Example from 2002 [for those who want to see what to
expect] To begin your search, you may want to check out the
library's subject guide for cell and molecular biology,
which offers basic searching tips and information on
databases: You need to use your user ID and PIN for some databases.
If you have difficulty, make a brief visit to the reference
desk in the library for assistance. If you want to just jump
in, try PubMed: In addition to the linked sites above, check out
additional links on the Links
page. [Let me know if you find useful sites which should
be added.] You can save your selected search results in a log, as
you do for sequence searching. This is handy for making a
useful printed short list to take to the library, or for use
when in other databases or accessing on-line journals. Some questions are general enough to allow you latitude
in your searches; others are specific and allow fewer
options in obtaining your information. All tools for doing
literature searches are open to you. If you don't know how
to approach a particular question, see me. THE HONOR
SYSTEM DOES APPLY. The point of this exercise is, in
part, to learn how to do a literature search. So- do your
own search. Carpooling for library field-trips for
journal access, or sharing information on database use or on
finding on-line journals, is certainly acceptable. You have several choices in getting the actual papers.
You can use our library and other libraries, such as UCD and
UCSF. You can access some on-line journals for free, some
on-line journals have limited access, and some charge a fee.
PubMed is now providing direct links to journals on-line,
and the free ones are marked. In addition, our library is
part of some consortia which allow us access to specific
journals. Particularly useful are Elsevier and Wiley
Interscience. Other resources for free access are NewJour
[linked on the library's Journal & Database page,
lower right column] and Highwire Press: www.highwire.org.
You can request documents at the library from journals not
available locally or free electronically. You can order
papers on-line, but this is usually the most expensive
solution, if you have a significant list of articles. When
in a real, not virtual, library, be kind- don't make other
people's searches a royal pain- there is plenty of space for
all. Replace references on the central re-file shelves for
journals when you are finished with a volume. That way
others may locate them more easily. Citations of your references are required, unless
otherwise stated. (Be precise! You can count on us looking
up some of these. Try copy/pasting from your log to avoid
typos.) An example of a reference citation is as
follows: Group your reference citations for each question with
your answers to that question. They may precede or follow
your answers as you choose, but they MUST BE PRECISE. A
general bibliography without citation notes within your
answers is not acceptable. Use either a number or the first
author, and year if necessary, within your answer to refer
to your references. Papers are to be typed in a standard font style
[please avoid script styles]; 12 pt is preferred, 10
pt is tolerated. Clearly indicate which questions are being
answered and collate them in order. [E.g.: question 1
before question 3; a before b.] Check to be sure all
subsections are answered and all parts of questions are
answered, or points will be lost. Page limit: 12, including
answers and citations. Please- no report covers or binders.
[Saves you $$ & saves me time.] Just a single
staple in the upper left-hand corner will do fine. Although most would assume that a statement on plagiarism
is neither required nor needed, I unfortunately discovered
otherwise. I direct you attention to the University's
catalogue for campus policy on plagiarism. I expect answers
in your own words, not that of the journals cited, or others
not cited. I expect some thought and synthesis of
information, not a regurgitation of phrases quoted. Quotes
are permissible in appropriate circumstances and when
referenced, but they should be used sparingly, if at all.
Use your log appropriately. You can use it to collect papers
and references. It is one useful way of organizing citation
lists, which can then be copied to your paper chase file.
But don't use it as a source of transferred blocks of text
into your answers. If I find an answer is plagiarized, it
will receive NO CREDIT. For help on this, check out the
following: If you find writing a problem, or you have difficulty
organizing notes into coherent text, the Writing
Center can be a lifesaver. They are very good at cutting
to the chase of what the problem is, and offering workable
solutions in a minimum of time. PART A. Choose either question 1 or 2 below. [30
pt] 1. Several researchers have been investigating the
mechanism of prion folding and the relationship of altered
prion protein structure to the development of
neurodegenerative diseases. a. Two different mechanisms of prion protein
folding have been recently reported. S.K. DebBurman has
examined the conversion of prion protein structure by a
chaperonin. Y. Cordeiro reported on the involvement of DNA
in the folding of prions. Briefly summarize the methods and
results of these studies. How do these papers compare in
terms of explaining the formation of prions? Is it possible
that two mechanisms exist that are responsible for prion
protein folding and that both result in essentially the same
product? Support your answer. b. What are the latest views of S.B. Prusiner, the
"father" of prions, regarding the connection of prions and
different neurodegenerative diseases, such as scrapie and
Alzheimer's disease? What are the latest views of Prusiner
on the actual formation of prions? c. Describe the major hypotheses on fibril
formation and briefly summarize the data supporting them.
K.J. Knaus's recent crystallographic analysis sheds some
light on the mechanism of fibril formation. How do his
results contribute to the debate on fibril formation? 2. The hemorrhagic fever viruses, which include
Marburg and Ebola viruses, have captured the attention of
epidemiologists in the past several years. The cause of the
sudden outbreaks as well as the disappearance of any sign of
the virus for extended periods of time are still a
mystery. a. C.J. Peters' career has been focused on the
Ebola group and their hemorrhagic fever relatives. Outline
the most recent understanding regarding the similarities and
differences of Ebola Sudan, Ebola Zaire, Ebola Ivory Coast,
and Ebola Reston. Include in your discussion molecular
comparisons, epidemiological comparisons, and outstanding
questions yet to be resolved. b. Following the Zaire outbreak in 1995, a renewed
effort was made to determine the reservoir for Ebola.
