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2015 COURSEBOOK
Molecular Genetics
UNIVERSITY OF TORONTO
Welcome!
We are thrilled you are joining us for this brand new online course!
In this course we are going to explore one of the most important subjects in all of medical science communicable diseases. This course was designed to meet the needs of second-year students interested in
infectious disease and older students who are interested in a basic microbiology class with a medical
perspective, perhaps to meet the prerequisites for a professional program in health sciences.
Over the course of the semester we will cover the basics of what microbes are and explain the differences
between parasites, fungi, bacteria, and viruses. We will discuss how to cultivate microbes, and how they are
identified in the lab. Importantly we will spend a lot of time discussing microbes of medical relevance
including how they cause disease and how they are diagnosed and treated.
The understanding of that microbes are the cause of disease was a revolution every bit as important to our life as
the industrial revolution. Since 1900 we have doubled our life-span, most of this is because of vaccines, widespread access to clean drinking water, better hygiene and food preparation practices, antibiotics, and the
emergence of public health agencies at all levels of government.
Many challenges remain, however. One challenge is that new infectious diseases emerge every few years.
Around 1980 we saw the emergence of a new and terrifying virus, HIV, that now infects millions of people on
every continent. We have also seen antibiotics that were effective against many bacterial or fungal infections
become useless as these microbes evolve resistance to almost every available treatment.
Another challenge is that the health gap between the wealthy and poor countries remains huge. Despite
considerable gains against hunger and disease in the poorest regions of the world, a combination of ineffective
or conflicting governments, weak public health systems, cultural barriers, and war, all contribute to inexcusably
high mortality rates due to infectious disease. Nowhere is this more evident than in the recent Ebola outbreak in
West Africa. Not only does poverty lead to more disease, but disease leads to more poverty.
This is the first time we are teaching this course and the first time any of the professors have ever taught
something online. That means were going to be soliciting frequent feedback to make sure everybody stays on
track. We know this is a work in progress but well do everything in our power to clearly state our expectations
and maintain open lines of communication. Things may change along the way if we find a certain approach
isnt working.
Looking forward to an exciting semester!
Professor Navarre
PREREQUISITES
This course assumes you have a basic understanding of what a cell is, what DNA is, what proteins do, and a
knowledge of some very basic biochemistry. If you dont know what a gene is (and that genes are encoded on
DNA) then you may struggle in this course. If you find you need a refresher on basic biochemistry please look
over Chapter 2 we will not be covering it because we assume you already have a basic understanding of the
most important concepts.
MARKING SCHEME
35% of the mark in this course will come from the final exam, 35% from the end of unit exams (long quizzes at
the end of each unit), which are open book, 30% from assignments and from participation in random discussions
and surveys (including, for example, 1% for simply completing the entry assessment quiz).
UNIT EXAMS ARE OPEN-BOOK AND WE EXPECT YOU TO DO THEM YOURSELF. ASSIGNMENTS ARE
TO BE YOUR OWN WORK AND IT IS EXPECTED THAT YOU WILL NOT COPY MATERIAL FROM OTHER
STUDENTS.
using your UTORid and password. Once you have logged in to the portal using your UTORid and password,
look for the My Courses module, where youll find the link to the MGY277 course website along with the link to
all your other Blackboard-based courses.
Activating your UTORid and Password
If you need information on how to activate your UTORid and set your password for the first time, please go to
www.utorid.utoronto.ca. Under the First Time Users area, click on activate your UTORid (if you are new to
the university) or create your UTORid (if you are a returning student), then follow the instructions. New
students who use the link to activate your UTORid will find reference to a Secret Activation Key. This was
originally issued to you when you picked up your Tcard at the library. If you have lost your Secret Activation
Key you can call 416-978-HELP or visit the Help Desk at the Information Commons on the ground floor of
Robarts Library to be issued a new one. Course instructors will not be able to help you with this. 416-978HELP and the Help Desk at the Information Commons can also answer any other questions you may have about
your UTORid and password.
Email Communication with the Course Instructor
At times, MGY277 course instructors may decide to send out important course information by email. To that
end, all UofT students are required to have a valid UofT email address. You are responsible for ensuring that
your UofT email address is set up AND properly entered in the ROSI system. You can do that by using the
following instructions:
To submit the information to activate your UTORid and password (see above), you will need to click the
Validate button. Follow the instructions on the subsequent screens to receive your utoronto.ca address. Once
you have your UofT email address, go to the ROSI system (www.rosi.utoronto.ca), log in and update the system
with your new UofT email address.
