College of Arts and Sciences
American University
Washington, D.C.
Winter 2013
www.american.edu/cas
catalyst
AMERICAN UNIVERSITY SCIENCE
EDITORIAL
Partnership Between McDonald’s and
Marine Stewardship Council Far From Sustainable
Mission Statement
By Jaclyn Yeary, biology/film and media arts, ’13
As organic and local options have become widely accessible, more and more consumers in
the United States are looking for responsible food options. As vendors search for ways to
make their products desirable, corporate notions of “sustainability” are often at odds with the
recommendations given by scientists.
In January 2013, McDonald’s announced that it would serve Marine Stewardship Council
Certified sustainable fish in all of its U.S. locations. This announcement made the company the
first national restaurant chain to bear the MSC’s blue eco-label on all of its packaging, providing
consumers with a visual cue that the seafood they are purchasing conforms to the highest
available standard for seafood sustainability and traceability. However, the wild-caught Alaskan
pollock that McDonald’s uses is far from sustainable and points to a bigger problem within the
MSC’s certification system—and, to some extent, the way we look at seafood as a whole.
The MSC was founded by the World Wildlife Fund and Unilever as a market-based solution
to overfishing. The council sets standards for “sustainable” seafood based on a variety of
factors, including health of the population, damage to the sea, and fishery management. If a
fishery wants to become certified by the MSC, it must hire a commercial auditor to assess
its stock. The process may take years and cost hundreds of thousands of dollars. At the end,
the auditor makes a recommendation based on the MSC’s standards. Despite checks and
balances implemented by the MSC, current practices have the potential to create a financial
conflict of interest. Independent auditors stand to earn a higher profit if they are more lenient
in their recommendations.
Despite the fact that the MSC claims to use the best available science in order to set its
standards, this system has led to the certification of several controversial fisheries. The Alaska
pollock fishery from which McDonald’s obtains its product is no exception.
A catalyst, as defined by scientists, facilitates chemical
reactions by bringing together substances that might not
interact in its absence. Similarly, Catalyst is one place
where all the sciences come together to relay exciting
scientific developments happening at AU, in the AU
community, and beyond.
Catalyst is a semiannual magazine created to promote
discourse and keep us up to date about how science at
AU affects and inspires us all. Our mission is to: serve
students and faculty in the sciences as a means to
inspire, inform, and promote discourse; share news and
accomplishments of students and faculty; inform students
of timely and valuable opportunities; raise the profile of
the sciences at AU; and expose students outside of CAS
to exciting science classes.
Our success will be measured by how useful and
informative you find this publication. So we want
to hear from you! Please send news items and
comments to catalyst.au@gmail.com.
Editors
Saba Tabriz, business administration and
premedical studies ’14
Jaclyn Yeary, biology/film and media arts ’13
Copy Editor
Khari Williams, MA ’11
Designer
Nicky Lehming
Faculty Advisor
Christopher Tudge
Pollock trawling fleets are known to have a major negative impact on the populations of Alaskan
king salmon in the form of bycatch. Thousands of salmon are caught and killed each year by
Pollock fishermen, only to be thrown overboard because they are the wrong species. Despite
efforts for bycatch reduction, the fishery supplying McDonald’s still reported that more than
(continued on inside back cover)
“The Hot Spot for Science Education”
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ON THE COVER
American University
4400 Massachusetts Avenue, NW
Washington, DC 20016
www.american.edu/cas/catalyst
Inspired by the film Batman, the cover features Zaid Tanvir, MS Biology ’13. Photo by Jeff Watts.
SCIENCE ISSUES: Partnership between McDonald's and Marine Stewardship Council Far From Sustainable . . . . . . . . . . . . Inside cover
SCIENCE STARS: Student Projects Affecting You!
Occupying “Occupy D.C.”: A Systematic Survey of the Occupy Movement at McPherson Square. . . . . . . . . . . . . . . . . . . . . . . . . . . 2
"Wading" for the Answer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Cellulose: Answering the Call for Sustainable Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Free as in Free Beer, Free as in Free Speech . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
On a quest for a PhD, a local student finds herself in a variety of DMV science networks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
PROFESSOR PROFILES
Catherine Stoodley: Deciphering the Cerebellum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Tips for Searching Databases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Inside back cover
A SYSTEMATIC SURVEY OF THE OCCUPY MOVEMENT AT MCPHERSON SQUARE
Photo by Daniel Lobo
By Saba Tabriz, business and premedical studies, ’14
Occupy D.C. Movement in McPherson Square
At the intersection of political science and
mathematical statistics stood David Rae, as
he and his partner, Michael Cassel, surveyed
the Occupy D.C. movement in McPherson
Square. Rae is particularly fascinated by
the inception and progression of politically
ideological movements.
