The Biomedical Sciences Cluster

The Metabolism Program at the University of Chicago embodies a unique structure that takes full advantage of the strengths and character of the University of Chicago. The Committee on Molecular Metabolism and Nutrition is an interdepartmental, degree-granting body that draws its faculty from the ranks of basic science and clinical science. This is possible because all these disciplines share the same campus and often the same building. This provides the student with the opportunity to acquire sound basic training in biochemistry. At the same time, this training is tempered by constant exposure to the impact of metabolism on human health and well being. This provides integrated training in the basic biochemical mechanisms through which foods and nutrients interact to optimize health, the pathological consequences of malnutrition, and the interplay of nutrition and human behavior.

The Committee on Molecular Metabolism and Nutrition is integrated within a cluster of graduate programs from the Committee on Cancer Biology, the Committee on Immunology, the Committee on Microbiology, and the Department of Pathology Molecular Pathogenesis and Molecular Medicine program. The five academic units share a joint Admissions Committee, several common courses, a seminar series, and additional common events for students and faculty within the cluster. The goal of the cluster system is to encourage interdisciplinary interactions among both trainees and faculty, and to allow students flexibility in designing their particular course of study.

In addition, students have extensive opportunities for interaction with the three other clusters within the Biological Sciences Division: the Molecular Biosciences Cluster; the Darwinian Sciences Cluster; and the Neurobiology Cluster. These clusters offer courses and sponsor seminars and symposia open to Metabolism students.

Program Philosophy

The philosophy of the program is to provide students with a wide range of educational opportunities in a research-rich environment that will stimulate the student to engage in the life-long pursuit of knowledge through self-learning. Didactic courses during the first year provide education in the principles of basic science. In the summer and continuing into the second year, coursework gives way to interactive training that stresses the evaluation of literature, effective communication, and hypothesis testing combined with early exposure to research. This is enriched by a strong seminar program that exposes the student to the national leaders in metabolism research and policy.

Prerequisites

Students may be admitted with deficiences, and students with a deficiency are encouraged to apply. Any such deficiences should be made up within 20 months of starting graduate study.

Formal Coursework

A minimum of 9.5 didactic courses are to be selected from 7.5 required courses plus electives. It is required that students maintain a minimum overall “B” average in their coursework. Any Cs must be offset by As to maintain a B average and a grade of B or better must be achieved in all programmatic courses.

The Programmatic Core in Metabolism (4.5 credits)

Metabolism Electives

Molecular Basis of Metabolic Disease (MOMN 30901). This course selects topics in nutrition in which modern molecular and cell biology provide a greater understanding of the regulation of these metabolic pathways. Wicksteed. Autumn.

Signal Transduction and Disease (MPMM 30600). Topics include receptor ligands, membrane receptor tyrosine kinases and phosphatases, G proteins, proto-oncogenes, signaling pathways, cytoplasmic protein kinases and phosphatases, transcription factors, receptor-nucleus signaling, development and cancer, genetic dissection of signaling pathways, cell growth and cell proliferation, interplay of cell cycle regulators, cell cycle progression and apoptosis, and sensing of hypoxia and mechanical stimuli. The role of signaling in disease is a theme throughout the course. Dulin. Winter.

Advanced Biotechniques (MOMN 30920). The Biotechniques course will focus on familiarizing students with cutting edge experimental techniques used in biomedical research. The course will comprise a combination of lectures, reading and discussion of primary literature and exposure to several core facilities located on campus. Topics to be covered include generation of transgenic animals, biosensors and cell imaging, genomic microarrays, proteonomics, protein overexpression, knockdown and detection. Roe, Sun. Spring.

The General Basic Science Core (3 credits)

Biochemistry
Proteins 1: Protein Fundamentals (BCMB 30400). The course covers the physico chemical phenomena that define protein structure and function. Topics include: 1) the interactions/forces that define polypeptide conformation; 2) the principles of protein folding, structure and design; and 3) the concepts of molecular motion, molecular recognition, and enzyme catalysis. Prereq: BCMB 30100, which may be taken concurrently, or equivalent. Koide, Keenan. Autumn.

Fundamentals of Structural Biology (BCMB 30500). This course emphasizes the basic principles of protein structure determination by X-ray crystallography and NMR spectroscopy. The underlying physical concepts of these methods will be introduced and the capabilities of each will be discussed and compared in context of their uses in de novo structure determination and protein engineering studies. Kossiakoff, Koide. Winter. (This course will not be offered in 2008.)

Proteins 2: Structure and Function of Membrane Proteins (BCMB 32300). This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading. Perozo, Roux. Winter

Cell Biology
Cell Biology 1 (MGCB 31600). Lecture/discussion course on fundamentals of protein translocation, protein and membrane sorting and transport, organelle biogenesis, and the cytoskeleton. Glick, Turkewitz. Autumn.

Cell Biology 2 (MGCB 31700). This course will cover cell cycle progression, cell growth, cell death, cytoskeletal polymers and motors, cell motility, and cell polarity. Glotzer, Kovar. Winter.

Genetics
General Principles of Genetic Analysis (GENE 31400). Coverage of the fundamental tools of genetic analysis as used to study biological phenomena. Topics include genetic exchanges in prokaryotes, eukaryotes, and their viruses and plasmids; principles of transformation; analysis of gene function. Bishop and Staff. Autumn.

Genetic Mechanisms (GENE 31500). Advanced coverage of genetic mechanisms involved in genome stability and rearrangement. Topics include genetics of transposons, site-specific recombination, gene conversion, reciprocal crossing over, and plasmid and chromosome segregation. Bishop. Winter.

