The University of Chicago
A Ph.D. candidate must fulfill certain formal coursework requirements, pass the preliminary and qualifying examinations, and present a satisfactory dissertation describing the results of original research.
The Committee expects a knowledge of and proficiency in microbiology. This requirement will normally be met by fulfilling the formal coursework listed below, but detailed degree programs are flexible. Courses taken at other institutions, in other departments, or as part of the Medical School curriculum may substitute for Microbiology courses with approval of the Chair of the COM.
Formal Coursework
To obtain a Ph.D. in the Division of Biological Sciences, nine graded courses are required. The Divisional requirement of nine course credits is maintained by the Committee on Microbiology. The Curriculum is as follows:
All COM graduate students are required to complete courses in three of four areas during the first year: 1) biochemistry, 2) cell biology, 3) genetics and 4) molecular biology. The following courses meet this requirement:
BCMB 30400: Protein Fundamentals (Proteins 1) [1] (Autumn)
GENE 31400: General Principles of Genetic Analysis [1] (Autumn)
MGCB 31600: Cell Biology [1] (Autumn)
BCMB 31000: Fundamentals of Molecular Biology [1] (Winter)
BCMB 31200: Molecular Biology 1 [1] (Winter)
BCMB 32300: Macromolecular Function (Proteins 2) [1] (Winter)
GENE 31500: Genetic Mechanisms [1] (Winter)
MGCB 31700: Cell Biology 2 [1] (Winter)
BCMB 31300: Molecular Biology 2 [1] (Spring)
Required Core Microbiology Courses are:
MICR 34000: Bacterial Pathogenesis [1] (Winter)
MICR 35000: Advanced Topics in Virology [1] (Spring)
COM Graduate Students are also required to attend the following events. Students must register in Year One (Autumn, Winter, Spring). One credit will be granted in Year One for both courses.
MICR 39000: Introduction to Experimental Microbiology [1]
MICR 40000: Microbiology Data Club
One additional Microbiology elective course is required. Students may take additional elective courses throughout the school year with the approval of the academic advisor. Microbiology electives include:
MICR 30600: Fundamentals of Bacterial Physiology
MICR 31200: Host Pathogen Interactions
MICR 31600: Molecular Basis of Bacterial Disease
MICR 33000: Molecular Genetic Analysis of Bacteriophage
MICR 34600: Introduction to Virology
General Education electives include:
BCMB 34300: Principles and Practices of Electron Microscopy
HGEN 46900: Human Genetics 2: Human Variation and Disease
IMMU 30800: Readings: Immunology
IMMU 31500: Advanced Immunology 1
IMMU 32000: Advanced Immunology 2
IMMU 35500: Selected Topics in Immunology
MCGB 35500: Developmental Genetics of Non-vertebrate Model Systems
MPMM 30800: Molecular Defense Mechanisms
Microbiology Research Courses are:
MICR 47000: Thesis Research
MICR 47100: Non-Thesis Research (Rotation)
Students are expected to maintain a grade average of "B" or higher. Students who fail to do so will be placed on academic probation with continuation in the program dependent upon improved performance. Students concluding their first year without a “B” average will be terminated from the program after Spring Quarter unless otherwise recommended by the Chair of the COM.
If a student fails to pass the Preliminary Examination or Qualifying Examination, the student will be terminated by the end of the respective quarter, unless otherwise recommended by the Chair of the COM.
Introduction to Research
All first-year students are required to participate in a Faculty Research Seminar (“All Stars”) held Autumn and Winter quarters. All Stars, BSDG 30000, is organized by the Biomedical Sciences Cluster. This seminar series is designed to provide incoming students with information on the variety of faculty research opportunities available. Students will attend these sessions in which faculty members will present their research. This course is offered pass/fail and confers no academic credit. Attendance is required for a passing grade in this course.
Scientific Ethics Course
All first-year students are required to attend a scientific ethics class organized by the Dean of Students Office. This course is offered during the Spring quarter only. These sessions on scientific ethics often involve examining a set of case studies. All first year graduate students must register for this course. The Dean’s Office will distribute announcements with the title of each talk and the name of the faculty members who will be giving presentations.
