IMMUNOLOGY

BIO 306

FALL 2008

Instructor:

Dr. Christine White-Ziegler
Office:	Sabin-Reed 457 (enter through SR456 to get to office)
Office phone:	585-3815
E-mail:	cwhitezi@smith.edu (a good way to contact me)
Office hours:	By appointment on Monday, Wednesday, or Friday

Course information:

BIO 306 Immunology
Course credit:	4 hours
Class time:	MWF 9-10:20 a.m.
Location:	McConnell 102
Prerequisites:	A cell biology course or permission of instructor
Recommended:	A genetics course A microbiology course

Course description:

This course will encompass how the immune system recognizes and overcomes pathogenic invaders, primarily bacteria and viruses. Innate, B-cell, and T-cell mediated immunity will be covered along with special topics such as how pathogens evade the immune system, transplantation, allergies, HIV, immunotherapies, and the role of the immune system in cancer. A number of special topics are also covered through student presentations and papers.

Lecture text:

The text for the class is Immunobiology: The Immune System in Health and Disease by Charles Janeway and Paul Travers, 7^th edition. It will serve as the primary reference for the course. The accompanying CD offers excellent short video clips. Additional readings may be assigned and will made available to students in the class through Moodle or the Young Science Library. An extremely helpful resource for the writing assignments in this class is A Short Guide to Writing About Biology by Jan Pechnik, 3^rd edition. It is on reserve for this course at the library.

Appointments/contacting me:

Right after class is an ideal time to meet, but we can set an alternate time on Monday, Wednesday, or Friday by appointment. When you want to set an appointment, please let me know a few time slots you are available on those days so we can find a time that matches both of our schedules. Feel free to contact me in class, by email, or by phone. Do, however, make sure that any important information you need to get to me (e.g. appointment times, paper topics, etc) is written down on something and handed to me! I promise you that I will promptly forget anything simply told to me. Also, I do not necessarily check email/voicemail on the weekend, in the evening after 4 pm, and (sometimes) not before class, so plan on a lag time in response to emails sent to me at these times.

Evaluation:

Immunology Instant	25
Quiz	50
Exams (3 x 100 points)	300
Annotated outline/synopsis	50
Peer reviews (2 x 25 points)	50
Paper	100
Oral presentation of paper	50
Total points	625

Immunology Instants

Each student will present an “Immunology Instant” during the course of the semester. This will be a short (approximately 3-5 minute) talk with a different student presenting each class meeting. These serve to relate the course information to recent discoveries regarding immune system function, diseases specific to immune system, or immunologically based treatments/diagnostics. Guidance will be provided on what information should be covered in these instants.

Exams

The Quiz, Exam 1, and Exam 2 will be self-scheduled exams. During the time period in which an exam is given, the exams will be available starting at 1:00 p.m. on the first day until library closing time on the last day. Students can obtain the test in the Young Science Library at the desk. The exam must be completed within two hours and returned to the Science Library desk. If students have questions pertaining to the exam material, these questions must be asked before the test is made available.

Exam 3 will cover the content of the last third of the course, primarily student papers. All of the student papers’ will be placed on reserve in the Young Science Library. Each student will be responsible for writing a test question and answer on her individual paper that will be used in formulating the exam. Exam 3 will be given out on the last day of class and must be returned to the Science Library desk during final exam week by the date given in the course outline.

Annotated outline/Peer review/Final paper

Each student will write a paper on a subject of interest within the field of immunology and that reflects the most current research on the topic. To do this, one needs to explore the current literature, primarily journal articles and reviews. This project will allow you to develop your skills in pursuing independent literature research and synthesizing information from a variety of sources to give a cogent, concise synopsis of the current research in the area you choose to explore.

Students may come up with their own topic or choose one in consultation with the instructor. Each student needs to talk to the instructor to get approval of her topic by the date stated in the schedule. This is done primarily to prevent duplication of topics as well as to increase the diversity of special topics. An annotated outline will be written for the paper to delineate the focus of the paper, emphasizing the cellular immunology. The majority of references (but not all) cited should have been written in the past 3 years. The outline is due by the date stated in the schedule, but can be submitted earlier. The paper, limited to 8-10 pages, should be typed, double-spaced, and include a list of references. The paper should be written from the primary literature and should give the latest information available on the subject.

The paper is to be handed in on the date stated in the syllabus. Each student in the class will be responsible for reviewing two other student’ papers. Each student will fill out a review of the presenter’s paper that includes comments for the writer on ways to improve the paper. The review will include a brief overall summary/critique of the paper along with specific comments on how the draft could be improved. Edits within the draft itself will help to clarify the comments. The reviews will be handed in to the instructor and then the instructor will return them to the writer such that she can use the comments for improving her paper. In addition, the instructor will also be reviewing and grading the paper. Thus, the paper should be as complete as the student can write such that the reviewers can give constructive comments and it will earn a good grade.

