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Committee on Cellular and Molecular Physiology

This is an archived copy of the 2012-13 catalog. To access the most recent version of the catalog, please visit http://catalogs.uchicago.edu.

Chair

  • Eric Beyer

Professors

  • Eric Beyer, Pediatrics
  • Francisco Bezanilla, Pediatrics
  • Eugene Chang, Medicine
  • Aaron Fox, Neurobiology, Pharmacology and Physiology
  • Benjamin Glick, Molecular Genetics and Cell Biology
  • Steve Goldstein, Pediatrics
  • Christopher Gomez, Neurology
  • William Green, Neurobiology
  • Dorothy A. Hanck, Medicine
  • Ratnesh Lal, Medicine
  • Alan Leff, Medicine
  • Karl Matlin, Surgery
  • Jeffrey Matthews, Surgery
  • Elizabeth McNally, Medicine
  • Deborah J. Nelson, Neurobiology, Pharmacology and Physiology
  • H. Clive Palfrey, Neurobiology, Pharmacology and Physiology
  • Eduardo Perozo, Pediatrics
  • Louis H. Philipson, Medicine
  • Nanduri Prabhakar, Medicine
  • Marsha Rosner, Ben May Dept of Cancer Research
  • Eric A. Schwartz, Neurobiology, Pharmacology and Physiology
  • Julian Solway, Medicine
  • Wei Jen Tang, Ben May Dept of Cancer Research
  • F. Gary Toback, Medicine
  • Jerrold Turner, Pathology
  • Mitchel Villereal, Neurobiology, Pharmacology and Physiology

Associate Professors

  • James Brorson, Neurology
  • Mahesh Gupta, Surgery
  • Akira Imamoto, Ben May Dept of Cancer Research
  • Stephen Kron, Molecular Genetics and Cell Biology
  • Philip E. Lloyd, Neurobiology, Pharmacology and Physiology
  • Jeremy Marks, Pediatrics
  • James Mastrianni, Neurology
  • Daniel McGehee, Anesthesia and Critical Care
  • Gopal Thinakaran, Neurobiology
  • Aaron Turkewitz, Molecular Genetics and Cell Biology

Assistant Professors

  • Konstantin G. Birukov, Medicine
  • Matthew Brady, Medicine
  • Nikolai Dulin, Medicine
  • Kathleen Goss, Surgery
  • James Holaska, Medicine
  • Richard Baker Jones, Ben May Dept for Cancer Research
  • Piers Nash, Ben May Dept of Cancer Research
  • Jalees Rehman, Medicine
  • Martin ter Beest, Surgery
  • Mirjam Zegers, Surgery

Emeritus Faculty

  • Harry A. Fozzard, Neurobiology, Pharmacology and Physiology


Students are no longer being admitted to the program in cellular and molecular physiology.  Research on the structure and function of biological systems at the molecular, cellular, and sub-cellular level is being conducted by faculty with membership in the Institute for Integrative Physiology.   IIP is not a graduate program. These faculty have membership in graduate programs that would prepare students for a PhD on topics of cellular and molecular physiology.  Interested students should consult the listings for more detailed information concerning those individual programs.

Today’s cell physiologist is motivated by the need to understand how cells work in the context of organs and organisms. The intricate interactions within and between cells provide a fascinating framework and countless unanswered questions. Thanks to recent advances in technology and experimental approaches, we are identifying fundamental cellular processes that were only theorized just a few years ago. In today’s research environment, quality training in cell physiology requires interdisciplinary approaches using state of the art techniques. The graduate training program in Cellular and Molecular Physiology at the University of Chicago provides a supportive research community that fosters cooperation while encouraging individual excellence and creativity. In short, this program is an ideal training environment for individuals interested in joining this exciting field. The program provides training and instruction for students over a wide range of topics, leading to the Ph.D. degree, which is granted through the Department of Neurobiology, Pharmacology and Physiology. Major research areas in which training can be received include electrophysiology of ionic channels in excitable and nonexcitable cells; membrane transport systems; signal transduction and second messenger systems; regulation of cell growth in normal and transformed cells; biophysics and biochemistry of muscle contraction; molecular biology of muscle proteins and ionic channels; and mechanisms of endocytosis and secretion. A common focus of this committee is the interest in the integration of the specific phenomena in the behavior of the whole cell.

