PhD Program

Course Descriptions

Your coursework for our PhD in Microbiology and Immunology combines a strong foundation with flexible options. All required courses and common electives are listed below.

MIC 512 Fundamentals of Immunology, 2 credits

Requires successful completion of BCH 503 or BMS 503 with a grade of B or better.

This course covers the anatomy and function of the immune system, cell interactions, antibody formation, antigen-antibody reactions, cell-mediated immunity and biological effects of immunological reactions.

MIC 513 Eukaryotic Pathogens, 2 credits

Requires successful completion of MIC 512 AND BMS 503 with a grade of B or better.

This course is for students with a strong background in biochemistry and cell biology as well as experience reading and presenting papers from the current scientific literature. It focuses on the basic biology and host interaction of select eukaryotic pathogens. The pathogens covered will vary, but will include both parasitic protozoans and fungal pathogens. Discussion encompasses aspects of molecular biology, biochemistry, cell biology and host-parasite interaction. Students will be expected to gain a working knowledge of major ideas and select primary literature in molecular parasitology, mycology and host-pathogen interactions, and be able to discuss questions, experimental approaches and evaluation of results. Several faculty members present in their areas of expertise.

MIC 515 Virology, 2 credits

Requires permission of instructor.

This course focuses on mechanisms of viral pathogenesis and the host response, as related to human disease. It covers the scientific approaches used to investigate these processes and involves studying viruses at their molecular biology and genetic levels as well as from a biophysical and evolutionary perspective. Several faculty members present in their areas of expertise. Material is based on the latest information from cutting-edge research, providing students with an awareness of the latest problems of interest in the field. Topics include, for example, virus structure, binding and entry, and alteration of host function; replication of RNA viruses; RNA virus transcription and translation; retroviruses; DNA virus life cycle and transcription; replication of DNA virus genomes; antiviral agents; emerging viruses; chronic and latent infections; and viral pathogenesis.

MIC 516 Bacteriology, 2 credits*

Requires permission of instructor

This advanced course briefly introduces general principles of bacteriology before progressing to a more comprehensive analysis of various virulence factors and specific mechanisms of bacterial pathogenesis that lead to disease. The course also covers the scientific approaches used to investigate these processes.

MIC 599 Supervised Teaching, 1 credit

Students will be given the opportunity under faculty guidance to prepare and present short, introductory lectures and laboratory recitations, direct execution of experiments in the laboratory, and participate in student evaluation and improvements to course design.

MIC 607 DNA Replication and Repair, 2 credits

Requires successful completion of BCH 503 OR BMS 503 with a grade of B or better.

This advanced seminar focuses in-depth on DNA replication, repair and damage responses. The course aims to increase knowledge in areas of DNA metabolism; improve and refine presentation skills; and hone abilities to read primary research articles and critically evaluate the work. Students also learn to organize and present a lecture independently without using a textbook as a guide.

MIC 608 Advanced Eukaryotic Pathogens, 2 credits

Requires permission of instructor.

Each year, this participatory seminar focuses on different aspects of gene expression in eukaryotic pathogens. Weekly discussions are based on the most recent primary literature. Each student selects and presents a paper of high importance to the field. The presentations include relevant background information concerning the questions to be addressed.

MIC 609 Current Topics in Immunology, 2 credits

Requires successful completion of MIC 512 with a grade of B or better.

This seminar offers a forum for discussing current scientific literature in immunology. Students present selected research papers approved by the course director. Classes are organized around groundbreaking research on topics such as vaccine development, transplantation, autoimmunity, neuroimmunology and immunopharmacology.

MIC 610 Critical Analysis, 1 credit

Requires permission of instructor.

This course introduces students to the process of writing a grant application. Discussion sessions follow faculty lectures on all stages of this process — from the initial steps of preparing an application to grant submission and review. In conjunction, students write short grant applications on subjects other than their thesis projects, with help from their major professors. At several stages, students submit the documents for peer evaluation and discussion, facilitated by a faculty member. Students also prepare written reviews for the final documents following the format of the National Institutes of Health, emphasizing strengths and weaknesses of their applications. In addition, students prepare and deliver short PowerPoint presentations on their proposals.

MIC 611 Advanced Microbial Genetics, 2 credits

Requires successful completion of BMS 501 AND BMS 502 AND BMS 503 with a grade of B or better.

This course is designed to develop a working knowledge of a broad range of genetic approaches applicable to model bacteria. It covers principles and approaches used in the genetic dissection of complex biological processes in these bacteria. Participants lead in-depth discussions of the reasoning, uses and limitations of diverse methods of genetic analysis commonly used with model bacteria. These discussions are reinforced by journal club presentations that highlight the use of the technique. The course aims primarily to increase the depth of knowledge about established techniques in microbial genetics. Students also hone their abilities to read, understand and critically evaluate research articles as well as improve presentation skills.

