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

MRI：收购台式下一代测序平台以加强希望学院的本科生研究和教育

• 批准号: 1229585
• 负责人: Aaron Best
• 金额: $ 17.19万
• 依托单位: Hope College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2015-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1229585&HistoricalAwards=false
• 关键词: MRI; Acquisition; Benchtop; Next; Generation

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.

测序技术的进步极大地改变了生物学许多领域的科学研究方式，这也改变了下一代科学家的教育方式。然而，测序数据的生成仅限于大型实验室、实验室联盟和核心测序设施，限制了本科生接触这些技术。最近推出的台式下一代测序平台有望为许多个体研究实验室和小型机构提供中等高通量的测序。这笔重大研究仪器拨款支持希望学院收购 Ion Torrent 个人基因组机 (Ion PGM) 测序平台。 Ion PGM 将为教师和本科生研究人员提供负担得起的高通量测序能力，用于现有和新兴的研究和教育项目，从而对希望学院的本科生研究和培训产生重大影响。这些项目包括以下研究重点：1）感染细菌（分枝杆菌噬菌体）的病毒基因组序列，由一年级大学生作为生物学入门实验室课程的一部分发现； 2) 对当地马卡塔瓦湖流域进行长期环境研究，通过新型细菌分离株的全基因组测序来识别和追踪微生物污染源； 3) 增进对哺乳动物寄生虫贾第鞭毛虫基本基因表达机制的理解； 4）了解世界各地发现的枫树之间的系统发育和生物地理关系； 5)测试寄生植物与其光合宿主之间质体基因的潜在水平基因转移。这些项目促进了对广泛的生物和环境问题的科学理解，这些问题可以通过不同规模的 DNA 测序来解决。每个项目都将通过 Ion PGM 的内部可用性变得更加有效，Ion PGM 具有独特的多功能性，能够以成本有效的方式生成不同规模的序列数据。该测序平台将使希望学院能够有效地培训本科生需要测序数据的实验设计；使用下一代测序技术生成必要的数据；在研究实验室和课堂实验室环境中分析、解释和传播大规模数据集。 Ion PGM 将立即加强每个学年影响 100 多名本科生的项目和计划。一年级学生将受到希望学院非常成功的为期一年的噬菌体基因组学研究课程的影响，该课程旨在留住 STEM 领域的高素质学生。各级学生都将参与 PI 及其合作者的研究实验室。高级生物学课程的学生将在基于课堂实验室的研究项目中使用该技术。希望学院已建立的夏季研究项目将使我们能够扩大全国学生和科学界代表性不足群体的学生使用前沿测序技术的机会。教师将通过利用下一代测序技术将项目推进到新的创新领域并为维持校外资助的研究项目生成初步数据的能力而受到影响。学生与教师的合作研究将通过地方、区域和国家/国际科学会议和同行评审出版物向科学界传播，并通过基于社区的大众研讨会向公众传播。序列数据将被存入适当的可公开访问的数据库。地区和国家合作者将使用 Ion PGM，将其影响力从希望学院扩大到西密歇根州乃至全国的学生。