Acquisition of Automated Genotyping and Sequencing Equipment

赫尔古尔特的生态学、群体遗传学和植物分子遗传学研究小组在分子方法的使用方面前所未有的增长，代表了三个生物学部门，这促使了对DNA测序和分子基因分型自动化设备的支持。这一增长是由三股力量推动的：序列数据带来的令人兴奋的科学可能性——其中许多是拟议用户第一次绘制的，自动化测序的技术创新，以及芝加哥大学三个生物学小组的战略增长。为了进一步提高研究的卓越性和领导力，并提供研究培训机会，我们制定了一个“动手”多用户设施的计划，该设施将包含执行DNA测序和基因分型所有步骤所需的设备。除了现有的ABI 373A测序仪外，该设施还将包括两台新的DNA测序仪和一台用于自动样品处理的工作站。该设施还将拥有高容量温度循环机，用于进行测序反应，离心机和这项工作所需的其他设备。为了适应研究产生的数据编辑、统计分析和数据库比较的需要，该设施将容纳4台Macintosh PowerPC和2台Silicon Graphics工作站。这些工作站提供的计算速度将确保该小组在快速发展的模拟分子种群遗传学和进化过程领域的领导地位。它还将促进互补优势的协同作用-计算（群体遗传学家）和信息学（分子遗传学家）。该基金将由陈立伟博士管理，在克雷特曼博士和一个三人工具政策委员会的监督下。这些现代仪器将对大学社区产生广泛的影响。13个主要教师用户属于6个研究生培训项目，目前有22名博士后研究助理，39名研究生和26名本科生在他们的实验室工作，其中包括34名女性和8名少数民族成员。9个二级用户有博士后14人，研究生28人，本科生13人。所有符合条件的用户每天24小时都可以使用测序设备。每年将有100多名本科生，其中一半以上是女性，通过必修课程、独立研究和其他培训机会使用该仪器。该大学是美国国家科学基金会REU的一个站点，并且还支持霍华德休斯医学研究所，皮尤基金会和生物科学部的夏季本科生研究。生物科学部还参加了夏季研究机会计划（SROP）和DBS少数民族夏季奖学金计划，这两个计划都为少数民族提供了研究机会。在生物过程分析中使用自然发生的DNA序列变异是一个共同的主题，它将主要用户所代表的三个研究领域联合起来-分子群体遗传学，分子生态学和植物分子遗传学。自动化数据采集的能力在这三个研究领域都带来了巨大的科学进步，同时也以前所未有的规模促进了跨学科的互动。跨学科研究和研究生培训一直是芝加哥大学教育理念的标志。最近在生态和进化系的跨学科进化遗传学和生态学小组的增长，在有机生物学和解剖学系建立了一个发育进化遗传学小组，以及由e&e和分子遗传学和细胞生物学（MGCB）部门联合扩展植物遗传学，所有这些都建立在这一哲学基础之上，并为创新的新研究提供了战略机会。几年前，E&amp；E系成功招募了两名分子进化遗传学高级教员，M . Kreitman和C-I Wu，这促进了其他研究小组将分子方法纳入研究的转变。与此同时，E&amp；E已经开始了一项战略计划，通过招募六名教员，S PruettJones, M Leibold, E Simms, C Pfister， T Wootton和J Bergelson，来发展生态学的卓越研究。有几个人在他们的研究中使用分子方法，而J . Bergelson的工作被公认为定义了分子生态学的一个新领域。同时，MGCB已经招募了两名优秀的植物分子遗传学家B Keith和D Preuss加入赫尔院，目前正在寻找一名高级植物发育遗传学家，他也将在赫尔院工作。实现这些不断扩大的研究小组的研究潜力的关键是基因分型和DNA测序设施的发展，这是所有这些研究小组的交汇点。

Unprecedented growth in the use of molecular methods by the ecology, population genetics, and plant molecular genetics groups in Hull Gourt, representing three biology departments, motivates this proposal for support of automated equipment for DNA sequencing and molecular genotyping. This growth has been propelled by three forces, the exciting scientific possibilities made accessible with sequence data - many of which are being charted for the first time by the proposed users, technological innovations in automated sequencing, and the strategic growth of the three biology groups at the University of Chicago. To further enhance research excellence and leadership, and to provide research training opportunities we have developed a plan for a "hands-on" multi-user facility that will contain equipment needed to carry out all steps in DNA sequencing and genotyping. The facility will include two new DNA sequencers and a workstation for automated sample processing, in addition to an existing ABI 373A sequencer. The facility will also have high capacity temperature cycling machines for carrying out sequencing reactions, centrifuges, and other equipment needed for this work. To accommodate the requirements for data editing, statistical analysis and database comparisons generated by the research, the facility will house four Macintosh PowerPC and two Silicon Graphics workstations. The computing speed afforded by these workstations will assure the group's leadership in the rapidly growing field of simulating molecular population genetics and evolutionary processes. It will also promote the synergistic interaction of complementing strengths - computation (population geneticists) and informatics (molecular geneticists). The facility will be managed by Dr. L-W Zen, under the supervision of Dr. M. Kreitman and a three person Instrument Policy Committee. These modern instruments will have broad impact on the University community. The 13 primary faculty users belong to si x graduate training programs, and currently have 22 postdoctoral research associates, 39 graduate students, and 26 undergraduates working in their labs, including 34 women and eight members of minority groups. The nine secondary users have 14 postdoctoral research associates, 28 graduate students and 13 undergraduates. All qualified users will have access to the sequencing facility 24 hours a day. More than one hundred undergraduates, over half of whom are women, will use the instrumentation annually through required courses, independent research, and other training opportunities. The University is an NSF REU site, and also supports summer undergraduate research with grants from Howard Hughes Medical Institute, the Pew Foundation, and the Biological Sciences Division. The Biological Sciences Division also participates in the Summer Research Opportunities Program (SROP) and the DBS Minority Summer Fellowship Program, both of which provide research opportunities for minorities. The use of naturally occurring DNA sequence variation in the analysis of biological processes is a common theme that unites the three areas of research represented by the primary users - molecular population genetics, molecular ecology, and plant molecular genetics. The ability to automate data acquisition is leading to dramatic scientific advances in all three areas of research, and at the same time is promoting interdisciplinary interaction on an unprecedented scale. Interdisciplinary research and graduate training have been hallmarks of the University of Chicago's educational philosophy. The recent growth of interdisciplinary evolutionary genetics and ecology groups in the Department of Ecology and Evolution, the creation of a developmental evolutionary genetics group in the Department of Organismal Biology and Anatomy, and the joint expansion of plant genetics by the departments of E&E and Molecular Genetics and Cell Biology (MGCB), all build on this philosophical foundation, and pro vide strategic opportunities for innovative new research. The successful recruitment of two senior faculty in molecular evolutionary genetics by the E&E department several years ago, M Kreitman and C-I Wu, have catalyzed the conversion of research by other groups to incorportate molecular approaches. At the same time, E&E has embarked on a strategic plan to develop research excellence in ecology by recruiting six faculty members, S PruettJones, M Leibold, E Simms, C Pfister, T Wootton and J Bergelson. Several are using molecular methods in their research, and J Bergelson's work is being acknowledged as defining a new field of molecular ecology. At the same time, MGCB has recruited into Hull Court two excellent plant molecular geneticists, B Keith and D Preuss, and is currently searching for a senior plant developmental geneticist, who will also be housed in Hull Court. Crucial to the fulfillment of research potential of these expanding groups is the development of a Genotyping and DNA Sequencing Facility, a point of convergence for all these research groups.