigenetic mechanisms that may alter gene expression in early stage urchins on a rapid time scale. For the environment-organism interaction, the PIs will focus on co-occurring multiple abiotic factors (pCO2, oxygen and temperature) that are ecologically relevant, are highly variable in the purple urchin nearshore habitat, and are projected to change drastically in future climate change scenarios. The project will explore ecological epigenomics in a global change context. Methodologically, the PIs plan to do the following: (1) raise cultures of sea urchins at variable pCO2 and temperature conditions followed by assays to test physiological tolerances of the progeny (growth, metabolic rate and lipid content), (2) use two screening assays for global patterns of DNA methylation: an ELISA-based method that measures levels of 5-methylcytosine (5-mC) in samples of genomic DNA, and the methylation-sensitive amplification polymorphism (MSAP) assay, (4) use RNA-Seq to assess gene expression patterns, and (5) perform concurrent profiling of the larval transcriptome and methylome using Illumina® sequencing technology, in this case, RNA-Seq combined with whole genome bisulfite methylation sequencing.