Download - Symposium Abstract Book 2012
NORTH CAROLINA SCHOOL OF SCIENCE AND MATHEMATICS’
27th Annual Research Symposium
MAY 18, 201210:30 a.m. - 2:30 p.m.
NCSSM Research Symposium 2011-2012
Avi Aggarwal, Amy Xie, Tyler Hayes, Whitman Groves
Teachers/Mentors: Myra Halpin, NCSSM; Florence Gold, NASA Johnson Space Center
Human Spinal Elongation in Space - The goal of this experiment is to observe the behavior of the human spine in
microgravity. Because astronauts frequently report back pain, and astronauts are known to “grow” 2-3 inches in
space, we seek to identify ways to relieve the strain through testing the forces exerted on the spinal column. It is
hypothesized that increased thoracic curvature created by holding one’s knees to his chest as well as fluid shift
changes force distribution. Force probes and piezoelectric strips quantify the forces on a realistic model of the
human spine. Video recording provides qualitative observations. A relationship between gravitational acceleration
and lumbar load exists.
Avi Aggarwal
Teachers/Mentors: Myra Halpin, NCSSM; Heileen Hsu-Kim, Andreas Gondikas, Duke University Department of Civil
& Environmental Engineering
Effect of Thiols on Silver Nanoparticle Fate - Silver nanoparticles are widely used in consumer goods for their
antimicrobial properties, yet little is known about their environmental impact. In aquatic systems, ligand groups in
organic matter may adsorb to particle surfaces and affect their bioavailability and reactivity. Surface-modified
silver nanoparticles may aggregate and settle out of water or dissolve into potentially more bioavailable forms of
silver. The thiol (S-H) ligand group has high affinity for silver and is likely to react with silver in water. We assessed
the effect of thiols on citrate-coated silver nanoparticles using glutathione, a low molecular weight peptide and
antioxidant. Aggregation of silver nanoparticles was measured with time-resolved dynamic light scattering (DLS).
Dissolved silver was determined by filtering batch suspensions to separate dissolved from particulate silver and
measured with inductively coupled plasma mass spectroscopy (ICP-MS). Zeta potential measurements (DLS) and
dissolved glutathione concentrations (measured with high pressure liquid chromatography - HPLC) were used as
indicators of sorption and surface charge. Results indicate that glutathione enhanced aggregation and dissolution
by sorbing on the surface of silver nanoparticles. Overall, these results suggest that thiols could play a critical role
in the reactivity and bioavailability of silver nanoparticles. In environments such as sediment pore water and
wastewater treatment plant effluent water, thiols are present in nanomolar to micromolar concentrations and
should be included in risk assessment studies. Moreover, the transformations studied here occurred
simultaneously, and our results stress the need for a multi-level approach for transport and fate models of metallic
nanomaterials.
Saima Akbar
Teachers/Mentors: John Kirk, NCSSM; Hiroaki Matsunami, Ting Zhou, Duke University
Genetic Expression in the Carotid Body - The carotid body is a small chemosensory organ that lies between the
bifurcations of the carotid artery. This organ senses changes in the levels of blood oxygen, CO¬2, and pH and sends
signals to the brain to regulate breathing and blood pressure. Because the organ is so small, we have yet to
understand its gene expression. The lab has previously completed a transcriptome analysis of a single sensory cell
from the mouse carotid body using single-cell derived cDNAs. From the sequencing data, we saw that essential
components of the G protein dependent pathway are highly enriched, including an olfactory receptor MOR18-2. To
test the validity and specificity of the MOR18-2 expression, we performed in situ hybridization to observe gene
expression.
NCSSM Research Symposium 2011-2012
Grishma Alakkat
Teachers/Mentors: John Kirk, NCSSM; Kate Scholberg, Duke University, Physics
Energy Drop in Supernova Events - The energy levels of a supernova as it passes through different phases of its life
cycle are measured as a function of the energy of a neutrino emitted from the supernova that is detected on Earth.
These neutrino events are extremely rare, and therefore we must be able to work with the data that is available.
One of the major steps in the life cycle of a supernova is the accretion to cooling transition. this step marks a large
drop in the energy level of the supernova. However, if there are too few neutrino events, it is impossible to say
with precision the time this transition occurred. This information is often essential in better understanding the
properties of the supernova, and therefore it is necessary to optimize the number of events. One method of doing
this is to take the mean of all the number of events per unit time, and create 2 subsets of data: one above the
mean and one below. Then, the mean of each of these subsets can be taken, and the difference between the mean
minus any error for both means gives a measure for calculating the precision of a certain number of events. The
lower this number, the lower the precision.
Marc Arrambide
Teachers/Mentors: David Green, NCSSM
Guitar Strings:Tonal Quality vs. Perceived Quality - I am conducting an experimental study investigating the
correlations between the perceived quality and tonal quality of an electric guitar string. The loudness, distribution
and distinctiveness of a string’s harmonics determine its tonal quality. I will compare these acoustic properties
using Fourier analysis with the strings’ professional reviews by Guitar Center, Musician’s Friend and Guitar World
magazine. A literature element will review the physics of simple harmonic motion, Fourier analysis, and vibrating
strings. I will also study a new hybrid string structure consisting of a cobalt coating on a steel string, which a recent
Guitar World magazine evaluated. I am conducting this experimental investigation under the mentorship of Mr.
David Green in IE378 Research Experience in Physics.
Forrest Ashworth and Monal Depani
Teachers/Mentors: Myra Halpin, NCSSM
PET/PEG Microwave Copolymer Synthesis - The main goal of our project was to lower the amount of catalyst
(tetrabutyl titanate) needed in an esterification reaction of polyethylene glycol (PEG) and poly(ethylene
teraphthalate) (PET) to produce a PET/PEG block copolymer. We used microwave-assisted synthesis to produce
copolymers at different catalytic percent amounts, 10 and 5 percent catalyst. We created thin films using a
hydraulic laboratory press to test our reactants in the FTIR spectrometer and used these spectra for product
verification. Inferring no change in product quality in varying catalytic amounts from our results, this reaction may
be carried out with even lower amounts of catalyst.
NCSSM Research Symposium 2011-2012
Robert Baraldi
Teacher/Mentors: John Kirk, NCSSM
Modeling the chromatin spring - Metaphase is a crucial part of mitosis, or cell division. One of the least
understood yet essential components of this phase is the chromatin spring, which is responsible for balancing the
kinetochore microtubules while the chromosomes prepare for segregation. Earlier research has concluded that the
chromatin and proteins form a spring. The true nature of this spring is unknown, although it has been widely
assumed that it is a simple Hookean/linear spring. In order to efficiently map this, we have created a program
using Matlab software that allows us to model many different parameters within the cell during metaphase only.
While initial testing seemed conclusive, it was determined that the linear spring could only model length of spindle
fibers and the spring. The exclusion of this large amount of variation exhibited by wild type cells suggests that a
linear model is not correct. Upon further examination, we concluded that the data actually follows two spring
constants. When reaching a certain threshold, the spring jumps to another constant as it is unbound by proteins
found in the chromatin, specifically condensin and cohesin.
Adele Bernard
Teachers/Mentors: John Kirk, NCSSM; Nancy Zucker, Duke University
Social Cognitive Rehab for Anorexia Nervosa - People with Anorexia nervosa (AN) tend to associate with rejection
and are prone to difficulties relating with others. The aim of this study is to pilot a hypothesized intervention that
would help subjects increase success in their interpersonal relationships, widen their range of social comfort, and
learn to subdue life-restricting aspects of AN. Using knowledge about increased local processing in brains of those
with AN and increased association with negative stimuli, we piloted a daily task that measure their reaction rate
selecting a positive image from a rejecting one or an emaciated distraction. The study also involved pre-treatment,
treatment, and post-treatment surveys and personal assessments that aimed to guide our subjects towards
engaging in their personal lives. Our study led to a variance in results where some aspects of the subjects' disorder
improved while some deteriorated. About 2/3 of the subjects demonstrated interpersonal improvement and
improved in their negative rejection reaction rate. Also, those who had AN for the longest period of time and
greater severity did not respond to the intervention as well as others, leading us to re-evaluate our target patient
group and approach to social rehab.
Christopher Bernedo
Teachers/Mentors: John Kirk, NCSSM; Evelyne Huber, UNC - Chapel Hill
The "Great Transformation" of Ollanta Humala - Ollanta Humala’s victory as President of Peru arose amidst a
continuing momentum of leftist governments rising within Latin America in what scholars refer to as the “pink
tide” or “post-neoliberalism.” Since the late 1990s, the region has seen Hugo Chavez, Evo Morales, Luiz Inacio Lula
da Silva, and other leftist political figures assume the leadership of their respective nations. Yet, Humala did not
see victory in his first attempt at presidency in 2006, when he was still seen as a radical leftist. Running again in
2011 as a more moderate candidate, he managed to secure the election. Certain factors that may have caused this
shift to the center are electoral constraints, legislative alliances, and the constraints of capitalism present in the
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Peruvian government. I argue that these factors not only caused Humala's shift to the left-of-center, but they will
keep him on a track towards the moderate throughout his presidency.
Emily Boaz, Emily Chen, Nicole Serem
Teachers/Mentors: Joan Barber and Steve Warshaw, NCSSM
Mindfulness at NCSSM - NCSSM’s environment nurtures academic success, commitment to community service,
and exposure to different cultures, the rigors of this environment may also create unique challenges for the
students.The possible effects of these new adjustments may manifest outwardly in behaviorisms such as sleeping
habits, eating habits, as well as emotional well-being. These conditions may indicate it prudent to look into ways to
buffer these reactions specific to this type of environment.
A form of evidence-based stress management called mindfulness has been proven to alleviate these stress
symptoms. Mindfulness is a state of “non-doing” and living in the present. As described by Dr. Jon Kabat-Zinn,
mindfulness is the “complete ‘owning’ of each moment of your experience, good, bad, or ugly.” Mindfulness
fosters a more accepting view of each individual’s present condition. This new perspective reduces stress related
to one’s preoccupation with the future and past, and instead allows the individual to focus on the present. Dr.
Kabat-Zinn’s Mindfulness-Based Stress Reduction program has demonstrated high effectiveness and success rates
in clinical settings, and has, inadvertently, proven to facilitate better quality of life in participants.
Mindfulness is not a recent development, however little research has been conducted on mindfulness in
adolescents, and even less so on stress in residential high school students. Since mindfulness has had such success
(especially in adults), it has the potential to be extremely effective in helping students manage their stress and live
a greater well-balanced lifestyle while at these residential schools.
Catherine Bradley
Teachers/Mentors: John Kirk, NCSSM; Amy Joh Leigh Spivey, Child Learning Lab
Inhibitory Control in Preschool Aged Children - Inhibitory control develops throughout childhood, but the most
significant development is between 3 ½ to 5 years of age (Simpson, & Riggs, 2005; Carlson, & Moses, 2001). There
are many different types of specialized inhibitory control and the development of the specialized types could
depend on a general inhibitory mechanism in the brain. This hypothesis was tested by giving children aged 3.5 to 4
years of age three inhibitory tasks, and studying the relationships between the tasks. The Day-Night task measured
verbal and cognitive interference inhibition, the Card Sort task measured cognitive interference inhibition, and the
Frog-Monkey task measured motor inhibition. 38 participants were given the inhibitory measures, and results
showed a positive correlation between the Card Sort and Frog-Monkey tasks, but no relationships between the
Day-Night task and the other two tasks. The data suggests that there is not a general inhibitory mechanism that
controls the development of specialized inhibitory control. Instead, specialized types of inhibitory control may
develop independently of each other.
