Aresty Research Center for Undergraduates
2015 Summer Science Student Abstracts
Listed alphabetically
Abdulraouf Abdulraouf
Professor Zhiping Pang
Stress Enhanced Activity Based Anorexia Animal Model: The Role of Stress in Altering the Mesolimbic
and Hypothalamic Circuitry Axis
Stress about body image and body weight causes compulsive dieting behaviors and sometimes leads
to eating disorders as Anorexia Nervosa (AN). AN is a life threatening eating disorder that affects
approximately 8 per 100,000 women in the U.S, and has the highest mortality rate of all psychiatric
illnesses. We developed a novel animal model, termed enhanced Activity Based Anorexia (eABA)
model that strongly mimics the most apparent symptoms of AN such as chronic weight loss,
decrease in food intake, and hyperactivity. This model is based on the already widely used ABA
model. In the classical ABA model, when a rodent is placed in individual cage, fed on a restricted
hourly schedule, and provided with a running wheel it will show a paradoxical increase in running
wheel activity (RWA), decrease in food intake, and chronic loss of body weight. eABA is different than
ABA in that it adds the emotional covalence. eABA is based on the notion that after stress, serum
leptin levels increase. Leptin is an adipocyte derived peptide hormone and a product of the obese
(ob) gene. Leptin is an anorectic hormone that decreases food intake via its actions on the Lateral
Hypothalamic Area (LHA), and LHA subsequent actions on the mesolimbic DA system. The
mesolimbic system is mediating region of reward for actions as feeding and we believe it is
disrupted in AN. Furthermore, another important subject that can relate to AN is how Hypothalamic
Pituitary Axis activation during stress, which increases glucocorticoids and Corticoreleasing
hormone (CRH) levels, can lead to microglial proliferation and activation. Microglias are immune
system cells that protect and nourish neurons and their synapses. When they are activated they will
decrease their branching and thus their overall surrounding of neurons which can lead to synapse
remodeling. Because AN is associated with elevated stress levels we believe activation of microglia
might lead to synapse remodeling which might be related to AN symptoms. Our result indicate that
our eABA model is very much better than the classical ABA model in inducing AN symptoms in
rodents. Moreover, our preliminary data also indicate microglial proliferation and activation in the
Hippocampus (CA1), LHA and Arcuate nucleus (ARC). Our work also suggests that sEPSC in the LHA
of eABA become insensitive to exogenous leptin application, when compared to fasting, control, and
ABA conditioning.
Ezra Ablaza
Professor Stephen Garofalini
Atomistic Mechanisms of Dissolution Reactions in Oxide Glasses
Silicate glasses are sturdy and resistant to corrosion or dissolution. We study silicon dioxide (SiO 2)
glass dissolution in water using Molecular Dynamics (MD) computer simulations to determine the
energy barrier and structural characterization of dissolution sites deeper within the glass surface. A
connection is observed between increasing energy barriers and increasing sizes of siloxane (Si-O-Si)
rings. Future work for the year will include similar studies on glasses with a more complex chemical
structure.
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Raheel Ahmad
Professor Spencer Knapp
Synthesis of New Antimalarials
Malaria is caused by protozoa in the genus Plasmodium, and is spread by infected blood transferred
through mosquito bites.1 It continues to be a threat to many populations globally, especially to those
in third world countries. The World Health Organization estimates that in Africa a child dies of
malaria every minute.2 Due to this apparent crisis, numerous drugs have been developed to treat the
disease. Unfortunately, increasing resistance stimulates production of new antimalarial drugs to
provide adequate treatment. (+)-SJ733 is an antimalarial drug candidate that has been approved for
clinical trials. In intermediate steps for the synthesis of this compound, we have investigated
optimizing conditions for the epimerization and hydrolysis of the main scaffold for the drug in one
reaction. We also attempt to improve reaction conditions for the synthesis of the main scaffold by
reducing usage of a lewis acid reagent and instead using it catalytically in conjunction with another
reagent. This prepares for a enantioselective reaction in which an asymmetric scaffold can be
synthesized using a chiral catalyst. The use of only catalytic quantities of reagents and optimization
of reactions as stated previously would enable us to create a lower cost antimalarial, allowing far
reaching availability in less wealthy nations.
Maximilian Ashkenazi
Professor Vladimir Pavlovic
Fully Automated Airborne Drones with Peripheral Technology
Drone technology is quickly emerging and highly relevant in today's world. From package delivery to
soil testing, the civil applications of unmanned aerial vehicles in particular are quite promising. Our
group's goal is to create autonomous drones out of existing quad-rotor helicopters. The helicopters
are equipped with Pixhawk PX4 Flight Management Units (FMUs) and peripherals sold by 3D
Robotics, Inc., which include radio controller receivers, telemetry radios, and global positioning
systems. Programs were written using a BeagleBoard-xM computer in the PX4 development
environment to dictate the autonomous flight of a helicopter. A Gopro camera was also used for
video capture. In result, our group was able to create an automated aerial vehicle with basic
functionality such as video feed and waypoint recognition.
Marissa Berger
Professor Shishir Chundawat
Pretreatment of Plant Biomass Increases Hydrolytic Activity
Plants constitute an extensive and renewable resource suited for energy production and
transportation fuel needs; however, the biological conversion of lignocellulosic biomass to fuels is
hindered by plant recalcitrance to sugar extraction. Cellulose consists of a long chain of glucose and
is the most abundant organic molecule in plant cell walls that, in its natural cellulose-I form, remains
resistant to enzymatic hydrolysis, the breaking down of sugars. Altering cellulose from its native
form to the alternatively-structured cellulose-III through ammonia-based treatment is shown to
decrease hydrolytic resistance. Still, the amount of enzymes needed to achieve high sugar yields
remains costly, so it is necessary to improve pretreatments and reduce enzyme requirements. By
analyzing and comparing the glucose yields of the enzymatic hydrolysis of untreated and treated
cellulose-I and III and corn stover samples through DNS assay, one can determine which method of
biomass pretreatment is most efficient. Results from the assays at various loadings of C.Tec2
enzyme confirm the increased hydrolytic activity of C-III versus C-I and of the pretreated Avicel
samples versus C-I. Surprisingly, these data indicate a lower recalcitrance of the Avicel 25-AT
(treated with ammonium thiocyanate at 25°C) samples versus the Avicel 50-AT (treated at 50°C)
samples. Corn stover responds similarly, with the untreated CS being much more recalcitrant than
the treated, but overall glucose yields for CS were lower than for cellulose. With this data, there is a
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potential for more cost- and energy-efficient recalcitrance treatment of plant biomass by optimizing
the treatments for lower protein loadings.
Jaclyn Bird
Professor Michael Sukhdeo
The Development of Haemonchus contortus, a Gastro-intestinal Parasite of Goats
Haemonchus contortus is a parasitic nematode infecting ruminants, especially sheep and goats.
Infection with this parasite often leads to anemia and can cause death, which is of economic concern
to sheep and goat farmers. This parasite’s ability to evolve rapidly allows populations of H.
contortus to quickly become resistant to anthelminthic treatments. The goal of my project was to
establish baseline data on H. contortus development. The life cycle of the parasite consists of eggs,
5 larval stages (L1-L4), and adults. Thus far I have successfully cultured the nematode up to the L3
stage. I collected eggs from the feces of goats from the Cook Campus farm and cultured the eggs in
petri dishes, where I manipulated variables such as temperature and bacteria presence. The results
suggest that eggs must be submerged in water, be maintained at a temperature near 22 C, and have
access to bacteria extracted from feces in order to develop to L3 larvae. The long-term goal of this
project is to determine the aspect of ruminant physiology that triggers the infective L3 stage of H.
contortus to exsheath from its protective cuticle and establish itself in the abomasum of ruminants.
This physiological trigger of exsheathment may be developed into a prophylactic application to
reduce infective stages on the field.
Emma Brush
Professor Olaf Jensen
Comparing Abiotic Factors of Historic Spawning Rivers of Alosa sapidissima and A.
pseudoharengus to Determine Ideal Spawning Conditions in the Raritan River
American shad (Alosa sapidissima) and River herring (A. pseudoharengus) are historical anadromous
fish, spending the majority of their lives at sea, returning to their natal rivers during the spring to
spawn. In colonial times, shad and river herring supported some of the largest and most important
commercial and recreational fisheries in the Mid-Atlantic. Since then, spawning rivers, like New
Brunswick’s own Raritan, have been blocked by dams and physically affected by climate change,
leading to the rapid decline of shad and river herring populations. The purpose of this project is to
describe the maximum yield of shad and river herring as the carrying capacity of the Raritan, which
we established by determining the life-supporting conditions of the Raritan through comparison of
current conditions of other rivers in the northeast U.S. By defining those conditions we will be able
to realize a plan to reclaim and restructure the Raritan as needed to achieve maximum carrying
capacity. In the Raritan, we have done species abundance sampling through techniques of catchand-release fishing, and monitoring video footage taken at the fish ladder at Island Farm Weir in
Bridgewater. Data have been used from the United States Geological Survey’s National Water
Information System (USGS NWIS) to determine current conditions of the Raritan, Potomac, Penobscot,
and Chowan Rivers.
Brinley Burdge
Professor George Carman
The Role of Pah1 Phosphatidate Phosphatase in Lipid Metabolism
The synthesis of lipids is important for the growth and metabolism of all organisms. The Pah1
phosphatidate phosphatase (PAP) enzyme plays an essential role in the regulation lipid synthesis by
catalyzing the dephosphorylation of phosphatidate to form diacylglycerol, which are precursors to
phospholipids and triacylglycerol, respectively. Mammalian cells defective in PAP are typified by
metabolic disorders such as lipodystrophy (i.e., selective loss of body fat) and inflammation. The
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yeast Saccharomyces cerevisiae is used as a model system to study the PAP enzyme. Synthetic
complete growth medium was prepared and autoclaved to prevent non-specific microbial growth.
Wild type and the pah1D mutant cells defective in PAP were cultured and growth curves were
prepared by measuring the cell density at 600nm. The pah1D mutation caused an inhibition of
growth. Cells were harvest at the exponential and stationary phases of growth, and the lipid fraction
was extracted by a chloroform/methanol/water phase partition. The chloroform fraction was
applied to a thin-layer chromatography plate and subjected to chromatography using the solvent
system hexane/diethyl ether/acetic acid (80:20:2, v/v). The phospholipids (Rf 0) remained at the
origin followed by the ascension of diacylglycerol (R f 0.16) ergosterol (Rf 0.20), fatty acids (Rf 0.38),
triacylglycerol (Rf 0.67), and ergosterol ester (Rf 1.0). At stationary phase, the major effects of the
pah1D mutation were an increase in phospholipids (16.6 %) and fatty acids (10.3%), and a decrease
in triacylglycerol (25.9%).
