SGER: Profile of Signal Molecules in a Soil Microbial Community

SGER：土壤微生物群落信号分子概况

• 批准号: 0454823
• 负责人: Jo Handelsman
• 金额: --
• 依托单位: University of Wisconsin-Madison
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-11-01 至 2006-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0454823&HistoricalAwards=false
• 关键词: SGER; Profile; Signal; Molecules; Soil

This is a Small Grant for Exploratory Research (SGER) award to identify and sequence metagenomic clones derived from Alaskan soil that produce biologically active small molecules. This exploratory project was stimulated by two recent events: first, the development of a rapid intracellular assay to identify clones that produce signaling molecules; and second, recently published studies of the metagenomes of the Sargasso Sea and an acid mine drainage community, respectively, that illustrate the power of obtaining vast amounts of sequence data from metagenomic sources.Slicing complex microbial communities many ways is necessary to construct a comprehensive portrait of them. Some of the most fruitful approaches to obtain slices of microbial communities include: culturing, PCR amplification of 16S rRNA sequences, identification of phylogenetic anchors on metagenomic clones, and analysis of random end sequences of metagenomic clones. The phylogenetic anchor approach involves sequencing all clones that contain a certain phylogenetic marker. The collection of clones containing 16S rRNA phylogenetic information provides the basis for inferences from nucleotide sequence about functions performed by the organisms from which the fragments of metagenomic DNA originated. By contrast, this project will introduce the use of a functional anchor - the converse of the phylogenetic anchor approach. The function anchor approach will be used to identify all clones in a library that express a certain function and then sequence them to obtain phylogenetic information about their origins. If successful, this will become a new standard of analysis of metagenomic libraries that will provide access to new genes whose functions might not have been suspected by inspection of their sequences and phylogenetic inference about the origins of those functions. Undergraduate students will also be involved in the project, with the investigators utilizing and evaluating two different approaches to attracting and incorporating members of underrepresented groups in science.

这是一个探索性研究（SGER）的小额赠款奖，用于鉴定和测序来自阿拉斯加土壤的宏基因组克隆，这些克隆产生生物活性小分子。 这一探索性的项目是由最近的两个事件刺激的：第一，快速细胞内分析的发展，以确定产生信号分子的克隆;第二，最近发表的关于马尾藻海和酸性矿井排水群落的宏基因组的研究，这说明了从宏基因组来源获得大量序列数据的能力。切割复杂的微生物群落的许多方法是必要的，对他们进行全面的描述。 获得微生物群落切片的一些最有成效的方法包括：培养、16 S rRNA序列的PCR扩增、宏基因组克隆上的系统发育锚的鉴定以及宏基因组克隆的随机末端序列的分析。系统发育锚方法涉及对含有某一系统发育标记的所有克隆进行测序。包含16 S rRNA系统发育信息的克隆的集合提供了从核苷酸序列推断宏基因组DNA片段起源的生物体所执行的功能的基础。 相比之下，本项目将引入功能性锚的使用--与系统发育锚方法匡威。功能锚方法将用于鉴定文库中表达某种功能的所有克隆，然后对其进行测序以获得关于其起源的系统发育信息。如果成功，这将成为宏基因组文库分析的新标准，将提供对新基因的访问，这些基因的功能可能不会被怀疑通过检查它们的序列和关于这些功能的起源的系统发育推断。 本科生也将参与该项目，研究人员利用和评估两种不同的方法来吸引和融入科学中代表性不足的群体。