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: 0853746
• 负责人: DeEtta Mills
• 金额: $ 9.43万
• 依托单位: Florida International University
• 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=0853746&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.

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。化学和生物分离计划的NSF奖项支持了琳达B教授的工作。McGown和DeEtta K.米尔斯分别在伦斯勒理工学院（RPI）和佛罗里达国际大学（FIU），以提高DNA分析方法的能力，揭示真正的多样性的微生物群落。复杂的微生物群落和生物膜在环境，工业，医药，农业和市政应用工程系统中的重要性日益认识到创造了一个新的方法和技术来表征这些复杂的生活系统的需求。量化群落中微生物的数量和类型及其对环境压力的响应的能力对于理解任何含有微生物群落的自然或工程生态系统的结构和功能是至关重要的。由于微生物种群在时空尺度上运行，远离典型的人类感知，因此过去很难研究它们在复杂系统行为中的作用。这已经成为分析化学和生物分离前沿的一个挑战。分析微生物群落和了解它们对环境刺激的动态相互作用和反应的最有力的方法之一是通过检查它们的DNA图谱，或者？宏基因组？。然而，社区DNA分析与现有的方法的有效性是有限的，因为分类无关的生物可能会产生相同长度的DNA，导致低估了社区的真实多样性。然后必须对相同长度的DNA进行测序，以揭示分布图中隐藏的多样性，并获得采样群落的真实多样性。本计画研究利用鸟苷化合物自结合形成一种新的凝胶介质，以解析相同长度不同序列的DNA。在毛细管凝胶电泳中将新凝胶与常规筛分凝胶相结合将导致群落DNA的长度和序列的前所未有的分辨率，这将揭示先前被掩盖的群落多样性，而不必对微生物群落的整个宏基因组进行测序，从而与当前方法相比大大减少了时间和费用。RPI的研究将由一名研究生，一名本科生和两名高中生进行，他们每年将通过RPI的科学技术入学计划（STEP）招募。STEP让地区初中和高中中代表性不足和经济上处于不利地位的学生参与旨在在进入中学后学校之前发展解决问题的技能和广泛的知识基础的活动。FIU是一个少数民族机构，将由两名本科生进行研究。在该项目的夏季学期，将有来自两个机构的学生实习/实验室交流。FIU学生将在RPI学习4-6周的分离技术，McGown学生将前往FIU学习PCR、qPCR和DNA提取等分子技术。这次交流将大大提高这些学生团体的呼吸和知识的深度。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传播和交叉到工程的关键领域。分子生物学和分离科学的融合是麦高恩和米尔斯实验室当前工作的自然发展。通过为少数民族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扩大他们的知识基础。