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The Scripps Research Institute Graduate Program Advanced Immunology and Microbial Science (1/5/12) Contact Information Course

Directors: David Nemazee, Juan Carlos de la Torre Office location: Immunology 220B Phone: 49529 E-mail: nemazee@scripps.edu Teaching Assistant: Students who would like additional help for understanding any paper prior to the designated class meeting are asked to directly contact one of the following people TBA Course Information Semester & year: Spring 2012 Meeting days & time: Monday & Wednesday 9:45 am to 11:15 am Meeting location: Conference Room of the Graduate School Office Course Description Each class involves the discussion of a significant paper from the recent literature. The class discussion will be guided by one student from the class and a knowledgeable faculty discussant. The list of discussion papers will span the breadth of host defense, immunology and microbiology, and will cover myeloid and lymphoid cell development, innate immunity, immune recognition, immune tolerance and memory, leukocyte signaling, virology, bacteriology, microbial evasion and immune mediated pathology. Background Preparation (Prerequisites) Students will find it helpful to read relevant background material for each class from the Janeway textbook. Even students who have not previously taken an Immunolgy and Microbiology course will be able to successfully take this course, if they read relevant background material from the book. It is essential that students unfamiliar with immunology read Appendix I of Janeway before the course starts, as this chapter describes methods that are integral to the course material. Also, students with little background in the area of virology could use the book Essentials of Virology to get familiar with basic principles in this area. Texts and Journals References Background reading 1. Janeway's Immunology 7th edition textbook 2. Essentials of Virology (S. Ram Reddy and S.M. Reddy) Specific recent primary research papers will be chosen for each session To be announced for each Unit by the Professor of the class 1

Course Learning Outcomes By the end of the course students will be able to: 1. analyze papers in the literature, 2. conduct critical analysis of contemporary basic research in immunology and microbial science, 3. discuss essential concepts in immunology and microbial science, 4. demonstrate proficient verbal communication skills that reflect scientific analysis of the literature (oral presentation rubric), 5. demonstrate proficient scientific writing skills that reflect scientific analysis of the literature (scientific writing rubric), and 6. design experiments that provide interpretable information. Course Requirements & Assignments "Next experiment": For every class (except for the first class of the course, see below), students will submit a written document describing one or two next experiments that represent a logical follow up of the work presented in the paper of the day. These will be graded by the faculty discussant of the day, and the composite scores from these submitted papers (for a total of 18 classes) will comprise each students course grade. Each next experiment should produce an amount of data corresponding to what it would be expected to be a figure in a follow up paper. The short description of each next experiment should include a) a rationale for doing the experiment, b) a brief description of the experiment, including experimental methods, and c) the expected outcome(s), and a rationale of why they are expected. The description of the two next experiments should be short (e.g. 4-6 sentences each) and together, the text for both next experiments should be about 1/2 page of single-spaced printed text (12 point, Times New Roman). Brevity is preferred and concise, focused descriptions are better. Oral presentation: Each student will make 1-2 fifteen minute presentations introducing a paper prior to discussion and a second presentation after the presentation to discuss the implications, other approaches being used to study the problem, conflicting conclusions from other studies, etc. Time permitting, the student will also discuss suggested next experiments. class participation: Students are expected to be active participants in the discussion, to ask questions, and to be prepared to answer questions posed by the Professor. Grading Student progress will be assessed on the basis of: 1. weekly next experiment writing assignments 2. evaluation of participation in discussion, and 3. evaluation of the quality of scientific oral presentation.

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Point grades for each category will be: 3 points = excellent (A+), 2 points = very good (B+), 1 point = fair (C+), 0 points = unsatisfactory. Grading of "next experiment" papers is based on overall clarity, logical presentation, demonstration of understanding of the subject matter, reasonableness and probability of success of the experimental approach proposed. Participation and presentation grades will be assessed by taking into account the input of course directors, faculty participants, and teaching fellows. Presentations will be evaluated on content, organization and delivery, which should demonstrate accurate knowledge, clear understanding and ability to explain the significance, strengths and weaknesses of the research, and the ability to communicate in a clear and engaging manner. Class participation will be evaluated on the quality and quantity of participation in discussion.

