Microbiology, Immunology and Molecular Genetics

Degrees Offered
Doctor of Philosophy

Dual-Degree Program
Students with outstanding academic records who have been accepted into the MD program may apply for admission to a combined degree program leading to the MS and MD or to the PhD and MD degrees. Completion of the dual-degree program usually requires a minimum of seven years.

Program Admissions Requirements
In addition to the general Graduate School admission requirements, this program has additional specific requirements.

Students enter the graduate program in the Department of Microbiology and Immunology through the Interdisciplinary Program in Biomedical Sciences (IDP). Admission to this program is based on undergraduate achievements in science and mathematics courses, performance on national examinations, and research experience. The Interdisciplinary Program in Biomedical Sciences provides students with a strong foundation in the fundamentals of cell biology, biochemistry, and molecular genetics before they choose a dissertation research mentor. Students who choose a mentor in the Department of Microbiology and Immunology will enter the department upon satisfactory completion of a written mock research proposal and an oral qualifying examination.

Fields of Research
The following areas of research in the Department of Microbiology and Immunology offer excellent opportunities for graduate dissertation projects:

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  Molecular Biology of Bacterial Pathogenesis
  • Characterization of the molecular properties of bacterial exotoxins, with the goals of defining their mode of action and how toxins modify host cell physiology. (Dr. Barbieri)
  • Identification of host and bacterial proteins involved in attachment of Borrelia burgdorferi and Leptospira interrogans to human cells, and the consequences of these interactions for the host. (Dr. Coburn)
  • Investigation of the secretion and function of bacterial virulence factors encoded by Pseudomonas aeruginosa. (Dr. Frank)
  • Studies of the pathogenesis of Mycobacterium tuberculosis, with particular emphasis on defining the genetic determinants required for establishment, maintenance and reactivation from latent infection. (Dr. Zahrt)
  • Investigation of genetic determinants and signaling pathways required for antimicrobial resistance in Enterococcus faecalis. (Dr. Kristich)
  Molecular Genetics of Human Viruses
  • Studies of the vaccinia virus, with particular emphasis on understanding viral DNA replication and on the regulation of the viral life cycle by protein kinases and phosphatases. Also, investigation of the role of the cellular VRK kinases in cell proliferation, gametogenesis, and mammary oncogenesis. 
  • Investigation of the molecular mechanisms employed by human herpesviruses to escape detection by the immune system. (Dr. Hudson)
  • Investigation of how proteins from simple human RNA viruses (e.g., picornavirus) interact with host cell pathways to facilitate intracellular membrane rearrangements. These studies help us understand the basic cellular pathways and identify potential targets for anti-viral therapeutics. (Dr. Jackson)
  • Characterization of interactions between cancer-associated viruses and host systems that function in tumor suppression. Specifically, study of the crosstalk between mouse gammaherpesvirus-68, a rodent virus closely related to human Epstein-Barr virus and Kaposi’s Sarcoma associated virus, and the DNA damage response, a host network that safeguards the cellular genome. (Dr. Tarakanova)
  • Investigation of proteins involved in establishing a permissive environment for herpesvirus replication using mass spectrometry. (Dr. Terhune)
  Cellular and Molecular Analysis of the Immune Response
  • Studies of the immune regulation of inflammation in immunity and autoimmunity. (Dr. Dittel)
  • Investigation of the immunobiology of bone marrow transplantation, graft versus host disease, autoimmunity, and graft versus leukemia reactivity. (Dr. Drobyski)
  • Investigation of the immunobiology of chemokines and chemokine receptors in mucosal inflammation, host defense, and metastasis. (Dr. Dwinell)
  • Investigation of the role played by B cell anergy in autoimmune diseases and the molecular mechanisms that maintain B cell anergy. (Dr. Gauld)
  • Memory T cell function and development. (Dr. Gorski)
  • Viral infections have been associated with the development of allergic diseases, such as asthma. The lab is focused on trying to understand how a lung anti-viral immune response leads to the development of allergic disease, and determining ways to inhibit this process. (Dr. Grayson)
  • Investigation of type 1 diabetes (T1D), an autoimmune disease that targets the insulin-producing beta cells of the pancreas. Studies focus on the factors that make the beta cells good targets as well as factors that make the immune system overly aggressive. The laboratory uses functional genomics, genetics, immunological and histological approaches to study diabetogenesis in a rat model as well as human subjects. (Dr. Hessner)
  • Minor histocompatibility antigens and CD8+ T cells in transplant rejection and tumor clearance. (Dr. Malarkannan)
  • Regulation of CD4+ cell response by vaccine adjuvants. (Dr. Malherbe)
  • Investigation of the structure and function of Platelet Endothelial Cell Adhesion Molecule (PECAM)-1, also designated CD31, with the goal of identifying ways to manipulate these signaling pathways to control inflammatory diseases or those that are due to defects in platelet function, such as bleeding and thrombosis. (Dr. Newman)
  • Investigation of the immunogenicity of adenovirus E1A and its use as a vaccine strategy and the etiology of lymphoproliferative diseases that occur in the context of primary immunodeficiencies. (Dr. Routes)
  • The role of defensins in innate mucosal immunity. (Dr. Salzman)
  • Basic mechanisms of immune regulation, mechanisms of inflammation and immune deficiencies. (Dr. Verbsky)
  • Investigation in the function of signal transduction pathways of cytokine and B-cell receptors. (Dr. Wang)
  • T-cell tolerance, thymocyte selection, and maintenance of the peripheral repertoire. (Dr. Williams)
  • Investigation of the genetic basis of the autoimmune disease type I diabetes. (Dr. Ghosh)
  Molecular Mechanisms of Gene Expression
  • Studies of the role of cellular factors in the control of cellular and retroviral RNA processing reactions, particularly RNA splicing and polyadenylation regulation. (Dr. McNally)
  • Studies of the mechanisms and consequences of signal transduction: endothelin-mediated signaling through small GTPases, cycloxygenase-2, and the prevention of apoptosis. (Dr. Sorokin)
  • Investigation of the mechanisms of transport and anchoring that result in the asymmetric localization of mRNA between mother and daughter cells. (Dr. Long)
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  Required Courses

