Jumat, 26 Agustus 2011


Your assignment is to survey the primary literature in a well-focussed area of virology and to write a literature research paper (also known as a "term paper") of approximately 3000-4000 words reviewing the current state of knowledge in the chosen area. The purposes of the assignment are to acquaint you with the current literature in virology, provide you with in-depth knowledge in an area of virology that is interesting to you and to familiarize you with some "cutting edge" research in virology.

The term paper assignment is separate and distinct from the oral report assignment although there is some overlap in purpose between the two assignments.



A: Selection of topic

There is no restriction as to topic except that it must involve some aspect of viruses and it must be approved by the instructor. The latter restriction is enforced to keep topics well-defined and manageable and to ensure that no two students select an identical topic.

The "first come first served" rule is in effect here. Students who make a topic selection early are less likely to run into conflicts with other students. Register your choice with the instructor to receive priority. Email is a good option here.

In order to keep to a schedule, the term paper topic must be elected fairly early in the semester. This means you will need to carry on some extra reading outside class and consult with the instructor as you define your interests and narrow your choices. The deadline date for topic selection is given in the Term Paper schedule.

Your term paper topic may be related to but not identical to the topic of your oral report. For graduate students, your term paper topic may be related to but not identical to your thesis topic. I will expect an OK from your major advisor that the term paper topic you have chosen is not too closely related to your thesis. These may be subsequently revised, if necessary.


B. Library Research

You will need to survey the primary literature in order to write your paper (and perhaps to select your term paper topic in the first place). Some scientific journals devoted to reporting the results of studies with viruses include (but are not limited to) the following.

Virology: publishes mechanistic and molecular reports on all types of viruses; perhaps the most prestigious virological journal

Journal of General Virology: publishes studies on all aspects of virology, including studies considered too biologically oriented to be accepted for Virology; because of the wide range of studies published here, this tends to be the most interesting virological journal

Journal of Virology: concentrates mainly on medical aspects of virology and on animal virology, but does publish studies on plant and bacterial viruses; papers with molecular, biochemical, structural, biological orientation may appear here

Intervirology: publishes fewer articles, but does accept a wide range of topics; this is the journal in which matters of taxonomy, nomenclature, classification are usually discussed

Phytopathology: publishes a few papers each issue pertaining to plant viruses, usually reporting biological studies

Journal of Bacteriology: publishes papers on various aspects of bacterial viruses

Journal of Clinical Microbiology: publishes a few articles each issue strictly on medical aspects of virology

Journal of Medical Virology: devoted to a wide range of aspects of medical virology, including case studies

Journal of Virological Methods: reports new methods for the study of animal, plant and bacterial viruses

Cell: the most widely-cited journal in all the biological sciences occasionally publishes an article pertaining to virology, when the studies reported have very great significance

These journals are by no means the only ones which contain papers on viruses. They are merely the leading journals in the field. Unfortunately, the IUP library receives few of them. Obtaining copies of articles which appear in other prominent journals is thus made somewhat problematic.

There are several ways to deal with this difficulty. The most effective way is to travel to a university-level library in another community (Pittsburgh, State College, Morgantown, to name a few) and look up the article there. The second way, which is less reliable and ultimately more time-consuming, is to use the inter-library loan service (ILLIAD). The third way, the slowest and least reliable of all, is to use reprint request cards to ask authors directly for a copy of the needed article. Your instructor will demonstrate the use of these cards. Another way that may prove effective is to download from the internet, when possible.

Your paper MUST be based mainly on primary articles published within the last few years. Primary articles are those which make the initial report of original research and have undergone a process of checking by other scientists that is called peer review. Primary reports contrast with secondary, or review reports, which make use of primary sources to discuss and summarize the current state of information in an area. They bring together many primary articles to present an overall, up-to-date picture of a topic. Secondary articles are often helpful in locating primary articles or defining a topic. Because it will be based upon primary sources, your term paper will ultimately resemble one of these review articles. You should consciously model your term paper on a review article such as those which appear in the “Annual Review” series, available electronically on the IUP campus.

Tertiary sources, such as textbooks, will be of little help in your work, since they are usually outdated by years at the time of publication

You will probably find that internet searches of the literature will make your job much easier. You will also probably find that there are many pages and sites that deal with different aspects of virology. You may use these sites for background information but the main thrust of your paper should deal with reports in the primary literature. Unlike web sites, these reports have been reviewed by peers and may be assumed to be of greater value and accuracy.

Web sites such as Wikipedia are not acceptable sources. Your citations must come from peer-reviewed materials.

