The Committee on Microbiology - Curriculum

Ph.D. in Microbiology

Students interested in graduate training in the Committee on Microbiology must apply by December 28 to the Biological Sciences Graduate Division at the University of Chicago.  Students are typically interviewed by faculty in the month of February for admission in autumn of that same year.  Students are admitted according to recommendations made by the faculty of the Committee and the faculty of the Biomedical Sciences Cluster.  After arriving on campus, students are advised by the Graduate Advisor of the Committee on Microbiology regarding which classes they should take.  The Committee on Microbiology aims to admit between four and eight graduate students per year.  Funding for Committee on Microbiology graduate students is guaranteed throughout their doctorate study.

Graduate Curriculum of the Committee on Microbiology

The Committee on Microbiology requires graduate students pursuing a Ph.D. in Microbiology to take a minimum of nine courses.  Even so, the basis of graduate training in microbiology is the performance of original laboratory research.  The philosophy of graduate classroom training in microbiology is to develop a knowledge base for the first-year graduate student.  The courses MICR 30600, MICR 31600, MICR 33000 and MICR 34600 are designed for graduate students (and upper-level undergraduates) that do not have profound knowledge of the subspecialties of microbiology.  These classes are designed to teach students the available experimental tools and to define the experimental frontier in a field. Upper-level graduate classes examine the most current scientific literature or the development of original research problems.  Of course, microbiology classes are complemented by a set of courses in other disciplines in the Biological Sciences Division.  Interdisciplinary study is encouraged.

I. Lecture Classes for Graduate Students of the Committee on Microbiology

Autumn Quarter: Students will take two or three classes as assigned by the graduate advisor. Students are also encouraged to do a laboratory rotation. Examples for these classes are:

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

MCGB 31600  Cell Biology 1
A lecture and discussion course on fundamentals of protein synthesis and translocation, protein and membrane sorting and transport, organelle biogenesis and the cytoskeleton.  Drs. Turkewitz and Glick.  Autumn.

MICR 30600  Fundamentals of Bacterial Physiology
This course introduces bacterial diverstiy, physiology, ultra-structure, envelope assembly, metabolsm, and genetics.  In the discussion section, students review recent origianl experimental work in the fiield of bacterial physiology.  Dr. Missiakas.  Autumn.

MICR 31200  Host Pathogen Interactions
This course will explore the basic principals of host defense against pathogens and pathogens' strategies to overcome host immune mechanisms.  The course will address evolutionary aspects of innate and adaptive immune responses, while also studying specific examples of viral and bacterial interactions with their hosts.  The reviews of relevant immunological mechanisms necessary for appreciation of host/pathogen interactions will be incorporated in teh studies of specific cases.  Dr. Chervonsky.  Autumn.

Winter Quarter: Students will take two classes assigned by the graduate advisor.  Students are also encouraged to do a laboratory rotation.  Examples for these classes are:

BCMB 30500  Fundamentals of Structural Biology
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.  Drs. Kossiakoff, Koide.  Winter.

BCMB 32300  Proteins 2: Structure and Function of Membrane Proteins 
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.  Drs. Perozo, Roux.  Winter

GENE 31500  Genetic Mechanisms  
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.  Dr. Bishop.  Winter.

IMMU 31500  Advanced Immunology 1  
Lecture/discussion course that explores the genetic and molecular basis of immune recognition by B and T lymphocytes. Specific topics to be discussed include the expression of the antigen specific receptors on B and T lymphocytes, immunogenetics, the differentiation of lymphocyte subsets, MHC restriction, cellular interactions and effector mechanism in immune responses, and the role of accessory molecules in cellular interactions.  Dr. Bendelac.  Winter.

MGCB 31000  Fundamentals of Molecular Biology  
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.  Drs. Storb and Staley.  Winter.

MGCB 31200   Molecular Biology 1 
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.  Drs. Rothman-Denes.  Winter.

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

MGCB 35500  Developmental Genetics of Non-vertebrate Model Systems 
This course explores the use of genetics in three different model systems, C. elegans, Drosophila melanogaster and Arabodopsis thaliana, to elucidate developmental mechanisms.  The class will focus on a series of interrelated topics: for each topic, introductory material presented by the lecturer will be followed by student-led discussions of individual papers.  Drs. Ferguson, Du, and Greenberg.  Winter.

MICR 34000  Bacterial Pathogenesis  
Bacterial pathogens of human, animal and plant organisms, their infectious strategies and molecular mechanisms of causing disease. Dr. Schneewind. Winter. 

MICR 34600  Introduction to Virology
This class on animal viruses considers the major families of the viral kingdom with an emphasis on the molecular aspects of genome expression and virus-host interactions.  Our goal is to provide students with solid appreciation of basic knowledge as well as instruction on the frontiers of virus research.  Dr. Pilipenko. Winter.

