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  • 1. BIOLOGY 107 - IMMUNOLOGY COURSE GREEN SHEET Spring Semester – 2006 San Jose State University Tues. / Thurs. 9:00-10:15 DH135 Instructor: Ruth Kibler, Ph.D., Duncan Hall 251; Phone - 924-4892 (Office): Phone - 924-4900 (Biology Office); E Mail Address: Office Hours: Mon. 12:30 – 2:30 Tues. 10:15 – 12:15; Thurs. Other times by appointment. Course Description Catalog course description: Immunology, Concepts and principles. Mechanisms of cellular cooperation and regulation of immune responses. Practical considerations and applications. Course description: Biology 107 is a general immunology course designed to provide information about all areas of immunology. Emphasis is on the basic concepts. The material presented will provide you with the vocabulary of immunology and a general knowledge of the subject. The course is designed to give you the basics needed to take advanced courses in immunology. Biology 107 has one three-hour/week laboratory component that must be taken with the lecture. Prerequisites 1) BIOLOGY 3 (Cell Biology) WITH A "C OR HIGHER". Grades of a B or higher in upper division courses such as Bio 135, Bio 116, Bio 124 MAY substitute for the "C or better requirement" in Bio 3. See me about Bio 3 substitution courses. 2) Completion of both semesters of organic chemistry with a AC@ OR HIGHER. Concurrent enrollment in the second semester of organic chemistry is acceptable. 3) Micro 101 with a grade of a C or HIGHER is a Prerequisite for Bio 107. Permission from the instructor is needed to take Micr 101 concurrently with Bio 107. Second bac. and graduate students without this prerequisite should see the instructor. 4) Completion of Bio 6 or concurrent enrollment in Bio 6 is required. Textbook The textbook for this course is Immunology by R.A. Goldsby, 5th edition, published by W.H. Freeman and Company, 2002. Read the book to clarify what you do not understand in the lecture and the Handouts. • At the beginning of each handout there are questions assigned for the chapters from this book. The answers to these questions are found in the back of the book. At least 10% of each exam will be taken directly from these questions. • Case studies found in the book are assigned by chapters. Questions on the case studies will appear in the exams. • You will be held responsible for the material presented in the lecture, the textbook and the Handouts. You are not responsible for topics in chapters not covered in the lecture. This means that you can read the textbook chapters selectively. 1
  • 2. Handouts and Laboratory Manual The Handouts can be purchased in class from the Biology Student Association. Bring the Handouts for each lecture to class with you. I will be referring to figures in the Handouts during lecture. The text and figures were generated to give you information about the areas that I feel are important to understand the subject. The Handouts are designed to lead you through the material for each Lecture. Use These Handouts to Learn the Material. The laboratory manual can be purchased from the Biology Student Association. Appendix to the Handouts • Look in the appendix at the back of the Handouts. You will find: One Scientific American article with questions to be submitted. • Worksheet for Handout 4 on flow cytometry to be submitted. • One Patient Oriented Problem Solving assignment on Tetanus with questions to be submitted. • Study questions for the four exams • Questions on the lecture material on antigens to help you study for that part of the exam. Exams Exams: There will be three midterm exams and a final exam. Make up exams are given only with a medical excuse or consulting me BEFORE the exam. All make-up exams will be taken on the same day. This day will be after the 3rd midterm exam. Please notify me as soon as possible if there is a problem. Approximately 80% of the final exam will cover the material after the 3rd exam. Approximately 20% will be cumulative. The material covered in each exam will be announced. In general, questions from material covered after the previous exam will be emphasized. The subject of immunology builds on the material presented in each Handout starting at the beginning of the course. Exam questions can be multiple choice, fill in, true/false, short answer and drawing experimental conclusions. I try to return all exams within 10 days so that you can go over them during the laboratory. I keep all exams, so you must return them to me at the end of the laboratory class period. FAILURE TO RETURN AN EXAM TO ME DURING THE CLASS LABORATORY PERIOD WILL RESULT IN A SCORE OF A0" FOR THAT EXAM. The exams are available in my office for you to review at any time. If you believe an exam has been scored incorrectly, please bring this to my attention immediately after the exam has been returned to you. Write the questions you wish reviewed on the back of the exam along with your reasons for asking for the review of the question. I will periodically total your points, so you will know how you are doing in the course. Drops If you wish to drop this course, please do so by the stated University Guidelines University and Department guidelines require a serious and compelling reason to drop a course. A failing grade, alone, does not constitute sufficient reason to drop a course. You must submit a form to drop a course. My signing of the form is mainly informational and does not constitute approval of your dropping of the course Expectations What you can expect from me. 2