David Rae completed his undergraduate degree
in political science and history at Purdue
University before joining the mathematics and
statistics community at American University as
a graduate student. Therefore, when he was
deciding the subject of his final statistics project
with Cassel, surveying Occupy D.C. was the
obvious choice.
The Occupy movement, though having stated
goals of restoring economic and social justice,
has been contrarily interpreted by the media to
have vague goals and ideologies.
“Rather than focusing on the movement as
a whole, prior surveys have been mostly
anecdotal,” says Rae.
Ultimately, the goal of Rae’s and Cassel’s
study was to conduct a statistically robust
survey on Occupy D.C. in order to “make
more precise estimates on what the people
at Occupy think about various political
issues and to ascer tain if the movement has
concrete views.”
Catalyst Winter 2013 2
Occupy D.C., which is in accordance with the
nationwide Occupy movement, primarily took
root in McPherson Square and Freedom Plaza.
Though Rae and Cassel originally wanted to
survey both locations, all researchers have to
face the grueling task of narrowing down their
research to the bounds of their resources and
time. Ultimately, the pair selected the larger and
more highly reported occupation of McPherson
Square. Rae and Cassel received no outside
funding, began their survey in late October, and
completed their sampling of McPherson Square
in approximately three to four weeks.
Unlike most of our memories of statistics
class—filled with exacting hypotheses,
testing, and p-values—the most challenging
aspect of Rae’s and Cassel’s research was
not actually statistical. The pair strategically
used a simple random sample, providing
an equal likelihood for a member of the
population pool to belong to the sample,
and they utilized the help of the statistical
software package, Stata, thus making data
analysis a fairly simple task. Collecting this
data and interpreting it, however, proved to
be quite a demanding endeavor.
The survey sought to answer a number of
questions with the primary aim of “obtain[ing]
basic information about the political beliefs
and demographics of Occupy D.C.” General
information was also requested from each
respondent regarding age, race, and gender.
Sampling the protesters also proved to be a
difficult task. Initially, Rae and Cassel performed
their simple random sample at the kitchen, a
location with a high volume of individuals. Upon
requesting a survey from every fourth person
who passed by, the pair found that many of
the individuals they surveyed were not directly
involved in the Occupy movement; many were
homeless, and others were simply passersby picking up food. To obtain a representative
sample, Rae and Cassel moved to the center of
the square, asked every fourth person whether
they were part of the Occupy D.C. movement,
and requested a survey from them if they were.
“A major goal of surveying is to have control
over the sampling population, but protest
movements are very dynamic,” Rae says.
The population was very transient; at times
there would be no available subjects, and at
other times Rae would be overwhelmed with too
many subjects to survey. The sampling process
Created by David Rae and Michael Cassel
In order to address issues such as the
protesters’ support of Congress, banks, labor
unions, and President Obama, the survey
asked basic approval/disapproval questions.
A second type of question, which tested the
range of importance of political beliefs, asked
protesters to state whether issues such as
the environment, corporate influence, racism,
financial reform, police brutality, and war were
very important, somewhat important, or not
important in regards to their participation in
the Occupy movement. Initially, the pair used
a five-level agreement scale rather than the
three-level scale to obtain responses; however,
this scaling method seemed to produce a high
volume of non-responses. Rae believes that this
result could have been due to the discomfort
that arose from sharing the specifics of one’s
personal beliefs.
ultimately required spending hours upon
hours on site.
Rae and Cassel determined that the Occupy
D.C. movement was overwhelmingly male,
with a slight overrepresentation of whites in
relation to the population of Washington, D.C.
The majority of members were between 20 and
40 years old. The percentages and proportions
resulting from Rae’s and Cassel’s study of
Occupy D.C. were deemed to be very similar
to national figures. For example, answers
to questions regarding the approval of the
president, Congress, and labor unions were
“eerily similar to the national average.” These
results were surprising to the pair—while the
Occupy movement received a great deal of
media attention for its radical beliefs, Rae’s and
Cassel’s study demonstrated that the radical
nature of these beliefs is not necessarily true.
In addition to gaining from the practical
experience of performing research, Rae had
Catalyst Winter 2013 3
a profound personal experience with his
study of Occupy D.C. Rae was moved by
the passion that the protesters had towards
those issues that affected their lives.
Par ticipants provided stories that described
why they became involved and how they had
been functioning throughout the occupation.
While performing his survey, Rae also
watched as occupants put on costume plays
and engaged in marches as a unit. Not only
were these acts enter taining, but Rae was
also impressed with the level of coordination
required among the occupants to engage in
such activities.
