Microbiology 430/530 [3 cr.]

Microbial Symbiosis. Professors Nicole Koropatkin and Marcy Balunas. Humans and other animals exist in constant contact with microbes. Although some microscopic partners cause disease, most host-microbe interactions are benign and, in many cases, beneficial. This course will provide a detailed look at the many interactions between animals, including humans, and our microbial symbionts. We will also focus on techniques used in interrogating experimental systems of microbial symbiosis. This course is highly interdisciplinary and will draw classes you may have already taken, such as microbiology, immunology, physiology, ecology, genetics, and biochemistry.

Overall Objectives: This course will provide a detailed understanding of the composition and function of host-microbe symbioses moving from model systems to the human microbiota, as these bacterial communities have a profound influence on health and disease.

Course Format: This course will include interactive lectures in which students will be expected to participate by answering questions and/or discussing experimental details, including reading and discussing papers from the primary literature. A semester-long group project will result in a proposal for a new research direction with group presentations. Taking the Graduate level course (530) requires an extra project.

Topics Covered: 1) Microbial ecology of different animal model systems as well as across human body sites, 2) physiological outcomes of beneficial host-microbe associations (e.g., immune development, nutrient digestion, infection resistance), and 3) molecular evolution of pathogenic and beneficial microbial symbionts.

Winter 2025, M/W, 10–11:30 AM

Microbiology 460 [3 cr.]

Eukaryotic Microbiology. Course Director: Tom Moore. This upper level undergraduate course which can be taken for graduate credit with permission will cover the biology of eukaryotic microbes and the environments in which they live. Eukaryotic microbes include single-celled protozoa, multi-cellular helminths (worms), and fungi. This course will cover the complex life cycles (intermediate hosts, insect vectors) required for survival of many protozoa and helminths. Eukaryotic microbes are also a significant cause of human disease throughout the world (e.g. Malaria, Leishmaniasis, Trypanosomiasis, Giardiasis, Histoplasmosis, Blastomycosis). We will examine the evolutionary relationship between eukaryotic pathogens and their mammalian hosts, including the complex relationship between host immunity and pathogen immunoevasion. We will also discuss the renewed interest in Neglected Tropical Diseases (NTDs). NTDs are a group of diseases causing substantial illness in more than one billion people globally. The most common NTDs include Lymphatic Filariasis (Elephantiasis), Onchocerciasis (River Blindness), Schistosomiasis, Soil-Transmitted Helminths, and Dracunculiasis (Guinea Worm Disease). This course is cross-listed as INTMED 460. Fall term only.

Pharmacology 502 [2 cr.]

Introduction to Scientific Communication. Course Director: Lori Isom. This course introduces graduate students to essential scientific communication skills. Beginning with the relatively easy task of learning to search the literature over the Internet and ending with the challenges of writing an NIH style grant application and giving a short seminar, each student will develop confidence in both written and spoken scientific communication. Class meetings alternate between presentations by local experts on various topics and student presentations of their work in progress. In-depth analysis of student writing and presentation skills will be provided in class by the instructor, by other students working in small groups, as well as by guest scientists. Through a series of assignments, each student will write a grant over the course of the term on a topic of his or her choice. By the end of the term each student will have polished and revised the proposal to a high quality product that will be presented both orally and in written form to the rest of the class. Finally, each student will participate in a mock study section to constructively evaluate each other's grants. Prerequisite: Must be in the second year or higher of a PIBS-related graduate program. Winter term.

Microbiology 599 [1-8 cr.]

Independent Non-Dissertation Research for Graduate Students. Permission of instructor. Students may undertake independent library or laboratory research study under the supervision of an appropriate faculty member. May be taken any term as a pre-candidate, for a letter grade.

Microbiology 607 [2 cr.]

Microbial Pathogenesis. Course Director: Vern Carruthers. Prerequisite: Introductory microbiology or permission of course director. Topics include regulatory mechanisms of pathogens, toxins and toxinogenesis, secretion, adherence and invasion. The course is literature-based, although each session begins with a discussion by the instructor to provide context and background for papers under discussion. Primarily covers bacterial pathogens. Winter term.

Microbiology 612 [3 cr.]

Microbial Informatics. Course Director: Pat Schloss. Prerequisites: Graduate standing and undergraduate Microbiology, Biochemistry, Cell Biology, or Genetics. Increasingly, microbiologists are generating large and varied datasets and must be integrated with data from traditional approaches to test hypotheses and identify new avenues of research. This course will give microbiologists the background they need to design robust experiments, implement traditional statistical approaches for small and large datasets, and utilize statistical programming software. Course is taught in fall and includes lecture and laboratory components. Contact instructor for timing as this is often taught over a short time frame.

