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BIOL671: Molecular and Immunological Techniques (MIT) Course Syllabus for Spring 2013 Course instructors: David T.

Gauthier, Ph.D Office: MGB 202E Telephone: (757) 683-3822 e-mail: dgauthie@odu.edu Office hours: by appointment Credits: 4 Course location and schedule: Lecture/Laboratory:

M 1300-1700, W 1300-1800 MGB249 (wetlab/lecture) or BAL1013C (computer lab)

Course objectives: In this course, students will learn fundamental skills and techniques of molecular biology and immunology. Molecular techniques will include DNA extraction, Polymerase Chain Reaction (PCR), cloning, and DNA sequencing (Sanger dideoxy and next-generation methods). Additionally, students will learn basic skills in bioinformatics, including sequence alignment, primer design, searching of sequence databases, and assay design. The Geneious (Biomatters Ltd., New Zealand) bioinformatics suite will be the primary software tool used in the course, but students will be exposed to other, web- and Unix-based software packages. All techniques taught in Molecular and Immunology portions of the course lay the foundations for more complex, specialized techniques that students will use in their future research. A major portion of this course will be a specialized group project. The instructor will provide ideas for projects at the beginning of the course, and students are encouraged to change/modify projects with discussion with the rest of the class and instructor. Projects are subject to instructor approval and logistic/expense limitations, but the goal is to generate a substantive, creative inquiry that approaches a real-world question or problem. Communication: The course instructor will be communicating with students via Blackboard and student email. Students are responsible for regularly checking Blackboard for course announcements, and are responsible for all information conveyed thereby. Honor code: By enrolling in this course, you are agreeing to abide by the University Honor Code. Information about the University Honor Code, including explicit definitions of various forms of cheating including plagiarism and unauthorized collaboration, is available at: http://orgs.odu.edu/hc/pages/Honor_Code.shtml. You are responsible for reading and understanding this material. Cheating in any form will not be tolerated during this course. Any instances of cheating will be referred to the Office of Student Judicial Affairs, and grade sanctions will be imposed up to and including failure of the course.

Attendance: This is primarily a laboratory course, and every lab session will build on the one previous. Therefore, it is extremely important that you attend every laboratory session, and I will be taking attendance. As each laboratory session is 4-5 hr. long, students making up laboratory activities create serious difficulties for the course instructor. Therefore, I will not offer the opportunity to make up lab sessions unless I am notified of the absence a) at least three calendar days in advance, or b) you have a signed doctors note or other official excuse for why you were absent. Laboratory sessions will start at 1300 sharp. You are expected to be present and ready to work at that time. Up to 50 points will be given at the instructors discretion for attendance and participation in discussions. Electronic devices and food: Laptops are welcome in the class, and I encourage you to play with the software packages we use in the computer lab on your own computers. It is expected that laptops are being used at all times (except during breaks) for class-related purposes. Talking on cell phones, texting, etc. during class or in labs is expressly prohibited. Electronic devices of any kind are prohibited during practical exams or quizzes, unless specifically indicated otherwise by the instructor. All food/drink is expressly prohibited within MGB249 and within the BAL computer lab. Assignments/class projects: Course grades will be determined on the basis of exams, group exercises, individual methods presentations, and a group project including presentation of results. Unless otherwise arranged, late assignments will be penalized 10% per day. Exams: Exams will include multiple choice and short answer, and will be designed to reinforce concepts taught in the course. Three in-class, closed book exams will be given during the course. Methods presentations: Students, working individually, will each be assigned a molecular or immunological method. Students will prepare a 12 minute PowerPoint presentation explaining a) the method, b) its uses/application, and c) advantages and drawbacks compared to similar methods. At least 3 minutes will be left for questions from the instructor and class. Group projects: A major activity in this course will be the completion of group projects. These are intended to be real-world projects, rather than canned laboratory exercises, and will require critical thought and creativity on the part of students. Projects are to be performed with guidance of the instructor, and written up as a Short Communication style publication. This Short Communication must include 1) a title and author page, 2) an abstract (<200 words), 3) an Introduction presenting background literature and the purpose of the study, 4) Materials and Methods, 5) Results, 6) Discussion of results, 7) Literature Cited, and 8) Figures and Tables. Items 3)-6) should be no more than 10 manuscript pages in length. Figures and Tables must be original, include a fully explanatory legend, and be referenced in the text. Only include Tables and Figures directly relevant to the presented results. Formatting should be as follows: 1.5 spacing,

Times New Roman 12 pt. font, 1 inch margins, left-justified. Format of bibliography and in-text citations can follow the journal of your choice, but must be consistent and correct. Textbook and equipment: No textbook is assigned for this course. Appropriate readings will be provided by the instructor. Laboratory notebooks: You will need a laboratory notebook for this course. It must follow these rules: Permanently Bound Notebook (spiral notebooks and 3 ring binders are NOT acceptable) Labeled with your name, email address, class name If pages are not numbered, be sure to number them (usually in the top corner at the edge of the page) Write in blue or black ink only Never, under any circumstance, should you remove a page. This rule is to prevent unscrupulous researchers from "losing" data that might not have been favorable to their research objectives. If you rip out some pages you thought were unnecessary, colleagues might view the gaps as suspicious. Mistakes are to be crossed out but left on the page. The mistake must remain visible/legible. Write legibly! Your notebook does not have to be a work of art, but it should be easily readable by another scientist. Do not work on scratch paper, then transfer your notes to your notebook. All work should be done in the notebook. Evaluation and grading: Your overall grade will be based on the following: Attendance and participation Exams (3 50 pt.) Methods presentation Group project and presentation 100 pt. 150 pt. 100 pt. 200 pt. 550 pt.

