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MGY277H1

An Introduction to Medical Microbiology

2015 COURSEBOOK

photo - Dr. Julie Claycomb

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.

HOW THE COURSE IS ORGANIZED


Since this is an online course we have decided to eliminate constraints that normally exist in a traditional
classroom. In a traditional classroom, for example, you are supposed to meet two or three times a week for a set
amount of time. This puts a lot of limitations on what can be covered. Professors in traditional classrooms are
bound to package their material into inflexible units that may not really fit the material. What if a topic only
needs 15 minutes of lecture? What if it needs 70? Sometimes things get rushedother times you feel as if the
professor is just filling in the time because what if, god forbid, the professor did not use up all of the allotted 50 minutes
and actually let you out early?
The fact were online allows us to abandon the 50 minute lecture three times each week format. We will
instead have video vignettes that are 5 15 minutes each and are designed to supplement readings from the
textbook and other materials we will provide you. The vignettes also enable us to have interviews with experts
and take you on virtual field trips to particular places like the labs at Public Health Ontario or the Hospital for
Sick Children.
We will also send you off to do your own online research using resources at the Centers for Disease Control, the
World Health Organization, Health Canada, as well as online resources within the U of T library system.
The course is organized into learning units that we expect you to complete within a given time frame. The
intro unit takes about a week. The unit on basics of bacteria takes a week and a half. These units are punctuated
with quizzes and small assignments.
The course is designed to start with the general principles of microbiology going so basic that we will define
the differences between prokaryotes and eukaryotes and viruses. After that we will cover how microbes are
cultivated and identified in the laboratory. We will then move on to cover the basics of the immune system and
then do a quick unit on the fundamental themes of pathogenesis prior to engaging in a series of individual units
that each focus on a specific pathogen.

POLICY ON DISTRIBUTION OF THE MATERIALS OUTSIDE OF THE COURSE


At the University of Toronto and the Department of Molecular Genetics we take pride in the fact that we have unique, highlevel and up-to-date expertise in the course topics. Students should be aware that the videos materials are the Intellectual
Property of the lecturers. Access to this material (slides, handouts, videos, recordings) is something you have earned
through your previous efforts that got you into this course, and is also a significant component of what you are paying for
with your tuition.
Further distribution of the lecture materials (e.g. on other web sites, in computer or paper files accessible by
other students or the public, or by giving paper copies to others not registered in the course) without permission
constitutes an academic offence, and the instructors have the right to pursue disciplinary action.

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.

HOW TO GET HELP


Given that this is an online course you are certainly encouraged to explore the wide variety of online resources
available for free on the internet. We provide specific readings from reliable sources that have been selected for
their accuracy and how well they communicate at the appropriate level. Weve avoided highly technical and
specialized literature for this course because of the introductory nature of the material being covered.
We have opened up the discussion board on Blackboard for questions, comments, and discussions. We will not
use Facebook or Twitter as a means of communication simply because many students do not opt to have
accounts on those sites. The Blackboard discussion board is the only place we will answer questions. We may
periodically release clarifications and/or updates if something we presented does not make sense or has errors.
There are a number of wonderful YouTube videos that can explain a variety of concepts both clearly and
accurately. However there are also lots of videos that are just plain wrong or deceiving. These include a large
number of pseudo-science videos that have a buried political or social agenda often containing a confusing mix
of half-truths and facts selected merely to support the position of the author (while ignoring the facts that do not
support their position). For the purposes of the course we strongly suggest you stick with the textbook and the
readings we provide. Wikipedia is usually quite accurate but sometimes has information that is completely
wrong. One of the worst sources of information is Yahoo answers which solicits advice from random people
on the internet almost all of it is garbage. If there is a conflict between something you read on the internet and
something weve provided you in this course you can ask for clarification and we will be happy to discuss.
However we will only consider the material we recommend or provide as valid for the purposes of
examinations and marking.

Policies for behaviour and academic integrity


Academic misconduct at the University of Toronto is defined by the Code of Behaviour on Academic Matters.
Generally, academic misconduct is any behaviour, intentional or otherwise, that gives a student unearned or
unfair advantage in academic work over other students.
As a student, you alone are responsible for ensuring the integrity of your work and for understanding what
constitutes an academic offence. Not knowing the Universitys expectations is not an excuse. Educate yourself!