Upon completing his work in McPherson
Square, Rae considered continuing his
research at the other Occupy locations in
Washington, D.C. Once he recognized that
the movement was dismantling in other
states, however, Rae realized that putting
for th his effor ts into a second phase of
research would be fruitless. ¢
Photo by Jaclyn Yeary
Nicholas Connor
WADING
FOR THE ANSWER
By Jaclyn Yeary, biology and film and media arts ’13
One might say that Nicholas Connor really
knows how to go with the flow—literally. After
a diverse array of professional experiences,
this Wisconsin native landed in the laboratory
of AU professor Stephen MacAvoy, where he is
currently conducting research on the sources of
pollutants in the Anacostia River.
Connor completed his bachelor of science
degree in biology at the University of
Wisconsin–Milwaukee. Like many students,
he decided to travel after graduation, visiting
New Zealand, Australia, Tasmania, Fiji, Hawaii,
and California. When he returned stateside,
Connor held a slew of jobs in a variety of
Catalyst Winter 2013 4
fields that eventually brought him to American
University, where he is pursuing an MS in
environmental science.
Connor worked as a seasonal field biologist
for the National Parks, holding positions as a
black bear field researcher in the Great Smoky
Mountains and completing population surveys
of woodpecker, lynx, and goshawk at Helena
National Forest. He also spent time in Alaska
surveying pollock. “You know the ‘Deadliest
Catch’ boats?” said Connor. “Picture those
boats—only with fish, not crab.” (A pollock is
a fish whose tasteless meat is used as a filler
in fake crab meat, chicken nuggets, etc.)
Connor said he enjoyed his time in the field,
but after a few years, he was ready for a
change. “Field biology is nice,” he said, “but
I was either living in the woods for five days
or on a boat for 30 days at a time. I decided I
needed a change.”
Afterwards, Connor worked in surgical
consulting for roughly five years. “It was more
the medical part of science,” Connor said. “I
recently decided that it was too far away from
the environment. I wanted to be able to do
something that keeps me in the city but allows
me to be working with the environment.”
In looking at the industry, Connor realized that
he was interested in environmental consulting,
which encompasses areas such as risk
assessment and remediation (e.g., cleanup
of toxic waste) and typically requires an
advanced degree.
“It all happened at the right time, because
my wife was star ting her residency at
John Hopkins and we were moving,” said
Connor. “We just decided, ‘Let’s just be
broke together.’”
“All three of those were interesting to me,
but I got along with Dr. MacAvoy best,”
Connor said with a laugh. “I liked him up
front because he was the only one that
actively engaged me. He said, ‘Here’s what
I’m doing, here’s what you could do, and I’d
like to see you here.’ He knows his stuff and
he’s really intelligent. He’s really dedicated to
working in the D.C. watershed area. This is
a long-term project for him.”
Although quite different from his experience
as an undergraduate, Connor says he is
enjoying his time at AU. He likes the smaller
class sizes, and he has noticed how open and
engaging the professors in the Environmental
Science Department are. “I really see a lot of
student access to professors, and professors
are really willing to bring any student into the
lab who is interested in their research and help
them further their interests. I think that’s one
of the things I like most about AU.”
Connor’s research with MacAvoy focuses
on the anthropogenic sources of pollutants
in the Anacostia. Every one to two months,
they go into the field to gather samples from
three sites: one upstream, one midstream, and
one downstream. Samples include water with
particulate matter, sediment, and mussels.
The sediment samples are dried in an oven and
put through an extraction process. Afterwards,
they look for bacterial communities. If they
can determine what types of communities are
present, they can sometimes correlate the
various communities to certain pollutants.
Photo by Jennifer Boyer
Connor said that when searching for a
master’s degree program, there are many
different degrees that allow you to focus on a
lot of different areas. He was intrigued by the
research going on in several different programs.
One, in Rochester, focused on the developed
environment and bordered on environmental
engineering. Another, at UMD, looked at using
vines and green canopies to save energy.
Finally, at AU, his interest was piqued by
MacAvoy’s work with the Anacostia.
The water samples are filtered through glass
filters. The suspended par ticulate matter
is put through an extraction process and
analyzed through gas chromatography and
mass spectrometry.
Mussels collected from the three sites are
dried out and subjected to the same extraction
process. Since mussels are bivalves, they filter
the water in their environment, and the materials
that they filter are held in their tissues. When
the fatty acids that make up the mussels are
analyzed, differences can be seen between
mussels living in different environments.
The results from these tests are compared
to the baseline levels of organic carbon,
nitrogen, and other materials in the Anacostia,
which have been determined by MacAvoy in
his research over the years. “Once you have
the baseline,” said Connor, “you can start to
determine where the ‘extras’ are coming from.”
Their research has some preliminary results,
but Connor said it’s too early for correlations.
One of the things that he said is a possibility
is that some of the increased sodium levels
seen in the river could be coming from runoff
on concrete. Increased nutrients, such as
nitrates and phosphates, may be correlated
with sewage, along with the high estrogen
levels seen throughout D.C.’s waterways.