The program in Cellular and Molecular Physiology includes faculty with diverse research interests who are dedicated to graduate education. All students receive concentrated attention from faculty mentors, advisory committee members and course instructors. The research interests of the program faculty range from cell development and structure to signal transduction across the plasma membrane.

Cell physiology students are required to take 9 courses, selecting at least one course from each of the following categories: biochemistry, cell biology, molecular biology and physiology. In addition, students take two courses in genetics. Elective courses are offered in neurophysiology, membrane transport, ionic channels, control of cell growth, neuropharmacology, and psychopharmacology. In addition to this didactic course work, all first year students are required to attend a course in scientific ethics and integrity in research, usually offered in Spring Quarter. Before completion of the degree program, students in the Biological Sciences are required to be a teaching assistant in two courses without remuneration in order to gain experience in organizing and leading a class.

Laboratory Rotations

Students are required to complete two lab rotations, which together will receive a total of one course credit. Additional rotations may be taken, but will not receive credit.

Preliminary Exams

Students will submit a written thesis proposal before the start of the third year. Successful students will be admitted to candidacy for the Ph.D.

Thesis Proposal

Submitted before the start of the third year.

Frequency of Thesis Committee Meetings

Bi annual thesis committee meetings.

The Committee welcomes medical students interested in a Ph.D. There are two M.D./Ph.D. programs available to Pritzker School of Medicine students. Interested students are encouraged to apply for the Medical Scientist Training Program at the same time they file their application with the Pritzker School of Medicine. Interested MSTP students, would follow the medical school curriculum for two years and then enter the Cellular and Molecular Physiology research program for their dissertation research. After the completion of the Ph.D., the students return to medical school to complete the work required for the M.D. Another combined degree program is available after matriculation to medical school. Medical students are allowed elective research courses during the third quarter of the first year during which time many discover an interest in scientific research. Application to the Cellular and Molecular Physiology Program may be made during the second year of medical school. Once accepted to the program and after securing funding from the several fellowship sources available to medical students within the University, the student takes a leave of absence for the length of time required to complete the Ph.D.

More information on the combined M.D./Ph.D. degree programs is available from the Dean of Students Office of the Biological Sciences Division.

Admission Information

Students initially are admitted to the Biological Sciences Division and must meet divisional requirements. The application consists of a statement of interest, three letters of recommendation; transcripts from all post secondary institutions attended; official notification of GRE general examination scores; and official notification of TOEFL if the applicant’s native language is not English.

Financial Aid

Fellowship support is provided by means of University and endowed fellowships, federal training grants, and programmatic support awarded to the individual laboratory. In most cases, this support includes a full stipend, the required student supplemental health insurance and health center fee, and full tuition which varies according to the number of quarters a student has been in registration. Notification of fellowship support is sent with the admissions packet. Highly qualified applicants are also encouraged to apply for fellowships from outside agencies such as the Howard Hughes Medical Institute and the National Science Foundation.

Funding is guaranteed to each student for the first four years and traditionally has been continued through the completion of the Ph.D. as long as satisfactory progress is certified. The student is responsible for reporting and paying applicable state and federal income taxes.

Biochemistry and Molecular Biology Courses

BCMB 30266. Units.

Equivalent Course(s): IMMU 30266

BCMB 30400. Protein Fundamentals. 100 Units.

The course covers the physical‑chemical phenomena that define protein structure and function.  Topics include:  the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology.  Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation.

Instructor(s): Robert Keenan, Shohei Koide, Joseph Piccirilli     Terms Offered: Autumn
Equivalent Course(s): GENE 30400,HGEN 30400,MGCB 30400

BCMB 31000. Fundamentals of Molecular Biology. 100 Units.

This course covers the structure of genetic material, chromatin, replication, DNA repair and transcription, including its regulation, RNA processing, post-transcriptional regulation, and protein synthesis. Third- or fourth-year standing is required for undergraduates; any graduate student may enroll.

Instructor(s): U. Storb, J. Staley     Terms Offered: Winter
Prerequisite(s): Basic knowledge of genetics and biochemistry
Equivalent Course(s): BIOS 21208,GENE 31000,MGCB 31000

BCMB 31100. Evolution of Biological Molecules. 100 Units.

