Stockton University NAMS Research Symposium Abstracts – Spring 2013 [Not This Year’s Abstracts]

1. Stormwater Design and Planning on a Barrier Island (Ocean City, NJ)

Adams, Robert

Faculty Advisors: Baker, Tracey; and Moscovici, Dan

Environmental Science

Recent storm events have brought attention to stormwater induced flooding in the Merion Park neighborhood in Ocean City, NJ. An analysis of existing infrastructure has exposed multiple design and planning failures as a result of developing at low elevations. A stormwater discharge analysis was carried out using the Natural Resource Conservation Service (NRCS) Rational Method (TR-55) and changes in impervious parcel cover were considered. A comparison of tide heights to a known outfall elevation was looked at and compared to the calculated culvert size for design feasibility. Out of this assessment, recommendations were offered utilizing changes in parcel impervious cover and other technologies.

2. Understanding the binding interaction of Caspase-1 kinase to control acute Inflammation of Orthodontic Appliances

Augello, Ashleigh; Benjamin III, Earl; and Benjamin, Ellis


Orthodontics is a branch of dentistry that uses tensile force from intraoral or extraoral orthodontic appliances to resolve dental malocclusions. The use of tensile force seeks to remodel periodontal ligament and alveolar bone however this process initiates acute inflammation and necrotic conditions in the periodontium. This acute inflammation arises through multiple mechanisms including that of the inflammasome conversion of pro- interleukin 1β (IL-1β) to the active form. Inhibition of one major protein found in the inflammasome, Caspase-1, has been found to block the activation of IL-1beta thereby blocking the acute inflammation initiated by appliance tightening. This research sought to understand binding interaction of pharmaceuticals to the protein kinase functionality of the Caspase-1. 22 crystal structures of the kinase of the Caspase-1 protein were docked using IGEMDock to FDA, Alkaloids, Lactams, Lactones, Flavinoids, Sulfanilamide, Cyclic Imides, and NSAIDs drugs to determine structural correlation for the most effective binders. Structural similarities were determined with IGEMDock and vROCS and partition coefficient was determined using DRAGON program. This data found a cluster of approximately 10 drugs to preferentially bind to the Caspase-1 kinase for use as targeted anti-inflammatory treatments.

3. Characterization of Marine Plankton in Great Bay, New Jersey

Berezin , Maria; and Luke, Tara H.


Marine plankton play a significant role in the food webs of shallow marine and brackish communities. Characterization of these communities can result in a more detailed understanding of the health of an ecosystem, as well as lead to the discovery of species that have not been described in a particular area. In addition, characterization of these communities globally can result in a better understanding of species distribution. Sea water samples were collected in Great Bay, New Jersey and DNA was extracted. After extraction of DNA from the samples, polymerase chain reaction (PCR), gel electrophoresis, and DNA sequencing were performed. DNA sequences were then compared to the sequences of known organisms found by using the BLAST algorithm.. DNA sequence alignments and Phylogenetic trees were constructed using MEGA 5.10 software, and analyzed. Of the samples collected, one contains a nucleotide sequence more closely related to copepods than to other organisms.

4. “Flipping the Classroom” In An Introductory Physics Classroom Using Collaborative In-Class Problem Solving Exercises

Bland, Jared; and Trout, Joseph

Applied Physics

In this pilot project, one hour of lecture time was replaced with one hour of in-class assignments, which groups of students collaborated on. These in-class assignments consisted of problems or projects selected for the calculus-based introductory physics students. The first problem was at a level of difficulty that the majority of the students could complete with a small to moderate amount of difficulty. Each successive problem was increasingly more difficult, the last problem being having a level of difficulty that was beyond the capabilities of the majority of the students and required some instructor intervention. The students were free to choose their own groups. Students were encouraged to interact and help each other understand. The success of the in-class exercises were measured using pre-tests and post-tests. The pre-test and post-test were completed by each student independently. Statistics were also compiled on each student’s attendance record and the amount of time spent reading and studying, as reported by the student. Statistics were also completed on the student responses when asked if they had sufficient time to complete the pre-test and post-test and if they would have completed the test with the correct answers if they had more time. The pre-tests and post-tests were not used in the computation of the grades of the students.

5. Paleomagnetism of Mesozoic Basalts in the Pomperaug Basin, Connecticut

Cesta, Jason M.; and Hozik, Michael J.


The Pomperaug Basin is a small Mesozoic basin in west-central Connecticut, filled with sedimentary rocks separated by three lava flows: South Brook, Orenaug, and East Hill. These lava flows are generally considered to be of the same age as the three lava flows in the Hartford/Deerfield Basin and the Newark Basin. Paleomagnetic work in the Hartford/Deerfield, Newark, and Culpeper Basins indicates that one of the lava flows (middle flow in the Hartford and Newark Basins, only flow in the Deerfield Basin, and upper flow in the Culpeper Basin) has a magnetic inclination that is shallower than that of the other flows. They also have a corresponding paleomagnetic pole at a lower latitude than those for the other units. These data suggest a magnetic excursion event during the short interval of time when these flows were cooling. Preliminary data from the lava flows in the Pomperaug Basin show a similar relationship, supporting the hypothesis that the Pomperaug Basin flows are correlative with the lava flows in the other basins, and adds weight to the suggestion of a magnetic excursion in the early Jurassic.

6. Geoarchaeology: Origin of Abandoned Meander Sediments, Río Verde, Oaxaca, Mexico by Mineralogical Analysis

Cesta, Jason M.1; Severs, Matthew J.1; Mueller, Raymond G.1; and Joyce, Arthur A.2

1Geology; 2Department of Anthropology, University of Colorado, Boulder, Boulder, CO

The Río Verde is one of the largest rivers on Mexico’s west coast. Its upper drainage contains the important archaeological site of Monte Alban among many others. The lower portion of the drainage contains the similarly important Río Viejo site. Previous geoarchaeological research showed that the river shifted course and altered the environment over the last few millennia. The Río Verde has shifted from the west to its present location but doesn’t appear to have ever shifted to the east. At different periods in time the archaeology of the east side of the river has differed from the west side. One question is whether these temporal changes were influenced by changes in the position of the Río Verde. A recent rise in the watertable caused by a new irrigation project has revealed many buried meanders east of the river. Sourcing these abandoned meander sediments offers insights to the archaeology and geomorphological evolution of the region. Sand samples were collected by bucket auger from the center and on either side of five meanders. Samples were also collected from modern depositional environments, including the Río Verde, Río San Francisco, and Río Yutanana. Mineralogical analysis of both grain shape and mineral species provides a means to determine the origin of the eastern meanders. Local streams drain only two main bedrock types, granite and grano-diorite with small areas of gneiss. On the other hand the Río Verde drains multiple bedrock types, most notably sedimentary and high grade metamorphics. Observation and measurement of minerals provides answers to the origin of the meanders. Mineralogy of the sediments was determined by oil immersion microscopy. Mineralogy of the buried meander sediments was primarily quartz, feldspars, muscovite, biotite, and amphibole, with notable percentages of volcanic glass. Accessory minerals include zircon, chlorite, and various opaque minerals. Mineral assemblages and compositional percentages observed within the meander scar sediments display similarities to those observed in sediments of the Modern Río Verde. Preliminary mineralogical analysis of the meander scar sediments alludes to origins relating to the Río Verde, and not those of local streams.

7. Survey and Analysis of Microgobius thalassinus Population Increase in a South Jersey Estuary: A Response to Climate Change?

