RII Track-2 FEC: G2P in VOM: An Experimental and Analytical Framework for Genome to Phenome Connections in Viruses of Microbes

RII Track-2 FEC：VOM 中的 G2P：微生物病毒基因组与表型组连接的实验和分析框架

基本信息

批准号：
1736030
负责人：
K. Wommack
金额：
$ 599.91万
依托单位：
University of Delaware
依托单位国家：
美国
项目类别：
Cooperative Agreement
财政年份：
2017
资助国家：
美国
起止时间：
2017-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1736030&HistoricalAwards=false
关键词：
RII Track FEC G2P VOM

项目摘要

Non-technical descriptionThe viruses in soils, sediments, and water environments infect microbes and impact the ecosystems. While there is a high-level understanding of viral impacts on ecosystems, the details of the viral-microbe interactions are largely unknown. The ability to predict the biological and ecological features, or phenome, of any particular virus-microbe system based on DNA sequence alone is highly limited. This Research Infrastructure Improvement Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC) award seeks to advance the ability to predict the phenomic features of the viruses of microbes (VoMs) from genomic data. A collaborative team of researchers from Delaware, Rhode Island, Nebraska, and Hawaii will study viruses that infect marine and freshwater phytoplankton, and viruses that infect a bacterial group that forms a symbiosis with important legume crops, most notably, soybean. Collectively, global phytoplankton populations are responsible for creating vast stores of biomass that support the nutritional needs of larger aquatic organisms. In this process phytoplankton sustain half of the oxygen within the atmosphere. Enhanced understanding of genome to phenome links within phytoplankton viruses will aid in improving models that predict the impacts of excess carbon and nutrients on ecosystems. Within the food supply chain, legumes, soybeans in particular, are an extraordinarily important source of plant protein supporting the nutritional needs of billions of people. Better understanding of genome to phenome connections for viruses infecting bacterial symbionts of legumes could eventually lead to new technologies for improving the productivity of critical agronomic crops such as soybean. The project team includes faculty, postdocs and students who will engage in collaborative research and share methodologies, best practices, and results through workshops and meetings. Four early career faculty will be mentored by six other well-established faculty investigators. The entire project team will prepare educational materials and provide summer camp opportunities for middle and elementary schools students.Technical descriptionThis RII Track-2 FEC award is for a collaborative effort among University of Delaware, University of Nebraska-Lincoln, University of Hawaii, and Roger Williams University. The planned research seeks to connect genomic features of viruses of microbes (VoMs) with phenotypic life-history traits and use these connections to advance scientific understanding of the role of VoMs in ecosystems. The project team will test several genome to phoneme hypotheses in VoMs, focusing on phenomic features such as host range, burst size, latent period and infectivity. An integrated high-throughput approach including emulsion-droplet microfluidic technologies, next generation sequencing, and bioinformatics, will be used to study viral-host systems representative of picophytoplankton, eukaryotic phytoplankton, and diazotrophic bacteria. The project team will collect samples across environmental gradients from soybean fields, tropical oceans, and lakes, hypothesized to select for different VoM phenomic traits. The researchers will build a new bioinformatics analysis tool known as the Viral Informatics Rulebook for Genome Organization ? VIRGO and incorporated it into an existing community resource for bioinformatic annotation of viral metagenomes known as the Viral Informatics Resource fOr Metagenome Exploration (VIROME). Four early-career faculty members engaged in this project will be mentored by successful mid and later career faculty. The team will work together in training postdocs, graduate students and undergraduate students as well as in communicating the importance of environmental virology to diverse audiences including K-12 students and the general public.