Seminars
In addition to formal courses and seminars, there are many regularly scheduled research seminars that will help keep students updated on new developments in microbiology and related disciplines.
Students are expected to attend weekly Committee on Microbiology Seminars and the Microbiology Data Club throughout the course of their matriculation.
The Committee on Microbiology Seminar, given by invited speakers, are held on Mondays during the academic year from 12:00-1:00 p.m. in CLSC l19.
The Committee on Microbiology Data Club meets every Wednesday during the academic year from 12:00-1:00 pm in CLSC 119. At each Data Club meeting, one student, postdoctoral scholar or faculty member will present the research they are working on.
You will find seminar notices posted on the Committee bulletin board outside CLSC 607, 707, 1111, as well as on the first floor of Cummings. Additionally, both the Biomedical Sciences Cluster and the Biological Sciences Division Academic Computing Office has instituted an on-line calendar of events throughout the Division.
Course Descriptions
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 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. Drs. Koide, Keenan. Autumn.
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.
MGCB 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, Glick. 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. (This course will not be offered in 2008.)
BCMB 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.
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 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 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. Getz. 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.
Fundamentals of Bacterial Physiology BIOS 25206
This course introduces bacterial diversity, physiology, ultra-structure, envelope assembly, metabolism, and genetics. In the discussion section, students review recent original experimental work in the field of bacteria physiology. Biweekly lab required. Drs. Missiakas and Christianson. Autumn.
Introduction to Virology BIOS 25287
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.
Molecular Basis of Bacterial Diseases BIOS25216
This course meets one of the requirements of the microbiology specialization. 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.
Dr. Martinez. Spring.
Molecular Genetic Analysis of Bacteriophage BIOS 25307
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.
Medical Microbiology
The Committee on Microbiology offers Medical Microbiology 160-35900 to second year Medical Students at the University of Chicago. The course is comprised of fifty lecture components (MTWThF 8:30-9:20 AM) and ten laboratory components (W 1:30-3:30 PM) in the Autumn quarter. Dr. Olaf Schneewind is the course director and Dr. Kenneth Thompson is the laboratory director. Medical Microbiology is a required component of medical student education. Listed below is a list of lectures and laboratories for the academic year 2005-06.Microbiology
For University of Chicago Second Year Medical Students IIStudent Required Reading/Performance:
- Course Reader and Laboratory Manual
Student Suggested Reading
- Microcards By: Harpavat/Nissim
- Medical Microbiology Made Ridiculously Simple By: Gladwin/Trattler
Performance Evaluation
Lecture Attendance, Midterm Examination, Final Examination (weighted 80%)
Laboratory Performance, Lab Tests & Lab Exam (weighted 20%)Schedule of Lectures MTWRF 8:30-9:20 AM
Day Date Subject Instructor Monday 9/25 Bacterial Classification and Structure Schneewind Tuesday 9/26 Bacterial Growth and Genetics Schneewind Wednesday 9/27 Pathogenesis of Bacterial Infections Schneewind Thursday 9/28 Antibacterial Therapy & Resistance Mechanisms Alexander Friday 9/29 Staphylococcal Diseases Schneewind