  • 3. • fairness and impartiality in all grading I grade all homework and exams by ID numbers. The only reason for this is that I do not wish to know whose papers I am grading. This way, I do not have preconceived ideas about how you should do on the exam. • prepared handouts for each lecture. • tests given on the dates announced in the Green Sheet - no surprise changes. • study questions provided for each exam - some questions on the exam taken from the study questions. • up to date assessments of how well you are doing in class. Cumulative point scores are calculated after each exam. • return of exams within 10 days after the exam • trying to make the material interesting - incorporation of current information from meetings attended and literature reviewed. • helping you to understand the material and provide resources when requested. Office hours are to be used by students to obtain help or to go over material. The numbers of students sometimes make this difficult, but I encourage you to use this opportunity. What I expect from you. • timely attendance at lectures - students who attend class usually do better. Although much of the material is covered in the handouts and the book, material which is added in lecture can appear on exams. • reading Handout material before class. You do not have to understand everything, but it will help you if you have some idea of what material will be covered before you come to lecture. • take exams on time and on announced dates. • keep track of when homework is due and turn in assignments on time. • try to learn and understand the material. Most of my satisfaction in teaching comes from observing students who have an interest in learning. • try to achieve the highest grade possible. The most discouraging statement that I can hear from a student is that you are satisfied with a D. • inform me of personal concerns or emergencies that affect your performance in the class. Honesty (my policy) See last page for University Policy Cheating will not be tolerated in this class. You do not learn by cheating. Please think about this statement, and do not place me in the position that I must bring this subject to your attention. The penalty for an infraction of the policy can be very severe. Penalties can include a A0" for an exam and not being allowed to drop the course as well as a report to Judicial Affairs where the report is kept on file. Repeat offenders will be given a failing grade in the course and referred to the Judicial Affairs for administrative sanctions which may include expulsion. I will inform studenst of any action taken against them. An appeal is urged if you feel falsely accused. Honesty is required on written material. You must do your own work. Your answers using the same sentences and wording as an article or another student=s answers is known as plagiarism. It is appropriate in some cases to use the same terminology as the article, but it is inappropriate to use complete sentences from the article. It is never appropriate to use the words of another person unless it is used as a quote. Requirement for the course: Five points on the first exam will be questions on this. Tutorial on plagiarism: Each of you must go to the following site at our library and go through the tutorial on plagiarism. Grading and Points for Course Lecture Exams: Exam 1 150 points Feb. 21 Tuesday 3
  • 4. Will include at least 5 points on the tutorial on plagarism Exam 2 200 points March 14 Tuesday Exam 3 200 points April 18 Tuesday Final Exam 250 points May 19 Friday 7:15 a.m. Total Exam Points = 800 Scientific American Reading Questions: 17 points See Appendix to the Handouts. Clonal Selection - Scientific American 257:62, 1987. Answers to the questions are due on Feb. 7. Questions on this assignment are included in Exam 1. Flow Cytometry Worksheet: 10 points See Appendix. Turn in on February 14. Questions on this assignment are included in Exam 1. Patient Oriented Problem Solving and Post-Test: See Appendix Tetanus Problem Solving: A problem solving set on immunity to tetanus is in the Appendix of your Handout packet. Included in this material are: a) a pre-test with answers, b) four immunologic problems relating to tetanus, c) a post test without answers. Answers to the post-test will be graded. Questions from this problem solving will be included in the second exam. It is a more interesting learning experience if you do this exercise in groups of 2 to 4. If you do this as a group, turn in one post- test for the group. You will each individually receive the same grade. I recommend that you do it as a group. The Post-Test on Tetanus is due on March 2. Points = 15 Total Lecture Points = 842 Laboratory There is a lab fee of $25 for this course. If a laboratory assignment is turned in late, 10% of the grade will be taken off each day it is late. If you miss a laboratory, you will receive 0 points for that assignment unless you have a medical excuse AND discuss it with your laboratory instructor. It is possible to make up a missed laboratory in one of the other sections if you discuss it with your instructor. Laboratory Exams: Two Lab Exams, 125 points and 125 points = 250 Poster Session: = 50 The last laboratory session of the course will be a presentation of material in a Poster Session. You will prepare a poster in pairs from one scientific article. For detailed instructions, see Lab Exercise 14 Lab Exercises You are responsible for turning in material = ~114 from various exercises and your flow charts from most of the labs. Total Laboratory Points = ~414 TOTAL COURSE POINTS = ~1256 4