Connor said he and MacAvoy are examining
these questions: “How much of these nitrates
are there in the system? How much could be
coming from the sewage outflows, and how
Catalyst Winter 2013 5
Anacostia River
might they be affecting the organisms living in
the river?”
After Connor completes his degree, he is
hoping to get into environmental consulting by
working with companies that do environmental
risk assessments for industries.
“For example, if you are putting up a wind
farm, before you put up the farm, you have
to do surveys on how the turbines will affect
the bat population,” Connor said. “Or, if you’re
building a factory, you need to know how the
runoff from the factory will affect a stream that
runs through the property.”
Connor says he would also like to get involved
in the sustainability work done by these
companies by putting up solar panels and green
roofs, and finding ways to close energy loops.
“If I’m doing that in five years,” he said,
“that’d be great.” ¢
By Alexandra France, public health and premedical studies, ’14
What do silicon, fire, and cellulose all have
in common? Just ask Laura Flynn, a senior
biochemistry major who is working on a
research project with American University
professor Douglas Fox to modify cellulose so
it can be used as an all-fiber flame retardant.
You may be wondering what is so great about
a flame-inhibiting product made solely from
the naturally abundant plant material cellulose.
Well, not only is cellulose readily available in
the natural environment, but it also serves as
a very effective insulation material. And with
the chemical modification that Fox’s team is
currently working on in Beeghly Laboratory, it
can be quite successful in inhibiting fire. The
team in Fox’s lab, consisting of three to four AU
students from varying science backgrounds,
hopes to contribute to growing evidence proving
the effectiveness of environmentally abundant,
non-artificial flame retardants in order to promote
sustainability and energy consciousness.
Cellulose, a naturally abundant organic
compound, is the structural component of
plants and bacterial cell walls. It is useful in
the production of products like paper, textiles,
or insulation because the abundance of polar
hydroxyl groups in each cellulose molecule
gives it the ability to interact with adjacent
molecules in order to form fibers. When woven
together in long, linear structures, cellulose
makes a physically strong and durable building
material, ideal for building insulation. However,
in its natural form, cellulose is extremely
flammable and therefore does not meet the
federal government’s safety standards for
insulation that is protective against the threat
of fire. Before being used, it must first be
modified or treated, oftentimes with borate
salts, to decrease its flammability. This is
where Flynn’s research comes in. The first year
of the research project, according to Flynn,
“consisted mostly of chemical research,”
centered on attaching side chains to produce
the desired chemical substance and then
utilizing the technique of Fourier transmission
infrared spectroscopy (FTIS) to determine
whether the correct substance was in fact
obtained. Now, in a later stage of research,
the main focus of the project is to determine
the effectiveness of their all-fiber polymers at
retarding flame. While in the lab, located in
the Beeghly Chemistry Building, Flynn spends
many long hours using FTIS to determine the
exact chemical composition of the substances
she works with, as well as a machine called
an extruder to push cellulose into materials in
order to decrease their flammability. She hopes
her work will contribute to the growing drive for
sustainable sources of building insulation by
proving chemically modified cellulose to be an
ideal candidate.
Flynn began working with Fox after she
took his Biophysical Chemistry class last
year. As a professor in both the Chemistry
and Environmental Science departments,
Fox is interested in “green chemistry,” and
Catalyst Winter 2013 6
his interests related to the use of natural,
environmentally sustainable products for
everyday purposes inspired Laura to join his
research team. Fox and his student laboratory
assistants are drawn to the specific research
of increasing cellulose’s ability to resist fire,
primarily because of its high potential for use as
an exceedingly sustainable form of insulation.
The usage of cellulose as a fire-resistant
insulation in building material promotes
environmental sustainability in two different
ways. Firstly, the pure abundance of
cellulose in the natural environment renders
it an ideal candidate for widespread use in
many aspects of everyday life. Each day it
is estimated that plants produce nearly 50
kg cellulose for each person on ear th, so
there is plenty of cellulose to go around,
Since cellulose is found in abundance in
plant materials, constructing insulation out
of it results in far less carbon emission than
the production of its synthetic insulation
counterpar ts. For example, while fiberglass is
both effective and widely used as a fireproof
insulation material, its production requires
energy for the acquisition of the raw materials
that go into making it, as well as for the
actual manufacturing process. This energy
most often comes from the combustion of
fossil fuels—those nasty but undeniably
useful fuels that cause the emission of
carbon dioxide. Finding sustainable sources
of production and seeking new ways to
reduce CO2 emissions has been all the rage
in recent decades since the environmental
consciousness movement began picking up
steam around 1970, the year of the first Ear th
Day. Flynn’s use of cellulose insulation as a
substitute for synthetics will undoubtedly help
decrease greenhouse gas emissions.
of ozone-depleting greenhouse gases is
therefore reduced.
of options for sustainable flame retardants with
low environmental and health safety risks.