Information about Portal/Blackboard and e-mail communications


Logging in to the Blackboard Course Website for MGY277
Like many other courses, MGY277 uses Blackboard for its course website. To access the MGY277 website, or any
other Blackboard-based course website, go to the UofT portal login page at http://portal.utoronto.ca and log in

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:

MGY277H1 UNIT OVERVIEW WINTER 2015


DATES
Jan 5 Jan 9
Jan 12 Jan 16
Jan 19 Jan 23
Jan 26 Jan 28
Jan 30 Feb 4
Feb 6
Feb 9 Feb 13

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

Feb 16 20: FAMILY DAY AND READING WEEK


Feb 23
Feb 25 Feb 27
Mar 2 Mar 4
Mar 6 Mar 9
Mar 11
Mar 13 - Mar 16
Mar 18 20
Mar 23
Mar 25
Mar 27
March 30
April 1

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

HOW TO TAKE THIS COURSE:


As we progress through the course the units will be made available. Content this year is still being built and
added so we cant upload it all at once. On Blackboard all the information and content is available through the
Course Materials link.
Each unit will start with the expectations for the unit by listing what videos you are to watch, what readings are
assigned, and what the assignments are. Assignments range from short quizzes to more in-depth research into a
particular subject. Every unit ends with a unit exam that will ask multiple choice or fill in the blank questions
about the material covered in the unit. These are open book/open video exams that you can save and return to.
There is no excuse for not doing very well on them.
The units will also contain a slide packet that gives you a pdf file of all the slides in the unit. You should
probably have that file open (print it if you can) while you watch the videos so you can annotate as we move
along. You can also simply take written notes. You should definitely work towards organizing the information
as you hear/read it. You should probably start a binder in which you keep all of your printed slides and notes.
Because you have to retain this information for the final exam its best if you take notes as you go along rather
than simply jump to the unit exam and hunt for the answers among the videos, etc.
There are places where we might ask how many people died of Ebola in October and have you look it up in a
table for an assignment. Very specific numbers are not something you will be required to memorize for the final
exam so dont waste your time on those. After you take a few unit exams you should have a good sense for the
depth of knowledge that will be required for the final.

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.

Alexander Ensminger, Ph.D.


Like Dr. Navarre, Dr. Ensminger was also born and raised in Ann Arbor, Michigan (they didn't know each other
then). After completing his Ph.D. at MIT in 2006, Alex began postdoctoral work with Dr. Ralph Isberg (Tufts
University). During this time, he established the laboratorys expertise in next-generation sequencing
technologies and developed a powerful experimental evolution approach to uncover new bacterial genes that
influence host range and virulence. Based upon these foundations, he started his independent research program
in the Department of Molecular Genetics at the University of Toronto in March, 2011. Alex is a co-coordinator of
MMG1010, Molecular Genetics Colloquium, a mandatory course for all of our first-year graduate students and a
co-instructor for MGY434, a fourth-year undergraduate microbiology course. He is also an avid barefoot waterskier and fearless DIYer.

Scott Gray-Owen, Ph.D.


Scott is our only representative from the prairies, raised in Calgary and obtaining both his BSc and Ph.D. from
the University of Calgary. He did postdoctoral work in the lab of Tomas Meyer at the Max Planck Insitut fr
Biologie in Germany before joining the Department of Molecular Genetics. His lab aims to understand how
human-restricted bacterial and viral pathogens colonize host tissues and evade an otherwise effective immune
response. Studies from his lab have provided a detailed description of molecular processes that occur
downstream of the host-pathogen interface, and to the development of more relevant models of infection and
disease.

Sadhna Joshi, Ph.D.


Dr. Sadhna Joshi completed her Ph.D. and D.Sc. from Universit Paris Diderot, France. She joined Allelix
Biopharmaceuticals, Mississauga, Ontario, in 1983 where she worked as a Senior Research Scientist &
Principle Investigator on AIDS and Immune Regulation. In 1989 she joined the University of Toronto as
Associate Professor in the Department of Molecular Genetics. She is also cross-appointed in the Department of
Laboratory Medicine and Pathobiology.

Patrick Paladino, Ph.D.


Dr. Paladino is an expert virologist who did post-doctoral work with Dr. Lori Frappier in the Department of
Molecular Genetics after competing his Ph.D. in the lab of Dr. Karen Mossman, the current Chair of
Biochemistry at McMaster University. He has an interest in online education and facilitated the design and
construction of this course. He delivers the introductory unit on virology for this course.