Dr. Michael Sanderson
IGERT Program in Genomics
University of Arizona
Biosciences West. 328
1041 E. Lowell Street
Tucson, AZ 85721-0088
All new students are expected to have an IGERT faculty advisor. If your departmental advisor is already on the IGERT faculty, this requirement is fulfilled. If the department advisor is not on the IGERT faculty, then an IGERT faculty member will be assigned to provide advice on IGERT matters.
This IGERT program brings together faculty from eleven departments (Anthropology, Biochemistry, Cell Biology and Anatomy, Computer Sciences, Ecology and Evolutionary Biology, Entomology, Management and Information Systems, Molecular and Cellular Biology, Pediatrics, Pharmacology and Toxicology, and Plant Sciences) in six colleges (Agriculture and Life Sciences, Medicine, Pharmacy, Science, Social and Behavioral Sciences, and the Eller College of Management). Many students will come from within these eleven departments, but students in any Ph.D. program at the University of Arizona are eligible for IGERT support.
Each new student has a faculty mentor who serves as chair of the initial guidance committee. Entering students are required to form an interdisciplinary IGERT guidance committee consisting of one faculty member from each of the three core areas; composition of this committee needs to be approved by the IGERT steering committee. The guidance committee should meet with the student during the first month of the student's first term to prescribe a plan of study consistent with the student's background and needs. Following this meeting, it is the responsibility of the student and the chair of the committee to complete FORM A and submit it to the IGERT Director. The guidance committee should also meet at the beginning of the student's second semester. Students are encouraged to meet on a monthly basis with committee members one-on-one; we believe that it is especially important for students at the outset of an interdisciplinary training program to interact with faculty mentors coming from different perspectives. At the end of the first year, students choose their thesis advisor and form their thesis committee. This committee will then meet annually to provide advice and guidance. This committee provides a written report of the annual meeting (FORM B) to the IGERT steering committee, describing the student's progress and accomplishments.
The graduate college of the University of Arizona stipulates that all Ph.D. committees consist of five faculty members. Students entering through this IGERT program are required to form inter-disciplinary thesis committees by including at least one representative from each of the three core areas among the five faculty members. Students obtain the Ph.D. through existing departments and graduate programs but interact with other students in this program through the various channels.
RESEARCH ROTATIONS AND COLLOQUIA
Ph.D. students in most participating programs are already required to undertake three research rotations, usually completed in laboratories of faculty within their department. IGERT students adapt the research rotation requirements of their degree program in order to acquire interdisciplinary research experience in genomics. In particular, all IGERT students are required to perform one research rotation in each of our three core areas, thus ensuring exposure to fundamentally new perspectives. For example, a student working on patterns of gene expression might undertake a rotation in evolutionary theory, while a computer science student might complete a rotation in molecular biology. These hands-on experiences and participation in activities of different laboratory groups foster interactions among researchers in different disciplines. Each rotation is a half-semester long and occurs on a fixed schedule. At the end of each of the three rotation periods, there is a colloquium, run by the IGERT director, in which each student presents a fifteen-minute talk about their recently completed research. This colloquium is advertised within participating departments and is open to all faculty and students. These colloquia are scheduled at the end of each rotation period, typically on the second Friday in October, December, and March.
All new students are required to take the course "Functional and Evolutionary Genomics" in the Fall semester. This course surveys the basic findings and approaches in the field, including the conceptual, methodological and technical advances that are central to obtaining genome sequences and understanding genome function and evolution. The class meets twice weekly, each time for a three hour session combining lecture and computer laboratories. It is team-taught by three IGERT faculty, representing each core area.
This course has three objectives. First, we are interested in providing a core of background information relevant to evolutionary, functional, and computational issues in genomics. This provides an assurance that all students in our program are equipped with a standard base of knowledge across our three areas and will provide the necessary lexicon so that students from these different areas can communicate with each other. This goal is achieved by a series of lectures in each of the three core areas as well as by reading and discussing the primary literature.