Christensen, Dana; Able, Ken; Hagan, Roland; and Grothues, Tom


Populations potentially experience range shifts when the physical conditions of their preferred habitat undergoes a change. Along the coast of Southern New Jersey different types of southern fish species have been increasing in abundance while northern fish species have been diminishing with respect to their original known distributions. These population shifts have been associated with long term climate change. The green goby fish, Microgobius thalassinus is an example of a southern species in which larval individuals have been identified in New Jersey since 2002. This species had not been previously found in juvenile form, or in adult form since ichthyoplankton sampling started at Rutgers Marine Field Station in 1989. According to a majority of the literature this species northern limit is the Chesapeake Bay where it’s preferred natural habitat and spawning habitats are low salinity estuaries. The larval data, coupled with presence of adults indicates that this species may currently inhabit areas of the Southern New Jersey coast. Rutgers University Marine Field Station (RUMFS) has gathered weekly quantitive data from ichthyoplankton sampling since 1989 at Little Sheepshead Bridge where plankton nets are used to capture larval fish in Tuckerton, NJ. Great Bay is connected to Little Egg Inlet by Sheepshead Bridge where water temperatures and tidal fluctuations are relatively consistent and well understood. Because sampling is done on Sheepshead Bridge during flood tides, the larva gathered represents the species that utilize the estuary as at some point during their lifespan. From these samples larval fish are continually collected, measured and identified. Multiple variables are recorded generating the ability to observe and identify multiple factors about various species that inhabit the region including but not limited to: increase or decrease in abundance, early or late spawning periods, elongated spawning periods, and or increase or decrease in larval sizes. Therefore, long term changes for each species are represented in great detail by the respective gathered data. Potential correlations between factors within this data, can be utilized, specifically trends found over time relating larval M.thalassinus presence to long term temperature changes. Adult individuals have also been captured during trawling which contribute to the survey. In order to identify correlations between population increase and climate change, temperature data must be gathered, prepared and analyzed. The System Wide Monitoring Program (SWMP) consists of a network of buoys which record temperature, salinity, nutrient content, dissolved oxygen content as well as turbidity as often as every fifteen minutes at various locations in the Great Bay- Little Egg harbor Estuary. The SWMP data is unique to marine scientists due to the buoy placement successively up the river from the inlet, it is also of importance to those scientists in need of large time series data sets to observe changes over time in respect to the marine environment. At this point the SWMP data is currently being prepared using computational methods. This time series will be used to identify correlations between green goby population change and a variety of variables (including temperature). Sampling for the gobies through ichthyoplankton sampling, identification and trawling will continue at Rutgers marine field station. Due to the nature of this project and the ability for expansion due to a large growing data set as well as accessible time series data, multiple factors and multiple species will be analyzed for correlation. The final analysis will include population survey and potential correlations between the other main species of goby found within the estuary: Gobiosoma bosc, the naked goby and Gobiosoma ginsburgi, the Ginsburg goby.

8. Controlling Cell Fate: Genetic Determinants of Synthetic Pseudohyphal Growth

Ciccaglione, Kerri; and Law, Michael J.

Biology, Biotechnology concentration; UMDNJ, Molecular Biology

Cell fate decisions require cells to first recognize multiple extracellular stimuli, and then respond in a manner that is appropriate. Central to these responses are highly regulated transcriptional responses. In budding yeast Saccharomyces cerevisiae, two cellular differentiation pathways are controlled by nutritional response. The first, pseudohyphal differentiation, is induced when yeast are cultured on medium containing limited nitrogen. The second, meiosis, is induced when yeast are cultured without fermentable carbon and nitrogen. These two differentiation pathways share similar response to nutrition, as evidenced by partially overlapping transcriptional cascades. To determine how RNA polymerase is targeted to specific transcripts, a yeast two-hybrid analysis was performed using a component of the RNA mediator complex, UME3, as bait. This screen identified KDM5, a histone demethylase, as an interacting partner of UME3. To understand the nature of this relationship, yeast strains were constructed lacking both KDM5 and UME3. Interestingly, these mutant yeast exhibited pseudohyphal growth even in rich media, to yield a “synthetic pseudohyphal” phenotype. To identify the genetic targets of these mutants, we employed a high copy suppressor screen. In this screen, genomic yeast DNA is digested into random pieces and inserted into a multiple copy plasmid. Approximately 4,300 yeast transformants were screened for pseudohyphal suppression which yielded 17 plasmids that contain genomic suppressors. Of these, 5 plasmids were sequenced to identify potential genes that suppress the phenotype and revealed that there are some regions of overlap, supporting saturation of the screen. Currently, the identified genes are being tested individually to identify suppressors.

9. Role of Sample Preparation in In Vitro Cytotoxicity Responses to Silver Nanoparticles

Clendaniel, Alicea; Kumar, Girish; Degheidy, Heba; Casey, Brendan; and Goering, Peter

Faculty Advisor: Moscovici, Dan


Metallic nanoparticles readily agglomerate in aqueous media and this effect can influence their physical properties and in vitro biological responses. The goal of this study was to: 1) compare effects of cell culture medium containing 10% FBS and DI water as suspension vehicles on AgNP size and agglomeration, and 2) compare effects of pre-mixing of medium and AgNPs on their biological responses in L-929 fibroblasts compared to direct addition of nanoparticles to the cells. To assess the effects of premixing on agglomeration, AgNPs were pre-mixed with cell culture medium or DI water for 1 min, or 1, 5, 24, or 120 hr. Results of dynamic light scattering analysis showed that pre-mixing AgNPs with medium maintained particle dispersion better than DI water. The hydrodynamic diameter of AgNPs increased proportionally to the pre-mixing time. AgNP agglomeration was size-dependent; 10 nm AgNPs agglomerated more readily than 100 nm and 200 nm particles. To assess the effects of premixing on biological responses, AgNPs pre-mixed with cell culture medium for 1 min, or 1, 5, or 24 hr were added to L-929 fibroblasts, or were added to the cells without premixing. After 24 hr exposure, cell viability was assessed by using the standard MTT assay. After 4 and 24 hr exposures, the degree of cell necrosis (via 7 AAD dye) and apoptosis (via Annexin V dye) was assessed using flow cytometry. AgNPs produced a mass concentration (μg/ml) dependent decrease in MTT reduction. Pre-mixing of AgNPs with cell culture medium did not affect cell viability compared to controls; however, AgNPs added directly to the media without premixing were cytotoxic. The degree of necrosis and apoptosis of L-929 cells when exposed to AgNPs depended on mass concentration, exposure time, and size of AgNPs. Cells treated with 10 nm particles at 50 μg/ml showed 22-fold and 33-fold increases in the percentage of apoptotic and necrotic cells, respectively, after 24 hr. Thus, the data show that different sample preparation for AgNPs can affect particle agglomeration and biological responses. Note: this research was completed during an internship with the food and drug administration.

10. Geochemical Investigation of Anatectic Melts in Low-Pressure Migmatites

Dubnansky, Michael; Favorito, Daniel; Price, Patrick; Makin, Sarah; and Severs, Matthew J.


The study of melt inclusions is vital to understanding igneous processes. Inclusions trap and preserve melts prior to subsequent processes including crystallization, diffusion, and any potential disequilibria the crystals may be subjected to, as well as chemical weathering or alteration at the surface. In many cases, they also retain their concentration of volatile elements. These advantages make melt inclusions highly valuable in studying the evolution of magmatic systems. Although they have been utilized extensively in volcanic systems and in some felsic plutonic systems, recent studies have suggested they may be found in other plutonic rocks and potentially in metamorphic rocks undergoing partial melting. Questions remain regarding the latter due to the difficulty in distinguishing between silicate melts and Si-rich hydrothermal fluids at high pressures. Additionally, these melt inclusions are usually completely crystallized and are difficult to identify. The focus of this study aims at finding and determining the geochemistry of melt inclusions in low-pressure migmatites. These trapped melts would thus represent the exact conditions present at the time of anatexis. Migmatites are unusual rocks as they are partially melted and represent a transition between igneous and metamorphic. Samples were collected over the course of a week from previously described field locations in New Hampshire and Maine. This project will explore the geochemistry and petrogenesis during the initial stages of anatexis. Homogenization experiments of potential melt inclusions will determine whether they truly represent melts that subsequently crystallized or trapped solids. Samples were crushed and separated to identify potential melt inclusion-bearing crystals of peritectic minerals such as garnet, cordierite, and spinel that are preserved over the course of melting and subsequent crystallization. Finally, the geochemistry of both the inclusions and their host crystals will be determined via electron microprobe that will allow for in-situ analysis of major and minor elements.

