Microbiology: Bacteria and Viruses
Bio
254
Spring
2005
Instructors:
Dr. Christine White-Ziegler |
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Office: |
Sabin-Reed 457 |
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Office phone: |
585-3815 |
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E-mail: |
cwhitezi@science.smith.edu |
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Office hours: |
The best times to
contact me are immediately after lecture/lab on Monday or Wednesday. If these times conflict with your
schedule, please contact me for an appointment. |
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Dr. Esteban Monserrate |
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Office: |
Sabin-Reed 435 |
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Office phone: |
585-3851 |
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E-mail: |
emonserr@science.smith.edu |
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Office hours: |
By appointment or stop
by my office. |
Lecture
class:
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Course credit: |
3 credits |
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Class times: |
MWF 10:00- 10:50 am Th 4:00-4:50 pm |
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Location: |
McConnell 404 |
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Prerequisites: |
CHM 111, BIO 111 or
equivalent |
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Co-requisite: |
BIO 255 (Microbiology: Bacteria and
Viruses Laboratory) must be taken concurrently |
Course
description and objectives:
This course will focus on the biology of
bacteria including prokaryotic cell structure, diversity, metabolism, growth,
and genetics. The different
environments in which bacteria are found, and the role bacteria play in these
environments, is also addressed.
Additionally, an introduction to the biology of viruses will be
included. A particular emphasis is
placed on medical microbiology in which the role of bacteria and viruses in
disease is discussed. Special
topics covered in this class include antibiotic resistance, evolution of
pathogens, virulence factors, emerging infectious diseases, gene regulation,
and bacteria in unusual or extreme environments.
In addition to learning important
information about the biology of a variety of microorganisms, students will
have the opportunity to write a paper on a topic of their interest. Through this assignment, students will
experience the research process from the concept stage to a culminating final
paper and oral presentation on the topic, giving students the opportunity to
practice and improve their written and oral communication skills. The exchange of information learned by
individual students will be facilitated oral presentations and reading of each
otherÕs papers. Also, students
will orally present "Microbial Moments" that will allow a more casual exchange
of information and discussion of specific microorganisms.
Appointments/contacting
us:
As stated
above, we can meet with you for appointments. When you want to set an appointment with either one of us,
please be prepared with a few time slots you are available on those days so we
can find a time that matches our schedules. Feel free to contact us in class, by email, or by phone. Do, however, make sure that any
important information you need to get to us (e.g. appointment times, paper
topics, etc) is written down on something and handed to one of us! We promise you that we will promptly
forget anything simply told to us.
Also, Dr. White-Ziegler does not check email on the weekend, in the
evening, and (sometimes) not before class, so plan on a lag time in response to
emails sent at these times.
Lecture
text:
The
text for the class is Microbiology by Prescott, Harley, and Klein, 6th
edition. It will serve as the
primary reference for the course.
Additional readings may be assigned and will be available on reserve in
the Young Science Library. An
extremely helpful resource for the writing assignment in this class is A
Short Guide to Writing About Biology by Jan Pechnik, 3rd edition. It is on reserve for this course at the
library.
Evaluation:
|
Assignment |
Points |
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Microbial
Moments (2 x 25 points) |
50 |
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Abstract |
30 |
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Exam
1 |
100 |
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Exam
2 |
100 |
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"Near
perfect" draft of paper/writing conference |
25 |
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Final
paper |
100 |
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Presentation
of paper |
50 |
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Exam
3 |
100 |
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Total |
555 |
Microbial
moments
To
introduce specific microbes in the class, each student will present 2
"Microbial Moments" during the course of the semester. This will be a short (approximately 3-5
minute talk) about a specific bacterium or virus that will include such
information as the unique characteristics of the bacterial genus (or species)
and it role in its environment. A
handout will be provided as to what information should be covered in these
moments. Each class meeting a
different person will present.
Microbial moments will be started in February.