MIC 613 Advanced Virology, 2 credits

Requires permission of instructor.

This seminar for advanced graduate students covers multiple aspects of virology at the cutting edge of current research. Students obtain a detailed understanding of various topics related to the history and process of vaccine development, including impacts on global health, economic and social issues. They critically analyze and critique the literature as well as identify novel problems in current research. Classes are organized around recent papers in the virological literature, encompassing topics such as emerging viral diseases and the hepatitis viruses. Students present, participate in discussions at a high level and demonstrate critical thinking skills.

MIC 616 Advanced Fungal Pathogenesis, 2 credits

This in-depth study of scientific literature relates to all aspects of fungal pathogenesis. Students will read, understand, interpret and critique primary scientific literature relating to the human pathogenic fungi. The course emphasizes understanding factors that contribute to host susceptibility, epidemiology and treatment, as well as fungal taxonomy and basic fungal biology. Topics range from fungal molecular biology, cell biology and biochemistry to immunology, antifungal susceptibility and clinical trials. Each course meeting will focus on a different paper chosen from the current, peer-reviewed scientific literature. Students will select papers, organize and deliver presentations, and answer questions about the paper. They are expected to attend all Journal Club meetings, participate in discussion and engage in critical questioning and scientific exchange.

MIC 619/620 Microbiology and Immunology Seminar, 1 credit

Through this journal club experience, each student selects a scientific paper(s), organizes and presents relevant material, and manages a question-and-answer session. Students participate in discussion, critical questioning, scientific exchange and constructive evaluation of peer presenters.

MIC 622 Protein-Nucleic Acid Interaction, 3 credits

This course is cross-listed in the departments of microbiology, biochemistry and biology. Interactions between proteins and nucleic acids facilitate all aspects of genome maintenance, including genetic recombination; DNA replication and repair; and all facets of transcription and associated mechanisms of gene regulation. Recognizing that a detailed, quantitative understanding of these interactions is key to studying and understanding all aspects of nucleic acid metabolism, this course familiarizes students with all relevant aspects of proteins and how they interact with nucleic acids, as well as with state-of-the art approaches to performing quantitative studies. It is taught by a team of faculty with expertise in these areas. 

Initial lectures cover nucleic acid structure and dynamics and protein structure as it relates to interactions with nucleic acids (that is, recognition elements). Content then progresses to cover physical biochemical aspects of protein-nucleic acid interactions, including thermodynamics, kinetics, site-size determination, binding constants, cooperativity, the kinetics of motion, the role of ATP binding and hydrolysis in regulating these interactions and comparison between bulk-phase and single-molecule studies of protein-nucleic acid interactions.

MIC 623 Current Topics in Global Health Infectious Diseases, 2 credits

This graduate seminar course will cover topics in infectious diseases with a focus on global health inequity in under-resourced countries. Students will draw from primary, peer-reviewed scientific literature to learn about various infectious diseases that impact under-resourced regions, and place the microbiology and immunology of these pathogens within the context of global health, health care inequity (drug access, infrastructure, malnutrition) and public health (prevention, screening, safe water and hygiene). 

MIC 624 Modern Topics in Bacterial Pathogenesis, 2 credits

Requires permission of instructor.

This seminar involves presentation, review and discussion of current scientific articles related to bacterial pathogenesis. Students will be introduced to methodologies and state-of-the-art techniques.

MIC 627 Molecular Parasitology, 2 credits

Requires permission of instructor.

This participatory seminar focuses on different aspects of molecular parasitology each year. Topics usually center on molecular biology or host-parasite interaction and reflect the most current primary literature. Each student selects a recent paper of high importance to the field and organizes and gives a presentation about it. Presentations include relevant background information about the questions to be addressed. Other students in the class are expected to ask and answer questions about the material presented.

MIC 700 Research, 1-12 credits

Through this tutorial experience, students work one-on-one with faculty mentors to conduct research in one of the following areas:

  • fungal pathogenesis
  • immune dysregulation
  • immunology/immunobiology
  • medical and molecular parasitology
  • medical microbiology
  • microbial pathogenesis
  • microbial pathology/immunology
  • molecular immunology and mucosal immunology
  • molecular parasitology
  • molecular virology
  • non-enteric E. coli infections
  • oral microbiology
  • recombination and repair
  • signal transduction in bacterial pathogens
  • tumor immunology