The project in Fox’s lab is funded by the
National Institute of Standards and Technology
(NIST), which has its headquarters in
Gaithersburg, Md. As an agency of the U.S.
Department of Commerce, NIST promotes
innovation that improves economic security
and enhances our quality of life. The institute is
funding this project because of a current lack
This spring, Fox presented his work at the
American Chemical Society National Meeting
and Exposition in San Diego, Calif. As the global
science community continues to focus on
environmental conservation and efficient use of
resources, projects such as this, which promote
sustainable development, will shape the future
of scientific research. ¢
Photo by Emily O’Connor
A second reason that cellulose insulation is
environmentally sustainable is that it is an
exceptionally effective insulator. Because of
its high density, it can be quite successful
at minimizing air leaks between the interior
of a building and the outside environment.
As a result of more effective insulation,
buildings require less heat during the winter
and less air conditioning during the summer.
When the usage of electricity is decreased,
carbon dioxide emissions and the production
Cameron Cook
FREE AS IN FREE BEER,
FREE AS IN FREE SPEECH
By Emily O’Connor, film and media arts, ’14
Software that is “free” as in “free beer” and
“free” as in “free speech”: This is computer
science major Cameron Cook’s area of expertise.
The junior is creating an open-source software
collaboration project called Gravel for his
capstone. Cameron’s approach will allow people
with little experience to contribute software to his
open-source project.
Catalyst Winter 2013 7
Cook describes his area of research as “getting
people to understand computer science.” With
this in mind, he is good at breaking down his
project and describing how it works. Cameron’s
basic definition of open-source software is
“free as in beer and free as in speech.” In other
words, there are neither monetary costs nor
restrictions on the way the software can be
used and altered. Because of this philosophy,
individuals can take the source code of a project
and make it their own. Cook lists examples
such as Firefox and Google Chrome, popular
open-source Internet browsers that resulted in
many personalized options. The alternative to
open source is closed-source, or proprietary,
software. Examples would include software
produced by Microsoft or Apple. Closed-source
software is created by employees of a company,
allowing access to relatively few individuals.
Open-source software, therefore, is an
opportunity to use the wider community to fix
software bugs quickly while fostering creativity
and engagement. However, there are obstacles
to open source. Cook points out that it could
take knowledge of millions of lines of code to
alter software. “If a ‘noob’ wanted to contribute,
you’d have to get in touch with the people at the
top,” he explains.
To alleviate this problem, Cook is taking a
radical, untried approach that will “maximize
people’s intelligence” while minimizing the
amount of information and experience they need
to contribute. His project, Gravel, is a program
that helps organize edits for other software.
Users can divide the edits needed by opensource projects into small segments called
“problem sets.” Cook demonstrates the concept
of problem sets with the visual of a smiley face.
He draws arrows to various parts of the face.
“Say you want to change the color of this eye,”
he says. “That would be a problem set I could
send out through Gravel for someone else to do.”
Anyone who wants to code these problem sets
can complete the micro-project and submit
his or her work. Then Gravel connects all the
problem sets back together, completing the edit.
This way, an individual editor can perform one
simple task and avoid dealing with massive
amounts of information.
Cook drew inspiration for his project from Libre
Office Wiki, which lists bugs that need to be
fixed in open-source software. However, his
collaborative, organized approach is something
entirely new. The project itself has been in the
works for a few semesters; this is Cook’s third
capstone project. Computer science requires
students to complete two capstones, but Cook
extended this project from his second one, in
which he created the command line interface.
This is the backbone of the software, where the
information is contained. Now, he is building the
graphical user interface—or as he describes
it, “making it look pretty.” He illustrates with
another diagram: A rectangle represents the
inputted code that creates a button that a user
will see. From the button, he draws an arrow
back to the code; when a button is clicked, it
references what to do in the code.
Cook uses Java, a programming language
taught in AU’s computer science classes. His
work process includes writing code, running
what you have, checking for bugs, then writing
some more. In contrast to writing a paper,
where anything you write can be considered a
finished project, Cook says that “in [computer
science], you can work on something for eight
hours and have nothing to show for it.” He
might very well work on something for eight
hours at a time: Cook says he “lives here [in
the Sports Annex] from 10 p.m. to 3 a.m.”
and has 24-hour swipe access. When he is
not creating Gravel, Cook also has a job at
Defense Advanced Research Projects Agency
(DARPA), a branch of the Department of
Defense, working on Android code.
Cook is using the open-source community to
spread the word about his project. He suggests
that places such as Firefox and Android can
have a Gravel “hub” that would allow them to
communicate the edits they need.
Gravel is itself open source, so after his project
is complete at the end of the semester, Cook
will submit it to the open-source community.
