How Many Semesters

Microbial Ecology and Evolution

Course Number: MCB 435

Instructor: Dr. Rachel Whitaker email: [email protected] office: C222 CLSL phone: 244-8420

Meeting Place and Time: CLSL A446 Tuesday, Thursday 10:00-11:30. Office Hours: C222 CLSL Wednesday 3:00-4:00.

Course website: http://www.life.uiuc.edu/mcb/435/index.html Username: mbc435 Password: MEE2010

Course Summary: This course will focus on evolutionary and ecological principles as they apply to microorganisms. Examples from both medical and environmental microbiology (from emerging pathogens to global climate change) will illustrate critical applications of these basic principles. We will introduce an array of quantitative and molecular tools that facilitate the study of microbial population and community dynamics.

Readings: Microbial ecology and evolution are new and rapidly progressing fields – no single textbook provides the background you will need. Weekly background articles to support lecture material will be provided on the website or handed out in class. These materials are intended to broaden topic areas and present information in a different way. Students are not responsible for background reading material on examinations unless otherwise noted.

In addition, we will read and discuss five articles from the primary literature. Students are responsible for the material covered in these articles on examinations.

Suggested Texts:

A Primer of Population Genetics – Daniel L. Hartl, 2000 Sinauer Associates, Inc. Sunderland, MA.

For those not familiar with microbiology

Brock Biology of Microorganisms – 12th edition Madigan and Martinko, 2009 Prentice Hall Upper Saddle River, NJ Evaluations:

Exam 1 25 Exam 2 25 Final Project 25 Participation 20 Debate 5 Total 100

Exams – 25 pts each

Exams will cover the material presented in class. This includes lectures, paper discussions, and workshops. The first will cover weeks 1-7 and the second will cover weeks 8-14, including material from our debate. There will be no cumulative final.

Final Project – 25 pts

Students will write a grant proposal on a topic of their choosing that is relevant to the material covered in class. This proposal will be a maximum of 15 pages in length including an Abstract, Background, Description of two to three specific hypotheses to be tested, Methods, Relevance and References. During the final exam period students will present their proposal to the class in a 10 minute presentation.

Participation – 20 pts (Paper Discussion + Questions and Answers)

Paper Discussions – 15 pts

Throughout the semester we will discuss five research papers from the primary literature. For each discussion, pairs of students will be assigned different parts of the paper (introduction, figures, tables, methods) that they will be responsible for presenting in class. Presentations include discussion of the relevance of material to the overall conclusion of the paper. Each presentation will be worth three points.

Questions and Answers – 5 pts

We will maintain an online discussion where students can pose and answer questions. For each question or answer, students will receive 1 point toward their final grade. Questions must apply to the material discussed in class (lecture, papers, workshops, debate), but are not limited to specific details, i.e. questions may extend material in new directions. To receive credit, questions must not have been asked previously. Credit will be given for each answer to a question that has not been previously answered to the satisfaction of the person who posed it.

Debate – 5 pts Some of the most hotly contested questions in microbial ecology and evolution revolve around the definition of microbial species. Some esteemed scientists believe that microbial species do not exist. Some believe it doesn’t matter. Some believe microbial species do exist and must be defined in order to continue rigorous investigations of microbial ecology and evolution. We will have a debate in class -- Do microbial species exist and does it matter? Three weeks before the debate, I will divide the class into two sides. Each side will be responsible for putting together an argument for their position based on data from the literature. After the debate each student will write a 1 page statement of their personal position (referencing materials discussed during the debate).

Quiz questions:

Five times throughout the semester, class will begin with a single quiz question. Answers to the quiz will not be graded but will be used to evaluate whether material is being understood. Quiz questions will provide examples of the style of question that will be asked on exams.

Workshops:

Two in-class workshops will allow students to work with evolutionary and ecological data. These workshops will meet in the computer lab 164E Burrill Hall. Worksheets completed during these workshops will be evaluated but not graded. Syllabus:

Tuesdays Thursdays Week January 19 January 21 1 Introduction The Woesian Revolution

Week January 26 January 28 2 Tree thinking Molecular tools for analysis Genomics and metagenomics

Week February 2 February 4 3 Genomics and metagenomics (continued) Paper discussion #1 Mutation

Week February 9 February 11 4 Natural selection and genetic drift Recombination/horizontal gene transfer Migration

Week February 16 February 18 5 Evolution of emerging diseases Paper discussion #2

Week February 23 February 25 6 Population genetics workshop Experimental evolution (Meet in Burrill Hall 164E)

Week March 2 March 4 7 Species concepts Paper discussion #3

Week March 9 March 11 8 Review/ Species debate preparation Exam

Week March 16 March 18 9 Species debate preparation Species debate

Spring Break Spring Break Week March 30 April 1 10 Measuring diversity Community structure (Topics due for final project)

Week April 6 April 8 11 Community structure workshop Human microbiome (Meet in Burrill Hall 164E) Ecology of health and disease

Week April 13 April 15 12 Interactions/symbiosis/coevolution Paper discussion #4 Week April 20 April 22 13 Viruses Discussion of paper topics (Outline of paper topics due)

Week April 27 April 29 14 Paper discussion #5 Review

May 4 Exam

Friday May 7 8 to 11 AM Final project presentation

Paper discussion #1

H. Tettelin, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial ‚"pan-genome". Proceedings of the National Academy of Sciences. 2005. 102(39). 13950-13955.

Paper discussion #2

A. Rambaut, et al. The genomic and epidemiological dynamics of human influenza A virus. Nature. 2008. 453(7195). 615-619.

Paper discussion #3

H.J.E. Beaumont, et al. Experimental evolution of bet hedging. Nature. 2009. 462(7269). 90-93.

Paper discussion #4

P.J. Turnbaugh, et al. A core gut microbiome in obese and lean twins. Nature. 2009. 457(7228). 480-484.

Paper discussion #5

K.M. Oliver, et al. Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism. Science. 2009. 325(5943). 992-994.