Biology 4583F: Molecular Genetics Laboratory

Contact Information:
Instructor - Prof. Shiva M. Singh, WSC 307, x83135, ssingh@uwo.ca
Lab Supervisor – Kim Loney, BGS 3070, x81322, kgrant4@uwo.ca

Background and objectives

Inspiring progress in the field of genetics and associated technologies have offered extraordinary insights into
biological complexity from molecular and cellular to populations and evolution, and unified biology. These
developments have changed the way problems are approached in such diverse areas as agriculture,
biotechnology, environment, evolution, forensics, medicine, pharmaceuticals and reproductive biology. They
have begun to generate ever increasing number of complete genome sequences and help develop genomic
methods for a variety of uses and applications. The scope of the genomic industry doubles every five years,
driven by the discovery of new genomic concepts and development of innovative genetic technologies. These
technologies will form the focus of this course. Specifically, it will focus on methods and approaches used in the
study of DNA (genome, including epigenome) and RNA (transcriptome). Specifically, the technologies covered
will provide hands on and individualized experience in the form of following three modules:

1) Epigenetics and DNA methylation

2) Gene expression patterns (from whole genome to single genes)
3) Genome editing with CRISPR/Cas systems

Prerequisite
Unless you have either the prerequisites for this course or written special permission from your Dean to enroll in
it, you may be removed from this course and it will be deleted from your record. This decision may not be
appealed. You will receive no adjustment to your fees in the event that you are dropped from a course for failing
to have the necessary prerequisites. The prerequisite for this class is a minimum mark of 70% in each of Biology
3596A/B and 1.0 course from: Biology 3466B, 3592A, 3593B, 3594A, 3595A, 3597A/B; and registration in
year 4 of an Honors Specialization in Genetics or permission of the Instructor and/or Genetics Undergraduate
Coordinator.

Course Format
This is a laboratory course. The emphasis is given to hands-on experience.
Four hours/week are devoted to this course (1 tutorial hour, 3 lab hours)
Lab sections: Monday, Tuesday, and Wednesday 1:30 to 4:30 pm (BGS 3065). Students will attend their own
section, one day per week
Tutorial hour: Thursdays 2:30 – 3:30 pm in P&AB 106. Tutorial/discussion hour (as appropriate) will include
conceptual and technical background beyond what is covered in the lab. This material is testable.

Required Materials
Laboratory outlines, protocols and associated readings will all be posted to the course site on OWL. You must
also provide your own hard-bound lab book as well as lab coat and safety glasses.

Course Communication
Announcements will be frequently posted to the OWL website (with an email notification), so please check
regularly. Questions can be directed in-person or through email to the teaching assistants, lab supervisor, or
course instructor. Please make sure to use your Western email account.

1
Methods of evaluation

Category Percent of
Final Grade
Project 1 Report 20%
Project 2 Report 20%
Project 3 Poster Presentation 20%
Assignments (3 in total, 5% each) 15%
Lab Book 10%
Lab Quiz (3 in total) 10%
Lab performance and participation 5%

Lab performance and participation (5%)

Your participation mark is based on your punctuality/presence in tutorials and labs, pre-lab preparation
for lab exercises, interpersonal skills, polite & courteous behavior towards others (teaching assistants
and classmates), contribution to class discussions, and compliance with WHMIS. Each lab will be
worth a total of 0.5% (x 10 labs = 5%)

Lab assignments (15%)

Each project will have a corresponding assignment that will test your ability to follow lab protocols,
background theory, and their application in solving genetic problems related to the project material.

Lab book (10%)

Every student will work on an individual basis. A detailed record of your lab experiments will be
documented in a bound book. This lab book serves as the single most valuable resource and reference
for the activity during the course. A properly maintained lab book helps recall important information
that would otherwise be lost. Your lab book will:
 be up-to-date and neat, but NOT rewritten prior to submission
 have numbered pages
 have a table of contents at the beginning of the book
 have all techniques clearly outlined prior to your arrival to the lab
 outline the weekly purpose of the lab, results, interpretation and discussion
 have formulae, graphs, pictures etc. included in the appropriate week’s lab. Any references that
were used should also be noted.
The lab books will be evaluated at the end of the term. Your lab book may be checked during your lab
to ensure that it is up-to-date.

