The Committee on Microbiology - Curriculum
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
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:
BCMB 30400 Proteins 1: Protein Fundamentals
covers the physico-chemical phenomena that define protein structure and
function. Topics include 1) the interactions /forces that define
peptide conformation; 2) the principles of protein folding, structure
and design; and 3) the concepts of molecular motion, molecular
recognition, and enzyme catalysis. Drs. Koide, Keenan.
GENE 31400 General Principles of Genetic
Coverage of the fundamental tools of genetic analysis as used to study
biological phenomena. Topics include genetic exchange in
eukaryotes, and their viruses and plasmids; principles of
transformation; analysis of gene function. Drs. Bishop and
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.
Fundamentals of Bacterial Physiology
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
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
Fundamentals of Structural Biology
emphasizes the basic principles of protein
structure determination by X-ray crystallography and NMR spectroscopy.
underlying physical concepts of these methods will be introduced and
capabilities of each will be discussed and compared in context of their
de novo structure determination and protein engineering studies.
Drs. Kossiakoff, Koide. Winter.
BCMB 32300 Proteins
2: Structure and Function of
This course will be an in depth
assessment of the structure and function of biological membranes. In
to lectures, directed discussions of papers from the literature will be
The main topics of the courses are: (1) Energetic and thermodynamic
associated with membrane formation, stability and solute transport (2)
protein structure, (3) lipid-protein interactions, (4) bioenergetics
transmembrane transportmechanisms, and (5) specific examples of
protein systems and their function (channels, transporters, pumps,
Emphasis will be placed on biophysical approaches in these areas. The
literature will be the main source of reading. Drs. Perozo, Roux. Winter
31500 Genetic Mechanisms
Advanced coverage of genetic mechanisms involved in genome stability
rearrangement. Topics include genetics of transposons,
recombination, gene conversion, reciprocal crossing over, and plasmid
chromosome segregation. Dr. Bishop. Winter.
Advanced Immunology 1
Lecture/discussion course that explores the genetic and molecular basis
immune recognition by B and T lymphocytes. Specific topics to be
include the expression of the antigen specific receptors on B and T
lymphocytes, immunogenetics, the differentiation of lymphocyte subsets,
restriction, cellular interactions and effector mechanism in immune
and the role of accessory molecules in cellular interactions. Dr. Bendelac. Winter.
31000 Fundamentals of Molecular Biology
The course covers nucleic acid structure and DNA topology, recombinant
technology DNA replication, DNA damage, mutagenesis and repair,
site-specific recombination. Prokaryotic and eukaryotic transcription
regulation, RNA structure, splicing and catalytic RNAs, protein
chromatin. Drs. Storb and Staley. Winter.
Molecular Biology 1
structure and DNA topology; methodology;
nucleic-acid protein interactions; mechanisms and regulation of
in eubacteria, and of replication in eubacteria and eukaryotes;
genome and plasmid segregation in eubacteria. Drs.
31700 Cell Biology 2
This course will
cover cell cycle progression, cell growth, cell death, cytoskeletal
and motors, cell motility, and cell polarity. Glotzer,
35500 Developmental Genetics of
Non-vertebrate Model Systems
course explores the use of genetics in three different model systems,
elegans, Drosophila melanogaster and Arabodopsis thaliana, to elucidate
developmental mechanisms. The class will
focus on a series of interrelated topics: for each topic, introductory
presented by the lecturer will be followed by student-led discussions
individual papers. Drs. Ferguson, Du,
and Greenberg. Winter.
34000 Bacterial Pathogenesis
Bacterial pathogens of human, animal and plant organisms, their
strategies and molecular mechanisms of causing disease. Dr. Leber.
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. 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:
31300 Molecular Biology 2
Topics include transcription and post-transcription, changes in
structure during gene activation, tissue- and developmental-specific
transcription regulators, and post-transcriptional regulation of gene
expression. Prereq: MGCB 31200 or consent of
Singh and Staley. Spring.
46900 Human Genetics 2: Human Variation and Disease
This course focuses on
principles of population and evolutionary genetics and complex trait
they apply to humans. It will include
the discussion of genetic variation and disease mapping data. Drs. DiRienzo, Hudson, and Pritchard. Spring.
Explores the molecular and biochemical mechanisms by which lymphocytes
activated in response to antigen. Dr. Clark, Kee. Spring.
MGCB 31300 Molecular Biology 2
The content of this course will cover the mechanisms
regulation of eukaryotic gene expression at the transcriptional and
post-transcriptional levels. Our goal is to explore with you research
and evolving methodologies. Rather than focusing on the elemental
aspects of a
topic, the lectures and discussions will focus on the most significant
developments, their implications and future directions. Drs. Singh,
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
virus-host interactions. Our goal is to
provide students with solid appreciation of basic knowledge as well as
on the frontiers of virus research. Drs.
Golovkina and Roizman. Spring.
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
to infection and the viral functions which enable the pathogens to
host. Drs. Golovkina, Roizman. Spring.
course describes the basic mechanisms involved in defense against and
pathogenesis of human diseases. Topics to e covered include
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
III. Research Forum 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
IV. Upper-Division Classes of the Committee on
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
Dr. Missiakas. Autumn.
MICR 31600 (BIOS 25216) - Molecular Basis
of Bacterial Diseases.
Dr. Martinez. Winter.
MICR 34600 (BIOS 25287) - Introduction to Virology.
Dr. Golovkina. Spring.