Microbiology 4141: Biology, Genetics and
Pathogenesis of Viruses
Quarter Prerequisites- Biol. 5003 and one of the following: Biol. 5004 or Biol. 5013 or
MicB. 5105
Semester Prerequisites- Biol. 4003 (Genetics) and one of the following: Biol. 4004 or
MicB 3301 (Biology of Microorganisms)
In order to understand the mechanisms by which viruses take advantage of and subvert
the host biosynthetic machinery, you need a good understanding of some basic
biochemical, genetic and molecular biological principles. Given the prerequisites for this
course, you should have a firm grasp of the definitions/concepts underlying the following
list of common scientific terms.
If you can not describe most of these terms, then you will have alot of difficulty with the
factual and conceptual material in this course: DNA, mRNA, amino acid, protein,
nucleotide, promoter, 5', 3', transcription, semiconservative DNA replication, translation,
codon, reading frame, splicing, recombination, plasma membrane, endocytosis,
endoplasmic reticulum, lipid bilayer, hydrophobic.
Can you draw a DNA replication fork? If not, check out the molecular biology tutorial
section of the class Web site!
Credit hours: 3
The university defines 3 credit hours as 3 contact hours plus 6 additional hours of work
outside of class per week for an average student to achieve an average grade in the
course. You will not do well in this upper division course unless you are willing to spend
the requisite amount of time preparing for class and working on assignments.
Office and phone: 1425 Mayo Building; 624-9933
Please feel free to stop by my office to ask questions if I am not busy. I appreciate the
opportunity to get to know you outside of class. You can call me to make an
appointment to stop by (I have voicemail), but to avoid playing "phone tag", it may be
easier and quicker to email me through the class Web site (see below).
Email: Private Email access to instructor is through the "Private class email" tool
in the course WebCT web site. Do not use other University email addresses.
Office hours: Flexible
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I am happy to meet with you at a mutually convenient time. My lab/office door is usually
open so you can also take your chances and stop by to make an appointment or to chat
briefly if I am not busy. I respond very well to e-mails (see above). Please come to
discuss questions, concerns, confusions, etc., or just to chat!
Catalogue description:
Structure, composition and properties of bacterial, plant and animal viruses; interaction
with cells, effects on host cell metabolism; molecular biology of virus replication and
genetics; techniques for studying virus properties; viral pathogenesis and
tumorigenesis.
Extended description and course objectives:
This is the second year that this course is being offered. My goal is to help you learn
about the diverse characteristics and ingenious replication strategies of animal viruses.
We will also investigate the mechanisms by which viruses cause disease. As a field,
virology is only about a century old, but it is growing exponentially. Many facts about
cell biology and molecular processes (for example, RNA splicing) were first discovered
in virus-infected cells. Still, there are many unanswered questions and interesting
problems. I hope this course will raise your curiosity about the field.
Despite the relative youth of the field of Virology, there is way too much information to
pack into this upper division course, even in a whole semester. As a consequence, my
hope is that you finish this course with a working understanding of important concepts in
virus biology, rather than a dazzling array of facts about specific viruses that you can
recall for the final exam but will forget soon after. This is not to say that there aren't
important facts that you will need to master. A certain factual knowledge base is
essential for you to be able to understand complex concepts. Towards this goal, we will
use a textbook that is organized around important topics in virus biology, rather than by
individual virus families.
Teaching methods:
To achieve the course objectives, we will combine lectures with a variety of active
learning techniques. These techniques will help you (and me) assess your
comprehension as the class is progressing. They are designed to keep us both
engaged in the process of learning and to keep the course flexible and fun. I look
forward to intelligent questions and thoughtful discussion. The variety of classroom
techniques should facilitate learning by those who favor different styles. For example,
some of you learn better by listening, some by writing. Some work better in groups,
others need more time to analyze and process information.
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It will be necessary for you to complete the assigned reading before class; otherwise
you will not be able to take effective notes and contribute to the discussions and
classroom activities. Quite often, you will be asked to write something in class, either
about assigned reading or the material presented in class. You might be asked to bring
to class a short exam question and answer, based on the assigned reading or you might
be asked to summarize the most important point from the lecture. You will need to bring
to each class session a few 4x6 index cards. Please do not turn in cards of other sizes
or answers on small slips of paper!! Only answers on 4x6 cards will receive credit.
The "writing intensive" component:
Learning to write is a lifelong process that is refined through your personal and
professional experiences. Through writing you gain knowledge and communicate your
ideas. The University of Minnesota is committed to the belief that writing and learning
are inseparable and that learning to write effectively is one of the most intellectually
empowering components of a university education. Thus, the University has established
a "writing across the curriculum" program. The goal of writing intensive courses, such as
this, is to prepare you to communicate effectively in a variety of situations in your future
employment and as a citizen.
