ABR: Evolution of Left-Right Asymmetry in Chordates using Cephalochordates as a Proxy for the Ancestral Chordate

琳达Z.荷兰，P.I. 提案编号：1353688 提案标题：ABR：用头节脊索动物作为祖先脊索动物的替代物研究脊索动物左右不对称性的演化 脊索动物（文昌鱼和文昌鱼）与脊椎动物密切相关，但在结构和基因水平上都比较简单，因为它们的基因组没有经历祖先脊椎动物中发生的两轮全基因组复制。虽然这些重复对人类很有用，因为一个基因的缺陷通常可以通过重复来弥补，但文昌鱼中缺乏基因重复使其成为确定单个基因如何共同创造胚胎和成人的理想选择。因为文昌鱼是如此的像脊椎动物，例如，肾脏或大脑的遗传机制在两个群体中基本上是相同的。不同之处在于，脊椎动物通过对这些基本机制的阐述，创造了额外的复杂性。 一个主要的悬而未决的问题是左/右（LR）不对称是如何演变的。脊椎动物表面对称，但内部器官在左/右（LR）轴上不对称排列。本研究旨在阐明LR不对称性的遗传机制，使用两个遥远的文昌鱼属（文昌鱼和文昌鱼）。重要的是，这两个属之间的杂交产生幼虫中间不对称。这项研究对于理解基因网络及其如何进化具有深远的意义。与生物信息学家的合作将有助于确定在特定发育阶段活跃的基因。它将给本科生提供研究经验。在2013-2014年，13名本科生，包括6个代表性不足的少数民族参加了荷兰实验室的研究。培养博士后1名。研究结果将在会议上提出，并发表在科学期刊上。与斯克里普斯的桦树水族馆和圣地亚哥联合学校的“通过技术加强科学教育"项目的外联活动将为中学生提供荷兰实验室的虚拟图尔斯之旅，并通过SKYPE进行直接互动。 这项工作将通过PI和合作者之间的学生/博士后交流促进跨学科教育，让生物信息学学生学习生物学，让生物学学生学习生物信息学。长期以来，人们一直认为底脊索动物文昌鱼是脊椎动物起源的线索。这一建议解决了一个主要的悬而未决的问题：什么是在脊索动物LR不对称性的遗传基础，它是如何改变在进化过程中？具体的目的是阐明的LR不对称的进化脊索动物使用两个遥远的文昌鱼属（Branchiostoma和Aparthon）作为代理祖先脊索动物。除了Nodal、Lefty和Pitx保守三联体在脊椎动物和文昌鱼胚胎中的左侧表达外，脊索动物LR模式化的基本遗传基础尚不清楚。建议LR不对称的规范从倾斜的母体节点开始，并通过BMP抑制右侧的节点来细化。文昌鱼胚胎的简单性允许从卵开始到脊椎动物样胚胎结束的基因网络的解剖。Branchiostoma和Aparthon提供了“金发女孩原则”-相似足以确保两种结构是同源的，而不同足以阐明LR不对称的遗传差异。两属间的杂种具有中间不对称性。荷兰实验室是研究B的先驱。floridae，是第一个在实验室中研究Aestheton发育并建立两个物种全年繁殖的物种。 测序A. lucayanum基因组，目前正在对A. lucayanum基因组。这两个属是相似的，但LR不对称性在几个方面有所不同。重要的是，文昌鱼的生殖腺在两侧，但阿龙只有在右边。该方法结合了原位杂交，抗体标记，操纵基因功能，RNA-Seq和生物信息学。LR图案和生殖细胞迁移的分子基础在这两个物种的比较将阐明LR不对称的脊索动物的基本基础和测试的整体假设，脊椎动物进化从文昌鱼样的祖先。这些结果不仅适用于头索动物，也适用于脊椎动物，并可能改变对脊椎动物无数变化的进化的看法，这些变化增加了一个小的非卵黄胚胎通过内陷原肠胚的基本主题。

Linda Z. Holland, P.I. PROPOSAL NUMBER: 1353688 PROPOSAL TITLE: ABR: Evolution of Left-Right Asymmetry in Chordates using Cephalochordates as a Proxy for the Ancestral ChordateNontechnical description/broader impacts Cephalochordates (amphioxus and lancelets) are closely related to vertebrates but simpler both structurally and at the gene level as their genomes have not undergone the two rounds of whole-genome duplication that occurred in ancestral vertebrates. While these duplications are useful for humans as a defect in one gene can often be compensated for by a duplicate, the lack of gene duplication in amphioxus makes it ideal for determining how individual genes work together to create an embryo and adult. Because amphioxus is so vertebrate-like, the genetic mechanisms that pattern, for example, the kidney or brain are fundamentally the same for both groups. The difference is that vertebrates have created additional complexity by elaborating upon these basic mechanisms. A major outstanding question is how left/right (LR) asymmetry evolved. Vertebrates are superficially symmetric, but internal organs are asymmetrically arranged across the left/right (LR) axis. This study aims to elucidate the genetic mechanisms of LR asymmetry using two distant amphioxus genera (Branchiostoma and Asymmetron). Importantly, hybrids between the two genera yield larvae intermediate in asymmetry. This study has far reaching implications for understanding gene networks and how they evolve. A collaboration with bioinformaticians