Collaborative Research: New medium for DNA separation of microbial communities

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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.