11. Impacts of Derelict Crab Traps in the Mullica River-Great Bay Estuary: Patterns of bycatch and progress towards preventing future trap loss

Duffy1, Maureen; Berezin2, Maria; and Friedman3, Duane

Faculty Advisors: Sullivan, Mark2; Evert, Steve3; and Straub, Peter2

1Marine Science & Environmental Science, 2Biology, 3Marine Science

Every year hundreds of crab traps are lost in the Mullica River–Great Bay Estuary (New Jersey) presumably due to recreational boat traffic and seasonal storms. These derelict or “ghost” pots may continue to capture marine life and adversely affect local populations long after their surface buoy connections have been lost. A Klein 3900 side-scan sonar system was used to locate derelict pots in the Mullica River-Great Bay Estuary. With the help of local commercial watermen, derelict traps are in the process of being removed from various habitats within the estuary. The objectives of this project are to (1) inventory bycatch species identified from recovered ghost pots (2) relate patterns of bycatch to trap variables such as location, condition, status of escape vents in a GIS framework (3) propose initial solutions to help mitigate future trap loss. This work is important for determining the variables that best predict the causes and locations of future loss. Reducing the frequency of trap loss will help sustain local estuarine populations, as well as benefit the fishers that make a living in these systems.

12. Amphidromous Fishes of Puerto Rico: Post Larval Morphology and Recruitment Timing

Duffy1, Maureen; and Engman2, Augustin

Faculty Advisor: Sullivan, Mark

Marine Science Program

A large number of the freshwater fish species that occur on oceanic tropical islands have an amphidromous life cycle. These fish species are important to tropical island stream ecosystems and to the people live on the islands. They are also important components of biodiversity and they play a role in structuring stream ecosystems. There are five native amphidromous species of freshwater fish in Puerto Rico, the Mountain Mullet (Agonostomus monticola), River goby (Awaous banana), Sirajo goby (Sicydium plumieri), Bigmouth sleeper (Gobiomorus dormitor), and Smallscaled spinycheek sleeper(Eleotris perniger). There has been little research on the early life histories of the amphidromous fish species of the island of Puerto Rico. Three species of Puerto Rico amphidromous fishes were raised in a laboratory setting from the time of recruitment to a juvenile phase in order to document the morphological changes that occur over this period of their life history, the relationship of the lunar cycle to post larval migration was also investigate. In the two rivers were this study was conducted more migrating post larvae were captured during the last quarter of the lunar cycle than other cycles. The ability to identify the post larvae of amphidromous species of Puerto Rico and knowledge of recruitment timing will allow for further ecological studies of these fishes as well as improve fisheries management practices.

13. Cloning, Sequencing, and Analysis of the ITS region of the Northern Star Coral (Astrangia poculata) from Coastal New Jersey

Fasy, Brian; Joyal, Sara; and Luke, Tara H.


The purpose of this research was to observe variation in the internal transcribed spacer (ITS) region of Northern Star Coral. Coral samples were collected in Great Bay, New Jersey in September of 2011 using a bottom grab. Genomic DNA was extracted from individual polyps, and PCR reactions were performed. The PCR products were cloned and four individual polyps were sequenced.These sequences were compared to other known sequences in Genbank using BLAST, aligned, and analyzed. The Northern Star coral was similar to other corals, but not identical in its ITS region.

14. Geochemical Analysis of Melt Generation in Maine Migmatites

Favorito, Daniel A.; Price, Patrick F.; Makin, Sarah A.; Dubnansky, Michael G.; and Severs, Matthew J.


Migmatites are rocks that represent the first occurrence of crustal anatexis in orogenic events and preserve characteristics of both their metamorphic precursors and the products of their melting. The presence of migmatites has important implications for how mountains and the continental crust are created during orogenies. However, many questions concerning these processes are not fully understood, including the actual mechanism for heating such rocks and the nature of the geochemistry of the first stages of anatexis. The geochemistry is particularly problematic because the leucosome that represents the “molten” portion of the migmatite may have been subjected to fractional crystallization and re-crystallization processes. As a result, bulk rock studies of migmatites may not necessarily indicate what is happening over the course of melting from beginning to end. This study aims at addressing this question by conducting geochemical microanalysis of a group of migmatites collected from the Tumbledown and Weld Anatectic Domains, Maine. Bulk rock geochemistry of these samples has been determined by previous authors, but there is a lack of microanalytical data to compare and constrain the results of melting models. Thin sections were made in order to study the petrography of the samples and subsequent electron microprobe analysis (EPMA) was conducted in order to determine the exact chemical composition of various minerals within the samples and examine chemical zonation of these minerals as well. Using this data, specific mechanisms responsible for melt generation and variations over time were determined.

15. Hatching Trends in Coturnix japonica

Fisher, Timothy; Wessels, Jessica; Mcveigh, Ryan; Aaronson, Neil; and Barbato, Guy


Five lines of Japanese quail, Coturnix japonica, were set and incubated to determine potential differences in hatching time. The lines used were high (HS) and low (LS) stress, high (HR) and low (LR) plasma cholesterol response, and an unselected control line (AR). The eggs were set over the course of six days, and left in an incubator until the developed quail broke through the eggshell, referred to as a pip. The results displayed a quantifiable difference in hatching times, reflecting hour of pip. The HS quail pipped later in the day on average when compared to the LS quail. The plasma cholesterol response lines showed similar findings; the LR line showed pips earlier in the day as opposed to the HR line. The control group, AR, had pip times that were in between the high and low groups respectively. For a nidifugous species that displays hatching synchronization, these data provide insight into a potentially critical relationship between genetic background and its influence on hatching times in Japanese quail. In addition to monitoring pip times, experimental methods will expand to recording the sound mechanism that triggers hatching synchrony. Prior research has found that both select avian and reptilian species exhibit this form of development synchronization. As such, these data will be used as a precursor for the development of a method to research synchronous hatching trends in the turtle species, Malaclemys terrapin.

16. Modeling the Human Papillomavirus (HPV) with Female and Male Protected Classes

Gaudiello, Arielle

Faculty Advisor: Rapatski, Brandy


HPV is sexually transmitted disease that affects an estimated 75% of the world. We created an ODE model for HPV, focusing on the female and male population between the ages of 13 and 26, the class highest at risk for infection. The population was split into 7 different groups: susceptible, protected, inactive, and infected females, and susceptible, inactive and infected men. With this model, we investigated how effective protecting females via vaccination would be in reducing R0, the reproduction number of the disease, below 1, the quantity needed to change the epidemic to an endemic. Improvements were then made regarding the structure, assumptions, and classifications of groups. This modified model allowed more flow between the groups, particularly changing the movement between the susceptible, protected, and inactive females. We determined the equilibrium solutions and their stability. From there, we added and 8th group, a male protective class, and determined the effectiveness in reducing R0. The addition of the male protected class significantly played a role in the in altering the prominence of HPV among the population.