Lisa Chang
Professor Jean Hartman
Impact of Forest Structure on Watershed Performance
Understanding how land use affects watershed performance is essential to managing water quality
and pollution. This is important for many reasons, like promoting public health and safety, as well
as preserving natural habitats and ecosystems. The goal of this project was to uncover the
connection between different classes of land use and stream water quality. Water quality was
measured using both biological and visual assessments of streams in two headwater areas of New
Jersey. It was then compared to percentages of seven different land cover classes in a 300 feet
buffer zone around the stream and to the entire sub-watershed. The biological assessment consisted
of collecting and identifying stream macroinvertebrates to the order level. The visual assessment
consisted of observing stream width, depth, and velocity at given points along a one hundred meter
area of a stream. Both assessments could be translated into a numeric score that would indicate
water quality. Percentages of each land cover class in the stream buffer zone and in the overall
watershed were calculated in Geographic Information Systems (GIS). The study found significant
positive relationships between percentage of forest cover and water quality, as well as significant
negative relationships between commercial land use and water quality and inconclusive relationships
between agricultural or developed land use and water quality.
Shawn Chen
Professor Daniel Seidel
The Reductive Amination Synthesis of a Thiourea Catalyst
Organocatalysis utilizes small organic molecules to catalyze organic reactions and provides an
alternative to traditional transition-metal catalysis. Organocatalysts are more flexible in varying
reaction conditions, more readily accessible, and have multipoint recognition capabilities, allowing
them to function similarly to enzymes. They also allow the enantioselective synthesis of chiral
molecules, as certain isomers of specific compounds allow differing functions and reactivity. A
current popular organocatalyst is a bifunctional thiourea bearing a tertiary amino group, which
currently takes a multistep process to synthesize and results in a relatively low yield. We are
searching for a more optimal way to create this compound. Our current research project shows a
simplified synthesis by formulating a monothiourea derivative, which was then followed by reductive
amination to acquire the desired product. Only two steps were needed for this synthesis which
allowed a significant increase in net yield. These findings provide a basis into the future synthesis
and optimization of organic catalysts.
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Alexia Ciarfella
Professor Richard Ludescher
Translating Research on Luminescence of GRAS Probes into Educational Tools in Photophysics
Current research on fluorescent food molecules can be used as an effective and intriguing
mechanism through which photophysics can be taught to elementary school students. In our
research, luminescent properties of azo (artificial) and natural food dyes, are explored as potential
probes to monitor food quality and safety and to elucidate the biophysics of digestion. For instance,
azo dyes’ fluorescence intensity is highly dependent on physical properties of their
microenvironments; thus, they can be used as nonintrusive sensors for food quality. In order to
expose students to photophysics in the context of food fluorescence, this project translated our
research into an educational kit with the instructions and supplies necessary for five laboratory
activities. Each laboratory activity demonstrates one of the following concepts: the electromagnetic
spectrum, luminescence of GRAS probes, the general function of a luminescence
spectrofluorometer, the use of filters in refining spectrofluorometric data collection, and
luminescence quenching as a function of matrix rigidity manipulation. For each topic in
photophysics, researchers gained a thorough understanding of the principle, practiced various
laboratory methods that employed the idea, and designed an engaging experiment to clearly
demonstrate the concept. Because the application of luminescent probes is becoming increasingly
more prevalent in countless areas of research, it is imperative that students have an early
introduction to photophysics. By introducing the physics of light through fluorescent properties of
food, the complex principles and applications of photophysics can be made more relatable and
stimulating for young students, increasing their understanding of these important ideas.
Melanie Cotton
Professor Aaron Mazzeo
A Multigait, Soft Robotic Jellyfish That Exhibits Passive Energy Recapture
Jellyfish are the most efficient swimmers on the planet due to passive energy recapture (PER), the
ability of some jellyfish to demonstrate two distinct periods of acceleration in each swimming cycle.
In this research, the design, fabrication, and characterization of a soft robotic jellyfish that exhibits
PER deepens the understanding of the propulsion mechanism of jellyfish and has interesting
implications in the fields of soft robotics and efficient underwater vehicles. Two types of silicone
rubber used in the construction of the jellyfish robot mimic the shape and flexibility of biological
jellyfish, and the hydraulic system used to power the robot replicates the swimming behavior of
jellyfish capable of PER. The subsequent testing of the biomimetic robot to obtain displacement and
velocity plots, to visualize vortex formation, and to measure efficiency facilitates the analysis and
comparison of three gaits: fast, moderate, and slow. Both the moderate and slow gaits demonstrate
PER, and further analysis indicates that varying the gait has a significant impact on vortex formation.
Based on the calculated cost of transport (COT) values, the slow gait is the most efficient of those
tested. The first successful replication of PER in a robotic system and the discovery of a unique
pattern of vortices associated with each gait suggest that further optimization of the design of the
robot and its gait will yield future propulsion systems with even higher efficiency.
Molly Cunningham
Professor Yair Rosenthal
Small Plankton, Big Impact on Climate Studies (551A.D. – 1793A.D.)
Climate change is a serious concern. It is important to understand how the climate has changed in
the past to make better predictions and to take action to prevent further negative changes to the
climate and environment. The Atlantic Ocean plays an important role in determining climate because
when the flow of the ocean currents changes, the temperature changes as well. Temperature
changes can be mapped out by taking measurements of Magnesium to Calcium ratios (Mg/Ca) and
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changes in the amount of Oxygen-18 to Oxygen-16 (δ18O) from plankton shells. Shell weights also
provide a glimpse of how reliable the Mg/Ca ratio will be as well as carbonate ion concentrations.
The plankton specie used for this project is Globigerina bulloides. The G. bulloides shells came from
the RAPiD-17-5P core which was taken from the bottom of the ocean off the coast of Iceland. The
North Atlantic Current brings warm salty nutrient waters to the G. bulloides. The information
obtained from the plankton shells will complete preexisting records and extend records back for
2000 years. These records can be analyzed and studied to understand how and why Earth’s climate
has changed from cold periods to warm periods. The data collected supports the climate changes
during years of the Medieval Warm Period (about 1000 A.D.-1400 A.D.) and the Little Ice Age of
Europe (about 1400 A.D.-1900 A.D.) and it provides information about past climates as far back of
551A.D. An even more complete understanding of climate change can be mapped out, analyzed,
and understood after comparing the results from RAPiD-17-5P to other cores.
Marissa DelRocini
Professor David Margolis
Imaging the Acute Effects of Ketamine on Cortical Network Activity in Mice
Ketamine is a non-competitive NMDAR antagonist used as a dissociative anesthetic in both humans
and animals and sometimes as a drug of abuse. Ketamine can also cause temporary schizophrenialike symptoms in high doses and has been found to have long-term anti-depressant effects in low
does, suggesting widespread effects on brain networks. NMDARs have been found to regulate
connectivity in areas including the orbital prefrontal cortex, subgenual and posterior cingulate
cortices, and the nucleus accumbens. In addition, electrophysiology studies have shown that
ketamine induces increase neuronal burst firing. However, it is not known whether ketamine has
uniform or diverse effects on excitability and connectivity across the entire extent of cortex because
it has not been possible to record cortical activity with complete coverage and high spatiotemporal
resolution. New generation transgenic reporter mice with a GCaMP6f calcium indicator allow for
imaging of calcium signals across large areas of cortex with high spatiotemporal resolution. Five
mice were imaged before and after a single 30 mg/kg dose of ketamine. Analysis of the location of
cortical activation, mapped areas of correlated activity and compared changes in the brain after the
ketamine injection indicates that neural activity in these areas are reduced in magnitude but
generally increased in frequency when compared to the data of mice before the ketamine injection.
In addition, there is a significant increase in neural activity identified as double peaks in which the
time interval between both peaks is very small. Future studies focusing on the dose-dependency of
ketamine effects could help clarify the uncertainty behind the diversity of ketamine induced
symptoms at different potencies.
Akash Desai
Professor Mona Zebarjadi
Active and Passive Cooling
Our project is part of alternate cooling technology undergraduate program that focuses on ways of
cooling to harvest full potential of modern central processing units. Thermal radiation runs rampant
in electronic circuits due to electricity passing through millions of connections. There are two major
means used for cooling, passive and active cooling. (1) Passive cooling is a heat dissipation method
that relies on the principle of cooling an object without depending on a power source. While, (2)
active cooling is an alternative method that focuses on heat-gain control and heat dissipation
through an additional power source. These methods have been used independently; however, when
combined, makes the cooling process more efficient. This project aims to maximize the cooling
efficiencies of electronic circuits using a thermoelectric cooler as an active cooling agent and a heat
sink as a passive cooling agent. A thermoelectric cooler, when supplied with appropriate voltage,
produces a temperature gradient around the semi-conductors attached to the electrodes. Others
have done similar kinds of set-ups, however very few people have tried to run this set-up with
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varying thermoelectric cooler sizes and scenarios. Once the experiment is set up, sufficient tries
have been run to measure the cooling efficiency with different designs. Several statistical analyses
were conducted to further strengthen and verify the results of the setup. Use of active and passive
cooling with the use of thermoelectric materials in smaller scale circuits is a step forward in creating
a system with reduced thermal radiation and improved performance.
Shweta Dipali
Professor Karen Schindler
The Effect of Inhibition of PLK1 on AURKC Localization
Aneuploidy is the presence of an abnormal number of chromosomes due to errors in meiosis and is
the leading genetic cause of infertility. There are many regulators of chromosome segregation that
work to prevent aneuploidy in oocytes. One of which, Aurora Kinase C (AURKC) is a mammalian
germ-line specific protein that functions in correcting improper kinetochore-microtubule attachment
and localizes to the kinetochores and inter-chromatid axis (ICA) during metaphase of meiosis I. Our
lab has determined that the Haspin Kinase regulates AURKC localization at the ICA, but it is still
unclear what drives AURKC localization at the kinetochores. A likely candidate is Polo-like Kinase 1
(PLK1), which is another important regulator of the cell cycle that functions similar to AURKC and
also localizes to the kinetochores during Met I. To visualize the effect on AURKC localization, we
inhibited PLK1 in mouse oocytes with the specific small molecule inhibitor BI2536. First, we
determined appropriate working doses of the inhibitor by maturing cells in the drug at varying
concentrations on a live cell imager and assaying for G2/Meiosis transition and meiosis I
completion, to indicate PLK1 inhibition. Furthermore, we stained oocytes matured in the working
doses of BI2536 for markers indicating AURKC, the outer kinetochore, DNA, as well as the spindle
and imaged under a confocal microscope. The images revealed that the intensity of AURKC
decreases at the kinetochores in cells treated with the drug, as compared to control oocytes. These
preliminary data suggest that PLK1 activity drives AURKC localization to kinetochores.
