Bio 343 – Microbiology Spring 2008

Course Syllabus

Professor: Peter Kennedy

Phone: (503) 768-7509
E-mail: pkennedy@lclark.edu
Office hours: Mondays 11:30-12:30 220 BioPsych, 2-4 Dove Cote

Teaching Assistant: Jehan Yahya

E-mail: jyahya@lclark.edu

Course objective:

This course will examine the biology of microbial organisms, with a primary focus on
bacteria and fungi. Lectures will emphasize key aspects of microbial life, including
energetics and physiology, genetics and diversity, and interactions with the environment
and other organisms. Laboratory exercises will emphasize ways in which microbes are
studied using culture dependent and independent methods. By the end of the course, I
expect you to have gained a clear understanding of the diversity of microbial organisms
(taxonomic, metabolic, and genetic), the roles microbes play in human and other hosts’
lives, and the ways in which microbes interact with different environments. This course
will provide a diverse array of learning experiences to help you meet these expectations.

Course outline:

The course will be divided into four sections. The first section will examine the
fundamental aspects of prokaryotic life. This includes cellular structure, genetics, and
metabolism. This section will also examine the diversity and evolutionary history of
microbes as well as the challenges of cultivating and identifying them. The second
section of the course will focus on human-microbe interactions. This section will
examine microbial populations of the human body, human defense systems, and
infectious diseases. The third section of the course will focus on microbes in the
environment. This section will discuss ways of analyzing microbial communities,
phototrophic microbes, invertebrate-microbe interactions, plant-microbe interactions, and
microbial community dynamics. The final section of the course will focus on fungi.
Lectures will cover aspects of fungal taxonomy and diversity, mechanisms of dispersal,
and human-fungal interactions.

Course readings:

There are two recommended textbooks for this course. The first is the seven edition of
Prescott, Harley, and Klein’s Microbiology and the second is the third edition of Bryce
Kendrick’s The Fifth Kingdom. Prior editions of either text may also be used, but you
will be responsible for identifying the correct sections of the text that correspond to the
lectures. In addition to these texts, there will be a number of assigned readings from
primary research articles and literature reviews.

Course logistics:

On my webdisk space (pkennedy), you will find a folder entitled Bio 343 – Spring 2008.
This will have copies of the syllabus, lab handouts, lecture pdfs, and other course related
material. The syllabus and list of readings are tentative, since some lecture topics may go
faster or slower than others and the literature is constantly changing. I will announce the
readings for the upcoming week in Friday’s class and update the syllabus as needed. If
you have any trouble reading of the assigned papers, Dr. Deborah Lycan has prepared an
excellent step-by-step guide to reading the primary literature that I strongly encourage
you to check out (http://www.lclark.edu/~lycan/Bio311/howtoreadprimary.html).

Laboratory projects:

There will be five lab projects in the course. Rather than doing a series of “canned” labs,
we will do a series of inquiry-based research projects. For the first four projects you will
need to complete a group lab write-up (you will work in groups of four each time) (10
points each). For the fourth project, you will write-up a formal research paper based on
the data you have collected (50 points). In some of the exercises you will need to grow
bacteria or set-up PCR reactions and then come in on a subsequent day and analyze
results. This means that the time you spend in lab will not be restricted to the time
scheduled for your particular section. You will most likely need to spend time in the
laboratory on more than one day per week, but the accumulative time will not be more
than what was originally scheduled.

Course Assignments:

There will be one writing assignment. The goal is to give you a chance to learn a good
deal more about the biology of one microbial species. You will do a review of the
literature about this species to learn about 1) where it grows (e.g. what are its habitat
requirements? what kind of metabolism does it have?), 2) how it reproduces and
disperses (e.g. what are the unique features of its life cycle? does it reproduce sexually
and asexually?), 3) how it interacts with other organisms in nature (e.g. does it have any
important symbioses? does it change the environment in which it lives?), and 4) how uses
of get used by humans (is it important in medicine?, food production?, toxic waste clean-
up?). Your species account will be five single-spaced pages, references included (15
references max). You can definitely use the internet as a place to get started, but all of
your cited literature must come from either research articles in peer-reviewed journals or
books (use the citation format of the journal Science). This assignment is worth 25 points.
It is due May 8th. You will also complete a formal two page write-up from one of the
biology seminars offered in the spring semester. See the Webdisk folder for further
instructions about this assignment (worth 10 points due April 18 th). Assignments will
lose a letter grade for each day they are late.

Course Examinations:
There will be four exams in the course. The exams will be based primarily on lecture
material, so regular attendance will greatly improve your ability to answer the questions.
Test questions will be a mix of short answer (mainly terminology and concepts) and short
essay/data analysis (requiring synthesis and original thinking) questions. Sample test
questions will be provided at the end of each lecture to help prepare for the types of
questions that will be on the exams. Each exam will be worth 50 points and must be
completed in one hour. If you have a diagnosed learning ability, you may be entitled to
additional time or other accommodation on the exams. To receive this, however, you
must notify me of your situation at the beginning of the semester. This information will
be strictly confidential.

Academic integrity:

Science depends on academic integrity and you will be held to that same high level of
honesty. I am required by the college to report cases of suspected cheating to the Honor
Board. If I suspect you of cheating or copying ideas, I will talk to you, explain my
concerns, and then fill out and forward the required form to the Dean of Student’s Office.
The Honor Board will then schedule a hearing to determine the appropriate outcome.
Please don’t cheat or plagiarize, it’s not worth it.

Grading:

Your grade will be based on your % of the possible points from the course (350). 30
points will be allocated towards attendance and for participation in discussions of
assigned readings. Grades will not be made on a curve, so all of you have the
opportunity to get an A if you work hard. The grading categories will be as follows: A
>93, A- 90-92, B+ 87-89, B 83-86, B- 80-82, C+ 77-79, C 73-76, C- 70-72, D 60-69, F
<60. Please see the Lewis and Clark College Catalogue for interpretation of letter grades.