MICROBIOLOGY – 40857 – BIOS 3120-500
Credit Hours: 5
Syllabus for Spring 2012
Class Information – Lecture (3 credit hours)
Time: 8 - 9:15am, Tue & Thurs
Location: Wood Hall 01710
Recommended Text:
Brock Biology of Microorganisms, Global Edition, 13th Edition (~$50)
http://www.amazon.fr/Brock-Biology-Microorganisms-Michael-Madigan/dp/032173551X
OR
Brock Biology of Microorganisms, 13th Edition (~$149)
http://www.amazon.com/Brock-Biology-Microorganisms-Michael-Madigan/dp/032164963X
Instructor:
Dr. Kathryn Docherty
Email:
kathryn.docherty@wmich.edu
Office:
Wood 3159
(see Professional Emailing section below)
Office Hours: by appointment
Phone:
269-387-5654
Elearning website: https://elearning.wmich.edu/
Class Information – Laboratory (2 credit hours)
Location:
CHEM 03802
Lab Coordinator: Vivian Locke, vivian.locke@wmich.edu
Required Text: Microbiology Lab Theory and Application, 3rd Edition. Leboffe and
Pierce. Complete/Long Edition
Section
Time
TA
TA email
BIOS 3120-540
10-11:50am TR
Mary Thwaites
mary.ansorge@wmich.edu
BIOS 3120-545
1:30-3:20pm TR
Mary Thwaites
mary.ansorge@wmich.edu
BIOS 3120-550
4:00-5:50pm TR
Miles Rogers
miles.t.rogers@wmich.edu
BIOS 3120-555
6:00-7:50pm TR
Miles Rogers
miles.t.rogers@wmich.edu
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Course Description
This course is an introduction to basic microbiology with an emphasis on the diversity,
physiology, genetics and pathogenicity of microorganisms. Also included are fundamental
concepts of virology and the hose immune response to infection. The laboratory component
provides hands-on instruction in basic techniques used in bacteriology.
Pre-requisites: BIOS 2500, CHEM 3750, CHEM 3760 with a grade of “C” or better in all prerequisites. Recommended pre-requisite: Biochemistry
Grading
Your grades will be determined based on the following formula:
Exam Grade 1
Exam Grade 2
Exam Grade 3
Exam Grade 4
Literature Quizzes
Participation
Lab Grade
DROP lowest exam grade
DROP lowest Lit. Quiz grade
TOTAL POINTS
85 points
85 points
85 points
85 points
50 points
5 points
200 points
(-85 points)
(-10 points)
500 points
Grading Details
Exams. (255 points, 85 points each) There will be FOUR exams given throughout the
semester. Each exam will be comprehensive, with emphasis on the most recent material and
guidelines for comprehensive topics to study provided before each exam. Exams will focus on
material covered in my class lectures and handouts from class and from literature quizzes and
assignments. I will provide a study guide at least 1 week before each exam is scheduled with
practice questions and suggestions for comprehensive topics of focus.
Make-up exam policy. There will be no make-up exams, even for excused absences. You are
required to take all 4 exams, but your lowest exam grade will be dropped. If you are unable to
take an exam, it must be for a university-sanctioned and documented reason (i.e. military
service, religious obligation, sporting event, major illness or injury, death in immediate family,
job or school interview). If you miss an exam for an undocumented or unexcused reason, your
lowest exam grade will not be dropped at the end of the semester. If you miss more than one
exam, even for an excused reason, you will receive a zero on any exams beyond one that you
miss. Please check the schedule of exams and plan accordingly. Each exam is worth 85/500
points of your total grade and will consist of multiple-choice and short-answer questions.
Literature Quizzes. (40 points, 8 points each) There will be SIX assigned primary literature
readings throughout the semester. The citations for these literature assignments are provided
below in the schedule. They are all available online through the WMU library. I will briefly go
over doing a literature search to find these articles today. Quizzes will be conducted at the
beginning of the class during which they are assigned. You will then have an opportunity to
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discuss the paper for ~15 minutes with a break-out group and with me. You will then take
another quiz on the paper. Your final grade for each quiz will be the AVERAGE of attempt 1
and attempt 2. Concepts and results presented in the primary literature assignments will also
appear on your exams. If you miss 1 quiz during the semester, that grade will be dropped. If
you miss 2 or more of these quizzes, then you must turn in a typed, 2-page summary of the
paper on the next scheduled class day. ½ total points will be deducted for each calendar day
that the summary is late beyond that day, barring excused and documented absences, as
above.
