Applied Molecular Genetics (MBG*4240) W14

Applied Molecular Genetics (MBG*4240) W14
The lab is no place for experiments!
Objectives: In this course we will learn how to conduct complex experiments. The course provides
solid theoretical knowledge on cutting-edge techniques and methods that are used in contemporary
biology, medicine and biotechnology. In-depth understanding of these methodologies is our key
objective. We will study how to write a research proposal and how to understand, present and
criticize research at the expert level. The course will promote self-learning and team work.
Some of the techniques in this course have been studied in MBG*2040/MBG*3350/MBG4080.
These will be revisited with an emphasis on practical applications, scope, advantages and potential
flaws. Discussion of recent research papers will be used to exemplify these techniques and to achieve
profound professional level of understanding of modern technology.
Instructor:
Lectures:
Office hours:
K. Yankulov SCI3245
TTH
11:30-12:50
TTH
13:30-14:30
[email protected]
MACK115
SCI3245
ext. 56466
Important dates:
January 07
January 17
January 21
February 11
February 28
March 06
March 12
First class
Enroll for PRESENTATION or for WRITING OF A RESEARCH PROPOSAL
Assignment of presentations
Assignment of research proposals
Research Proposal due
Midterm
Peer review of research proposals due
Format: The course consists of lectures (seven modules, topics are shown below) and 9-11 original
research papers. The list of papers will be finalized on Jan. 21. These research papers will be
presented in class by your peers. You need to read and understand all these papers.
Lecture Topics
1. DNA and RNA. Hybridization techniques for the analysis of DNA and RNA. DNA and RNA
modifying enzymes. Cloning of DNA and vectors. Preparative and quantitative PCR.
2. Advanced analysis of DNA. Contemporary DNA sequencing. Epigenetics and analysis of
DNA methylation. In vitro mutagenesis. Mapping of regulatory elements on DNA. Analysis
of protein-DNA interactions. Analysis of chromatin structure.
3. Advanced analysis of RNA. RT-PCR. Microarrays. Transcriptome sequencing. Northern
blot and RNAase protection.
4. Genetic screens. Genomic and cDNA libraries. Screening of libraries. Forward and reverse
genetic screens. Examples of contemporary reverse genetic screens.
5. Generation of transgenic organisms: yeast, plants, Drosophila, mammals.
6. Recombinant proteins. Tagging and expression of cloned genes. Analysis of tagged proteins.
Functional biochemical analyses. Identification of Proteins by Mass spectrometry.
7. Selected Higher Order Techniques and Applications: Chromatin Immunoprecipitation, 3C
(Chromosome Conformation Capture). High-throughput protein arrays. Vectors for Somatic
Cell Gene Therapy.
Readings: Detailed Lecture handouts (posted on Courselink) and the original research papers are
your main source of information. There is no assigned textbook for this course. If needed, additional
reference readings for different lecture modules will be provided in class.
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TERM ASSIGNMENTS
Assignment #1 (25/100 marks): You will participate in the presentation of an original paper OR
write a research proposal. By Jan. 17 EACH OF YOU SHOULD ENROL FOR ONE OF THE TWO
OPTIONAL ASSIGNMENTS using GROUPS on the navigation bar on Courselink.
OPTION #1. Presentation of a research paper. Half of the class will form teams of three.
Each team will present one original research paper. The list of papers and detailed
instructions on this assignment are posted in Courselink. You will use GROUPS to selfenroll and select three papers from the list. You can use DISCUSSIONS to form groups. The
final selection of papers will take place in class on Jan. 21. There will be a draw if more than
one group has selected the same paper. You can also propose a paper of your choice but you
need my approval. The team will prepare a presentation (15-20 min, PowerPoint) and send
the PowerPoint file to [email protected] not later than 24 hours before the
presentation. Penalty for late submission is 2 MARKS per hour.
