EMERGING INFECTIOUS DISEASES

BIO 321 Topics in Microbiology/BCH 380 Topics in Biochemistry

“Outbreak: Understanding the Pathogenic Strategies of Emerging and Reemerging Infectious Diseases”

Spring 2009

Instructor:

Dr. Christine White-Ziegler

Office: Sabin-Reed 456 (office within lab)

Office phone: 585-3815

E-mail: cwhitezi@smith.edu

Office hours: By appointment- please contact me by email or phone to set up a time.

Seminar class:

Course credit:	3 hours
Class meeting times:	Thursdays 1:00-2:50 pm
	Poster presentation in Microbiology class
Location:	McConnell 403
Prerequisites:	A molecular genetics biology class or
	A microbiology class
Recommended:	An immunology class

Course description:

This semester the course investigates the pathogenesis of microbes of recent concern, focusing on the particularly innovative molecular processes these organisms use to ensure their success in surviving and multiplying in the host.

This course is divided into two parts. The first part of the course will investigate specific pathogenic strategies of microorganisms and relate this to the larger global picture of how this impacts detection, treatment, and public health. The pathogens chosen are those you have read about in the news from current outbreaks. Students will be introduced to these topics through a variety of required readings with student led and interactive discussions.

In the second part of this course, we will learn about a variety of pathogens through student-directed discussions and presentations on their specific pathogens they have researched through the semester.

Readings:

This seminar will rely upon articles from the primary journal articles, reviews, book chapters, and textbooks. Each week there will be assigned readings chosen by the students that will be placed on the Moodle website (http://moodon.smith.edu/) or on reserve (Young Science Library in Bass Hall). There will be additional books and videos on reserve that may be helpful as background material or for independent research projects. These resources are listed at the end of the syllabus.

Evaluation:

Attendance and participation	120
Leading of discussion	100
Introduction/annotated bibliography	30
“Near perfect” draft of project	20
Peer review of projects (2)	50
Final project	100
Oral presentation for seminar class	75
Poster presentation for microbiology class	40
Total points	535

Attendance and participation

Attendance and participation in a small class such as this is critical for lively, informative discussion. Beyond the first meeting, my intention is not to lecture, but rather to have all of us do the same readings and discuss the ideas and experiments put forth in the readings. Therefore, participation will be judged based on attendance, preparedness for class, meaningful involvement in the discussion, getting any outside resources/help needed to complete the research paper, and self motivation in following through on assignments.

Leading of discussion

After the first class meeting, groups of 2 students will be responsible for leading discussion each class time. The students will meet with the instructor prior to class (approximately 10 days before) to go over ideas that they have to initiate conversation in class, discuss the papers they will assign for the class to read, and to clarify any questions they have about the material. It will be the responsibility of the students to set up the meeting time with the instructor.

The leading of discussion will consist of:

• Discussing the main concepts of the review article(s) assigned to the class. All of the students in the class should be prepared to be able to explain figures/main points from the review material
• Presenting a primary article related to the pathogenic strategy covered in the review, focusing on the experimentation performed. All of the students in the class should have read the article assigned.

• Delineating the overall impact of the pathogen, with a focus on particular aspects related to public health. This can include case studies, epidemiology reports, tracking strategies, treatment/vaccine strategies, public health measures, health policy, politics, etc. There is significant flexibility here on what material is presented and how it is presented.

Pathogen Project

The project will be to complete an in-depth project on a particular pathogen and its strategy for multiplying and surviving within a host. This project may be a paper or a PowerPoint/web page presentation with significant explanation in the notes section such that it can be viewed as a webpage (see Moodle site for examples). The oral presentation at the end of the course is based upon your project.

Assignment	Due date
Paper topic chosen	2/12
Introductory paragaph/annotated bibliography	2/26
Draft of project	3/12
Peer review	3/26
Final draft	4/30

The project will have its main focus on an aspect of the molecular basis of virulence. The molecular microbiology should form a substantial portion of your paper. It should cover an aspect of how the microorganism functions in the host to cause disease, focusing to the molecular mechanisms and processes used by the organism and, when appropriate, how the immune response plays into the pathogenesis. This should be based on what is currently known from the primary literature. Basically, you should be writing a scientific, but also persuasive essay as to why this is a critical area of investigation regarding your pathogen of interest.

Other elements that can be included within the paper should illustrate and be presented in a manner that supports why the research on the specific molecular pathogenesis aspect you have covered is important. These elements include:

1. Why is this pathogen considered of top concern, either in a specific region and/or worldwide?
2. What is thought to be the reason(s) for the emergence of this pathogen? Has it recently emerged or reemerged?
3. What events or outbreaks have brought it to the public eye? Is it endemic /epidemic in a particular region?
4. Basic biology of the pathogen and transmission of the pathogen
5. Clinical presentation of the disease(s) it causes, linking these symptoms to the pathogenic strategies of the organism and immune response of the host
6. Methods used to detect and work with the pathogen
7. Successful treatment or vaccines
8. Public health strategies/control measures that are being used/ or being developed
9. Impediments- financial, political, social- that prevent or limit prevention of the disease and its spread

Paper topic- Each student will choose a microorganism and it pathogenic strategy that will be the focus of her project for the class. Students should have 2-3 topics in mind so that we can ensure that there is no overlap between students within the class.

