Transcript A One Semester First Year Seminar: An Interdisciplinary

A One Semester First Year
Seminar: An Interdisciplinary
Study of the SARS Virus
Julie B. Ealy
Assistant Professor of Chemistry
Pennsylvania State University
Lehigh Valley
2005
First Year Seminar at PSU
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Required of all freshman
Skill development
Academic integrity
Sense of community
Active and collaborative learning
Technology
• 8 months in preparation
Introductions
• A sense of community
– Listen and interact with different people
who individually, but more so
collectively, can contribute to a better
understanding of disease
I really never had a class at our university
where I really got to know the class, in
class. The class setting was so
comfortable.
Primary Literature
• Objective:
– Develop techniques for tackling problems
students know little about such as reading a
journal article or focusing on a table or graph
or figure
Science 2003, 302:1519-1522 “Are We Ready for
a Pandemic Influenza?”
Some words from the article: pandemic, influenza,
H7N7, pathogenic, conjunctivitis, serologic,
H5N1, virus, vaccine, seroarchaeology, amino
acid, cloned
Passages
• “Influenza viruses are typed according to
their hemagglutinin (H) and neuraminidase
(N) surface glycoproteins.”, p.1519
• “Transmission from aquatic birds to humans
was hypothesized to require infection of an
intermediate host, such as the pig, that has
both human-specific (α2-6 sialic acid) and
avian-specific (α2-3 sialic acid) receptors on its
respiratory epithelium.”, p. 1520.
Student Comment
One of the first projects that Professor Ealy
gave us was just to read over a four page
article. My first reaction was confusion. I
thought I would be taking notes and writing
everything Professor Ealy said down.
Instead, we learned how to read every
detail of an article. This task might sound
easy but it was much harder than it
sounded since we had to define words that
we had never heard of before.
Comments
• I haven’t been asked to read and
understand articles that are above
my knowledge level in any other
class. I learned to recognize and
examine important points.
• Learning how to comprehend a
seemingly unapproachable article
was a very valuable technique that
I learned from this course.
Graph/Figure/Table Interpretation
www.niaid.nih.gov/sars_meeting.htm
Malik Peiris, University of Hong Kong
Comment
• In this course we developed techniques
for… tackling problems that we knew little
about. We read articles that weren’t
written for normal readers, we researched
those articles, understood them,
summarized them, and made clear
statements about them. We studied
subjects in details where we learned how
to understand and make statements about
graphs, tables, and figures
Molecular Modeling – Spartan Pro
– utilize computer generated software that permits
3D visualization of molecular images that
enhances understanding of molecular structure
• Organic bases of RNA – 3D structure, formula,
hydrogen bonds
• 20 amino bases – name, abbreviation
• 21 nucleotides of cDNA for the spike glycoprotein
of SARS – identify complementary RNA – aa
• Build a beta sheet – 3 amino acids
• Build an alpha helix – 8 amino acids
Comments
• The thing that astonished me was that there are
approximately 1256 amino acids that make up
the spike glycoprotein. Now that I have seen
what a single amino acid looked like, then to
think of 1256 of them all linked to each other (for
the SARS spike glycoprotein) is amazing.
• The Spartan Pro program is a great tool to
generate a visual aid as a backup to what we are
discussing in class. Because my science
background is limited, comprehension of
structures is difficult without a picture as
reinforcement.
Comment
• Finally we constructed what is known as an
alpha helix. We did this by choosing 8 amino
acids…At first glance it looked like something
that was unorganized with no structure or
shape to it. Although as we proceeded to orient
this structure into a different view or angle so
we could see down the center I began to see
that I was totally wrong about my assumption.
…it looked as though there was a clean cut
circle that looked right through the middle of all
8 connected amino acids. Also, almost all the
nitrogens, oxygens, and some of the carbons
and hydrogens were organized around the
center.
Drugs and Side Effects
• Drug assigned – name, side effects, administration, what it
treats, structure
Lipitor
Treats Alzheimer’s patients for memory, thinking, and everyday activities
Side effects are nausea, diarrhea, not sleeping well, vomiting and others
Drug is administered by mouth in 5mg or 10mg doses
Comments
• This past week has been very interesting.
Every person in the class has talked about
a different pharmaceutical drug. It was neat
learning about the structures of them and
all of the crazy side effects that go along
with them.
• I must say, doing the assignment of
researching the drugs is one that I honestly
enjoyed. It was interesting learning more
about all the drugs and what made it more
interesting was that I was really familiar
with the drugs already.
SARS Main Proteinase – Atom/AA
Comment
• Once again, my understanding of this
class has been strengthened by the use
of 3-dimensional visual aides on the
computer. Very similar to the first
series of computer exercises I found
this one very fascinating and I found
that this information will aid in better
understanding of this course. I also
began to understand from this exercise
exactly how complex the protein can
be.
