Pathobiology 552; Spring 2009

Course Title: Cell biology of pathogens and their hosts.

Course description (Revised 01/02/09):

Goal:  The goal of this course is to expose graduate students to important concepts in cell biology as they relate to infectious disease and host-pathogen interactions.  The emphasis will be on understanding the primary literature and learning how experiments in cell biology are designed, performed, and interpreted.  Students should be prepared to read primary literature each week in addition to textbook material.  Students should have had some exposure to molecular biology, immunology, and biochemistry.  Students who are not in the Pathobiology graduate program should email jais@u.washington.edu for permission to register.

Format of classes:  Classes meet Tuesday and Thursday from 11:00 AM to 12:50 in the South Campus Center (SCC) room 309.  Each topic will be covered with a 50 - 60 hour lecture covering a basic cell biology topic and a 35 - 45 minute discussion/analysis of one or more papers from the primary literature (assigned in advance).  These papers will typically illustrate pathogen cell biology relevant to the lecture topic.  Discussion format is up to individual lecturers:  they may have students discuss specific figures, or they may approach the questions raised by the paper in a more global manner.  Student participation during discussion or primary literature is required.  Students will also be assigned sections of textbooks and a review for most classes. Please review the syllabus from last year's course to be sure you can handle the assigned primary literature before signing up for this course!

Format of Literature Presentation Sessions:  A couple weeks before each presentation sessions, selected students choose a primary paper for discussion.  Students will choose their paper for discussion from a list of papers put together by the instructors.  These papers will illustrate concepts in the cell biology of pathogens that were presented in lectures or introduce new concepts that we didn't have time to cover in class.  The goal is to give students experience in doing short focussed presentations of primary literature in cell biology.

Exams and Final Proposal:  There will be a single one-week, take-home exam in this course (midterm), and a final grant-style proposal.  The emphasis in the exam will be on understanding concepts in cell biology, reading and analyzing primary literature, and experimental design.  Students will be on the honor system to work alone on the exam and not discuss the exam with anyone else.  The completed exam should be submitted, coded by student number (no names), and will be graded before matching the student numbers with names.

Students will also write an NIH-style grant proposal on a cell biology topic that is covered in one of the lectures and is relevant to infectious disease or pathogenesis.  Students are allowed (and encouraged) to discuss their proposal with anyone before they turn it in, but they are not allowed to copy (verbatim or in concept) proposals or sections of proposals written by others.  Students should not use topics you have used or seen used in the laboratories in which you have worked.  Likewise, they should not use topics you have written about for other classes or topics that have or are being studied by your colleagues, friends, or lab-mates.  The proposal should be novel and consist of 5 pages single-spaced (excluding figures and references) including: 2-3 Specific Aims (1 page); Background and Significance (1 page); Research Design and Methods (3 pages).  Topics will need to be approved in advance.  Proposals should be identified by an anonymous alias name only.  Students will be assigned to a proposal review session and will asked to read and critique in specific proposals that are written by students in a different session and identified only by alias names.  Each review session will meet once to discuss and score assigned proposals.  We will do our best to give students written feedback on their proposals from instructors, copies of the relevant student critiques, and feedback on comments that arose during proposal review sessions.  There are sample grant proposals posted on the course website.

http://courses.washington.edu/pabio552/

The goal of the proposal is to familiarize students with the grant writing and reviewing process, and to give them an opportunity to use what they have learned in this course to generate hypotheses and design experiments.  Grading of proposals will be based on clarity, logical design, likelihood of successful outcome, originality, creativity, and relevance to cell biology topics covered in the course.

Grading:  10% participation in class discussions; 10% oral presentation session assignments (9% for the oral presentation; 1% each for the discussion assignment); 30% midterm exam; 30% final proposal; 10% participation in study section; 10% written critiques for study section. 

How to contact us:  The course organizer is Dr. Jaisri Lingappa, Associate Professor, Dept. of Pathobiology and the TA is Beth Thielen, Pathobiology graduate student/MSTP student.  Feel free to discuss any issues related to the course (material, format, etc.) with us.  Jaisri's office is in at 1616 Eastlake Ave., Suite 305.  Jaisri and Beth will be available after classes for questions, or you can reach us by e-mail (jais@u.washington.edu, bthielen@u.washington.edu) to make other appointments to see us as needed.