Genome Organization, Mutageneis and DNA Repair

Biology 3594A
Fall 2016

This course will cover concepts related to DNA organization, replication, mutagenesis and repair in
both prokaryotic and eukaryotic organisms. Lecture topics will include current literature in DNA
mutagenesis and repair designed to permit direct examination of concepts, experimental design,
methodology, data analysis and future trends.

Prerequisites: Biochemistry 2280A; Biology 2581B

Instructor: Dr. Patrick McDonald (pmcdona5@uwo.ca)

Assistant Professor, Department of Biology

Office: Collip room 209

Office Hour - Wednesday 10:30 – 11:30 am

Lectures: Tuesday and Thursday 12:30 – 1:20 pm (P&AB-106)

Lecture slides will be posted on OWL

Tutorials: Monday 1:30 – 2:20 pm (B&GS-1056)

Thursday 2:30 – 3:20 pm (P&AB-150)

Teaching Assistants: Mandana Miri (smiri3@uwo.ca)

Keegan Leckie (kleckie3@uwo.ca)

OWL site: http://owl.uwo.ca will be the central location for materials relating to Bio3594A. The
OWL forum is the primary location for students to ask questions about the course
and lecture material. Students are responsible for checking OWL on a regular basis.

Course Evaluation:
Poster Presentation 10% Due: October 6
Mutation Report 10% Due: October 13
Mutation Science Blog (Mutablog) 10% Due: November 3
Term Paper (Science Perspectives) 20% Due: November 22
Final Exam 40% December Exam Period
Participation 10%
– 3% attending appointment at Writing Support Centre
– 2% tutorial participation (Research Proposal)
– 1% term paper topic submission
– 4% attendance
Course Description:
This course is designed to build upon principles and concepts covered in Introductory Genetics
Biology 2581b. In 2016, Biology 3594a will cover concepts related to DNA organization,
replication, mutagenesis and repair in viral, prokaryotic and eukaryotic organisms. Lecture topics
will use primary research articles to present key concepts, experimental design, methodology, data
analysis and future trends. Mechanisms, methods of detection and consequences of mutations will
be covered. Molecular approaches for the analysis of DNA at the level of primary sequence, gene,
chromosome and genome will be examined. Tutorials will have a workshop format and will aim to
develop skills in studying primary research articles, investigating the origins, mechanisms and
consequences of mutations and effectively writing reports and short perspectives articles. The
tutorial sessions, assignments, discussion, debates and final exam will allow students to apply the
concepts and principles to a variety of biological problems. This course does not have a mid-term
exam. Evaluation is based on assignments and a final examination.

Key Topics in 2016:

– Genome sequencing approaches - Copy Number Variation
– Genome origin and evolution - Origin and mechanisms of mutation
– Synthetic biology - Mutation signatures in cancer
– Molecular techniques for analysis of genome organization, mutation and repair

Required Reading: Posted on the Biology 3594A OWL website

Review Resources:
Biology 2581b text Genetics: from Genes to Genomes 4th Edition Hartwell et al. Jones and
Barlett Publishers: Chapters: 6, 7, 9, 10, 11, 17

Available Resources:
Genetics: From Genes to Genomes 4th edition
- On reserve in the Taylor Library
Lewin: Genes X
- On reserve in the Taylor Library
Genomes 2nd edition
- Online: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=genom
Comparative Genomics
- Online: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=comgen

Writing Resources:
From the Student Development Centre
- Online: http://www.sdc.uwo.ca/writing/undergrads/writing_resources.html

Assignments and Evaluation

For all assignments, an electronic copy is submitted online by the OWL course website deadline
and the hard copy is handed in prior to the start of the lecture on the due date. Both formats must
be submitted on time otherwise 1% of the final course mark is deducted for each day the
assignments are late. The hard copy with the written evaluation will be returned to the student. The
electronic copy will remain on the OWL course website as the permanent record of the completed
assignment.
Student Participation
It is expected that students have read the required readings prior to lecture discussions and it is
expected that all students attend lectures and tutorials. Participation will be evaluated in several
areas of the course eg. attending lectures and tutorials; participating in class and tutorials;
submitting assignments by assigned deadlines according to posted instructions. As well, 3% of the
participation mark is recorded for students attending an individual appointment for an effective
writing session at the Student Development Centre [The Writing Support Centre]. Please take a
sample of your writing [blog or term paper] for any of the writing assignments in this course and a
staff member at the Writing Support Centre will record your visit for receipt of 3% toward your
participation in this course. The intent is to have your writing reviewed and common errors
corrected in order to improve your marks on class assignments. Book your appointment early! To
ensure an appointment, be sure to book two weeks in advance. The cut off date for appointments in
the Writing Support Centre is November 17th, 2016. Appointments may not be available if you
delay.

