O F F I C E O F ... JMU Students Attend Colonial Academic Alliance Inside this issue:

O F F I C E O F S P O N S O R E D P RO G R A M S
Summer 2005
JMU Students Attend Colonial Academic Alliance
Inside this issue:
Student Abstracts
“Undergraduate
research lets
students expand
their own mindschallenging
themselves to find
answers to the
questions no one
has asked.”
2
The third annual Colonial Academic Alliance
(CAA) Undergraduate Research Conference was
held April 8th and 9th, 2005 at Hofstra University in Hempstead, New York. The yearly conference brings together student representatives from
the ten CAA institutions to present their scholarly
and research endeavors to a gathering of their
peers in a professional setting. Areas of study
represented at the conference included a wide
array of subjects from the traditional sciences to
the humanities, fine arts, social sciences, and professional schools. Out of 130 undergraduates
attending the conference, 12 students represented the diversity of undergraduate research
and scholarly inquiry that James Madison University has to offer. Biology, Chemistry, Psychology,
Sociology, Anthropology, and Integrated Science
and Technology were just a few of the disciplines
presented by JMU students.
Over the last ten years there has been a strong
emphasis on improving the educational experience of college students to better prepare them
for their professional careers. The importance of
providing undergraduate students with in-depth
mentored research experiences has been a major
focus to improve on high quality collegiate education. At research conferences such as CAA,
students in turn have the opportunity to present
their academic studies in a professional environment that encourages guidance and criticism from
research experts from different CAA schools.
JMU contingency included 12 stellar undergraduate researchers.
CAA Students Excel with Faculty Guidance
OFFICE OF
SPONSORED
PROGRAMS
For additional information,
contact Patricia Buennemeyer,
Director
MSC 5728
JMAC Bldg. 6, Suite 26
1031 S. Main Street
Phone: 540-568-6872
Fax: 540-568-6240
Email: [email protected]
Find us at URL:
http://www.jmu.edu/
sponsprog/
Gregory Clark, ISAT, (Dr. Ron
Raab) - Cloning, Expression,
Purification, and Characterization
of Y. Pestis Chaperone-Usher
Proteins in E. Coli As Recombinant
Vaccine Candidates.
Mohammad Heydarian, ISAT,
(Dr. Ron Raab) - Cloning, Expressing, and Purifying the sGP
Allison Abbot, Sociology &
Protein of the Ebola Virus for use
Anthropology, (Dr. Fletcher
in Development of Diagnostic
Linder, Dr. Jennifer Coffman) Tests for the Ebola Virus.
Ethnohistories of Newton: Excavating and Reconstructing Harri- Susanna Hoffer, Chemistry, (Dr.
Gina MacDonald) - Nucleotide
sonburg, VA’s Radicalized Past
Binding to RECA-SSDNA FilaNaheed Ahmed, Sociology &
ments.
Anthropology (Dr. Fletcher
Sarah Horsey, Psychology, (Dr.
Linder) - Female Circumcision:
Kenneth Barron, Dr. Tammy GilliLegitimate Practice or Human
gan) - Moving Beyond Predicting
Rights Violation
Academic Outcomes and Learning
Martin Brakke , Chemistry (Dr.
Gina MacDonald) - Monitoring Strategies: The Impact of
the Assembly and disassembly of Achievement Goals on Middle
School Students’ Psychological
RECA-DNA Filaments.
Well-Being.
Undergraduates are given the opportunity to excel in research
initiatives under guidance of a
faculty member. Following is a
list of students, their associated
faculty mentors, and the research they presented:
Adaku Iwueze, Biology, (Dr.
Judith Wubah, Dr. Daniel
Wubah) - Generation of a Deoxyguanosine Kinase3-GFP Expression Plasmid.
Heather Johnson, Chemistry,
(Dr. Dan Downey) - Stream Water Chemistry in the St. Mary’s
Wilderness Following Limestone
Treatment.
Linsey Mayhew, Sociology &
Anthropology, (Dr. Fletcher
Linder) - Free Community Radio:
Imagining Community and Reconciling Difference Through Radio
Narrative
Ellen White, Chemistry, (Dr.
Gina MacDonald) - Monitoring
Subtrate Binding of Yeast
Phosphoglycerate Kinase.
Vera Wubah, Biology, (Dr.
Charles Bieberich) - Profiling
Kinase Activity in Prostrate Tumor
Cell Lines by In-Gel Kinase Assay.
