IMUN 605 Topics in Cell and Molecular Immunology

605:  Course Organizers:  Phil Scott, Larry Turka & Yongwon Choi

Purpose of the course: The purpose of this course is to develop skills in: critically reading papers; orally presenting papers in a journal club format; and writing reviews of papers. 

Components to the course:

1. Presentations:  Everyone will have two presentations to give to the class: one to present the background for a paper, and the other to present a paper. Students will have an opportunity to meet with one of the course directors the week before the presentation to help answer questions about the paper and the area of work.
2. Future Studies:  For each class, students not presenting the background or the paper will be required to submit a brief description of what questions were raised by the paper that should be pursued, and an outline of what experiments you might do to address these questions.
3. Class Discussion: Everyone will have to pick one paper to lead a discussion of the future studies that are suggested by the students.
4. Class Participation: Each student is expected to participate during the class presentations, asking and answering questions related to the papers/topic being covered. 
5. Manuscript Reviews: Two reviews will be done by each student during the semester.  The first one will be due at the beginning of March.  The second will be due in mid-April.  Each student will pick one paper from two selected by the course organizers for each of these reviews.

How to prepare presentations:

The following is a general guide to how you should present the background and the paper in class.  It is a format that should work for presentations given in any journal club.  [It should also help you think about how to present your data in the first and second preliminary exams.]

Background: 20- 30 minutes- no powerpoint, but handout.  Use the board.

• Give a brief overview of the field that is covered by the paper.
• Describe the major questions that are associated with the field.
• Provide the specific history that led the authors to do the experiments that are described in the paper; or that led the authors to address the questions raised in the paper.
• Provide a background for any unique approach used in the paper (but not the methods used).
• Utilize the introduction of the paper as a primary source (but not the only source) for your presentation.  The papers picked by the authors to reference in the introduction very often provide clues (certainly should) as to how the authors got to where they are in their thinking. 

Paper Presentation: 20- 30 minutes- powerpoint

• Introduce the paper by stating what specific questions this study addresses and, referring back to the background presentation, why these are important.
• Show a model of what the paper is addressing (if possible). 
• Avoid the use of text slides.
• Present figures and tables from the paper.  Describe why the specific experiment was done, and what the conclusions are from the data presented.  If the specific method is unusual or complicated, explain prior to showing the data.   Are the conclusions reached by the authors appropriate?  Is there an alternative explanation of the data?  Are the controls appropriate? The authors want the data to fit the story they are telling, but are there aberrant pieces of data that do not fit.  Are they significant, or can they be ignored?
• Summarize the results of the paper. Did they make their case?  Are they over-interpreting their results?  What experiments should they have done that would have increased your confidence about their conclusions?  (Were these feasible?) Where would you go from here? 

Class Discussion: 20- 30 minutes

Presentation issues:

• When using powerpoint, do not use small font sizes that can not be read.  Check that they will be seen when projected.  What can be seen on the screen is not necessarily visible when projected, even in a small room.
• Be completely sure of the methods used for each figure, so that if a question arises you can answer it without re-reading the paper during the presentation.
• Presentation of the background and the paper must be coordinated prior to class.  Whether you are presenting the background or the paper, you need to be familiar with both parts of the presentation.  [When you come to class, you should be able to switch who gives the background and who goes over the paper.]

Responsibility of class during and after presentation:

• Be on time for class.
• You should ask questions about things that you do not understand.  The presenters have spent time researching the background for the paper, and if there are points that are not clear ASK FOR A CLARIFICATION. If there is something about the data that is not clear, ask about it.  If there is a point that you think has not been raised about the data, make the point.  The success of the class will be determined by how interactive the discussions are. 
• At the end of the class, students will rank the paper based upon their reviews (would they accept, reject, ask for revisions).  Is there something that they saw as a problem that was not discussed during the presentation?  On the basis of the presentation, would they change their reviews?  This discussion will be lead by a student.

How to write reviews of papers (see attached Nature Immunology instructions):

• First paragraph- For the editor, very briefly describe what the paper shows (or the authors think it shows) and why this is important (if it is) to the field.
• Following paragraphs- Describe the major issues of the paper- what is particularly good or particularly bad that should influence whether the paper should be published.  If the paper is not appropriate for this journal (i.e. too specific for Science, or topic better suited to another journal), state so.  This is often only one paragraph.
• Specific comments. These should be numbered and review the issues that you think need to be addressed in the paper.  If you ask for additional experiments, be sure that they are practical.  Are you asking for too much for one paper?  What controls might be missing? What Figures are unclear?  Is the appropriate literature cited?
• If you recommend a return for revision, be clear about what it will take for you to accept the paper.  You may well be asked to review it again, and if the authors address your concerns, be sure you would be willing to accept the paper.  If this is not the case, it should be rejected in the first place. 
• Reviews do not need to be long to be good reviews.  Most importantly, they need to highlight the importance of the paper, so that even if there are problems that need to be addressed the editors can get a sense of whether it is worth asking for revisions. 
• Reviews should not be inflammatory.   

