Ecology of Infectious Diseases
Fall 2013
Course: BIOL490 Office: HH 722
Professor: Andrea Swei, PhD Office Hours: Wednesday 1-3
Time: Tues and Thurs 2-3:30, HH 501 Email:
Lab: Wed 10-12, SCI 249
Prerequisites: Biol 230 and 240
Text Materials:
Disease ecology: community structure and pathogen dynamics. Edited by Sharon K. Collinge and Chris Ray. Oxford University Press 2006. New York. (ISBN: 0-19-856707-3)
Additional selected primary literature available on iLearn
Course description:
In this course, we will examine the ecological and evolutionary processes that govern the transmission of pathogens in animal and plant systems. Topics that will be covered include factors that lead to disease emergence, the impact of diseases on host populations, and the role of community ecology and biodiversity on pathogen transmission. The course will cover the theoretical underpinnings of disease ecology, case studies and examination of research methodology, as well as laboratory exercise on executing quantitative/modeling methods in disease ecology.
Student Learning Objectives:
Knowledge and understanding
1. Able to describe the basic principles that determine the invasibility, persistence, and transmission of pathogens in a variety of systems
2. Understand the parameters involved in estimating disease transmission and persistence
3. Critically read scientific papers on patterns and processes that shape disease transmission and spread
4. Be able to comprehend and explain methods and principles from primary literature
5. Describe how habitat change, climate change, and other disturbances influence the spread of pathogens
6. Understand and be able to describe key examples of human, wildlife, domestic animal, and plant disease systems and the factors that regulate their transmission and prevalence
Skills
1. Give an oral presentation on the ecology of an infectious disease
2. Group presentation
3. Be able to execute and parameterize basic epidemiological models in R
Course work: 600 Total Points
Exams: Two midterm exams, 100 points. Final exam, 100 points. All exams will be in class. Questions will consist of multiple choice and short essay. (total 300 points)
Oral Presentation: Details TBA, 100 points.
Pop Quizzes: 4 closed-note in-class quizzes, 5 points each (total 20 points)
Lab: Write up of lab problems sets, 20 points each (total 160 points)
Participation: Participation in lecture and discussions, 20 points
Extra Credit: Extra credit may be given to students who participate in additional departmental seminars at SFSU, UCSF, UC Berkeley or Stanford and write short reviews of the lectures. You must see the instructor for approval of extra credit ideas.
Missed Test: If a student misses a midterm without either a certified medical excuse or prior instructor approval, the student may take a makeup test at a designated time at the end of the semester. Only one makeup test/quiz will be given. It will be fair but challenging! Tests missed with certified medical excuses or prior instructor approval will be dealt with individually. If a student misses the final exam without a valid excuse, a zero will be averaged into the grade. Missed labs cannot be retaken.
Grading:
Final grades are computed as a letter grade, plus or minus where appropriate: A (93.00-100%), A- (90.00-92.99%), B+ (87.00-89.99%), B (83.00-86.99%), B- (80.00-82.99%), C+ (77.00-79.99%), C (73.00-76.99%), C- (70.00-72.99%), D+ (67.00-69.99%), D (63.00-66.99%), D- (60.00-62.99%) and F (59.99% or below). Work that is turned in late will lose 10% of total points per day past due.
At the end of the semester, if a student is borderline between 2 grades (for example, between an A- and a B+), discretionary criteria will be used to determine which of the two grades, the student receives. These criteria will include class participation, class attendance, and the student’s willingness to seek help.
Attendance: Attendance and punctuality are required for the class. All quiz questions are derived from class material.
General Classroom Policy: Mobile phones must be switched off.
Honor Code: By your signature on the attendance sheet, you are agreeing to abide by a class honor code. This means that you agree not to cheat or participate in any type of academic misconduct (plagiarism etc). In addition, if you become aware that a classmate has cheated or engaged in academic misconduct, it is your responsibility to bring it to the instructor’s attention. In this way, you and your classmates are responsible for each other’s academic behavior. Any student caught
Disabilities: Students with disabilities who need reasonable accommodations are encouraged to contact the instructor early in the semester. The Disability Programs and Resource Center is available to facilitate the reasonable accommodations process. The DPRC, located in SSB 110, can be reached by telephone at 338-2472 (voice/TTY) or by e-mail at .