17. Native bees in the N.J. Pinelands: Diversity and habitat relations

Hamblin, April; Fan, Weihong; and Cromartie, W.J.

Environmental Sciences

Even though concern is spreading about worldwide pollinator decline, much is still unknown about native bee populations and their density, abundance, and diversity. The New Jersey Pine Barrens are a highly distinctive ecosystem whose native bees have not been thoroughly studied. We sampled using fifteen transects of ten blue, ten white, and ten yellow bee bowls filled with water and dish detergent at three sites in the New Jersey Pinelands monthly from May to October, 2012. The thirty bee bowls were placed at each site for about a twelve hour period during each sampling. Specimens were collected in 80% ethanol, then washed in water plus detergent, dried, and pinned. We found 57 species of bees in 2012. The largest number were found during June at the Richard Stockton College site. Over half belong to the family Halictidae. Several rare species are present, including some associated with deep sand. We conducted a preliminary analysis using GIS to relate bee species richness to fire, soils, and landuse. Because of their variability, future study sites were not proposed through this analysis, yet these data suggest that more diverse, fragmented landscapes provide for a more diverse bee community.

18. Fracturing in the Stockton Formation, Stockton, New Jersey

Hozik, Michael J.; Cesta, Jason M.; Donley, Tara L.; Dykstra, Rebecca J.; Favorito, Daniel; Makin, Sarah; and Stinson, Robert J.


The Field Geology class at the Richard Stockton College of New Jersey mapped joints and fractures in the Stockton formation exposed in Wickecheoke Creek at Stockton, New Jersey. The dominant joint system strikes N30°E; an approximately orthogonal system strikes N60°W. In addition, the western part of the area has a third joint set striking approximately East-West, but with more variation than in the N30°E set. The joints appear to be Mode I (tensile) joints for the following reasons: 1) Many of them, particularly in the N30°E set, exhibit plumose structures; 2) Joints terminate at lithologic boundaries; and 3) Younger joints truncate against older ones. The N30°E set is the oldest; both the N60°W set and the East-West set are younger, but the age relationships between the latter two is unclear.Spacing (the distance between nearly parallel joints) is generally related to grain size in the rocks, with larger spacing in coarser grained rocks. Some of the finer siltstones have very closely spaced joints. Shaley layers have minimal jointing; they are characterized more by irregular fractures. None of the joint set was observed to cross a shaley layer. Within the shaley layers are arcuate fractures with well-developed slickenlines. The arcuate fractures occur in almost any orientation, and the slickenlines are consistent with normal motion. We interpret these features to indicate that the shaley layers were softer than the siltstones and underwent compaction and lateral extension, consistent with the apparent normal faults. These weaker layers also served as boundaries to limit the propagation of the joints.

19. The Chitinase Activity in Grapes

Huynh, Nhan

Faculty Advisor: Keenan, Kelly


Fruit bearing plants are constantly predated by fungi and insects especially when fruits are ripening. The fruits become sweeter, and the skins become softer, attracting the predators and leaving the fruits vulnerable. Chitin is a major polymer found in the cell walls and exoskeletons of fungi and insects. Many fruits and plants produce chitinase as a defence against these predators. The enzyme hydrolases chitin at the β(1,4)glycosidic bond, degrading the cell walls and exoskeletons. The objective of the experiment was to study the chitinase activity in grapes. This was completed by chitinase assay, and using a spectrophotometer to measure the absorbance at 550 nm. Various types of grapes were used to study the chitinase levels.We tried to optimize the chitinase assay by only using crude extract without any dilution in the sample.

20. Metabolic Profiling of cold shocked Chlamydomona reinhardtii

Keating, Ryan; and Pollock, Elizabeth

Biochemistry and Molecular Biology

Chlamydomona reinhardtii is a single cell green alga adapted for growth in warm fresh waters and soil. C. reinhardtii is related to the cold water adapted C. altera which can be found growing in frozen lakes in upper North America. The cold resistance properties of C. altera are of interest to researches who wishes to find ways to incorporate cold resistance properties into temperate crops and organisms. Metabolites produced by an organism’s metabolic pathways have been shown to serve as an indicator of environmental stress. Changes in metabolite concentrations in C. reinhardtii subjected to cold shock and provide insight into the metabolic processes affected by cold environment. We developed a method that utilizes nuclear magnetic resonance (NMR) to provide metabolite profiles of C. reinhardtii that have undergone cold shock. We created a 1:3 Methanol:Water extraction and quenching mechanism to extract the metabolites. PCA score plot analysis showed similar metabolite profiles amongst algae that were subjected to cold shocks compared to normal grown algae. NMR has been shown to provide accurate and reproducible metabolite fingerprints for the algae. PCA loadings provided an insight into metabolites that were increased and decreased due to cold shock.

21. Sexual dimorphism of humeri in Nasalis larvatus: Evidence for bending and torsional stress similarity

Keelen, Belinda; and Lague, Michael R.


Nasalis larvatus males are twice the size of females, which may cause allometric differences between males and females due to potentially greater stresses experienced by males. In this study, size and shape dimorphism in the humerus of Nasalis larvatus was studied to determine whether patterns of humeral dimorphism follow expectations based on the biomechanics of weight-bearing (i.e., maintaining stress similarity). Two-dimensional landmarks and semi-landmarks were used to quantify mid-shaft cross-sectional properties and bone length, and to compare levels of dimorphism to isometric expectations and expectations for bending/torsional stress similarity. The mid-shaft cross-sectional shape of the humerus between males and females scales isometrically, but robusticity, total area, sectional moduli, etc. scale to the expectation for bending and torsional stress similarity. This holds true, however, only when estimated pregnancy weight is added on to female body mass. Overall, male proboscis monkeys are accommodating changes to the overall thickness of the humerus without changing cross-sectional diaphyseal shape so as to bear greater forces due to body mass while maintaining similar stress levels as females.

22. Comparative Analysis of Spring Breeding Amphibian Reproductive Success in Varying Hydroperiods

Kiska1, Ryan; Baker2, Patrick J.; and Baker3, Tracy J.

1Sustainability, 2Biology, 3Environmental Science

A diversity of wetland habitats are found on Stockton’s campus including natural and anthropogenic vernal ponds. Vernal ponds are ephemeral depressions, typically filling in late fall and drying by mid-summer and provide habitat critical to the breeding success of several amphibian species. The hydroperiod, the length of time a vernal pond holds water, is a crucial factor in amphibian breeding success. Successful breeding was determined based on presence of eggs and successful metamorphosis within hydroperiod. Beginning in January 2012, vernal ponds and the phenology of the obligate and facultative amphibian species that use them were examined. Each pond was described using a consistent survey procedure and amphibian species were identified based on sighting, call, and capture by net. Survey methods consisted of water quality monitoring, species observations, and monthly pond perimeter measurements. GPS polygons were generated monthly to monitor changes in water level and pond perimeter. In 2012, low precipitation totals resulted in inactive ponds, short hydroperiods, and unsuccessful breeding. As of April 2013, breeding of wood frogs (Rana sylvatica), spring peepers (Pseudacris crucifer), New Jersey chorus frogs (Psuedacris triseriata kalmi), and Southern Leopard frogs (Rana utricularia), have been observed. Fowler’s toads (Bufo fowleri) have been observed, but without evidence of breeding. Pseudacris crucifer and Psuedacris triseriata kalmi were observed breeding in two ponds that were not active in 2012. Comparison with 2012 shows increased occupancy and breeding. Successful breeding is predicted for 2013 and water levels are anticipated to persist well beyond 2012 hydroperiod. Future directions include generating and comparing chemical and soil analyses of natural and anthropogenic ponds to explain differences in species composition.