Evaluation:

• Presentations- after the first presentation you will be reviewed by one or both of the course organizers for pointers on how to improve; after the second presentation you will also be reviewed and given a grade (Excellent, A; Good, B; Fair, C; Poor, F). 
• Future Studies- each description of proposed future studies that is handed in will be graded.
• Two full reviews will be graded. 
• Class Participation- graded by course organizers; mid-course any deficits in class participation will be pointed out to allow for improvement (Class attendance is mandatory).
  

All classes will be held in Room 301, Hill Pavilion

January 14: 3-5  Introductory Class

January 28:  3-5

            Garrett, W. S., G. M. Lord, S. Punit, G. Lugo-Villarino, S. K. Mazmanian, S. Ito, J. N. Glickman and L. H. Glimcher. 2007. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131:33-45.

February 6: 3-5  WEDNESDAY

            Scott-Browne, J. P., S. Shafiani, G. Tucker-Heard, K. Ishida-Tsubota, J. D. Fontenot, A. Y. Rudensky, M. J. Bevan and K. B. Urdahl. 2007. Expansion and function of Foxp3-expressing T regulatory cells during tuberculosis. J Exp Med 204:2159-69.

February 18: 3-5

            Deane, J. A., P. Pisitkun, R. S. Barrett, L. Feigenbaum, T. Town, J. M. Ward, R. A. Flavell and S. Bolland. 2007. Control of toll-like receptor 7 expression is essential to restrict autoimmunity and dendritic cell proliferation. Immunity 27:801-10.

February 25: 3-5 

            Yu, D. and et. al. 2007. Roquin represses autoimmunity by limiting inducible T-cell co-stimulator messenger RNA. Nature 450:299.

March 5: 3-5  WEDNESDAY

            McGeachy, M. J., K. S. Bak-Jensen, Y. Chen, C. M. Tato, W. Blumenschein, T. McClanahan and D. J. Cua. 2007. TGF-beta and IL-6 drive the production of IL-17 and IL-10 by T cells and restrain T(H)-17 cell-mediated pathology. Nat Immunol 8:1390-7.

March 17: 3-5

            Anthony, R. M., J. F. Urban, Jr., F. Alem, H. A. Hamed, C. T. Rozo, J. L. Boucher, N. Van Rooijen and W. C. Gause. 2006. Memory T(H)2 cells induce alternatively activated macrophages to mediate protection against nematode parasites. Nat Med 12:955-60.

March 24: 3-5

            Collison, L. W., C. J. Workman, T. T. Kuo, K. Boyd, Y. Wang, K. M. Vignali, R. Cross, D. Sehy, R. S. Blumberg and D. A. Vignali. 2007. The inhibitory cytokine IL-35 contributes to regulatory T-cell function. Nature 450:566-9.

March 31: 3-5

            Kim, H. S., M. S. Han, K. W. Chung, S. Kim, E. Kim, M. J. Kim, E. Jang, H. A. Lee, J. Youn, S. Akira and M. S. Lee. 2007. Toll-like receptor 2 senses beta-cell death and contributes to the initiation of autoimmune diabetes. Immunity 27:321-33.

April 7: 3-5

            Pham, T. H., T. Okada, M. Matloubian, C. G. Lo and J. G. Cyster. 2007. S1P(1) Receptor Signaling Overrides Retention Mediated by Galpha(i)-Coupled Receptors to Promote T Cell Egress. Immunity.

April 14: 3-5

            Sokol, C. L., G. M. Barton, A. G. Farr and R. Medzhitov. 2007. A mechanism for the initiation of allergen-induced T helper type 2 responses. Nat Immunol.

April 21: 3-5

            Stemberger, C., Huster, K.M., Koffler, M., Anderi, F., Scheiemann, M., Wagner, H., and D.H. Busch. 2007. A single naïve CD8+ T cell precursor can develop into diverse effector and memory subsets. Immunity.  27:985

April 28: 3-5

            Van Laethem, F., S. D. Sarafova, J. H. Park, X. Tai, L. Pobezinsky, T. I. Guinter, S. Adoro, A. Adams, S. O. Sharrow, L. Feigenbaum and A. Singer. 2007. Deletion of CD4 and CD8 coreceptors permits generation of alphabetaT cells that recognize antigens independently of the MHC. Immunity 27:735-50.