Student Poster Presentation

Each student will prepare a poster typical of those seen at research society meetings. The poster
topic is due prior to September 22th 2016 and requires approval. The poster will be prepared
using Powerpoint and guidelines for the preparation of the poster will be reviewed in a tutorial.
Each student will submit 1) a hard copy of the poster on (8½ x11) letter paper in landscape setup
and 2) the electronic Powerpoint file for the poster. Students submit the electronic version through
the OWL course website. The due date for the poster hard copy and electronic file is October 6,
2016. Submit both by the posted deadline.

Student Mutation Report

Each student will be given a short DNA sequence. In a tutorial on mutation reporting you will be
introduced to online databases to identify the DNA sequence, identify any mutation in that sequence
and complete a report to provide a comprehensive investigation of the possible mutagens and
mutational mechanisms leading to that mutation and the functional relevance and phenotype of the
organisms carrying the mutation. As part of your report you will be asked to complete a
questionnaire/survey regarding the mutation. Your Mutation Report is a “takehome” assignment due
October 13, 2016. Submit the hard copy report in class and the electronic form through the
OWL course website by the posted deadline.

Student “Mutablog”
This format and style of writing will permit you to comment on a recent news item relevant to our
course topics and published since January 2016. The original news coverage must have been
published since January 1, 2016. Grammar and spelling will be evaluated. An image, photo or
diagram are optional and in addition to the text. Provide a web link to the news item that caught
your eye and prompted you to write the Mutablog. We will review science blogs in lecture or
tutorial prior to the due date. The hard copy of your Mutablog (500 to 600 words) is due November
3rd 2016. Submit the hard copy Mutablog in class and the electronic copy through the OWL
course website by the posted deadline.
Term Paper
Each student will prepare a term paper in the style of a Science Perspectives article.
Your Science Perspectives article will be based on a primary research paper in a high impact journal
[impact factor >10]. The primary research paper must report discoveries in the field of Genome
Organization, Mutagenesis and DNA Repair. The primary research article must be published
since January 1, 2016. The primary paper must be approved by Dr. McDonald. (The topic is due
October 20th, 2016 for review and approval and the final student term paper is due November
22nd, 2016). The hard copy of the final term paper is submitted in class prior to lecture on
November 22nd, 2016. You must submit the electronic file for the term paper online to the course
OWL website site prior to the class to coincide with the hard copy submission (assignment day
and time deadlines are also provided on the course website with each assignment).

“Science Perspectives” (up to 1000 words plus 1 figure and figure legend) highlight recent exciting
research, but do not primarily discuss the author's own work. They may provide context for the
findings within a field or explain potential interdisciplinary significance. Perspectives should add a
dimension to the research and not merely be a summary of the experiments done in the paper.” This
article format has 1] a concise, descriptive and creative title and 2] a longer descriptive “take home”
message or newspaper headline type of title.

Important Note: the primary papers upon which you base your poster and perspectives
articles are to be different and unique from those selected by the rest of the class.*** During
the topic selection process, Dr. McDonald will check the class records to remove any duplicates
that might occur.

Penalties: If you do not hand in assignments on time (topic, paper, poster, report, blog etc.): 1% of
the course final mark is deducted per day until the assignment is handed in. Assignments are due in
lecture to Dr. McDonald or the teaching assistant and online on the specified dates and times.

Plagiarism:
Students must write their essays and assignments in their own words. Whenever students take an
idea or a passage from another author, they must acknowledge their debt using proper referencing
such as footnotes or citations.

Scholastic offences are taken seriously and students are recommended to be familiar with the UWO
policy:
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf

Accessibility Statement:
If you require any arrangements to make this course more accessible, contact Services for Students
with Disabilities (SSD). Email: ssd@uwo.ca Phone: (519) 661-2147

Absence From Final Exam:

If you are unable to write the final exam due to illness or other serious circumstances, you must
inform your instructor by email and provide valid medical or supporting documentation to the
Academic Counselling Office. It can be contacted at 519-661-3040 or scibmsac@uwo.ca.

For further information, please consult the university’s medical illness policy at
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_illness.pdf.
Support Services:
Learning-skills counsellors at the Student Development Centre (http://www.sdc.uwo.ca) are ready
to help you improve your learning skills. 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.uwo.ca/uwocom/mentalhealth/) 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 Registrarial Services is http://www.registrar.uwo.ca.

Additional Statements:

Accommodation for work worth less than 10% will be referred to the student's Dean's Office or
Academic Counselling unit.

No electronic devices will be permitted for tests or exams.