NCSSM Research Symposium 2011-2012
Ashleigh Caison
Teachers/Mentors: John Kirk, NCSSM; Charlie Gersbach, Dave Ousterout, Duke University
The Synthesizing of TALENs for Gene Therapy - Transcription activator-like effector nucleases can be used to edit
the genome in very specific chosen places. The Gersbach Lab uses these, combined with zinc-finger nucleases
(which act for the same purpose) to try and “fix” muscular dystrophy by editing the dystrophin gene. The TALENs
are designed through a five day process of putting repeat variable di-residues together with a Fok1 cutting domain
to create the nuclease. One of two designed TALENs was successful, and can be used in combination with ZFNs to
edit DNA.
Jiexi Cao
Teachers/Mentors: John Kirk, NCSSM; Gary Bishop, UNC Chapel Hill
Syllable Pop: Decoding Polysyllabic Words - Literacy is a key component to living and surviving in the modern
world. Without the ability to read, people often endanger themselves by not understanding the world around and
are more susceptible to fraud and deceit. However, not everyone can naturally become literate. As public
education becomes more standardized, a larger portion of students are blocked from attaining the knowledge in a
suitable, efficient way for them. Syllable Pop provides a different alternative to memorizing a list of vocabulary for
those who need a different approach. The simple JavaScript game logically breaks down polysyllabic words and
presents it to the user in a fun, enjoyable way where the user controls a bird casually flying around in the sky,
collecting balloons with chunks of the word, piecing the word back together.
Landon Carter
Teachers/Mentors: Myra Halpin, NCSSM; Rahman Tashakkori, Appalachian State University
Modeling Tephra Fallout - Volcanoes are highly destructive, causing hundreds of deaths and billions of dollars of
damage annually. Even more dangerous is the supervolcano, a massive volcano that ejects at least 1000 cubic
kilometers of tephra (volcanic rock and ash). Yellowstone is the most well-known supervolcano in the United
States. Using Gaussian atmospheric dispersion models, it is estimated that a Yellowstone eruption would cover
much of the United States in at least a millimeter of ash, causing direct damage in the form of building collapse and
respiratory problems. The atmospheric effects would last far longer, on the order of decades or even centuries,
causing an extended cooling period and wiping out up to 99% of the human population worldwide.
NCSSM Research Symposium 2011-2012
Landon Carter
Teachers/Mentors: Myra Halpin, NCSSM
Thermal Decomposition of Polyethylene - Polyethylene’s decomposition products are hydrocarbons, so leftover
polyethylene represents apossible source of fuel. Alkanes are more useful than unsaturated hydrocarbons in fuel,
thus, substances that can influence production of saturated versus unsaturated hydrocarbons are useful (SH/UH
ratio). Previous studies show that radical mechanisms govern polyethylene’s thermal decomposition, raising the
possibility of antioxidants hindering radical propagation. Therefore, I hypothesized that adding ascorbic acid would
produce larger hydrocarbons and greater SH/UH ratios. In order to determine these ratios, products were analyzed
with UV-Vis spectroscopy. Results using UV-Vis spectroscopy are inconclusive. Planned work includes using GC-MS
for thorough analysis of products.
Sarah Chao
Teachers/Mentors: John Kirk, NCSSM; Michael Jarstfer, UNC Eshelman School of Pharmacy
Mitochondria and TERT - The possibility of a link between mitochondria and TERT (telomerase reverse
transcriptase) was investigated, with the use of online programs Ensembl, Mitoprot, and Clustawl. Mitochondria
are known to play a large role in apoptosis, and TERT is known to have Caspase-6 and 7 cleavage sites which, when
cleaved, result in apoptosis. TERT protein sequences for 32 different vertebrate organisms were obtained from
Ensembl. On each, Mitoprot was used to calculate the possibility of mitochondrial targeting sequences and
cleavage sites. Clustawl was then used to align the sequences to check for conservation of the “TVTD” Caspase-6
cleavage site and for any correlation with the existence of the mitochondrial targeting sequence. Hints of a
correlation were seen, but not enough to be conclusive. Future work could include retesting with a new set of
protein sequences, to account for the possibility of errors in the sequences from Ensembl.
Vivian Chen
Teachers/Mentors: John Kirk, NCSSM; Khanh Nhat Tran Viet, Terri Young, Duke Center of Human Genetics
Genetic Analysis of ATOH7 to ONH - The atonal homolog 7 (ATOH7) gene codes for transcription factors involved
directly with the optic nerve and ganglion cell development according to previous research. Optic nerve hypoplasia
(ONH) was the focus of this research, a disease with no current genetic linkage concerning the underdevelopment
of the optic nerve and one of the leading causes for blindness. Using a variety of polymerase chain reactions and
gel electrophoresis, the single exon of ATOH7 along with the untranslated region of the gene were analyzed in 54
different DNA samples from Duke, Australia, France , and Ohio. The sampling group contained both affected and
nonaffected subjects with ONH. Splitting the gene into three overlapping regions, there was a 44%, 91%, and 94%
success rates in PCR. Using a computer program Sequencher, the results of the successful PCRed DNA samples
were analyzed to determine the base pair sequences and search for any novel coding single nucleotide
polymorphisms (SNPs) or other mutations and variations. Two novel non-coding synonymous SNPs were found as
well as an already reported coding synonymous SNP, rs146898613. Further troubleshooting needs to be conducted
on failed DNA samples, but potential genetic therapy methods can be developed in the future with the help of
further research.
NCSSM Research Symposium 2011-2012
Kayla Christianson, Katie Helm, Israel Nelson, and Juliana Ruggiero
Teachers/Mentors: Marion Brisk, NCSSM
Synthesis of Nanotubes - Our research focused on testing and improving the procedure Dr. Yue Wu developed in
his laboratory at the University of North Carolina at Chapel Hill to synthesize titanium dioxide nanotubes. This
procedure was the first half of a two-step process that involved application of a dye to TiO2 nanotubes to produce
a photovoltaic electrochemical cell that electrolyzes water. The high surface area results in significant production
of hydrogen gas. To begin the process of nanotube preparation, we mixed NaOH pellets, distilled water, and
titanium dioxide in a specially designed autoclave with a Teflon one liter vessel. The autoclave was heated in an
oven for three days. After cooling the white caked material was separated from the highly basic solution and then
pulverized. The titanium dioxide nanotubes where then separated into centrifuge tubes where they were washed
with 0.10 N HCl and distilled water until the pH was lowered to about 7.0. The process involved washing, shaking,
and centrifuging. After each wash the pH was determined. After the titanium dioxide material was neutralized, we
brought them to unc for imaging using a scanning electron microscope. The results indicated a successful synthesis
of titanium dioxide nanotubes.
Hannah Cornell
Teachers/Mentors: Ershela Sims, NCSSM
Biomechanics of Jump Landing - In this project, 6 subjects (3 males and 3 females) will have their kinetics from
takeoff to landing measured as they jump and land on a 2D force plate. The following variables: takeoff ground
reaction force, loading rate, and landing ground reaction forces will be calculated. Subjects will also be recorded as
they jump and land so that their joint kinematics during landing can be measured. Video analysis will be
completed in Logger Pro to determine the knee flexion angle at landing. The data obtained from female subjects
will be compared to that of the male subjects in order to determine the differences in landing mechanics. This
project is being done in an attempt to better understand the differences in how males and females land after
jumping in the air. This is important because previous studies have found that adolescent females who participate
in sports that involve jumping maneuvers sustain anterior cruciate ligament (ACL) injuries at a higher rate than
males in the same sports. The study hypothesis is that women will land with a greater knee flexion angle than men,
and that women will have a higher loading rate than men.
Jerry Cui and David Wang
Teachers/Mentors: Bob Gotwals, NCSSM; Gary Churchill, Sue McClatchy, Jackson Laboratory
Computational Investigation of the Igf2r Pathway - Aging is not a simple process, and there are numerous
pathways and genes involved in the senescence of cells. Many studies have confirmed that one way to increase
lifespan is to follow a dietary restriction (DR) regimen, which has been well-studied in mice. There are several key
pathways and genes involved that contribute not only to longevity, but also to a reduced risk of cancer. Our goal
was to identify genes related to the Insulin-Like Growth Factor-1 (IGF-1) pathway and identify their relationship to
dietary restriction and extended lifespan. An expression quantitative trait locus (eQTL) analysis of genes with
known relations to the IGF pathway was conducted from a B6 x BTBR cross. From the eQTL analysis, a list of genes
related to key IGF genes in the IGF-1 pathway was built by analyzing the regions surrounding the eQTL peaks. This
NCSSM Research Symposium 2011-2012
list was refined by comparing expression data and determining the correlation between gene interactions. After
further analysis of the identified genes, we were able to create a list of six genes that are highly correlated with the
Igf2r pathway.
Raj Desai
Teachers/Mentors: John Kirk, NCSSM; Jonathan Pillai, Sarah Mueller, Joseph DeSimone, UNC - Chapel Hill
Synthesis of MPLA Loaded Nanoparticle Vaccines - A recently developed top down process for the synthesis of
nanoparticles has introduced many new potential applications of nanomedicine and material synthesis. This new
process, known as PRINT Technology, was developed by the DeSimone Lab at the University of North Carolina at
Chapel Hill. PRINT Technology introduced greater control over particle synthesis. This study highlights some of the
major new innovations of PRINT Technology on particle synthesis including control over size, surface chemistry,
shape, and particle composition and studies the synthesis of MPLA-loaded nanoparticle vaccines. MPLA
nanoparticle vaccines were developed using 80x180 nm series molds and tested for incorporation of MPLA into the
80x180 HP4A nanoparticles. This study focuses on the potential of PRINT Technology produced nanoparticle
vaccines and provides insight into the further potential of the use of nanoparticles as vaccines.
Caroline deSaussure
Teachers/Mentors: John Kirk, NCSSM; Nelson Chao, Benny Chen, Divino Deoliveira, Duke University
An Ear Punch Model for Combined Radiation Injury - Combined radiation injury presents a major clinical obstacle
for patients receiving radiation treatment who have preexisting wounds. To treat malignant tumors, surgery is
often combined with radiation treatment. However, the wounds from the surgery often become extremely
infected and the healing process is severely impeded by the radiation. These effects can be seen historically by
events like Hiroshima and Chernobyl, where many people were poisoned by the severe amounts of radiation
exposure and also suffered from additional wounds, such as burns and cuts. The purpose of this study was to
develop a mouse model that would investigate the mechanisms of wound healing through an ear punch model. To
determine the efficacy of the implemented treatment methods, we investigated several different drug and cell
therapy options. We implemented these options in different strains of mice that were subject to varying degrees
of irradiation and analyzed results through microscope imaging.
Katy Drews, Caitlin Seyfried and Katie Helm
Teachers/Mentors: Steve Warshaw, NCSSM; Ernie Swanson, Triangle J Council of Governments
NCSSM Waste Assessment - We performed a solid waste reduction assessment of the NCSSM campus, consisting
of an on-site facility audit and a comprehensive survey report with cost benefit analysis. We researched potential
reuse, reduction, and recycling strategies on campus. First, the main solid waste streams were identified, and
analyzed as to their reduction or recycling potential. We quantified the amount of waste currently produced, and
then quantified the tonnage of waste potentially able to be diverted from landfilling. The potential cost savings of
each waste stream change were identified.
NCSSM Research Symposium 2011-2012
Denise Elizondo
Teachers/Mentors: John Kirk, NCSSM; Chris Kontos, Sarah Frazier, Duke University Medical Center.
Phosphorylation of Caskin2 and Tie1 interactions - Research was done on the interaction between Tie1 and
Caskin2. Not much is known about Caskin2, however previous data indicates that it binds to Tie1 but not Tie2. The
goal is to see if Akt phosphorylation of T794 on the Tie1 receptor has any effects on the Caskin2-Tie1 interaction.
Based on preliminary data in zebrafish, phosphorylation of the T794 site is critical for proper vascular
development. Knowing its effects on Caskin2 will help in the understanding of the regulation of the essential roles
of the Tie receptors in angiogenesis.