Sanjita Ekhelikar
Professor Patricia Buckendahl
Comparing Response to Hindlimb Unloading in the Presence and Absence of Osteocalcin
Skeletal unloading is a condition caused by prolonged disuse of the musculoskeletal system, and
can lead to many physiological complications. Astronauts enduring microgravity, patients suffering
from spinal cord injuries, and people with limited mobility experience inactivity for extended periods
of time, particularly of their lower limbs.This results in skeletal unloading, which inhibits new bone
formation and causes existing bone to deteriorate, leading to osteoporosis and triggering
inflammatory response. A rodent hindlimb unloading (HLU) model was developed to study the
impacts of unloading on mice in a laboratory setting. Research studies are underway in the
Buckendahl lab to investigate the role of the protein osteocalcin in coping with the effects of skeletal
unloading. Secreted by osteoblasts, osteocalcin has been linked to bone formation and to
inflammatory response mediation. For the experiment, wild type and genetically altered mice that
lack osteocalcin were used. Mice were randomly assigned to a control group with no treatment, and
an experimental group in which they were suspended from their tails for a week to prevent hind
limbs movement and induce unloading. The mice were then euthanized, and several bones and soft
tissues were extracted to analyze both bone structure and gene expression of various markers of
bone formation and inflammatory response. The results of the analysis will help assess if there is
any correlation between osteocalcin and unloading. The goal of this study is to determine the role of
osteocalcin on the body’s ability to deal with the physiological impacts of skeletal unloading.
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David Estrin
Professor Mark West
Single Body Part Neurons in the Dorsolateral Striatum of Mice
Neurons in the dorsolateral striatum have been shown to process single body part (SBP) movements
or cutaneous touch within various laboratory species like monkeys, cats, and rats. It has been
hypothesized that normal motor behavior relies on the proportionate and precise firing of opposing
pathways in the striatum. According to this hypothesis, the direct pathway is thought to contain
primarily D1 receptor expressing neurons, which propel signals to the Globus Pallidus internal
segment (GPi) and on to motor thalamus exciting movement. Furthermore, the indirect pathway is
believed to contain primarily D2 receptor expressing neurons which project signals to the Globus
Pallidus external segment (GPe), then through the sub thalamic nucleus (STN) before projecting to
the motor thalamus, ultimately inhibiting movement. Dysfunction or imbalance in these circuits is
thought to be the cause of a multitude of neuropathological diseases such as Parkinson’s
disease. However, anatomical evidence for the specificity of these pathways (D1->GPi / D2->GPe) is
limited and very little is known about the contribution of SBP neurons to each pathway. To test the
specificity of each pathway, our laboratory plans to use genetically modified mice along with
optogenetics, in order to independently activate D1/D2 pathways in vivo via laser pulses. Currently,
we have been determining if SBP neurons may be discriminated in the mouse, and assessing whether
or not they belong to the direct or indirect pathway or both. We have been studying this
electrophysiologicaly in mice by utilizing 16 microwire arrays which are implanted into the striatum
of D1-Cre and D2-Cre C57BL/6 mice. By performing “body exams” on mice, our lab has been
measuring neuron activity in relation to body part movement and cutaneous touch. During body
exams, the body of the mouse was broken down into several major categories such as head, trunk,
front paw, back paw, etc. Neurons associated with these body parts exhibit action potentials when
the body part is touched and/or moved (direction specific). Ultimately, if body part sensitivity can
be discriminated unambiguously in the mouse, we can move forward in determining whether they
belong to the direct and indirect pathways. By ascertaining the process of motion by analyzing
the relationship between direct/indirect pathways and D1/D2 expressing neurons, our lab hopes
to contribute to the scientific understanding of neuromotor pathologies and motion as a whole.
Jennifer Fang
Professor Michael Verzi
YY1 is Required for Intestinal Organogenesis, Functioning Independently of the mTOR Pathway
Yin-Yang1 (YY1) is a critical transcription factor for intestinal organogenesis through regulation of
mitochondrial function. YY1 loss in embryonic endoderm results in underdeveloped, translucent
intestines, drastically shortened villi, and deformed mitochondria. We hypothesized that YY1
functions downstream of the mTOR (mammalian target of rapamycin) pathway in maintaining
metabolic functioning. mTOR deregulation is correlated with cancer, type 2 diabetes, and
neurodegeneration. While mTOR signaling has been shown to function upstream of YY1 in other
tissues, the role of mTOR in gut development is unexplored. Elucidating the role of transcription
factors during intestinal organogenesis will shed light on the causes of developmental diseases such
as necrotizing enterocolitis and intestinal atresia. We inhibited mTOR by rapamycin administration
and Raptor (Regulatory-Associated Protein of mTOR, a critical component of the mTOR complex)
knockout. In both these methods, the embryonic intestines failed to phenocopy the YY1 intestinal
knockout, as ascertained by villus height measurements, electron microscopy ultrastructure
analysis, and immunohistochemistry staining. These results thereby suggest that YY1’s role in
organogenesis is independent of mTOR.
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Amanda Gallagher
Professor Amrik Sahota
Molecular Pathophysiology of Bladder Outlet Obstruction
Cystinuria is a rare autosomal recessive disorder characterized by high concentrations of cystine in
urine and repeated cystine stone formation in the kidney, bladder, and/or ureter. We are using male
Slc3a1 knockout mice of different ages to acquire information about the production and
development of the disorder. Males are more severely affected than females, making our mice an
ideal model system. The exact pathology of how urinary stones cause bladder obstruction is not
fully understood, but we know bladders of male knockout mice over 3 months of age exhibit
hypertrophy, decreased compliance, and decreased contractile responses. We hypothesize that the
urothelial cell surface, possibly because of injury and/or increased proliferation, causes gene
expression changes. This brings about inflammation, interstitial fibrosis, and smooth muscle
hypertrophy. To determine if the presence of cystine stones in the bladder leads to qualitative and
quantitative variations in gene expression in bladder cells, we examine the expression of interleukin1β (IL-1β), transforming growth factor-β (TGF- β), and insulin growth factor (IGF-1). IL-1β is a
proinflammatory cytokine that induces TGF- β and insulin growth factor IGF-1, which contribute to
tissue fibrosis and muscle hypertrophy respectively. Starting with RNA extraction then conversion to
cDNA, we utilize RT-PCR and qPCR to test, record, and analyze the expression levels of the genes.
These changes in expression with age underlie histopathological changes associated with the
dysfunctions found in mice with Cystinuria, and studying them will provide further information
about the disorder and others of its kind.
Nakul Gangolli
Professor Eric Gawiser
Image Reduction of the CW1256 Field of the MUSYC Collaboration
We are using image reduction techniques to process images of the CW1255 field of the MUltiwavelength Survey Yale Chile (MUSYC) collaboration to catalog high-redshift Lyman-Alpha Emitting
(LAE) galaxies at redshifts of z≃2.1 and z≃3.1. LAEs are young galaxies that have high star
formation rates (SFR) and emit Lyman-alpha radiation, a form of radiation in which an electron in the
second energy level of hydrogen drops down to the lowest energy level, emitting a photon of
wavelength 121.6 nm. The images were taken using the MOSAIC II CCD camera at the CTIO 4 m
telescope with O2 and KO3 narrowband filters, centered at wavelengths of 372.7 nm and 501.5 nm;
respectively. We used the MSCRED package in IRAF to subtract bias, flat field the image, remove
cosmic rays and satellite trails, project the images on a tangent plane, stack (both unweighted and
weighted) multiple exposures into single images, and remove background sky. The purpose of this
project is to reduce the images so that we can use them to catalog LAE and analyze them for star
formation rates, stellar masses, ages, and dark matter halos.
Anna Harootunian
Professor Karin Struwe
Examining the Effects of Mowing on Urban and Rural Queen Anne's Lace Populations
In an increasingly urbanized world, we must understand the impacts of human activity on plant
evolution in order to conserve and protect natural vegetative resources into the future. Queen
Anne’s lace (Daucus carota) is a weedy herbaceous plant that is abundant in rural meadow and
urban grassland habitats throughout North America. Urban plant communities containing Queen
Anne’s lace populations are commonly managed through intense mowing or weed-whacking. To test
for urban adaptations to mowing pressure, Queen Anne’s lace seeds gathered from five urban and
five rural environments across New Jersey were grown in a common garden on Rutgers University
New Brunswick campus. The treatment group plants were trimmed with scissors to 10 centimeter
height to simulate mowing or weed-whacking pressure. After three weeks of post-treatment growth,
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plants in the treatment group from rural maternal environments were significantly shorter than
those in the control group, while there was no significant difference between the heights of trimmed
and un-trimmed plants from urban maternal environments. These results may suggest that urban
Queen Anne’s lace populations have adapted to maximize growth in the face of intense mowing,
weed-whacking, and other disturbances. Future work should determine if increased post-disturbance
growth rates in urban Queen Anne’s lace populations leads to increased fitness in anthropogenic
habitats and/or divergence between rural and urban populations.
Anthony Hoang
Professor Edward Arnold
Structural Studies of the HIV-1 Initiation Complex
Human immunodeficiency virus (HIV) is the causative agent of AIDS. HIV-1 reverse transcriptase is a
crucial enzyme involved in the virus’s life cycle. HIV-1 RT interacts with the viral genomic RNA and
host-cell tRNAlys,3 to form the HIV-1 Initiation Complex (HIC), a key structure for the regulation of
reverse transcription. The molecular structure of the HIC is not yet characterized, and may be a good
drug target. We produced highly pure, reproducible, structurally homogeneous tRNAlys,3 and viral
genomic RNA by in vitro transcription from DNA templates. Size exclusion chromatography replaced
denaturing urea-PAGE as the primary means of purifying the RNAs. By manipulating variables such
as annealing temperature, MgCl2 concentration, and other polycation (spermin and spermidine)
concentrations, native PAGE will be used to determine conditions that produce RNA conformation
and homogeneity. This will allow for further structural analysis of the HIC through crystallography,
small angle x-ray scattering, and hydrogen-deuterium exchange coupled to liquid chromatographymass spectrometry.
Brandon Jones
Professor Mitsunori Denda
A 2-Dimensional Vortex Approach to Model Insect Flapping Flight
The need for efficient surveillance in hostile environments inaccessible from the ground has inspired
the development of Micro Aerial Vehicles (MAVs). Researchers are studying insects with the goal of
reverse engineering flapping flight in order to manufacture the smallest possible MAVs.
Conventional airfoil theory ignores the effects of unsteady aerodynamics such as vortex shedding,
interaction with the wake vortices, and other undiscovered phenomena. Insect wings interact with
their shed vortices so computational models must be based upon unsteady fluid dynamics. This
project uses a MATLAB 2-dimensional model of insect flight, which divides the wing’s periodic
motion into time steps, with the leading and trailing vortices shed at every time step and the
resulting forces calculated from the Biot-Savart equation. This simulation provides accurate results
with a notably shorter runtime than the full viscous fluid solvers and allows for the optimization of
flight parameters. The honey bee and crane fly were studied to identify initial input parameters such
as wing span, chord length, flapping frequency, and stroke plane angle. The simulation was then
run numerous times and the lift forces for each trial was compared. The data suggests that wingwake interaction, whether constructive or destructive, plays a pivotal role in overall lift generation
and dictates if flight is possible. For the crane fly, the largest lift forces correlated with a 20 degree
stroke plane angle and were proportional to the size of the wing and flapping frequency. Future
research should investigate the effects of other parameters, such as advanced or delayed supination
and pronation, on the wing-wake interaction.