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Page 2
ETHNOHISTORIES OF NEWTOWN: EXCAVATING AND
RECONSTRUCTING HARRISONBURG, VA’S RACIALIZED PAST
Allison J. Abbott (Dr. Fletcher Linder and Dr.
Jennifer Coffman), Department of Sociology
and Anthropology
In the Great Migration of the early 20th century, many African-Americans moved North
and the segregation of urban areas in the
North and South began. During this period
in Harrisonburg, VA, a large number of socalled blacks settled into an area of Harrisonburg called Newtown. Residential segregation based on race continued until
1960 to 1963, when Newtown’s 741 residents were forced to relocate and watch
their houses be torn down and burned in
the name of urban renewal. This project
uses archival research and ethnohistorical
interviews collected from Harrisonburg’s
black and white communities to excavate
Newtown’s cultural lifeways and (re)
establish its “sense of place”. This research suggests that the black neighborhood torn down in the early 1960s was a
mixed use, lower-to-middle-class neighborhood with businesses, social “hang-out”
spaces, and family residences. In this area,
we see the influence of extended kinship as
evidenced in the sharing of everyday material objects, social reciprocity, and shared
care-giving, as well as basic economic support. When the segregated neighborhood
was obliterated, the black community of
Harrisonburg was forced to either acculturate themselves within the existing white
community or become social outliers cut off
from their established community networks
of support.
Female Circumcision: Legitimate Cultural Practice or Human
Rights Violation?
Naheed Ahmed (Dr. Fletcher Linder), Department of Sociology and Anthropology
Controversy surrounding female circumcision centers on questions of cultural integrity and human rights. Can we take cultural
relativity too far? Are there inherent
“rights” associated with being human? Is it
ethnocentric to label “foreign” cultural practices as human rights violations? These are
some of the questions I broach in this
study. Through conversations with members of communities that practice female
circumcision, and document reviews at the
national and international levels, I examine
why female circumcision persists, and how
government (GO) and non-governmental
(NGO) organizations have mobilized to stop
this practice. My findings include: contrary
to popular misconceptions, there are girls
who willingly undergo this ritual and women
who believe its practice should be continued. And, according to individuals of practicing communities and officials at GOs and
NGOs, the success of circumcision eradication programs varies. Successful programs
tend to take a local approach and do not
openly condemn the practice of female circumcision, but instead use more discreet
methods, such as discussing the health
complications of the practice. These findings only serve to underscore the difficulties
of classifying cultural practices as human
rights violations.
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MONITORING THE ASSEMBLY AND DISSASEMBLY OF
RECA·DNA FILAMENTS
Martin H. Brakke, (Dr. Gina MacDonald),
Department of Chemistry
The Escherichia coli protein RecA is a multifunctional enzyme that plays an important
role in the process of DNA strand exchange
and repair. To date, it is not clear how ATP
hydrolysis is coupled to protein conformational changes and the DNA strand exchange reaction. Fourier Transform Infrared
spectroscopy (FT-IR) and Attenuated Total
Reflectance (ATR) were used in an attempt
to monitor changes in protein and phosphate vibrations that arise as ATP hydrolysis
occurs in active RecA filaments. Infrared
spectra were collected over time on active,
ATP-RecA-DNA nucleoprotein filaments.
Multiple DNA substrates were used to correlate rates of hydrolysis and infrared
changes that occur over time. Assay results
confirm that the rates of hydrolysis using
ssDNA are much faster than dsDNA due to
a slow assembly of RecA on dsDNA with the
experimental conditions used. In addition,
control experiments were performed on
ADP-RecA-DNA filaments. Reproducible
changes in IR spectra were observed in the
1400 - 900 cm-1 region that are consistent
with vibrations arising from the hydrolysis of
ATP and/or changes in DNA phosphate vibrations affected by the assembly/
disassembly of RecA filaments. Future
studies will attempt to identify vibrations
associated with hydrolysis and assembly.