Human Genetics 1: Human Genetics (HGEN 47000). This course covers classical and modern approaches to studying cytogenetic, Medelian, and complex human diseases. Topics include chromosome biology, human gene discovery for single gene and complex disease, non-Mendelian inheritance, mouse models of human disease, cancer genetics, and human population genetics. The format includes lectures and student presentations. Cox, Ober, Millen. Autumn.

Molecular Biology
Fundamentals in Molecular Biology (MGCB 31000). The course covers nucleic acid structure and DNA topology, recombinant DNA technology, DNA replication, DNA damage, mutagenesis and repair, transposons and site-specific recombination. Prokaryotic and eukaryotic transcription and its regulation, RNA structure, splicing and catalytic RNAs, protein synthesis, and chromatin. Staley, Storb. Winter.

Molecular Biology 1 (MGCB 31200). Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria. Rothman-Denes. Winter.

Molecular Biology 2 (MGCB 31300). The content of this course will cover the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore with you research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions will focus on the most significant recent developments, their implications and future directions. Singh, Staley. Spring.

Electives (2 credits)

The remaining two (or more) courses may be selected from available courses in the areas listed below. At least one advanced metabolism course must be selected (denoted by *). Statistics is recommended. Students who have completed their academic requirements are encouraged to formally audit additional advanced courses.

Students may petition the Ph.D. Curriculum Committee regarding changes in required areas of coursework. Up to two (2) required areas may be modified to provide a specific focus of study in metabolism. Specific changes and the justification for those changes must be submitted in writing.

Reading and Laboratory Rotations

In the winter and spring of their first year, students are required to perform 10-week, graded rotations through laboratories of interest. Since the student will choose their thesis lab during these rotations, it is critical that serious thought and effort (reading papers, talking to the PI and lab members, etc.) be given before choosing the labs. Students should contact prospective laboratories in the preceding quarter to ensure that space/resources are available. In the following quarter, students will present an overview of their project and results from their rotation. A third, optional rotation can be performed during the summer quarter. It is expected that a student will have chosen their thesis research lab no later than the end of their first year.

Current Topics in Nutritional Research (0.5 credit)

The Committee holds a seminar series/journal club biweekly throughout the year. Student attendance and participation are required autumn, winter and spring quarters of their first two years. At the end of the second year, students will be graded pass/fail. Continued student participation in this series is expected until graduation.

In the autumn, CMMN faculty members will give research talks to further expose students to research being conducted by Committee members. In the winter through summer quarters, faculty presentations will either comprise research talks or presentation of a high profile, recent journal article related to Metabolism research. Additionally, prominent outside speakers will be invited periodically to give research seminars, and students will meet with the speaker immediately after the talk.

Students are also required to present twice yearly. In the first year, presentations will be based on the laboratory rotation performed the previous quarter. Second year students will present a mock grant proposal in the winter (see below) and a journal article in the spring. In subsequent years, students are required to present on their thesis research project once a year. The second presentation can either be discussion of a journal article, or for more advanced students, a second presentation of their own research.

Student Teaching

Students are required to teach as part of their doctoral training. This requirement may be met by assistant teaching two courses that meet the Divisional requirement for a full TA-ship or taking the Divisional TA training course and assistant teaching one course. The TA requirement should be completed by the third year of residence. Teaching performance is evaluated by the course director and filed in the Graduate Affairs Office.

Mock Grant Proposal

In the winter of the second year, students are required to complete a mock grant proposal, consisting of a 10 page, NIH-style grant proposal and a 45-minute oral presentation. The proposal should define an unaddressed research area in Molecular Metabolism and Nutritional Biology, propose 2-3 specific aims to explore the problem and describe experiments that would be conducted over a 5-year period. Previous proposals will be available to be used as templates. The topic chosen cannot be directly related to the student’s thesis research and must be approved by the CMMN Chair. The student will present and defend their mock grant proposal to the Metabolismn Committee faculty and students. A committee comprising of three CMMN faculty members chosen by the CMMN Chair will evaluate each mock grant proposal and oral presentation. The student will meet privately with the committee members after the oral presentation to discuss the proposal and to answer questions. Any deficiencies in the written proposal, oral presentation and/or background knowledge of the research area will have to be addressed before the student is passed. All required revisions must be completed by the end of the following quarter.

Thesis Requirements

Starting in the summer/autumn after the second year, a student should begin in earnest, research work towards their thesis project. By autumn of the third year, the student should form their thesis committee and submit their thesis proposal.

The thesis committee will comprise of four members: the student’s advisor, a committee chair (not to be the advisor) and two other members of the Metabolism Committee. The thesis proposal should consist of a detailed background of the research area to be studied, preliminary data demonstrating the feasibility of the proposed experiments, 2-3 specific aims and a supporting experimental plan to address the research area. Total length should be approximately 20 pages. The proposal should be given to committee members at least two weeks before the oral defense of the thesis proposal. The student will make a public presentation to students and faculty of CMMN, and then meet with their committee in private to answer questions and discuss the proposed experiments in detail. Once accepted by the committee, the student will then formally enter the Ph.D. program.

Thesis

Each student will be required to complete a dissertation documenting original research within 6 years of the thesis proposal defense. However, it is expected that students will complete their thesis during their fifth year in the program. The thesis should consist of 2-3 chapters, and it is expected that at least two of these chapters will result in first author publications in prominent journals. Students failing to meet these time limits must apply for readmission to the Ph.D. program.