MIMM MOLECULAR MICROBIOLOGY LAB

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McGILL UNIVERSITY DEPARTMENT OF MICROBIOLOGY AND IMMUNOLOGY MIMM 384 - MOLECULAR

1 McGILL UNIVERSITY DEPARTMENT OF MICROBIOLOGY AND IMMUNOLOGY MIMM MOLECULAR MICROBIOLOGY LAB LABORATORY MANUAL Fall 2016 Dr. Benoit Cousineau and Dr. Greg Marczynski

2 MIMM 384 MOLECULAR MICROBIOLOGY LAB This course presents the student with a series of laboratory exercises in molecular biology and microbial genetics. In addition, through a mentored term paper project, students will explore, with the guidance of a leading researcher in their fields, present- day research subjects in bacteriology, microbiology, virology, mycology, parasitology and immunology. The general objective is to provide practical and theoretical introduction to technology used in bacteriology, microbiology, virology, mycology, parasitology and immunology research. SPECIFIC OBJECTIVES By the end of this course, students will be able to: - Follow an experimental protocol. - Perform laboratory techniques commonly used in microbiology and immunology. - Design experiments with appropriate standards and controls. - Analyze properly microbiology and immunology research data. - Present research results in a clear and efficient manner. - Use a scientific approach to problem solving. - Search efficiently the scientific literature. - Analyze, interpret, summarize and clearly present scientific information. PREREQUISITES: MIMM Biology of Microorganisms, MIMM Laboratory In Microbiology COREQUISITES: MIMM Microbial Physiology and Genetics, MIMM 324 Fundamental Virology COURSE CONTENT AND INSTRUCTIONAL APPROACHES 1. Two consecutive sections of lectures and laboratory exercises - Molecular biology (labs 1-6) - Microbial genetics (labs 7-12) 2. Term Paper Project Writing of a term paper on a topic in the general area of bacteriology, virology, mycology, parasitology or immunology. Each student will be assigned a topic by a professor from the Department of Microbiology and Immunology who will supervise the writing of the term paper. TIMETABLE Mondays, 2:30-3:30 pm: Pre- Laboratory Lectures Lyman Duff Medical Building Amphitheatre. Wednesdays, 1:30-5:30 pm: Laboratory exercises Laboratory Cubicles, 4 th floor of the Lyman Duff Medical Building. days, 1:30-2:30 pm: Experimental laboratory follow- up periods (as required) Laboratory Cubicles, 4 th floor of the Lyman Duff Medical Building days, 2:30-3:30 pm: Lectures (as required) Lyman Duff Medical Building Amphitheatre. 2

3 COURSE COORDINATORS Molecular biology (labs 1-6): Prof. Benoit Cousineau Lyman Duff Medical Building, Room 617 Microbial genetics (labs 7-12): Prof. Greg Marczynski Lyman Duff Medical Building, Room 506 Term paper project: Prof. Dalius Briedis Lyman Duff Medical Building, Room 502 TEACHING ASSISTANTS (Fall 2016) Andreea Damian Shantelle Lafayette Marija Landekic Débora Vieira Parrine Sant Ana Teaching assistants can be reached by for consultation or for any other problems students may have regarding this course. LABORATORY STAFF Aghdas Zamani Richard Arthur Shan Hong Zhang 3

4 COURSE CALENDAR Fall 2016 LECTURERS: D. Briedis (DB), B. Cousineau (BC), A. Koromilas (AK), G. Marczynski (GM) DAY DATE TIME / ROOM / ACTIVITY 2 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Introduction to MIMM 384 (BC) 9 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: The Term Paper project (DB). Learn your supervisor s name. Make an arrangement to meet with him or her (by 23 Sept at the latest). Mon Wed Mon Wed Mon Wed 12 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Protein assays (BC) 14 Sept. 1:30 p.m. Laboratory cubicles Laboratory: Protein assays (BC) 16 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Endonuclease restriction analysis (BC) 19 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: On-line search of the scientific literature (DB) 21 Sept. 1:30 p.m. Laboratory cubicles Laboratory: Endonuclease restriction analysis of plasmid preparations (BC) 23 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Organizing your term paper (DB) 26 Sept. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: PCR analysis (BC) 28 Sept. 1:30 p.m. Laboratory cubicles Laboratory: PCR to determine gene orientation in plasmids (BC) 30 Sept. Mon 3 Oct. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Bacterial transformation (BC) Wed 5 Oct. 1:30 p.m. Laboratory cubicles Laboratory: Transformation of E. coli with a plasmid (BC) 7 Oct. 1:30 p.m. Laboratory cubicles: Count transformed colonies (BC) 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Purification, electrophoresis and transfer of GST fusion protein (AK) Meeting with term paper supervisor to occur 7-14 Oct. Hand in outline (10% of grade). Meetings to be scheduled by the students and supervisors. Mon 10 Oct. THANKSGIVING Wed 12 Oct. 1:30 p.m. Laboratory cubicles Laboratory: Purification, electrophoresis and transfer of GST fusion protein (AK) 14 Oct. 4