Letter Grade Grade Point

A B C F 4.0 3.0 2.0 0.0


Learning Outcome

Superior Achievement Exemplary Satisfactorily demonstrated ability in Proficient field of study Below average,work not at level expected of a TSRI graduate student Developing Not acceptable Fail

Attendance No late submission of the next experiments will be allowed, except under extenuating circumstances approved by the course director. Students should contact the course director immediately if they have to miss class. Unexcused absence will result in a grade of 0 for the session. If you do not submit the next experiments page for a particular class, your grade will be diminished by 1/17th. Scientific and Professional Ethics The work you do in this course must be your own. Be aware when you are building on someone else's ideas, including ideas of classmates, professors, and authors you read. You must explicitly acknowledge the ideas of others. Feel free to build on, react to, criticize, and analyze the ideas of others but, when you do, make it known whose ideas you are working with. If you ever have questions about drawing the line between others' work and your own, ask me and I will give you clear guidance. Expectations and Logistics Student teams The class will be divided into teams of two students each. These teams will rotate over the duration of the course, such that every team will lead 1-2 classes. The student team assigned to each paper will meet with the relevant faculty discussant 1-2 weeks before the paper is presented, to get help and suggestions in identifying and understanding the literature that will be used to prepare the introduction and the perspectives PowerPoint presentations for each class (see below). Each of the students in the team should send their PowerPoint presentation to the faculty discussant at least 3 days before their presentation, so the faculty can give them feedback for modifying it, if necessary. Class format At the beginning of each class, one student will give an introduction of 10 minutes (PowerPoint format), to present background material for the discussion paper and to frame the problem being studied. Next, the faculty discussant will project slides of the figures from the paper, and will elicit discussion from all members of the class to evaluate the data. After the figures have been discussed, the student will make a short perspectives presentation of 10 minutes, in which the person discusses other approaches being used to study the problem, conflicting conclusions from other studies, etc. Finally, the student and faculty discussant will lead a discussion of next experiments, which students will already have proposed on documents that they submitted at the beginning of class. Every student in the class will be responsible for reading the days discussion paper prior to class, and should be prepared to discuss each figure. Also, each student must submit a next experiments document when arriving in class (below). A short review(s) related to the topic of the discussion paper will be provided on the reading list. More basic background may be obtained by reading relevant section of the: 1) Janeway's Immunology 7th edition textbook, and 2) Essentials of Virology (S. Ram Reddy and S.M. Reddy) 3

Selection of Papers The discussion paper for each class (together with a related short review) will be posted on the Advanced Immunology and Microbial Science Course website. Students are asked to review this list, and send an email to Diane Kreger in the graduate office indicating 1st, 2nd, and 3rd and 4th choices. Every effort will be made to assign students to the paper(s) of their choice; however, decisions will be made on a first come/first served basis. Students may submit choices as individuals (and end up with a second team member arbitrarily) or as a team with a second person with whom they would like to work. Everyone will have the chance to present 1-2 times. If students do not sign up for specific papers, they will be assigned to paper(s) randomly by the course director. First Class of the Course The goal of the first class is to provide everyone with a clear sense of the class format, by providing a guided template. We will assign one discussion paper for each class (to be read by all class members beforehand), but our two student TAs (instead of class members) will perform the job of the student team. Moreover, class participants are not asked to submit written next experiments documents for this first class. We will discuss examples of appropriate next experiments. Schedule Unit Intro 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 xx 6/4 6/6 4/23 4/25 4/30 5/2 5/7 5/9 5/14 5/16 5/21 5/23 5/30 Date Mon Wed 4/2 4/4 4/9 4/11 4/16 4/18 General Research Topic Overview Innate immunity in lower organisms Innate immunity in mammals Lymphocyte development Antigen presentation, MHC Structure/function of immune molecules Signal integration in T cells CD4 T cell differentiation Immunological memory Mucosal immunity Autoimmunity CD8 T cells, tumor immunology Immune tolerance Future vaccines T cell responses to microbes and evasion HIV and AIDS Virus mutation and evolution: implications for virus-host interactions and disease Viral engineering Human viral infections Professor David Nemazee Nathalie Franc Peter Tobias Nick Gascoigne Luc Teyton Erica Ollmann Saphire Karsten Sauer Charles Surh M. McHeyzerWilliams Wendy Havran Dwight Kono Linda Sherman David Nemazee Mansun Law Lindsay Whitton Michael Zwick Juan C. de la Torre Glen Nemerow Oldstone Confirmed ? ok ok ok ok ok ok ok Professor email prefix (suffix @scripps.edu) nemazee nfranc tobias gascoign lteyton erica ksauer csurh mcheyzer havran dkono ok ok ok? ok ok Date? ok lsherman nemazee mlaw lwhitton zwick juanct gnemerow mbaobo