Lab reports/presentations (60%)

You are required to prepare two lab reports and one poster presentation. All detailed guidelines to
preparation of the lab reports and poster will be posted on OWL.
i. Reports: Will be written in the form of a research article containing abstract, introduction,
methods, results, discussion, conclusion and references. It will be based on your own work in
the labs. This exercise will teach you how to present your own research work to the scientific
community in written form, review scientific literature to better understand the genetic concepts
involved, and discuss genetic techniques in light of real-life biological problems.
ii. Poster presentation: Will take place during the last week of classes in your assigned lab time.
Each individual is responsible for preparing a poster. This format will give you experience in
presenting data in poster format and discussing its contents and fielding questions through face-
to-face contact with observers, which is common practice at research conferences. Posters will
be evaluated by Dr. Singh and TAs (50%) as well as by peers (50%).

2
Lab Quiz (10%)
Lab quizzes will be conducted by the Instructor during the last week of each of the three
modules/projects during the lab period (see schedule). It will cover methods being used, special caution,
trouble shooting, problem solving and potential applications of the technology being worked on.
Quizzes will be administered in informal one-on-one conversation style with the Instructor at the bench.

Note on evaluation: Scholastic offences are taken seriously and students are directed to read the
appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at this website:
http:// www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf.

Course materials
Lab manuals, tutorial/lectures, assignments and reading materials will be available on OWL
(https://owl.uwo.ca). Students are responsible for checking OWL on a regular basis for news and updates. This
is the primary method by which information will be disseminated to all students in the class.

Lab Attire/Safety
All students in the lab are required to wear appropriate lab attire at all times. This includes lab coat, safety
glasses, long pants, closed-toed shoes and gloves (as necessary). Long hair should be tied back. Those with
prescription glasses are still required to wear appropriate safety glasses or goggles to fit over top.

Accessibility
Please contact the course instructor if you require lecture or printed material in an alternate format or if any
other arrangements can make this course more accessible to you. You may also wish to contact Services for
Students with Disabilities (SSD) at 661-2111 ext. 82147 if you have questions regarding accommodation. The
policy on accommodation for students with disabilities can be found at
www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_disabilities.pdf

Missed Course Components

If you are unable to meet a course requirement due to illness or other serious circumstances, you must provide
valid medical or supporting documentation to the Academic Counselling Office of your home faculty as soon as
possible. If you are a Science student, the Academic Counselling Office of the Faculty of Science is located in
WSC 140, and can be contacted at 519-661-3040 or scibmsac@uwo.ca. Their website is
http://www.uwo.ca/sci/undergrad/academic_counselling/index.html.
 The policy for accommodation for religious holidays can be found at
www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf.
 A student requiring academic accommodation due to illness must use the Student Medical Certificate
(https://studentservices.uwo.ca/secure/medical_document.pdf) when visiting an
off-campus medical facility. For further information, please consult the university’s medical illness
policy at http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_illness.pdf

Absence from lab (prior knowledge or sudden event):

Prior to the missed lab, the student is to immediately inform Prof. Singh or Kim Loney by email of their
expected absence and schedule into another lab section during the same week. Due to the nature of the lab
experiments and time constraints a lab CANNOT be repeated after the designated week is over. Missed
labs will be reflected on your participation and assignment marks.
Absence or late submission of labs, assignment or reports/presentations due to non-medical issue will be
dealt with on individual basis that may include a grade of zero.