CLONING, EXPRESSION, PURIFICATION, AND
CHARACTERIZATION OF Y. PESTIS CHAPERONE-USHER
PROTEINS IN E. COLI AS RECOMBINANT VACCINE CANDIDATES
Gregory A. Clark, (Dr. Ron Raab), Integrated
Science and Technology, and Cpt. Jeremy
Goodin, United States Army Medical Research Institute of Infectious Diseases
[USAMRIID]
In this experiment, two genes from Y. pestis,
the causative agent of plague, were expressed, purified, and tested for their potential as vaccine candidates. The proteins
Caf1A and Caf1M function together in vivo
for the secretion and assembly of outer
membrane proteins. This function, coupled
with their high theoretical antigenic determinant values, makes them likely to provoke
an immune response that could provide
resistance to infection by Y. pestis. Both
genes were cloned into E. coli independently
in a fusion protein expression system and
together in a dual-expression vector. Purification of Caf1M was expected to be uncomplicated because of its predicted solubility in the fusion protein expression system. Caf1A was expected to become soluble when expressed with its chaperone protein, Caf1M. The presence of Caf1M was
also hoped to protect the cell from Caf1A,
which has been observed to be toxic to E.
coli cells. This experiment revealed an unusual cell lysing effect when Caf1A was
expressed independently minus its leader
sequence that resulted in soluble Caf1A
available in the growth medium. Additionally, a sizable amount of Caf1A was observed in the insoluble fraction when fulllength Caf1M was expressed with Caf1A
minus its leader sequence.
JMU’s 2005 CAA participants:
Top row (left to right): Naheed Ahmed, Ellen White,
Heather Johnson, Susanna Hoffer, Patricia Buennemeyer
(Advisor), Vera Wubah, Adaku Iwueze, Sarah Horsey,
Allison Abbot, Linsey Mayhew, Fletcher Linder (Advisor–
at back), Greg Clark
Front: Martin Brakke, Mohammad Heydarian
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CLONING, EXPRESSING, AND PURIFYING THE sGP
PROTEIN OF THE EBOLA VIRUS FOR USE IN
DEVELOPMENT OF DIAGNOSTIC TESTS FOR THE
EBOLA VIRUS
Mohammad Heydarian, (Dr. Ron Raab),
Integrated Science and Technology
The Ebola virus is the causative agent of
hemorrhagic fever; one can become infected with hemorrhagic fever by being in
contact with the blood and secretions of an
infected person. By being easily transmitted
from one host to another the Ebola virus is
a potential biological weapon. JMU is working with USAMRIID (United States Medical
Research Institute of Infectious Diseases)
to develop diagnostic tests. Researchers at
JMU are working on cloning, expressing, and
purifying the sGP protein of the Ebola virus
for USAMRIID to use in developing diagnostic tests for the Ebola virus in the event that
it is used as a biological weapon. We used
affinity purification methods, co expression
of various combinations of chaperone proteins, and free expression to obtain sGP for
USAMRIID to use in developing diagnostic
tests. The sGP samples that were obtained
are currently being tested at USAMRIID for
antigenic activity against the immunoglobulins of their diagnostic tests.
NUCLEOTIDE BINDING TO RECA-SSDNA FILAMENTS
Susanna Hoffer, (Dr. Gina MacDonald), Department of Chemistry
All of the functions of the E. coli protein
RecA require the formation of a RecA-ATPssDNA nucleoprotein filament. The active
conformation can also form in the presence
of ATPyS. However, RecA-ADP and RecADNA-ADP complexes are inactive. One major structural difference between the two
conformations is that the active conformation has a larger pitch of the protein helix
than that of the inactive conformation.
There is little other information about the
structure of the active complex. To investigate the structural changes that occur during nucleotide binding to RecA-ssDNA filaments we utilized difference FTIR spectroscopy. Our results show changes in the
structures of both the nucleotide and the
RecA protein during the binding of nucleotides to RecA-ssDNA filaments. Our results
enable us to better understand RecA and
the structural changes the protein undergoes during the binding of different nucleotides.
Colonial Academic Alliance
Page 5
Preparing students to be educated and enlightened citizens...
MOVING BEYOND PREDICTING ACADEMIC OUTCOMES
AND LEARNING STRATEGIES: THE IMPACT OF
ACHIEVEMENT GOALS ON MIDDLE SCHOOL STUDENTS'
PSYCHOLOGICAL WELL-BEING
Sarah E. Horsey, (Dr. Kenneth Barron & Dr.
Tammy Gilligan), Department of Psychology
The academic goal orientations and life satisfaction of middle school students is investigated. Previous research has discussed and
debated goal orientations in academics to
determine what types of goals should be nurtured and fostered. This study aims to replicate and extend the findings of three distinct
achievement goals: performance-approach,
performance-avoidance, and mastery goals.
These goals are measured in a personal context as well as a classroom induced context.
This study plans to extend research by analyz-
ing the effects of goal orientations on students’ life satisfaction in five separate areas:
life satisfaction with family, friends, school,
living environment, and self. It is hypothesized that personally adopted and classroom
adopted mastery goals will result in the
greatest life satisfaction in all areas. Performance-avoidance goals will result in the
least life satisfaction in all areas. Performance-approach goals may result in high life
satisfaction, to the extent that the student is
doing well in school. The impact of pursuing
combinations of goals will also be explored
to better capture complex motivational dynamics.