Peter Fan and Aakash Indurkhya
Teachers/Mentors: Myra Halpin, NCSSM
Genetic Toggle Controllers using Zinc Finger Trans -The activation or repressions of key genes, controlled by gene
regulatory networks, often cause genetic diseases during stem cell differentiation and DNA replication. Synthetic
biology holds promise for advances in gene therapy through the engineering of novel gene regulatory networks.
Using synthetic zinc finger transcription factors, we increased functionality and added an interfacing component,
called the “controller,” to an established network topology, the genetic toggle switch. The bacterial-two-hybrid
assay, a standard method in zinc finger characterization, was tested and found to be too cumbersome for use in
fast paced and high throughput synthetic biology. Hence, we proposed a modified experimental protocol and
presented a computational BLASTn screening and protein-DNA docking characterization method that efficiently
selected nine viable zinc finger transcription factors. We used TinkerCell, a CAD network modeling software, to
construct a stochastic model for the toggle switch controller and found that all defining characteristics of the
genetic toggle switch were maintained with reduced transcriptional noise. The use of synthetic zinc finger
transcription factors establishes synthetically generated biological parts as the key to next generation gene
regulatory networks. The full development of the toggle switch controller will serve as a major step towards
personalized medicine and gene therapy.
Warren Feng
Teachers/Mentors: Myra Halpin, NCSSM
Engineering a Multifunctional Quantum Dot - The preliminary procedures are currently being completed within
the lab which consists of quantum dot synthesis and designing a genetic sequence in Molegro. The overall goal is
to engineer a multifunctional quantum dot affixed zinc finger nuclease transfer vector for cancer detection,
imaging, and gene therapy. Quantum dots are preferred over other methods of imaging because of the robust
yield and precise targeting towards a cell of interest. We plan to synthesize quantum dots with a polymer coating
and covalently bind ligands to the polymer shell. These quantum dots once synthesized, will be encapsulated
within a polymeric nanoparticle which will be produced using a double emulsification process. This nanoparticle
will also encapsulate our specially designed ZFNs and plasmid containing hBAX. This nanoparticle as a whole will be
attracted to a cancer cell once the ligand transferrin is covalently binded to the outside shell. Once the
nanoparticle approaches the cancerous cell, endocytosis will be initiated and the cell will enter. Once the
nanoparticle degrades from within, apoptosis will be induced via the ZFNs and tailored plasmid.
NCSSM Research Symposium 2011-2012
Alyssa Ferris
Teachers/Mentors: Amy Sheck, NCSSM; Beth Sullivan, Duke Institute for Genome Sciences and Policy
Histone Modifications and Centromere Activity - Most chromosomes have a single centromere, but some, called
dicentrics, have two functional centromeres. This usually leads to cell death; in human dicentrics, however, one of
the centromeres is turned off and the cell remains functional. To determine if the presence of histone methylation,
(a mechanism for inactivation) correlated with centromeric function, I measured the levels of euchromatic and
heterochromatic methylation at active and inactive centromeres of the naturally dicentric human Chromosome 17.
I used four hybrid mouse cell lines, derived from two distinct human cell lines that had a different active
centromere (either centromere Z1 or Z1B) on each homologous chromosome. To quantify the levels of histone
methylation, I used chromatin immunoprecipitation to pull down DNA that was tagged with specific methylation
groups and then measured the levels of methylation using semi-quantitative PCR. I found that the levels of
heterochromatic methylation increased when centromere Z1 became inactive, but I did not find a similar trend at
the other centromere (Z1B) or with euchromatic methylation. I also found that the levels of methylation were not
constant in different cell lines, indicating that each cell line had a unique epigenetic profile instead of a set level of
methylation. These results have long term implications for cancer medications and gene therapy.
Justin Finkelstein and Halston Lim
Teachers/Mentors: Jonathan Bennett, NCSSM; Caleb Marsh, Appalachian State University
A Statistical Evaluation of GRB Afterglows - Gamma Ray Bursts (GRBs) are the some of the most luminous and
distant events observed in our Universe. By studying these high energy relics of the past, a greater understanding
of our cosmological origins can be gained. In this study, we investigated the afterglow properties of long duration
GRBs. Using Minitab 16 statistical software as well as Logger Pro to generate and analyze light curves, we took a
sample of 30 GRBs and conducted a statistical analysis on the bursts to test if they all exhibited an intermediate
plateau decay. We generated light curves using data from the Swift X-Ray Telescope (XRT), and then separated the
curves into their different decay phases and generated decay indices. When we split the GRBs in two categories
based on whether they superficially featured a plateau decay region, the variations observed in the pre plateau
decay index and pre plateau break were significant between the two groups. However, the variations in the
intermediate plateau decay index, the post plateau break, and the post plateau decay index were insignificant
between the two categories of GRBs. Our results show that the plateau region decay index is independent from
the initial decay index, suggesting a possible secondary emission in the intermediate plateau decay region.
Zachary Fowler
Teachers/Mentors: John Kirk, NCSSM; Allison Ashley-Koch, Karen Soldano, Duke Center for Human Genetics
BBS7 SNPs as Genome-Wide Anencephaly Cohorts - Neural tube defects occur when the neural tube fails to close
during embryogenesis, resulting in fetal death. Anencephaly occurs when an infant is born without a posterior
neurological region due to a neural tube failure. It has been speculated that this failure is a result of a mutation in
the BBS7 gene, which, when involved in the onset of Bardet-Biedl syndrome, results in ciliopathy. We have
hypothesized that because cilia are needed to seal the neural tube and connections between BBS7 and ciliopathy
have been made, that single nucleotide polymorphisms in BBS7 must be associated with anencephaly etiology. A
NCSSM Research Symposium 2011-2012
genotypic analysis carried out on 22 SNPs following allelic differentiation, in order to determine the association
between “at-risk” genotypes and an anencephaly carrier, revealed association between BBS7 SNPs and
anencephaly. Furthermore, statistical analysis revealed that association between BBS7 SNPs and anencephaly
occurs 99.2% of the time.
Aakash Gandhi
Teachers/Mentors: Amy Sheck, Bob Gotwals, NCSSM
Rational Design for Targeted QSI - Through a process known as quorum sensing, Gram-negative infections rely on
the activity of a synthase and receptor of small-molecule autoinducers to regulate pathogenicity. Quorum sensing
inhibition (QSI) in such bacteria inhibits virulence factors such as swarming motility and biofilm production through
competitive antagonism, a process that does not actively select for resistance. In this study, a targeted inhibition
scheme was evaluated as a model for quorum sensing inhibition through computational screening and in vivo
assay of compounds found in naturally-available anti-quorum sensing products. Structural validation of existing
crystallographic data for the LasI synthase and LasR receptor for the quorum-regulated infection P. aeruginosa was
performed to create secondary structures, and molecular dynamics software was used to assess the binding
affinities of synthetic, furanone, and flavonol compounds. A quorum sensing inhibition assay was also developed
to screen for in vivo potency (IC¬50) against the quorum sensing activity of Vibrio fischeri MJ11, but experimental
protocols require further development. Docking results validate the computational model against previous
experimental data, and identified luteolin and furanone C30 as candidate inhibitors of (respectively) the QS
receptor and synthase. Additionally, analysis of conserved ligand-active site residue binding demonstrates critical
H-bonding on primary amine, valerolactone, and phenolic moieties. This functional pattern identifies the
mechanism of competitive antagonism for targeted inhibition of LuxIR-type quorum sensing, homologous to all
Gram-negative infections, and suggests a rational design for the selection of drugs belonging to a novel class of
anti-pathogenic treatment.
Anita Gandhi
Teachers/Mentors: John Kirk, NCSSM
Heparin-Induced Thrombocytopenia - Heparin-Induced Thrombocytopenia (HIT) is an immune-mediated disorder,
which usually occurs anywhere between four to ten days after heparin exposure. The problem that HIT faces
currently is that it is extremely difficult to diagnose1, 2. As HIT patients have an incredibly low platelet count, or
thrombocytopenia, it may seem easy to pick them out7. This, however, is not the case. For one thing,
thrombocytopenia is a common symptom for many disorders5. Currently, research is being done in order to find
the optimum amount of heparin that binds to the PF4 protein and creates the most complexes. This was done by
absorbance techniques. So far, it has been noted that, after consistent experimentation, that the peak of the most
complexes occurs at 5 microliters of heparin for both distilled water and HBSS. This experiment has been done in
other research labs other than the one at Duke University and is therefore a reliable source of measurement. We
are repeating the tests in order to say that there is consistency with the results and that there is no error regarding
faulty machines or false data. So far, the results that our lab has produced matches up with the other labs. Upon
future research, we hope to find out more about the pathogenesis of HIT.
NCSSM Research Symposium 2011-2012
Hailey Gosnell
Teachers/Mentors: John Kirk, NCSSM; Simon Gregory, Duke Center for Human Genetics
Genetic Factors Contributing to NTD Occurrence - Fumonisin B1 is a carcinogenic toxin found in corn throughout
the world [Marasas et al., 2004]. FB1 prevents the biosynthesis of sphingolipids through inhibiting ceramide
synthase, an enzyme that plays a crucial role in sphingolipid and glycerophospholipid metabolism. Sphingolipids
play an important part in cell signaling events and are vital components of cell membranes. A connection between
maternal fumonisin ingestion through consumption of tainted corn, during the early stages of gestation and
increased frequency of birth defects, specifically NTDs (neural tube defects) has been indicated in areas for which
corn is a dietary staple [Marasas et al., 2004]. Neural tube defects are defined as malformations caused by failure
of proper neural tube closure during the first few weeks of pregnancy. Common forms of NTDs include
anencephaly (failure of the anterior neural tube to close properly resulting in an absence of the brain at birth) and
spina bifida (incomplete closure of the posterior neural tube). Numerous research studies in this field have shown
that both environmental and genetic factors are manifested in the occurrence of neural tube defects.
In consideration to the above summary of what is known of neural tube defects, the objective of this study is to
discover and validate unique and measurable biochemical and genetic biomarkers that predict increased risk for
teratogenicity in areas where fumonisin-contaminated corn consumption is high. Fumonisin will be evaluated as
an environmental contaminant that significantly contributes to neural tube defect development. My presentation
details the mouse model of this ongoing project.
Katrina Gutierrez and Brian Iezzi
Teachers/Mentors: Myra Halpin, NCSSM; Brian Cooper, UNC Charlotte
Validation of Transcription Factor Binding Sites - Scientists have already mapped out complete genomes for
multiple organisms, but have not yet mapped out all the transcription factor binding sites. Without this
knowledge, we cannot completely understand development, evolution, and other biological processes. In order to
expand the list of known binding sites, our research goal was to verify predictions of potential binding sites
generated from a researcher’s computational algorithm.
We attempted to detect binding at the predicted binding site sequences by using capillary electrophoresis, where
substances moving through a thin tube are separated according to their charge to density ratio. This means that
negatively-charged DNA would be detected at a different time from DNA bound to positively-charged transcription
factors, so we can determine if something is binding to the DNA.
The challenge was working with multiple unknowns because, unlike previous research, we did not know which
transcription factors were supposed to bind or the binding conditions necessary. Our screening for binding was
also hindered by binding from other proteins that were not transcription factors. However, we found that we
could differentiate between the specific binding we were searching for and this unwanted binding because the
latter would be detected around the same time with every DNA sequence. We have not yet validated the binding
site predictions, but we hope to do so by making our samples more closely reflect the cellular conditions, where
binding could potentially occur.
