EAGER: Application of transcriptomics to investigate organism-environment relationships in marine zooplankton

EAGER:应用转录组学研究海洋浮游动物的生物体与环境关系

基本信息

  • 批准号:
    1040597
  • 负责人:
  • 金额:
    $ 21.4万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2010
  • 资助国家:
    美国
  • 起止时间:
    2010-07-15 至 2014-06-30
  • 项目状态:
    已结题

项目摘要

Intellectual Merit: This project will develop transcriptomics approaches to investigate gene regulation as a function of environmental cycles and in response to experimental manipulation. Currently, there are few tools to establish physiological state of marine zooplankton, in particular for oceanic species. Molecular approaches based on quantifying the transcriptome could serve as powerful tools to obtain a physiological profile for individuals and groups of individuals collected in the field. In combination with laboratory experiments, transcriptome analysis will provide a new approach to understanding organism-environment interactions in the pelagic zone.The PI will focus on a model planktonic crustacean, Calanus finmarchicus, to develop the molecular tools. C. finmarchicus, a calanoid copepod, is highly abundant in the North Atlantic, with populations extending from the Gulf of Maine and Labrador Sea to the North Sea. Pyrosequencing and microarray technologies will be used to develop a diagnostic tool to determine physiological state in C. finmarchicus. The goal of having a measurement of physiological state is to determine if individuals in the population are growing, are synthesizing or catabolizing storage lipids, and are metabolically active and/or experiencing environmental stress. Specific objectives of this project include:1. High throughput sequencing of C. finmarchicus transcriptome from pre-adult (copepodid stage V [CV]) individuals representing distinct phases of the annual cycle (late spring-early summer, early fall, diapausing individuals).2. Analysis of the sequence data for discovery of seasonally regulated genes for the development of an ecologically relevant microarray. Probes for this microarray will include seasonally regulated genes, genes involved in the environmental stress response and control genes.3. Preliminary testing of microarray on existing samples collected from the Gulf of Maine and stored in liquid nitrogen, as well as on experimentally manipulated animals.Broader Impacts: 1) Training of graduate and undergraduate students in these techniques will occur. At least two graduate students in Marine Sciences/Biological Oceanography will participate in the project and be trained in transcriptomics at the bench and in bioinformatics. Undergraduate students will participate in the project at the Mount Desert Island Biological Laboratory through the NSF REU-site funding. Undergraduate training will be interdisciplinary and include both biological oceanography and molecular biology techniques. 2) Results and sequences obtained in this study will be contributed to databanks and made available to the general public. Sequences will be analyzed using clustering tools and annotated using gene ontology software, followed by sequence submission to the National Center for Biotechnology Information (NCBI) database. Gene sequence data for copepods in general are still sparse, and the planned submission will increase information available for calanoid copepods by ten-fold or more.
智力优势:该项目将开发转录组学方法来研究基因调控作为环境周期的函数和对实验操作的响应。目前,很少有工具来建立海洋浮游动物,特别是海洋物种的生理状态。基于定量转录组的分子方法可以作为强有力的工具,以获得在该领域收集的个人和群体的生理概况。转录组分析与实验室实验相结合,将为理解远洋区生物与环境的相互作用提供一种新的方法。PI将专注于一种模式浮游甲壳动物,Calanus finmarchicus,以开发分子工具。C. finmarchicus是一种哲水蚤类桡足类,在北大西洋非常丰富,种群从缅因州湾和拉布拉多海延伸到北海。焦磷酸测序和微阵列技术将用于开发一种诊断工具,以确定生理状态的C。finmarchicus。测量生理状态的目的是确定群体中的个体是否正在生长,是否正在合成或分解代谢储存脂质,以及是否代谢活跃和/或经历环境应激。本项目的具体目标包括:1.高通量测序C. finmarchicus转录组来自成体前(桡足类阶段V [CV])个体,代表年周期的不同阶段(春末夏初,初秋,滞育个体)。分析序列数据以发现季节性调节基因,从而开发生态相关的微阵列。该微阵列的探针将包括季节性调控基因、参与环境应激反应的基因和控制基因。对从缅因州海湾收集并储存在液氮中的现有样本以及实验操作的动物进行微阵列的初步测试。更广泛的影响:1)将对研究生和本科生进行这些技术的培训。至少有两名海洋科学/生物海洋学研究生将参加该项目,并在实验室接受转录组学和生物信息学方面的培训。本科生将通过NSF REU网站的资助,在荒岛山生物实验室参加该项目。本科生培训将是跨学科的,包括生物海洋学和分子生物学技术。2)在这项研究中获得的结果和序列将贡献给数据库,并提供给公众。序列将使用聚类工具进行分析,并使用基因本体软件进行注释,然后将序列提交到国家生物技术信息中心(NCBI)数据库。桡足类的基因序列数据总体上仍然稀少,计划提交的数据将使哲水蚤类桡足类的信息增加10倍或更多。