During the first year, students take courses in biochemistry, cell and molecular biology, signaling, and genetics as described for the Interdisciplinary Program in Biomedical Sciences. Additional courses taken in the second and third years vary with the field of research chosen by the student. These courses are taught at a more advanced level that includes discussions of current research in areas such as microbial pathogenesis, molecular genetics of cancer, protein structure and function, cell biology, and immunology.

Course requirements for students in dual-degree programs (PhD and MD or MS and MD) and for students entering with an advanced degree may differ from the above.

  Overall Course Requirements

A requirement of this program is to fulfill two credits in Bioethics by completing Course (10222) Ethics and Integrity in Science and Course (10444) Research Ethics Discussion Series. For course descriptions of 10222 and 10444 see listing within the Bioethics Program.


25210 Principles of Laboratory Animal Science. 1 credit.
A one-credit hour course surveying the issues fundamental to the successful use and care of animals in biomedical research. Students will gain knowledge of an array of core topics in laboratory animal science, including: understanding and navigating ethical and regulatory frameworks in which animal research occurs; basic biology and care of common laboratory species; managing rodent breeding colonies; contemporary issues in laboratory rodent genetics; important sources of non-experimental variables in animals research, including nutrition, microbial status, and pain; strategies for minimizing pain and distress in animal subjects; and basic techniques in laboratory rodent handling and restraint.

25230 Current Topics in Microbiology and Immunology. 2 credits.
This advanced course consists of introductory lectures on a selected topic followed by in-depth discussions of original research articles on topics such as bacterial invasion, virulence factors, immune evasion, virus-host interactions, T-cell functions, and viral regulatory proteins.

25234 Cellular and Molecular Immunology. 3 credits.
This course is an introduction to the experimental basis of immunology through readings from texts and current immunological journals. Topics covered include the cellular basis of the immune response, antigens, antibodies, and molecular basis for generation of immunologic diversity, and regulation of the immune response.

25236 Cellular Microbiology. 3 credits.
This course, offered in alternating years, explores contemporary concepts of cellular microbiology and microbial/viral pathogenesis through a series of formal lectures and discussions of original research articles. The emphasis is on host/pathogen relationships and the interface between bacterial or viral infection and the molecular biology of eukaryotic cells. Students will gain an appreciation of the basic properties of bacterial and viral pathogens, the processes leading to acute and chronic infections, the strategies that these agents utilize to enter and traffic through cells, and how these agents exploit host cell mechanisms to regulate gene expression and genomic replication.

25251 Advanced Molecular Genetics. 3 credits.
Specific topics in molecular genetics are explored through a combination of lectures and sessions in which research papers are presented and critically evaluated. Emphasis is placed on developing the ability to critically read and evaluate experimental results from original research papers. Specific topics for this course, which vary from one year to the next, include: cancer genetics, gene therapy, meiotic recombination, and DNA repair.

25259 Mucosal Immunity. 1 credit.
This focused immunology course on the mucosal immune system introduces students to advanced concepts and biomedical research relevant to human health and disease at the mucosal surface.