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Pranav Haravu
Teachers/Mentors: Myra Halpin, NCSSM; Diane Fels, Kenneth Young, Duke University Radiation Oncology
Dysadherin's Role in Cancer Metastasis - Though cancer treatments have significantly progressed, metastasized
tumors still pose a significant challenge to modern therapeutic methods, resulting in poor prognoses and lower
survival rates for patients with metastasized cancers. In this study we investigated the role of dysadherin in a
possible mechanism for both hypoxia- and hyperthermia-induced metastasis. Dysadherin is a cell-membrane
protein found highly expressed and glycosylated in cancer cells, but expressed only in a few normal cells. It down-
regulates E-cadherin mediated cell-cell adhesion, facilitating metastasis. We treated Panc-1 and PC3 cells with 43
hyperthermia and .5% O2 hypoxia. Western Blots, with actin as a loading control, showed a significant increase in
expression of glycosylated dysadherin in Panc-1 cells exposed to hypoxic and hyperthermic conditions. However,
unglycosylated dysadherin expression was not affected, leading us to believe unglycosylated dysadherin does not
play a significant role in metastasis. IF imaging of PC3 cells also showed a significant increase in dysadherin
expression in samples treated with hypoxia or hyperthermia, quantified by the ratio of fluorescence of the
secondary, FITC, to that of DAPI. The results suggest hypoxia- and hyperthermia-induced metastasis function by
increasing the expression of glycosylated dysadherin, which in turn down-regulates E-cadherin and promotes
metastasis. Inhibiting key steps within this mechanism could serve as a potential drug target, greatly reducing the
metastatic potential of malignant tumors. To our knowledge, this is the first report indicating that hypoxia- and
hyperthermia-induced metastasis may occur by increasing glycosylated dysadherin expression.
Brian Hart
Teachers/Mentors: John Kirk, NCSSM; William Keech, Duke University
Fiscal Policy over the Last Decade - Since 2001 the United States has seen a resurgence in the use of discretionary
fiscal policy. My research compiles experts' research on the major fiscal policies of the Bush and Obama
Administrations in order to get a better understanding of their effects on the macro economy, as well as the
effectiveness of active fiscal policy in general. These policies have attempted to improve the troubled economy
that has persisted over the past decade, but because there is a general lack of understanding with respect to fiscal
policy, the stimuli have been poorly designed and generally ineffective in comparison to their costs. Economists, as
well as policymakers, do not have enough experience and data to fully understand the effects of fiscal stimuli, and
because of that there is strong disagreement among economists as to what amount, if any, stimulus is needed to
improve a recessed economy. Presidents Bush and Obama passed three main fiscal policies: the Bush Tax Cuts, the
Emergency Stimulus Package, and the American Recovery and Reinvestment Act. My research shows that these
policies failed to have their desired effects and only improved the economy marginally at best. Lastly, this paper
will attempt to assess the long-term effects of the massive deficits that were created in order to implement these
policies.
Justin Hendrick and Pooja Potharaju
Teachers/Mentors: Bob Gotwals, NCSSM
Computational Analysis of Type 2 Diabetes - Inflammation has emerged as one of the key factors of human health
as increasing data suggest a potential role for inflammation in the pathogenesis of T2D. This is supported by the
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results of both preclinical studies and new clinical trials using anti-inflammatory approaches to treat the disease.
Through our research, we investigated the relative contribution of genes directly correlated to inflammation in the
development of T2D using C57BL/B6xBTBR expression qtl data and developing a causal model for inflammation in
adipose. From this, we identified specific loci and genetic markers to look at the relative contribution of these
genes in the pathogenesis of T2D. Analysis of main scans and QTL analysis showed that the most significant peaks
were under chromosomes 9 and 13. The genes Leptin and TNF seemed to have the most significant
correspondence to T2D according to the BIC models, but we are still unsure of all the implications.
Austin Hopkins
Teachers/Mentors: John Kirk, NCSSM; Peter Klopfer, Duke University
Reproductive Behavior of Fat-tailed Dwarf Lemur - The inter-sexual social interactions of fat-tailed dwarf lemurs
(C. medius) were observed after emergence from seasonal torpor. Two mating C. medius pairs were observed for
general social interactions, sexual behaviors, and any interaction between members of separate pairs. C. medius is
a monogamous species, but extra-pair mating occurs. The question of if and how male individuals express
preference for extra-pair mates remains unanswered as the project has not been completed, and the current data
is not enough to draw conclusions. However, the notion that sexual behavior begins during emergence from torpor
was reaffirmed.
Morgan J. Howell
Teachers/Mentors: Myra Halpin, NCSSM
Engineering a Multifunctional Quantum Dot - The preliminary procedures are currently being completed within
the lab which consists of quantum dot synthesis and designing a genetic sequence in Molegro. The overall goal is
to engineer a multifunctional quantum dot affixed zinc finger nuclease transfer vector for cancer detection,
imaging, and gene therapy. Quantum dots are preferred over other methods of imaging because of the robust
yield and precise targeting towards a cell of interest. We plan to synthesize quantum dots with a polymer coating
and covalently bind ligands to the polymer shell. These quantum dots once synthesized, will be encapsulated
within a polymeric nanoparticle which will be produced using a double emulsification process. This nanoparticle
will also encapsulate our specially designed ZFNs and plasmid containing hBAX. This nanoparticle as a whole will be
attracted to a cancer cell once the ligand transferrin is covalently binded to the outside shell. Once the
nanoparticle approaches the cancerous cell, endocytosis will be initiated and the cell will enter. Once the
nanoparticle degrades from within, apoptosis will be induced via the ZFNs and tailored plasmid.
Alice Huang
Teachers/Mentors: John Kirk, NCSSM; Shane Dikolli, Duke Fuqua School of Business
The Effects of Social Media on Modern Businesses - With social media on the rise, business leaders are quickly
incorporating this powerful social phenomenon in their marketing strategies. Social media, and Twitter in
particular, is changing the way business leaders interact with their customers, how they market their products, and
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what their business priorities are. The goal of this project was to determine the reason CEOs choose to use Twitter,
as opposed to other social engines, and whether they tweet for personal gain, professional gain, or a combination
of the two. Finally, I looked at the success of Twitter Campaigns by correlating business revenue to number of
tweets.
Suqi Huang
Teachers/Mentors: Myra Halpin, NCSSM; Andrey Khlystov, Duke University
Activity Coefficients of Wood Smoke Tracer - Aerosols are known to affect the climate and have been linked to
adverse health effects. An effective way of reducing air pollution is to determine and to control the sources of the
harmful particles. The chemical mass balance (CMB) receptor model is a method of source apportionment that
uses tracer compounds, which should be distinct to certain sources and conserved in the atmosphere. In this
experiment, the Integrated Volume Method developed by Saleh and Khlystov (2009) was used to predict the
volatility of a wood smoke tracer, levoglucosan, and the interaction of the tracer with artificial and ambient semi-
volatile organic aerosols. Artificial mixtures were made with monocarboxylic acids, and ambient particles were
collected using a filter and extracted in ethanol. Aerosols were generated from mixtures with different mole
fractions of levoglucosan and sent through a heated thermodenuder. The change in volume was calculated by
comparing measurements before and after heating and was graphed versus the mole fraction. Aerosol generated
from levoglucosan exhibited a change in volume, which suggests that it is semi-volatile. Mixtures of levoglucosan
and monocarboxylic acids do not form a solution. Mixtures of levoglucosan and ambient extracts showed
interaction and did not display ideal behavior, and the activity coefficients of levoglucosan were determined.
Mariya Husain
Teachers/Mentors: John Kirk, NCSSM; Alison Adcock, Betsy Johnson, Duke University
Hippocampus-Dependent Learning: CAARMS+ Subjects - OBJECTIVE: In this experiment, relational memory was
tested for its correlation to generalization performance in people at ultra high risk for schizophrenia.
METHODS: 62 subjects at ultra high risk for schizophrenia and 34 healthy controls were administered the Acquired
Equivalence task, which teaches associations and tests overlapping generalizations. The use of fMRI was
implemented to track hippocampal activation.
RESULTS: Hippocampal activation was equally observed between both types of subjects. Hippocampal activation
positively correlated with trend levels for healthy subjects but not or ultra high risk subjects. Hippocampal
activation negatively correlated with PANSS scores for ultra high risk individuals, and positively correlated with
HiSoC scores. HiSoC scores also strongly correlated with generalization performance.
CONCLUSIONS: People at ultra high risk for schizophrenia have impaired ability to generalize in comparison to
healthy subjects. Future implementation of this experiment could predict whether people at high risk for this
disorder will actually develop the disorder.
NCSSM Research Symposium 2011-2012
Ashley Jernigan
Teachers/Mentors: John Kirk, NCSSM; Dan Richter, Paul Heine, Duke University
Phosphorus Fractionation in Pocosin Restoration - Juniper Bay is a pocosin located near Lumberton in North
Carolina. My research focused on the phosphorus content of this pocosin. Juniper Bay was drained and farmed for
decades, and has recently started to be restored back to its natural wetland form. I conducted a phosphorus
fractionation on the soils to determine how the farming practices affected the element levels in the soil.
The phosphorus fractionation is a multistep process that includes four different extractions. The four extractions
are the HCO3-Pt extraction, the NaOH-Pi extraction, the NaOH-Po extraction, and the HCl-Pi extraction. These
procedures must be completed in this order since it is a building process.
From the fractionation we found that, in comparison to a pocosin that had never been farmed, Juniper Bay had
significantly higher levels of phosphorus in the soil, especially in the upper layers of the soil. This may affect the
restoration process since the bay is not drained anymore and the water levels are rising. Having significantly higher
levels of phosphorus in the soil, and therefore in the water table, could cause algae blooms and devastate the
restoration process. Juniper Bay is continuing to be sampled and the restoration will continue to be monitored.
Mary Ann Jin
Teachers/Mentors: John Kirk, NCSSM; Gary Bishop, UNC-Chapel Hill
Word Blaster: Improving Literacy with a Game - Many children with dyslexia and other disabilities have difficulty
with reading large words because they have trouble breaking them down. Due to this, they often become stuck at
a second grade reading level. In order to remedy this problem in a way that the children would enjoy, Word
Blaster, a browser-based JavaScript game, was created. The game implements morphological awareness training
to help children visualize the breakdown of words and familiarize them with the parts of words. Word Blaster is
customizable so that the teacher or parent can input the words they want the child to practice with, allowing for
flexibility to suit each child’s reading level and weaknesses.
Sara Johnson
Teachers/Mentors: John Kirk, NCSSM; James Peacock, UNC - Chapel Hill
Muhammadiyah's Role in Muslim Indonesia - This presentation will discuss Muhammadiyah, a large Muslim
organization on Java, Indonesia. It will cover Muhammadiyah’s political role in Indonesia and how it has changed
since the fall of Suharto in 1998. I will discuss Muhammadiyah’s social role in the Indonesian home and the role of
the women’s movement, especially Aisyiyah, the women’s branch of Muhammadiyah. I will also discuss what sets
Muhammadiyah apart from any other religious organization, and Muhammadiyah’s interaction with other religious
organizations of Indonesia.
NCSSM Research Symposium 2011-2012
Varqa Kalantar
Teacher/Mentor: Jon Bennett, NCSSM
Single-bubble Sonoluminescence in Various Liquids. - Single-bubble sonoluminescence is a process by which
resonant sound waves in a flask of water create a bubble with a pulsating radius. The bubble "collapses",
compressing the air inside and generating light. The goal of this project was to create a setup to observe single-
bubble sonoluminescence, and then to investigate the effects of using various liquids other than water in an
attempt to increase the intensity of light emitted from the bubble in a regular water flask.