OPTION #2. Research proposal. Half of the class will form teams of two and will write a
research proposal on an assigned topic. Three research projects will be announced in the
beginning of the course. During the classes in the first half of the semester you need to relate
the lecture material to these projects. On Feb. 11 one of these projects will be randomly
assigned to your team. You need to go to https://www.uoguelph.ca/peartool/user/signon and
upload a PDF file of your proposal by noon on Feb. 28. After submission, your proposal
will be directed to your classmates for peer review. You will receive their comments and
marks for information only. The final mark of your proposal will be given by K. Yankulov.
Assignment #2 (10/25 marks): Peer review of the research proposals. On Feb. 28 all of you will
receive one research proposal written by your peers. By noon on March 12 you shall upload your
marks and your comments. The authors will receive your review and marks for information only.
Eventually, K.Yankulov will mark the reviews. The whole review process is completely confidential.
Midterm exam (15/100 marks): A midterm will be conducted in class on March 06. It will consist of
several multiple choice questions and 1-2 short answer questions. The final exam (50/100 marks) will
consist of several multiple choice questions and 8-10 short answer questions.
Bonus marks (maximum 5 per person). To promote discussion and focus, occasionally I would ask
questions in class. The correct answer to such questions will be awarded a bonus mark of 0.5. During
presentations of research papers you could earn 1 bonus mark if make an insightful comment or ask a
smart question that the presenters can not ask.
Evaluation
Presentation of a research paper OR writing a Research proposal
Review of research proposal
Midterm
Final exam
25 %
10%
20 %
45 %
Communication: Messages will be sent to your …@uoguelph.ca e-mail addresses as supplied by
Courselink. Failure to read and respond to these messages may preclude academic consideration.
General messages regarding class presentations, assignments etc. will be placed in Courselink NEWS.
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POLICIES
Academic Consideration: Students who are absent from classes during the term are expected to make
up for missed lectures via their own reading. Students requesting academic consideration need to
advise the course instructor in writing and provide the appropriate documentation. See
http://www.uoguelph.ca/registrar/calendars/undergraduate/current/c08/c08-ac.shtml for information on
regulations and procedures:
Use of electronic devices and recording of lectures: Electronic recording of classes is forbidden
without the consent of the instructor. When recordings are permitted they are solely for the use of the
authorized student and will not be reproduced, or transmitted to others, without the express written
consent of the instructor.
Academic Misconduct: The University of Guelph is committed to upholding the highest standards of
academic integrity and it is the responsibility of all members of the University community, faculty,
staff, and students to be aware of what constitutes academic misconduct and to do as much as possible
to prevent academic offences from occurring. University of Guelph students have the responsibility of
abiding by the University's policy on academic misconduct regardless of their location of study;
faculty, staff and students have the responsibility of supporting an environment that discourages
misconduct. Students need to remain aware that instructors have access to and the right to use
electronic and other means of detection. Please note: Whether or not a student intended to commit
academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of
assignments does not excuse students from responsibility for verifying the academic integrity of their
work before submitting it. Students who are in any doubt as to whether an action on their part could be
construed as an academic offence should consult with a faculty member or faculty advisor. The
Academic
Misconduct
Policy
is
detailed
in
the
Undergraduate
Calendar:
http://www.uoguelph.ca/registrar/calendars/undergraduate/current/c08/c08
Accessibility: The University of Guelph is committed to creating a barrier-free environment.
Providing services for students is a shared responsibility among students, faculty and administrators.
This relationship is based on respect of individual rights, the dignity of the individual and the
University community's shared commitment to an open and supportive learning environment. Students
requiring service or accommodation, whether due to an identified, ongoing disability or a short-term
disability should contact the Centre for Students with Disabilities as soon as possible.
For more information, contact CSD at 519-824-4120 ext. 56208 or email [email protected] or see the
website: http://www.csd.uoguelph.ca/csd/
Course Evaluation Information: Please refer to the Course and Instructor Evaluation Website.
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