Introductory paragraph and annotated bibliography- The introductory paragraph should be written and handed in along with an annotated bibliography that includes 10 references, at least 6 of which are primary articles. The project should be based upon the primary literature and should give the latest information available on the subject. Thus, a majority of the references cited should have been written in the past 5 years, and should focus on the molecular pathogenesis of the organism. A good introduction on writing an annotated bibliography can be found at:

http://www.library.cornell.edu/olinuris/ref/research/skill28.htm

Peer review- Students will be put together in groups of 3 people for the purpose of reviewing each other’s drafts. A “near perfect” draft of the project will be due and given to the other members of a student’s group. A copy should be given to the instructor as well. A “near perfect” project should be as complete a project as the student can create such that the reviewers can give constructive comments. Projects that meet this expectation will receive full credit when handed in; those projects that do not meet this expectation will be not be given these points.

Each member of the group will fill out a review of the presenter’s project that includes comments for the writer on ways to improve the project. The reviews will be handed in to the instructor on the due date, and then the instructor will return them to the writer such that she can use the comments for improving her project.

Final project-The final draft of the project is due on the last day of class. It may be submitted any time prior to this, but will be penalized by a loss of 5 points for every day it is late.

Optional writing conference- I am willing to meet to offer comments regarding a student’s project. In order to have a fruitful meeting, I will need to read over your near perfect draft and thus require ~ 48 hours notice before we meet. This writing conference must occur prior to when the student presents in class.

Presentations to seminar class

During the end of the course, students will be presenting their research. Two-three students will present at each class meeting. Each student will have a 30-minute time period to present and lead discussion about her pathogen. The main focus will be towards the molecular pathogenesis with each student providing a detailed summary as to how the pathogen succeeds within the host and causes disease. Student should plan to talk for 20 minutes with the remaining time for questions.

Presentations to Bio 204: Microbiology

In an effort to facilitate the exchange of information, students in this class will also be giving a short presentation of their research to the Microbiology class in a poster session format. The Microbiology class lasts for 50 minutes and ~ 7 of you will have posters for each session. Your poster will not be able to cover every point made in your paper. Therefore, students will want to present the most interesting and important points about their pathogen to the Microbiology class. These presentations will need to be scheduled during the microbiology lecture meeting times which are MWF 10-10:50 and R 4-4:50. These talks will take place in April; specific scheduling for these talks will be determined by mid- semester.

Let’s Chat (The Microbiological Way!)

Extra credit can be earned in the course by bringing to class a article from the past week that highlights a new finding or event related to emerging infectious disease and summarizing the article verbally for the rest of the class. This opportunity is available for the first 7 class meetings and earns up to 3 points/class. Extra credit information cannot pertain to topics we are discussing in class.

This is an outline of topics we will cover in this class. It is subject to change.

Date	Topic	Assignment	Readings
1/29	Introduction to class	·
2/5	Discussion 1: Community acquired, methicillin resistant Staphylococcus aureus	PAPER TOPIC DUE
2/12	Discussion 2:
2/19	Discussion 3:	INTRODUCTORY PARAGRAPH AND ANNOTATED BIBLIOGRAPHY DUE
2/26	Discussion 4:
3/5	Discussion 5:
3/12	Discussion 6:	NEAR PERFECT DRAFT DUE
3/19	Spring Break!
3/26	Discussion 7:	PEER REVIEW DUE
4/2	Student presentations (3)
4/9	Student presentations (3)
4/16	Student presentations (3)
4/23	Student presentations (3)
4/30	Student presentations (2)	FINAL DRAFT DUE

BIO 321/BCH 380- Books on reserve at the Young Science Library

Author

Title

W. M. Scheld, D. A. Armstrong, J. M. Hughes, Editors W. M. Scheld, W. A. Craig, J. M. Hughes, Editors W. M. Scheld, W. A. Craig, J. M. Hughes, Editors W. M. Scheld, W. A. Craig, J. M. Hughes, Editors W. M. Scheld, W. A. Craig, J. M. Hughes, Editors Lansing Prescott, John P. Harley, Donald A. Klein S.J. Flint [et al.] Bernard N. Fields, David M. Knipe, Peter M. Howley, Editors-in-Chief Charles A. Janeway, Jr., Paul Travers C. Robert Horsburgh, Jr., Ann Marie Nelson, Editors Ann Marie Nelson, C. Robert Horsburgh, Jr. Alan J. Cann Felissa R. Lashley and Jerry D. Durham., Editors

Emerging infections Emerging infections 2 Emerging infections 3 Emerging infections 4 Emerging infections 5 Microbiology Principles of virology: molecular biology, pathogenesis, and control Fundamental virology Immunobiology : the immune system in health and disease Pathology of emerging infections Pathology of emerging infections 2 Principles of Molecular Virology Emerging infectious diseases : trends and issues

BIO 321/BCH 380 Videos– Please let me know if you would like to borrow any of these.

1999 Howard Hughes Medical Institute (HHMI) Holiday Lectures

Lecture 1- Microbe Hunters: Tracking Infectious Agents

Lecture 2- The Microbes Strike Back

Lecture 3- Outwitting Bacteria’s Wily Ways

Lecture 4- Emerging Infections: How Epidemics Arise

1996 Howard Hughes Medical Institute (HHMI) Holiday Lectures

Lecture 1- How Immune Cells Create Trillions of Receptors from a Few Hundred Parts

Lecture 2- How the Immune System Detects Invaders

Lecture 3- How the Host Avoids ‘Friendly Fire’

Lecture 4- Stalking the Elusive Pathogen

2000 American Society for Microbiology Intimate Strangers: Unseen Life on Earth Series

1. The Microbial Universe

2. The Unity of Living Systems

3. Metabolism

4. Reading the Code of Life

5. Genetic Transfer

6. Microbial Evolution

7. Microbial Diversity

8. Microbial Ecology

9. Microbial Control

10. Microbial Interactions

11. Human Defenses

12. Microbes and Human Diseases