Mark Kirollos
Teachers/Mentors: Amy Sheck, NCSSM; Paul Magwene, Duke University
Ammonia Signaling and Colony Morphology of Yeast - Saccharomyces cerevisiae is often classified as a unicellular
organism, however, this species displays complex behavior such as cellular differentiation and cell signaling often
associated with multicellular organisms. Carbon limitation in media causes yeast colonies to form complex
morphology, believed to be an adaptation for surviving stressful conditions. Ammonia signaling has been shown to
synchronize complexity in yeast colonies alongside other transcriptional changes triggered by carbon limitation
that effect complex colony formation. By submitting yeast strains grown on high and low dextrose levels to varying
levels of extracellular ammonia, the effect of each treatment on variation in complexity and colony size could be
determined. Increasing ammonia exposure time decreased the strength of morphology in certain strains and
promoted growth, contrary to prior published finding. Ammonia levels also affected colony diameter in some
strain, causing colonies to become larger as ammonia exposure time increased. These findings may further the
treatment of pathogenic biofilms by identifying potential pathways that effect the growth and transcriptional
changes that increase survivability of fungal diseases.
Tyler Kissinger
Teachers/Mentors: Jon Bennett, NCSSM; Kate Scholberg, Duke University High-Energy Physics Neutrino Group
Long-Distance Supernova Sensitivity at DAEdALUS - In this study, we use the Monte Carlo method to investigate
the expected long-distance supernova sensitivity at a proposed neutrino research facility, DAEdALUS. A burst of
neutrino interactions in a detector during a short time interval (t < 10 s) is indicative of a supernova event, as
supernovae produce massive amounts of neutrinos in a very short time interval during their death. As part of the
DAEdALUS experiment, three neutrino beams (active according to a particular time structure) will pass through a
300 kiloton water Cherenkov neutrino detector. We investigated the number of double and triple events, pair
interactions appearing to be signals from long-distance supernovae, expected to occur as a result of the three
neutrino beams passing through the detector from the cyclotron accelerators. This was determined through the
creation of a program which incorporated a random number generator and statistical methods to model the
estimated ten-year runtime of the DAEdALUS experiment according to the time structure of the cyclotrons. This is
compared to the number of double and triple events expected to occur simply as a result of other various
background sources and the number of true long-distance supernovae events to create a measure of the
sensitivity of the detector.
NCSSM Research Symposium 2011-2012
Jennifer Kronmiller
Teachers/Mentors: John Kirk, NCSSM; Peter Ornstein, Hillary Langley, UNC-Chapel Hill
Conflict and Emotional Talk in First Grade CIN's - This study was designed to explore first graders’ emotion- and
conflict-related speech when talking about positively and negatively valenced past events. In this study, 114
racially and socioeconomically diverse first grade children completed a Child Independent Narrative (CIN) task with
an experimenter, in which they were asked to recall details from specific, past events. Transcripts of these
conversations were then coded to identify all emotion- and conflict-based language used when describing positive
and negative past experiences. Results indicate that there were significant group differences based on gender,
race, and socioeconomic status. Specifically, results reveal that girls used significantly more total specific emotive
talk and more specific negative talk than did their male peers. Boys, on the other hand, used more total conflict
talk in their narratives than did their female counterparts. African-American children displayed significantly more
conflict talk than did their Caucasian peers. Children below the poverty level used more general emotive talk than
children above the poverty level, particularly when referring to negative instances. Finally, children from below
poverty families used significantly more total instances of conflict than those whose families were above poverty.
These results replicate previous findings that girls use more emotion language than boys. This study extends what
we know about children of different ethnic and socioeconomic groups, and how they may be differentially
socialized to talk about emotional experiences.
Debanjali Kundu
Teachers/Mentors: John Kirk, NCSSM; David Brizel, David Yoo, Pretesh Patel, Duke University Medical Center,
Radiation Oncology
Radiotherapy Treatments for Parotid Gland Tumors - Postoperative radiotherapy (PORT) is usually employed for
malignant salivary gland tumors (SGTs) when high risk features such as high grade, positive surgical margins (PSM),
perineural invasion (PNI), nodal involvement, and advanced T stage are present. We have evaluated factors
correlated with disease recurrence following surgery and PORT. Dosimetric comparisons of intensity modulated
radiotherapy (IMRT) vs en face mixed electron-photon techniques were performed. Overall survival (OS), local
control (LC) and 5-year disease free survival (DFS) rates were measured.
Jaehyeong Lee and Rob Gourley
Teachers/Mentors: Sangmin Lee, Cree Incorporated
Quantum Efficiency Using an LED Spectrophotometer - Fast and cheap spectral response measurement systems
are required in solar cell manufacturing lines in order to produce high quality solar cells. Using LEDs as light sources
is the most promising technique. However, since LEDs inherently have 10 - 15 nm spreads in wavelength, the
resolution for the wavelength is about 10 times worse than conventional spectrophotometers. In this report, a
method to compensate for the wavelength spread of LEDs has been developed. The output power from a solar cell
can be expressed where the input power is the distribution function of LED light power, where E(lambda) is the
efficiency of a solar cell, lambda is the wavelength and a^i is the coefficient of an nth order polynomial
approximation of E(lambda). Since 8 different wavelength LEDs were used, the maximum value of is 7. With the
same method, quantum efficiency was also approximated. Two different sizes of Si single crystal solar cells were
NCSSM Research Symposium 2011-2012
examined with this method. For the larger solar cell, the effect of spatial distribution of LED light intensity was also
calibrated. By comparing the data from larger solar cell with existing data sheet, it was confirmed that the solar cell
efficiency can be accurately measured by an LED spectrophotometer without assuming monochromatic light
sources.
Jaehyeong Lee and Tejas Sundaresan
Teachers/Mentors: Myra Halpin, NCSSM
Amphipathic Films for Water Collection - Providing clean water in arid regions is a difficult task. One eighth of the
world population does not have access to potable water, leading the most impoverished to consume diseased,
pollutant-laden water. In fact, 80% of illnesses in developing countries can be traced to dirty water. Current efforts
to provide clean water focus on groundwater extraction, but are limited by groundwater depletion and militant
control of aquifers. Another method of water collection is atmospheric collection. Our proposal is an amphipathic
film with localized hydrophobic and hydrophilic regions that can extract water from the atmosphere. The base of
the film will be a gold substrate extracted from recordable compact discs while the hydrophobicity of the film will
change based on the thiol self-assembling molecule that binds to the gold surface. The amphipathic film offers
many benefits when compared to current technology, namely avoidance of groundwater depletion, cost-
efficiency, and a light-flexible design.
Bryant Lin
Teachers/Mentors: Bob Gotwals, NCSSM; Tim Shafer, Lyle Burgoon, Cina Mack, Andrew Johnstone, EPA
On Chemical Classification of Spike Trains on MEAs - Microelectrode arrays(MEAs) detect chemical induced
changes in action potential “spikes” in neuronal networks and can be used for neurotoxicity screening. Analytical
“fingerprinting,” using Principal Components Analysis(PCA) and chemical class prediction using Support Vector
Machine(SVM) on spike trains may improve the utility of MEAs to classify unknown chemicals by mode of action.
The current study developed such approaches using MEA data from well-understood chemicals (bicuculline,
carbaryl, lindane, RDX, picrotoxin, muscimol, verapamil, fipronil, fluoxetine, chlorpyrifos oxon, domoic acid, and
deltamethrin, dimethyl phthalate) and “negative” controls (nicotine, acetaminophen, and glyphosate).
Concentration-response relationships, bursting parameters (e.g. rate, duration, interspike intervals, #spikes/burst)
and synchronization of activity were computed and averaged to yield parameter values as a function of
concentration, then standardized to control. These data were combined with spike rate and synchrony data and
PCA was performed across concentrations above each chemical’s IC/EC50 for spike rate. The first 3 principal
components accounted 68.1942%, 18.6860%, 6.6974% of the data variability and were used to identify separation
between chemical classes through spatial proximity and intersection of 95% confidence ellipses. The separation of
chemicals within chemical classes and between different chemical classes indicates that the sets may be
distinguishable. Using SVM, the test set was classified into the chemical classes of
increasing/decreasing/unchanging spike rate or no activity with a mean accuracy of 74.66% with 10-fold cross-
validation. The separation of different chemical classes through PCA and high prediction accuracy in SVM of a
small dataset demonstrates promising approaches for identifying neurotoxicological modes of action for unknown
chemicals.
NCSSM Research Symposium 2011-2012
Matt Litzsinger and Nathan Sanders
Teachers/Mentors: Myra Halpin, NCSSM
Wastewater MFCs - The utilitarianism of modern society and limited fuel reserves dictates new methods for
producing energy. The condition of the environment will affect descendants far into the future; therefore, it is
crucial to set a precedent of increasing alternate energy production. This is the fundamental motivation of our
project.
The goal of this project was to determine whether or not the addition of a modified-kaolin catalyst would increase
breakdown or organic material and increase the energy output of a microbial fuel cell in order to enable
commercial harvesting of energy from wastewater that could be applied in the wastewater treatment process. We
have run initial tests of our cell with K12 E. Coli bacteria and Potassium Ferrocyanide ions. We plan to test our cell
with wastewater from the North Durham WRF with our synthesized Cu2O–CoO–PO4 3− catalyst in the near
future.
Pranav Maddi
Teachers/Mentors: Jon Bennett, NCSSM; Michael Falvo, Timothy O'Brien, UNC Chapel Hill-Dept of Physics
Using Blocking Peptides to Analyze Fibrin Fibers - Fibrin is the main structural protein involved in blood clotting,
and exhibits strength and elasticity that rival engineering materials. Fibrin study traditionally focuses on entire
clots, whereas we employ new AFM-based “nanoManipulation” techniques to study single fibrin fibers. The
unstructured alpha regions and alpha;-helices within the coiled-coil regions of fibrin’s monomers are known to
extend when fibrin stretches, though it is not known exactly how they contribute to fibrin’s mechanical properties.
We isolated these regions using 4-residue peptides that interfere with the “knob-hole” interactions that connect
the coiled-coil regions and a 12-residue peptide that interferes with the alpha interactions. We found that the
alpha interactions and the knob-hole interactions are equally important for the assembly of fibrin. Our data
suggest that the coiled-coils are responsible for fibrin’s extension at low strains, and that the alpha regions account
for the majority of fibrin’s strain-stiffening behavior at higher strains. These findings advance the fibrin extension
model and may lead to better treatment and prevention of deep-vein thrombosis and pulmonary embolism.
Alyssa Mathewson
Teachers/Mentors: John Kirk, NCSSM; Neil Vidmar, Duke University Law School
The Insanity Defense - This project discusses how the insanity defense was applied in past and modern US court
systems and how it developed in common law England. Throughout the paper, research by other authors is read
and examined in order to gain a better understanding of how the insanity defense we know today was created. A
careful examination of these documents paints a picture of common law passed down to a young United States
that developed into its own very different law. Major cases in the past century are discussed in order to
understand how public opinion changed the law.
NCSSM Research Symposium 2011-2012
Daniel Mattox
Teachers/Mentors: John Kirk, NCSSM; Teresa Tarrant, Thurston Arthritis Research Center- UNC-CH
Functional Difference between GRK2 and GRK3 - In order to establish functional regulatory differences between
GRK2 and GRK3, a Phospho Erk assay was first tried but rejected due to background signaling. A SRE Luciferase
reporter assay system was also tried but was not successful due to other signaling pathways within the cell
interfering with the assay and causing inconsistent data. The TANGO assay was determined to be a successful
functional assay system with a clear and separate response curve for CXCR4 exposed to SDF-1 after the V2 tail
containing the vasopressin domain was removed.
Grant Means
Teachers/Mentors: John Kirk, NCSSM; Christopher Bonino, RTI
Efficiency of Hydrolysis in a PEM Electolysis Cell - The efficiency of hydrogen production through water
electrolysis was studied using a Polymer electrolyte membrane (PEM) assembly. Two different factors were
tested: flow rate of the water and the presence of a conductive solution in place of the traditional pure water. The
following electrolytic solutions were evaluated: deionized water (our control), potassium nitrate (KNO3, and
sulfuric acid. Flow rates of 583, 76, and 90 mL/hr were also tested. Both factors were found to be statistically
insignificant in terms of hydrogen production. The negligible effect that the conductive solutions had on the
efficiency of production is because the ion-transfer mechanism is determined by the ion-transfer membrane, and
not the solution.
