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University of Alberta
BIOL 392/592
SEM B1, LAB H1
Winter Term 2013
Instructor:
Office:
Phone:
E-mail:
Dr. David Coltman
CCIS2 5-065
(780) 492-7255
dcoltman@ualberta.ca.
Instructor:
Office:
Phone:
E-mail:
Dr. Corey Davis
CCIS2 5-009
(780) 248-1099
cordavis@ualberta.ca.
Teaching Assistant: Joshua (Josh) Miller
Office:
CCIS2 5-010
E-mail:
jmm1@ualberta.ca
Office Hours: By appointment only
Lecture Room & Time: SEM B1; BS M 557 1:00-1:50 PM Wed
LAB H1; BS M 557 2:00-4:50 PM Wed, Thu
Course Description: A laboratory course introducing students to current molecular
biology techniques and associated analyses used to study population genetics,
systematics, and evolutionary biology in natural populations. Students will develop
microsatellite marker systems and use them to examine the genetic structure of a natural
population. A comparative bioinformatic approach will be used to generate sequence data
to investigate the use of single nucleotide polymorphisms in candidate gene analysis and
in phylogenetic inference. Prerequisite: BIOL 207, 208 and consent of instructor,
corequisite: BIOL 380. Note: BIOL 392 and 592 cannot both be taken for credit.
Course Prerequisites: Prerequisite: BIOL 207, 208 and consent of instructor,
corequisite: BIOL 380. It is important to prepare yourself for this course through a review
of the prerequisite material. Students who do not have the required prerequisites at the
time of taking this course should not expect supplementary professorial tutoring from the
instructor.
Course Objectives and Expected Learning Outcomes: In Biology 392/592 students
will be introduced to the basic theoretical and experimental techniques used in the study
of molecular ecology. Students will learn the theory and techniques required to develop a
DNA based marker system and use the system to investigate population structure in a
natural population. In addition, students will generate single gene sequence and will type
gene based SNP markers for use in genetic association analysis.
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The Projects: The course is divided into four components. In the first section, students
will develop microsatellite markers by building an STR (short tandem repeat) enriched
genomic library. This section will introduce students to common molecular biology
techniques including; genomic DNA isolation, DNA quantification, enzymatic reactions,
agarose gel electrophoresis, culturing bacteria and sterile technique, plasmid isolation,
PCR, hybridization, ligation, transformation, library screening, and sequencing.
During the second component students will use developed microsatellite markers to
genotype individuals from a natural population. The data generated will be used to
demonstrate basic population genetic analysis techniques.
The third laboratory component will involve using comparative genomics to generate
sequence of a gene to facilitate SNP discovery.
Component four will consist of SNP genotyping and basic theoretical analysis techniques
for association analysis.
Week
Laboratory Schedule:
Date
Day Tasks
1
1
2
Jan 9
Jan 10
Jan 16
1
2
1
2
Jan 17
2
3
Jan 23
1
3
Jan 24
2
4
Jan 30
1
4
Jan 31
2
Pipetting exercise, Start genomic DNA isolation
Complete genomic DNA isolation
DNA quantification
Restriction enzyme digestion of genomic DNA
Prepare and plate dilution series of DH5, Streak out DH5
(pBS II SK+)
Mungbean nuclease and Antarctic phosphatase treatment of
genomic DNA
Ligate linkers to processed genomic DNA
Test PCR of linker ligation
Agarose gel preparation
Set up overnight culture of DH5 (pBS II SK+)
Agarose gel electrophoresis of genomic DNA, ligations and
test PCR
Prepare “binding and washing (B&W) buffer”
pBS II SK+ plasmid isolation, quantification, and restriction
digestion
Enrichment hybridization (to be set up on Tuesday January
31)
Biotin bead attachment and hybridization washes
Enrichment PCR
Linker digestion of amplified enriched genomic DNA
Prepare LB-Amp, X-gal, IPTG plates
Agarose gel preparation
3
5
Feb 6
1
5
Feb 7
2
6
Feb 13
1
6
Feb 14
2
7
8
Feb 18-22
Feb 27
1
8
Feb 28
2
9
9
10
10
11
Mar 6
Mar 7
Mar 13
Mar 14
Mar 20
1
2
1
2
1
11
12
Mar 21
Mar 27
2
1
12
13
13
14
Mar 28
Apr 3
Apr 4
Apr 10
2
1
2
Agarose gel electrophoresis of pBS II SK+ and amplified,
digested, enriched genomic DNA
Ligation of amplified, digested, enriched genomic DNA into
pBS II SK+
Set up overnight culture of DH5
Preparation of competent cells
Plate genomic/plasmid ligations and controls
Pick colonies and amplify inserts by “colony PCR”
Pour agarose gel
MIDTERM LAB EXAM
Agarose gel electrophoresis of “colony PCR”
Gel purification of inserts
Set up sequencing reactions
READING WEEK – NO LABS
Set up small scale genomic DNA isolations
Microsatellite sequence analysis and primer design –
COMPUTER LAB
Complete small scale genomic DNA isolations
Microsatellite PCR
Capillary electrophoresis of microsatellite PCR
Microsatellite genotyping – COMPUTER LAB
Analysis of microsatellite data – COMPUTER LAB
392 Open Lab, 592 Assignment
Candidate gene selection, comparative genomics, NCBI
(Genbank), CATS primer design – COMPUTER LAB
Single Gene sequencing
ASSIGNMENT 1 DUE
Single gene sequencing
Sequence analysis, SNP discovery, SNP assay design –
COMPUTER LAB
SNaPshot reactions
392 Open Lab, 592 Assignment
SNP genotyping – COMPUTER LAB
SNP typing and analysis – COMPUTER LAB
FINAL LAB EXAM, ASSIGNMENT 2 DUE
Required Textbook: none
Recommended or Optional Learning Resources: copies of
Sambrook et al., Molecular Cloning, a laboratory manual 2nd Ed. and 3rd Ed.