Others will be able to modify it and use it for
their own projects. “Gravel could have its own
Gravel!” Cook explains. However, because
this is his capstone project, for now he must
perform all the necessary edits; he cannot reap
the benefits of his own idea by sending out
problem sets to other programmers.
Ultimately, Cook hopes to “engage people
who would otherwise be disengaged.” He
references how physicists and chemists
publish their work in scholarly papers to
publicly share their knowledge, and he opines
that if software is meant for the public, it
should be free and open source. The benefit
of this approach is that problems in software
Catalyst Winter 2013 8
“get fixed like this,” Cook says as he snaps
his fingers. “It gets people to contribute.”
To what exactly will people be contributing?
There is a wide range of open-source projects,
but one option includes software designed
for community service. Cook himself is part
of an open-source project based in India that
is developing a health care platform for rural
villagers. The project, Raxa JSS, allows rural
health providers to transfer their medical
records from paper files to tablet technology.
Cook volunteers his time helping to edit the
code that makes this project possible.
In addition, Cook feels he can generate
interest in computer science through these
bite-sized projects. Logic and puzzles, he
says, appeal to many philosophy majors,
who then become interested in computer
science. In addition, graphic design students
are often attracted to working with computer
science students on the design aspects of
their projects. Cook is closely involved in this
partnership of talents as the Treasurer of the
Association of Computational Machinery, an
organizational body for students that fosters
collaboration between computer science and
graphic design students.
Cook has received positive feedback on
Gravel from others at AU. He will present
his finished project to the computer science
community, others working on their capstone,
and his advisor, assistant professor Michael
Black. By the end of the semester, he will
have a working version of Gravel “with no
bells and whistles.” That simplicity should
not be a problem—Cook can simply use
Gravel itself to create problem sets. Then
individuals of varying experience levels from
around the world can each contribute a bell
or a whistle themselves. ¢
ON A QUEST FOR A PHD,
A LOCAL STUDENT FINDS HERSELF IN A
VARIETY OF DMV SCIENCE NETWORKS
Photo by Jaclyn Yeary
By Jackson Farmer, biology ’14
professor Kathleen DeCicco-Skinner. Originally
a post-baccalaureate student considering
medical school, Jung switched from studying
for medical school to conducting biomedical
research. “Not only was Dr. DeCicco-Skinner
one of my favorite professors at AU, but her
research was particularly interesting for me,”
Jung says. “So I became a master's student,
and she became my advisor in 2010.”
DeCicco-Skinner has been dutifully studying
the Tpl2 gene for years and has discovered
ties to skin cancer and tumor formation. “It
has been shown in previous studies that
the loss of this gene, Tpl2, leads to higher
incidence of skin tumor formation and
progression,” she says. “Sarah’s project
involves identifying the mechanism behind this
increased susceptibility to skin cancer.”
a year as a chemist, and then found herself
back in school at the teaching labs of American
University in 2009.
Going to graduate school and writing a
master’s thesis at AU is not just going to
grad school and writing a master’s thesis
at AU. In Jung’s case, like with many other
graduate students, her research took her up
the Red Line and onto the campus of the
National Institutes of Health (NIH), where she
volunteered in a laboratory at the National
Cancer Institute (NCI), a branch of the NIH.
During her final two years at AU, from
2010–12, Jung was working with biology
At NIH, Jung had the oppor tunity to analyze
cDNA microarray data using the sophisticated
Sarah Jung
A Washington, D.C., native hailing from
Cleveland Park, Sarah Jung has been all
around the many science networks in the D.C.Maryland-Virginia (DMV) area. She received her
bachelor of science degree in chemistry from
the University of Maryland in 2008, worked for
Catalyst Winter 2013 9
Photo by Jaclyn Yeary
supercomputers not present on the American
University campus. However, at AU, Jung
performed a variety of molecular biology
experiments, including qPCR (real-time
polymerase chain reactions), Western
blotting, zymography and endothelial tube
formation assays.
The microarray experiments that Jung
performed at the NIH were used to look at
how other genes may be related to the Tpl2
gene and whether these genes also play a
role in cancer. Cancer is a very complex
condition that can be caused by irregularities
or mutations on a number of genes and
pathways. That is, there is no single cause
for cancer, and because there are so many
types of cancers, different genes can play
a role for specific cancers or even multiple
types of cancer.
Jung’s microarray tests thousands of different
genes using different cancer stimuli and
compares the level of expression of the
gene between mice that have the Tpl2 gene
and mice that do not. This allows Jung to
determine which genes may play a role in
cancer development and tumor formation, and
that is when the research can proceed fur ther.
The more genes and pathways to cancer
formation that are known, the more research
can be done on controlling these genes so
that tumorigenesis may be inhibited.
Jung’s work with Tpl2 knockout mice is
another example of her genetic research.
