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Undergraduate Course Listing

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The following is a list of Cornell courses in host-microbe biology that may be of interest to advanced undergraduate and graduate students.



Locker Rooms, Kitchens and Bedrooms: The Microbiology of College Life
BioMI 1100
Instructor: I. Hewson
Offered every Spring (3 credits)
Microbial habitats are literally everywhere on a college campus – and college students interact with microorganisms daily. From the athlete locker room, to the kitchen, to the bathroom, to between the sheets, college students are exposed to a plethora of microorganisms that are benign, beneficial, and pathogenic. The goal of this class is for students to learn about microbiology and microbial ecology as it relates to them – in the college campus environment. Students will learn about viruses, bacteria, eukarotes and metazoans that cause common illnesses (i.e. gastroenteritis, influenza and STDs), the microbially-driven elemental cycling of alcohol production, and ecology of microorganism that spoil food. Students will take away a practical understanding of the microorganisms that they can apply to their own lives.

Dynamic Models in Biology
Instructor: S. Ellner
Offered spring, odd years (4 credits)
Prerequisite: two majors-level biology courses and completion of mathematics requirements for biological sciences major or equivalent.
Introductory survey of the development, computer implementation, and applications of dynamic models in biology and ecology. Case-study format covering a broad range of current application areas such as regulatory networks, neurobiology, cardiology, infectious disease management, and conservation of endangered species. Students also learn how to construct and study biological systems models on the computer using a scripting and graphics environment.

Pathogenic Bacteriology
BioMS 4040 / BioMI 4040
Instructor: D. Debbie
Offered every Spring (2-3 credits)
Course in medical microbiology, presenting the major groups of bacterial pathogens important to human and veterinary medicine. Emphasizes infection and disease pathogenesis. Topics include disease causality; interactions of host, pathogen, and environment, including immunity to bacteria; and principles of antimicrobial therapy and drug resistance. Recommended for those planning to attend medical school, graduate school, or veterinary medical school, or those just interested in how bacteria cause disease.  A companion seminar addresses the current and classic literature related to the pathophysiology of medically important bacterial pathogens on the cellular and molecular levels.

Cellular and Molecular Microbial Pathogenesis: The Host Pathogen Interplay
BioMS 4340
Instructor: D. Debbie, D. Russell, G. Whittaker
Offered Spring, odd years (2-3 credits)
This course will integrate the immune response of the host to challenges from medically important pathogens, including viruses, parasites and bacteria, to provide a unified view of microbial pathogenesis. The lectures will integrate concepts from the disciplines of immunology, bacteriology, virology, and parasitology, to cover aspects of host cell biology and the innate and acquired immune responses of the host to infection. A range of medically relevant human and animal pathogens will be detailed, focusing on the host’s response to commensalism versus disease, the mechanisms of host invasion, nutrient acquisition, and modulation of the host’s immune response. The course will also discuss current disease interventions and the challenges facing antimicrobial therapy and vaccine development. This integrated and comparative view of the cellular and molecular interaction between infectious agents and the host’s immune response will be a capstone of the student’s exposure to infection biology.

Diet and the Microbiome
NS 4200
Instructor: A. Poole
Offered Spring semesters (3 credits)
In this course, students will acquire a present-day overview of the reported effects of diet on the microbiome with an emphasis on host physiology outcomes. The microbiome field is rapidly evolving, and this course has no textbook; we will mainly be assessing primary literature and scientific reviews. Students will learn to critically analyze the conclusions drawn from microbiome studies to empower them to make informed judgements as new research findings are reported. For more information including feedback from last year’s students, please see:

Microbial Pathogens Versus Plants: Molecular Weapons, Defenses, and Rules of Engagement
PLPPM 4010
Instructor: C. Casteel
Offered every Spring ​(3 credits)
The co-evolutionary molecular battle between microbial pathogens and plants has game-like properties whose rules are emerging from recent genomic, biochemical, and cell biological advances. This course explores the molecular pieces and collective behaviors of pathogen virulence and plant immune systems, similarities between interaction mechanisms in plant and animal pathosystems, and the application of this knowledge to sustainable agriculture. The course emphasizes the development of professional skills, such as the management of scientific literature, creative design and critical evaluation of research, communication of complex scientific concepts to diverse audiences, and discussion of environmental issues associated with transgene-based disease management strategies. Students write and peer review research proposals.

DNA Targeting: Applications, Reagents, and Impact
PLPPM 4250
Instructor: A. J. Bognadove
Offered Spring (3 credits)
Recent advances in our capacity to direct molecules to specific DNA sequences in vitro and in living cells give us an unprecedented ability to probe and modify the genetic material. Through primary literature, this course considers applications of DNA targeting, ranging from systems biology to genome editing; reagents, including zinc finger proteins, TAL effectors, the CRISPR/Cas9 complex and others; and impact, reaching basic science, agriculture, and medicine. Regulatory, ethical, intellectual property, and public perception considerations are also discussed.