项目成果

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Petra Lenz其他文献

Products of anti-CD3/anti-CD28 activated lymphocytes induce differentiation and maturation of dendritic cells and have adjuvant-like activity <em>in vitro</em> and <em>in vivo</em>
  • DOI:
    10.1016/j.clim.2008.06.003
  • 发表时间:
    2008-10-01
  • 期刊:
  • 影响因子:
  • 作者:
    Kristina M. Harris;Petra Lenz;Kim G. Hankey;Thomas MacVittie;Ann Farese;Kaori Nakajima;Kenichiro Hasumi;Dean L. Mann
  • 通讯作者:
    Dean L. Mann
Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions
  • DOI:
    10.1016/j.ajhg.2024.10.005
  • 发表时间:
    2024-12-05
  • 期刊:
  • 影响因子:
  • 作者:
    Bin Zhu;Avraam Tapinos;Hela Koka;Priscilla Ming Yi Lee;Tongwu Zhang;Wei Zhu;Xiaoyu Wang;Alyssa Klein;DongHyuk Lee;Gary M. Tse;Koon-ho Tsang;Cherry Wu;Min Hua;Chad A. Highfill;Petra Lenz;Weiyin Zhou;Difei Wang;Wen Luo;Kristine Jones;Amy Hutchinson
  • 通讯作者:
    Amy Hutchinson

Petra Lenz的其他文献

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{{ truncateString('Petra Lenz', 18)}}的其他基金

Collaborative Research: Zooplankton restarts in a high-latitude marine ecosystem: species-specific recruitment and development in early spring
合作研究:浮游动物在高纬度海洋生态系统中重新启动:早春物种特异性的补充和发育
  • 批准号:
    2222376
  • 财政年份:
    2022
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Standard Grant
Intergovernmental Mobility Assignment (11/12/19 - 11/11/20)
政府间流动分配(11/12/19 - 11/11/20)
  • 批准号:
    2010264
  • 财政年份:
    2019
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Intergovernmental Personnel Award
THE DRIVE TO SURVIVE: COPEPODS vs ICHTHYOPLANKTON
生存的动力:桡足类与浮游鱼类
  • 批准号:
    1235549
  • 财政年份:
    2012
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Standard Grant
Collaborative Research: BEHAVIORAL AND NEURAL MECHANISMS FOR PREDATOR EVASION IN CRUSTACEAN ZOOPLANKTON
合作研究:甲壳类浮游动物逃避捕食者的行为和神经机制
  • 批准号:
    0451376
  • 财政年份:
    2005
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Standard Grant
Collaborative Research: Sensory Reception and Predator Evasion in Crustacean Zooplankton
合作研究:甲壳类浮游动物的感官接收和捕食者躲避
  • 批准号:
    9906223
  • 财政年份:
    1999
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Continuing Grant
Sensory Reception in Crustacean Zooplankton
甲壳类浮游动物的感觉接收
  • 批准号:
    9521375
  • 财政年份:
    1995
  • 资助金额:
    $ 21.4万
  • 项目类别:
    Continuing Grant

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