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Shyam Kalaria
Professor Richard Riman
Up-Conversion Nanoparticles Doped with Gadolinium
Rare-earth (RE) doped up converting nanoparticles (NaYF₄: RE) produced through solvothermal
methods can revolutionize bio-imaging. The nanoparticles allow for cheaper, more portable, safer,
and less invasive means of scanning for abnormalities in the body in real time. Brighter and smaller
nanoparticles enable more accurate pinpointing of smaller foreign objects in the body. To obtain
smaller and brighter particles we examined the influence of adding a third rare-earth dopant,
gadolinium (Gd), along with Ytterbium (Yb), and Erbium (Er). The presence of gadolinium promotes
hexagonal phase formation, which allows brighter up-conversion (UC) light emission. UC is a
process by which the nanoparticles absorb energy from two photons to emit one higher energy
photon. However, the nanoparticles are not bright enough even with the recent changes. This
problem originates from the fact that a large amount of the energy is lost through non-radioactive
(non-light producing) processes or just not absorbed completely to begin with. The issue can be
remedied by researching new base structures that are more effective than NaYF₄ at limiting nonradioactive energy loss and by testing different RE dopant combinations for maximum energy
absorption and emission.
Samir Kamat
Professor Wilma Olson
Genetic Information Encoded in DNA
RNA serves important functions in relaying information between DNA and proteins, protein
synthesis, and controlling gene activity. Unlike its DNA counterpart, RNA is a single-stranded chain
that forms a convoluted structure of twists, helices, bulges, and other motifs. It is thought that the
manner in which RNA folds contributes highly to its function, though there is still much to be
learned. RNA junctions, which arises from the intersection of multiple helices, are of particular
interest. Using DSSR, RNA structure analysis software, we survey junction-types from a
representative sample of RNA. Through pymol, we also attempt to classify junctions through
structural alignment, observing great similarities among junctions that share common base-pair
arrangements (spacers).
Daniel Kats
Professor Martin Schwander
The role of DFNA5Gene in Progressive Hearing Loss
Hearing loss is the most common sensory disorder in humans, present in about 1 out of every 500
newborns. In addition, a large fraction of the elderly population suffers from progressive hearing
loss. Aside from environmental factors such as excessive noise, genetic factors play an important
role in hearing loss. DFNA5, a member of the gasdermin gene family, has been identified as a gene
responsible for progressive hearing loss. Different DFNA5 mutations have been identified, but
detailed information on the expression and mechanism through which DFNA5 acts is still missing
due to the lack of a suitable mouse model. Here, we have generated a transgenic mouse line that
allows for the expression of either the naturally occurring wild-type or mutant human DFNA5 in
specific cell lines over time by a breeding mechanism known as Cre-LoxP-technology. To assess
hearing function in wild-type and DFNA5 mutant mice, we measured the auditory brainstem
response (ABR) and determined auditory thresholds. Genotyping of the mice was performed by
polymerase chain reaction (PCR) to verify the presence of both Cre recombinase and the DFNA5
transgene. Based on our preliminary results, we currently cannot conclude whether DFNA5 mutant
mice develop progressive hearing loss, as the small number of Cre-positive mice analyzed showed
normal hearing thresholds. However, a better understanding of the role of DFNA5 in inner ear
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function and dysfunction will, in the long-term, provide opportunities to intervene in human
progressive hearing loss and to prevent or treat this disorder.
Megan Kenny
Professor Karin Stromswold
A Link between Speaking and Understanding
BACKGROUND: Sentences are often temporarily ambiguous. For example, the pig was kiss__ could
be the beginning of an active sentence (The pig was kissing the sheep) or a passive sentence (The
pig was kissed by the sheep). English-speaking preschoolers rarely say passives, and frequently
misunderstand them, and even adults say fewer passives and misunderstand passives more than
actives. This project investigates the link between sentence comprehension and production in adults
and children. ADULTS: Previous work reveals that adults say passive verb stems (E.G., the kiss in
kissed) more slowly than active verb stems (E.G., the kiss in kissing). Perhaps adults can use this
acoustic difference to predict whether a sentence is active or passive while it is still syntactically
ambiguous. In our study, adults listened to truncated sentences (E.G., The pig was kiss__) and
guessed whether the truncation came from a passive or active sentence. After completing this task,
they said each sentence. Analyses reveal that adults were better than chance at “guessing” whether
an ambiguous truncation was active or passive. We have begun to analyze adults’ production data.
CHILDREN: We have designed a sentence-picture matching comprehension task to determine the
speed and accuracy with which children understand full actives and passives. We have designed
another task to elicit children to produce actives and passives. PREDICTIONS: We predict that people
who lengthen passive verb stems more will comprehend active and passive sentence faster and more
accurately than people who lengthen passive verb stems less.
Hyejin Kim
Professor Richard Ebright
In Vitro Activity of RNAP Inhibitors against Bacterial Biofilms
Bacterial biofilms are frequently involved in serious chronic infections and medical device-related
infections. They place a significant burden on healthcare because bacteria in biofilms are much more
resistant to antibiotics than bacteria in suspension and are very difficult to eradicate. Interestingly,
the RNA polymerase (RNAP) inhibitor rifampin has been shown to be effective at eradicating certain
biofilms. The bacterial RNAP is a well-established target for drugs because a) it is essential for gene
expression, b) highly conserved across species, allowing for broad-spectrum activity against
pathogens, and c) not so highly conserved in human RNAPs, allowing for therapeutic selectivity. It is
unclear, however, if this activity against biofilms is due to the specific properties of the antibiotic
rifampin (a bacterial RNAP inhibitor) or if this is evidence of the RNAP as a favorable target for
clearing biofilms. This study thus seeks to characterize the in vitro activity of various bacterial RNAP
inhibitors against biofilms of clinically relevant S. epidermidis (Gram-positive model) and P.
aeruginosa (Gram-negative model). The Minimum Biofilm Eradication Concentrations (MBEC) and the
Minimum Inhibitory Concentrations (MIC) of these inhibitors will be compared to those of rifampin
and of reference antibiotics that do not target the RNAP. This comparison will help determine if the
RNAP is indeed a promising target for biofilm-active antimicrobials and if other bacterial RNAP
inhibitors are effective at eradicating biofilms.
Yoon Mi Kim
Professor Ruth Steward
The Effect of Tet on Larval Locomotion in Drosophila
TET genes are essential for the maintenance of stem cells in Drosophila. Tet is an essential gene
because Drosophila without Tet is lethal; Tet null Drosophila die in pupa stage. Tet proteins are
highly conserved in mammals and flies. In mammals they control the addition of a hydroxyl group
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onto methylated Cytosine in DNA. Drosophila do not have DNA methylation and
hydroxymethylation, and Tet in flies is postulated to regulate 5hmC in RNA, and apparently has an
important role in neuron development. In flies, the gene is specifically expressed in the central
nervous system. Therefore, this larval locomotion project was conducted to investigate the
requirement of TET in larval locomotion. According to the data I obtained, the differences between
the sample means (contractions, line crossed, turns, and wiggles) of Control (CG3444) and
Experimental groups (Tet null, Tet DBD, and Tet 2) for the Drosophila larval movements (n=100)
were statistically significant (p-values <0.05). T-tests were executed to determine the statistical
significance of the results. The Steward lab has recently found that loss of Tet results in abnormal
axons in the central nervous system. In support of the possibility that Tet regulates nerve input that
controls muscle movement, my results show that loss of Tet results in abnormal larval behavior.
Future directions are to continue investigating the Tet gene in more depth by conducting
experiments on the abnormal turning behavior and behavioral plasticity in Drosophila larvae of
normal and Tet loss of function animals.
Viktor Krapivin
Professor Girsh Blumberg
Investigation of URu2-xFexSi2 with Raman Spectroscopy
The Uranium based superconductor URu2Si2 has a second order phase transition below the
temperature of 17.5 Kelvin into a new phase of matter referred to as the "hidden order" (HO) state.
[1, 2] In order to study the phase transition, one can use Raman spectroscopy to determine the
associated order parameter. Here we measured samples of [attached picture] with variable Iron
doping in order to investigate the effects of replacing Ruthenium with Iron. The samples under
investigation were cleaved in order to obtain a smooth and stress free surface. Measurements done
with x=0.05 and 0.10 suggest that the hidden order state disappears near the x=0.10 Fe doping.
Citations:
1. T. T. M. Palstra et al., Phys. Rev. Lett. 55, 2727, (1985).
2. N. Kanchanavatee, et al., Phys. Rev. B. 84, 245122, (2011).
Gaurav Kumar
Professor Bonnie Firestein-Miller
The Role of Cypin in Functional Recovery of Neurons Following Traumatic Brain Injury
Traumatic brain injury (TBI) affects approximately 1.7 million people each year in the United States,
and of which 52,000 die and 275,000 are hospitalized (1). TBI is primarily caused by deformations
of the brain tissue (primary damage) due to mechanical trauma, followed by rapid release of
glutamate. Glutamate is a non-essential amino acid, a crucial component of cellular metabolism, and
most common excitatory neurotransmitter. Nearly all excitatory neurons in the central nervous
system are glutamatergic, and it is estimated that over half of all brain synapses release this agent.
Under normal conditions, glutamate allows for communication between neurons as it is released at
the presynaptic site into the synaptic cleft from which it travels to postsynaptic membrane of
another neuron and effectively activates its target receptors, such as NMDA receptors (NMDARs).
Overactivation of NMDARs leads to excess calcium signaling and causes cell death (secondary
damage) (3). Formation of large varicosities (focal swelling) within dendrites and loss of dendritic
spines are the earliest indications of glutamate induced excitotoxicity in vitro. The Firestein
laboratory has shown that while overexpression of cytosolic PSD-95 interactor (cypin) increases the
number of varicosities per micrometer, it also decreases the size of varicosities, which appears to be
neuroprotective. On the other hand, knocking down cypin decreases the amount of beaded neurons,
decreases the number of varicosities per micrometer, and increases the size of the varicosities,
which is detrimental to cell health and survival following TBI. Additionally, the mTOR/Akt pathway
has been implicated in the modulation and regulation of synaptic strength, synaptic activity,
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maturation, and axon regeneration, all of which might contribute to recovery of neural morphology
and health when subjected to TBI. To mimic either primary or secondary injury as a result of TBI in
rat cortical neurons, we grew cells on silastic membranes or glass coverslips and subjected them to
stretch or NMDA-induced injury. To investigate cypin activity on varicosity formation in NMDAinduced injury model, we treated neurons in vitro with novel small molecule drugs that modulate
cypin’s activity. To manipulate mTOR/Akt pathways, we used several compounds, such as the PTEN
inhibitor bpV, the Akt inhibitor MK2206, and the mTORC1 inhibitor Everolimus (a rapamycin analog),
and assessed their effects on neural morphology following injury. Since both cypin and mTOR/Akt
have shown great potential for neuronal recovery in our TBI models, our research has potential to
produce novel treatments for patients who have suffered a TBI.