Microbiology 615 [2 cr.]

Molecular and Cellular Determinants of Viral Pathogenesis. Course Directors: Christiane Wobus, Adam Lauring and Andrew Tai. Concepts of viral pathogenesis and controls. Early events, entry, receptors, tropism determinants. Replication and interactions with host defenses. Transmission in populations; smallpox as a paradigm. The format includes a combination of lecture and critical analysis of primary literature. Winter term.

Microbiology 619 [1 cr.]

Special Topics: These one-credit courses will be one-time offerings, each covering an area of current microbiology, immunology or related research, to be held 4 weeks of winter or fall term, respectively.

Human Genetics 630 [1 cr.]

Short Course—Special Topics in Genetics. Lectures are open to anyone interested, but only Genetics Training Grant students and CMB students may register for this course. Please contact the Cellular and Molecular Biology department for fall term schedule and the Human Genetics department for winter term schedule.

Microbiology 640 [3 cr.]

Molecular and Cellular Immunology. Course Director: Malini Raghavan. This three-credit course is focused upon molecular and cellular aspects of vertebrate immunology. Topics covered include: Mechanisms of antigen recognition in innate and adaptive immunity, antigen processing and presentation, the MHC, generation of diversity in immune receptors, B and T cell development, activation, differentiation, death and effector functions; mechanisms of homeostasis and immunosuppression; NK cells and other innate immune cell types, immunological tolerance and its breakdown; microbial immunity; and immune cell signal transduction. The course includes both didactic lectures and discussion-type seminars based upon contemporary research papers. A previous introductory course in immunology is recommended and summer learning information can be provided if needed. Fall term.

Microbiology 641 [1 cr.]

Advanced Immunology. Course Director: Cheong-Hee Chang. Prerequisite or corequisite: MICRBIOL 640. Mechanisms that regulate immune cell development and function in health and disease will be covered in this advanced level immunology course, primarily through discussion of contemporary research papers. Together with MICRBIOL 640, this course is expected to lead to an in-depth understanding of the immune response at molecular and cellular levels.

Microbiology 812 [1 cr.]

Microbiology Seminar. Microbiology and Immunology Graduate Students. An analysis of advances at the frontiers of microbiology. Every microbiology graduate student is required to enroll in this course each term. Students give one seminar per year on a journal article or their own research. All terms, taken for a letter grade.

Microbiology 813 [1 cr.]

Science in the Clinics. Prerequisite or corequisite: MICRBIOL 607, 615, 640 or permission of instructor. Course Directors: Vern Carruthers and Adam Lauring. This course brings students into the real world of infectious diseases to help them connect basic pathogenesis research and training with clinical and therapeutic features of infectious disease medicine. The sessions are run by two faculty members, a physician and a basic scientist. Each class begins with a case presentation by the physician, who takes the class through ID cases, including history, laboratory and physical findings, etc. During this discussion, students learn and discuss the meanings of specific clinical findings, learning why different tests are performed and how physicians ultimately build a differential diagnosis. Following the case presentation, an assigned paper is covered in detail by the basic scientist through discussion with the students. The discussion is aimed at interpreting the findings with regard to their basic science implications, in addition to clinical implications in light of the case discussions just carried out.

Microbiology 995 [8 cr.]

Candidate Dissertation Research. Prerequisite: Graduate School authorization for admission as a doctoral candidate. Election for dissertation work by Microbiology and Immunology doctoral students who have been advanced to status as candidates. All terms, taken as an S/U course.

INF 500

INF 500 is the Infectious Diseases and Microbiology sequence for M1 students. It is taught by faculty in the Departments of Microbiology & Immunology, Internal Medicine, Pharmacology, and Pediatrics. It involves a combination of lectures, multidisciplinary conferences, and small group meetings in which lab exercises are performed and case studies are presented.

IMM 501

IMM 501 is the Medical Immunology sequence for M1 students. It is taught by faculty in the Departments of Microbiology & Immunology and Pathology. The sequence comprises of lectures, small group meetings and patient presentations.

DENT 533

DENT 533 is the Infection and Immunity course for D1 students, and is taught by faculty from the Department of Microbiology and the School of Dentistry. It consists of lectures and discussions of case studies.

Microbiology 350 [1 cr.]

Introductory Laboratory in Medical Microbiology . Lab Course in College Biol. and Chem. Course Director: Dr. My-Hang Huynh. An introduction to the techniques and principles of the isolation, cultivation, identification and properties of microorganisms relevant to human health and disease. (This course should be accompanied or preceded by one of the following: Micro. 301 or equiv.) This class is offered in Fall and Winter term.

