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THE VIROLOGY SHOW -
produced by JW & ET Spring, 2004
Prerequisites: Completion of the lower-division core in
Biology or equivalent. Strongly recommended: at lease one
semester of Organic Chemistry. Open to non-majors with
consent of instructor.
Approach: A balanced broad introduction to the
general field of molecular virology is my aim. Bacteria
phage, plant viruses, and insect viruses will be discussed
in addition to animal and human pathogens. Based on the
surveys, lectures will be tailored to fit the class as much
as possible. (Some restrictions do apply. J)
Structure: Lecture plus discussion. Discussion is
more than simple discussion- it includes demonstrations,
computer lab and wet lab exercises. [Please see
discussion schedule following the lecture schedule.]
Web-accessible course materials include schedule &
syllabus, study aids, links to resources, assignments, and
interactive exercises.
1. Lectures will be based on material drawn from
the texts, from other reference sources including current
literature, and from Web sources.
2. Discussion sections will include a variety of
activities, including "hands-on" exercises with modeling,
computers, and lab methods; focused discussion topics; short
presentations; and reviews.
3. To insure everyone stays on his/her toes and
doesn't wait until a midterm to read several chapters, six
short self-quizzes are available for copying and will be
reviewed in discussion sections during the term. [These
will not count in your grade.] In addition, there will
be short problem discussions throughout the term to help
with and expand upon the study guide problem sets. Study
guide problems are posted on-line.
4. The two midterms will be essay and will require
synthesis of information and thought. A sample exam will be
posted and will be available for copying.
5. There will be a series of exercises designed to
expose you to Web-based resources and database searches,
especially involving "bioinformatics" [translation:
protein and genomic sequence searches and analysis]. For
more information, check out "Computing" from the menu
bar.
6. Each student will present a journal paper in
their discussion group based on a designated topic. See
"Journal Presentation" below for more information.
7. "The Great Paper Chase" is a literature search
and information gathering exercise, with six weeks allowed
for completion. [The assignment will be posted on-line
by 3/2.]
8. The final will be one-half "midterm" covering
the last lectures, and one-half comprehensive. The lowest
score from the midterms and the final will be dropped.
[For the brave and the industrious, this makes the final
optional.]
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Assessment
& Grading
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Bioinformatics
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40
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Journal presentation
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20
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Discussion
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40
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2 midterms (100 pt each)*
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200
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1 final(100 pt)*
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1 paper chase**
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100
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Total
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400
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* One midterm or the final may be dropped. [This makes
the final "optional".] No make-ups on exams. If you have
a problem, see me well in advance.
** See below for description. Do pay attention to the
deadline schedule.
Note on final grade calculation: Grades will be
assigned based on an adjusted percentage. An adjustment
factor will be calculated for the highest undergraduate
points received. [If the total points possible is the
highest score, the factor = 1.000]. This factor will be
averaged with the adjustment factors from past years. Each
student's raw score will be adjusted by the averaged factor
and grades assigned as follows:
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A
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B
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C
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D
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F
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100-90%
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89 - 80%
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79 - 70%
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69 - 60%
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59-0%
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Cheating and plagiarism: This will result in
dismissal from class and a failing grade.
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Course Requirements
Bioinformatics:
Bioinformatics is the descriptive term now used for
web-based computer searches and analysis of protein, nucleic
acid, and genomic databases. Powerful search engines and
analysis software are now available which allow us to
consider questions which once, not very long ago, were
beyond our reach to answer. The exercises will allow you to
explore what has been discovered about viruses at the gene
and protein level. Perhaps you will make some discoveries of
your own!
These exercises are being updated and will be reposted
prior to lab sessions. Check the "Announcements" box on the
Home Page periodically for updates. Points will be earned
for completing the exercises.
- 10 pt- Computer exercise
1: Introduction & molecular modeling of viral
proteins
- 15 pt- Computer exercise 2: Sequence databases and
tools
- 10 pt- Computer exercise 3: Class projects
- a5 pt- Bioinformatics
survey
Grading on these is lenient; the key point is to learn
something in the process of doing them. You will be able to
explore while you gain some familiarity of how to find
sequences, to make comparisons of sequences, and to locate
original literature related to the sequences. You will be
shown where and how to continue learning more about
bioinformatics beyond the brief introduction given during
this course. You will also gain experience which should help
you in completing the Great Paper Chase. You may find that
learning virology just got a lot more interesting!
Journal Presentation:
Each student will select one paper on a topic related to
immunology. This paper will be discussed in your discussion
section. Check the Journal
topics schedule and the description
for details. Full points are earned, provided that the
presentation is given and that the paper presented was both
reasonably current and relevant to the topic.
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Discussion Sections:
To facilitate information flow and to establish two-way
communication, there will be short forms to return in each
section meeting. These will have space for input and
questions. Although I won't be taking attendance per se, do
see me if you have missed a meeting or if you would like to
sit in on the other section as a substitute. The activities
planned for discussion sections are integral to the course
and are expected to add interest as well as enhance the
learning process.
In addition to the discussion meetings, there will be a
variety of opportunities to participate in on-line
discussions. I will throw out some topics to get things
started. You are invited to add others as we progress
through the course.
Grading for discussion will be based on participation,
both in discussion section and on-line. It is a fairly easy
way to earn points while doing some things which will make
learning virology easier, and maybe even fun.
Midterms:
Two one hour exams will be primarily short essay format,
covering major principles and concepts. Thought and analysis
will be stressed. Memorized material will be restricted as
much as possible to short questions and diagrams. A
representative example of a midterm will be posted in the
case outside D234. Use of Study Guide 1, Study Guide 2, and
the timely use of the on-line self-quizzes will help in
keeping up with the material and reviewing for the
exams.
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Final:
A choice of questions will be offered. The focus of
one-half of the exam will be on material covered after the
last midterm. The balance of the exam will be questions
requiring synthesis of material covered throughout the
semester. See Study Guide 3 for aid in preparation.
The Great Paper Chase:
This exercise carries the value of one midterm or the
final. However, two points should be made clear. One, you
have control over the quality and content of this effort,
and I have control over the exams. Second, past students
consider this to be the most significant learning experience
of the course. The Paper Chase is a computer and library
literature search exercise and is in 3 parts. All but the
last part total 70 points. The first part is worth 30
points; the second part is worth 40 points and may or may
not cover a summary essay question. Some questions are
general enough to allow you latitude in your searches;
others are specific and allow fewer options in obtaining
your information. The last part is worth 30 points and is
based on a question you write, submit for approval, and then
answer. All tools for doing literature searches are open to
you. The questions for the Paper Chase will be posted by 3/5
and are due 4/18. For papers returned by the deadline,
feedback will be given by the last class, perhaps sooner. 10
points per day, including Saturday & Sunday, will be
lost for lateness.
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