This introductory graduate-level course connects evolutionary changes in genes and genomes with the structure, function and behavior of the protein and RNA molecules they encode.  Our central themes will be the mechanisms and dynamics by which molecular structure and function evolve, how protein/RNA architecture shapes evolutionary trajectories, and how patterns in present-day sequences can be interpreted to reveal the interplay data of evolutionary history and molecular properties.  We will teach core concepts in both macromolecular biochemistry (folding and stability of proteins and RNA, structure-function relationships, kinetics, catalysis) and molecular evolution (selection, mutation, drift, epistasis, effective population size, phylogenetics) and specifically explore the interplay between them. Students will derive and simulate evolution using molecular-level models; analyze empirical structure, function and sequence data in an evolutionary framework; and, through discussion and reading of classic and recent literature, trace the development of key ideas in molecular evolution up to the present day.

Instructor(s): D. Allan Drummond, Joseph Thornton     Terms Offered: Winter
Prerequisite(s): Comfort with basic computer programming (course will use Python and R); undergraduate biology, chemistry, calculus, and introductory statistics.
Equivalent Course(s): HGEN 31100,ECEV 31100

BCMB 31200. Molecular Biology-I. 100 Units.

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.

Instructor(s): L. Rothman-Denes     Terms Offered: Winter Quarter
Equivalent Course(s): MGCB 31200,DVBI 31200

BCMB 31300. Molecular Biology-II. 100 Units.

The content of this course covers the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions.

Instructor(s): J. Staley, J. Holaska, A. Ruthenburg     Terms Offered: Spring Quarter
Equivalent Course(s): MGCB 31300,DVBI 31300

BCMB 31358. Simulation, Modeling, and Computation in Biophysics. 100 Units.

This course develops skills for modeling biomolecular systems.  Fundamental knowledge covers basic statistical mechanics, free energy, and kinetic concepts.  Tools include molecular dynamics and Monte Carlo simulations, random walk and diffusion equations, and methods to generate random Gaussian and Poisson distributors.  A term project involves writing a small program that simulates a process.  Familiarity with a programming language or Mathlab would be valuable.

Instructor(s): B. Roux     Terms Offered: Spring
Prerequisite(s): BIOS 20200 and Bios 26210-26212, or consent from instructor
Equivalent Course(s): BIOS 21358,CPNS 31358

BCMB 31400. Genetic Analysis of Model Organisms. 100 Units.

Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes.  The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature.

Instructor(s): A. Palmer, D. Bishop, E. Ferguson, J. Malamy     Terms Offered: Autumn
Equivalent Course(s): DVBI 31400,HGEN 31400,MGCB 31400

BCMB 31600. Cell Biology I. 100 Units.

Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis,and mechanisms and regulation of membrane fusion.

Instructor(s): A. Turkewitz, B. Glick     Terms Offered: Autumn Quarter
Equivalent Course(s): MGCB 31600,DVBI 31600

BCMB 31800. Current Seminar Topics in Biochemistry & Molecular Biology. 50 Units.

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students.

Equivalent Course(s): BPHS 31800

BCMB 31900. Introduction to Research. 100 Units.

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students

Instructor(s): Staff     Terms Offered: Autumn, Winter Quarters
Equivalent Course(s): MGCB 31900,DVBI 31900,GENE 31900,HGEN 31900

BCMB 32200. Biophysics of Biomolecules. 100 Units.

This course covers the properties of proteins, RNA, and DNA, as well as their interactions. We emphasize the interplay between structure, thermodynamics, folding, and function at the molecular level. Topics include cooperativity, linked equilibrium, hydrogen exchange, electrostatics, diffusion, and binding.

Instructor(s): T. Sosnick     Terms Offered: Spring
Prerequisite(s): Consent of instructor
Equivalent Course(s): BIOS 21328,BPHS 31000

BCMB 32300. Macromolecular Function. 100 Units.

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.

Equivalent Course(s): MGCB 32300

BCMB 32500. Bioorganic Chemistry. 100 Units.

A goal of this course is to relate chemical phenomena with biological activities. We cover two main areas: (1) chemical modifications of biological macromolecules and their potential effects; and (2) the application of spectroscopic methods to elucidate the structure and dynamics of biologically relevant molecules.  Not offered in 2012-13.

Equivalent Course(s): CHEM 32500