Add/Drop/Withdrawal:
For complete schedule see: http://www.sfsu.edu/~admisrec/reg/regsched134.html
Class start: August 27, 2013
Drop deadline: Monday, September 9
Add deadline: Monday, September 9 (last date to add with permit numbers).
Withdrawal: September 10-November 22. After that, no withdrawal unless seriously ill, in case of accident, or circumstances beyond the student’s control.
Final exam:
Thursday December 19th 1:30-4pm in HH501
Lecture Schedule
Week / Date / Topic / Reading1 / Aug 27 / Tues: Introduction to disease ecology and evolution
Aug 29 / Thurs: Community ecology and host-pathogen systems / Collinge Ch 2
2 / Sep 3 / Tues: Foundations of disease ecology: SIR models and R0 / Anderson and May 1991
Sep 5 / Thurs: Macroparasite systems / King et al. 2006, Collinge Ch 10
3 / Sep 10 / Tues: Host population regulation by parasite / Hudson et al. 1998
Sep 12 / Thurs: Parasite induced behavioral modification / Moore 1983
4 / Sep 17 / Tues: Guest lecture on amphibian declines (Dr. Vance Vredenburg, SFSU) / Wake and Vredenburg 2008
Sep 19 / Thurs: Wildlife disease and seasonality / Collinge. Ch 3, Dobson and Meagher 1996
5 / Sep 24 / Tues: Spatial-temporal dynamics and networks: rabies / Collinge Ch 12
Sep 26 / Thurs: Midterm
6 / Oct 1 / Tues: Evolution of virulence / Galvani 2003, Ewald 1993
Oct 3 / Thurs: Student presentations
7 / Oct 8 / Tues: Heterogeneity and transmission: superspreaders and AIDS / Lloyd-Smith et al. 2005 Nature
Oct 10 / Thurs: Biodiversity and the dilution effect / Keesing et al. 2010
8 / Oct 15 / Tues: Vector-borne diseases: Lyme disease, malaria, West Nile Virus / Collinge Ch 3, Druilhe et al. 2005
Oct 17 / Thurs: Student presentations
9 / Oct 22 / Tues: Guest lecture on Dengue virus (Dr. Shannon Bennett, CAS) / Bennett 2010, Ch 9
Oct 24 / Thurs: Seasonality and Conservation / Altizer et al. 2006
10 / Oct 29 / Tues: Student presentations
Oct 31 / Thurs: Midterm
11 / Nov 5 / Tues: Disease control: herd immunity and culling
vaccinations / Lloyd-Smith et al. 2005 TREE,
Mackinnon et al. 2008
Nov 7 / Thurs: Novel pathogens, prions and infectious cancers / McCallum and Dobson 2002
12 / Nov 12 / Tues: Coevolution and antibiotic resistance: tuberculosis / Levy and Marshall 2004
Nov 14 / Thurs: Guest lecture on avian malaria (Dr. Ravinder Sehgal, SFSU) / Collinge Ch 13
13 / Nov 19 / Tues: Guest lecture on viral discovery (Dr. Samia Nacacche, UCSF) / TBD
Nov 21 / Thurs: Guest lecture on physiology and disease (Dr. Rudolf von May, UC Berkeley) / TBD
14 / Nov 26-28 / Thanksgiving break
15 / Dec 3 / Guest lecture on white nose bat syndrome (Tina Cheng, UCSC) / TBD
Dec 5 / Guest lecture on African frog declines (Dr. David Blackburn, CAS) / Collinge Ch 11
16 / Dec 10 / Guest lecture on Sudden Oak Death (Dr. Margaret Metz, UC Davis) / TBD
Dec 12 / TA-led Review
Final Exam / Thursday December 19th 1:30-4pm / Location: HH 501
Lab Schedule
Week 1 / No lab
Week 2 / Lab 1: Introduction to R part I
Week 3 / Lab 2: Data analysis and plotting
Week 4 / Discussion / GA led
Week 5 / Midterm review / GA led
Week 6 / Lab 3: Difference equation model
Week 7 / Lab 4: Chain binomial lab
Week 8 / Lab 5: SI lab
Week 9 / Discussion / GA led
Week 10 / Midterm review / GA led
Week 11 / Lab 6: SIR Lab
Week 12 / Lab 7: R0 lab
Week 13 / Lab 8: GLMM analysis
Week 14 / Discussion / GA led
Week 15 / Open Lab / GA led
Week 16 / No lab