Participation. (5 points) I will not take attendance in class. However, I strongly encourage you
to attend as much as possible. There will be at least 1 break-out question every lecture. My
opinion is that there are no wrong answers in the context of these questions, and the more you
discuss during these opportunities the better everyone will learn the material. If you are a
regular contributor, you will receive these participation points. If you find that you are struggling
in class and would like extra help on a particular topic from me, and make appointments to see
me and get help in a timely fashion, you will also likely receive these participation points. On
the contrary, if you do not come to class regularly or you are disruptive during class, you will
subtract from your participation points.
Microbiology Laboratory. (200 points) This is a crucial part of the course, as you will apply
the knowledge you gain in class in a hands-on laboratory setting. Turning in your lab reports on
time and your regular attendance in class is necessary for your success in the lab. You will
learn a variety of microbial culture techniques that are used in clinical microbiology laboratories.
By the end of the course, you will be able to isolate pure cultures of bacteria and identify
particular microorganisms based on their physical characteristics and growth capabilities. Your
lab section is run by the microbiology laboratory coordinator (Vivian Locke) and by the teaching
assistant for your section (Miles Rogers or Mary Thwaites). Your TAs are responsible for
grading your laboratory materials and you should approach them first with questions related to
lab assignments and grades. If your TA cannot resolve your question, I encourage you to make
an appointment with me to discuss the issue. Your TA will go over the requirements for
laboratory in detail on your first day of lab. (Thursday, January 12)
Final Grade. Your final letter grade that appears on your transcript will be determined out of
500 points as follows:
Letter Grade
Start %
A
92
BA
86
B
80
CB
76
C
70
DC
66
D
60
E
59 and below
Ground Rules
Academic Dishonesty. Students are responsible for awareness and understanding of the
policies and procedures in the Undergraduate Catalog or Graduate Catalog that pertain to
Academic Integrity. These policies cover cheating, fabrication, falsification, forgery, multiple
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submission, plagiarism, complicity, and computer misuse. If there is reason to believe a student
has been involved in academic dishonesty, the student will:
•
•
•
be referred to the Office of Student Judicial Affairs
given the opportunity to review the charge(s)
o if charges are accepted, I will assign your grade accordingly
o if charges are denied, you will have the opportunity for a hearing
If students are uncertain about an issue of academic honesty prior to the
submission of an assignment or test, they should consult the class instructor
We will go over several instances of plagiarism today. They will be posted on e-learning
for your reference. Pay particular attention to this when writing your lab reports.
Disability Services Statement. Any student with a documented disability (e.g. physical,
learning, psychiatric, vision, hearing, etc) who needs to arrange reasonable accommodations
must contact the professor and Disability Services at the beginning of the semester. You must
provide me with written documentation from Disability Services to arrange for these
accommodations.
Other Accommodations. If you are a student athlete, are in active military service, have a
religious obligation, or will miss class for any other reason that is acceptable in accordance with
university policies, please inform me of this at the beginning of the semester and provide written
documentation for your absence. I will do my best to accommodate your needs. If you are
having a personal issue that interferes with your academic success or health, I encourage you
to arrange to meet with me so we can work to resolve the issue.
Diversity Statement. Western Michigan University’s College of Education maintains a strong
and sustained commitment to the diverse and unique nature of all learners, and to maintaining
high expectations for each student.
Computers in class. I encourage you to use laptops, iPads, etc in class if they help you with
note-taking. There are two caveats: 1) While the internet is a great source of information, and it
is great if you are so motivated by something being covered in class to look up more information
during class, I do not know all the information that is out on the internet. If you find something
that is contrary to something I have said on the internet during class, please ask those
questions after class, as they can be disrupting. 2) Computers and the internet can be misused
and distracting to you and your classmates during class. Please only use them for note-taking,
or they will be subject to confiscation.
Cell phones in class. Turn off your phone (no calls, no texting) during class. They are
distracting to everyone, including me.
Eating and extended whispered conversations. Both of these are distracting to everyone –
please do not do them. If you have a question – ask it out loud! Probably someone else has
the same question.
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Lateness Policy. This class is scheduled from 8-9:15am. I will start lecturing at 8:01am. You
are not required to come to class, unless there is an exam. Consistent lateness will result in
loss of participation points and missed material. It is also extremely disrupting to me and to your
classmates. If you are going to be more than 10 minutes late, please do not come to class. If
you do come in during the first 10 minutes after lecture has started, please do so quietly and sit
down as quickly as possible.
Professional Email Protocol. I will check my email at least once a day on weekdays. I will not
respond to emails sent over the weekend until Monday. I will only respond to emails which
follow these guidelines:
•
•
•
It is sent from a .wmich.edu account. All communication between professors and
students must be using the WMU email system, as per university policy.
You put MICRO 3120 in the subject line of the message. I will miss your email if this
is not included.
You use professional email protocol, addressing me with something like “Hi Dr.
Docherty,” and then using complete, grammatically correct sentences, and signing it
with your name. I will go over some examples.