José Medrano
Teachers/Mentors: Jon Bennett, NCSSM
Effect of Wall Material on Ocarina Sound Quality - It is generally accepted among musicians that an instrument's
wall material affects the sound it makes. In order to test this, we used human listeners and Fourier analysis to
compare the sounds made by 3 identically-shaped ocarinas, a type of early woodwind. The Fourier analysis was
used to compare the frequencies and overtones for all 18 notes on the ocarinas, and we found that the
frequencies varied randomly around the accepted frequencies for each note. No ocarina varied systematically.
In order to test this result and the hypothesis that any perceived differences in sound are due to cognitive biases,
we had 24 volunteers attempt to differentiate between the sounds in blind tests. We played 15 notes to each
listener and had them choose the ocarina of origin. They were correct on average 4.8 ± .6 times of 15, nearly
consistent with random chance (5/15). We also had the listeners rank 15 pairs of notes according to how similar
they perceived them to be. We found that listeners were only slightly more likely to rank notes from the same
ocarina as similar than they were to rank notes from different ocarinas as similar.
We have found that although the variations in sound from each ocarina are random, the differences between
them are not discernible to humans in blind tests. However, humans could tell when the ocarina was switched,
even if they could not say what it was switched to or from. Further testing is necessary to explain this.
NCSSM Research Symposium 2011-2012
Charlie Mize
Teachers/Mentors: John Kirk, NCSSM; Karl Fetter, UNC - Chapel Hill
Tulip Tree Types - There are three recognized variations of the North American tree Liriodendron tulipifera. In this
study, shape data from leaves and samaras from the three populations was studied as part of a project to
investigate the intraspecific variation and map reproductive barriers of the species. Hundreds of Liriodendron
tulipifera leaves and samaras from the collection at the Herbarium of the University of North Carolina were imaged
using a digital scanner. Leaf shape data was collected and analyzed using geometric morphometrics, and samara
length and width measurements were compared using traditional morphometrics. Preliminary analyses suggest
significant shape variation between three populations.
Jackson Mower
Teachers/Mentors: Amy Sheck, Korah Wiley, NCSSM
DNA Methylation in Queen and Worker Honey Bees - Apis mellifera queen and worker bees are both female that
are very similar if they are from the same hive. However, their genes are expressed differently. The results of
recent research suggest that DNA methylation is the cause of this dichotomy. DNA methylation is an epigenetic
phenomenon that involves silencing genes with the addition of methyl groups to DNA through DNMT. The goals of
this project were to determine if DNMT is active in worker honey bees, and compare the amount of DNMT activity
in queen and worker larvae. The first step of the test was extracting the cytoplasmic and nuclear proteins from the
samples. An ELISA-based test was used to analyze the extracts. The results of this study suggest that worker honey
bees possess a working DNMT system and DNMT is more active in queen larvae than worker larvae. This is
significant because epigenetics is a largely unknown phenomenon that could be better understood through
studying organisms, such as honey bees, that contain a DNMT system similar to the one found in humans.
Epigenetic knowledge could one day be implemented in health care.
Tosin Omofoye
Teachers/Mentors: John Kirk, NCSSM; Gabriel Lopez, Lu Gao, Leah Johnson, Duke University
Assembly of Microparticles for Acoustic Separation - This project deals with the generation of mono-dispersed
PDMS particles and the assembly of the microfluidic device that is used to create the particles. The particle
generation device is created from a PDMS slab with embedded channel patterns that is plasma bonded onto a
glass slide. The same sylgard solution that is used to create the device is also pumped through one of its channels,
along with water which is pumped through a perpendicular channel. Their interaction at the channel juction is
what creates the mono-dispersed particles. Particles can then be separated using another microfluidic device
which produced an acoustic wave perpendicular their path. As the solution of particles is run through the device,
compressible particles are pushed to the antinodes of the acoustic wave which occur at the walls of the channel,
while incompressible particles are pushed to the node of the wave which is at the center of the channel. Several
tests were performed where particles were successfully separated. The process that was used to calculate the bulk
modulus of the PDMS is also explained. This was used to confirm that PDMS is a compressible material.
Unfortunately, problems with the plasma bounding process and SU-8 mold of the silicon wafer kept us from
successfully assembling a particle generation device and consequently from generating mono-dispersed particles.
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More work is needed in order to create the particle generation device, but success in the other parts of this project
holds promise for the future of acoustic separation in micro-fluidic devices.
Chisimdi Onwuteaka
Teachers/Mentors: Karen Glumm, NCSSM
Assimilating into Modern America - My research project explores and examines what cultural aspects and
problems do first, one and one half adolescents (ages: 7-18 years) of immigrant families face and adopt when
assimilating and transitioning into modern American society? And also, how are these adolescents affected when
they have to balance modern American culture and their culture that they have been taught by their parents?
Using the responses that I received from members of the NCSSM student body, I analyzed and put together a list
of results that I discovered through the details of the interviews and surveys that I conducted.
Sarah Parsons
Teachers/Mentors: John Kirk, NCSSM; Frank Fee, UNC-Chapel Hill
Julia Griffiths: Feminist or not? - Julia Griffiths was a British woman who assisted Frederick Douglass, an American
newspaper editor and former slave, with his two abolitionist newspapers during the antebellum period. Upon
returning to the United Kingdom in 1855 after working and living with Douglass in Rochester, NY, Griffiths began
writing “Letters from the Old World.” From 1855 to 1863, Griffiths wrote 87 letters to Douglass who published
them as a column in his Frederick Douglass’ Newspaper and Douglass’ Monthly. In February 2012, I began studying
31 extant letters of Griffiths’ “Letters from the Old World” to determine whether or not she was a feminist of her
time. After examining the column for two months with my mentor, Dr. Frank Fee, Associate Professor Emeritus of
UNC-CH, I concluded that Griffiths was not a “feminist,” but that she did extend women’s place in the public
sphere by playing an influential role in the abolition movement.
Jacob Pawlik, Edward Zhao and Isaiah Stackleather
Teachers/Mentors: Amy Sheck, NCSSM; Paul Magwene, Amy Schmid, Duke University
Yeast/Halobacteria Response - Halobacteria and Yeast are made up of complex systems of 'signaling pathways'
conjoined functionally to meet a goal or induce an action. These pathways are activated or inactivated in direct
proportion to environmental conditions, and so the question of the effect of varied environmental stresses on the
signaling pathways of test subjects like yeast and halobacteria could highlight some of the characteristics of
response in each organism. Experimentation was performed by exposing cultures to varied environments such as
glucose and sucrose, along with strains lacking necessary inducers for pathways to be carried out, such as trmB and
ura3, and observing overall growth. By using a combination of these environmental stresses, we were able to
discover pieces of the nature of yeast and halobacteria, and ultimately reveal the effect of pathways on growth.
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Steven Philips
Teachers/Mentors: John Kirk, NCSSM; Sheryl Moy, UNC - Chapel Hill
Sociability in Three Inbred Mouse Models of Autism - Deficits in social interaction are important early markers for
autism and related neurodevelopmental disorders with strong genetic components. We measured social
interaction with three inbred mouse strains: C57BL/6J, DBA/2J, and FVB/NJ. To measure sociability, each mouse
was placed in a three-chambered box. One side chamber contained an unfamiliar mouse (stranger 1) in a wire
cage, and the other side chamber was empty. To test for social novelty, the test was performed with a familiar
mouse in one side chamber and an unfamiliar mouse in the other side chamber. Parameters scored included time
spent in each chamber and number of entries into the chambers. The three strains showed significant levels of
sociability (spending more time in the chamber containing stranger mouse than in the empty chamber) and a
preference for social novelty (spending more time in the chamber containing the stranger mouse than in the
chamber containing the familiar stranger mouse). This experiment may allow us to develop a method to treat
social deficits in mouse models of autism.
Joshua Potter
Teachers/Mentors: John Kirk, NCSSM; Howard Rockman, Duke University
What is the Role of Fibroblasts in TREK-1 KO? - The hearts of wild-type mice, after tying of the aorta to stimulate
pressure overload, have been seen to develop cardiac hypertrophy and significant fibrosis. Yet, when the same
procedure is done to thehearts of TREK-KO mice, despite the hypertrophy developed, neither fibrosis nor heart
failure occurs. To ascertain the role of TREK in the hearts of these knockout mice, we have excised the cardiac
fibroblasts present in the hearts in order to test the collagen synthesis that is associated with fibrosis. The amount
of collagen synthesized can be determined by measuring hydroxyproline which is found in collagen fibers. Final
attempt at measuring hydroxyproline in samples led to negative results.
Emily Price
Teachers/Mentors: John Kirk, NCSSM; Stefan Zauscher, Zerah Parlak, Duke University
Viscosity Compensation in the QCM - Varying concentrations of glycerol solutions were run through the quartz
crystal microbalance (QCM) and the second frequency of the first, third, and fifth harmonic were measured and
compared to the average of the center frequencies. As the concentration of the solutions in the system increased,
viscosity increased, but not mass. In the QCM, the second frequency was much less sensitive to the viscosity
change and therefore shifted significantly less than the center frequency. The second frequency of the third
harmonic showed especially significant results as it showed the lowest average shift. These results meant that the
percent concentration calculations were much more accurate when using data from the second frequency than
the traditionally used center frequency. The data was collected from August 2011 to January 2012 at Duke
University. For QCM experiments in liquids, especially highly viscous liquids, the second frequency yields much
more accurate results than center frequency and is suggested to become the new standard for data collection in
liquids.
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Taylor Rosenfeld
Teachers/Mentors: John Kirk, NCSSM; Leonel Medina, Mikhail Lebedev, Duke University
Brain-machine Interface Research With Primates - Brain-machine interfaces (BMIs), present an interesting
opportunity to treat an array of neurological diseases, such as quadriplegia, paraplegia, and limb loss. Simply put, a
BMI works by allowing the user to control a given external device by the act of thinking. Using BMI's and a
technique called intracortical microstimulation, researchers have begun investigating the possibility of sensorizing
a neural prosthetic limb that can be interfaced with a BMI. The advantage of such an innovation is that it helps
establish a bi-directional line of communication between the brain and the external device (in this case a
prosthetic limb). Such communication allows the brain to receive feedback on the environment from the limb that
can be interpreted, for example, as physical stimuli. As a result, this makes it possible for the prosthetic limb to
both act and feel just like a normal human arm or leg. Research is conducted with rhesus macaques who are
trained to perform various tasks, mostly involving a joystick and a "game." Future research points towards the
development of a full body neural prosthetic "suit" to restore motor function to individuals suffering from
quadriplegia.
Nicole Savignac
Teachers/Mentors: Bob Gotwals, NCSSM; Gary Churchill, Susan McClatchy, The Jackson Laboratory
Effects of FMO-family Genes on Artherosclerosis in - Atherosclerosis is a chronic disease that is caused by the
progressive buildup of fatty deposits in the arteries. After the age of 35, two in three Americans have some degree
of plaque buildup which could eventually lead to coronary heart disease, which is the leading cause of death in the
US. For our project, we wanted to look into this disease and try to find another possible way of treating the disease
through Fmo-family genes. We got the idea for our project from a paper by Wang et al. In his paper, he stated that
there have been signs to indicate that Fmo genes have some relationship to atherosclerosis, but that relationship
has not been explored thoroughly. Through this project, we were hoping to look into relationships between Fmo
genes in mice and whether they could lead us to a better understanding of the Fmo genes effect on
atherosclerosis. Through our research, we have found that there is a single nucleotide polymorphism on
chromosome 1 for Fmo1 showing that there is something significant between the two. Further explorations also
other significant genes to be Myoc, 2810422O20Rik, Dcaf6, Brp44, Mpzl1, Rcsd1, Creg1, Pou2f1, Ildr2, Fmo1,
Fmo3, Fmo2, Fmo5, and Abl1. We performed BIC modeling to find the most significant models. Through our
experiments, our models have shown that the possible pathways are related. Our plans for further research
include more tests and compare our current results to a data set of mice with atherosclerosis to determine what
role each gene plays.
