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Colgate University Libraries Digital Commons @ Colgate Faculty Syllabi Fall 2015 BIOL 374 Geoffrey Holm Colgate University, [email protected] Follow this and additional works at: http://commons.colgate.edu/syllabi Part of the Immunology and Infectious Disease Commons Note: This syllabus may not be applicable to the current semester. Be sure to verify content with the professor(s) listed in the document. Recommended Citation Holm, Geoffrey, "BIOL 374" (2015). Faculty Syllabi. Paper 43. http://commons.colgate.edu/syllabi/43 This Syllabus is brought to you for free and open access by Digital Commons @ Colgate. It has been accepted for inclusion in Faculty Syllabi by an authorized administrator of Digital Commons @ Colgate. For more information, please contact [email protected]. BIOLOGY 374: IMMUNOLOGY SYLLABUS LECTURE: T/TH TIME: 12:00PM-1:15 PLACE: BLDG. 10, FAES CLASSROOM 7/8 (NOTE: CLASS WILL BE HELD IN BLDG. 31 ROOM 2A48 ON 12/8) Instructor: Geoff Holm (Bldg. 50 Room 2537, [email protected]) Office hours: T/Th 4:30-5:30 in Bldg. 50 lobby or pre-arranged location, and by appointment Text: Primer to The Immune Response, 2nd Edition; Mak, Saunders, and Jett, 2014, AP Cell Press. Primary literature readings will be made available as assigned. Goals and Objectives In Immunology, we will study the molecular and cellular components of the human immune system. We will investigate the general principles that govern different components of the immune system, and integrate those principles to create a broad picture of how the immune system functions to eliminate infectious diseases. We will examine the consequences of malfunctions in the immune system, and how researchers and clinicians can manipulate the immune system to positively impact human health. In addition, we will emphasize how immunologists understand what they do about immune system function, as well as discuss research methods that allow for investigation of new questions about how the immune system functions. Additionally, this course aims to enhance your ability to communicate your knowledge to classmates and a general audience, and to work efficiently in groups. Upon completion of this course, you will be expected to: 1 Recognize the basic cell types and macromolecules that comprise the immune system. 2. Understand how the innate immune system functions to control nascent infections. 3. Describe how the adaptive immune system responds to pathogens and understand the processes by which these pathways generate immunologic memory 4. Understand how cells of the immune system communicate with the extracellular environment, and integrate signals from the environment to cause changes in cell structure and/or function. 5. Analyze how various components of the immune system work together to form an integrated response to infectious diseases. 6. Explain how malfunctions of the immune system impact human health. 7. Describe how the immune system can be manipulated to positively impact human health. 8. Analyze important techniques used by immunologists and apply this knowledge to novel experiments probing immune structure and function. 9. Critique primary journal articles within the field of immunology, and communicate your insights orally and verbally. 10. Effectively communicate your knowledge of immunology to a general audience. Format: Lecture and discussion/workshops. Occasionally throughout the semester, the class will divide into smaller groups to discuss a current journal article relevant to the week’s theme, or to solve an in-class group problem. These problems may be given without prior notice, and the results will be reflected in the final grade assessment. Course Information Determination of Grades: Course grades will be based upon scores earned on the following assignments in the lecture portion of the course. Assignment: 2 unit exams (100 pts ea) Cumulative final exam Weekly quizzes (10 pts each) Seminar summaries (20 points each) Total Points Point Value 200 pts 200 pts ~80 pts 60 points ~540 pts Unit and Final Exams: Exams I and II will be unit exams covering material presented in the lectures, reading assignments, and discussions. They will take place in class on the dates indicated on the syllabus. A comprehensive final (50% covering unit III and 50% cumulative) will be self-scheduled during finals week. Exam questions will require you to independently integrate material from topics presented across multiple lectures. Exams also will require you to apply the major concepts to situations not covered directly in class. Quizzes: Educational literature indicates that concept retention is enhanced when students are routinely quizzed on their knowledge. To accomplish this in a low stress manner (rather than having “pop quizzes” in class), and to reinforce the main themes of the course, there will be routine Moodle quizzes (10 points each) based on the assigned readings, which must be completed by noon on the date indicated on the syllabus. Group discussion problems: Throughout the semester, we will set aside class time for “process oriented guided inquiry learning” (POGIL)-style workshops, based on a current primary literature paper. During these class meetings, you will work in groups to assess/analyze the paper, and relate it to the material covered in previous lectures. These problems will allow you to apply your knowledge and extend it to novel situations. All students should