23. The Vulnerability of Underground Storage Tanks during Extreme Weather Events

Kiska1, Ryan; Clendaniel2, Alicea; Kondrk3, Jackie; List3, Alexandra; and Stopen3, Michael

Faculty Advisor: Chirenje3, Tait

1Sustainability, 2Chemistry, 3Environmental Science

In the wake of Hurricane Sandy, the structural integrity of Underground Storage Tanks (USTs) has become a significant concern for environmental degradation in Southern coastal New Jersey. Using publicly available spatial and other data regarding USTs, typical underlying soil characteristics and chemistry, and the regulations governing them, we were able to evaluate the threat extreme weather events have on USTs. Analysis showed that abandoned and unmonitored USTs are at risk of corroding and flooding with water during extreme weather events. Tanks in compliance were determined to be at risk for only short periods of power loss during storms. There was a correlation between USTs not in compliance with regulation and poverty rates in the four counties analyzed. We recommend that USTs that are abandoned or not in compliance with regulation in the flood risk zone be protected or removed.

24. The effects of essential oil compounds on bacterial growth and associated metabolic changes as analyzed through NMR spectroscopy

Kong, Eric; Gazzara, Robert; and Pollock, Elizabeth C.


Natural food substances have long since been purported to contain compounds which confer health benefits. Of these compounds, essential oils have been heralded as powerful antimicrobial agents and many oils have already been researched and characterized as such. However, much of this research only reveals the efficacy of essential oils to eliminate bacterial colonies (MLC) or inhibit their growth (MIC); little research is done into the exact chemical effects of these oils on bacterial growth. In this study, the effects of Lemon Oil, Ginger Oil and Nutmeg Oil on the growth of Escherichia coli in a liquid media were examined. A clear inhibition of growth was seen in media inoculated with the essential oils. Metabolic compounds were then extracted via a polar extraction method and analyzed through Nuclear Magnetic Resonance (NMR) spectroscopy. Results thus far have yielded noticeable differences in the NMR spectra, though further analysis of the data is still needed in order to elucidate specific differences attributed to the essential oils.

25. Using the Weather Research & Forecasting Model (NCAR) to Model the Atmosphere over the North Eastern United States and Investigate the Effects of Land Use on the Atmosphere

Lutes, Tiffany; and Trout, Joseph

Physics and Computational Science

In this pilot project, the Weather Research & Forecasting Model (WRF) from the National Center for Atmospheric Research (NCAR) is being used to investigate the effects of land development on the weather and climate. New Jersey, especially New Jersey coastlines and NJ pine barrens, have seen a rapid amount of development in a very short period. Historical, long-term, hourly surface temperature data is being analyzed using Wavelet and Fourier analysis to search for trends. WRF model simulations are being created and will be used to compare to data collected. This data will include variables such as temperature, wind direction, and wind speed. Observations and simulations will be compared over areas of different land use.

26. Cloning and Sequencing of the COI gene in members of the family Colubridae

Manna, Vincent

Faculty Advisor: Luke, Tara H.


The family Colubridae is the largest snake family, containing approximately 70 percent of all snake species. This wide range of diversity makes it difficult to describe any family characteristics that hold true for all members of the family. Members of this family are found worldwide, and they occupy a wide variety of habitats. With the advent of phylogenetic analysis a more in-depth characterization of the Colubridae family is possible. Here, we investigate the taxonomic stability of several genera in the Colubridae family using the slow evolving mitochondrial gene for the Cytochrome C Oxidase subunit 1 (COI) protein. Cytochrome c participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. This work contributes to the overall knowledge of genetic variation within this widespread group of reptiles.

27. Metabolic Profiling of Radish Seedlings Exposed to the Ionic Liquid 1-Butyl-3-Methyl Imidzolium Bromide

Michaelson, Stephanie; and Pollock, Elizabeth


Ionic liquids, which are liquid forms of an ionic salt at room temperature, play a concern on today’s environment because they are used as biocatalysts in huge manufacturing companies. To determine the effect of these ionic liquids on the environment, radish seedlings were hydroponically germinated in the presence of 1-butyl-3-methyl imidazolium bromide. The seedlings grew anywhere between three to seven days and they were subjected to three treatment groups: control, treatment of 1/500 ml of ionic liquid, and treatment 1/1000 ml of ionic liquid. A height/weight analysis and NMR-based fingerprinting were used to assess the metabolic effects of the ionic liquid treated plants compared to the control. Results showed significant reduction of 9-41.7% in the height and weight of the treated group as well as a significant difference in the chemical composition in the NMR data.

28. Measuring Growth of the Northern Star Coral (Astrangia poculata) using Gene Expression

Mitchell1, Sage A.; May2, Stephen N.; and Luke, Tara H.2

1Marine Science, 2Biochemistry and Molecular Biology

This research examines the impact of environmental conditions on the growth rate of Northern Star Coral (Astrangia poculata). The overall health of coral reefs are notable environmental indicators, as they represent an incredibly diverse ecosystem and support approximately one third of all marine fish species, clearly presenting as vital elements in the ecosystems around the globe. Despite this, global warming and climate change has destroyed or threatened nearly 70% of reefs around the world, and global ocean temperatures and acidity rise yearly, further threatening these ecosystems. However, determining ideal conditions that would permit growth, or regrowth, of these corals would be extremely beneficial to many ecosystems, and could lead to global initiatives to restore coastal and deep-water reefs. Growth of the Northern Star Coral under various conditions will be analyzed by examining the expression Nad4L and MSH1, genes directly associated with growth processes.

29. Biomechanical analysis of bones

Monticelli, Taylor

Faculty Advisor: Sharobeam, Monir

Computational Science

Biomechanics is the mechanical study of the living body, which includes the forces exerted by the muscles and the gravitational forces on the skeletal structure. Using the programs Solidworks and COMSOL, the biomechanics of a bone can be modeled visually using Solidworks and then be put under physical forces using COMSOL. Solidworks is a 3-D mechanical CAD (computer-aided design) program used to either build or alter a model and its properties. COMSOL is a simulation software that uses the finite element to solve and analyze a given model. By applying the concepts and laws of physics, structures and mechanisms can be modeled and studied. The aim is to understand how bones will react to force in different ways, as well as to test the model to see if the mechanics of the bone such as compression, tension, shear, torsion, and bending are modeled correctly. The result of this analysis should lead to better understanding of the effect that any force can have on a bone.

30. Characterization of Calorimetry for an Alternating Magnetic Field at Radiofrequencies

Nusbaum, Charlie; Attaluri, Anil; and Ivkov, Robert


Purpose: To determine proper temperature measurement and data analysis techniques in a quasi-adiabatic calorimeter for an alternating magnetic field at radiofrequencies (155kHz-165kHz). The methods developed will be used to measure the specific loss of power (SLP) of magnetic nanoparticles developed for cancer treatment. Materials and Methods: Rate of temperature rise due to induced eddy currents was measured (n=5) for a copper wire of radius 0.99mm and length of 3.379mm in an AMF of varying amplitude (200 Oe, 250 Oe, 300 Oe, and 350 Oe). The AMF was generated by applying an alternating current to a 13.5-cm vertical solenoid. The calorimeter was placed in the solenoid and subjected to the AMF until the temperature of the copper increased by 10°C. The temperature of the samples was measured at 0.30-second intervals using optical fiber temperature probes. The specific absorption rate (SAR) of the samples was calculated, normalized by, and averaged for comparison to calculated theoretical values. Results: We report that normalized SAR data had a percent error of less than 10%, except for data corresponding to 200 Oe which had a percent error of 22.53% due to fluctuations in the system. Normalized experimental data followed a linear trend approximately parallel to theoretical values with an R2-value of 0.9955. Conclusion: We demonstrated that copper can be used to calibrate quasi-adiabatic calorimetric systems used for SLP measurements of magnetic nanoparticles for a field range of 200 Oe-350 Oe at 155kHz-165kHz.