In MICB4141 you will be asked to write both formally and informally. Writing will help
you organize your thoughts and assess your own understanding. Daily in-class
exercises are viewed as informal writing. In these exercises I am interested in your
thoughts, ideas and ability to integrate course materials. I am less interested in
grammar, punctuation and the structure of your sentences (as long as you are clear!).
Formal written assignments, on the other hand, will be evaluated on the basis of
substance, clarity and presentation. These formal assignments will range in length from
one page to five pages. The following are some of the objectives of the writing
assignments and activities in MICB4141:
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To communicate scientific knowledge clearly and accurately
To demonstrate proper use of grammar, mechanics, and general English
language usage
To understand conventions of writing within the discipline of Microbiology
To appropriately address specified audiences. For example, to communicate
technical knowledge to a non-technical or general audience.
To communicate appropriately to a specific purpose: for example, to inform,
persuade, instruct, compare, contrast or recommend
To write a research paper that thoroughly reviews relevant literature and
articulates an argument
To collaborate effectively with other students
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There are a variety of campus writing resources that can help you with the mechanics of writing.
Links to these are available on the class web site (see below) under the MicB4141 Tools icon.
[Teaching Assistant name] will be the teaching assistant for MICB4141 in 2001. She is a
graduate student in the field of virology and she is an excellent writer. Her major focus
as a TA will be to assist you with your writing and to help evaluate it. Jen will be holding
help-sessions to assist you with your writing. In order to take advantage of these,
however, you will have to be prepared in advance and avoid the temptation to
procrastinate!! You can contact Jen to discuss your writing and arrange help by using
the Contact TA forum in the bulletin board tool of the class Web site.
Note-taking: Dynamite Learning Tool or Dinosaur? There is controversy in the memoryresearch field about whether the process of taking notes serves an "encoding function"
(by helping students to process and remember information). However, results of an
informal survey taken in this class last year indicated that students who took notes in
class scored significantly higher in the class than students who did not take notes. In
1983, Carol Carrier, an education researcher, reviewed some of the available notetaking research. She found that students who take notes learn more than those who
simply listen to a lecture. This is because note-takers are active learners who must
select, interpret and connect information with other things they know. She also found
that students who reviewed their own notes scored higher on tests than those who
reviewed a detailed set of notes provided for them. Avoid the temptation to be a
passive learner in class or when you are reading.
WebCT- MicB4141 Web site:
This course has a web site. Click on course listing and then Microbiology. You should
see MicB4141 listed there. You can login with your x500 login and password. Netscape
is the browser that is recommended by the staff who maintain the WebCT sites.
This course web site is under continuous development, and will be modified as the
semester progresses. It includes a number of useful course tools. Your feedback is
requested in order to make the web site as useful and user-friendly as possible.
Syllabus and assignments- The course syllabus is on the web site. It includes the
reading assignments, which may be modified as the course proceeds. Writing
assignments are also described on the site.
Electronic mail- The WebCT environment allows private message transfer among
course participants and the instructor and between course participants. If you would like
to contact Dr. Schiff by email, you should do it through the web site. If you would like to
contact one of your fellow classmates, you can do it through the class web site, too.
When you have mail, the icon on the first page of the web site will have a "halo" around
it. Check it out!!
Course bulletin board- This very useful tool can be used to carry on an open, online
discussion ("chat"). It is a place where the instructor may choose to clarify an
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assignment, discuss students' questions about class material, or post study guide
information. There is a special bulletin board forum for contacting the TA for help with
your writing. The bulletin board is also a place where students may discuss questions
among themselves or ask fellow classmates for clarification of material, assignments,
etc. Material discussed on the bulletin board can be viewed by all class participants.
When there is a new posting on the bulletin board, the icon on the first page of the web
site will "light up".
Lecture note outlines- In general, I will try to make brief outlines of lectures available
at some time the day before the lecture. These should help facilitate note-taking. In
some situations, more extensive information may be posted on the Web site after class.
Reference and writing tools- Links have been generated to a variety of reference
materials, including scientific journals, virology web sites and university writing
resources. These provide interesting browsing and may be useful when working on
assignments.
Glossary- a glossary is under development.
Grade tool- Each student can view his/her grades. For some assignments/exams,
students will have access to minimum, maximum and average grades.
Calendar tool- A course calendar will contain useful reminders about course activities
and assignments.
Attendance and participation:
Learning is an active process that requires your presence as well as mine. It is
impossible for you to participate if you are not in class! 15% of your final grade will be
derived from participation in daily classroom exercises. So that I can keep track of your
participation, these exercises will be turned in at the end of class. Bonus points will be
awarded towards your final grade if you have perfect or near-perfect attendance. Don't
forget to turn in your 4x6 index cards at the end of class!