Letter grades will be assigned on the following scale: 93.0-100%=A; 90.0-92.9%=A-; 87.089.9%=B+; 83.0-86.9%=B; 80.0%-82.9%=B-; 77.0-79.9%=C+; 73.0-76.9%=C; 70.0%-72.9%C-; <60%=F. There will not be a curve. Exams, attendance/participation, and methods presentations will be graded on an individual basis. A single score will be given to student teams for exercises and Group project/presentations. Concerns about group dynamics and scoring should be brought to the attention of the instructor. Paper discussions: At least once per month, we will discuss a technique-intensive paper from the primary literature. You will be given this paper at least one week in advance of discussion. We will discuss the paper in class, and all students are expected to make a substantive contribution to the discussion.

Conflict resolution: The course instructor will make every effort to resolve conflicts or difficulties in a timely and fair manner. Issues that cannot be resolved by discussions with Dr. Gauthier should be brought to the attention of the Biological Sciences department chair, Dr. Wayne Hynes. Changes to course schedule and/or content: The instructor reserves the right to make appropriate changes to the course schedule and/or content following timely notification of students.

Lecture/Laboratory schedule: *note: This syllabus schedule is subject to change as group projects take shape. 1 (M; 1/14) 2 (W; 1/16) (M; 1/21) 3 (W; 1/23) No class, instructor will be absent Course introduction; Safety briefing; Pipetting laboratory; Intro to projects MLK Holiday, no class Begin extraction of animal tissue with silica column; DNA extraction (lecture); Finish DNA column-based extractions, spectrophotometric analysis of DNA yield and purity; Paper discussion #1 Polymerase Chain Reaction (PCR; lecture); Set up PCR reactions to amplify extracted DNA Gel electrophoresis; Electrophorese and analyze PCR reactions from Day 4; Real-time PCR (lecture); SybrGreen real-time PCR Exam 1; TA cloning (lecture); DNA sequencing (lecture); perform ligations and transformations E. coli must be restreaked from colonies M13 amplifications of cloned products from restreaks; electrophoresis of M13 products, PCR product cleanup for sequencing; Next-Gen sequencing (lecture) DNA sequencing reactions; load sequencer; Discussion of group projects Recommended goal: Literature search and initial plan for group project Intro to Geneious (BAL); Analysis of chromatograms; sequence alignment and assembly; BLAST searching; intro to phylogenetic analysis (BAL) Design of PCR assays; primer and probe design; Paper discussion #2 Breakout session for group projects Group project work

4 (M; 1/28)

5 (W; 1/30)

6 (M; 2/4)

(T; 2/5) 7 (W; 2/6)

8 (M; 2/11)

9 (W; 2/13)

10 (M; 2/18) 11 (W; 2/20) 12 (M; 2/25)

13 (W; 2/27)

Exam 2; In situ hybridization (lecture/lab); Fluorescence and confocal microscopy (lecture); Group project work Recommended goal: Initial experiments (preliminary data) and plan for next step. Completion of a draft Introduction. Introduction to the Unix command line; de novo assembly of next-gen data (BAL) Reference assembly of next-gen data with SHrIMP2; intro to comparative genomics (BAL) Spring Break, no class Quantifying proteins: Bradford assay; Group Project work Detecting antibody and antigen: ELISA lab; Paper Discussion #3 Protein extraction and SDS-PAGE separation of proteins; Group project work Exam 3; Analysis of SDS-PAGE gels and western blotting of proteins; Group project work Recommended goal: Final experiments in planning stage. Begin outlining remaining paper sections. Immunodetection of protein on western blot membrane; Group project work TBA TBA TBA TBA; Paper discussion #4 Methods presentations Methods presentations Project presentation and discussion Project presentation and discussion; Short Communications are due to instructor no later than 5pm.

14 (M; 3/4)

16 (W; 3/6)

(MW; 3/11, 3/16) 17 (M; 3/18) 18 (W; 3/20) 19 (M; 3/25)

20 (W; 3/27)

21 (M; 4/1)

22 (W; 4/3) 23 (M; 4/8) 23 (W; 4/10) 24 (M; 4/15) 25 (W; 4/17) 26 (M; 4/22) 27 (W; 4/24) 28 (M; 4/29)