  • 5. BIO 107 GRADING POLICY The following is my grading policy so that there is no confusion as to how I grade. All exams are graded by an ID number so that I do not know whose exam I am grading. The purpose of using this method is so that I do not have any preconceived ideas about how people should be doing when I grade. From the beginning of the course, I guarantee that any student with: 90% or above will receive an A or A-. 80 to 89.9 B+, B or B- 70 to 79.9 C+, C or C- 60 to 69.5 D+, D or D- less than 60 F This means that if all of you are between 80 and 89.9, all students will receive a B, B+ or B-. I will NEVER up the percentage necessary for that grade. I really wish that all students in the class would attain this level or higher. I go over the scores at the end of the semester. I look at averages of the different exams, trends in scores over the years that I have taught the class, presence of graduate students in a certain area of the grade scale. It is possible that when I look at the scores at the end of the course I may lower the percentage required in each grade category. This means that 89 or 88 might become an A- or 79 or 78 might become a B-. (Over the last 8 years, the lowest percentage that became an A- was 87%. The other grade ranges were lowered consistent with that percentage.) I also try to look at exam scores for you as individuals, particularly if you are on the borderline of a grade range. I try to take into consideration if one exam was low and all others were high. A plus or minus grade will have an approximately 1.5% span. Example: C- could be 70 to 71.5%. A C+ could be78.5 to 79.9%. I do not give extra credit. Homework and laboratory assignments should receive high scores to increase your score in the course. 5 5
  • 6. Schedule of Lectures - Idealistic TEXT DATE TOPIC HANDOUT CHAPTER 1-26 Introduction 1 Basic Concepts in Immunology 2 1 1 - 31 Basic Concepts in Immunology 2 1 Antibodies, Antigens, Monoclonal Antibodies - An Parts of Introduction 3 3,4 2-2 Monoclonal Antibodies - An introduction 4 Cell Membranes and Membrane Molecules, Flow Cytometry 4 6 2-7 Innate Immunity - Complement Pathways (Turn in answers to questions on Clonal Selection article, Scientific Amer. 257:62, 1987) 5 13 2-9 Innate Immunity - The cells Video on phagocytic cells 6 1,2 2-14 (Innate Immunity - Continued) 1,2 (Turn in flow cytometry analysis information) 6 2-16 Development of Hematopoietic Cells 7A 2 Organs, Tissues and Cells of the Lymphoid System 7B 2,15 2-21 Exam 1 through Handout 6 150 points Will include at least 5 points on the tutorial on plagiarism 2-23 Organs, Tissues and Cells of the Lymphoid System 7B 2,15 Antigens and Antigenic Determinants 8 3,18 2-28 Antigens and Antigenic Determinants, Vaccines Immunoglobulin Structure and Function 8 3,18 9 4 3-2 Immunoglobulin Structure and Function (Continued) 9 4 (Turn in answers to Tetanus Problem Solving) 3-7 Immunoglobulins (continued) 9 4 3-9 Antigen-Antibody Interactions 10 6 3-14 Exam 2 through Ag-Ab interactions (Handout 10) 200 points 3-16 Variable Region Genes 11 5 3-20 Variable Region Genes (con’t) 11 5 3-23 Constant Region Immunoglobulin Genes 12 5 (Lab Exam 1 on March 21, 22, 23 through Lab 6 125 points) Spring Break - March 27 through March 31 4-4 Major Histocompatibility Complex 13 7,8 4-6 MHC (continued) 13 7,8 6
  • 7. T Cell Receptor, T cells 14 9,10 4-11 T Cell Receptor, T cells (continued) 14 9,10 4-13 Cytokines 15 10,13 4-18 Exam 3 through Handout 14 or 15 200 points 4-20 Cytokines (continued) 15 11 Cell-cell interactions 16 4-25 Cell-cell interactions (continued) 16 11 4-27 Cell mediated Immunity 17 14 5-2 Cell mediated immunity (continued) 17 14 Immunodeficiency (Lab Exam 2 on May 2, 3, 4 125 19 19 points) 5-4 Immunodeficiency 19 19 Allergy 18 16 5-9 Allergy 18 16 HIV (Poster Session - Labs on May 9,10,11) 20 19 5-11 HIV 20 19 Infection and immunity 21 17 5-16 Infection and immunity 21 17 5-19 7:15 am Friday, Final Exam (through Handout 21) 250 points 7 7
  • 8. University, College, or Department Policy Information Academic Integrity Statement “Your own commitment to learning, as evidenced by your enrollment at San Jose State University, and University’s Integrity Policy, require you to be honest in all of your academic course work. Faculty members are required to report all infractions to the office of Judicial Affairs. The policy on academic integrity can be found at: Campus policy in compliance with the Americans with Disabilities Act “If you need course adaptations or accommodations because of a disability, or if you need special arrangements in case the building must be evacuated, please make an appointment with me as soon as possible, or see me during office hours. Presidential Directive 97-03 requires that students with disabilities requesting accommodations must register with DRC to establish a record of their disability.” Department Policy on Repeating Classes Students will be allowed to repeat biology majors= classes ONLY ONCE. This includes repeating classes for Academic Renewal and repeating them at other institutions. Note that failure to successfully complete a required major’s class in the second attempt may result in disqualification from the major. Department Policy on Late Adds The Department of Biological Sciences does not approve Late Adds (adding classes after the end of the add period indicated in the schedule and directory). You are responsible for adding classes before the last day to add and for confirming via Touchtone that you are in the class. When your instructor gives you an add code, you should use it as soon as possible to avoid problems. 8
  • 9. 8 9