Acquisition of Automated Genotyping and Sequencing Equipment

代表三个生物部门的赫尔古尔生态学、种群遗传学和植物分子遗传学小组对分子方法的使用空前增长，促使这项支持DNA测序和分子基因分型的自动化设备的提议。这种增长是由三种力量推动的，通过序列数据获得令人兴奋的科学可能性-其中许多是由拟议的用户首次绘制的图表，自动测序方面的技术创新，以及芝加哥大学三个生物学小组的战略增长。为了进一步加强研究的卓越性和领导力，并提供研究培训机会，我们制定了一项“动手”多用户设施的计划，其中将包括执行DNA测序和基因分型所有步骤所需的设备。该设施将包括两台新的DNA测序仪和一个用于自动样本处理的工作站，此外还有一台现有的ABI 373A测序仪。该设施还将拥有高容量的温度循环机器，用于执行这项工作所需的测序反应、离心机和其他设备。为了满足研究产生的数据编辑、统计分析和数据库比较的需求，该设施将配备四台Macintosh PowerPC和两台Silicon Graphics工作站。这些工作站提供的计算速度将确保该组织在模拟分子群体遗传学和进化过程这一快速增长的领域中的领先地位。它还将促进优势互补的协同作用--计算(群体遗传学家)和信息学(分子遗传学家)。该设施将由L博士管理，并由M.Kreitman博士和一个三人仪器政策委员会监督。这些现代化的工具将对大学社会产生广泛的影响。13名初级教师用户属于six研究生培训项目，目前有22名博士后助理研究员、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名少数族裔成员。9个二次用户中有14名博士后研究助理、28名研究生和13名本科生。所有符合条件的用户都可以全天24小时使用测序设施。100多名本科生，其中一半以上是女性，每年将通过必修课、独立研究和其他培训机会使用这种乐器。该大学是NSF REU的一个网站，还由霍华德·休斯医学院、皮尤基金会和生物科学部资助夏季本科生研究。生物科学部还参与了夏季研究机会计划(SROP)和星展少数民族夏季奖学金计划，这两项计划都为少数族裔提供研究机会。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，它将主要使用者代表的三个研究领域--分子种群遗传学、分子生态学和植物分子遗传学联系在一起。自动化数据获取的能力正在所有三个研究领域带来巨大的科学进步，同时正在以前所未有的规模促进跨学科互动。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，生态与进化系跨学科进化遗传学和生态学小组的发展，组织生物学和解剖学系发展进化遗传学小组的成立，以及E&amp；E和分子遗传学与细胞生物学(MGCB)系对植物遗传学的联合扩展，所有这些都建立在这一哲学基础上，并为创新的新研究提供了战略机遇。E&A；E系几年前成功招聘了分子进化遗传学的两名高级教员M Kreitman和C-I Wu，推动了其他小组的研究向非相关分子方法的转变。与此同时，E&amp；E已经开始实施一项战略计划，通过招聘六名教职员工，S·普鲁特·琼斯、M·莱博尔德、E·西姆斯、C·菲斯特、T·伍顿和J·伯格森，发展卓越的生态学研究。有几个人在他们的研究中使用了分子方法，J·伯格尔森的工作被认为是定义了分子生态学的一个新领域。同时，MGCB已向Hull Court招聘了两位优秀的植物分子遗传学家B Keith和D Preuss，目前正在寻找一名高级植物发育遗传学家，他也将住在Hull Court。这些不断扩大的研究小组发挥研究潜力的关键是开发基因分型和DNA测序设施，这是所有这些研究小组的汇合点。

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.