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School of Science

Faculty Research Mentors and Projects

Summer Research Program 2019


Dr. Jason Adolf

Endowed Associate Professor of Marine Science


Project Title: Harmful algal blooms in Monmouth county coastal lakes, estuaries, and ocean

Project Description:

Phytoplankton are an essential component of aquatic ecosystems, transforming sunlight and inorganic nutrients to food for numerous species at higher trophic levels. However, a handful of the ~25,000 species of phytoplankton can cause troubling ‘Harmful Algal Blooms’ (HABs) that affect human health, sicken or kill aquatic organisms and disrupt aquatic ecosystems. Marine, estuarine and freshwater systems have seen an increase in HABs in recent decades, with significant ecological and economic impacts.

Monmouth County, New Jersey has experienced HABs in its coastal ocean, estuaries, and coastal lakes and provides an excellent location for researching HABs in varied aquatic environments. This SRP project will build on HAB research in aquatic environments of Monmouth County that started last year, including the Navesink / Shrewsbury River estuaries; Deal Lake (coastal lake); and the near shore ocean off Monmouth County beaches. Students will work as a team with their professor, with individual students taking lead responsibility for HAB research in different environments. Students will learn to characterize the physical and chemical environments where HABs occur, and to analyze water samples for the presence of HAB species using microscopy and flow cytometry. Projects will be coordinated with activities of the NJ DEP HAB monitoring program. This research will provide students with hands on field and laboratory experience in a real-world field of marine science, improve our understanding of HAB formation, and will aid prediction and management of HAB events.

Dr. Pedram Daneshgar

Associate Professor, Biology

Project Title: Exploring the Role of Maritime Forests as a Carbon Sinks

Project Description:

Maritime forests can be defined as dune successional climax communities dominated by woody vegetation found primarily on barrier islands and ocean-fringing sand dune systems.  These ecosystems have tremendous value both ecologically and for society in the services they provide.  Compared to other ecosystems, there has been limited research on maritime forests and most literature that describes the ecology of maritime forests does so poorly as the ecology of barrier islands is explained instead. Preliminary work in the literature suggests that these ecosystems are valuable for storm protection, bird and mammal habitat, and nutrient and groundwater conservation, but there are several unknowns that remain including the roles maritime forest play in the global carbon cycle as a sink and how these ecosystems will respond to climate change.

Dr. Keith Dunton


Project TitleConservation and demographics of New Jersey coastal sharks and sturgeon

Project DescriptionWorldwide, species with k-selected life history traits (long live, late maturing) are of great conservation need due to the drastic declines in populations from various anthropogenic threats.  The coast of New Jersey has been shown to be a migratory corridor for many of these species including sturgeons, coastal sharks, and rays.  By collecting information on their population demographics (size, age, sex, species) and spatial/temporal habitat uses along the New Jersey Coast, we can gain a greater understanding of their population ecology, which is essential for both the conservation and management issues.

Currently Atlantic Sturgeon (Acipenser oxyrinchus), is listed as endangered under the US Endangered Species Act.  It has been previously shown, that while endangered, large aggregations of this species occur in nearby coastal waters and the Hudson River (essential nursery and spawning area).  Sandy Hook Bay, an urbanized embayment important for commercial and recreational fishing, trafficked by high-speed ferries as a hub for NYC transport, and is the location of Naval Weapon Station Earle, a weapons loading terminal for the US Navy, is located within close proximity to these areas of known Atlantic Sturgeon aggregations and freshwater spawning/nursery sites.  While, Atlantic Sturgeon, have been historically documented to occur in Sandy Hook Bay, no formal surveys have been conducted to identify their presence/absence.  Using acoustic receivers over the last 2 years, we have been able to detect numerous Atlantic sturgeon within this region.  This project will build off current and previously funded UCI research to focus on looking at the population demographics in this regional as well as spatial and temporal habitat use.  This is essential for the conservation and recovery of the species.

Sharks and Rays
The NJ coast is home to numerous shark species as well as supports both a large recreational and commercial fishery.  Coastal sharks, Sandbar shark (Carcharhinus plumbeus), Sand Tiger (Carcharias taurus), are of particular interest because they are currently prohibited from harvest and also have the potential overlap with humans (e.g. bathing beaches) since they typically occupy shallow coastal waters.  Although prohibited, these species are also incidentally captured in the recreational, land-based, hook-and-line shark fishery, which has been increasing in popularity in recent years.   Due to the nature of this fishery, the collection of information about specific species can be difficult.  We will work directly with this recreational community to continue to collect information of population demographics as well as tag sharks with conventional and acoustic tags to monitor movements after release.  Last years SRP focusing on this was very successful with our single recreational angler capturing and tagging over 70 sharks with us.  Understanding the population demographics of specific shark species as well as migratory pathways along the coast of New Jersey can be used to create better management and conservation efforts for the shark fishery.  Additional species such as Atlantic Angel Shark (Squatina dumeril), Spiny Butterfly Ray (Gymnura altavela), Roughtail stingray (Dasyatis centroura) have been shown to be rising locally and but are considered “data-poor” in NJ coastal waters. These species will be opportunistically sampled within our surveys as well as through cooperative efforts with NJDEP for additional information such as age and diet.

Please note, this project may require long hours on at least one day of week due to travel to field location and will require work at night and possibly inclement weather.   Because of that, hours may be condensed to only 2-3 days per week depending on field work activities.