Brandon Schneider
Teachers/Mentors: John Kirk, NCSSM; Anil Gehi, UNC-Chapel Hill
Rhythm Control in the Elderly with AF - Atrial fibrillation guidelines suggest conservatively treating elderly patients
with atrial fibrillation, tending to favor a rate-control strategy. Studies have shown that rhythm control in the
elderly is effective but the extent of symptom relief is unknown. Outpatients were recruited into an atrial
fibrillation registry at UNC-Ch. Medical records and questionnaires measured demographic, comorbidity, health
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statuses, and AF Symptom Severity. Elderly patients were defined as those greater than 70 years old. Despite more
comorbidities, decreased baseline symptom severity, and higher risk of recurrence, a rhythm control strategy in
elderly patients with atrial fibrillation is still warranted given the substantial symptom relief.
Nishkala Shivakumar
Teachers/Mentors: Jon Bennett, NCSSM; Matthew Sharpe, NC A& T University
The Acoustic Performance of Smart Foams - Smart foam is an emerging active-passive noise control technology
with applications in the transportation industry. Smart foam consists of passive foam with an embedded curved
piezoelectric film. The piezoelectric film uses electrical energy to mechanically deform the foam and generate
acoustic signals. This signal can destructively interfere with a primary source of noise. In this research, we
experimented with three geometries of smart foams, constructed using melamine foam and 28 μm thick
polyvinylidene fluoride films with Cu-Ni surface electrodes. An AC voltage provided by a signal generator and
amplifier drives the smart foam. An omnidirectional microphone mounted at a distance 100mm from the foam
surface measured the sound pressure (dB) and harmonic distortion generated by the smart foam. Experiments
were repeated for voltages, 40V-140V, and frequencies, 300Hz-2000Hz. The results show the acoustical pressure
generated by the smart foams to peak between 900 to 1,100 Hz and a characteristic frequency response common
to all geometries.
Erica Shook
Teachers/Mentors: Linda Schmalbeck, NCSSM
Using Old Leaves to Teach New Climate Science - For my project I created an educational lesson for Earth and
Enviromental Science students to study the Paleocene Eocene Thermal Maximum and the use of Leaf Margin
Analysis to study climate change we are facing today. In this presentation I will cover the need for Climate change
science to be incorporated into high school science curriculum. I will also cover a summary of the lesson I created
and the expected and recieved results of my lesson.
Param Sidhu, Tejas Sundaresan, and Yu Wang
Teachers/Mentors: Myra Halpin, NCSSM
Stellar Strips - Conrad SOI - Stellar Strips are starch based, edible strips that enhance the flavor of space food and
provide essential nutrients for astronauts. Currently, astronauts have dulled sensations of taste due to the food
packaging process and microgravity induced nasal congestion. While there are no current solutions to these
problems, their negative effects can be minimized through enhancing and strengthening the flavor of foods to
overcome the dulled taste sensation. Stellar strips are designed to meet this need and be used on long-term stays
in space. Through their convenience, cost efficiency, and space-saving properties, the strips fill a unique niche in
the aerospace nutrition market and will not only help to improve the quality of life and health of astronauts but
also mark a significant development that will increase the feasibility of long term space travel.
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Connor Smith
Teachers/Mentors: Karen Glumm, NCSSM
Students' Perception of Culture at NCSSM - This project was designed to compare students' cultural experiences
at NCSSM with their experiences at their home schools. It has been expanded to study how NCSSM has changed
over the years in terms of cultural opportunities such as events and clubs. A survey was given to students in early
February to measure their participation in cultural groups and events and how their perception of culture changed
upon arriving at NCSSM. It is my hope that Student Life will be able to use the research to better the cultural
experience at NCSSM.
Greeshma Somashekar
Teachers/Mentors: Myra Halpin, NCSSM; Stavros Garantziotis, NIEHS
ITIH4: functional response to lung injury - ITIH4, a serum protein, has been shown to have elevated
concentrations in patients with diseases such as early stage ovarian cancer, breast cancer, and chronic obstructive
pulmonary disease (COPD). Recent studies have therefore identified ITIH4 as a potential biomarker for these
diseases. The goal of this study is to better understand the role of ITIH4 as a biomarker and specifically, how it
affects the immune response to lung injury.
Wild type mice (ITIH4+/+) and ITIH4 knockout (ITIH4-/-) mice were exposed to lipopolysaccharide, an endotoxin
used to induce inflammation in the lungs. Based on immunohistochemistry, we found that ITIH4 is expressed in the
lung in bronchial epithelia and in alveolar macrophages and neutrophils. Tissue injury levels, cytokine and cell
counts, and cell migration data were analyzed. These indicate that ITIH4 slows the migration of inflammatory cells
to the site of an infection. Results suggest that ITIH4 is a biomarker of containment: it serves to localize the
immune response to an infection. This information adds to the growing body of knowledge about ITIH4 and may
also allow physicians to learn more about the unique immune response in an individual based on the
concentration of ITIH4 present.
Andrew Stowe
Teachers/Mentors: John Kirk, NCSSM; Erica Davis, Duke University
Mutations Affecting Ciliopathies - Ciliopathies are genetic disorders of the cilia or ciliary function. Mutations in
genes that code for proteins that operate the cilia in cells can alter or prohibit cell movement, communication, and
growth. This can cause serious phenotypes in developing infants such as renal cysts, retinal degeneration, and
developmental problems. By using an assay involving zebrafish embryo injection, the effects of a certain mutation
can be seen. This was done by developing a sample of the gene, TTC21B, and inserting the desired mutation. Then
this gene was injected into zebrafish embryos that had the original gene suppressed to be rescued. We compared
this rescue to that of the normal wild type TTC21B gene to observe any adverse effects there might be. We found
that the wild type rescue did not perform as expected or was as normal, so the results of the mutant gene rescue
are inconclusive until further trials can be performed.
Bei Sun
NCSSM Research Symposium 2011-2012
Teachers/Mentors: John Kirk, NCSSM; Jun Chen, Esther Lee, Duke University
Nucleus Pulposus Differentiation of Mouse iPS Cell - Induced pluripotent stem cells (iPSCs), reprogrammed from
somatic cells with specific transcription factors hold great promise for regenerative medicine as a source of
autologous cells. Of particular interest is the ability of iPSCs to differentiate into Nucleus Pulposus-like (NP) cells for
use in treatment of the intervertebral disks in human spines. This study follows attempted differentiation of mouse
iPSCs into an immature NP-like phenotype through hypoxic incubation and culturing in a Notochordal conditioned
medium. There is also a 3T3 mouse fibroblast culture grown concurrently for comparison of iPSC to a non-
pluripotent cell type benchmark. Histology of the cell cultures, including H&E, Saf. O, Collagen II, and Vimentin,
offer promising results with expression of Vimentin and Collagen II in the NCCM medium, both of which are
characteristic of an NP-like phenotype. The 3T3 fibroblast group also displays unexpected transdifferentiation
ability, displaying many characteristics of an NP-like phenotype as well.
Nicholas Tobey
Teachers/Mentors: John Kirk, NCSSM; Don Smith, UNC Chapel Hill Computer Science Department
RAPID: A Modern Protocol for Data Transmission - Modern advancements in computer network infrastructure
have revealed that existing protocols for data transmission across networks are inefficient at high bandwidth levels
and high round trip times.
RAPID, a new TCP-like congestion control protocol that uses precisely spaced packets to estimate available
bandwidth within a few dozen round trip times, has been developed at the University of North Carolina. Multiple
different TCP-like congestion control protocols were evaluated in a private network to test their ability to react to
sudden reductions or increases in available bandwidth when in a high bandwidth-delay product environment.
Natalia von Windheim
Teachers/Mentors: Amy Sheck, NCSSM
Enhancing Oil Degradation by B. cereus - Biostimulation, the boost of naturally occurring bacteria that degrade oil
by the addition of nutrients or other deficient requirements, has emerged as a viable solution for the clean up of
oil spills. Uric acid and lecithin (nitrogen and phosphorus sources, respectively) have shown promise as
biostimulation agents in marine environments. While many catastrophic spills occur in water, an even greater
amount of spills occur on land. The goal of this work was to determine if biostimulation can work in a terrestrial
environment such as what might happen when oil spills on land, such as burst pipelines. For this study, kerosene-
contaminated soil was inoculated with B. cereus and one of two biostimulation treatments - either uric acid and
lecithin treatment or S-200, a commercially available biostimulation agent. Both biostiumulation treatments were
compared to a control, with no additional nutrients. Soil samples were then removed for evaluation after 11 days
of incubation and again after 22 days. In each case, dichloromethane and water were used as solvents to extract
the liquid from the soil and then the organic phase was separated from the aqueous phase. Subsequently, the
organic phase samples were prepared for gas chromatography to quantify the degradation of hydrocarbons in the
kerosene. Upon analysis of the chromatography data, the uric acid and lecithin treatment showed the most
significant degradation while there was no significant difference between the control and the S-200 treatment.
NCSSM Research Symposium 2011-2012
Rebekah Wells
Teachers/Mentors: John Kirk, NCSSM; Sue Jinks-Robertson, Kevin Lehner, Duke University
Effects of Chronic Low-Dose Radiation on Yeast - DNA damage is something that occurs regularly. The cell has
different mechanisms for repairing this damage. In this experiment we look at the damage induced by Chronic
Low-Dose Ultraviolet Radiation (CLUV). We were interested to see in the rate of mutagenesis was increasing with
exposure to CLUV even if growth rate did not change. In order to do so we developed an assay that compared
growth rate, transference rate, and number of colonies mutated to determine the rate of mutation. We
determined that rate of mutagenesis was increased although growth rate did not reflect it. Once we accomplished
this we looked at strains where specific DNA damage-repair mechanisms had been blocked to see if a trend could
be seen that would suggest that one repair mechanism is more vital in repairing damaged induced by CLUV. We
have yet to determine which repair mechanism is most important. But we do have results that suggest some
mechanisms are more involved than others. We have also shown that our assay can be used to determine rate of
mutation and can be applied to virtually any situation.
This experiment was carried in the Microbiological and Molecular Genetics department at Duke University in the
Sue Jinks-Roberston Lab. The experiment began August 25, 2011. The project is unfinished and will be carried into
summer of 2012.
Kathryn Wheeler
Teachers/Mentors: John Kirk, NCSSM; Robert Jackson, Jonathan Karr, Duke University
Methane Contamination and Hydraulic Fracturing - The techniques of hydraulic fracturing, also known as fracking,
and horizontal drilling have significantly increased the amount of available shale gas. Fracking is a process where
water and chemicals are injected at high pressures underground to fracture the geological formation. Last year,
Osborn, Vengosh, Warner, and Jackson of Duke University published a paper that found an association between
the distance groundwater is from a well and methane concentration in the groundwater. This study was a
continuation of the 2011 Duke University study. We have been testing samples of groundwater at various
distances from fracking wells to see if these samples also indicate an association between distance and
groundwater methane contamination. The data is still incomplete, but we have found less of an association
between distance and methane contamination. Factors such as geology may prove to have a larger impact on
groundwater methane contamination from fracking than distance does.
Sara White
Teachers/Mentors: John Kirk, NCSSM
Hypotheses on Breast Cancer Growth Rate Models - The proficiency of two breast cancer tumor growth models,
the Gompertzian and the stochastic Gompertzian, are investigated using theoretical methods. Based on the
findings clinical data, it is generally accepted that breast cancer tumors do not grow with exponential rates.