非技术描述土壤，沉积物和水环境中的病毒感染微生物并影响生态系统。尽管对病毒对生态系统的影响有高级的了解，但病毒 - 微生物相互作用的细节在很大程度上尚不清楚。仅基于DNA序列的任何特定病毒 - 微生物系统的生物学和生态特征或现象的能力都受到了高度限制。这项研究基础架构改进Track-2集中的EPSCOR合作（RII Track-2 FEC）旨在提高从基因组数据中预测微生物（VOM）病毒（VOM）现象特征的能力。来自特拉华州，罗德岛，内布拉斯加州和夏威夷的研究人员的合作团队将研究感染海洋和淡水浮游植物的病毒，以及感染细菌群的病毒，该病毒与重要的豆类作物形成同伴，最值得注意的是大豆。总体而言，全球浮游植物种群负责创造大量的生物量存储，以支持大型水生生物的营养需求。在此过程中，浮游植物在大气中维持了一半的氧气。对浮游植物病毒内基因组与现象联系的了解增强，将有助于改善预测过量碳和养分对生态系统的影响的模型。在食品供应链中，豆类，尤其是大豆，是植物蛋白的极为重要的来源，可支持数十亿人的营养需求。更好地理解豆类感染细菌共生体病毒的基因组与现象连接最终可能导致新技术，以提高关键农艺作物（例如大豆）的生产力。该项目团队包括将通过研讨会和会议进行协作研究并共享方法，最佳实践和成绩的教职员工和学生。另外六位成熟的教师调查员将指导四个早期职业教师。整个项目团队将准备教育材料，并为中学和小学的学生提供夏令营的机会。技术描述这一RII Track-2 FEC奖是因为特拉华大学，内布拉斯加州大学，夏威夷大学和罗杰·威廉姆斯大学的合作努力。计划的研究旨在将微生物（VOM）病毒（VOM）病毒的基因组特征与表型生活创造特征联系起来，并使用这些联系来促进对VOM在生态系统中的作用的科学理解。项目团队将测试VOM中的多个基因组对音素假设，重点关注现象特征，例如宿主范围，爆发尺寸，潜在时期和感染力。一项综合高通量方法，包括乳液 - 滴滴微流体技术，下一代测序和生物信息学，将用于研究代表皮皮氏浮游生物，真核浮游植物浮游生物的病毒宿主系统。该项目团队将从大豆田，热带海洋和湖泊中收集样品，假设选择不同的VOM现象性状。研究人员将建立一个新的生物信息学分析工具，即基因组组织的病毒信息学规则手册？处女座并将其纳入现有的社区资源中，用于对病毒宏基因组的生物信息学注释，称为元基因组探索的病毒信息学资源（Virome）。成功的中后期职业教师将指导四名从事该项目的早期职业教师。该团队将共同努力，培训博士后，研究生和本科生，以及将环境病毒学的重要性传达给包括K-12学生和公众在内的不同受众的重要性。

项目成果

期刊论文数量（37）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

N -glycans from Paramecium bursaria chlorella virus MA-1D: Re-evaluation of the oligosaccharide common core structure

来自草履虫小球藻病毒 MA-1D 的 N-聚糖：寡糖共同核心结构的重新评估

DOI：
10.1093/glycob/cwab113
发表时间：
2021
期刊：
Glycobiology
影响因子：
4.3
作者：
Speciale, Immacolata;Di Lorenzo, Flaviana;Notaro, Anna;Noel, Eric;Agarkova, Irina;Molinaro, Antonio;Van Etten, James L.;De Castro, Cristina
通讯作者：
De Castro, Cristina

Near-atomic structure of a giant virus

DOI：
10.1038/s41467-019-08319-6
发表时间：
2019-01-23
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Fang, Qianglin;Zhu, Dongjie;Rossmann, Michael G.
通讯作者：
Rossmann, Michael G.

CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes

DOI：
10.1128/mbio.02651-18
发表时间：
2018-12
期刊：
mBio
影响因子：
6.4
作者：
Daniel J. Nasko;Barbra D. Ferrell;Ryan M. Moore;Jaysheel D. Bhavsar;Shawn W. Polson;K. E. Wommack
通讯作者：
Daniel J. Nasko;Barbra D. Ferrell;Ryan M. Moore;Jaysheel D. Bhavsar;Shawn W. Polson;K. E. Wommack

Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.).