These experiments were also done at the
NIH, and they involved the use of mouse
pups that were genetically engineered not to
have a Tpl2 gene, which is called MAP3K8
in humans. These mice were analyzed to see
any metastatic (cancer growth) potential that
may occur if they didn’t have the Tpl2 gene.
Anne Ballard and Sarah Jung
The data collected could be a good indicator
of what may happen when the MAP3K8 gene is
lost or damaged in humans.
It’s not just genes and pathways that cause
cancer formation. Jung also experimented
with matrix metalloproteinases (MMPs), which
are enzymes in the body that play a role in
cell growth, movement, and differentiation.
As with genes and pathways, there are many
different families and types of MMPs; some
are good, but others have been linked with
aggressive cancers. Jung, once again, dived
back into genetics and researched which
genes are related to those dangerous MMPs.
Understanding these connections is vital for
future research on treatment and prevention of
cancers and tumorigenesis.
Catalyst Winter 2013 10
As for her life outside of school and research,
Jung says, “I lead a rather active life, playing
soccer in a few coed leagues and sometimes
traveling with teams to places like Orlando, New
Orleans, and Virginia Beach.”
She also loves to travel.
“I haven't been out of the country in a few
years, but I try to travel as often as I can,” Jung
says. “Just last month I went to Orlando [for a
soccer tournament], Aspen—I went on a ski trip
with my friends—Indianapolis, and Boston.”
Jung has since graduated from AU and
moved out of the area to Tufts University for
PhD studies in molecular microbiology, once
again diversifying her research goals and
science networks. ¢
DECIPHERING THE CEREBELLUM
AN AMERICAN UNIVERSITY PROFESSOR’S EFFORT TO
REDEFINE THE BRAIN’S STRUCTURE AND FUNCTION
Photo by Ariana Stone
By Laura Lee, biology ’12
Professor Catherine Stoodley has no
small ambitions, as she is out to rewrite
neuroscience textbooks. She wants to change
the way academics think about the cerebellum
by demonstrating just how much thinking it
actually does.
“We’ve got to change the science books,”
she says. “The cerebellum does more than
just movement.”
Stoodley came to American University after
an impressive academic career. She majored
in biology and minored in child development
at Tufts University before earning both her
master’s and doctoral degrees in neuroscience
at Oxford University in England. Before leaving
Oxford, she performed her first postdoctoral
research, which was then followed by a
second postdoctoral position in a collaborative
program between Massachusetts General
Hospital and Harvard University. Now, within
AU’s Psychology Department, she intends
to apply her considerable academic chops
and her background in neuroscience towards
redefining the relationship between motor and
cognitive function.
Catherine Stoodley
Catalyst Winter 2013 11
We are currently taught that the cerebellum
mainly performs in areas of motor control.
Yet Stoodley, along with a growing group
of neuroscience researchers, now believes
that the cerebellum performs significant
cognitive functions as well. She explains that
“every outcome of thought is movement.
The dichotomy between motor and cognitive
[function] is a false dichotomy.”
To divide cognitive and motor function is to
deny their relationship as integral parts of one
larger process, Stoodley says. She considers
this to be a “philosophical problem” facing
neuroscience, and she intends to help resolve it.
Stoodley’s research has practical and clinical
applications for those who suffer from
developmental disorders such as autism,
ADHD, and dyslexia. Each of these disorders
features developmental differences in the
cerebellum in conjunction with behavioral
and learning difficulties. With regard to earlier
work examining these disorders, Stoodley
explains, “We were looking at the cerebellum
as a big kind of unit and not looking at the
different subsystems.”
The consequence of this was a misunderstanding
of the variations between structural abnormalities
of the cerebellum and the nuance and variety
of the forms that such developmental disorders
can take. “Because the cerebellum is traditionally
thought of as a motor structure, I think [that]
when people were finding differences in autism,
ADHD, and dyslexia, they generally were seen
as incidental findings instead of a potentially
important part of the etiology of the disorder,”
Stoodley says.
Now, with a new framework emphasizing the
roles of the different subsystems within the
cerebellum, it is clear to Stoodley that such
variations between patients cannot simply
be dismissed. “When you look at where the
findings are commonly seen in the cerebellum
for dyslexia, they’re in the region that we find
is very often engaged in reading,” she says. In
this way, these variations may hold the key to
unlocking the cerebellum’s secret workings.
In order to further this research, Stoodley
has a number of projects under way. Her
main focus at the moment is to map the
relationships between lesions in the cerebellum
using magnetic resonance imaging (MRI)
and clinical observations of patients. She has
also implemented behavioral measures of
performance in an effort to tie the cerebellum’s
structure to its function. By examining MRI
scans from healthy patients and patients
with cerebellar tumors, she hopes to find a
correlation between cerebellar abnormalities
and specific clinical and behavioral outcomes.