Ausubel et al., Current protocols in molecular biology are available in the lab as references.
Past Evaluative Material:
Examples of Past exams will be posted on the class website.
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Grade Evaluation:
The University of Alberta uses a letter grading system with a four-point scale of
numerical equivalents for calculating grade point averages. BIOL392 and BIOL592 are
graded separately based on the GFC suggested distribution of grades in undergraduate
(3rd year) and 500 level courses respectively.
Task
Primer Note
Assignment #1
Assignment #2
Midterm lab exam
Final lab exam
*Practical assessment
392
n/a
17.5%
17.5%
20%
25%
20%
592
15%
10%
10%
20%
25%
20%
Due Date
April 15, 2013
March 20, 2013
April 10, 2013
February 13, 2013
April 10, 2013
Throughout
Comments
See below
Microsatellite analysis
Association analysis
Weeks 1-5
Weeks 6-13
See below
* Practical assessment will include assessment of your laboratory notebook, organization skills
and time management, self-sufficiency, cleanliness, how carefully and successfully you carry
out the exercises, how safely you work, and how well you cooperate with others in the lab.
 Students registered in Biology 592 will be required to write a draft manuscript in the format of
a “Molecular Ecology Resources” permanent genetic resource note. Primers designed from
clone sequences generated during library cloning will be used to assess genetic variation in the
species used for cloning (focal species) and closely related species (cross species amplification).
Data generated from these primer tests will be used to write a primer note.
Students will be required to perform additional laboratory work that will be completed
under the instruction of the teaching staff. This additional lab time will be performed on
March 14th, March 28th.
Note: Grades are unofficial until approved by the Department and/or Faculty offering the
course.
Format of Exams:
Midterm and final exams will be a combination of multiple choice and short answer
questions.
Missed Term Exams and Assignments:
A student who cannot attend a laboratory period, write a midterm or final laboratory
examination or complete a term assignment due to incapacitating illness, severe domestic
affliction or other compelling reasons can discuss these reason with the instructor(s) to
determine if it is appropriate to apply for a deferred examination, deferral of the midterm
weight to the final laboratory examination, extension of time to complete an assignment
or participate in a make-up mock laboratory.
Deferral of term work is a priviledge and not a right; there is no guarantee that a deferral
will be granted. Misrepresentation of Facts to gain a deferral is a serious breach of the
Code of Student Behaviour.
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Deffered midterm examinations will be held on Monday February 25th 2013.
Deffered final examinations will be held on Friday April 26th, 2013.
Student Responsibilities:
ACADEMIC INTEGRITY: ‘The University of Alberta is committed to the highest
standards of academic integrity and honesty. Students are expected to be familiar with
these standards regarding academic honesty and to uphold the policies of the University
in this respect. Students are particularly urged to familiarize themselves with the
provisions of the Code of Student Behaviour (online at
www.ualberta.ca/secretariat/appeals.htm) and avoid any behaviour which could
potentially result in suspicions of cheating, plagiarism, misrepresentation of facts and/or
participation in an offence. Academic dishonesty is a serious offence and can result in
suspension or expulsion from the University.’
All forms of dishonesty are unacceptable at the University. Any offense will be reported
to the Senior Associate Dean of Science who will determine the disciplinary action to be
taken. Cheating, plagiarism and misrepresentation of facts are serious offenses. Anyone
who engages in these practices will receive at minimum a grade of zero for the exam or
paper in question and no opportunity will be given to replace the grade or redistribute the
weights. As well, in the Faculty of Science the sanction for cheating on any examination
will include a disciplinary failing grade (no exceptions) and senior students should
expect a period of suspension or expulsion from the University of Alberta
CELL PHONES: Cell phones are to be turned off during lectures, labs and seminars.
Cell phones are not to be used during exams
STUDENTS WITH DISABILITIES: Students who require accommodation in this
course due to a disability are advised to discuss their needs with Specialized Support &
Disability Services (2-800 Students’ Union Building).
ACADEMIC SUPPORT CENTRE: Students who require additional help in
developing strategies for better time management, study skills or examination skills
should contact the Academic Support Centre (2-703 Students’ Union Building).
Policy about course outlines can be found in section 23.4(2) of the University Calendar.
Disclaimer: Any typographical errors in this Course Outline are subject to change and
will be announced in class. The date of the final examination is set by the Registrar and
takes precedence over the final examination date reported in this syllabus.
Note: Recording is permitted only with the prior written consent of the professor or if
recording is part of an approved accommodation plan.