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

海洋通常被认为是巨大的和不可改变的，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很多事情（例如，通过提供海鲜，甚至我们呼吸的氧气来自数十亿海洋浮游植物的活动），而且，这些海洋服务受到海洋化学变化的威胁，因为大气中二氧化碳的增加。为了扩大我们对海洋生态系统脆弱性的了解，该项目的目标是研究海洋生物对环境变化的适应能力，方法是检查它们的早期阶段（胚胎和幼虫）对海洋压力的耐受性，例如温度升高和海洋化学变化。这个项目的研究生物是紫色海胆，一种常见的海洋无脊椎动物，发现于加州海岸。虽然这看起来像是一个奇怪的选择，但紫色海胆一直是发育生物学中的模型研究生物，科学家们对它们的胚胎发育有很多了解。对于该项目，研究人员将使用分子生物学工具，其中一些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环境压力下的成功率。该项目的新见解可能会为海洋生物如何以及如何快速适应海洋环境的变化带来一些光明和希望。该项目的目标是研究“基因组到表型组”的概念，并研究有助于生物体生理能力快速变化以应对环境变化的机制，这些机制将在生态而不是进化的时间尺度上运作。该模型系统是早期的生活史阶段的紫色海胆Strongylocentrotus purpuratus，和PI将集中在两个过程：代内可塑性和跨代可塑性（TGP），他们将专门询问表观遗传机制，可能会改变基因表达在早期阶段的海胆在快速的时间尺度。对于环境-生物相互作用，PI将侧重于共同发生的多个非生物因素（pCO 2，氧气和温度），这些因素与生态相关，在紫海胆近岸栖息地中变化很大，预计在未来气候变化情景中会发生急剧变化。该项目将在全球变化的背景下探索生态表观基因组学。在方法上，PI计划进行以下工作：（1）在不同的pCO 2和温度条件下培养海胆，然后进行测定，以测试后代的生理耐受性（生长、代谢率和脂质含量），（2）对DNA甲基化的总体模式使用两种筛选测定：基于ELISA的方法，测量基因组DNA样品中5-甲基胞嘧啶（5-mC）的水平，以及甲基化敏感性扩增多态性（MSAP）测定，（4）使用RNA-Seq评估基因表达模式，和（5）使用测序技术，在这种情况下，RNA-Seq与全基因组亚硫酸氢盐甲基化测序组合，进行幼虫转录组和甲基化组的同时分析。

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.