5 Mon 17 Oct. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Immunodetection of GST fusion protein (AK) Wed 19 Oct. 1:30 p.m. Laboratory cubicles Laboratory: Immunodetection of GST fusion protein (AK) 21 Oct. Mon 24 Oct. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Medical Bacteriology, Staph. & Strep. (GM) Wed 26 Oct. 1:30 p.m. Laboratory cubicles Laboratory: Staph. & Strep. (GM) 28 Oct. 1:30 p.m. Laboratory cubicles Follow-up: Staph. & Strep. (GM) Meeting with term paper supervisor to occur 28 Oct-11 Nov. Hand in paper draft (10% of grade). Meetings to be scheduled by students/supervisors. Mon 31 Oct. 2:30 p.m. Amphitheatre Lyman-Duff Lecture: Medical Bacteriology, Staph. & Strep. (GM) Wed 2 Nov. 1:30 p.m. Laboratory cubicles Laboratory: Staph. & Strep. (GM) 4 Nov. 1:30 p.m. to 3:30 p.m. To be announced Midterm exam Molecular biology section (labs 1-6) Mon 7 Nov. 2:30 p.m. Amphitheatre Lyman-Duff Wed 9 Nov. 1:30 p.m. Laboratory cubicles Follow-up: Staph. & Strep. (GM) 11 Nov. 1:30 p.m. Laboratory cubicles Mon 14 Nov. 2:30 p.m. Amphitheatre Lyman-Duff Wed 16 Nov. 1:30 p.m. Laboratory cubicles 18 Nov. 1:30 p.m. Laboratory cubicles Mon 21 Nov. 2:30 p.m. Amphitheatre Lyman-Duff Wed 23 Nov. 1:30 p.m. Laboratory cubicles 25 Nov. 1:30 p.m. Laboratory cubicles Mon 28 Nov. 2:30 p.m. Amphitheatre Lyman-Duff Wed 30 Nov. 1:30 p.m. Laboratory cubicles 2 Dec. 1:30 p.m. Laboratory cubicles Term papers need to be submitted to supervisor directly by 4:00 by hard copy or electronic as determined by supervisor. Mon 5 Dec. 2:30 p.m. Laboratory cubicles Wrap-up: Bacterial Genetics, Caulobacters (GM) 5

6 COURSE MATERIAL Required Texts The laboratory manual can be purchased at the Microbiology and Immunology Department office (Lyman Duff Medical Building, room 511) in early September. COURSE EVALUATION Laboratory reports 25% Pre- lab quizzes 5% Midterm Exam (labs 1-6) 25% Final Exam (labs 7-12) 25% Term paper 20% - Laboratory Reports: A 3- page report per laboratory session that includes purpose, introduction, result and discussion sections. Laboratory reports are due 1 week after the completion of the laboratory exercise and are jointly submitted by the laboratory partners. - Pre- Lab Quizzes: 5 short- answer type questions at the beginning of each laboratory exercise. - Midterm (Molecular biology) and Final (Microbial genetics) Exams: Two- hour written examinations. - Term paper: A 10- page review of original papers in the scientific literature on an assigned topic. Important notes: - 5% deduction will be applied for each day of late submission of the laboratory reports and term paper. - A documented excuse (e.g. Doctor s note) for missing a lab session or an exam should be submitted to the course coordinator. The mark for a missed lab session or exam without a documented excuse is zero. Note regarding missed laboratory exercise: As the material in all the laboratory exercises will be covered on the exams, it is strongly recommended that you obtain the data for any missed exercise from your laboratory partner and that you also contribute to the writing of the laboratory report. This will ensure that you understand the scientific principles, technical details and logical analysis of this exercise for the exams. 6

7 MCGILL UNIVERSITY POLICY STATEMENTS 1) McGill University values academic integrity. Therefore all students must understand the meaning and consequences of cheating, plagiarism and other academic offences under the Code of Student Conduct and Disciplinary Procedures (see for more information). L'université McGill attache une haute importance à l honnêteté académique. Il incombe par conséquent à tous les étudiants de comprendre ce que l'on entend par tricherie, plagiat et autres infractions académiques, ainsi que les conséquences que peuvent avoir de telles actions, selon le Code de conduite de l'étudiant et des procédures disciplinaires (pour de plus amples renseignements, veuillez consulter le site 2) In accord with McGill University s Charter of Student s Rights, students in this course have the right to submit in English or in French any written work that is to be graded. Conformément à la charte des droits de l étudiant de l Université McGill, chaque étudiant a le droit de soumettre en français ou en anglais tout travail écrit devant être noté (sauf dans les cours dont l un des objets est la maîtrise d une langue). 3) In the event of extraordinary circumstances beyond the University s control, the content and/or evaluation scheme in this course is subject to change. 4) McGill has policies on sustainability, paper use and other initiatives to promote a culture of sustainability at McGill. 5) If you have a disability please contact the instructor to arrange a time to discuss your situation. It would be helpful if you contact the Office for Students with Disabilities at before you do this. 6) Instructor generated course materials (e.g., handouts, notes, summaries, exam questions, etc.) are protected by law and may not be copied or distributed in any form or in any medium without explicit permission of the instructor. Note that infringements of copyright can be subjected to follow up by the University under the Code of Student Conduct and Disciplinary Procedures. 7) End-of-course evaluations are one of the ways that McGill works toward maintaining and improving the quality of courses and the student s learning experience. You will be notified by when the evaluations are available on Mercury, the online course evaluation system. Please note that a minimum number of responses must be received for results to be available to students. 8) Additional policies governing academic issues which affect students can be found in the McGill Charter of Students Rights and Responsibilities ( Rights-and-Responsibilities-2010.pdf). 7

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