25260 Mucosal Pathogenesis. 1 credit.
Mucosal Pathogenesis is an upper-level, one-credit hour Microbiology course that focuses on the interactions of microbial pathogens with cells of the mucosal epithelium. Students gain a detailed and comprehensive understanding of specific infectious microbial pathogens, and the mechanisms utilized by the microorganisms to associate, invade, and/or cause disease at the mucosal surface. Microorganisms to be discussed include those that target the respiratory tract, the gastrointestinal tract, and the genital/urinary tract.

25261 Bacterial Toxin-Mucosal Cell Interactions. 1 credit.
Bacterial Toxin-Mucosal Cell Interactions is a one-credit hour upper-level Microbiology course that addresses the interactions between bacterial toxins and mucosal cells. The goal of this course is to provide students an appreciation of how bacterial toxins that target mucosal cells function as virulence factors and are utilized as vaccines and for clinical therapies. The course format includes formal lectures and paper discussions.

25262 Tumor Immunology. 1 credit.
This focused immunology course introduces students to advanced concepts and biomedical research relevant to human health and disease.

25263 Signaling in the Immune System. 1 credit.
This focused immunology course introduces students to advanced concepts and biomedical research relevant to human health and disease.

25264 Developmental Immunology. 1 credit.
This focused immunology course introduces students to advanced concepts and biomedical research relevant to human health and disease.

25265 Immunological Tolerance. 1 credit.
This focused immunology course introduces students to advanced concepts and biomedical research relevant to human health and disease.

25266 Clinical Immunology. 1 credit. Prerequisites: 25234.
Clinical Immunology is an upper-level, one-credit hour Microbiology course that will provide advanced information and conceptual knowledge regarding the human immune system in health and disease. Specific topics will include primary and secondary immunodeficiencies, autoimmune diseases (systemic autoimmune diseases and autoimmune disease of the skin and gastrointestinal tract), atopic diseases, HLA and bone marrow transplantation. The course will comprise a combination of formal lectures by instructors, and group discussions of scientific papers from the recent literature.

25269 Advanced Bacterial Physiology. 1 credit. Prerequisites: 25236
Advanced Bacterial Physiology is a 1 credit hour Microbiology course that focuses on fundamental and diverse aspects of bacterial physiology. Students will gain an understanding of the mechanisms bacteria use to execute, coordinate and control basic cellular processes such as macromolecular synthesis, nutrient utilization and metabolism, signal transduction, and stress responses. The course focuses on critical evaluation and discussion of papers from the primary literature. These discussions will be augmented by short didactic presentations of background material by the course director to place the paper's topic and findings in context.

25270 Advanced Virology. 3 credits.
Concepts in virology are illustrated by selected appropriate model systems of animal viruses. Topics include viral replication, genetics, antivirals, and virus-host interactions.

25271 Membranes and Organelles. 1 credit. Prerequisites: 16244
Membranes and Organelles is an upper-level, one-credit hour Cell Biology course that focuses on the topics of membrane protein trafficking and membrane biogenesis. Students will gain a detailed understanding of organelles and membrane protein trafficking and degradation, membrane vesicle fusion, secretion, and membrane biogenesis. The course will consist in part of readings of seminal papers describing the genetic screens for sec and vps mutants, as well as the Rothman in vitro vesicle fusion experiments. These experiments provide the first description of the proteins we know today to be involved in membrane protein fusion, secretion, and trafficking. After gaining grounding in the design and outcome of these historic screens, the class will focus on what is known today about the initial proteins identified in the original ground-breaking screens. The newer areas of membrane biology will follow similar format, examining the discovery of paradigm, and delving into what is known today. Students will be evaluated by participation in paper discussion (40%) and an in-class paper presentation (60%). The course will meet twice a week for 6 weeks.

25295 Reading and Research in Microbiology. 1-9 credits.

25299: Master Thesis. 6 credits.

25300: Seminar. 1 credit.

25399: Doctoral Dissertation. 9 credits.

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MCW Microbiology & Molecular Genetics News

Enduring pain for someone she loves

Nov. 18 - Microbiology and Molecular Genetics graduate student Kristen Westdorp had run two marathons in her life prior to 2016, but the second one was more than eight years in her past, and she was ok with that. She was diving in to her graduate studies, running a casual five miles three times per week, and doing the types of things other students do to fill their time. But then her mother, Cheryl, was diagnosed with Huntington’s disease in 2014 at age 50, and, as can be expected, her perspective began to be shaped and colored by the human devastation taking place before her eyes.