Winter 2016: BIO 144 - Life: decoded. Genomics in Society  Draft syllabus

Image credit: Barbara Denef
Course objective/goals:Highslide JS   Our genome is the blueprint to our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. But it is more than a static information store: our genome is a dynamic, tightly regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how is the genome constructed and how do we identify the genes that make up our genome? How do we determine their function? How do organisms differ or match and what does genomics teach us about the evolutionary relationships between different organisms? What does our understanding of genomics mean in terms of our future health and wellbeing?

“Life: decoded. Genomics in society” aims for students, who will not necessarily focus on a career in science, to acquire an understanding of how the genomics revolution has transformed many facets of our society. From the more obvious impacts on the way we conduct scientific research, to its impacts on the medical practice, which is moving towards human genome-based personalized medicine; from its impacts on agriculture (domestication, genetically modified organisms) to ethical considerations regarding genetic discrimination; and from genomic insights into the microbial inhabitants of our body to genomic insights into the microbes that sustain our planet’s environmental health.

Instructor: Prof. Vincent Denef (Department of Ecology and Evolutionary Biology)

Time/Location: Mon/Wed/Fri,


Prerequisites: None

Required reading: The textbook used for this course is Introduction to Genomics (Oxford University Press, USA; 2nd edition ISBN-10: 0199564353 | ISBN-13: 978-0199564354) and will be supplemented by articles from the popular and scientific media. If readings are assigned prior to lecture / discussion, these are expected to be read before the class they will be discussed in.

Independent project: To enable a more active learning experience, 30% of this class’ credit will be based on a group-based short documentary, which the students will prepare throughout the semester and present during the last week of classes. This group project will allow students to actively investigate the impacts of genomics in today’s world of science, ethics, policy, art, law, anthropology, journalism, medicine, agriculture, etc. Students will be divided in groups of 4-5 and choose a field impacted by genomics and investigate the impact of genomics based on articles in the popular/scientific media, interviews with experts in the field, as well as with people not active in the field. The final product will be a 10-minute short documentary movie. While this will be a group project where all group members will be expected to contribute to all aspects of the project, each member of the group will take on a role that carries the responsibility for overseeing part of the project (literature research, screenplay writing and production, camera and editing, expert interviews, layman interviews).

Fall 2016: EEB 446 - Microbial Ecology  Full syllabus

Course objective/goals:Highslide JS   A greater focus on the microbial component of the biosphere is warranted, since “microbes run the world”(1). If we are to build comprehensive and predictive models for ecosystems important to environmental and human health, we need a better understanding of how microbial communities assemble and operate. This course will cover the ecology of microbes by highlighting their interactions with each other and the environment, and will present the latest insights into their role in ecosystems ranging from thawing permafrost to the human gastrointestinal tract. Ecological and evolutionary concepts and tools used in microbial research, including novel “omics” techniques, will be introduced. The course also aims at uncovering how concepts developed in plant and animal ecology do and do not translate to the microbial world.

Instructor: Prof. Vincent Denef (Department of Ecology and Evolutionary Biology)

Time/Location: Tue/Thu, 10-11:30am, 3733 CCRB

Website: ctools or LSA courseguide

Prerequisites: Introductory Microbiology (BIO 207 or the equivalent) and one 300 level biology course; Microbial diversity (EEB470) and general ecology (EEB281/381) are recommended.

Required reading: There is currently no comprehensive textbook available to support a microbial ecology class. Required readings include all papers posted on the course’s website and handouts.  Additional readings will be distributed throughout the course.

Independent project: Part of the grade will be based on an independent project, carried out individually or in groups, depending on the class enrollment. Students will develop a concept from plant/animal ecology in the microbial field, written as a short research proposal, and presented during the last week of classes.