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BIOL 412

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The Ecology of Infectious Diseases

 

BIOL 412 is a 3 credit course

Fall Semester 2013

Tues./Thurs. 8.00-9.15

112 Buckhout Lab 

Office Hours: Tue. & Thur. 12.10-1.10pm 

 

Instructor

Dr. Isabella Cattadori

128W Millennium Science Complex

Phone:  865-9594

Email: through Angel (cms.psu.edu)

 

Course approach

This course will take an ecological approach to the study and control of infectious diseases. We will look at the dynamics of disease, how parasites (worms, bacteria and viruses) spread through a host population, the consequences for the hosts and the consequences for the parasite from both an ecological and evolutionary viewpoint. We will use the ecological insights to discuss and identify effective means of controlling the parasites. We will learn how to develop basic mathematical models to describe the dynamics of a parasitic infection and discuss how these models can be applied to make predictions and optimize control-strategies for infections. This will be illustrated with numerous work examples of human, veterinary and wildlife diseases. We will also look at the role of parasites in the ecosystem and how environmental changes affect parasite transmission. At the finer level we will look at how host-parasite interactions and multi-parasite species infections are modulated by host immunity and what may cause rapid changes in infectiousness and transmission. We will touch on a range of current issues that include pandemic outbreaks, emerging diseases and the role of parasites in ecosystem functioning. Our ecological approach involves applying the principles of population biology to understand infectious diseases and develop new perspectives on epidemiology: thus the title “Ecology of Infectious Diseases”. This course is designed for ecology, biology and animal science majors to obtain insights into the ecology of parasitism, and for pre-meds to provide biological foundation to the study of epidemiology.

 

Course goals

Upon completion of this course, students will understand the mechanisms, patterns and dynamics of disease spread and persistence. They will understand how to construct and apply models to specific infections and to predict and optimize effective control measures. They will cover the major concepts in parasitology and population dynamics including the basic reproductive number (R0), the critical community size, threshold densities, the consequences of aggregated parasite distribution or host heterogeneities and epidemic metapopulation dynamics. Students will gain knowledge of the epidemiology of a range of infectious agents, including macro- and micro-parasites and agents with direct, vectored and complex life-cycles. They will also consider key features of disease emergence and major threats to human populations. They will be able to understand the relative measures and drawbacks of various control procedures. Finally, students will know the difference between density-dependent and frequency-dependent transmission and understand non-linear dynamics and the processes that generate heterogeneities in exposure and susceptibility. 

 

Course Materials

This is a fast moving field with new epidemics and data becoming available weekly or even daily so to keep up to date the majority of the reading will be through pdf files from on line material. I will provide handouts/ papers to read for the assignments. Additional pdf will be provided as complementary background reading.

Angel website: https://cms.psu.edu. The syllabus, lecture notes, pdfs of scientific publications and additional material will be posted on Angel the day before. It is your responsibility to check Angel regularly.

                                                                                                                                           

Communication

If you need to communicate with Dr. Cattadori (please do so through Angel), please use your own Penn State email account to send and receive messages. Never give out your personal user identification to roommates or other friends, since this information would allow another individual to access your personal university records (i.e., grades, class registration, etc.) as well as your email account. Keep your virus protection software up to date. Office hours are Tuesday and Thursday, if this conflicts with your classes an off-office-hour appointment can be arranged. 

 

Exams and Assignment of Grades

There are 4 exams during this course. The first 3 will address issues related to macro- and micro-parasite lectures, the last one will be the FINAL exam and will include questions on the ENTIRE course. Every question is one point, there are ~40 questions in the first 3 exams and ~80 questions in the final exam, since is comprehensive of the entire course. All exams are weighed in the same way. The final grade is based on the average of the 4 exam percentages (for example: (87%+95%+91%+84%)/4= 89.25. Attendance at exams is mandatory.

