Virology
Biology 319, Spring 2005
Text:
Dimmock, Easton, Leppard, Introduction to Modern Virology, 5th edition. Blackwell Science.
Instructor:
Roger Denome, Associate Professor of Biology, rdenome@stonehill.edu
Office hours: M-F 8:30-9:30, T-F 11:15-12:00, and by appointment.
Room 213 Science building. Office phone: 565-1196. Lab phone: 565-1171
Web site: http://faculty.stonehill.edu/rdenome/index.htm
Class Place and Times: M, W, F, 10:30-11:20
Lecture Schedule
19 January What are viruses? Chapter 1
21 January
24 January Techniques to study viruses Chapter 2
26 January
28 January
31 January
2 February Virus structure Chapter 3
4 February
7 February
9 February Viral genomes Chapter 4
11 February
14 February
18 February Test #1, over Chapter 1-4 (Topic for paper due. 5 points)
21 February Viral attachment and infection Chapter 5
23 February
25 February Genome replication for DNA viruses Chapter 6
28 February
2 March
4 March Genome replication for RNA viruses Chapter 7
Spring Break 3/5-3/13
14 March Genome replication involving reverse transcriptase Chapter 8
16 March
18 March
21 March
23 March Test #2, over chapters 5-8 (Paper rough draft due. 10 points)
30 March Gene Regulation in DNA viruses Chapter 9
1 April
4 April
6 April Gene regulation in RNA viruses Chapter 10
8 April
11 April
13 April Virus assembly Chapter 11
15 April
18 April
20 April Student Presentations (50 points) Paper due (35 points)
22 April
25 April
27 April
29 April
2 May
4 May Test #3, over chapters 9-14
Grading, Tests and Written Assignments: Your grade for this class depends on 3 lecture tests (each worth 100 points), one paper and the associated class presentation (100 points), and a cumulative final (200 points). Lecture tests will emphasize the material covered in the previous section (11-13 lectures) of the course. It is impossible to keep these tests from being cumulative; there is a great deal of overlap in the material from section to section. The format for the tests will depend on the material, although standard multiple choice and short answer questions will make up the bulk of the tests.
The final exam is comprehensive; all of the material that is covered in the course will be tested, in proportion to the number of lectures on that area.
The paper (50 points) and presentation (50 points) for this class will be on a virus of your choosing. This topic must be addressed in several ways.
1. You need to deal with the biology of the virus, in depth.
2. You need to deal with how that virus affects it's host.
3. You need to address the broader implications of the virus in terms of humans. (e.g. What are the socioeconomic effects? How has the virus altered how people act? What treatment strategies have worked, and how are those distributed?)
Obviously, the way you approach these topics depends to a great extent on what virus you choose. You must pick your virus by the first lecture exam and you must turn in a rough draft of your paper (with complete reference list) by the second exam. The paper is due on April 20th at 10:30 a.m.
During the last 6 lecture periods, you will present a summary of your work on your paper to the class. You will be graded on this presentation, so it should be complete and done to the standards of a paper presentation at a scientific conference. We will discuss the details of these expectations in class.
Grading:
540-600 points (90-100%) = A
480-539.9 points (80-89.9%) = B
420-479.9 points (70-79.9%) = C
360-419.9 points (60-69.9%) = D
< 360 points (below 60%) = F
Those students who have 90% of the possible points after the third test do not need to take the final. Their grades (A- or A) will be based on the percentages given above for the material on the first three tests.
Students may substitute the final exam grade for their entire grade in the class on the following grading scale:
180-200 points (90-100%) = A
160-180 points (80-100%) = B
140-159.5 points (70-79.9%) = C
120-139.5 points (60-69.9%) = D
<120 points (below 60%) = F
The intent of this policy is to supply a “safety net” for students who have one "less than good" test because of illness or emergency. Don't plan on using this method of grading. My experience has been that students who do so are very rarely happy with the results.
Objectives
There are 4 major objectives in this course.
Cell Biology of Viral Infection. Each major group of viruses has unique mechanisms of infection, replication and maturation. These have evolved to produce productive viral infections in particular host cells, which have their own unique characteristics. You are expected to combine your knowledge of cell biology with new material on each viral group so that you understand viral infection as an extension and perturbation of normal cellular processes.
The Molecular Genetics of Viruses. Some viruses have incredibly simple genomes. Others have genomes nearly as large and complex as those of prokaryotes. You are expected to know the genomic organization of the major groups of viruses and how those genomes are able to "hijack" cellular molecular biology to create more virus.
Organismal Responses to Viral Infection. Organisms have evolved an array of responses to viral infection. These responses are more or less successful at allowing the organism to survive viral infections. You are expected to understand these defense mechanisms, from the points of view of the organism and the virus.
Secondary Effects of Viral Infection. Viral infection frequently has effects other than simply killing the cell and producing more virus. These include long term effects on the immune systems of mammals, development of cancers and modification of host cell genome structure. You are expected to know these effects and understand the normal or aberrant conditions that produces them.
Notes on plagiarism.
You may discuss written assignments with each other. However, it is essential that the final product of the written assignments be individual projects. Please note the following rules for plagiarism.
1. Make sure that you are responsible for your wording. It is your responsibility to make sure that you put concepts in your own words, not those of a common study group or text. Similar wording and sentence structure are indicators of plagiarism. Copying, then altering a passage slightly so that the wording is not exactly the same as the original is still plagiarism.
2. Give credit to sources. If you do use wording or a significant body of ideas from another source, you must give credit to that source. This means including correct references and page numbers for the source. Using someone's work without giving credit is plagiarism.
In this class, you can't use the instructor, another student or the textbook as a referenced source. This means that you must come up with ways of saying things that are very different from the text. I realize that this is a departure from requirements for other classes, but it is necessary in this case. Written assignments are to see if you understand the material. If all you do is quote from outside sources, you haven't shown me that you understand the material. Work to express the concepts and facts of genetics in your own words.
There are only so many ways to describe many phenomena. The use of jargon words and phrases in genetics is not plagiarism. Plagiarism is the use of significant sections (a sentence or more) from another source without giving credit to the person who produced the original.
3. Response to plagiarism. If I encounter written assignments that seem to be plagiarism, the student(s) involved will be given the opportunity to explain. If the explanation is not satisfactory to all parties involved, an independent member of the science faculty will review the material. If the material is deemed plagiarism, then all of the papers involved will be given a score of 0 (zero). In addition, college rules for dealing with plagiarism will be enforced. This involves reporting the infraction to the Academic Review Board. A second offense will result in a grade of “F” for the course.