31. Comparative Computational Analysis of Staphylococcus aureus Metabolic Proteins using Sugar Alternatives for use in Diabetic Conditions

Patel, Goonja; Wright, Avery; Ryan, Jacqueline; Perryman, Anthony; Sowers, Louise; Benjamin, Ellis; and Benjamin III, Earl


Health conditions such as diabetes are complicated by secondary bacterial infections which increase mortality/morbidity rates. Hyperglycemic environments have been shown to enhance bacterial growth while weakening the body’s immune response. The overall goal of this project is to perform a computational analysis of bacterial metabolism using established sugar alternatives such as Acesulfame potassium, Alitame, Aspartame, Cyclamate, Dulcin, Glucin, Neohesperidin dihydrochalcone, Neotame, Saccharin, Salt of aspartame-acesulfame and Sucralose to better treat S. aureus infections. The results were compared to values of natural sugars including glucose, fructose, sorbitol and sucrose. Computational analysis included 2D/3D structural comparison and protein docking studies to S. aureus glycolytic proteins. The results suggest energetically favorable docking of natural sugars at for the introductory proteins with basal level docking energy for sugar alternatives. These results can lead to improved treatment options for bacterial infections in diabetic patients.

32. Apiary Research Project

Pawling, Christopher; Ordner, Jamie; Sturts, Adam; and Sedia, Ekaterina


Honeybees are an exemplary organism for studying animal behavior, developmental biology, entomology, pollination ecology, biochemistry, and agricultural science and ecology. Having European Honeybees on campus will allow students to get involved with a variety of research projects. In addition, managing an apiary is an extremely rewarding experience. Having an apiary at Stockton will aid in pollination at the arboretum and organic garden. The beehives are self-sustainable once established, and adding an apiary to Stockton will be an asset for research, giving students with different interests (botany, biology, ecology, environmental science) the opportunity for hands-on research on a variety topics, including hygienic behaviors of bees, pollination ecology, and medicinal applications of honey and other bee products. The past autumn, winter, and spring have been used to lay the groundwork for a sustainable apiary of European Honeybees to use for research. There are currently four beehives located at the Stockton Arboretum. They were installed on March 30, 2013 and the bees are currently in the process of building honey comb and starting their first brood cycle. This poster presentation documents our experience in establishing the apiary at Stockton, and we hope that it will encourage current and future students as well as faculty to get involved with research using this new resource on campus.

33. Molecular Identification and Phylogenetic Analysis of Aquifer Bacteria

Perez, Michelle; Siconolfi, Dominick; and York, Karen


The Richard Stockton College of New Jersey utilizes a geothermal energy storage system for heating and cooling the academic buildings. After ten years of operation, an increase in the temperature of the aquifers was observed because more heat was deposited underground than extracted. To explore the impact of the temperature increase on aquifer microbes, aquifer samples were collected from the monitoring well with the greatest temperature increase. Preliminary identification of microbes using the 16S ribosomal RNA gene sequence identified seven bacteria isolates as being related to bacteria of the genus Acidovorax. This study describes further characterization of those bacteria using the single copy protein encoding gene lepA and focuses on the isolates Cu 7, Cu 10, and Cu 24. Using polymerase chain reaction (PCR), the lepA gene was amplified from chromosomal DNA, cloned into a pGEM-T Easy plasmid, and transferred into E. coli. DNA sequences of the recombinant plasmids were determined using automated DNA sequencing. These DNA sequences were compared to known bacterial sequences in the National Center for Biotechnology Information (NCBI) database using the BLAST program (Basic Local Alignment Search Tool). The sequences obtained from Cu 7 lepA did not share a 100% similarity with any of sequences in the NCBI database, indicating that lepA from this bacteria has been sequenced for the first time. To determine the phylogenetic relationship between CU 7, other aquifer bacteria, and other bacteria in the NCBI database, a phylogenetic tree was constructed. These results indicate that the lepA sequence obtained for Cu 7 was distinct from other aquifer isolates and from all bacteria in the NCBI database.

34. Use of Wavelets to Analyze Long Term Temperature Data and Short Term Atmospheric Phenomena

Prouty, Roy; and Allen, Jeniffer

Faculty Advisor: Trout, Joseph

Applied Physics

An atmospheric front can be defined as a sloping zone of pronounced fluctuation in thermal, moisture, and/or wind fields present in the atmosphere. These transition zones (fronts) can be characterized by a strong, horizontal temperature gradient. To examine long term trends in the number and magnitude of these transition zones, the frequency, intensity and shape must be analyzed. When performing this analysis on temperature records, otherwise evident transition zones may be obscured by the more persistent diurnal and seasonal fluctuations in temperature. Where Fourier Analysis reveals the long term, very persistent tendencies of a signal, utilizing the compact, scalable nature of wavelets allows us to reveal both the long and short term transitions present in temperature fields, allowing us to examine the long term trends.

35. Retrospective analysis of Horseshoe Crab (Limulus polyphemus) egg density data from New Jersey beaches of Delaware Bay

Raymond, Eric; and Santoro, Michael

Faculty Advisor: Hernandez, Daniel


Horseshoe crabs are an important species: their blood is utilized as the only FDA-approved test of all injectable drugs for bacterial contamination and their eggs are a vital food source for migrating shorebirds, including the State-endangered Red Knot (Calidris canutus). Delaware Bay is the last major Spring migratory stopover for Knots traveling between Tierra del Fuego and the Arctic breeding grounds. It is here that the Horseshoe crab egg resource provides a vital fuel source to birds during the final leg of their annual migration. The purpose of this project was to analyze an eight-year egg density dataset in order to parse out egg availability trends for individual beaches, rather than the statewide index currently in use. Samples of horseshoe crab eggs were collected each spring using the USGS “core method” (the current standard procedure for Horseshoe Crab egg collection). Eggs in the samples were enumerated to produce density data (eggs/m^2) for a total of 12 beaches along Delaware Bay from 2005 to 2012. During this time period, nine of the beaches, including: Reeds, Kimbles, Cape Shore, East Point, Villas, Highs, Sunray, Pierces and Cooks all showed a decrease in their egg densities. Two beaches, Moores and Fortescue, showed an increase in their egg densities. Finally, the egg density for Gandys beach showed no trend. The negative trends observed at the majority of the beaches may be due to a number of factors including: excessive non-sustainable harvesting of horseshoe crabs, natural erosion of Bay beaches and increasing frequency and severity of storms, due to climate change. These data suggest that more aggressive measures need to be taken in managing Horseshoe crabs and spawning habitat in order for the population to stabilize and recover. An increase in population size should therefore lead to a proportional increase in eggs available to the birds on Bay beaches.

36. Development of a parallel genetic algorithm framework to bridge the gap between general purpose programming and high performance algorithms and computation

Roubos, Demetrios

Computational Science Program, MSCP

This framework enables general purpose programmers using the JAVA programming language to implement parallel genetic algorithms that can leverage the high compute capacity of graphics processors using the CUDA programming language (Compute Unified Device Architecture by NVidia). This project allows for the development and re‐use of several common genetic algorithm operators including selection, mutation, and crossover.