Plant Behavior and Biotic Interactions
PlSci 4460 / BioEE 4460 / BioNB 4460
Instructors: R. Raguso and A. Kessler​
Offered every Spring (3 credits)
​​​How do plants respond to antagonists, such as herbivores and pathogens? What are the checks and balances that keep mutualist organisms in their tight interactions? How are symbioses organized on molecular, metabolic and ecological levels? What are the molecular, plant hormonal, and metabolic mechanisms mediating plant biotic interactions with other organisms? What ecological and evolutionary consequences do these interactions have for the fitness of the plants and their interactors? This course provides an overview of plants’ myriad interactions with antagonists and mutualists, from microbes to multicellular organisms, and explains the underlying ecological and evolutionary concepts. It gives an introduction to the study of induced plant responses in the light of a behavioral biology framework.​

Plant Viruses and Disease – The fate of a virus: To be transmitted or to disappear
PlSci 4940
Instructor: K. Perry​
Offered Spring 2020 (2 credits)
​​​This course is designed to provide a comprehensive overview of plant viruses associated with disease and to provide advanced training for students interested in plant disease and plant-associated microbiology. Basic principles of virology (animal and plant) will be presented. Emphasis will be given to topics relevant to understanding and managing plant viruses and disease, including: transmission, replication, cell-to-cell and systemic movement within the plant, virus genome structure and gene expression, disease epidemiology, host resistance and responses to infection, gene silencing, viruses as vectors for foreign gene expression in plants, virus evolution, virus diagnostics and plant certification programs for clean planting stocks.

Advanced Immunology
BioMS 7050 / VetMI 7050
Instructor: C. Leifer
Offered Spring, odd years (3 credits)
This course covers selected topics in immunology at an advanced and in-depth level through lectures, papers, and case-based discussions.

Prokaryotic Biology: Bacterial Pathogenesis
BioMI 6905
Instructor: T. Dörr
Offered every Spring , 4 week session (1 credit)
Introduction to the fundamental concepts of bacterial pathogenesis including the normal flora, pathogen entry and colonization, the production and regulation of toxins, horizontal transfer of pathogenesis determinants, and the roles of both specific and nonspecific host defenses. Examples include bacterial pathogens of both animals and plants.

Seminar in Ecology and Evolution of Disease
Entom 6900 / BioEE 6900
Instructor: D. Peck
Offered every Spring (1 credit)
Graduate-level discussion of the ecology, epidemiology, genetics, and evolution of infectious disease in animal and plant systems. Weekly discussion of research papers published in the primary scientific literature. Participation in discussion and presentation of at least one paper required for course credit.



Biology of Infectious Disease: From molecules to ecosystems
BIOMI 2950
Instructor: T. Hendry
Offered every Fall (3 credits) – Letter grades only
A broad integration and overview of the origins, nature, and dynamics of infectious disease in humans, plants, and animals. An examination of the historical and contemporary concepts and impacts of infectious agents on hosts at multiple spatial and temporal scales and at different levels of biological organization. The ecology and evolution of pathogens, hosts, and vectors are also discussed. Consideration of newly emerging diseases in human, plant, and animal populations and the influence of human activities on global disease spread. Current and future issues and trends in disease monitoring and mitigation will also be addressed.

Essential Immunology
BioMS 4150
Instructor: Dr. B. Rhoades
​Offered every Fall (3 credits) – Student option grading, Fall 2020
Survey of immunology, with emphasis on the cellular and molecular bases of the immune response. Recommended for those planning to attend medical, graduate, or veterinary school, those pursuing careers in health-related fields, or those interested in how the body defends itself against disease.

Public Health Microbiology
BioMI 2500
Instructors: S. Merkel & J. Shapleigh
Offered every Fall (3 credits) – Student option grading, Fall 2020
This course will use a variety of teaching methods (including historical and current case studies and databases) to help students understand basic principles of microbiology as they apply to the emergence, transmission, pathogenecity, and control of infectious human disease. Major topics include water and food borne disease, zoonotic diseases, sexually transmitted diseases and antibiotic resistance.

Microbiology of Human Contagious Diseases
BioMI 2600
Instructor: S. Winans
Offered Fall & Spring semesters (3 credits) – Student option grading, Fall 2020
This course provides an introduction to the microbiology of microbial diseases. The primary focus is on molecular mechanisms of pathogenesis, including detection of the host environment, binding of pathogenic microbes to host cell surfaces and their invasion of host cells and tissues, and the delivery and functions of microbial toxins. It will include host defenses and microbial countermeasures against these defenses. We will also study the evolution of pathogens and the co-evolution of their hosts.