come to class having read the paper, and be prepared to answer questions regarding the paper content and the unanswered questions that the paper raises. More information on the POGIL workshops will be provided on the course Moodle site. Seminar Attendance: One of the major benefits of being at the NIH is the access to multiple seminar series on any number of different topics in the biological sciences (you may not appreciate this now, but trust me, as good as the Colgate Bio department and NASC seminar series are, one of the things I miss most about being at an academic medical center is the lack of seminars related to my scientific interests!). Unfortunately, I scheduled the Journal Club course at the same time as the weekly NIH Immunology seminar series (Wed. at 4:15…doh!). However, there are many other seminars on going, including some on immunology-related topics. Your assignment is to attend 3 seminars (on any topic, but ideally related to something we are discussing in the course) and write a ~3 paragraph summary of the seminar, including a description of two research-related questions you have based on the seminar and how you might go about answering these questions (i.e. what type of experiments would you do to address these issues?). These summaries will receive a “-“ (14 pts) , “+/-“(16 pts) , “+” (18 pts) or “++” (20 pts) grade, and the quality of the questions you propose will have a significant effect on your grade. Attendance Policy Attendance will not be taken at class meetings, but it is important to remember that class participation and open discussion are important components of this course. It is impossible to participate when absent. In addition, attendance at all class meetings is highly correlated to success in the course. I rely heavily on material covered in class (and sometimes NOT covered in the text book) when I write exams. Depending on relevance to the course, attendance may be required at occasional NIH seminars. Exam and Honor Code Policies All students must take the exam on the scheduled exam date. Please contact me prior to the exam if you have a serious conflict. Answers to the exam questions will be posted after each exam and students must consult the answer key before contesting a grading decision on a specific question. All such grading issues must be addressed within one week of receiving the grade. In addition, you are reminded of the Academic Honor Code in place at Colgate University. All tests and other graded assignments fall under the auspices of this policy. Unless otherwise indicated all graded materials must contain only work that you have completed yourself. Appropriate citation of the work or ideas of others is expected in all writing assignments. Cases of plagiarism will be referred to the Colgate Student Conduct Board. Students are reminded that convictions of violations of the Academic Honesty Policy of Colgate result in the grade of F for the entire course, not for the individual assignment. Plagiarism will not be tolerated. Other important policies and information: The classroom is a shared learning environment, and respectful and cordial interactions within the classroom are expected at all times. To show respect for the instructor and your fellow students, please: ensure that all cell phones are turned off during class; do not leave during class unless absolutely necessary; and restrict computer usage to material directly relevant to class. Polite constructive criticism of the course in general and of specific assignments and/or exercises is welcome. Expressing constructive criticism in this course will not adversely affect your grade. I will consider your suggestions but may or may not implement them. Students with documented disabilities needing academic adjustment or accommodation are encouraged to see one of us as soon as possible. All discussions will remain confidential. If you have not already done so, contact Lynn Waldman, Director of Academic Program Support (x7225), to discuss your request for accommodations. Schedule of Events Date Sept. Course Theme Lecture Topic Reading Cells of the Immune System Cells of the Immune System Chpt. 1; Chpt. 2, p. 21-34 15 B Cells 17 22 24 Antigen Presentation B Cell Receptor B Cell Development B Cell Functions/Paper #2 MHC I and II Chpt. 4 Chpt. 5, p. 111-123; Quiz 2 Chpt. 5, p. 123-140 Chpt. 6; Quiz 3 29 Antigen Processing and Presentation Chpt. 7 1 6 Mid-term Recess 8 13 T Cells 15 20 Exam I 1 3 Cell Communication and Movement Chpt. 2, p. 34-52 8 Innate Immune Responses Pathogen Recognition Chpt. 3, p. 55-66; Quiz 1 10 Complement and Inflammation/Paper #1 Chpt. 3, p. 66-81 Oct. 22 Peripheral Immune 27 Responses 29 Integration of Immune Nov. 3 Responses 5 10 12 17 Manipulation of Immune 19 Processes 24 Thanksgiving Dec. 1 Immune Disorders 3 8 10 Integration: HIV-1 T Cell Receptor T Cell Development T Cell Function/Paper #3 Chpt. 8 Chpt. 9, p. 197-211 Chpt. 9, p. 211-223. Tolerance Variations on a T cell theme Mucosal Immunity/Paper #4 Chpt. 10; Quiz 4 Chpt. 11 Chpt. 12 Immunity to Bacteria Immunity to Viruses, etc. Immune Evasion/Paper #5 Chpt. 13, p. 296-306; Quiz 5 Chpt. 13, p. 307-326 Chpt. 13, Evasion Strategies sections Exam II Vaccines Transplantation Chpt. 14, 333-348, 364-372 Chpt. 17 Tumor Immunology Immune Hypersensitivity/Paper #6 Autoimmune Diseases HIV -1 Chpt. 16; Quiz 6 Chpt. 18 Chpt. 19; Quiz 7 Chpt. 15 Unit III and Cumulative Final will be held at a time and place TBD.