Class atmosphere:
Risk taking: I will take a risk each time I stand up to give a lecture or start a classroom
exercise. You will take a risk each time you ask a question, enter into a discussion or
participate in a classroom exercise . I hope we can build a supportive environment in
which everyone is comfortable taking these risks so that we can maximize learning and
personal growth.
Required text:
We will use a relatively new textbook, Principles of Virology: Molecular Biology,
Pathogenesis and Control by Flint , Enquist, Krug, Racaniello and Skalka. Designed to
fill a gap between simple introductory texts and very advanced reviews of major virus
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families, the goal of this textbook is to introduce upper level undergraduates, graduate
students and medical students to all aspects of virology. Each of the authors has an
active virology research laboratory, and they have considerable expertise teaching
virology, molecular biology and biochemistry at both the graduate and undergraduate
levels. This textbook may be more difficult than others you have used. Consequently,
you may need to spend more time on your reading than you are accustomed to.
Recommended reference material: Fields Virology, Third edition. This reference book is
on reserve in the library. Virology is a fast-paced field. Resist the temptation to consult
older textbooks. They may contain material that is no longer accurate.
Grading:
Philosophy: As an undergraduate, I was not the greatest test taker. Thus, I am most
comfortable evaluating your progress based upon a variety of exercises. To encourage
you to keep up with the course material, the assignments and exams will be spread
throughout the semester. 55% of your grade will come from traditional exams, and the
other 45% will come from a combination of written assignments and classroom
exercises.
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Participation in daily exercises and other in-class activities: 15%
Written assignments: 30%
Three mid-term exams: 30%
Comprehensive final exam: 25%
Criteria for success: The University of Minnesota has established a uniform grading
policy. Grades are defined as follows:
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A- Achievement that is outstanding relative to the level necessary to meet
course requirements
B- Achievement that is significantly above the level to meet course
requirements
C- Achievement that meets the course requirements in every respect
D- Achievement that is worthy of credit even though it fails to meet fully the
course requirements
To encourage cooperative learning, grades will not be determined by a standard curve.
Rather, they will be based upon the percentage of the available points achieved. Cutoffs
will be based on the following percentages. You can check your progress on the
MicB4141 web site or you can make an appointment to talk with me. If you are having
trouble with the class material, please come to see me early!
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A range: 88-100%
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B range: 75-87%
C range: 60-74%
D range: 50-59%
Policies:
Written Assignments: Your written work should be typed or word-processed and
proofread for errors and clarity before you turn it in. Even if content is excellent, poorly
prepared written assignments may receive poor scores. Assignments that have not
been effectively proofread (i.e. papers with typographical errors or other serious flaws)
will be returned to the author for immediate revision and receive a maximum of 75% of
the available points. Now and in the future you will be judged based upon your written
work. There are no "second chances" when you submit a resume and cover letter for a
job!
Late Assignments: Since we all have complicated lives, you will each get one "free
late assignment" coupon which can be attached to an assignment that is turned in a
maximum of 2 days late. If the assignment is due on Tuesday, you can turn it in on
Thursday. If its due on Thursday....you can use the coupon to turn it in on Friday. Other
late assignments will not be accepted unless you and I have agreed on an extension
before the assignment is due (and only in extenuating circumstances). This policy is
necessary to be fair to those who do submit their work on time. If there are significant
assignment/exam conflicts that involve a majority of the class (for example with another
Microbiology course), please bring them to my attention and I will make an effort to
resolve the conflicts with the other instructors.
Class Participation: Participation in class exercises is expected. I can help you learn,
but the responsibility is yours. This means that you need to ask questions, offer your
opinion and join in discussions. My sense of the quality and level of your participation
(beyond just handing in evidence of daily work) will affect your final grade if it is
borderline. There is participation....and then there is PARTICIPATION!
Makeup Exams: According to University Senate Policies, makeup exams will be
provided for students who miss exams because of scheduled activities of an official
University student organization, a religious holiday, a verifiable illness, a serious family
emergency, jury duty or subpoenas. To be eligible for make-up tests, students must
furnish documentation that verifies the reason for their absences.
Incompletes: Incompletes will be granted to students for emergencies that are
documented. To receive an incomplete, students must file a written statement about the
work to be done and the expected date of completion.