Course Logistics
E-learning. We will be using the new university e-learning system (Desire-2-Learn or D2L)
which is accessible through gowmich.edu. I will post handouts for lecture, study guides, exam
keys and all grades to D2L.
Lectures. I will not be posting my lectures. However, I will post handouts containing all
relevant figures, tables, diagrams, etc., to help facilitate in-class note-taking. I will post these
handouts no later than the Sunday night prior to each class week so that you can print them in a
computer lab if you so desire. If you miss class, it is your responsibility to get notes from a
classmate who attended class.
Study guides. I will post a study guide for each of the 4 exams at least 1 week before the
exam. I will inform you in class and on e-learning when a study guide has been posted. I
strongly encourage you to work through the study guides before the exam, and ask me
questions in class or in a scheduled meeting in my office before the exam.
Individual meetings. I am available to you if you need extra help, or are just interested in
talking about microbiology. I strongly encourage you to meet with me if your first exam grade is
below a B. I request that you please email me to arrange such meetings and we will find a time
that is suitable for both of us. I do not have regular office hours because they are never
conducive to everyone’s schedule. If you ask me about arranging a meeting in person, I will
likely ask you to email me to schedule a time.
Canceled Class. If the university closes or I am unable to attend lecture, I will email the entire
class list as soon as possible, and arrange for a note to be placed on the door. For university
closures, you can also call X-71001 to find out if the university has closed.
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Schedule. Exam and quiz dates are set; topics covered are subject to change.
Date
1/10
1/12
1/17
1/19
1/24
Topic
Welcome, Assessment, Syllabus
Three Domains, Phylogeny, History of
Microbiology, Endosymbiotic Theory
Cell Walls of Bacteria and Archaea
Microbial Growth
Microbial Metabolism - Redox Chemistry
Suggested Reading in Brock
Chapter 1
Chapter 2, Chapter 16
Chapter 3
Chapter 5
Chapter 4
LIT QUIZ 1.; Microbial Metabolism - Variations
on Glycolysis and Electron Transport Systems
Chapter 4
1/26
1/31
2/2
2/7
2/9
2/23
2/28
3/1
3/6
3/8
3/11
3/13
3/15
3/20
3/22
Chapter 6
Chapter 6
Chapter 6
Viruses and Bacteriophage
Horizontal Gene Transfer
Chapter 8
Chapter 9
Chapter 10
Chapter 26
Chapter 26
Antibiotic Resistance
Chpater 26
LIT QUIZ 3., Intro to Immunology
Contagious Pathogens: Tuberculosis
Vector-Borne Pathogens: Lyme Disease
Chapter 28
Chapter 33
Chapter 35
Chapter 34
3/27
Microbial Species Concept
Methods in Molecular Microbiology (PCR)
Human Microbiome
Microbial Biotechnology, Assessment
Jenkins et al. 2005. Occurrence of
alternative fecal indicators and
enteric viruses in Michigan Rivers.
Journal of Great Lakes Research.
31(1):22-31. **posted on elearning**
Chapter 25
LIT QUIZ 6., Microbial Biodegradation and
Bioremediation
4/24
5/1
Colwell. 2003. Reduction of
cholera in Bangladeshi villages by
simple filtration. Proceedings of
the Natiaon Academies of Science
of the United States of America.
100(3): 1051-1055.
Chapter 24
Chapter 22
Chapter 12
4/10
4/17
4/19
Shales. 2004. Antibiotic
Discovery: State of the State.
ASM News. 70(6): 275-281.
EXAM 3 (administered by TAs)
LIT QUIZ 5., Microbial Metegenetics and
Metagenomics
4/12
Wolfe-Simon et al. 2011. A
Bacterium that can grow by using
arsenic instead of phosphorus.
Science. 332: 1163-1166.
EXAM 2
Antibiotic Discovery
Antibiotics
SPRING BREAK, no class
SPRING BREAK, no class
Mid-term grades due
LIT QUIZ 4., Water-Borne Pathogens: Cholera
3/29
4/3
4/5
Schimel. 2004. Playing scales in
the methane cycle. From microbial
ecology to the globe. Proceedings
of the National Academies of
Science of the United States of
America. 101(34): 12400-12401.
EXAM 1
Microbial Molecular Biology - DNA Replication
Microbial Molecular Biology - Transcription
Microbial Molecular Biology - Translation
LIT QUIZ 2.; Regulation of Gene Expression
2/14
2/16
2/21
Assigned Literature
Chapter 24
Chapter 15
Ley et al. 2005. Obesity alters gut
microbial ecology. Proceedings of
the National Academies of
Science of the United States of
America. 102(31):11070-11075.
EXAM 4 (in final exam week, 8-10am)
Final grades due at noon
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