It is imperative that you come to each lab fully prepared. Each week’s result is dependent on the previous
week’s result, so it is necessary that you complete all your work in the lab in order to move on to the next step.
The course may occasionally require that you perform some procedures outside of your designated lab time to
maintain the continuity of the experimental process. “Behind the scenes prep work” will be kept to a minimum
so you can follow the experiment from start to finish.
3
Course Content:

 Orientation to B4583F lab, lab safety, and WHMIS

__________________________________________________________________________________________

Project 1: Epigenetics and DNA methylation

Investigation of DNA methylation in the promoter region of the Mus Musculus gene Hnf1a (hepatic nuclear
factor 1 homeobox alpha) using two different molecular methods and bioinformatics techniques
 Isolation of DNA from mouse liver/brain tissues – Lab 1
 Check quality/quantity of DNA – Lab 2
 Use two methods to determine methylation:
1:Methylation-sensitive restriction digestion 2:Sodium bisulfite
- Enzyme Digestion (Lab 2) - sodium bisulfite conversion (Lab 2)
- Purify DNA (Lab 3) - PCR on converted DNA (Lab 3)
- Diagnostic PCR (Lab 3) - Agarose gel electrophoresis (Lab 4)
- Electrophoresis of PCR (Lab 4) - Isolation of band of interest (Lab 4)
- Bioinformatics (Lab 4) - Purification of DNA from gel (Lab 4)
- Sequencing & Bioinformatics
 Lab report due October 20
______________________________________________________________________

Project 2: Gene expression patterns from the whole genome to single genes

Part a) Bioinformatic analysis of microarray data using Partek Genomics Suite software.
 Identifying differences in whole genome expression between treatment groups. (Lab 5)
 Identify relevant gene pathways and functions using Partek Pathway and Gene Ontology (Lab 6)
Part b) Validation of high throughput experimental results using semi-quantitative RT-PCR and qPCR
 Multiplex semi-quantitative RT-PCR & demo of qPCR (Lab 7)
 Polyacrylamide gel electrophoresis & band quantification (Lab 8)
 Lab report due November 10
__________________________________________________________________________________________

Project 3: Genome editing using CRISPR/Cas systems

Mutation of the CAN1 gene in Saccharomyces cerevisiae using RNA-guided endonuclease activity of
CRISP/Cas technology
 Transformation of yeast with gRNA plasmid (Lab 8)
 Galactose induction of Cas9 (Lab 9)
 Observe mutant colonies and select colonies for DNA isolation (Lab 10)
 PCR amplify CAN1 gene (Lab 10)
 Run CAN1 PCR products on agarose gel and isolate DNA to be sent for sequencing (Lab 11)
 Use bioinformatics to determine where mutation is located.
 Poster Presentation – December 5, 6, 7
__________________________________________________________________________________________

4
Important Due Dates

Due Location
Project 1 Assignment September 29 Tutorial
Project 1 Report October 20 Tutorial
Project 2 Assignment October 26, by 1:30pm Lab or BGS 3070
Project 2 Report November 10 Tutorial
Project 3 Assignment November 24 Tutorial
Project 3 Poster presentations December 5, 6, 7 Lab
Lab Book Hand-In By 4:30pm on Dec. 7 Lab

Support Services
 Learning-skills counsellors at the Student Development Centre (http://www.sdc.uwo.ca)are ready to
help you improve your learning skills. They offer presentations on strategies for improving time
management, multiple-choice exam preparation/writing, textbook reading, and more. Individual support
is offered throughout the Fall/Winter terms in the drop-in Learning Help Centre, and year-round through
individual counselling.
 Students who are in emotional/mental distress should refer to Mental Health@Western
(http://www.health.uwo.ca/mental_health) for a complete list of options about how to obtain help.
 Additional student-run support services are offered by the USC, http://westernusc.ca/services.
 The website for Registrar Services is http://www.registrar.uwo.ca.

Support from Science Student Donation

This course is supported by the Science Student Donation Fund. If you are a BSc or BMSc student registered in the Faculty of Science or
Schulich School of Medicine and Dentistry, you pay the Science Student Donation Fee. This fee contributes to the Science Student
Donation Fund, which is administered by the Science Student Council (SSC). A number of grants from this Fund have allowed for the
purchase of equipment integral to teaching of this course. You may opt out of the Fee by the end of September of each academic year by
completing paperwork in the Faculty of Science’s Academic Counselling Office. For further information on the process of awarding
grants from the Fund or how these grants have benefitted undergraduate education in this course, consult the chair of the department or
email the Science Student Council at ssc@uwo.ca.