Virology class - Syllabus as of Oct. 1

Fall, 2001 -- Lecture Hall 3 -- Mondays 6-9:30

November 19

Everyone's papers are in your folders in the rack outside Betty's door.  There is also a notebook of interesting papers to be looked at there.


Evaluations will be based on class attendance and participation (including bringing in extra relevant material), making mini-presentations throughout the quarter, a quarter-end major small-group presentation (3 people, 45 minutes) and your self evaluation. You will be expected to maintain a Portfolio of your work and turn it in at Week 5 and again at the end of the quarter, with your draft self evaluation.

I have intentionally left this initial syllabus rather sketchy, and will give you a more detailed one once I have a chance to better see your interests and needs.

1 /September 24 First class: Introductions and goals; Setting the stage: Viruses in the natural world; 

Overview: viruses in the ecosystem (including in oceans, maintenance of microbial and insect populations); discussion of virus families; basic infection processes.

Readings from Ackermann
2 /October 1 A. Properties of viruses; Lytic phages

B. Introduction to the immune system tissues and cells: T and B cells

A. Brock: 236-259; "Bacteriophages"; "T-phages"

B. Brock: 801-826; Macrophages, dendritic cells, epitope presentation and superantigens

3 /October 8 Guest Speaker: Burt Guttman "Prophage and Lambda"

A. Lysogeny

B. HIV and AIDs 

C. Continue immunology discussion

A. Brock 259-267; handout

B. Brock 946-955; 875-881 

4 /October 15 DUE:
1. Short statement of research plan and team.
2. 1-2 pages about some aspects of your reading, other than the project.

A. Teams, topics and brief outlines for presentations due.

B. Guest speakers: Robin Moore, Naturopathic physician; Cheri Lucas-Jennings 

C. Communication in and with the immune system: cytokines; activation; apoptosis; tolerance

C. Brock 826-852 
Monday, October 22, 3:15 PM -- guest speaker -- Julian Davies -- Antibiotics and Antibiotic Resistance, LH 5

The use of antibiotics has transformed the treatment of infectious diseasesduring the last half-century and until recetly it was a rare infection that was refractory. Nowadays, resistant bacterial strains are more common and antibiotics often fail, particularly among the young, elderly and hosptalised patients. There are a number of reasons for this change (some will be discussed), but lack of knowledge of bacteria and their ability to survive catastrophes is perhaps the most important. We are now trying to understand how microbes evolve to survive antibiotics and I will summarise the current state of our comprehension. One thing is certain, antibiotic resistance is a very complex process! Will this knowledge help to expand the useful lifetime of existing antibiotics and find new and better ones? This remains to be seen. Finally I would like to present some ideas on the roles of antibiotics in nature; are they really antibiotics?

5 /October 22 Portfolio -- first half work --due during week 5 

A. Seminar: Book about AIDS, of your choice
Bring seminar presentation paper. Should contain three points or questions you feel are important. Write a paragraph about each point. Phrase carefully (precicely). Discuss why you feel each point is important and what questions they raise for you.

B.Continue cytokines discussion: review readings, discussion of questions from small groups and new ones.

A. AIDS book of your choice.

B. Brock 826-852

The 10th Annual Graduate School Fair, October 24, 10am-4pm, Library Lobbies

A. Large DNA viruses: Herpes, the "eukaryotic T4" 

A. Brock 276-279; 945-947, Herpes handout
DUE Nov. 5:

1.  3-page paper -- use the 2 handouts related to dendritic cells.  Summarize the material you understand in them as best you can, phrase questions about the parts you don't understand as sophisticatedly as you can, and distinguish carefully between what you do and don't understand.  You are welcome to use your notes, etc., and encouraged to use the colored figure of cytokines and the infection process that I gave you.  [Note that this is NOT intended to be a research paper -- you don't need to do further research of any sort to try to answer the questions you formulate -- the formulation is the idea!!]

2.  More detailed outline of presentations. Explicitly, who is going to be responsible for what sections?  Why is this topic of interest, and what are the main important points you are trying to make?  What are the main references you have been using to date?  What questions are you now focussing on in your research?  (One of the main factors in making a good presentation is defining your topic both narrowly enough and broadly enough.  Often, this means giving a general broad overview and choosing a few specific pieces or examples that you really focus in on.  These may be chosen because of their special interest or
current relevance.)  Expect to have about 15 minutes per person in your group -- but it often works best to intersperse pieces rather than just having each person complete theirs separately if your topics are closely integrated.  In other cases, the topics may be only loosely related, complementing each other somehow.

