BIOL453: IMMUNOLOGY LABORATORY        SPRING 2009

Dr. Marcia C. Coss                                                                               King Hall Room 3014
Office hours:  Mondays 4:30 – 6:00 PM or by appointment
Phone:    (703) 993-4031                                                                         E-mail: mcoss@gmu.edu

Text: Coss and Oates. 1996, Immunology Laboratory Exercises, Johnson Center Bookstore

►NOTE: The week of March 9, 2009 no labs are held – SPRING BREAK.

Occasionally, you and/or your lab partner(s) will be required to work in the laboratory between class meetings for short periods of time. The scheduling of these times will be arranged during the lab period. You are responsible for remembering to return and make your observations.

NOTE:  Attendance and prompt starting times for the Laboratory periods are very important to ensure that you will hear all the information and precautions the instructor has given. Attendance is mandatory and laboratory experiments cannot be set up at times other than already scheduled. If you are unable to attend your assigned section, contact the lab instructor to see if there is room available in the other lab sections. You may not attend a lab section you are not registered in unless the lab instructor has given permission.

I. COURSE GOALS:

• To become familiar with equipment used in today’s research and clinical laboratories
• To understand the underlying immunological principles of current laboratory techniques, both in medical/clinical and research laboratories
• To be able to analyze and interpret data generated using immunological techniques
• Improve written communication abilities while learning to write a paper in proper scientific format.

Final grade %                           TOTAL  EARNED POINTS/ 300 points

GRADING SCALE:             90-100% = A, 80-89% = B, 70-79% = C, 60-69% = D, < 60% = F

NOTE:  At the instructor’s discretion, the +/- grading system may be applied to the above grading scale.

A.   Attendance and completion of each laboratory period is worth 5 points. One point will be deducted from each exercise for each of the following infractions: 1) You are not present at the start of the lab period, 2) you are not prepared for the lab exercises  3) your lab bench is left unclean and/or equipment not put away,  4) any samples not properly labeled, 5) any samples/tests not discarded after the necessary incubation periods and 6) any noncompliance with the safety rules of the laboratory.

B.   Homework: Most labs that do not pertain to the research paper will require homework and/or an in-class assignment worth from 5-15 points (See Laboratory Schedule).  Homework consists of a combination of data analysis and written responses to questions posed in the lab manual.  NOTE: Homework assignments are due at the beginning of class the following week, unless stated otherwise in the laboratory schedule.  Homework is subject to a late penalty of one point per day.  If you miss a lab you are not allowed to turn in a homework assignment for that lab unless you have made formal arrangements with your instructor.  To receive credit for a lab, you must attend your regularly scheduled lab or make arrangements in advance to attend another lab during the same week.   

 Each student must do his/her homework individually.  Although we gather data in groups, each student must do the data analysis and written responses independently.  Violation of this rule will be considered a violation of the GMU honor code.  This applies to both the research paper and the homework. Cheating will not be tolerated and it is your duty as a GMU student to report any violations of the Honor Code to your instructor.

C. Papers:   Each student will write a short analytical review paper about an application for an immunoassay. Immunoassays are biochemical tests that rely on antibodies or other components of the immune system to bind to specific molecular structures (antigens). They have become the most commercially successful technology in diagnostics, from home pregnancy testing kits to AIDS testing.

The specific topic of the paper will change each semester and must be approved by the instructor. NOTE: HIV and pregnancy testing will not be acceptable topics for the papers.

The two drafts of the paper are worth a total of 120 points.  Each of the two drafts is worth 60 points.  Your instructor will deduct 2.5 points for each day the paper is late, including the weekends.

Your instructor will grade and return your first draft (worth 60 points) within 2-3 weeks. You will then revise the entire paper and submit it for grading on the last day of class.  The revised paper (again 2500-3000 words in length) is worth an additional 60 points.  In order to be graded, you must show that you have made a significant attempt to improve your paper and address the problems and mistakes pointed out by your instructor as graded in the first draft.  Therefore you must submit the edited first draft of the paper along with the second draft so that the instructor can compare the two versions.  Students who do not submit the first draft along with the second draft will receive a zero for the second assignment.

All papers must be submitted both electronically (please use Word) and in hard copy.  All papers will be put through plagiarism checking software.  Therefore make sure that your writing is your own.  Do not extensively quote or copy from your sources.  Do not consult with other students in the class.  Your paper should be yours and yours only.  If we find extensive plagiarism we will give you a zero on the assignment, and we reserve the option of turning your paper over to the GMU Honor Committee.

Do not take the word "draft" to mean that either assignment will not be seriously scrutinized.  This paper will be graded as if you had submitted it to a journal for publication and your instructor is an editor of that journal

            The paper accounts for 120 out of 300 points (40%) possible in lab.

                     First Draft        60 Points
                     Second Draft        60 Points
                        Total                   120 Points

III. PAPERS: Short Analytical Reviews typically deal analytically with recent developments in basic, translational and clinical interventional immunology of immediate interest to a broad range of clinical immunologists. The audience for your paper will be geared toward professionals in the field (doctors or clinicians) as well as persons, such as informed patients or first year biology students, who might not have the background of a physician.