The following are the only legitimate excuses accepted:

 - Verifiable illness (e.g., a receipt from your doctor is sufficient)

 - A University sponsored event (with a note from the sponsor)

 - A religious holiday recognized by PSU 

 - Verifiable death in the family (e.g., obituary, funeral card - with a date)                  

 

Academic Integrity/Academic Dishonesty:  

Academic dishonesty is not limited to simply cheating on an exam or assignment.  The following is quoted directly from the "PSU Faculty Senate Policies for Students" regarding academic integrity and academic dishonesty:  “Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution.  Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students.”

All University and Departmental policies regarding academic integrity/academic dishonesty apply to this course and the students enrolled in this course.  Refer to the following URL for further details on the academic integrity policies of the Department of Biology: http://science.psu.edu/current-students/Integrity/Policy.html. Each student in this course is expected to work entirely on her/his own while taking any exam, to complete assignments on her/his own effort without the assistance of others unless directed otherwise by the instructor, and to abide by University and Department of Biology policies about academic integrity and academic dishonesty.  Academic dishonesty either in lab or lecture can result in assignment of “F” by the course instructors or "XF" by Judicial Affairs as the final grade for the student.

 

Required Disability 

“Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/. In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at http://equity.psu.edu/ods/guidelines/documentation-guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.”

 

Assignment of Grades:

Grade Points %

A         93 - 100% B 83 - 86% C 70 - 76%

A-         90 - 92% B- 80 - 82%     D 60 - 69%

B+         87 - 89% C+ 77 - 79% F Less than 60%


Fall 2013, 412 Course Schedule

 

 

Tues./Thurs. 8.00-9.15     112 Buckhout Lab

 

 

 

 DATE

COURSE CONTENT AND CLASS TOPICS

1

 8/27

Course Introduction: Syllabus, general announcements.

Parasitism, the dynamical approach and the ecological perspective on parasitism. Definitions

2

 8/29

Macroparasite: fundamentals and definitions. Taylor’s power law and Negative binomial distribution

3

 9/3

Macroparasite: Causes of aggregation. Age-intensity and peak shift.

4

 9/5

Macroparasite: examples of aggregation/practice

5

 9/10

Macroparasite: Host-parasite models and host regulation. The Anderson and May model.

6

 9/12

Macroparasite: The Anderson and May model II

7

 9/17

Macroparasite: R0 and its significance in macroparasites. Control through anthelmintic application & Human cases

8

 9/19

Macroparasite: REVISION

9

 9/24

Macroparasite: EXAM on macros

10

 9/26

Microparasite: fundamentals and definitions

11

 10/1

Microparasite:  R0 and its significance in micro-parasites. The epidemic curve and SIR model part I.

12

 10/3

Microparasite: SIR Part II

13

 10/8

Microparasite: host heterogeneities (age, sex, etc), network

14

 10/10

ANDERSON LECTURE

15

 10/15

Microparasite:  Control and emergence, Vaccination, smallpox eradication, Critical host densities and threshold theorem. /

16

 10/17

Microparasite:  Measles a great example

17

 10/22

Microparasite: Heterogeneities in microparasites, superspreaders and dynamics of transmission

18

 10/24

Microparasite: REVISION

20

 10/29

Micro-parasite: EXAM on micros

19

 10/31

Micro-macro: Emerging Diseases Patterns and processes

21

 11/5

Micro-macro: Emerging Diseases Patterns and processes part 2

22

 11/7

Micro-macro: Vector borne diseases, malaria and dengue

23

 11/12

Micro-macro: Vector borne diseases, malaria and dengue  part 2

24

 11/14

Micro-macro: Influenza and genetic drift

25

  11/19

Micro-macro: Influenza and genetic drift part 2

26

 11/21

Micro-macro: Myxoma virus in Australia, the classical example of evolution of virulence

 

11/26

Thanksgiving

 

11/28

Thanksgiving

27

 12/3

Micro-macro: REVISION

28

 12/5

Micro-macro: exam on special topics

29

 12/10

Micro-macro: REVISION

30

 12/12

Micro-macro: REVISION

 

 

FINAL EXAM During week of finals