Monday 10/2 Streptococcal Diseases Schneewind Tuesday 10/3 Clostridial Diseases Schneewind Wednesday 10/4 Listeriosis, Legionnaire's Disease and Erysipeloid Schneewind Thursday 10/5 Zoonotic Infections/ Biological Warfare Schneewind Friday 10/6 Pneumococci and Bordetella Schneewind
Monday 10/9 Salmonellosis and Bacillary Dysentry Schneewind Tuesday 10/10 Escherichia coli, Pseudomonas & Klebsiella Infections Schneewind Wednesday 10/11 Cholera, Aeromonas & Plesiomonas Infections Schneewind Thursday 10/12 Antibiotic Selection in the Clinical Are Pt. 1 Alexander Friday 10/13 Antibiotic Selection in the Clinical Are Pt. 2 Alexander
Monday 10/16 Diseases caused by obligate intra-cellular bacteria Schneewind Tuesday 10/17 Mycobacterial Disease Schneewind Wednesday 10/18 Helicobacter, Campylobacter and Pasteurellacea Schneewind Thursday 10/19 Diphtheria, Nocardia & Actinomyces Schneewind Friday 10/20 Syphilis Schneewind
Monday 10/23 Non-veneral Treponematoses, Borrelia and Leptospira Schneewind Tuesday 10/24 Gonorrhea and other neisserial diseases Schneewind Wednesday 10/25 Midterm Examination
Thursday 10/26 Introduction to Virology Randall Friday 10/27 Viral Immunity/ Vaccines Randall
Monday 10/30 DNA viruses -- Papovaviridae
Randall
Tuesday 10/31 Herpesviridae (HSV, CMV, EBV)
Randall Wednesday 11/1 Adeno-, Parvo-, & Poxviridae Randall Thursday 11/2 RNA viruses -- Picornaviridae Randall Friday 11/3 Toga-, Flavi- Calici-, Coronaviridae
Randall
Monday 11/6 Reo-, & Orthomyxoviridae (Reo & Rotavirus, Influenza)
Randall Tuesday 11/7 Paramyxo & Rhabdoviridae Randall Wednesday 11/8 Retroviridae (HIV) Randall Thursday 11/9 Hepatitis viruses (HAV, HBV, HCV, HDV, HEV)
Randall Friday 11/10 Emerging/Re-emerging viruses: Ebola, Hanta, Smallpox Alexander
Monday 11/13 Clinical Antiviral Therapy Alexander Tuesday 11/14 Prions Mastrianni Wednesday 11/15 Introduction to Parasitology Benoit Thursday 11/16 Intestinal and urogenital protozoa Benoit Friday 11/17 Diversity Day No Class
Monday 11/21 Blood and Tissue protozoa Benoit Tuesday 11/22 Nematodes & Trematodes Benoit Wednesday 11/23 Cestodes & Arthropods Pitrak Thursday 11/24 Thanksgiving No Class Friday 11/25 Thanksgiving No Class
Monday 11/27 Hospital Acquired Infections Weber Tuesday 11/28 Infections in Immune-suppressed patients Pitrak Wednesday 11/29 Fungi-overview Schneewind Thursday 11/30 Systemic Fungal Diseases Schneewind Friday 12/1 Opportunistic Fungal Infections Schneewind
Monday 12/4 Finals Study Period
Wednesday 12/7 Final Examination
Schedule of Laboratories W 1:30-3:30 PM
Wednesday 9/27 Introduction to Microbiology Laboratory Techniques Thompson Wednesday 10/4 Respiratory Tract Infections Thompson Wednesday 10/11 Urinary Tract Infections Thompson Wednesday 10/18 Bacteriemia and Endocarditis Thompson Wednesday 10/25 Acute Meningitis Thompson Wednesday 11/1 Antibiotic Susceptibility Testing Thompson Wednesday 11/8 Mycobacteria Thompson Wednesday 11/15 Parasites and enteric pathogens
Thompson Wednesday 11/22 Mycology Thompson Wednesday 11/29 Final Practical Exam Thompson
Course Director: Olaf Schneewind (oschnee@bsd.uchicago.edu)
Laboratory Director: Kenneth Thompson (thompson@uchicago.edu)
Course Instructors:
Kenneth Alexander (kalexander@peds.bsd.uchicago.edu)
Jean-Luc Benoit (jbenoit@medicine.bsd.uchicago.edu)
James Mastrianni (jmastria@uchicago.edu)
David Pitrak (dpitrak@medicine.bsd.uchicago.edu)
Glenn Randall (grandall@bsd.uchicago.edu)
Kenneth Thompson (thompson@uchicago.edu)
Stephen Weber (sgweber@medicine.bsd.uchicago.edu)Teaching Assistnant: Kelly Riordan (kriordan@uchicago.edu)
Department of Microbiology, CLSC 1117, 920 E. 58th St. Chicago, IL 60637