37. Limiting Rheumatoid arthritis through the understanding and blockade of PI3K protein

Santaromita, Kim; Benjamin III, Earl; and Benjamin, Ellis


Rheumatoid arthritis (RA) is a chronic autoimmune disease that often causes inflammation of the synovial joints resulting in severe pain, bone erosion, and joint deformity which affects more than 2 million Americans. Current treatments for RA are based on anti-inflammatory treatments including steroids, non-steroidial anti-inflammatory drugs (NSAIDs), disease-modifying antirheumatic drugs (DMARDs), immunosuppressants, and TNF-alpha inhibitors. Side effects of current treatments can lead to heart problems, liver and kidney damage, bone marrow suppression, and severe lung infections. Improved pharmaceutical targeting of inflammatory proteins such as phosphphatidylinositol 3-kinase (PI3K) should yield drugs with increased efficacy and decreased side effects. This research sought to understand the pharmaceutical blockade of the PI3K kinase functionality to inhibit its function in the inflammatory pathway. 16 crystal structures of the tyrosine kinase of the PI3K protein were docked using IGEMDock to FDA, Alkaloids, Lactams, Lactones, Flavinoids, Sulfanilamide, Cyclic Imides, and NSAIDs drugs to determine structural correlation for the most effective binders. Structural similarities were determined with IGEMDock and vROCS and partition coefficient was determined using DRAGON program. This data found a cluster of approximately 10 drugs to preferentially bind to the PI3K kinase for use as targeted anti-inflammatory treatments.

38. Chemical Analysis of Seawater in an Anthropogenic Depression in Bass River

Sirak, Laura; Blood, Amy; Friedman, Duane; and Grguric, Gordan

Marine Science

An analysis of chemical parameters in a 12 m deep anthropogenic depression in Bass River was performed. Our data indicate a continuous increase in salinity with depth, starting from 15 ppt at the surface and continuing to 21 ppt at the bottom. The water column exhibits continuously decreasing dissolved oxygen concentrations, becoming anoxic below 7 m. Redox potential values show a similar drop, becoming negative soon after the onset of anoxia. These negative values indicate reduction of sulfate, which was verified by a drop in the sulfate concentration at deeper depths. The concentrations of silica, phosphate, and total alkalinity show a significant increase toward the bottom of the water column. Correlations of all these parameters to each other had coefficients of 0.80 or higher. This suggests the same source of these chemical species, which is likely sand and decomposition of organic matter, both coming from the sediments. Fluxes of these chemical species into the water column give this basin a distinct chemical signature.

39. A Study of Recombinant Frequencies in Sordaria fimicola With Mutant Spore Types

Sullivan, Alexis; Farrell, Douglas; and Hoang, Thien

Faculty Advisor: Barbato, Guy


In this experiment, two parental populations of Sordaria fimicola that contained mutant spore color genes, gray (ggt+t+) and tan (g+g+tt), were crossed under laboratory conditions to determine a linkage between the genes. Sordaria fimicola exists primarily in a haploid state with the only diploid pore being the zygote produced when the mycelia merge. The diploid zygote undergoes meiosis to produce ascospores. Sordaria fimicola are commonly used to demonstrate crossing over in a haploid organism. By using a dihybrid cross, ascospores can have the following phenotypes and genotypes, respectively: black (g+t+), tan (g+t), gray (gt+), and colorless or clear (gt). The mutant strains were crossed at room temperature until the cultures developed darkened coloration and a granular appearance, corresponding to the appearance of perithecia. The perithecia were transferred from the agar plates and, after being dispersed on a glass microscope slide, were viewed at 40X. Expected outcomes include the following phenotypes: a tetratype (T) ascus, with 2g+t+:2g+t:2gt+:2gt spores; a parental ditype (PD) ascus, with 4gt+:4g+t spores; and a non-parental ditype (NPD) ascus, with 4g+t+:4gt spores. A tetratype ascus (T) is considered anything that is not 4:4 asci. Parental ditype asci (PD) contain two genotypes like the parental strain while non-parental ditype (NPD) represent two genotypes that are unlike the parental strains. Digital photographs were taken of the resulting perithecia and both recombinant and nonrecombinant ascospores were counted. Recombination frequency was calculated corresponding to the genetic distance between the linked loci.

40. Understanding binding interaction of EGFR for the targeted treatment of lung cancer

Tarby, Shannon; Benjamin III, Earl; and Benjamin, Ellis


With over 174,000 new cases of lung cancer being diagnosed in the United States each year novel chemotherapy treatments with efficacy towards both small-cell and non-small cell lung carcinoma is of interest to increase the survival rate of cancer patients. Historically pharmaceutical treatments have been based on surgery, radiation therapy, and broad spectrum chemotherapies. New research is now focused on targeted approaches that seek to either inhibit specific proteins necessary for cellular proliferation or to initiate apoptosis for the removal of cancerous cells. The Epithelial Growth Factor (EGF) and its Receptor (EGFR) EGFR is protein that initiates cellular growth and has been found to be overexpressed in cancer cells which makes it an effective targeted approach to cancer treatment. Specifically, this research determined structural blockade of the tyrosine kinase receptor of the EGFR as a way to inhibit cancer propagation with the use of FDA approved drugs. 22 crystal structures of the tyrosine kinase of the EGFR protein were docked using IGEMDock to 714 FDA drugs to determine structural correlation for the most effective binders. Structural similarities were determined wih IGEMDock and vROCS and partition coefficient was determined using DRAGON program. This data found a cluster of approximately 25 drugs to preferentially bind to the EGFR tyrosine kinase for use as targeted cancer treatments.

41. Biofilm formation is effected by Shaking of Culture and can be inhibited by Plant Extracts

Tranor1, Brandon M.; Barbato1, Guy F.; and Walton2, Edward W.

Faculty Advisor: Rosche1, William A.

1Biology, 2Nursing

Plant extracts have been used for over a millennium to treat bacterial infections. Finding the mechanism(s) of these extracts will provide insight into drug/treatment strategies to cure bacterial infections. Background Bacterial infections can be controlled by (a) inhibiting bacterial growth, (b) being bactericidal, or (c) inhibiting bacterial adherence to biotic and abiotic surfaces. Once attached, bacteria are able to produce extracelluar substance to create biofilms. Biofilms are resistant to antimicrobial treatments. Materials Escherichia coli MG1655 was used to produce biofilms on plastic multi-well dishes. Extracts of cinnamon and cranberry (provided by Tournay Biotechnologies (Lamothe-Montravel, France)), were dissolved in sterile water then added to stationary-phase cells at varied concentrations. Plates were shaken at 175 RPM or allowed to incubate without shaking. Biofilms were quantitated by crystal violet incorporation and ethanol solubilization. The extracts were tested for their ability to kill cells or only keep them from growing. Results Biofilm formation can be inhibited by 60% by cinnamon extract and about 50% by cranberry extract. When combined, the two extracts can inhibit biofilm formation by up to 80%. At 1 mg/ml, both cranberry and cinnamon extracts are bacteriostatic. Conclusions Reduction in biofilm formation can prevent bacteria from adhering to surfaces. This reduces the infectivity of the bacteria because they can’t adhere to surfaces.

42. Purification and Characterization of Anti-Adhesion Molecules Isolated from Cranberry Extract

Ulejczyk, Jennifer; Kong, Eric; Barbato, Guy; Rosche, William A.; and Walton, Edward


The American cranberry, Vaccinium macrocarpon, has been reported to possess anti-bacterial/antibiotic activity. The bulk of the research on the antibacterial properties of cranberry juice focused on urinary tract infections, however there is a dearth of research regarding its effectiveness as a topical treatment on epidermal infections. A precursor to epidermal infection is bacterial adhesion to the wound site and prior studies in our lab have shown that cranberry extract inhibits E. coli adhesion to membrane proteins. A cranberry extract solution (containing 40% cranberry juice at 1 mg/ml) was passed over several ion exchange columns and aliquots collected; corresponding to positive, negative and neutrally charged fractions using ion exchange chromatography. The positive fraction yielded no significant inhibition of adhesion. Both the neutral and negatively charged fractions exhibited an inhibitory effect. Notably, the dose response for the neutral fraction had a greater slope but had smaller initial effect, implying that there are at least 2 classes of effective molecules, with differing pharmacodynamic properties. These data demonstrate that cranberry extract effectively inhibits adhesion of E. coli to membrane proteins with the effective compounds most likely lying within the neutral fraction. Further studies are needed to specifically isolate the effective compounds.