Kaitlin Leyble
Professor Pernille Hemmer
The Effect of Expectations on Pain Assessment and Interpretation
Almost everyone has visited a doctor for a problem at least once in their life. Over time, each person
develops a unique experience with illnesses. It is likely that these experiences determine when they
decide to seek care. With this in mind, individual health seems to be dependent on individuals
attaining accurate knowledge about illnesses. Previous studies focused on why individuals delay
seeking care; however, there is a relative lack of research on the expectations people have of
illnesses. To bridge this gap, we investigated how expectations impact an individual’s understanding
of illnesses and their symptoms. In this study, we included differing pain locations, durations, and
severities to test the accuracy of participants’ expectations for illnesses associated with abdominal
pain. In the first portion of the experiment, participants freely responded with an illness they
believed the pain level and location to indicate. In the second portion, they chose an illness from a
dropdown menu. We also asked participants to indicate how long they would wait to seek care
considering pain location and severity. Afterwards, they were asked about their background in order
to investigate how personal experience affected their interpretation of symptoms. We predicted that
illness judgements would influence likelihood to seek care. This study will help us to better
understand individual expectations for illnesses and whether or not those with accurate
expectations make better judgements about when to seek care.
Julia Lin
Professor Sharon Pine
Effect of Doxorubicin Chemotherapy Drug on Localization of Sox9 Transcription Factor in Lung
Cancer Cells
Lung cancer accounts for 27% of all cancer deaths and is the second most common cancer in both
men and women (1). In recent studies, the over-expression of developmental transcription factor
Sox9 has been correlated with poor survival in lung cancer patients. We and many other labs have
shown that Sox9 plays important roles in tumorigenesis, proliferation, and Epithelial-Mesenchymal
transition (EMT) (2). We found that chemotherapy drug Doxorubicin, a DNA topoisomerase II
inhibitor, degrades Sox9 in a time and dosage dependent manner. Our results indicate
administering .5uM and 1uM dosages of Doxorubicin to lung cancer cell lines H1299 and U20S
successfully degrades Sox9. By constructing a plasmid by ligating the Sox9 gene with a mCherry
fluorescence marker, we tracked the localization of Sox9 in cells. Since Sox9 needs to localize to the
nucleus for functioning as a transcription factor, the localization of Sox9 will shed light on its
regulation and functions under different conditions. After transfecting our specialized plasmid into
cells we treated cancer cells with Doxorubicin to delineate its possible effect on Sox9 localization, in
addition to its effect on Sox9 degradation. Future studies would focus on understanding and
interpreting the exact reasons why Sox9 degradation is inhibited at high Doxorubicin dosages.
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Sarah Lin
Professor Timothy Otto
Regional Distribution of Immediate-Early Gene Arc in Dorsal Hippocampus Following Object-Place
Learning
Episodic memory refers to the memory of past personal experiences, in particular the spatiotemporal contexts associated with them. This type of memory is dependent on a structure in the
medial temporal lobe of the brain known as the hippocampus and can be investigated using an
object-place learning (OPL) paradigm. While recent research has demonstrated that the acquisition of
object-place associations in rodents requires the involvement of the dorsal hippocampus, or the
upper region of the hippocampus when divided along its septotemporal axis, few studies have taken
the next step of looking into the different dorsal hippocampal subregions to characterize the extent
of each area’s involvement in OPL. To accomplish this, the lab examines the distribution of activityregulated cytoskeletal-associated protein (Arc), an immediate-early gene that is differentially
expressed in the subfields following hippocampal-dependent learning. This study specifically
predicts that there are elevated levels of Arc protein in the dorsal Cornu Ammonis 2 (CA2) region
relative to other subregions after OPL. This is based on anatomical evidence showing that afferent
nerves from both the medial and lateral entorhinal cortex, areas found to be involved in spatial and
non-spatial learning, converge at dorsal CA2. The lab used a modified OPL paradigm consisting of
an open field chamber with different sets of objects for the rodents to explore and then
immunohistochemical techniques to stain for Arc-positive cells and quantify Arc density in the
various regions of the hippocampus. While data analysis is still in progress, the lab expects findings
to reflect higher levels of Arc in the dorsal CA2 subfield.
Mengdan Liu
Professor Mehdi Javanmard
Optimizing Bead Based Immunoassays for application in Microfluidic Biosensors
Current standards for clinical diagnostics are slow and not sensitive enough to enable early
detection of disease. Dependence on fluorescent immuno-tagging as the primary means of detection
restricts these assays, or experiments, to laboratory analysis prolonging the return of meaningful
diagnoses to patients and practitioners. Our lab began prototyping and developing a microfluidic
biosensor, one that uses principles inherent to microscopic quantities of fluid, to improve on these
issues. The design uses microscopic beads coated in antibodies, changes in electrical fields, and
microfluidics condensed into a handheld, portable box decreasing costs, increasing sensitivity, and
delivering information faster. My work has been focused on optimizing the device’s bead-based
disease detection inside a variety of designs. Experimentation began by determining if aggregation
between magnetic and polystyrene coated beads as mediated by a specific antigen was possible.
Another chemistry was explored wherein beads were covalently coated with similar antibodies.
Qualitative observation confirmed that our design was functional inside and outside of our device.
Further analysis found the alternate chemistry as effective, and efforts are being made to
incorporate it into the device. With more development, we aim to introduce wearable health
monitoring devices and give wearable technology more credibility as viable and fast-approaching
improvements in medicine and quality of life of the general populace.
David Lo
Professor Barth Grant
Molecular Mechanisms of Recycling and Autophagy in Intestines of C. elegans
The purpose of this study is to identify relationships between the physical (phenotypic) and genetic
(genotypic) characteristics of intestines in free-living transparent nematode, Caenorhabditis elegans
(c.elegans), a model organism. The physical characteristics include red and green colored patches
when viewed under the microscope, while the genetic ones are the gck-2 genes that are lit up due to
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the red and green fluorescent proteins. This study uses c. elegans bombarded with genetic
constructs that produce progeny with this genetic variation. The two strains of worms that are
crossed are N2 males and hlh30GFP hermaphrodites that allow the later generations from that cross
to be examined. Analysis under a fluorescent microscope showed that parts of the intestine are lit
up by the green and red proteins. Further analysis can be used to find which genotypes correlate
with specific parts and properties within the c. elegans like size and intensity within the
intestines. The anticipated outcome of this project is the identification of the genotypes that affect
absorbance of substances – the brighter or bigger an area is, the higher the absorbance. The
findings may be useful in understanding the absorbance of certain medications or substances within
the intestine of humans.
Edward Looney
Professor Sevil Salur
Tagging Resonances from a Heavy Ion Environment at the CMS Detector
Quark-Gluon Plasma (QGP) is the hottest and densest state of matter known to man, but very little is
known about it. Scientists at CERN and Brookhaven National Laboratory are trying to learn about its
properties to ultimately understand more about how matter interacts with it and also understand
what all matter consisted of immediately after the Big Bang. This is done by analyzing data from
heavy ion collisions, little Big Bangs, collected by the CMS Experiment at CERN. For my summer
project, I identified and studied interactions of particles that decay into dimuon pairs using the
medium produced by these collisions. Muons offer us a clean signal for reconstructing their mother
particles since they do not interact with quarks and gluons.
Achmad Bakhtiar M Yuni
Professor Karl Kjer
DNA Barcoding of the COI gene in Trichoptera
DNA barcoding is a method to characterize species of organisms using a short DNA sequence from a
standard position in the genome. With DNA barcoding, scientists are able to speed up identification
of known organisms and facilitate recognition of new species. In the case of Trichoptera
(caddisflies), correctly identifying species is a difficult process because of their expansive diversity
and nearly identical physical characteristics. However, it is important because identified caddisflies
can be used to monitor water quality. This study aims to barcode the DNA of Trichoptera using the
cytochrome c oxidase subunit 1 mitochondrial region (COI). At the beginning of the study, adult
caddisflies are collected using the standard D-net procedure and light-trapping. Then, the specimens
are preserved using either pinning or alcohol preserving method. To make reliable classifications,
we used morphologically-identified adult caddisflies, extracted the mitochondrial DNA, and
amplified the COI gene using PCR. The amplified DNA are then tested using gel electrophoresis to
analyze their concentration levels and sent to Foran Hall to be sequenced. The resulting sequences
are edited using the ‘A Plasmid Editor (ApE)’ software and submitted to the Barcode of Life Database
(BOLD). By contributing to this public library of sequences linked to named specimens, DNA
barcoding will be increasingly practical and useful. Moreover, it will enhance public access to
biological knowledge.
Christopher Markosian
Professor Kenneth Irvine
Identifying the Mechanism of Interaction Between α-catenin and Ajuba LIM Protein
The Hippo signaling pathway controls growth during development by regulating the activity of
kinase Warts (Wts), which phosphorylates Yorkie (Yki) and prevents its nuclear translocation.
Yki is a transcriptional coactivator that promotes growth. Ajuba LIM protein (Jub) binds to and
inactivates Wts by promoting its localization to the adherens junctions. Upon the localization of
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Wts to the adherens junctions, Yki is no longer phosphorylated and hence is able to localize to the
nucleus, where it regulates growth-promoting genes. α-catenin, a protein involved in cell-cell
adhesion, is required for the localization of Jub to the adherens junctions. However, the mechanism
of interaction between α-catenin and Jub is not clear. Higher cytoskeletal tension correlates with
increased localization of Jub to the adherens junctions, suggesting that α-catenin may bind to Jub in
a tension-dependent manner. Two methods of determining the mechanism of this interaction in
Drosophila melanogaster are being utilized: 1. observing the effects of truncated versions of αcatenin on the localization of Jub in the wing imaginal disc and 2. conducting co
immunoprecipitation assays to assess the physical interactions between full-length and truncated
versions of α-catenin and Jub. Our study shows that in flies expressing α-catenin lacking the Nterminus of the VH2 domain (residues 273 to 509), localization of Jub at the adherens junctions was
increased compared to the endogenous punctate pattern. This result suggests that the N-terminus
of the VH2 domain of α-catenin may be responsible for an inhibition of interaction between α-catenin
and Jub.