A.  TOPIC: You will need to select an immunoassay technique to discuss in the context of a particular disease. You can either select a disease/disorder as the basis of your paper, and then discuss the pros and cons of the different types of immunoassays used, or select a specific immunoassay used to diagnose a particular disease.

For example, a general topic such as using an ELISA for HIV diagnosis could be based on the following paper: “Recombinant ORF66 and ORFK12 antigens for the detection of human herpes virus 8 antibodies in HIV-positive and -negative patients” by Yang et al. It is essential that you narrow down your topic and keep the focus of the paper on the immunoassay and not the disease. Remember that testing for HIV or pregnancy testing assays are not acceptable topics and your topic must be approved by your instructor by the fourth week of the semester (see Laboratory Schedule).

B.  FORMAT: The paper must be double-spaced and will consist of the following sections, each of which will be graded separately: 1) Title Page, 2) Abstract, 3) Introduction, 4) Methods, 5) Results, 6) Conclusions and Future Directions, and 7) References Cited.  The body of the paper (introduction, methods, results and conclusions/future directions) should be 2500-3000 words in length.  The paper should be double-spaced using a font of 10 or 12.  You will use the format for short analytical review papers published in the journal Clinical Immunology. The following is a link for these instructions which are summarized below:
http://www.elsevier.com/wps/find/journaldescription.cws_home/622806/authorinstructions

The title page (p. 1) should contain the title of your paper, your name, course name, course section, instructor's name and date submitted.

The abstract (p. 2) must be a single paragraph that summarizes the main findings of the paper. In the abstract you will attempt to condense the paper to one page in which you highlight your main points and conclusions.

The introduction should give general background to your assay, importance of assay and why we need it. This includes sufficient, basic information about the disease/disorder for the reader to understand the significance of the assay. Also you should include in this section definitions or descriptions of terminology or reagents relevant to the immunoassay. Figures can be included to assist with understanding the immunoassay. Figures should be numbered consecutively with Arabic numerals and include a figure legend. The introduction should conclude with the purpose of the paper.

Materials and methods should be taken from your primary paper that describes how the assay is carried out. There should be sufficient detail for the reader to understand how the assay is carried out but does not need to include every detail (amounts, concentrations etc unless critical for the reader to understand the assay). For example, it is not necessary to describe how a monoclonal antibody is made but it is important to understand what specific monoclonal antibody is being used.
Results should include the data generated by the authors. In this case you are to use the author’s data as your “own”. Include what you found out, what you are trying to prove and whether or not it was proven. Information regarding sensitivity, specificity etc should be included. If this is a newly developed assay then include the confirmatory data as well.

The conclusion and future directions should include a critical analysis of the topic as well as possible future directions. If you are discussing two or more assays for the same disease/disorder then compare and contrast the assays.

The literature cited (reference) section should exactly follow the format described in the Instructions to Authors for the Clinical Immunology journal and should include all papers you cited in the body of the text.  You should be making literature references in the text to any data or ideas that you gleaned from reading the literature.

You must refer to a minimum of 5 peer-reviewed papers.  You may refer to general texts and websites, but none of these will count toward the 5 peer-reviewed papers. 

References should be cited in the text by a number in brackets and listed at the end of the paper in numerical order. Abbreviations of journal names should follow the style of Chemical Abstracts Service Source Index 1985. Unpublished observations and personal communications should be cited in the text as such, and should not be included in the reference list. Please note the following examples.

[1] N. Alexis, K. Griffith, M. Almond, D.B. Peden, IL-4 induces IL-6 and signs of allergic-type inflammation in the nasal airways of nonallergic individuals, Clin. Immunol. 104 (2002) 217-220.

[2] K. Shortman, L.Wu, Thymic dendritic cells, in: M.T. Lotze, A.W. Thomson (Eds.), Dendritic Cells, Academic Press, San Diego 1998, pp. 15-28.

[3] A. Silverstein, A History of Immunology, Academic Press, San Diego, 1989.

Additional details will be discussed during the third lab period. It is strongly recommend that you contact the GMU Writing Center to ensure your spelling, grammar and references are correct.  Some websites that you might find helpful are as follows:

            GMU Writing Center:   http://writingcenter.gmu.edu/
            Council of Biology Editors: http://www.monroecc.edu/depts/library/cbe.htm

C.  Electronic submission: You must submit an electronic version to the instructor by the deadline. You will name your files as follows: email name and draft version.

Example: For a student named Iam Soconfused whose gmu email address is iamsoconf@gmul.edu, the students files would be: iamsoconfdraft.doc for the first draft and iamsoconfinal.doc for the final version.

D.  GRADING

The First and Second Drafts will be graded as follows:

                        Section                                        Points
                        Title Page & Word Count                 5
                        Abstract                                            10
                        Introduction                                     10
                        Methods                                          10
                        Results                                            10
                        Conclusion                                     10
                        Literature Cited                               5
                        Total                                                60

WRITING-INTENSIVE REQUIREMENT
This course fulfills the writing-intensive requirement for the BS degree with a Major in Medical Technology as mandated by the Faculty Senate and the GMU Board of Visitors.   It does so through a combination of homework assignments, most of which require written responses to questions posed at the end of each exercise, and through the research paper.  In the research paper you will experience the writing process in much the same way as scientists do.  That is, you iterate through several cycles of writing, criticism, and revision.
           
  Page last updated: January 24, 2009