GENERATION OF A DEOXYGUANOSINE KINASE3 - GFP
EXPRESSION PLASMID
Adaku F. Iwueze, (Dr. Judith A. Wubah & Dr.
Daniel A. Wubah), Department of Biology
Teratology is the study of causes and manifestations of abnormal development. In the
United States, 150,000 babies are born each
year with birth defects. It is not known
whether the 4,000 neonates born each year
affected by mitochondrial DNA defects are
included in this number. Deoxyguanosine
kinase (dGK), a mitochondrial gene, encodes
a rate-limiting enzyme in the mitochondrial
salvage pathway, a process for generating
dNTP precursors for mitochondrial DNA replication. Mutations in dGK lead to mitochondrial DNA depletion syndrome which causes
hepatic failure and early infantile death. An
isoform of the gene, dGK3 has been cloned
from early mouse embryos and the long-term
goal is to determine if there is a link between
dGK3 and birth defects. The objective of
this study is to determine the intracellular
location of dGK3. Using total RNA from adult
mouse liver, a full-length dGK3 cDNA with
EcoR1 sites at both ends was generated.
The dGK3 cDNA product was cloned into
pGEM-T vector and digested with EcoR1 enzyme to ensure creation of the sites. The
digested product was ligated into pEGFP
vector and colonies screened for inserts.
The dGK3-GFP expression plasmids will be
confirmed by sequencing and used in future
studies. (Financial support for this research
was provided by the Jeffress Memorial Trust
and the National Institutes of Health,
Bridges grant.)
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Page 6
STREAM WATER CHEMISTRY IN THE ST. MARY’S
WILDERNESS FOLLOWING LIMESTONE TREATMENT
Heather S. Johnson, (Dr. Dan Downey), Department of Chemistry
Water samples have been collected from
the streams of the St. Mary’s Wilderness,
Augusta County, Virginia and analyzed for
pH, acid neutralizing capacity (ANC), base
metal cations (Ca2+, Mg2+, Na+, K+), major acid anions (Cl-, SO42-, NO3-) and aluminum (AlT) concentrations. On March 20,
1999, the St. Mary’s River and five of its
tributaries were treated with 140 tons of
limestone (>99% CaCO3) delivered by helicopter. As a result of the limestone treatment the following changes have occurred: pH 5.53 ± 0.26 to 6.13 ± 0.30;
ANC 2.1 ± 4.7 to 21.8 ± 12.7 µeq/L; calcium concentration 21.8 ± 1.6 to 38.8 ± 9.2
µeq/L; calcium/hydronium ratios 8.6 ± 4.5
to 70.2 ± 52.0. As a result of the increased
pH, aluminum concentrations decreased
from 40 ± 17 to 22 ± 18 ppb. Hurricane
Isabel delivered 51 cm rainfall in 6 hours
into the wilderness. The limestone treatments were located at high elevations in the
watershed and avoided most of the disturbance. Yet in ten months since the hurricane, pH and ANC have averaged 5.75 ±
0.23, and 8.2 ± 8.0, respectively. As key
water chemistry values have returned to
near pre-liming levels, a second limestone
treatment is being planned.
FREE COMMUNITY RADIO: IMAGINING COMMUNITY
AND RECONCILING DIFFERENCE THROUGH RADIO
NARRATIVE
Linsey Mayhew (Dr. Fletcher Linder), Department of Sociology and Anthropology
In highly consolidated media markets, community representation and participation in
public discourse is becoming increasingly
rare. This paper focuses on Free Community Radio (FCR), an unlicensed radio station in Washington, DC, to explore how the
struggle over local participation plays out
on the ground and in the airwaves. Ethnographic data for this study were collected
through participant-observation in FCR’s
daily life, and interviews and focus groups
with FCR volunteers and community members at large. This research views
“community” as a contested sign that FCR
and other competing groups construct from
the area’s rich and complex past. I document and discuss how FCR imagines community within a common geographic space
and across ethnic, economic, religious, and
political borders. I argue that the imagination of community and the radio broadcasting of this memory form a narrative that attempts to reconcile ethnic differences while
resisting other forms of power apparently
opposed to FCR’s mission.