Comment
• We got the chance to look at the
different number of alpha helices and
beta sheets, along with loops which we
had never discussed before. It was
interesting to be able to view this image
as the cartoon representation, and then
switch it an atom view and a plastic
model view. These three images
allowed me to view them in different
aspects, which we didn’t do in our
previous computer exercises. It was
neat to be able to experience this.
Opening Paragraph for Docking
• What is seen on the screen is streptavidin, a
bacterial protein, complexed with biotin (purple), a
ligand (which in this case is a fancy name for a
molecule). The structure of the complex was
determined in 1989 by Weber, et al. An atom
model of streptavidin is displayed where all amino
acids and the side chains are visible. A space filling
model of biotin is displayed. Biotin is actually
vitamin H and is necessary for metabolism and
growth in humans. Biotin binds tightly to
streptavidin and makes the complex one of interest
in research. If the binding of biotin to streptavidin
can be understood better, it will aid in the design of
new drugs and ligands for proteins and nucleic
acids.
Biotin Docked into Streptavidin
Energy Values for Docking
Comments
• Another thing I got to use was ICM Pro. I got
to look at the structure of the bacterial
protein, streptavidin. I had the chance to see
biotin docked into the receptor, streptavidin.
• The other computer program that we worked
with really taught me a lot and I feel like I
understand that program. I got a pretty good
grasp of the concepts that were presented in
the computer exercise about drug docking. It
was interesting to see the drug trying to find
the perfect spot to dock in.
Poster Presentation
Topics: influenza, vaccines, economics, origin,
spread of SARS, structure of SARS
- share knowledge with others through a
poster presentation which requires
development of strategies for writing across
several disciplines
- understand that many people work together
and contribute to an understanding of a
general disease such as influenza, or more
specific diseases
Poster Presentations
• I learned a lot from working within a
group especially for this project.
• The poster presentations were easier
than I thought they were going to be.
The topic of our presentation was
interesting because it didn’t have to
deal with the virus of SARS itself but
how it affected the world economically.
• Group projects teach many things, with
an emphasis on working together with
others.
Final Comment
• When I first walked into this class I had the
attitude why do I have to take this class; it
has nothing to do with my major and it’s just
a waste of time. Although I soon would find
out that I was totally wrong with my
observations about the course and
everything else. I’ve learned more interesting
things in this class than I did in any other
throughout this semester.
References
• Abagyan, R., and M.Totrov. 2004. MolSoft, Molecules in
Silico. LaJolla, CA.
• Amino Acid references:
http://www.imb-jena.de/IMAGE_AA.html
http://www.biomed.curtin.edu.au/teach/biochem/tutorial/
AAs/AA.html
http://web.mit.edu/esgbio/www/lm/proteins/aa/aminoacids.
html
• Bowen, G. M., Roth, W.-M., & McGinn, M. K. 1999.
Interpretations of graphs by university biology
students and practicing scientists: Toward a social
practice view of scientific representation practices.
Journal of Research in Science Teaching 36: 10201043.
• Ealy, J. B. 1998. A student evaluation of molecular
modeling in first year chemistry. Journal of
Science Education and Technology 8: 309-321.
• Ealy, J. B. 2004. Students' understanding is enhanced
through molecular modeling. Paper accepted for
publication, Journal of Science Education and
Technology.
• Kozma, R. B. 1997. Multimedia and understanding:
Expert and novice responses to different
representations of chemical phenomena. Journal
of Research in Science Teaching 34: 949-968.
• Lowery, M. S. & Plesniak, L. A. 2003. Some like it
cold: A computer-based laboratory introduction to
sequence and tertiary structure comparison of
cold-adapted lactate dehydrogenases using
bioinformatics tools. Journal of Chemical
Education 80: 1300.
• Martin, N. H. 1998. Integration of computational
chemistry into the chemistry curriculum.
Journal of Chemical Education 75: 2, 241-243.
• NCBI Sequence Viewer. 2003. GenBank accession
numbers. AY274119. Available online at
http://www.ncbi.nlm.nih.gov/entrez/viewer.
• NIAID. 2003. SARS: Developing a research
response. May 30. Available online at
http://www.niaid.nih.gov/sars_meeting.htm.
• Peterson, R. R. & Cox, J. R. (2001). Integrating
computational chemistry into a project-oriented
biochemistry laboratory experience: A new twist
on the lysozyme experiment. Journal of
Chemical Education 78:1551.
• Roth, W.-M., Bowen, G. M., & McGinn, M. K.
1999. Differences in graph related practices
between high school biology textbooks and
scientific ecology journals. Journal of
Research in Science Teaching 36: 9771019.
• Shusterman, G. P. & Shusterman, A. J. 1997.
Teaching chemistry with electron density
models. Journal of Chemical Education 74:
771
• Wavefunction, Inc. Irvine, CA.
• Webby, R. J., and R. G. Webster. 2003. Are we
ready for pandemic influenza? Science 302:
1519-1522.