You will be required to keep the instructor up-to-date on the progress of your literature review and you will be graded on how well you do so. See the Term Paper Schedule for details.




C: Organization of paper

The final paper must organized into the four main sections listed below. To organize your paper further, use subheadings wherever possible within each section.

(1) Introduction

(2) Body

(3) Conclusion

(4) Bibliography


(1) In the Introduction, briefly review and describe the viruses you will discuss as well as the biological property being reviewed (replication or transmission for example). The general state of knowledge in the area and the pertinence of the topic should also be described. Include in the Introduction a list of the abbreviations you will use in the term paper.


(2) In the Body of your paper you summarize the knowledge in the field, discussing the pertinent contributions of each important primary report, one at a time. In essence, you use the Body to present the results of your literature review. In this part of the paper you are getting your message across, explaining the material to your readers. It is your job as writer to organize, reorganize, synthesize, paraphrase, summarize----whatever it takes to package the information in a form which is easy for the reader to understand.


(3) The Conclusion does two things. First, it summarizes the results of your literature review. Second, it pulls together the information you have collected to produce a "take-home message". In other words it synthesizes the important information.


(4) Bibliography lists the primary, secondary and tertiary literature you have consulted. For literature citations, use the same format as that used by articles in the Journal of Virology. I expect all students, both graduate and undergraduate, to do a professional job of searching the literature and I expect their bibliographies to show evidence of this. Microscopic bibliographies containing many tertiary sources or only a half-dozen or so references will count against your grade. I fully realize the difficulties of attempting to do library work at IUP and I also realize that the only way to surmount them is to start soon and to keep with it. Waiting until the last minute guarantees extra problems and lower grades.

Papers not conforming to format guidelines will be returned ungraded.

You will be expected to keep the instructor posted as you progress through the stages of writing your paper. See the Term Paper Schedule for details.


D. Style

The paper is to be written in the general style of a regular scientific review article (see the library's electronic collection of "Annual Review" serials for examples). Write the paper in standard scientific English, using jargon where appropriate and with definitions. Use complete sentences with correct punctuation and minimal spelling errors. Assume that your audience consists of a group of upper-division, advanced undergraduate students of at least your own level of education. If there are questions of style, usage, spelling, abbreviations, format, etc. refer to the Journal of Virology for guidance. Papers must be typewritten or neatly handwritten. Papers not conforming to stylistic guidelines will be returned ungraded.


E. Schedule

The deadlines for submitting various stages of the term paper are given below. These deadlines are in place to ensure that students make regular and steady progress toward completion of the paper and to discourage procrastination. Except in cases of dire emergency (as judged by the instructor on a case-by-case basis), failure to meet a deadline will result in a grade of zero for the appropriate segment of the term paper.

March 1 (Monday) at 4:30 PM This is the deadline for turning in a preliminary term paper topic in hard copy format and discussing it with me (aka First Progress Report). These may be subsequently revised, if necessary. You have to have a topic and a few references at this point. We will also discuss your literature search.

April 5 (Monday) at 4:30 PM At this time a brief outline of the paper is due (aka Second Progress Report) in hard copy format. The major subheadings of Introduction, Body, and Conclusion must be in place. The important points in each subheading should be listed. The bibliography should be well advanced, with all of the key references and most of the others listed. Subsequent revisions are permitted. We will have a more in-depth discussion of your literature search at this meeting.

May 3 (Monday) Finished papers due at 4:30 PM.

If you have any questions about the format or other requirements for brief outline, preliminary bibliography, and so on, feel free to contact me for clarification.



Your paper will be graded on a 100-pt. scale with points awarded according to the following schedule.

Source Points Due Date

Brief Outline/

First Progress Report 5 Monday March 1 at 4:30 PM

Final Outline/

Second Progress Report 5 Monday April 5 at 4:30 PM

Finished Paper 90 Monday May 4 at 4:30 PM

You will receive full credit for the term paper topic, the brief outline and the final outline as long as you turn them in ON TIME and written according to the guidelines established above.

Finished papers will be assigned first a letter grade and then a number grade from the range corresponding to the letter. Comments will be written on each individual paper Letter grades and their corresponding number range are given below.








Excellent; you conducted a thorough survey of the literature, concisely synthesized the data, communicated the results effectively, summarized and produced a take-home-message, used correct scientific terminology and followed the format



Above Average; you did many but not all of the above; see paper for more comments



Average; you did some but not all of the above; see paper for more comments



Below Average; you did not do most of the above; see paper for more comments



Far Below Average; you did few or none of the above, did not turn in a paper, or did not meet a deadline


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