If Stoodley is successful, this research
has exciting clinical applications. For one,
a better understanding of the pathology
of developmental disorders could lead to
better and more specific behavioral therapy
programs for sufferers of these developmental
disorders. Specific knowledge of abnormal
areas of the cerebellum could give therapists
insight into the unique challenges that each
patient faces. Also, knowledge of the vital
areas of the cerebellum for different functions
could help guide surgical practice. Armed
with an understanding of the functions of the
subsystems of the cerebellum, surgeons will
be able to make better judgments regarding
which areas are more vital to preserve.
It is with these goals in mind that Stoodley
is writing her grant applications. As a new
professor at American University, she has startup funding to get her research up and running,
but it won’t be enough to finish the job. To fill
the funding gap, Stoodley is applying for grants
from the National Science Foundation and the
National Institutes of Health, as well as several
private foundations.
Catalyst Winter 2013 12
Her current research involves reanalyzing
pre-existing MRI scans of children through
a collaborative effort with Massachusetts
General Hospital and, as such, is highly
economical. Stoodley would use new funding
going forward to perform original clinical
research and obtain new MRI scans—though
she needs to broaden her base of subjects to
truly understand her results.
“To look at what’s going on with such a dynamic
changing system, I start with adults,” Stoodley
says. “It’s difficult, if you don’t know what’s
going on in an adult stable system, to understand
what’s going on with kids.” It is necessary to use
functional imaging in healthy adults to determine
why the cerebellum is engaged in cognitive
tasks. It is the best way to delineate whether a
particular region is involved with motor planning
or a higher cognitive process.
She is helped along the way by AU students
eager to exercise their burgeoning research
abilities. They learn valuable techniques, such
as the ability to use computer programs to
analyze MRI scans. In addition to the research
assistance, Stoodley gains an immense sense
of satisfaction from mentoring students.
“I love having students in my lab,” Stoodley
says. “I find here [that] the students are really
enthusiastic about coming in and doing some
research, and having some fun.”
Stoodley’s work is impressive in both its
impor tance and its scope. As she seeks to
redefine our understanding of the brain, she
implicitly seeks to redefine the concept of
thought itself. Along the way, she may provide
greatly needed clarity to disorders that affect
the lives of countless children. With no
small effor t, Stoodley may be rewriting our
textbooks one day. ¢
McDonald's and Marine
Stewardship Council
(continued from front cover)
11,000 king salmon were killed as
a result of bycatch in 2012.
TIPS FOR
SEARCHING DATABASES
By Rachel Borchardt, Science Librarian
Other organizations that certify
the sustainability of seafood have
recognized the problems with the
certification of wild-caught Alaskan
pollock as well. Seafood Watch, a wellrespected list produced by the Monterey
Bay Aquarium, lists pollock as a “Good
Alternative” rather than a “Best Choice.”
They warn: “The Alaska Pollock
fishery is generally well-managed.
However, there are concerns about
trawling impacts, bycatch, and overall
population status.”
There are several search tools that are common to many science databases. Using these
tools can transform a simple keyword search into a complex, dynamic search tailored to
your specific need. They can be used to expand, narrow, and focus a search.
As the largest fast-food company in
the world, McDonald’s will introduce
millions of people to the blue MSC
label and to the concept of sustainable
seafood. However, while the company’s
efforts to provide consumers with
an environmentally friendly product
are admirable, the use of wild-caught
Alaskan pollock gives customers a false
sense of security.
e.g., (anatomy OR physiology)
e.g., (monkey OR primate OR gorilla)
Boolean Operators
Wildcard
AND—use to narrow a search and get fewer
and more relevant results.
Used to search for variations of a single
letter of a word—particularly handy for
British or translated words. Most databases
use a question mark (?), but some use an
exclamation mark (!).
e.g., evolution AND cockroach
OR—use to broaden a search and get more
results. Good for synonyms and words with
variant spellings. Add parentheses when
using OR.
NOT—use to narrow a search to get more
relevant results. Be careful not to eliminate
useful articles!
e.g., mouse NOT computer (could
eliminate articles related to computer
modeling of mice)
Truncation
Use to find words with different word
endings. Most databases use an asterisk
(*), but some use a dollar sign ($) or
question mark (?).
e.g., biolog* yields “biology,” “biologies,”
“biological”
e.g., bio* yields “biogenetics,” “bioevolution,”
“biography,” “biographical,” etc.
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e.g., colo?r yields “color” or “colour”
e.g., ?han?uk?ah yields “Hanukah,”
“Hanukkah,” “Channukah,” etc.
Subject Headings
Used to search for standardized vocabulary
on a topic. Searching on a subject heading
related to your search will narrow and focus
your results, eliminating off-topic articles.
In PubMed, these are called MeSH terms:
Medical Subject Headings.
e.g., using the MeSH term “myocardial
infarction” will help a topic search on
heart attacks
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