Spring Quarter: Students will take two classes assigned by the graduate advisor. Students are also encouraged to do a laboratory rotation. Examples of these classes are:

BCMB 31300  Molecular Biology 2  
Topics include transcription and post-transcription, changes in chromatin structure during gene activation, tissue- and developmental-specific transcription regulators, and post-transcriptional regulation of gene expression.  Prereq:  MGCB 31200 or consent of instructor.  Drs. Singh and Staley.  Spring.

HGEN 46900 Human Genetics 2: Human Variation and Disease 
This course focuses on principles of population and evolutionary genetics and complex trait mapping as they apply to humans.  It will include the discussion of genetic variation and disease mapping data.  Drs. DiRienzo, Hudson, and Pritchard.  Spring.

IMMU 32000  Advanced Immunology 2
Explores the molecular and biochemical mechanisms by which lymphocytes are activated in response to antigen. Dr. Clark, Kee. Spring. 

MGCB 31300  Molecular Biology 2
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. Drs. Singh, Staley. Spring.

MICR 31600  Molecular Basis of Bacterial Diseases
This lecture/discussion course involves a comprehensive analysis of bacterial pathogens, the diseases that they cause, and the molecular mechanisms involved during pathogenesis.  Students discuss recent original experimental work in the field of bacterial pathogenesis.  Martinez.  Spring.

MICR 33000  Molecular Genetic Analysis of Bacteriophage
Phage are the most abundant and fastest growing biological entities and are involved in many natural microbiological processes. This course will examine a series of bacteriophage that have been instrumental in our understanding of genetics and molecular biology with an emphasis on their properties and the methods for which they are used in current and potential biological studies and in biotechnology. Dr. Casadaban. Spring.

MICR 35000  Advanced Topics in Virology
The aims of this course are to examine viral host interaction using herpes simplex and retroviruses as models.  The course will focus on the means by which viruses take over the host cells, the mechanisms of host defenses to infection and the viral functions which enable the pathogens to overcome the host.  Drs. Golovkina, Roizman. Spring.

MPMM 30800 Molecular Defense Mechanisms 
The course describes the basic mechanisms involved in defense against and pathogenesis of human diseases. Topics to e covered include inflammation, coagulation, complement, wound repair, infection and immunopathology.  Dr. Boone. Spring. 

Summer Quarter: Most students will have selected a laboratory for their thesis research however, an additional rotation may be done during the summer quarter with consultation by the graduate advisor. Please see Committee on Microbiology Faculty and Research for faculty laboratories.

II. Seminars of the Committee on Microbiology

During the Autumn, Winter and Spring Quarters, the Committee on Microbiology will host a seminar series comprised of seven to ten presentations by faculty invited from other institutions.  A reading and discussion session will accompany the seminar series, MICR 39000 Introduction to Experimental Microbiology.  In the session, which meets for one hour on a day preceding each week's seminar, first year graduate students will discuss with their peers and a Microbiology faculty member three original research papers of the invited speaker.  Following the seminar and the conventional question and answer period, first year graduate students of the Committee on Microbiology are invited to question the speaker on her or his research and to discuss their own research for a period of 1 hour.  In this manner, we will provide students with an intellectual environment that reveals the discovery process and research frontiers in various laboratories and fields.  First year graduate students are required to register for the course, MICR 39000 Introduction to Experimental Microbiology, and will receive one credit for attending the seminar series (and the reading/discussion section) in the Autumn, Winter and Spring Quarters of the first year of graduate school.

III. Data Club of the Committee on Microbiology

All graduate students and honors undergraduate students of the Committee on Microbiology will present their research in a central forum, the data club, once each year.  The data club meets once a week (Wednesdays at noon in CLSC 119) during the autumn, winter and spring quarters. Students and postdoctoral fellows present their recent research data for critical evaluation by the faculty of the Committee on Microbiology.  This course provides a forum to ensure continued progress of graduate students in their thesis projects.  First year graduate students are required to register for the course, MICR 40000 Microbiology Data Club, and will receive one credit for attending throughout the Autumn, Winter and Spring Quarters of the first year of graduate school.

IV. Upper-Division Classes of the Committee on Microbiology

The classes listed below are upper division undergraduate classes that can be taken by graduate students with educational gaps in microbiology.

MICR 30600 (BIOS 25206) - Fundamentals of Bacterial Physiology.
Dr. Missiakas. Autumn.

MICR 31600 (BIOS 25216) - Molecular Basis of Bacterial Diseases.
Dr. Martinez. Winter.

MICR 34600 (BIOS 25287) - Introduction to Virology.
Dr. Pilipenko. Winter.