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Award Abstract #1229585

MRI: Acquisition of a Benchtop Next Generation Sequencing Platform to Enhance Undergraduate Research and Education at Hope College

NSF Org: DBI
Div Of Biological Infrastructure
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Initial Amendment Date: July 16, 2012
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Latest Amendment Date: July 16, 2012
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Award Number: 1229585
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Award Instrument: Standard Grant
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Program Manager: Robert Fleischmann
DBI Div Of Biological Infrastructure
BIO Direct For Biological Sciences
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Start Date: September 1, 2012
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End Date: August 31, 2015 (Estimated)
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Awarded Amount to Date: $171,877.00
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Investigator(s): Aaron Best best@hope.edu (Principal Investigator)
Jianhua Li (Co-Principal Investigator)
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Sponsor: Hope College
141 E. 12th Street
Holland, MI 49422-9000 (616)395-7316
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NSF Program(s): MAJOR RESEARCH INSTRUMENTATION
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Program Reference Code(s):
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Program Element Code(s): 1189

ABSTRACT

Advances in sequencing technology have dramatically shifted the way science is performed in many fields of Biology, which has also shifted the way education of the next generation of scientists must be conducted. However, the generation of sequencing data has been restricted to large laboratories, consortia of laboratories, and core sequencing facilities, limiting the exposure of undergraduates to these technologies. The recent introduction of benchtop next generation sequencing platforms promises to make moderately high throughput sequencing available to many individual research laboratories and smaller institutions. This Major Research Instrumentation grant supports the acquisition of an Ion Torrent Personal Genome Machine (Ion PGM) sequencing platform by Hope College. The Ion PGM will have significant impact on undergraduate research and training at Hope College by making affordable, high throughput sequencing capacity available to faculty and undergraduate researchers for use in established and emerging research and education programs. These programs include research focusing on: 1) the genome sequences of viruses that infect bacteria (Mycobacteriophage) that are discovered by first year college students as part of introductory biology laboratory courses; 2) long-term environmental studies of the local Lake Macatawa Watershed to identify and track microbial sources of contamination through whole genome sequencing of novel bacterial isolates; 3) advancing understanding of fundamental gene expression mechanisms of the mammalian parasite Giardia lamblia; 4) understanding phylogenetic and biogeographic relationships among maples found across the World; and 5) testing potential horizontal gene transfers of plastid genes between parasitic plants and their photosynthetic hosts. The projects advance scientific understanding of a wide range of biological and environmental problems that can be addressed through DNA sequencing at different scales. Each project will be made more effective by the in house availability of the Ion PGM, which is uniquely versatile in being able to generate sequence data at vastly different scales in a cost effective manner.

This sequencing platform will allow Hope College to effectively train undergraduates in the design of experiments requiring sequencing data; usage of next generation sequencing technology to generate necessary data; and analysis, interpretation, and dissemination of large scale data sets in both research laboratory and classroom laboratory settings. The Ion PGM will immediately enhance projects and programs that impact over 100 undergraduates during each academic year. First year students will be impacted through Hope College's highly successful yearlong course in phage genomics research, which is designed to retain high quality students in STEM fields. Students at all levels will participate in the research laboratories of the PI?s and their collaborators. Students in upper level Biology courses will use the technology in classroom laboratory-based research projects. Hope College?s established summer research programs will allow us to broaden exposure of students across the nation and of students from underrepresented groups in sciences in the use of leading edge sequencing technology. Faculty will be impacted through their ability to take advantage of next generation sequencing technology to advance projects into new and innovative areas and generate preliminary data for sustaining extramurally funded research programs. Student-faculty collaborative research will be disseminated to the scientific community through local, regional, and national/international scientific conferences and peer-reviewed publications and to the general public through community-based popular seminars. Sequence data will be deposited to appropriate openly accessible databases. Regional and national collaborators will use the Ion PGM, broadening its impact beyond Hope College to students in West Michigan and throughout the nation.

 

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