Second, we provide hands-on training and exposure to modern computational methods in genomics and bioinformatics. Our intent is that every student be conversant with bioinformatic methods, including proficiency in writing their own programs for data manipulation and analysis. In the computer laboratory, students learn to manipulate and analyze sequence data and large-scale gene expression and proteomic data. Students thus become familiar with the major genomic databases, and the methods for searching and interacting with these databases.
Third, we wish to foster meaningful interactions and collaborations among students from the three areas. Thus, in addition to lectures, discussions, and laboratories in each area, the foundations course incorporates exercises requiring the active collaboration of students based in different areas. To this end, the course incorporates research problems to be addressed by teams consisting of students with different expertise. For example, a group of three students might investigate whether rates of evolution differ between a set of "shared genes," present in all bacterial genomes sequenced, and a set of "unshared genes," present in half or fewer of the bacterial genomes sequenced. This problem would require an understanding of approaches to identifying gene function, an understanding of principles of molecular evolution, and a background in computation sufficient to retrieve, align, manipulate, and analyze huge amounts of data.
Lecture topics in this course include: gene structure and regulation, protein structure, gene and genome organization, gene duplication and loss, metabolic pathways, and evolutionary genetics. Lab topics include: programming, sequence retrieval, alignment, molecular evolutionary and phylogenetic analyses, expression analyses, database manipulation. Research topics are diverse, including such themes as comparative studies in gene expression, the evolution of genome organization, inferring metabolic systems from genome sequence data, and patterns of gene transfer among species. RETURN TO TOP
RESEARCH IN GENOMICS COURSE
All new students are required to take one or more semesters of a question-driven, workshop-style seminar, "Research in genomics." This course is offered each year in the spring semester for three credits and it focuses on a different topic each year.
The purpose of this course is for students and faculty to work together to apply the ideas developed in the foundation course to a real problem. The course is organized by one faculty member, but at least two additional faculty representing the other core areas also participate. In the semester preceding the course, students and faculty discuss potential projects and approaches, with a focus on the comparative genomics of closely related organisms. Students jointly consider both the conceptual framework and the sequencing strategy in designing these projects. For example, we may choose systems in which related, reference genomes are available, or in which we examine communities of organisms associated with a particular environment. Depending on the samples and project, we may choose small insert libraries, fosmids or BACs. After the students as a group have chosen a project, they prepare samples and clone libraries to be sequenced using 454 pyrosequencing technology available to the IGERT through the Arizona Genomics Institute. Based on current costs and technologies, we should obtain about 20 megabases of sequence, and these sequence data, generated before the course begins, form the basis of interpretation and analysis. The instructors direct and assist the students in bringing this work to the level of a scientific manuscript to be submitted for publication.
Staff at the Arizona Genomics Institute provide technical support if additional sequence or cloning is required (e.g., to help complete regions of missing or of poor quality data), and the expertise necessary to assemble, annotate and analyze sequences is already in place at the University of Arizona through the Arizona Research Laboratories. Students will have gained skills needed for analysis during the computational portion of the IGERT course in the preceding semester.
We envision two possible endpoints for this course. In many cases, the goal will be a research grant to support the work. It is possible that the group will become so excited about a research problem that they may decide to pursue it by submitting the application and collaborating on the project. In other cases, the endpoint for the course may be a multi-authored publication, either reviewing a topic or answering a question with data from the literature or from databases. In addition to the benefits of learning to critically evaluate a technique in a "real world" situation, this course shows students and faculty the value of collaborative interactions and efforts. RETURN TO TOP
BI-WEEKLY DISCUSSION GROUP
All new students are required to participate in a bi-weekly discussion group that includes IGERT faculty and fellows. This forum has been used for a variety of activities, including research seminars by students and faculty, panel discussions on a variety of topics including career development and ethics, talks by invited speakers, discussion of current literature and short research seminars by students and faculty. After the first year, all IGERT students are required to present an annual research seminar, many of which are in this bi-weekly discussion group. The group is organized and led by the senior IGERT fellows.
PARTICIPATION IN OTHER IGERT ACTIVITIES
All IGERT fellows are expected to participate fully in IGERT activities, including symposia, interactions with visiting faculty, informal discussion groups, and other scientific and social events that may be planned.
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