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Academic Dishonesty and Plagiarism: Plagiarism is deliberately handing in another
person's material/work as your own. It may be that of a classmate or it may be that of a
scientist whose work you read while researching a topic. It may be overt, in the form of
copying answers from a colleagues' test, or it may be subtle, in the form of paraphrasing
information from the textbook or another source. Students are expected to express
themselves and to sustain an argument in their own prose. They should not submit
written work that does not properly acknowlege transcription or quotation of the work of
others. If you want to quote from a published work, either because you think it makes
the point or you admire the author's turn of phrase, you must put the passage in
quotation marks and cite the reference. More often, you will want to express what an
author is saying in your own words. In this case you should include reference to the
author you paraphrase to indicate that the ideas are someone else's and not yours. If
you are not clear about the differences between scholarly citation, collaboration and
paraphrasing, please consult Dr. Schiff. Defining plagiarism can be somewhat difficult
when cooperative learning is encouraged. If you are studying with friends or working in
groups, remember, when you turn in an assignment and sign your name to it, you are
pledging that it represents your own work.
Evidence of academic dishonesty in any form will be forwarded to the Student
Scholastic Conduct Committee. According to the university policy, academic dishonesty
in any portion of academic work shall be grounds for awarding a grade of F for the
entire course. For helpful hints on avoiding plagiarism, check out the following writing
resources section of the class web site.
Students with disabilities: It is University policy to provide, on a flexible and
individualized basis, reasonable accommodations to students who have disabilities that
may affect their ability to participate in course activities or to meet course requirements.
Students with disabilities are encouraged to contact Dr. Schiff at the start of the
semester to discuss their individual needs for accommodations.
OK.....Let's learn some virology!
Tentative course outline and reading assignments, Spring Semester 2000:
Date
Topic
Reading
assignment
Tues.
1 Introduction
Jan 16
none
Thurs.
2 Properties of Viruses
Jan 18
Ch 1
Tues.
3 Analysis of Viruses
Jan 23
Ch 2
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Assignment Due
Dates
page 8
Thurs.
4 Virus Structure
Jan 25
Ch 3
Tues.
5 Virus Attachment
Jan 30
Ch 4
Activity: Virus Entry (Assignment
Thurs.
6
Feb. 1
1)
Ch 5
Tues.
7 Exam I
Feb. 6
Covers lectures 1-6
(Ch1-5)
Thurs.
Genome Replication and mRNA
8
Feb. 8
Production/RNA viruses I
Ch 6
Tues.
Feb.
13
Ch 6
9
Genome Replication and mRNA
Production /RNA viruses II
Thurs.
Reverse Transcription and
Feb.
10
Integration
15
Ch 7
Tues.
Feb.
20
Ch 11
11 Translational Control
Thurs.
Feb.
12 Activity
22
Tues.
Feb.
27
13 Exam II
Assignment 2:
Compare & contrast
paper (3-4 pgs.)
Covers lectures 811 (Ch 6,7,11)
Thurs.
Transcription Strategies/DNA
14
Mar 1
Virus Templates I
Ch 8
Tues.
Mar 6
Ch 8
15
Transcription Strategies/DNA
Virus Templates II
Thurs.
16 Processing of Viral Pre-mRNA
Mar 8
Ch 10
Tues.
Mar
13
Ch 9
17
Genome Replication
Strategies/DNA Viruses I
Assignment 1:
Jigsaw summary (23 pgs.)
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Assignment 3:
Public Health Web
site
Preliminary outline
and sources due
page 9
Thurs.
Genome Replication
18
Mar 15
Strategies/DNA Viruses II
Ch 9
Tues.
Intracellular Transport and
19
Mar 20
Assembly
Ch 12 & 13
Thurs.
20 Exam III
Mar 22
Covers lectures 1419 (Ch 8-10, 12,13)
Tues.
Apr 3
21
Assignment 3:
Public Health Web
site
First draft due
Transformation and Oncogenesis
Ch 16
I
Thurs.
Transformation and Oncogenesis
22
Ch 16
Apr 5
II
Tues.
23 Viral Offense Meets Host Defense Ch 14
Apr 10
Assignment 3:
Public Health Web
site
Final version due
Activity: Immune Evasion
Thurs.
24
Apr 12
(Assignment 4)
Assignment 4:
Jigsaw summary
due (2-3 pgs.)
Tues.
25 Pathogenesis
Apr 17
Ch 15 & 17
Thurs.
26 HIV Pathogenesis
Apr 19
Ch 18
Tues.
27 Antivirals and Vaccines
Apr 24
Ch 19
Assignment 5:
Debate position
paper due (3-5
pgs.)
Activity: Debate Preparation
Thurs.
28
Apr 26
(Assignment 5)
Tues.
29 Emerging Viruses
May 1
Ch 20
Thurs.
30 Activity: Debate (Assignment 5)
May 3
Schiff, Leslie. Microbiology 4141: Biology, Genetics and Pathogenesis of Viruses. University of
Minnesota. 11 Dec. 2002.
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