Collaborative Proposal: Decoding Virus Leviathans

巨型病毒的粗略定义是基因组大于280,000个碱基对(BP)，目前在这个大小范围内的完整病毒基因组序列不到20个。对这一组的粗略分析立即发现了各种各样的病毒，包括痘病毒、藻类病毒(藻类病毒)、疱疹病毒、噬菌体和尼玛病毒(对虾白斑综合征病毒)。迄今为止最大的病毒是棘阿米巴多噬病毒，直径750 nm，基因组长120万个碱基对。来自这些巨型病毒的基因组序列数据可以帮助阐明它们的分类位置。这些巨型病毒拥有新的、典型的非病毒基因，其中许多基因编码中央细胞功能和代谢途径。通过流式细胞仪的初步观察和对全球海洋采样(GOS)数据库的分析表明，巨型病毒在水生环境中极其丰富，已被有偏见的采样技术忽视。大多数病毒研究着眼于通过0.2微米过滤器的内容。长达0.75微米的巨型病毒将被这些过滤器捕获并逃避检测。W.Wilson博士(毕格罗海洋科学实验室)和S.Wilhelm博士(田纳西大学)对这一项目的中心假设是，巨型海洋病毒无处不在，种类繁多，包含大量新的遗传信息。该项目正在对目前采集的4种藻类病毒和从海水中分离的另外16种巨型病毒进行测序。采用单细胞分选技术对环境病毒进行分离和测序。一旦被分类，巨型病毒将被多重置换扩增(MDA)扩增，以产生巨型病毒单扩增基因组(GV-SAGs)，用于下游测序。为了完成这项工作，PI正在使用最先进的流式细胞术(Bigelow)和序列分析设施(田纳西大学/橡树岭国家实验室)，以及来自合作教授Jean-Michel Claverie的生物信息学专业知识，Jean-Michel Claverie教授是巨型病毒研究的世界领先者。这项研究正在一个非正式的CaféScience项目中讨论，该项目旨在向公众传授最新的科学思想。PI还将一个3个数量级(病毒、脂质/蛋白质和Amp；DNA)的模块整合到凯勒-毕格罗实验室数量级(Bloom)计划中，旨在向缅因州的高中生传授海洋生态系统。PIS正在与田纳西大学(UT)新闻学院合作，将本科生和研究生带入实验室，为公众记录这项研究。

Giant viruses are loosely defined as having a genome greater than 280,000 base pairs (bp) and currently there are less than 20 full virus genome sequences in this size range. A cursory analysis of this group immediately reveals a diverse range of viruses including poxviruses, phycodnaviruses (algal viruses), herpesviruses, a bacteriophage and nimaviruses (shrimp white spot syndrome virus). The largest to date is the Acanthamoeba polyphaga Mimivirus at 750 nm diameter with a 1.2-million bp genome. Genome sequence data from these giant viruses can help clarify their taxonomic position. These giant viruses possess novel and typically non-virus genes, many of which encode central cellular functions and metabolic pathways. Preliminary observations by flow cytometry and analysis of the Global Ocean Sampling (GOS) database suggest that giant viruses are extremely abundant in aquatic environments and have been overlooked by biased sampling techniques. Most virus studies look at what passes through a 0.2 micrometer filter. Giant viruses, up to 0.75 micrometers, will be caught on these filters and evade detection. The central hypotheses of this project by Drs. W. Wilson (Bigelow Lab for Ocean Sciences) and S. Wilhelm (Univ Tenn) are that giant marine viruses are ubiquitous, diverse and contain large amounts of novel genetic information. Four algal viruses from current collections and 16 additional giant viruses isolated from seawater are being sequenced in this project. The environmental viruses are being isolated and sequenced by adapting single cell sorting techniques. Once sorted, giant viruses are being amplified by multiple displacement amplification (MDA) to generate Giant Virus Single Amplified Genomes (GV-SAGs) for downstream sequencing. To accomplish this work, the PIs are using state-of-the-art facilities for flow cytometry (Bigelow) and sequence analysis (University of Tennessee/Oak Ridge National Laboratory) coupled with bioinformatics expertise from collaborator Professor Jean-Michel Claverie, a world-leader in giant virus research.This research is being discussed during an informal Café Scientifique program designed to teach the public about the latest ideas in science. The PIs are also incorporating a 3-orders of magnitude (virus, lipids/proteins & DNA) module into the Keller-Bigelow Laboratory Orders Of Magnitude (BLOOM) program, designed to teach Maine high school students about marine ecosystems. The PIs are partnering with the School of Journalism at the University of Tennessee (UT) to bring undergraduate and graduate journalism students into the lab to document this research for the general public.