Colonial Academic Alliance
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MONITORING SUBTRATE BINDING OF YEAST
PHOSPHOGLYCERATE KINASE
Ellen M. White, (Dr. Gina MacDonald), Department of Chemistry
ATP + 3-PG « ADP + 1,3-bPG 3Phosphoglycerate kinase (PGK) is a 45kDa
enzyme that catalyzes the reversible reaction in which a phosphate is transferred
from ATP to 3-phosphoglycerate (3-PG) to
form ADP and 1,3-bisphosphoglycerate.
(Banks, R. D.; Blake, C. C. F.; Evans, P. R.;
Haser, R.; Rice, D. W.; Hardy, G. W.; Merrett,
M.; Phillips, A. W. Nature. 1979, 279, 773777.) It has been proposed that when PGK
binds the two substrates, ATP and 3-PG, the
PGK enzyme has a hinge-bending motion
that brings two distant regions closer for the
phosphate transfer reaction. Crystal structures to date have not shown both the open
and closed conformation of PGK in the
same species. (Kovari, Z.; Vas M. Proteins.
2004, 55, 198-209.) NMR data, however,
have shown that there are significant conformational changes in the N-terminal regions and the hinge-bending region when
both substrates are bound. (Joao H. C.; Williams R. J. P. Eur. J. Biochem. 1993, 216,
1-18.) In order to better understand the
conformational changes due to nucleotide
binding to PGK, infrared spectra of PGK-ATP
and PGK-ADP were obtained. Preliminary
data show conformational changes in PGK
when ATP is bound and similar, but distinct
changes when ADP is bound. ATR experiments were also conducted to study vibrational changes that occur over time when
the both substrates are present. These
spectra may ultimately allow us to follow
the reaction catalyzed by PGK.
PROFILING KINASE ACTIVITY IN PROSTATE TUMOR
CELL LINES BY IN-GEL KINASE ASSAY
Vera B. Wubah, Xiang Li, (Dr. Charles J. Bieberich), Department of Biological Science,
University of Maryland, Baltimore County,
Baltimore, MD
Protein phosphorylation plays a crucial role
in the activities and properties of proteins
by allowing transmission of external signals
to regulatory proteins that govern cellular
processes including differentiation and
proliferation. Protein kinases are the enzymes that catalyze the transfer of a phosphate group from ATP to amino acid residues of serine, threonine or tyrosine. The
objective of this study was to examine the
kinase activity in tumorigenic and nontumorigenic cells derived from a model
adenocarcinoma of the mouse prostate
(TRAMP). Kinase activity was detected by
one dimensional and two-dimensional in-gel
kinase assays using a mixture of casein and
multide as a substrate. Two tumorigenic cell
lines were compared with one that is not
tumorigenic. A low molecular weight kinase
activity with stronger signal was detected in
the tumorigenic cell lines compared to the
non-tumorigenic line. In addition, a kinase
activity that was unique to the nontumorigenic cell line was also observed.
Characterization of differences in kinase
activity among the TRAMP cell lines may be
useful in identifying novel diagnostic markers for prostate cancer, and may provide
further understanding of the mechanisms
underlying the development of this disease.
Colonial Academic Alliance
Page 8
James Madison University will host the 2006 Colonial Academic
Alliance Undergraduate Research Conference.
Dates: Friday, March 31 - Saturday, April 1, 2006
Check the following URL for information on the event as it becomes available:
http://cit.jmu.edu/acadaffairs/caa/
Colonial Academic Alliance
The Colonial Academic Alliance is a consortium that links the twelve colleges and universities of
the Colonial Athletic Association in programs that improve the quality of teaching, learning and research for all.
The Alliance was created by the CAA presidents in 2002 and is administered by the provosts of
the member institutions. Collectively, the institutions comprise more than 200,000 students and
nearly 10,000 full-time faculty, including three Nobel Prize-winning professors. By leveraging the
strengths of each institution, the Alliance can build programs that no one college or university could
undertake on its own.
James Madison University in Harrisonburg, VA is hosting the fourth annual CAA Undergraduate Research Conference on April 1, 2006. The conference offers students from the CAA schools an opportunity to share their work with their peers in a professional setting. Students from all segments of
the sciences, the humanities, fine arts, social sciences, and professional schools -- present their
work at this twelve-institution event. The conference rotates among the participant campuses each
year. The participating institutions of the Colonial Academic Alliance are as follows:
University of Delaware
Drexel University
George Mason University
Georgia State University
Hofstra University
James Madison University
Northeastern University
Old Dominion University
Towson University
Virginia Commonwealth University
University of North Carolina Wilmington
College of William and Mary