Collaborative Research: New Medium for DNA Separation of Microbial Communities

合作研究：微生物群落 DNA 分离的新介质

• 批准号: 0853741
• 负责人: Linda McGown
• 金额: $ 25.55万
• 依托单位: Rensselaer Polytechnic Institute
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0853741&HistoricalAwards=false
• 关键词: Collaborative; Research; New; Medium; DNA

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).This NSF award by the Chemical and Biological Separations program supports work by Professors Linda B. McGown and DeEtta K. Mills at Rensselaer Polytechnic Institute (RPI) and Florida International University (FIU), respectively, to improve the ability of DNA profiling methods to reveal the true diversity of microbial communities. The growing recognition of the importance of complex microbial communities and biofilms in engineered systems for environmental, industrial, medicinal, agricultural and municipal applications has created a demand for new approaches and techniques for the characterization of these complex living systems. The ability to quantify the number and types of microorganisms within a community and its response to environmental stressors is fundamental to the understanding of the structure and function of any natural or engineered ecosystem containing microbial communities. Because microbial populations operate at spatio-temporal scales far removed from typical human perception, it has been difficult in the past to investigate their role in complex system behavior. This has emerged as a challenge at the forefront of analytical chemistry and bioseparation. One of the most powerful approaches for profiling microbial communities and understanding their dynamic interactions and responses to environmental stimuli is through examination of their DNA profiles, or ?metagenomes?. However, the effectiveness of community DNA profiling with existing methods is limited because taxonomically unrelated organisms may produce the same length DNA, resulting in an underestimation of the true diversity of the community. Same length DNA must then be sequenced in order to reveal the hidden diversity within the profiles and obtain the true diversity of the sampled community.This project investigates a new gel medium that is formed by self-association of guanosine compounds to resolve same length DNA with different sequences. Combining the new gel with conventional sieving gels in capillary gel electrophoresis will lead to unprecedented resolution in length and sequence of community DNA that will reveal previously masked community diversity without having to sequence the entire metagenome of the microbial community, thereby greatly reducing the time and expense compared to current methods. The research at RPI will be conducted by a graduate student, an undergraduate student and two high school students who will be recruited each year through the Science Technology Entry Program (STEP) at RPI. STEP engages underrepresented and economically disadvantaged students in area middle and high schools in activities designed to develop problem-solving skills and a broad knowledge base prior to entry into post-secondary schools. The research at FIU, a minority institution, will be conducted by two undergraduate students. There will be an internship/laboratory exchange of the students from both institutions during the summer semesters of the project. FIU students will spend 4-6 weeks at RPI learning separation techniques and the McGown students will travel to FIU where they will learn molecular techniques such as PCR, qPCR and DNA extractions. This exchange will greatly enhance the breath and depth of knowledge for these student groups. The coalescence, synthesis and dissemination of all data will be a combined effort of the PI, co-PI and their students. These interdisciplinary efforts will result in greater dissemination of information across scientific fields and crossover into critical fields of engineering. The merging of molecular biology and separation sciences evolves as a natural progression of the current work of the McGown and Mills laboratories. By providing support for knowledge development and mentoring of minority graduate and undergraduates, this research experience will strengthen and broaden their knowledge base by the laboratory interactions and student exchange between the two institutions.

该奖项根据 2009 年《美国复苏和再投资法案》（公法 111-5）提供资金。这项由化学和生物分离项目颁发的 NSF 奖项支持伦斯勒理工学院 (RPI) 和佛罗里达国际大学 (FIU) 的 Linda B. McGown 和 DeEtta K. Mills 教授分别开展的工作，以提高 DNA 分析方法揭示微生物群落真实多样性的能力。人们日益认识到复杂微生物群落和生物膜在环境、工业、医学、农业和市政应用工程系统中的重要性，这就产生了对表征这些复杂生命系统的新方法和技术的需求。 量化群落内微生物的数量和类型及其对环境压力源的响应的能力对于理解包含微生物群落的任何自然或工程生态系统的结构和功能至关重要。由于微生物种群的运作时空尺度与人类的典型感知相去甚远，因此过去很难研究它们在复杂系统行为中的作用。这已成为分析化学和生物分离前沿的挑战。分析微生物群落并了解其动态相互作用和对环境刺激的反应的最有力方法之一是检查其 DNA 谱或“宏基因组”。然而，现有方法进行群落 DNA 分析的有效性有限，因为分类学上不相关的生物可能产生相同长度的 DNA，导致低估群落的真实多样性。然后必须对相同长度的 DNA 进行测序，以揭示图谱中隐藏的多样性并获得采样群落的真实多样性。该项目研究了一种由鸟苷化合物自缔合形成的新凝胶介质，以解析具有不同序列的相同长度的 DNA。 将新型凝胶与毛细管凝胶电泳中的传统筛分凝胶相结合，将在群落 DNA 的长度和序列方面实现前所未有的分辨率，从而揭示先前被掩盖的群落多样性，而无需对微生物群落的整个宏基因组进行测序，从而与现有方法相比，大大减少了时间和费用。 RPI 的研究将由每年通过 RPI 的科学技术入门计划 (STEP) 招募的一名研究生、一名本科生和两名高中生进行。 STEP 让地区初中和高中中代表性不足和经济弱势的学生参与旨在在进入专上学校之前培养解决问题的技能和广泛的知识基础的活动。佛罗里达国际大学是一所少数族裔机构，这项研究将由两名本科生进行。项目夏季学期期间，两所院校的学生将进行实习/实验室交流。佛罗里达国际大学的学生将在 RPI 学习分离技术 4-6 周，而 McGown 的学生将前往佛罗里达国际大学学习分子技术，如 PCR、qPCR 和 DNA 提取。此次交流将大大提升这些学生群体的知识气息和深度。所有数据的合并、综合和传播将是 PI、co-PI 及其学生的共同努力。这些跨学科的努力将导致跨科学领域的信息更大程度地传播，并跨入关键的工程领域。分子生物学和分离科学的融合是麦高和米尔斯实验室当前工作的自然进展。通过为少数族裔研究生和本科生的知识发展和指导提供支持，这种研究经验将通过两个机构之间的实验室互动和学生交流来加强和拓宽他们的知识基础。