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

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，也改变了下一代科学家的教育方式。然而，测序数据的产生一直局限于大型实验室，实验室联盟和核心测序设施，限制了本科生接触这些技术。最近引进的台式下一代测序平台有望使许多个体研究实验室和较小的机构获得中等高通量测序。这项主要研究仪器拨款支持霍普学院收购离子激流个人基因组机器（离子PGM）测序平台。Ion PGM将对霍普学院的本科生研究和培训产生重大影响，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。这些计划包括研究重点：1）感染细菌的病毒的基因组序列（分枝杆菌噬菌体），发现了一年级的大学生作为介绍性生物学实验室课程的一部分; 2）长期的环境研究，当地的马卡塔瓦湖流域，以确定和跟踪污染的微生物来源，通过全基因组测序的新的细菌分离物; 3）推进对哺乳动物寄生虫蓝氏贾第鞭毛虫的基本基因表达机制的理解; 4）理解世界各地发现的枫树之间的系统发育和植物地理学关系;以及5）测试寄生植物及其光合宿主之间质体基因的潜在水平基因转移。这些项目促进了对各种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。Ion PGM的内部可用性将使每个项目更加有效，Ion PGM具有独特的多功能性，能够以具有成本效益的方式生成不同规模的序列数据。该测序平台将使Hope College能够有效地培训本科生设计需要测序数据的实验;使用下一代测序技术生成必要的数据;以及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将立即增强每个学年影响100多名本科生的项目和计划。一年级学生将通过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受到影响，该课程旨在留住STEM领域的高质量学生。各级学生将参加PI的研究实验室？和他们的合作者。高级生物学课程的学生将在课堂实验室研究项目中使用该技术。希望学院？我们建立的暑期研究项目将使我们能够扩大全国学生和科学领域代表性不足的学生使用前沿测序技术的机会。教师将通过他们的能力，利用下一代测序技术，以推进项目进入新的和创新的领域，并产生初步数据，以维持校外资助的研究计划的影响。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的出版物传播到科学界，并通过以社区为基础的流行研讨会向公众传播。序列数据将保存在适当的开放访问数据库中。区域和国家合作者将使用离子PGM，扩大其影响以外的希望学院的学生在西密歇根州和全国各地。

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.