Microbiology 405 [3 cr.]

Medical Microbiology and Infectious Diseases --- This course focus and scope is mainly geared to students interested in continuing onto post-graduate education in the areas of public health, medicine, biomedical research or other health-related areas. This lecture-based course covers topics on the biology of microbial cells, medical immunology, pathogenic virology and pathogenic bacteriology, and develops concepts on the types of interaction between host and pathogen that contribute to infectious diseases. Lectures will draw from both classic and newly emerging infectious diseases. Course Directors: Yasmina Laouar (fall semester) and Maria Sandkvist (winter semester).

Microbiology 415 [3 cr.]

Virology . Biol 162, and either Biol 311, Chem 451, MCDB 427, or permission of instructor is required. Course Director: Dr. Katherine Spindler. Viral pathogens are responsible for a significant number of human diseases ranging from the common cold to chicken pox to HIV/AIDS. This upper level undergraduate course will cover the history and discovery of viruses. We will review viral structure, replications and pathogenesis. This course will introduce students to bacteriophages as well as plant and animal viruses. We will introduce the similarities and differences between RNA and DNA viruses as well as explore the mechanisms responsible for viral entry into cells, viral protein expression, viral assembly and viral replication. We will discuss acute, persistent and latent infections. Students will learn about important viral diseases in humans and animals and will learn how viral infection can contribute to malignancy. In addition, the interactions between the host immune response and the viral virulence mechanisms will be discussed. Course grade will be based on both exams and a student project. Overall, students will gain a fundamental understanding of viral structure, biology, pathogenesis and control. This course is cross-listed as INTMED 415. Winter term.

Microbiology 440 [3 cr.]

Immunology . Biol 207, and either Biol 311, Chem 451, MCDB 427, or permission of instructor is required. Course Director: Dr. Tom Moore. This upper level undergraduate course will provide a broad overview of the rapidly advancing field of modern immunology in both the basic and clinical sciences. Topics to be covered include: Cells and Organs of the Immune System, Generation of T-Cell and B-Cell Responses, Immune Effector Mechanisms (including cellular and antibody-mediated responses), and The Immune System in Health and Disease (including AIDS and other immunodeficiencies, immune responses to infectious diseases, vaccines, transplantation and cancer immunology and autoimmunity). Lectures will emphasize experimental and clinical observations to highlight key concepts. Course will utilize lecture and textbook based learning complemented with web-based online resources directly linked to textbook, including chapter-by-chapter study guides, animations and molecular visualization of key concepts, and clinical case studies. Upon completion of this course, students will possess a solid understanding of immunological principles and concepts as they are applied to a growing cross-section of both the basic and clinical sciences. This course is cross-listed as INTMED 440. Winter term.

Microbiology 450 [3 cr.]

Global Impact of Microbes. Course Director: Professor Denise Kirschner, Ph.D. This course is made up of lectures, discussion and projects. Students will explore impacts of pathogenic viruses, bacteria, fungi or parasites.

The overall objective is that participants gain appreciation of the multiple factors that influence transmission, control and outcomes from encounters with microbes in different global sites. Course participants will better understand biological mechanisms of prevalent microbial pathogens and biomedical controls or prevention.

This course is ideal for those interested in infectious diseases, medicine, health, policy or related areas.

Microbiology 460 [3 cr.]

Eukaryotic Microbiology . Biol 207, and either Biol 311, Chem 451, MCDB 427, or permission of instructor is required. Course Director: Dr. Tom Moore. This upper level undergraduate course will cover the biology of eukaryotic microbes and the competitive environments in which they live. Eukaryotic microbes include fungi, protozoa, and helminths (worms). They are found in the soil, water (pond and tap), and even in our gastrointestinal tract. Fungi are critical for the nutritional cycle of life and act as the major composting organisms in the soil. They also are responsible for the production of bread, beer, wine, and "natural flavors" used by the food industry. A common feature of all eukaryotic microbes is that they have all developed strategies to outcompete other microbes (prokaryotes and eukaryotes) and survive in the environment and in hosts (animals, plants, insects). We will cover these biochemical and biological strategies, which include antibiotics, phase changes, and evasion of host defenses. Eukaryotic microbes are also a significant cause of disease in humans (e. g. malaria, AIDS-associated infections, allergies and chronic infections) and plants (e. g. dutch elm disease, potato blight, corn smut) and we will also highlight the mechanisms by which hosts defend themselves against these microbes. Overall, the student will gain an understanding of the impact of these organisms on the environment and on everyday life. This course is cross-listed as INTMED 460. Fall term only.