You can check your UofT email account from
1. The UofT home page http://www.utoronto.ca: From the Quick Links menu on the top right, choose
my.utoronto.ca. Enter your UTORid and password, and when the Welcome page opens, click WEBMAIL.
2. Email software installed on your computer, for example Microsoft Outlook or Mozilla Thunderbird. Visit the
Help Desk at the Information Commons or call 416-978-HELP for help with the set up.
Forwarding your utoronto.ca email to a Hotmail, Gmail, Yahoo or other type of email account is not advisable.
In some cases, messages from utoronto.ca addresses sent to Hotmail, Gmail or Yahoo accounts are filtered as
junk mail, which means that emails from your course instructor may end up in your spam or junk mail folder.
You are responsible for:
1. Ensuring you have a valid UofT email address that is properly entered in the ROSI system
2. Checking your UofT email account on a regular basis.
Accessibility Needs
The University of Toronto is committed to accessibility. If you require accommodations for a disability, or have
any accessibility concerns about the course, the classroom or course materials, please contact Accessibility
Services as soon as possible:
UNIT
1
2
3
4
5
6
7
TOPIC
Perspectives on microbiology and infectious disease
Bacteria
Viruses
Eukaryotic microbes
Microbial growth in the lab, in the environment, and how its controlled
Microbial identification and classification
Immunity
8
9
10
11
12
13
14
15
16
17
18
19
Principles of pathogenesis
Antibiotics and antibiotic resistance
Public Health and clinical microbiology
HIV the virus and the global epidemic
Sexually transmitted diseases herpes, gonorrhea, syphillus
Respiratory infections TB, influenza, SARS
Food and waterborne infections E. coli, Salmonella, Listeria, Cholera
Vector borne/zoonotic infections: malaria, plague, and Ebola
Skin and wound infections staph, strep, zoster
The human microbiome
Unexpected consequences of infection (cancer/ulcers)
Food microbiology and industrial microbiology
Your TAs
Epshita Islam
Hi! I grew up in Dhaka, Bangladesh before moving to Toronto where I completed
my undergraduate in Cell and Molecular Biology here at the University of Toronto.
During this time I developed a strong interest in infectious diseases, and I later
joined the Department of Molecular Genetics to pursue graduate studies in this
subject. As a PhD student in Dr. Scott Gray-Owens lab, my research involves
utilizing transgenic animal models to study infections by the bacterial pathogen,
Neisseria gonorrhoeae. Aside from science, I enjoy eating, travelling and playing with
cats.
Elizabeth Polvi
Hello! I am currently a PhD student in the department of Molecular Genetics, in
the lab of Dr. Leah Cowen. Our lab focuses on the fungal pathogen, Candida
albicans, and I am particularly interested in how this fungus acquires resistance to
antifungal drugs, and investigating drug combinations that can be used to
combat this resistance. I am also interested in studying the genes required for C.
albicans to form filaments. I did my undergraduate work at Dalhousie University
in Halifax, Nova Scotia. This is probably where I developed my love for rain, fog
and lighthouses. My other interests include synchronized swimming and
baking.
Sabrina Stanley
Hi! My name is Sabrina and I am one of your TAs this semester. I completed my undergraduate degree in
biochemistry at the University of Waterloo. I am currently a PhD student in the department of Molecular
Genetics under the supervision of Dr. Alan Davidson, where I study phage biology. In particular, I am figuring
out how a group of phage encoded proteins inhibit the CRISPR-Cas system of Pseudomonas aeruginosa. When
not in the lab, I volunteer with animals and play the saxophone in a community band.
Your instructors
William Wiley Navarre, Ph.D. (course coordinator)
William Navarre was born and raised in Ann Arbor, Michigan and attended the University of Michigan as an
undergraduate. He obtained his Ph.D. in the lab of Olaf Schneewind at UCLA studying the anchoring of surface
proteins in Gram-positive bacteria. He was a Damon Runyon Postdoctoral Fellow and did post-doctoral work
with Arturo Zychlinsky at New York University prior to joining the lab of Ferric Fang at the University of
Washington in Seattle. With Ferric he studied mechanisms of bacterial resistance to immune effectors. He
joined the Department of Molecular Genetics as an Assistant Professor in September of 2007 and was a CIHR
New Investigator. In 2012 he was promoted to Associate Professor and became head of the departmental
undergraduate program. He maintains an active role in teaching and is also the coordinator and lead teacher for
MGY377H1, the main bacteriology course on campus.