Exams
Exam
1 and Exam 2 will be self-scheduled exams. In a week in which an exam is given, the exams will be
available starting at 1:00 p.m. on the first day until library closing time on
the last day. Students can obtain
the test in the Young Science Library at the desk. The exam must be completed within two hours and returned to
the Science Library desk. Please
plan to allocate the full two hours provided to complete the exam. If students have questions pertaining
to the exam content, these questions must be asked before the test is made
available. Clarifications during
the exam could be asked if you can reach either Dr. White-Ziegler or Dr.
Monserrate. Therefore, we
recommend you plan accordingly.
Exam
3 will cover the content of the last third of the course, primarily student
papers. All of the student papersÕ
will be placed on reserve in the Young Science Library. Each student will be responsible for
writing a test question and answer on her individual paper that will be used in
formulating the exam. Exam 3 will
be on reserve at Science Library desk during final exam week. Material covered in Microbial Moments
will be tested on exams.
Paper
and oral presentation
Each student will write a paper on a
subject of interest within the field of microbiology (bacteriology or
virology). Students may suggest
their own topic or choose one from a list of suggested topics the instructor
will provide. Each student needs
to discuss with the instructor and get approval of her topic by the date stated
in the lecture outline. An
abstract, approximately 250 words, must be written for the paper to delineate
the focus and scope of the paper.
At least five references should be included with the abstract, three of
which should be primary journal articles.
The abstract is due on the date stated in the lecture outline, but can
be submitted earlier. The paper,
limited to 8 pages, should be typed, double-spaced, and include a list of
references. The paper should be
focused to a very specific topic.
The paper should give the latest information available on the subject
and thus should be written based primarily on journal articles from the past three
years.
Each
student will hand in a "near perfect" draft a week prior to when the student
presents. A "near perfect" draft
should be as complete a paper as the student can write. Any papers submitted later than this
time will be penalized. The student
is then responsible for scheduling a writing conference with the instructor,
prior to their presentation, in which the instructor will offer comments for
the writer on ways to improve the paper.
Peer review is highly encouraged so students should feel free to
exchange drafts and get comments from each other. The final draft of the paper is due one week after the
student's presentation.
Presentations
will be held between mid-March and the end of classes; a specific schedule will
be determined once class size has stabilized. Each student will give a 10-15 minute presentation of her
paper, followed by 5 minutes for questions and discussion. The presentations should be well
prepared, concise, and include any visual aids that would enhance the presentation. The presentation time will not be
enough to address every point made in the paper. Therefore, students will want to present the most
interesting and important points.
The purpose of the presentation is to give students a chance to speak in
front of others and promote an exchange of information and ideas.
On
Thursdays in the beginning of the semester, various professors from Smith
College/Five Colleges whose research involves prokaryotic and eukaryotic
microorganisms will give guest lectures about their work.
Students
from the seminar course BIO 360 Emerging Infectious Diseases "Biotechnology and
World Health" will be giving guest talks to this class on their research on the
top pathogens of concern and ways in which biotechnology can be used to
diagnose, cure, or prevent transmission of these pathogens.
Colloquia/Panel talks:
A
colloquium will be given on Monday, March 7 at 4:30 pm in McConnell B05 by Dr.
Nick Mantis, Division of Infectious Disease, Wadsworth Center, NY State
Department of Health. Extra
credit will be given for attendance at this talk along with a brief one-page
summary of the talks.
Web
page:
This
course has a web page which is a source for specific and general
information. More specific instructions
regarding the assignments for the class are found here. Useful links to immunology and
microbiology-related sites, literature reference databases, and internship
sites can be accessed through this page.
www.science.smith.edu/departments/Biology/cwhitezi/default.html
Late
policy:
Each
assignment is due on the date and at the time stated in the syllabus. An
assignment handed in late will be penalized 5 points for each day it is
late. Weekend days will be
included in this penalty.