7 /November 5 A. Small circular ds DNA viruses: Papovaviridae - papilloma viruses, warts and cancer

B. Hepatitis viruses: B (Hepadnaviridae family, circular ds DNA -- vaccination issue, especially); C  (Flaviviridae family;
linear + srand ssRNA); D (circular ssRNA; needs hepatitis B for envelope), (A (Picornaviridae family, like polio, + strand RNA);  E won't be discussed at this time)

C. Immunization

A. Brock 276-7; 886, Papilloma handout

B.  Brock 282; 988-989

C. Brock: 803-4, 847-9, 908-11

8 /November 12 A.  HIV and AIDS 

B. Psychoneuroimmunology 

A.  Handout from Principles of Virology (Flint) 632-661 World impact of viral diseases -- a discussion

B. Handouts from Psychoneuroimmunology, 3rd edition: (since one of the groups is dealing with PNI, exactly what is covered in this class discussion will be chosen to complement what they will be doing.)

November 19 Thanksgiving Break  none
9 /November 26 Time for you to meet with your group, practice, see what you still need to do or ask to prepare for an excellent presentation -- I will be back by Nov. 28 if you need further help from me in an way, and you can also email me. none
10 /December 2 PNI group; (rest of schedule to be determined Nov. 
10 /December 9 Student group presentations: (schedule to be determined Nov. 5)

Final quiz on viruses, etc. and discussion thereof (with study guide in advance)

Portfolios and draft self evaluation due

I have not found an appropriate single text for this program, so we will use a combination of suggested readings in:

Brock: Biology of Microorganisms (a very good, broad microbiology text which some of you already have and M2O will be using - or use any good recent micro book you have)

short readings handed out, readings and books on reserve, and your own explorations of the literature.

Good other resource books include:
G. L. Smith, W. L. Irving et al: New Challenges to Health: The Threat of Virus Infection (2001)
SJ Flint et al- Principles of Virology: molecular biology, pathogenesis and control (2000)
I have the older edition of Webster - Encyclopedia of Virology and the library is ordering the most recent division.

Immunology studies will be woven throughout the quarter. While we will only be studying certain aspects of immunology - primarily those most relevant to viral infection, + psychoneuroimmunology - a number of you may want to get an immunology book, both for use here and for future reference. They are available at for around $60. (There will be some immunology books on the reserve shelf as well.) Possible choices include:

Roitt and Rabson - Really essential Medical Immunology - 2000
Kuby's Immunology - 4th edition - Goldsby et al. - 2000 WH Freeman
Janeway - ImmunoBiology 5th edition -- Garland

PRESENTATIONS: Students will be required to give substantial presentations at the end of the quarter, preferably in groups of about 3, and will also be very much encouraged to give short individual presentations throughout the quarter as part of the general class sessions.

Questions to address in general in presentations: virus family, basic properties and infection cycle. modes of transmission, reservoirs, breadth of infectivity, ecological factors and effects; vaccine availability and effectiveness, nature and length of immunity induced by natural infection and from various available vaccine types;
Some suggested topics for student presentations:

Adenoviruses and gene therapy

Baculoviruses (plant viruses) and molecular biology

Cholera, filamentous and temperate phages, and pathogenicity islands

The Hantavirus epidemic: tracking down the etiology; social concerns

Morbilliviruses, world-wide agriculture and endangered species

Common family members: measles (MV), canine distemper virus (CDV - ferrets, mink, panda, seals), rinderpest ((RPV - ruminants - buffalo, kudu, eland); phocid distemper virus (PDV - seals); cetacean morbillivirus (CeMV - whales, porpoises, dolphins)

Mouse Mammary Tumor Virus (MMTV), mtv and the roles of superantigens


Rabies (a negative-strand RNA virus)

Rotavirus (a reovirus) and infant diarrhea in 3rd-world countries

Smallpox: infection process and consequences, vaccination, eradication and potential for bioterrorism

Betty Kutter, ext. 6099,

Contact Julie Farr to add links, or with questions or concerns.

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Last updated October 29, 2001