Conceptually, Gompertzian growth rates make sense; tumors grow faster the greater the tumor burden. The
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model fails to account for irregularity in growth rates. The stochastic Gompertzian model proposes random,
spontaneous changes in rate of growth or rate of decay. Both models are supported by clinical data. A growth
model of breast cancer tumor will lead to a better understanding of this aliment and aid in suggesting treatment
strategies.
Hun Wong
Teachers/Mentors: Amy Sheck, NCSSM; Paul Magwene, Duke University
Prions as a Mechanism of Yeast Stress Response - Prions are self-propagating amyloid proteins that are most
often associated with irreversible neurodegenerative diseases in mammals, but in Saccharomyces cerevisiae
(yeast) recent findings have suggested that prions may serve an evolutionarily beneficial role in responding to
stressful environments. This study attempts to discover a novel function of prions as a factor facilitating yeast
complex colony morphology (CCM) and pseudohyphal development- two known nutritional stress responses of
yeast. Twenty four strains were screened by growing them on media varying in nutritional stress (YPD, YPLD, and
SLAD-1%, low, medium, high stress respectively) with and without 1mM GuHCl, a chemical known as an effective
treatment to eliminate yeast prions. CCM and pseudohyphal growth were assayed as stress response indicators.
Eight of the 24 strains tested for CCM responded to GuHCl with changes in overall complexity as well as
morphotypes, and 5 of the 24 strains tested for pseudohyphal development displayed varying levels of
pseudohyphae in response to GuHCl. These results suggest that the strains that responded to GuHCl have prions
that play a novel role in stress management through CCM and pseudohyphal development.
Janice Wong
Teachers/Mentors: John Kirk, NCSSM; Pamela Maxson, Children's Environmental Health Initiative
Environmental Health GIS - Geographic Information Systems (GIS), a technology that combines cartography,
statistical analysis, and database technology, has many applications. It has been proven particularly effective in
analysis of health disparities and associated environmental risk factors by a number of studies. The experience of
partaking in GIS training, geocoding, and data acquisitions at the Children’s Environmental Health Initiative at Duke
University may be enriched by simultaneously reading related literature. The diverse applications of GIS, especially
in environmental health, call for further research, development, and spread of GIS technologies in the future.
Jessica Yoo
Teachers/Mentors: John Kirk, NCSSM; Timothy Haystead, Brittany Speer, Duke University
Dengue Fever: Search for a Cure - In recent years, with the onset of global warming, disease-carrying mosquito
populations have steadily creeped northward, bringing dengue fever to the US. Unfortunately, due to some
specific characteristics of the dengue virus, a cure or vaccine has remained elusive. In fact, the dengue virus is
notorious as "an immunologist's nightmare," for while its symptoms can lead to severe shock-and even death- the
search for a treatment has been hindered for various reasons.
NCSSM Research Symposium 2011-2012
In the Haystead Lab, we have the methods and means to conduct mass ATP-knockdown assays for various
compounds. Thus, we reasoned that if we managed to identify molecules that are essential to the viral infection
process that also happen to have high affinity for ATP, then we can create a small molecule inhibitor drug that
treats the disease by inhibiting viral replication.
These target molecules can be viral or host-derived, as long as they play crucial roles in the progression of dengue
infection. Hence, we chose to study the viral nonstructural proteins (NS3 and NS5), as well as the host-factor
(CCT7). Through various biotechnological methods, we proved that these molecules are not only present during
infection in high concentrations, but they also possess ATP binding sites, a necessary criterion for our purposes.
Therefore, a small molecule inhibitor drug that inhibits all three of these potential drug targets in conjunction
could potentially prove an effective treatment/precautionary measure against the dengue virus.
Grace Yook
Teachers/Mentors: John Kirk, NCSSM; Kelly Nelson, Duke University Dept. of Dermatology
With Applications in Skin Cancer Detection - My research project was on improving the Diffuse Reflectance
Spectroscopy model for future use in skin cancer detection. It was evident that the model needed improvement
due to the lack of light that was received by the corner pixels in the photodetectors. Because of this,
improvements were made to the DRS system to improve the light delivery to the photodetectors. Taking various
measurements of the current vs. voltage, along with power vs. wavelength, I was able to detect the changes that
needed to be made between the metal to quartz rods for future use.
Edwin Yun
Teachers/Mentors: John Kirk, NCSSM; Edward Tower, Duke University
Korea-U.S. Free Trade Agreement - The computational general equilibrium (CGE) model assumes perfect
competition, constant returns to scale, and product differentiation by country of origin. It uses analyzes the effects
by dividing the regions into Korea, the U.S., Japan, and rest of the world. The Michigan model contains differing
characteristics such as imperfect competition, monopolistic competition, increasing returns to scale, and product
variety. By studying the previous computational models, this paper aims not only to discuss the results but also to
draw original implications and insights based on the results. Such implications include a close examination on the
mechanisms behind each country’s welfare gains and the risk of frictional and structural unemployment in South
Korea as results of the KORUS-FTA. The analysis on the previously studied computational models estimates the
welfare gains based on both static and quasi-dynamic scenarios. The results suggest varying degree of increased
GDP, ranging from combined U.S. and South Korean welfare gains of $4.3 billion to $60.6 billion according to Choi
and Schott (2004) and Schott, Bradford, and Moll (2006), respectively. The welfare gains are also categorized by
the sectors, implying U.S. comparative advantage in agriculture and Korean comparative advantage in textile,
leather, auto parts, and chemicals. In addition, this paper discusses the complications arising from politically
sensitive issues such as the Investor-State Dispute Settlement and the Outward Processing Zone. Finally, this
paper examines functional tactics practicable by the U.S. investors for the Investor-State Dispute Settlement and
South Korea’s role as the United States’ strategic hub against China and North Korea.
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Ahmed Zaeem
Teachers/Mentors: John Kirk, NCSSM; Mary Roederer, UNC-Chapel Hill, Eshelman School of Pharmacy
Pharmacogenomics in Mexican Populations - The Pharmacogenomics for Every Nation Initiative (PGENI) aims to
use pharmacogenomics on a global scale to decrease adverse effects pf drugs. This study looks at the genetics
surrounding Mexican ethnic groups and compares them to United States Caucasians. The data was obtained from
literature that was filtered through the PGENI database. In order for data to be entered into the database, it needs
to contain information pertaining to the following criteria: sample size, country, ethnicity, gene, variant, and
frequency. The compiled data is computed and PGENI generates risk maps, showing the risk classification of
several variants throughout the countries of the world. Our study shows that the variants CYP1A1*2C and
CYP2E1*5 show an increased risk of adverse drug effects in Mexican populations than United States Caucasians.
CYP2E1*5 encodes the enzyme that is involved in metabolizing isoniazid, a medication used to treat tuberculosis.
Due to the increased risk of adverse drug effects associated with this variant, Mexican patients should be more
closely monitored for medication induced liver illness. CYP1A1*2C does not play a significant role in nicotine
metabolism, so the increased risk does not significantly affect Mexican populations.
Yiming Zhang
Teachers/Mentors: John Kirk, NCSSM; Liza Makowski, Gillings School of Public Health, UNC Chapel Hill
ID of a Pro-Inflammatory Macrophage biomarker - Obesity has become a worldwide epidemic and in 2008, it was
estimated that an alarming 33.8% of Americans were obese. Some of the leading causes of death in the US are
directly related to obesity, including heart disease, stroke, certain cancers, and type 2 diabetes. Macrophages
have been shown to be critical to the onset of obesity. In obese individuals, increased adiposity drives
macrophages to activate via the classical pathway (M1), leading to inflammation and further macrophage
aggregation. M1 macrophages metabolize glucose through glucose transporter 1 (GLUT-1), which may be the link
between macrophage metabolism/glucose uptake and the onset of inflammation and diet induced obesity. Our
study has shown GLUT-1 to be the main glucose transporter in macrophages and increases with M1 polarization.
The manipulation of macrophage fuel metabolism (via GLUT-1 expression alterations) has indicated that GLUT-1 is
a novel pro-inflammatory macrophage biomarker, driving M1 polarization when over-expressed. This has lead to
the discovery of pathways to regulate macrophage inflammation and the promotion of obesity which can lead to
new, targeted treatments and therapies for the treatment of obesity and diabetes down the road.
Yue Zheng
Teachers/Mentors: John Kirk, NCSSM; Jason Howard, Erich Jarvis, Duke University
Avian Vocal Learning and Microsatellites in dusp1 - Vocal learning, a complex behavioral trait once thought to be
unique to humans, is crucial for language acquisition. This behavior is also similarly found in three orders of birds:
parrots, hummingbirds, and songbirds. The genetic causes of this rare trait are still being elucidated; for example,
the dusp1 gene has been found to be highly up-regulated in response to vocalization learning in the song nuclei of
vocal learners, and studies suggest that microsatellites—short repeating DNA sequences found in the genome that
alter gene expression significantly—have an effect on dusp1 gene expression. To identify microsatellites and
determine their effect on the dusp1 promoter, we compared the dusp1 promoter sequences of vocal learning and
NCSSM Research Symposium 2011-2012
non-vocal learning avian models. Data collection took place in the Jarvis Lab at Duke University from July 11, 2011
to February 2, 2012. After isolating, cloning, and sequencing the dusp1 promoter sequence from various species,
we found that the number of microsatellites varied across both species and individuals of the same species. These
results were supported by computational analysis of the sequences and have implications for updating the
phylogenetic tree of bird evolution, increasing knowledge about avian vocal learning, validating sequences in the
Genome 10K Project, and eventually creating a better understanding of language problems in human beings.
Lisa Zheng
Teachers/Mentors: Leslie Brinson, NCSSM; Zachary Wissner-Gross, Harvard-MIT Division of Health, Science, and
Technology
An Inhibitory Model for Neuronal Symmetry Breaking - As neurons develop, several immature processes, or
neurites, grow out of the cell body and break symmetry by competing to become the neuron's single axon. To
explain how this symmetry breaking occurs, two contrasting ideas have been proposed: depletion and inhibition.
Depletion involves neurite competition for a collective pool of growth proteins, while inhibition includes additional
inhibitory signals. Several computational models have been proposed for depletion, but so far, no inhibitory
models have been developed. Here, we propose the first inhibitory models by adding negative feedback to a
previously published depletion model. Numerically, we find that inhibition based on both concentration and length
accelerate axon formation and induce axon formation over a larger range of parameters. However, only
concentration-based inhibition allows shorter neurites to regenerate. Analytically, we find that the strength of our
model's positive feedback must exceed a value related to the neurite count in order for symmetry breaking to
occur. Our work expands the current understanding of axon specification and growth mechanisms that are
important for nervous system development and relevant for treatments of Alzheimer's disease and nerve injury.
Connie Zhong
Teachers/Mentors: John Kirk, NCSSM; Sally Kornbluth, Erika Segear Johnson, Duke University
Caspase-2 Activators and Inhibitors - Caspase-2 plays a crucial role in apoptosis, programmed cell death. In these
experiments, we investigated the effects of adding different compounds to Xenopus laevis egg extract samples to
see how they would influence caspase activation. Through consistent caspase assays, we concluded that while
certain compounds such as LiCl, G6P, G6P+UO126, AOA, and AOA+UO126 slowed down caspase activation and
thus prevented cell death from occurring, UO126 and H2O2 had the opposite effect, instead speeding up this
process. Moreover, when UO126 and H2O2 were combined with other compounds including G6P and AOA, their
effects were partially shielded. This paper also outlines the methods of experimentation and possible sources of
error, as well as explores implications of this research in cancer therapy. Experiments were conducted starting in
June of 2011 until February of 2012 at the Levine Science Research Center on Duke University’s campus in Durham,
North Carolina.