43. Forelimb movements in Rattus norvegicus (white rat) and their relationship to pronation: implications for early mammal forelimb posture

Varadharajan, Radha; Pinkney, Kadeisha; Drake, Evan; and Bonnan, Matthew F.


Rattus norvegicus (the white rat) is a therian mammal with a forelimb morphology similar to that of early non-cursorial mammals. Currently, early mammal limb posture is controversial, with reconstructions ranging from sprawling to parasagittal. With this current ambiguity, the study of forelimb shape and movements in R. norvegicus may provide a model to infer the locomotor patterns of earlier mammals. Previous research, most notably by Jenkins (1971, 1974), indicates that the forelimb posture of rats does not follow simple, pendulum-like mechanics but rather a more complex, less-upright range of movement. For the first time, we will study the 3-D morphology and kinematics of the forelimb in R. norvegicus by utilizing three-dimensional moving X-ray animations generated through the XROMM (X-ray Reconstruction of Moving Morphology) technique. Specifically, we will focus on the three-dimensional movements of the scapula, humerus, and antebrachium (radius and ulna), and their combined contribution to pronation (placing the hand palm-side down). To this end, we will test three interdependent hypotheses on the contribution of each of these limb segments to pronation. For the scapula, we examined the serratus anterior, supraspinatous, infraspinatous, spinotrapezius, acromiotrapezius, and rhomboids major and minor. Data gathered on the rat scapula through literature and dissection lead to the hypothesis that this element contributes in a significant way to pronation. Specific features of the humerus distinguish the parasagittal from the sprawling stance in early fossil mammals: degree of torsion, condylar structures of the elbow joint, width of the intertubercular groove, and the relative sizes of the lesser and greater tubercles. These features are associated with major locomotor muscles such as the pectoralis major and minor, deltoids, and pronator teres. We hypothesize that the humerus will contribute in a significant way to the pronation of the hand in the white rat. In humans, the radius can rotate about the ulna to pronate the hand because these elements are bowed, creating the space necessary to allow such movements. The pronator teres and pronator quadratus pull on the radius and rotate it about the ulna, whereas the supinator and biceps brachii act as antagonists to return the bones to a parallel position. Unlike humans, the radius and ulna of Rattus norvegicus fit tightly together like two spoons stacked together, with little, if any, space available in which the radius can rotate about the ulna. Moreover, the pronator quadratus has not yet been described or identified in our rat dissections. Instead, the radius and ulna appear “fused” by the interosseous membrane and rendered incapable of supination. Rats have little need to supinate the forelimb because the forelimbs are primarily used in locomotion. It is therefore hypothesized that all pronation and supination occur in the humerus and scapula in rats because the radius and ulna are in such close proximity to each other that we infer they participate little, if any, to pronation. After we capture the three-dimensional movements of these bones with XROMM, we will test our hypotheses and perhaps gain insight into the posture of early mammals.

44. Identification of Microorganisms in Glacial Soils from Iceland using DNA Isolation and Sequencing

Wheeler, Casey

Faculty Advisor: Hutchison, Ron


Soil microorganisms such as algae, fungi, and single-celled eukaryotes can offer insight to the biological history of a glacier and have potential application in reconstructing successional timelines when a glacier is receding. DNA was isolated from samples of Icelandic glacial soil and sequenced in order to characterize the microorganisms present in the soil. The soil samples used in this experiment were collected from four different sites at the Vatna glacier in southern Iceland. In order to analyze the diversity of microorganisms represented in these samples, the soil was subjected to DNA isolation, purification, and amplification; the DNA product was sequenced and analyzed using a BLAST search to identify the organisms present in the samples. Two methods were used for cloning the DNA: the first followed the Invitrogen T-Easy protocol and the second followed the Clontech In-Fusion cloning protocol. The DNA isolated via the Invitrogen protocol was of high enough quality to be sequenced using a Beckman Coulter sequencer. The In-Fusion protocol gave poor cloning efficiencies. Using BLAST online database for comparison, the microorganisms that were most prominent in the soil samples included fungi from the genera Fusarium and Beauveria and protists from the phyla Cercozoa and Apicomplexa. The distribution of these organisms from the sample sites will be discussed. Future research on this topic will continue to analyze the DNA of soil microorganisms in order to create a biological timeline of glacial recession through identification of soil organisms.

45. Bone Modeling Using COMSOL and SolidWorks

Wolff, April

Faculty Advisor: Sharobeam, Monir

Computational Science

The purpose of the research is to use computer software to model the bones of animals and eventually be able to study the biomechanics. The research is in its preliminary stages as I am just learning the techniques needed to use the software packages together for the study of the bones. A scan of a rat humerus was done and the resulting stereolithography file(.stl) was imported into the 3D CAD software SolidWorks creating a completely solid representation of the bone. This rat bone has been the focus of the project so far. The SolidWorks program is used to manipulate the structure of the bone such as removing protrusions to create flatter surfaces to make it easier to test particular areas. Also, currently being worked on is trying to hollow out the center of the bone and adding material of different property to more accurately simulate the less dense internal structure of bones. The COMSOL multiphysics software was used to perform evaluations on the rat bone to see the effects of stress/strain and the deformation that will occur. The bone can be given specific material properties such as density and elasticity. The bone had forces placed on it specifically in areas where it was connected to other bones or connective tissues to simulate loading due to animal weight (normal situation) or an activity such as landing from a jump (stress situation). The SolidWorks software is linked to the COMSOL multiphysics software via an add-on tool so that the changes made in SolidWorks are automatically updated in the COMSOL file. This allows all other set parameters such as material properties and forces exerted on the bone to remain unchanged and the study to just be recomputed. This process will be used on larger animal bones further into the research project. In doing this, the further goal will be the ability to study the biomechanics of the various types of animal bones by creating models of them.

46. Ecology of Stockton’s Vernal ponds

Yeager, Jillena B.; Gordon, Sabol; and Gunn, Evan

Faculty Advisor: Cromartie, Jamie

Environmental Science

This study compared this year’s vernal ponds with previous years. The main goal was to investigate how changes in yearly weather patterns affect frog diversity and abundance. Data collection from the beginning of March was recorded and will proceed until the end of May. Water temperature, pH, and conductivity readings were measured to add to the existing compilation of measurements. Frog species were identified through recognizing specific frog calls and identification through capture. Approximation of the total population of a frog species in a particular pond was measured by estimating the total number of frog calls heard. Up until now, VPM, VPN, VPS, and VPE have had the most frog activity. Spring Peepers (Pseudacris crucifer), NJ Chorus frogs (Pseudacris triseriata), Wood frogs (Rana sylvatica), and Southern Leopard frogs (Rana sphenocephala) were the most abundant this year. 2012 was a drier and warmer year than 2013 and many vernal ponds including VPI, VPJ, VPK, VPN, and VPP were dried up. Last year’s dry conditions had no significant impact on this year’s frog abundance, as predicted. This year’s breeding season also began later than last year’s, and frogs were more spread out over the campus than last year.

One thought on “Stockton University NAMS Research Symposium Abstracts – Spring 2013 [Not This Year’s Abstracts]

  1. Pingback: Abstracts and Poster Numbers for Stockton NAMS Research Symposium now on-line | The Evolving Paleontologist

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