Briefly review the studies conducted by H. Leirs and P.
Reiter. What types of human encroachment on previously
undisturbed ecosystems expose people to new infectious
diseases? What must occur for a virus to cross from a
natural reservoir to human? What can be done to limit the
spread of disease locally and globally? c. As frightening as Ebola appears to be, the
outbreaks generally are quite limited. What changes could
occur which would allow Ebola to spread more broadly and
cause a more disseminated epidemic? What is the current
progress of vaccine development for these viruses? PART B. Choose either question 3 or 4 below. [40
pt] 3. The recent events involving the bioterrorist
attack using significant amounts of Bacillus
anthracis spores and the continuing threat of
international terrorism raises many issues regarding the
impact of a bioterrorist attack. Various studies have
attempted to predict the impact following a broadly
disseminated release of an agent. Post-attack estimates of
economic impact have been made of over $26 billion per
100,000 exposed to anthrax, for example. However, biowarfare
can be considered in two different lights. Besides the
threat of biowarfare and bioterrorism directed against
humans, there is also biowarfare directed against pests and
pathogens as a means of control, in lieu of chemical control
methods. a. When smallpox was first eliminated from the
world, it was hailed as a great accomplishment for world
health. Now, 25 years after that declaration, the world
population is no longer immune to smallpox. Smallpox has
been mentioned as a key potential agent which could be used
by terrorists. What are the major features which make this
an attractive choice for terrorists? What are the
drawbacks? b. How prepared is this country, or the world, for
such a possible attack? What types of prevention or
intervention programs exist against smallpox? Are these
sufficient to protect the US population; the world
population? What types of analyses have been made to
evaluate the impact or success of these programs? [What
is the estimate for the cost of this preparedness? Is it
worth it? Can any country afford it?] What could be done
to eliminate smallpox as a potential threat? Should the
remaining research stocks of smallpox be destroyed? Support
your answer. c. Cite another example of a virus which an
individual or government might wish to use to further their
political ends. Describe why the virus would work as a
weapon. Has it been listed in anyone's arsenal of bioagents?
If so, whose? What types of prevention or intervention
programs are possible against your example? What types of
analyses have been made to evaluate the impact or success of
these programs? d. With increased regulations and restrictions on
the use of chemical pesticides, there has been an increase
in the development and use of biopesticides, primarily
specific bacterial and viral insect pathogens. Give two
examples of viral insecticides. Discuss the efficacy of
their use. Are there any risks or disadvantages? If so, what
are they? a. Viruses may not always exist as they appear in
images with which we are familiar. J. Dubochet published
images of vaccinia which look quite different from the usual
images of pox viruses. He used cryoelectron microscopy. What
are the significant differences of these pictures of
vaccinia to those previously published? Briefly describe
cryoelectron microscopic techniques as applied to viruses.
How do cryoelectron images of other viruses compare with
images of the viruses prepared with other techniques, such
as conventional TEM and SEM? What are the limitations of
cryoelectron microscopy? b. Atomic force microscopy [AFM] is
another technique that yields high resolution images at the
nanometer scale. Describe briefly how this is accomplished.
Give some examples of AFM imaging of viruses. Compare and
contrast the utility of AFM and cryoelectron microscopy.
What are the limitations of AFM? c. By using AFM along with other methods, M.D.
Walkinshaw has recently reported on a bacteriophage protein
which acts as a structural mimic of DNA for the purpose of
inhibiting restriction enzymes. Give some other examples of
the application of AFM to the study of protein structure
and/or function. d. What other new types of imaging techniques have
been developed which might be of use in visualizing viruses,
their structural characteristics, and/or interaction with
their host cells? What are their individual advantages and
drawbacks in terms of technique and in terms of results?
Which method, in your opinion, holds the most promise for
future use on viruses and their macromolecules? Why? PART C. Design a question. [30 points] You
write a question concerning an area of your interest. I
review it, making comments or adding parts or whatever. Then
you do the search to answer your question. I've been asked if a question could be designed to
integrate the bioinformatics topic chosen. I think this is a
great idea, but by no means is it required. [See
Computing Exercise
3 for details of doing a combined bioinformatics
project/paper chase question.] In the past, some who did
this found that they got a lot more understanding out of the
information in the papers they were reading related to DNA
or structural details by doing some bioinformatics
searching. I am frequently asked if the paper chosen for journal
discussion can be connected to this part of the Paper Chase.
In short- yes. [Can they be unrelated?
Certainly.] b. The answer. Due on 4/18 along with the rest
of the answers. NOTE: Be sure to include your original
question, along with written comments,with your answers.
[Don't assume I'll remember everything about your
question out of the blue.]
[* Due date: Those in by 4/18 will be guaranteed
feedback by 5/16. Those in after 4/18 will be processed as
time allows. A 10-point/day penalty will be assessed,
including weekend days.]
INTRODUCTION
http://libweb.sonoma.edu/research/subject/cellmol.html
http://www.ncbi.nlm.nih.gov
Thatcher, E.F. and Gershwin,
L.J., 1989. Colostral transfer of bovine immunoglobulin E
and dynamics of serum IgE in calves. Veterinary
Immunology and Immunopathology 20:325-334.
http://www.indiana.edu/~wts/wts/plagiarism.html
THE QUESTIONS
4. New techniques in high resolution imaging are
being applied to study structural details of viruses and
macromolecules.YOUR QUESTION
a. The question. Turn in by 3/21. I will
return it by 3/26.
Updated 3/4/02 by thatcher@sonoma.edu