Outline
of course:
This outline should be
viewed as a flowchart of topics in the basic order that they will be
covered. It is subject to change.
|
Week |
Lecture |
Chapter
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M 1/24 |
Introduction |
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W 1/26 |
History of microbiology |
1 |
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R 1/29 |
TBA |
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F 1/28 |
Bacterial Diversity I:
Gram Ð and Proteobacteria |
21-22 |
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M 1/31 |
Bacterial Diversity II:
Gram +, Low-vs-High G+C |
23-24 |
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W 2/2 |
Microscopy: Visualizing
bacteria and viruses |
2 |
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R 2/3 |
Research in Microbiology
Guest Lecture
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F 2/4 |
Prokaryotic cell
structure and function |
3 |
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M 2/7 |
Prokaryotic cell wall:
Gram + versus Gram - |
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W 2/9* |
Taxonomic classification
of bacteria |
19, 15 |
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R 2/10 |
Research in Microbiology
Guest Lecture
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F 2/11 |
Archaea |
20 |
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*Approval of PAPER topic due by 10 am on 2/9
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M 2/14 |
Bacterial nutrition and
culture media |
5 |
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W 2/16 |
Measurement of bacterial
growth |
6 |
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R 2/17 |
Research in Microbiology
Guest Lecture
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F 2/18* |
Bacterial respiration |
9 |
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*Abstract of PAPER due at 10 am on 2/18
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M 2/21 |
Metabolic Diversity I:
Fermentation |
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W 2/23 |
NO CLASS- Rally Day! |
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R 2/24* |
Research in Microbiology
Guest Lecture
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F 2/25 |
Metabolic Diversity II:
Photosynthesis and Chemosynthesis |
10 |
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*Self
schedule EXAM 1 between 2/24-3/3 |
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M 2/28* |
Bacteria and their role
in the environment |
28-30 |
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W 3/2 |
Biogeochemical cycles
and bioremediation |
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R 3/3 |
Research in Microbiology
Guest Lecture
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F 3/4 |
Bacterial DNA
replication/transcription |
11 |
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M 3/7* |
Bacterial protein
translation |
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W 3/9 |
Gene/protein regulation
I |
12 |
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R 3/10 |
TBA |
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F 3/11 |
Gene/protein regulation
II |
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*Talk
by Dr. Nicholas Mantis, McC B05, Monday, 4:30 pm ÐEXTRA CREDIT! |
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M-F 3/14- 3/18 |
NO CLASS- Spring Break! |
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M 3/21 |
Genetic mutations |
11 |
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W 3/23 |
DNA repair |
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R 3/24 |
Student presentations
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F 3/25 |
Gene transfer I:
Transformation, Conjugation |
13 |
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M 3/28 |
Gene transfer II:
Transduction, Transposons |
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W 3/30 |
Antibiotics |
35 |
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R 3/31 |
Student presentations
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F 4/1 |
Antibiotic resistance |
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M 4/4 |
Viral Structure,
function and life cycle |
16 |
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W 4/6* |
Propagation of viruses:
Lytic versus lysogenic phages |
17 |
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R 4/7 |
Student presentations
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F 4/8 |
Eukaryotic viruses |
18 |
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*Self
schedule EXAM 2 between 4/5-4/13 |
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M 4/11 |
Viruses and disease |
38 |
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W 4/13 |
Cancer and HIV |
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R 4/14 |
Student presentations
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F 4/15 |
Special topics |
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M 4/18 |
Special topics |
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W 4/20 |
EID class presentations
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R 4/21 |
Student presentations
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F 4/22 |
EID class presentations
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M 4/25 |
EID class presentations
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W 4/27
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EID class presentations
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R 4/28 |
Student presentations |
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F 4/29 |
Last day of classes |
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*EXAM 3 due
5/5 by 5 pm |
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12. Bacteria and the environment
13. Replication, transcription, and translation
14. Gene and protein regulation
17. Dorit Research Talk (Antibiotic Resistance)