The choice to revise the paper is optional. The initial grade may be accepted. If a student chooses to revise the paper, they must provide a written rebuttal that, point by point, describes how they modified the paper to address the concerns of all of the reviewers. You are welcome to make an appointment with the instructor to review the comments made by your various reviewers. The modified draft will be read by the instructor, graded, and averaged with the initial grade to yield a final grade for the paper. The final draft of the paper, along with the drafts from the peer reviewers and the rebuttal, is due on the date stated in the schedule.

Presentations to class

During the last portion of the course, students will be presenting their research. Two-three students will present at each class meeting. Each student will give a ~ 15-20 minute presentation of her paper, followed by 5 minutes for questions and discussion. The presentations should be well prepared, concise, and include any visual aids that would enhance the presentation. The presentation time will not be enough to cover every point made in the paper. Therefore, students will want to present the most interesting and important points. The purpose of the presentation is to give students a chance to speak in front of others and promote an exchange of information and ideas.

Moodle/Website:

The majority of information for the course will be posted on Moodle (http://moodon.smith.edu/). In addition, this course has a web page that is a source for specific and general information. Useful links to immunology and microbiology-related sites, and literature reference databases can be accessed through this page. Look on the sidebar for “Useful Links” and click on it.

www.science.smith.edu/departments/Biology/cwhitezi/default.html

Colloquium:

A seminar will be given by Dr. Jon Goguen, University of Massachusetts Medical School on October 27 on his research examining the immune response to the bacterium that causes the plague Yersinia pestis. Significant extra credit will be given to those who attend his seminar and write a brief one-page summary of the talk.

Late policy: Each assignment is due on the date and in class at the time stated in the syllabus. Assignments will not be accepted by email; a written copy must be given to the instructor. Extensions are rarely given on an individual basis unless an email is received from your class dean. An assignment handed in late will be penalized 5 points for each day it is late.

Outline of course:

This outline should be viewed as a flowchart of topics in the basic order that they will be covered as time permits. It is subject to change.

Week	Lecture	Chapter
F 9/5	Introduction to course
M 9/8	Innate versus adaptive immunity: characteristics	1
W 9/10	Immune system cells/ Clonal selection hypothesis
F 9/12	Lymphatic system
	* Read chapter 1 by Friday 9/12
M 9/15	Phagocytes and function	2
W 9/17	Phagocytes and function/Pathogen evasion
F 9/19	Signal transduction/ Inflammation/Cytokines	6: 251-252
	*Self scheduled quiz between 9/12-9/19
M 9/22	Complement/Natural Killer Cells
W 9/24	Ig/TCR structure and antigen binding	3
F 9/26	MHC structure and peptide presentation
	*Immunology Instants start this week
	*PAPER topic due in class on 9/24
M 9/29	Ig diversity	4
W 10/1	TCR diversity
F 10/3	Isotype switching and Ig isoforms
	*Annotated bibliography of PAPER due in class on 10/3
M 10/6	Experimental techniques: Antibody techniques	Appendix I
W 10/8	Antigen processing pathways	5
F 10/10	MHC diversity: polygeny, codominance, polymorphism
M 10/13	NO CLASS- FALL RECESS
W 10/15	Experimental techniques: Transgenic/knockout mice
F 10/17	Transplantation	14
	*Self schedule EXAM 1 between 10/20-10/27
M 10/20	Transplant therapies
W 10/22	B/T cell development	7
F 10/24	T cell development and bone marrow transplants

M 10/27	T cell activation/ CTL effector functions
W 10/29	TH1 vs. TH2 T cells/ effector functions	8
F 10/31	B cell activation	9
	*Extra credit-seminar by Dr. Jon Goguen Monday 10/27 at 4:30 pm
	*PAPER due in class on 10/29
M 11/3	Basophils, mast cells, and eosinophils	13
W 11/5	Allergies
F 11/7	Experimental techniques: T cells	Appendix I
	*Peer reviews of papers due in class on 11/7
M 11/10	Vaccines	15, Appendix I
W 11/12	Vaccines
F 11/14	HIV and AIDS
	*Self schedule EXAM 2 between 11/13-11/20
M 11/17	HIV and AIDS	12: 527-545
W 11/21	Student presentations
F 11/23	Student presentations
M 11/24	Student presentations
W 11/26	NO CLASS- THANKGIVING RECESS!
F 11/28	NO CLASS- THANKGIVING RECESS!
M 12/1	Student presentations
W 12/3	Student presentations
F 12/5	Student presentations
	*Exam question on paper due on 12/5
M 12/8	Student presentations
W 12/10	Last day of class
	*OPTIONAL: Modified version of PAPER w/rebuttal due in class on 12/8
	*Exam 3 due at 5 pm on Thursday 12/18