Han Meng
Professor Kostas Bekris
Application of Immersive Reality in Human-Robot Interaction (HRI)
It is still quite challenging for robots to solve tasks, such as object recognition and detection,
automatically; human intelligence is still far superior in addressing these challenges. Thus, if a robot
communicates visual data to a remote human operator, it may be easier for the operator to locate
the target object. What is the best way, however, to provide this visual information in such a humanrobot interaction process? We have designed and implemented an intuitive user interface for robotic
teleoperation, which is also accessible to non-experts. The user interface is based on the use of
virtual reality that allows the operator to be immersed in the robot’s environment. Providing familiar
3D sensing information to the user makes the communication natural, and gives humans more
flexibility in controlling robots. For this project, we have assumed that the robot provides basic
operations (moving arms, grasping objects, etc.) and that its surroundings have been modeled. We
utilized the Robot Operating System (ROS) to create multiple connections among multiple devices (a
Baxter robot, an Oculus VR headset, an Arduino Uno microcontroller, two cameras, and two
computers). This allowed the reliable transmission of visual data from the robot to the human
operator. After that, we tested this immersive reality system for human-robot collaboration in cuppicking tasks. As a result, we found that the availability of immersive visual data in HRI helps the
operator to acquire high quality sensory information and simplifies the interaction with the robot.
Elena Mikhaylova
Professor Masanori Hara
Inorganic Polymers Modified via Cations and Ionic Liquids
My research entails creating a new type of polymer, with a chain comprised of silicate units. By
mixing the silica (SiO2) with strontium oxide (SrO) and rubidium oxide (Rb2O), some of the Si-O
covalent bonds within the silica are broken and replaced with ionic bonds. This silicate is further
modified with an ionic liquid (a salt in the liquid state), to significantly decrease its processing
temperature. The ionic liquid is considered as a processing agent and a plasticizer for the silicate
polymer. A polymer such as this can do wonders in both industry and the environment. By
essentially substituting the conventional carbon chain with silicon, a widely available and
inexpensive element, the resultant polymer would be significantly cheaper, easier to produce, and
better for the environment due to its biodegradable properties. Currently, my objective in this
project is to determine the effects of variables, such as SrO to Rb 2O ratios within the silicate,
processing temperature, ionic liquid components and ratios, on the structure and properties of
novel inorganic polymers.
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Cameron Mohrfeld
Professor Juan Dong
Are IQD15 and IQD16 Involved in BASL and Cell Polarity
Asymmetric cell division is extremely important for helping to differentiate plant cells, and also
creating and maintaining stem cell populations. Asymmetric cell division in plants is caused by what
is known as cell polarity. Not much is known about the mechanisms that drive cell polarity and that
is what this lab is working on. The main gene that we know to control cell polarity is BASL, and we
are trying to figure out what genes drive BASL. A large list of genes are being investigated to see if
they are an integral part of cell polarity, and the two genes that I have been working on are IQD15
and IQD16. It is known that these two genes are associated with the microtubules, so we are testing
to see if either of these two genes help establish or control BASL or if BASL helps control the IQD15
and IQD16. During my project, we created constructs of my two genes using pENTR, LR reactions,
e.coli transformations, and plasmid isolation. After we knew we had the right construct based on gel
electrophoresis results, we did an agrobacteria transformation for the next two steps which involved
injecting the transformed agrobacteria into tobacco plants and transforming them into Arabidopsis
to create transgenic plants. The results of the tobacco plant injection show us that the IQD15 and
IQD16 genes are in fact related to the microtubules. I did not have time to analyze my transformed
Arabidopsis, which is something I will have to do in the future. The results of this transformation,
using a confocal microscope, should help us to determine whether or not IQD15 and IQD16 are
involved with BASL and cell polarity.
Kimberly Ngai
Professor Ashutosh Goel
The Structure and Chemical Durability of Lithium Aluminum Borate Glasses
Borate-based glasses have only recently been researched for their potential applications in bioactive
glasses and liquid metal batteries. However, there is very little documentation on the chemical
durability and structure of borate glasses, specifically Lithium Aluminum Borate glass, and studying
the chemical durability is important to see a glass' capability for any application. Density tests,
Fourier transform infrared spectroscopy (FTIR), differential thermal analysis (DTA), dilatometry and
thermal expansion, nuclear magnetic resonance (NMR), X-ray photoelectron spectroscopy (XPS), and
chemical dissolution tests in deionized water were all performed on the glass series to test and
analyze their structures and durabilities. Chemical dissolution tests show a positive relationship
between Al2O3 content and weight loss of the glass after being submerged in the DI water. These
findings show that increasing Al2O3 while simultaneously decreasing B2O3 have a negative impact
on the glass' durability. Future research on the glass' other properties, such as mechanical strength,
microhardness, etc., will be done to see and confirm the possibility of its specific use.
Rebecca Padersky
Professor Kim McKim
Regulators of Mitotic Cohesion in Drosophila Meiotic Chromosome Segregation
Several proteins are known to regulate cohesion during mitotic segregation of chromosomes.
Among these proteins, CK1⍺, CK1 and San are believed to help regulate the cohesion between
chromosomes in meiosis as well. Therefore, mutations in these proteins are predicted to cause high
levels of nondisjunction, an inappropriate segregation of sister chromosomes, due to the inability to
regulate cohesion properly. We reduced the function of these proteins by doing RNAi knockdowns of
each gene with germline specific RNAi. Once each was created, flies were then crossed with an
appropriate promoter that would allow us to see if nondisjunction had occurred, and at what rate.
The CK1⍺ flies had very low fertility and lacked nondisjunction. This suggests that CK1⍺ may play a
role in mitosis and/or meiosis. Additionally, the CK1 flies showed low fertility, but showed 8.3%
nondisjunction with an NGTA promoter and 6.0% with a mat ⍺ promoter. This further supports that
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removing these proteins creates serious errors in meiosis. San has been looked at previously and
had very high levels of nondisjunction (23%), but the knockdown results did not correlate. Currently,
two new RNAi hairpins were successfully created for the San knockdown, which were both injected
into fly embryos which will be studied similarly in the near future. Our future plan is to look at the
oocytes from the flies to see the expression level of each gene as well as understand what
specifically is causing the nondisjunction.
Kush Patel
Professor Nicholas Bello
Validation of Anti-Obese Properties of Raspberry Ketone in Obese Mice
Excess body weight is a preventable risk factor for most diseases. Feeding suppression is often used
in laboratories to determine if a compound has anti-obesity properties. One problem with this type
of behavioral assessment is that compounds that can cause gastrointestinal illness also reduce
appetite. One way to distinguish appetitive from aversive mechanisms in feeding suppression is by
using a condition taste aversion (or avoidance) test (CTA). Previous studies in our lab have
determined that raspberry ketone (4-(p-hydroxyphenyl)-2-butanone) produced feeding suppression
and causes a CTA. However, exendin-4 (ex-4) is a glucagon-like peptide 1 (GLP-1) receptor agonist
used as an anti-obesity compound that also produces a CTA. In this study we planned on finding the
proper dosage of exendin-4 to do intraperitoneal injections on mice to reproduce a CTA. We
intraperitoneally injected 3 mice with 3.3 microliters (0.1 mg/kg) of ex-4 peptide with 0.3 mL of
saline and recorded food intakes on each mouse after 30 min, 60 minutes, 4 hours, and 24 hours.
We also injected the 3 mice with just 0.3mL saline and recorded food intakes at the same time
intervals to uncover the effects of ex-4 at the 0.100mg/kg dosage. Based on our research we found
that 0.1 mg/kg dose of ex-4 produced a significant reduction in chow intake. Currently, we are
preforming a CTA with saccharin + ex4 (CS+) and saccharin + saline (CS-). Data are forthcoming.
Daniel Peled
Professor Mehmet Uzumcu
Effects of Endocrine-Disrupting Chemicals on Rat Uteri
Animals and humans are exposed to endocrine-disrupting chemicals (EDCs) in the environment via
pharmaceuticals, plastics, and pesticides, among others. In this study, we examined methoxychlor
(MXC), a pesticide, and diethylstilbestrol (DES), a potent synthetic estrogen that used to be
administered to pregnant women to prevent miscarriages. These estrogen-mimicking EDCs cause a
range of reproductive diseases including uterine cancers, endometriosis, premature ovarian failure,
and overall reduced fertility. Recent studies from our lab showed that EDCs impact specific signaling
pathways, one of which is the PI3K signaling pathway that acts downstream of estrogen and IGF-1
signaling. To investigate the effects of MXC and DES on PI3K signaling in the uterus, animals were
(DMSO or oil) treatments from embryonic day 11 – postnatal day 7. Puberty, litter sizes, and estrous
cyclicity were observed and uteri were collected between 3-6 months of age. Histological and
immunohistochemical studies were conducted. Using ImageJ software, staining intensity from three
uterine regions (luminal and glandular epithelia, and stroma) was measured. It was found that the
luminal epithelial height was increased in the DES-treated uteri, suggesting uterine hypertrophy. In
addition, ESR-1 and PI3KR1 expression was increased in the mid and high doses. In contrast, PI3KR1
and ESR-1 expression was reduced in the in the low-dose-MXC treatment, but increased in the highdose-MXC, with no change in the luminal epithelial height. We also found that the effects of these
EDCs were epithelial compartment specific. With this information, we seek to further study EDCs’
effects on other members of the PI3K signaling pathway.
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Charles Rabolli
Professor Laura Fabris
Synthetic Parameters on the Optical Properties and Morphology of Gold Nanostars
Gold nanoparticles have recently jumped to the forefront of scientific research, as new syntheses
and new applications are being found to prove their unmatchable utility and durability. My project
focuses on the synthesis of gold nanostars, a new particle about which very little is known. Gold
nanostars have unique properties, which allow them to be utilized in various ways, from facilitating
drug delivery to cells, to enabling light propagation in ways seemingly contradicting classical optics.
I have studied the effects of varying parameters during the synthesis of nanostars, a seed-mediated
protocol, in an effort to better comprehend the role of each reagent in the synthesis. The seedmediated protocol I used prescribes the use of the following reagents: hydrogen tetrachloroaurate
trihydrate (HAuCl4·3H2O), hydrochloric acid (HCl), ascorbic acid, silver nitrate (AgNO3), and pre-made
12nm gold nanospheres acting as seeds. My research consisted of systematically altering the
concentrations of each reagent in the synthesis, one at a time, and, by analyzing the results via UVVis spectrophotometry, dynamic light scattering, and transmission electron microscopy, trying to
derive a comprehensive understanding of the role played by each reagent. To do so, I have analyzed
the size of the spherical core, the overall shape of the particles, and the morphology. My data have
the potential to be utilized by researchers because they are the first organized data collection that
correlates all these parameters to nanoparticle properties in a way that will be useful to other
researchers.
Dmitriy Ruckodanov
Professor Alexander Neimark
Synthesis of Transparent Conducting Electrodes with Silver Nanowires Embedded in a
Nafion Membrane
Indium Tin Oxide (ITO) is an inflexible and expensive, yet electrically efficient material used in
photovoltaic devices. Herein, we report on our group’s attempt to fabricate a Nafion membrane with
embedded silver nanowires (AgNWs) as a means of replacing ITO. Through measurements taken by
UV-vis spectrophotometer and multimeter, our goal is to create a flexible film with at least 95%
transmittance and minimal resistance respectively. We utilized several casting methods - blade
casting, drop casting, and spin coating - with the latter showing the greatest potential to achieve
maximum transmittance. As for the AgNWs, the ideal concentration by volume appears to be 5-10%.