will help identify genes that are active at particular developmental stages. It will give undergraduates research experience. During 2013-2014, 13 undergraduates including 6 under-represented minorities participated in research in the Holland laboratory. One postdoctoral fellow will be trained. Results will be presented at meetings and published in scientific journals. Outreach with the Birch Aquarium at Scripps and the San Diego Unified Schools' Enhancing Science Education through Technology program will give middle school students virtual tours of the Holland laboratory with direct interactions via SKYPE. The work will foster cross-disciplinary education via exchanges of students/postdocs between the PI and collaborators, allowing bioinformatics students to learn biology and biology students to learn bioinformatics. Technical descriptionThe basal chordate amphioxus has long been thought to hold clues to vertebrate origins. This proposal addresses a major unresolved question: What is the genetic basis of LR asymmetry in chordates and how has it changed during evolution? The specific aim is to elucidate the evolution of LR asymmetry in chordates using two distant amphioxus genera (Branchiostoma and Asymmetron) as proxies for ancestral chordates. Except for left-sided expression of the conserved triad of Nodal, Lefty and Pitx in embryos of both vertebrates and amphioxus, the fundamental genetic basis of LR patterning in chordates is elusive. It is proposed that specification of LR asymmetry begins with skewed maternal Nodal and is refined by BMP suppressing Nodal on the right. The simplicity of amphioxus embryos allows dissection of gene networks starting with the egg and ending with a vertebrate-like embryo. Branchiostoma and Asymmetron offer the "Goldilocks Principle"- alike enough to be sure that two structures are homologous and unlike enough to elucidate genetic differences in LR asymmetry. Hybrids between the two genera have intermediate asymmetry. The Holland lab pioneered research on B. floridae, was the first to study Asymmetron development and establish year-round breeding of both species in the laboratory. sequencing the A. lucayanum genome and is currently sequencing the A. lucayanum genome. The two genera are similar, but LR asymmetries differ in several respects. Importantly, Branchiostoma has gonads on both sides, but Asymmetron has them only on the right. The approach combines in situ hybridization, antibody labeling, manipulating gene function, RNA-Seq and bioinformatics. Comparisons of the molecular basis of LR patterning and germ cell migration in both species will elucidate the fundamental basis of LR asymmetry in chordates and test the overall hypothesis that vertebrates evolved from an amphioxus-like ancestor. The results promise to be applicable not just to cephalochordates but also to vertebrates and may transform ideas on evolution of the myriad variations vertebrates added to the basic theme of a small non-yolky embryo gastrulating by invagination.