Biology and Management of Plant Diseases
PLPPM 3010
Instructor: K. Cox
​Offered every Fall ​(4 credits) – Letter grades only
Introduction to the biology of the pathogens that cause plant diseases, and the diagnosis and management of plant diseases. Topics include the biology of bacteria, fungi, oomycetes, viruses, and nematodes; disease cycles; plant disease epidemiology; and the principles and practices of plant disease management. Intended for students who want a practical knowledge of plant diseases and their control, as well as for students preparing for advanced courses in plant pathology and plant-microbe biology. ​

Principles of Virology
BioMS 4090 / BioMI 4090
Instructors: J. Parker & N. Osterrieder
Offered every Fall (3 credits) – Letter grades only
This course covers principles of virology that will give a broad understanding of how viruses infect and cause disease. Topics include the classification of viruses, virus entry, genome replication and assembly, and virus pathogenesis. Particular emphasis is placed on virus-host cell interactions and common features between different viral families. Recommended for those planning to attend medical school, graduate school or veterinary college, or just interested in what viruses are and how they cause disease.

Principles of Infectious Disease for Public Health
VetMI 6111
Instructors: G. Whittaker & MPH Staff
Offered every Fall (2 or 3 credits, variable) – Letter grades only
This is a two secction course with the lecture section covering viral, bacterial and parasitic agents important for public health, as well as infectious disease countermeasures. The discussion section will address similar topics using cases and professional experiences to drive small-group discussion and applied learning.

Introduction to Disease Vectors
Entom 4520
Instructor: L.Harrington
Offered every Fall (3 credits) – Letter grades only
This course introduces vector taxonomy, evolution, biology, behavior, and the history of vector-borne disease control, with an emphasis on the Northeast USA. Some lectures will be taught by NEVBD collaborators and experts in vector control/public health via video link. Through a series of lectures and active learning projects, students will gain knowledge of the latest surveillance approaches, control methods, and challenges for controlling vector-borne diseases, which they will explore in greater detail through subsequent course offerings. In this course, students will gain an understanding of arthropod biology, body plan, organ systems, behavior and physiology, infection biology and immunity. Students will also gain practical skills with arthropod identification and demonstrate a solid understanding of disease vector evolutionary relationships. In addition, students will learn how to apply knowledge gained from the class in future roles as public health practitioners, or simply as informed citizens.

Introduction to Epidemiology
VTPMD 6640
Instructor: R. Ivanek-Miojevic
Offered every Fall (3 credits) – Letter grades only
This course covers fundamental epidemiology concepts and methods in the investigation of determinants of health or disease in populations. Topics include causation, measures of disease frequency and association, sampling methods, selection and interpretation of diagnostic tests, type and characteristics of observational and controlled studies, and bias and confounding.

Human Microbes and Health
BioMI 3210
Instructor: A. Hay
Offered every Fall (3 credits) – Letter grades only
The microbes on and in our bodies are as abundant as our own cells. These diverse microorganisms provide us with metabolic capacities beyond our own and are essential to good health, but can also play a role in disease. This course will introduce the microbes of the human body, discuss their origins, adaptations to the body, molecular interactions, and associations with health and disease.

Engineering the Microbiome
BME 6130
Instructor: I. Brito
Offered every Fall (3 credits) – Letter grades only
The human microbiome impacts human health in a multitude of ways. To achieve a specific health outcome, we can modify the compositions of the microbiome, the molecules microbes produce, how they interact or how our body interacts with them. Yet, our current toolbox is fairly limited. In this course, we will examine current methods for intervening in the microbiome, but focus primarily on cutting-edge technologies for microbiome-related therapeutics. This will include: probiotics, antibiotics, drug discovery, live bacterial therapeutics, biosensors, phage therapies, bacterial evolution and engineering immune responses. We will touch on the safety implications of using different biological technologies. This course is designed for graduate students or Masters and advanced undergraduate students (with advance permission). There will be a computational component to this course, although no prior computational experience is required.

Current Topics in Fungal Biology
PLPPM 6490
Instructor: G. Turgeon
Offered every Fall (1 credit) – S/U grades only
Weekly discussion of current scientific articles on the biology of fungi. Primarily directed at graduate students and senior undergraduates; postdocs, staff, and guests who have an interest in molecular and organismal biology of fungi are welcome.

Seminar in Ecology and Evolution of Infectious Diseases
Entom 6900 / BioEE 6900
Instructor: D. Peck
Offered Fall/Spring (1 credit) – S/U grades only
Graduate-level discussion of the ecology, epidemiology, genetics, and evolution of infectious disease in animal and plant systems. Weekly discussion of research papers published in the primary scientific literature. Participation in discussion and presentation of at least one paper required for course credit.