Films with higher concentrations showed segregation of the nanowires and thus greatly reduced
transmittance and conductivity, so we used SDS surfactant to disperse the AgNWs. Additionally, we
impregnated the membranes with Zinc Oxide nanoparticles (ZnO NPs) so that they would possess an
n type semiconducting material. We were able to verify the effectiveness of our deposition
techniques through X-Ray Diffraction. Finally, we employed thermal annealing, mechanical pressing,
and treatment with Hydrogen Chloride (HCl) gas at increased temperatures as methods of further
decreasing the resistance of these films. With further experimentation, we hope to develop a film
that can feasibly replace ITO in photovoltaics.
Anastasia Ryssiouk
Professor Chirag Shah
SOCRATES 2.0: Bridging the Gap between Researchers and Social Media Data through Natural
Language Interactions
Social media can be a valuable source of information, through which researchers can make
discoveries about peoples’ lives, thoughts, activities, intentions, and sentiments. Our open-sourced
web platform, the SOcial and CRowdsourced AcTivities Extraction System (SOCRATES), allows
researchers to start exploring their topics of interest in social media, without labor and time
intensive programming. The modular architecture of SOCRATES allows researchers to collect,
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analyze, and visualize their data, which is collected from an array of social media APIs (Application
Program Interfaces). Furthermore, SOCRATES offers a natural language layer, which has made the
system more “user-friendly”. Through a process of asking questions related to the users’ interests
and requests for certain analyses, the system generates one sentence about a possible research
statement and provides the collected data and analysis results with one click. Ultimately, SOCRATES
will become “smart” and will be able to extract, analyze, and show data from minimal input from the
researcher and can thus become a catalyst for a researcher’s investigation.
Kevin Shen
Professor Ah-Ng Kong
Effects of Cryptotanshinone on the Nrf2-ARE Pathway
Chemicals found in traditional Chinese medicine, often used as an alternative to treat various
diseases, are being shown to have anti-cancer effects. One such compound, cryptotanshinone, is
derived from the Dan Shen plant, and I investigated it for the activation of the Nrf2 pathway, a wellknown anti-cancer response. I treated HepG2 cells (liver cancer) with different dosages of
cryptotanshinone for 24 hours in a 96-well plate, then given MTS, a substance that is metabolized by
living cells. This creates a spectrum, according to how many living cells are left. Using this, I settled
on the dosages of 10uM, 5uM, 1uM, and a control, and treated plates of cells in sets of 4. I then
harvested the RNA and protein from the cells and used them to perform tests such as qPCR, which is
a method of quantifying the amount of a specific strand of RNA (such as RNA corresponding to anticancer genes) and western blotting, a process used to visualize the concentration of a specific
protein, in order to check for activation of the Nrf2 pathway. I also performed Luciferase Assays, a
method of testing for the expression of certain genes through luminescence. Results have been
mixed, with some trials showing opposite trends to other trials. However, cryptotanshinone
undoubtedly has an effect on the Nrf2 pathway, as even though trends may differ, there are clear
effects. These results show that cryptotanshinone impacts the Nrf2 pathway in an unclear way, and
should be further researched to clarify its effects.
Jeffrey Sheu
Professor Qian Cai
Mechanism of Defective Autophagy in Alzheimer’s Disease
A growing body of evidence suggests that defects in the autophagic pathway contribute to the
development of neurodegenerative diseases including Alzheimer’s disease (AD). AD brains display
defective autophagy, showing massive accumulation of autophagic vacuoles (AVs) along dystrophic
and degenerating neurites. It remains largely unknown the mechanism underlying autophagy
dysfunction in AD neurons. A recent study revealed that late endosome-loaded dynein-Snapin motoradaptor complexes mediate the retrograde transport of autophagosomes upon their fusion with late
endosomes to form amphisomes in distal axons of neurons. In this study, we sought to address
whether Snapin mediates retrograde transport of AVs toward the soma where mature lysosomes are
mainly located. Using biochemical approaches, our results showed that snapin deficiency results in
abnormal accumulation of AVs in the snapin conditional knockout (cKO) mouse brains with selective
deletion of snapin in neurons of the frontal cortex and hippocampus regions. Our documented
studies show striking defects in Snapin-mediated and dynein motor-driven retrograde transport of
late endosomes in AD neurons. Here we also demonstrated impaired Snapin-dynein coupling in AD
patient brains. We will next test whether Snapin-dynein uncoupling and defective retrograde
transport impact the removal of distal AVs containing aggregated proteins and damaged
mitochondria and lead to autophagic stress in AD neurons. Addressing this issue will conceptually
advance our knowledge as to how the defective late endosome-lysosomal system contributes to
pathological mechanisms underlying AD-linked neurodegeneration.
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Kate Sohn
Professor Gary Aston Jones
Effects of Exogenous Administration of Oxytocin on Initial Abstinence from Cocaine
The first day of abstinence from cocaine (Extinction Day 1, ED1) is considered a stressful event
resulting in drug-seeking and relapse (Calipari 2014). There are sex differences in ED1 drug-seeking,
where females seek more drug than do males (Feltenstein et al. 2011). The expression of Oxytocin
(OT) originating in the Paraventricular Nucleus (PVN) is sexually dimorphic and may reduce stress
(Rich and Caldwell 2015). We hypothesized that there may be differences in ED1 expression of OT,
and that administration of OT may reduce drug seeking. Rats were trained to self-administer cocaine
via lever presses. After 10 days of >10 lever presses, rats were tested for drug-seeking on ED1 and
euthanized. Brains were analyzed via immunohistochemistry for Fos+ (an indicator of neuronal
activity) and OT expression. OTC/Fos+ expression was reduced on ED1 compared to controls in the
PVN. We then hypothesized that administration of OT would influence drug seeking on ED1.
Oxytocin treatment (1mg/kg) resulted in a significant decrease in the number of lever presses on
ED1 for both male and female rats. Thus, increasing OT levels by exogenous administration is
effective in treating the drug-seeking phenotype. Future direction would include extending the
experiment to test the long-term effects of oxytocin on maintaining abstinence from a cocaine
addiction.
Divya Srivastava
Professor Ann Marie Carlton
Surface Validation of Space-Based CO2 Measurements
Greenhouse gases such as carbon dioxide have been rapidly warming the Earth since the Industrial
Age. Carbon sinks absorb carbon dioxide in the atmosphere through the carbon cycle, but human
combustion of fossil fuels is releasing more carbon than the sinks are able to absorb. While we
generally know what absorbs the atmospheric carbon, details as to where major carbon sinks are
located and how much they are absorbing are unknown. Measurements of CO2 taken at the surface
level of the earth have high resolution, but lack large-scale coverage. NASA’s Orbiting Carbon
Observatory-2 (OCO-2) was launched into orbit as the first satellite to take global, high resolution,
space-based measurements to characterize these sinks (and sources) on a regional scale. Because it
is the first of its kind, the data gathered from the satellite must be validated with surface level
readings. The objective of this project is to validate OCO-2’s data by bridging the gap between
ground-based and space-based approaches. This was done by creating a standard operating
procedure that utilized a drone and carbon dioxide sensors to take the CO2 levels in the lower
troposphere. Here we show that the OCO-2 is accurate in its readings, and demonstrate a proof of
concept validation experiment that can be applied to any space-based observatory. Using this
procedure and satellite, we can increase our understanding of carbon sinks and sources so that we
can better advise on how to handle global warming or other environmental policies that can be put
into place. Possible actions include strategically applying reforestation to aid carbon sinks, or
applying SOPs to alternate devices.
Dragos Stemate
Professor Siobain Duffy
Bacteriophage Φ6's Novel Host Range Mutations
Bacteriophages are viruses that only attack bacteria and have the potential to cure bacterial
infectious diseases. They can also serve as model viruses for studying the evolution and biology of
human viruses. The double-stranded RNA Pseudomonas bacteriophage phi6 is an excellent model
for fast-evolving RNA viruses like influenza and rotavirus. Studying the different kinds of mutations
phi6 can acquire to infect a novel host will give insights into their adaptability in novel
environments, and a better understanding of how phi6 expands its host range will help improve
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modeling and surveillance of emerging and epidemic-causing virus that affect many people every
year. Phi6 were raised on their original host, Pseudomonas syringae pv. phaseolicola, to obtain the
stock solutions, from which spontaneous host range mutants on Pseudomonas syringae pv.
atrofaciens (PA) were isolated. The P3 host attachment gene, which has been previously associated
with all known host range mutations, of all isolated mutants were sequenced and compared to the
ancestral sequence. We thus characterized the mutational spectrum of host range mutation of phi6
on the novel host PA. The regions of P3 implicated in expanded host range onto PA differ from those
previously noted for another novel host, Pseudomonas pseudoalcaligenes ERA and gives insight on
the diversity of options available to fast evolving viruses.
Xiaoou Su
Professor Melchi Michel
Visual Memory Capacity for Central and Peripheral Objects
Visual working memory (VWM) is defined as the ability to store and to actively manipulate relevant
information for a given task (Luck, 2008). We use VWM to complete countless natural tasks, such as
copy diagrams from a classroom blackboard, and keeping track of your place on a page of text, or
of the cursor is on your computer screen. These tasks require that we hold on to and combine
information across visual glances and changes in gaze. Although there exists a substantial body of
research suggesting that VWM capacity is limited (Luck, 2008) and we can quantify VWM this
capacity by looking at the measuring the ability of observers to faithfully retain certain visual
features of objects, such as orientation, shape, color, size across short delays, the mechanisms of
VWM remain opaque and many open questions remain unanswered. The current research focuses on
one of these outstanding questions: How does VWM capacity vary as a function of memory load and
retinal eccentricity? We use a change detection task, which is modeled after Sims, Jacobs, & Knill
(2012). In our task, observers are required to judge the orientation change of the stimuli by
comparing the sample array and the test array. Both the number of targets and retinal eccentricity
are manipulated across different blocks. We used an adaptive procedure to determine the
orientation change depending on the observers’ performance and measured the orientation change
threshold. Preliminary results from our study support published accounts in showing that the fidelity
and accuracy of remembered features decreases significantly as a function of increasing memory
load. However, we did not find any consistent effects of retinal eccentricity on performance. This
result, if it holds, is important because it provides the first evidence that an important but implicit
assumption of existing VWM models—that VMW does not vary systematically as a function of retinal
eccentricity—is true.
Patrick Tawadros
Professor Mimi Phan
Effects of Statins on Auditory Memories and Imitative Learning
In the past 30 years, obesity and corollary high cholesterol have become severe issues in children
and adolescents. The American Academy of Pediatrics has recently suggested the use of statins for
children who struggle to regulate their cholesterol levels through diet and exercise alone. However,
prolonged statin treatment may potentially result in a decrease in brain cholesterol, negatively
affecting the subject cognitively and neurologically. In this project, we will use an animal model to
measure how statins affect learning and memory in juveniles. For this study, we will breed birds in
order to produce juveniles. Approximately 45 days after birth, the male juveniles begin to imitate
and create their songs by listening to their fathers and their respective tutor songs. At this time, the
juveniles will then be divided into three groups. The first group will receive a high dosage of statins,
the second group will receive a low dosage of statins, and the third group will receive a water vehicle
as the control. To measure the effects of statins on learning and memory, we will study how the
birds learn and imitate their tutor songs. By measuring vocal imitation, we can determine whether or
not statins positively or negatively affect learning and memory. Ultimately, we expect that the statins
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will impair learning and memory at behavioral and neurophysiological levels. If statins do, in fact,
have a negative effect, then, statin treatment should be prescribed and administered to children and
adolescents with a much larger degree of caution.
Nicholas Townsend Haas
Professor Marianthi Ierapetritou
Advanced Model Predictive Feedforward/Feedback Control of a Tablet Press
The tablet press is one of the most critical but least understood unit operations involved in both
batch and continuous tablet manufacturing. Variables such as raw material characteristics, feeder
level, and shear history can all have significant impact on powder bulk density, lubricity and, by
extension, on tablet quality attributes. Therefore, an efficient advanced control system is highly
desirable. In industry, the Proportional Integral Derivative (PID) controller is the most common
controller used to accomplish this. However, a PID may not be able to deal with large process delays
and interactions in a system efficiently, and its parameters must be precisely tuned in order to
eliminate the error between a variable’s set point and output. Model Predictive Control (MPC)
remedies these problems by creating a mathematical model of the system and selecting the output
that optimizes the process as a whole. To demonstrate the effectiveness of MPC over PID, we use a
pre-existing feedforward/feedback simulation in Simulink that includes two master control loops for
tablet weight and hardness, a slave feedback loop controlling the force applied to each tablet, and a
feedforward loop that monitors granulation density. In this project, the PID controllers have been
replaced with a single two dimensional MPC. Graphs of the set point and output for critical variables
for both scenarios (with MPC and with PID) have been compared. We find that after initial high
overshoot, the MPC regulated simulation reaches the set point more quickly than the PID regulated
simulation.
Tyler Volpe
Professor Joachim Kohn
Characterization of Cell Infiltration to Polymeric Scaffolds
The regeneration of large tissue defects is still a clinical challenge. Current approaches include
grafts and synthetic polymeric scaffolds loaded with patients’ cells, but these can be timeconsuming and patient-specific. We focused on an alternative approach to optimally design scaffolds
that can promote tissue regeneration by harnessing the intrinsic regenerative capacity of the human
body. The ideal synthetic scaffolds attract favorable cell infiltration from the host tissue to support
tissue regeneration. The purpose of this study is to evaluate the effects of the chemical composition
of polymers on cell infiltration into scaffolds in vivo. The cell infiltrations to scaffolds made of
polymers with varying hydrophilic properties and degradability were analyzed. Scaffolds were
implanted subcutaneously in mice. After 3 weeks, the scaffolds were explanted and fixed. Cell
infiltration, which includes numbers of cells as well as types of cells, was analyzed by histology and
immunofluorescent staining (IF). Significantly more cells infiltrated to scaffolds made of the fastdegrading and hydrophobic polymer (E1001(1k)) compared to the slow-degrading and hydrophilic
polymer (E0006(1k)). The morphologies of cells are also different among explanted
scaffolds. Using antibodies specific to subpopulations of macrophages and to fibroblasts, IF
staining showed that more M1 (pro-inflammatory macrophages), fewer fibroblasts, and fewer M2
(anti-inflammatory macrophages) were present in E0006(1k) scaffolds compared to E1001(1k). Our
preliminary data demonstrated that the composition of the scaffold profoundly influences cell
infiltration in vivo.
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Yuwen Wang
Professor Kevin Chen
Compare genome segmentations derived from different methods
Some Single-Nucleotide Polymorphisms (SNPs) on the human genome are associated with the
expression level of genes, which is potentially related to certain diseases. Identifying interesting
SNPs are of great value in controlling and curing the diseases. However, due to the large amount of
SNPs and genes, testing correlations between every SNP and every gene will introduce substantial
multiple testing errors. Currently, people only test SNPs that locate near the genes. However, this
procedure has the risk of overlooking the influence of interesting SNPs that locate far away from
genes. One way to balance between multiple testing error and SNPs to be considered is to
concentrate on SNPs in enhancers and genes, since SNPs that are enriched in enhancers are likely to
be functional. On the analytical side, this work compares enhancer predictions from Spectacle and
that from eRNA method. The accuracy of two enhancer predictions is measured based on SNPs
enrichment and number of interactions with promoters. On the methodological side, this work
considers an implementation of simultaneous rank-one tensor decomposition method applied to
recover the parameters in Hidden Markov Model (HMM). HMM is the model that has been shown to
successfully give statistical model for genome annotations. The new method is expected to give
more accurate predictions about enhancers. Further analysis about its prediction accuracy in terms
of SNPs enrichment and interactions will be conducted if time permits.
Jonah Williams
Professor Charles Dismukes
Responses to Donor-Side Bromide-for-Chloride Substitution in the Water-Oxidizing Complex of PSII in
vivo
Photosynthetic water-oxidation is a process responsible for almost all present life on Earth. It has
also provided the fossil fuels which have driven our way of life and will likely be the source of our
renewable energy thereafter. Understanding the structure and function of photosystem II (PSII) is
essential for us to utilize its unique properties in the future. The purpose of this investigation is to
uncover the functionality of the two chloride ions positioned in PSII near the water-oxidizing
complex (WOC). The conventional hypothesis is that chloride is involved in channeling protons out
of the WOC and thus helps establish a proton gradient across the thylakoid membrane. We examine
the function of this ion through the use of in vivo bromine-for-chlorine atomic substitution in the
cyanobacterium Thermosynechococcus elongatus CP-47. By examining the effects of this bromide
(which is a larger ion and a softer, weaker base) substitution on oxygen evolution, charge
recombination, and Kok cycling, we were able get a better picture of chloride’s function. By
removing acceptor side limitations (through the use of exogenous quinones), we can observe that
bromide-substituted PSII systems suffer inactivation much faster than those seen in native (chloride)
culture if only constrained by the properties of the donor side. Additionally, Kok cycling has shown
that bromide culture has fewer double-hit transitions and more back-transitions than the control,
suggesting decreased proton removal from the WOC. Interestingly, rate-oxygen evolution analysis
has shown that bromide-grown culture responds less directly to energy input (in the form of heat),
indicating that this system is constrained by the ability to remove product (protons) rather than
energy required to produce said product.
Jenny Xu
Professor Eric Lam
Characterizing the Interaction between Duckweeds and Microbes in Nutrient-Rich Aquatic
Environments
Duckweeds are aquatic plant species that have the potential to become a useful source of biomass
for fuel and livestock feed. In addition to containing high levels of protein and starch, duckweeds
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clean wastewater as they grow by removing excess nitrogen and phosphate. Previous research has
shown that duckweed associated bacteria (DABs) aid in the growth of duckweed. Therefore it is
important to investigate what bacteria interact with duckweed collected from various environments.
Duckweed tissue and water samples were collected from the Princeton Meadows municipal
wastewater treatment plant, Passion Puddle at Rutgers, and a water retainment pond of a private
home site (Caldwell House) in a rural part of New Jersey. The duckweed tissue from each location
was genotyped for identification, maintained on nutrient media, and sterilized. Bacteria were
isolated from duckweed tissues for future identification and functional analysis. Genotyping results
thus far indicate that the duckweed collected from Princeton Meadows is Landoltia punctata.
Duckweed collected from the Passion Puddle is either Lemna japonica or Lemna minor. A method
has been optimized for maintaining duckweed tissue on nutrient media that includes sterilizing the
tissue before growing it in liquid cultures. Future experiments are being carried out to identify the
bacteria community members within the water samples as well as the bacteria phyla that are
enriched on the surface as well as within the duckweed tissue.
Michelle Yam
Professor Nicole Fahrenfeld
Improved Understanding of Contaminant Fluxes During Wet Weather Flows
Antibiotic resistance is a serious concern to public health because 2 million people are sickened and
23,000 people die of antibiotic resistant infections in the US each year. The purpose of this research
is to study antibiotic resistant genes (ARG) found in New Jersey surface water. The Fahrenfeld
Laboratory worked on two projects to study the fate of ARG in the urban water environment. The
first objective is to investigate the flux of ARG from combined sewer overflows across a storm event.
Water samples will be analyzed for total suspended solids and total organic carbon. To understand
the effectiveness of a Green disinfectant at eliminating ARG in CSO effluent, a disinfection study with
peracetic acid (PAA) will be performed. CSO samples will be treated with three different
concentrations of PAA at three different time intervals. Then, we will analyze the levels of ARG in the
water to determine which concentration of PAA and at which time interval would be most effective at
destroying ARG. The second objective is to determine the seasonal variation in ARG in wastewater
influent, wastewater effluent, and adjacent river water. qPCR will be used to determine the quantity
of ARG throughout this study. As a result, we may see a change in concentrations of ARG at different
times of the year. The ultimate goal of this research is to improve understanding of urban sources of
ARG and develop potential mitigation strategies.
Rachel Yang
Professor Fuat Celik
Low Pressure Flame Synthesized TiO2 Nanoparticles for Biomass Reforming
Finding renewable and sustainable energy sources with clean emissions is increasingly important
and hydrogen is at the forefront of alternative energy. To produce hydrogen gas, we focus on the
photocatalytic reforming of methanol, a simplified model for biomass, over modified TiO2
nanoparticles. TiO2 is a metal oxide semiconductor with high photocatalytic activity and stability
under irradiation, but with a band gap of 3.2 eV (anatase polymorph), is only effective in the UV
range. However, solar radiation is only 4% UV whereas 43% is visible light. In order to use the whole
visible light spectrum, we aim to lower the band gap of TiO2 to 1.7 eV. We investigate the low
pressure flame synthesis method that produces carbon-doped TiO2 with band gaps lower than that
of conventionally prepared anatase. This method uses a chamber filled with pre-mixed gases (H2,
N2, C2H4, and O2) at 20 torr with titanium isopropoxide (TTIP) as the TiO2 precursor. The flame
synthesized material has been found to have the same structure as anatase via X-ray diffraction
(XRD) analysis. After using the low pressure flame synthesis method to secure consistently viable
sample, we will find its band gap via UV-Vis spectroscopy analysis and test its capability as a
photocatalyst in reforming methanol via gas chromatography.
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