Dr. Martin Hicks

Assistant Professor, Biology


Project Title: Gene Therapy for the Treatment of Brain Tumors

Project Description:

This project focuses on the development and testing of AAV gene therapy vectors that encode novel RNA therapeutics to reduce the expression of oncogenic transcripts for the treatment of glioblastoma multiforme (GBM), the most common malignant primary brain tumor in adults. Individuals diagnosed with GBM have a short life expectancy of 12-14 months. Thus, a novel strategy that circumvents this barrier is necessary to effectively reach the CNS tumor microenvironment. Our approach is direct administration of AAV vectors that encode RNA therapeutics to deliver a persistent and constant dosage of treatment.

The proliferation of GBM is often coupled to the overexpression of tyrosine kinase receptors (TKRs). TKRs are cell-surface receptors that bind to their cognate ligand. Binding of the ligand stimulates TKRs, activating a signal-transduction cascade that leads to cell growth, migration and the formation of tumor vasculature.  As these receptors are often upregulated in GBM, an RNA therapy to modulate the expression and inhibit the translation of critical TKR domains would reduce the functionality of these oncogenic transcript in GBM.

Furthermore, with the advancement of nanopore sequencing technology, we are able to read longer transcripts. With this technology, we are examining the architecture of pre-mRNA transcripts to detect alternatively spliced and polyadenylated isoforms, as well the RNA structurome to reveal RNA elements within TKRs which may be better targets for RNA anti-sense directed therapy.

To this end, we have developed a strategy to identify novel targets within oncogenic transcripts and incorporate these therapies directed against novel targets into our AAV directed RNA gene therapy platforms. In this approach we are able to alter splicing as well as use RNA mimics to take advantage of the RNA interference pathway to modulate and reduce expression of oncogenic transcripts in animal models of GBM.

Dr. Cathryn Kubera

Assistant Professor, Biology


Project Title: The Role of GABA in Cerebellum Development and Fetal Alcohol Syndrome

Project Description:

Fetal alcohol spectrum disorders and Fetal Alcohol Syndrome (FAS) create significant social, economic, and medical burdens for the several million Americans that have these conditions.  In addition to having mental disabilities, individuals with FAS often have motor impairment and coordination deficits that are due to cell death-related abnormalities in the cerebellum.

This project will examine the role of alcoholism-related genes like the GABA receptor subunits during cerebellum development.  A chicken embryo model will be used to study timing of gene expression in relation to alcohol exposure, and determine patterns of cell death in the cerebellum. Part of the approach will entail using the CRISPR-Cas9 system to genetically engineer cells and initiate knockdown of gene function.  This project will facilitate understanding of the molecular mechanisms underlying the progression of FAS.

Dr. Dorothy Lobo and Dr. James P. Mack

Professors, Biology



Project Title: Effects of Essential Oils, Methylglyoxal and Cannabidilol on the Growth and Proliferation of a Variety of Human Cancer Cell Lines and Specific Multidrug Resistant Bacteria

Project Description:

One project to be addressed is the influence of essential oils, methylglyoxal and cannabidilol on the proliferation and survival of normal and cancerous cells grown in culture. Previous research has indicated that manuka and kumquat essential oils have growth-inhibitory effects on cancer cell lines. This summer, we would like to explore the potential for these essential oils to trigger apoptosis in these cancer cell lines, and to compare all results to normal cell lines. Here at Monmouth, there has been work performed to characterize the anti-bacterial role of essential oils, but we have the ability to expand this work to determine the effects on human cells. The proliferation and rate of apoptosis of normal human cells and cancerous cells exposed to essential oils will be measured. This work may lead to further evaluation of signaling pathways influenced by essential oil treatment.


We will also address the effects of specific essential oils (Cassia, Oregano, Cinnamon and Manuka Oil) and Methylglyoxal on the growth of multidrug resistant bacteria including: MRSA, Pseudomonas aeruginosa and ESBL-E.coli.

Dr. Megan Phifer-Rixey

Assistant Professor, Biology


Project Title: Evolutionary Genetics in the Wild

Project Description:

Genetic tools can provide insight into wild populations—everything from species’ ranges and distributions to specific adaptations to local environments.  This summer, my lab will use genetic tools to investigate two distinct research areas 1) environmental adaptation in wild house mice (Mus musculus domesticus) and 2) local marine and estuarine community composition. While these two systems are very different, they are united by common research methods, spanning molecular genetics, bioinformatics, and population genetics, and by a common research goal—using an evolutionary perspective to better understand wild populations of ecologically important species. The house mouse is one of the most widely distributed mammals and one of the most widely used genetic model organisms. Nevertheless, relatively little is known about genetic variation in natural populations. Recently, house mice have expanded their range in association with humans establishing populations in a variety of novel habitats, providing an exceptional opportunity to study the genetic basis of rapid evolutionary change. This summer, we will be investigating the traits that have enabled house mice to adapt to so many different climates and habitats.

To better understand local marine and estuarine communities, my lab will be part of collaborative projects using eDNA (environmental DNA) to survey the Navesink and Shrewsbury Rivers and using genetic markers to survey local populations of striped bass (Morone saxatilis).  Both of these projects will help characterize commercially and ecologically important systems and lay the foundation for future collaborative work in the region.

Dr. Sean Sterrett

Assistant Professor, Biology


Project Title: Reptile and amphibian surveys in urbanized ecosystems

Project Description:

Reptiles and amphibians are diverse groups of vertebrates that are experiencing global declines due to anthropogenic effects. Urbanization and suburbanization creates challenging environments for these animals to persist (i.e. habitat loss, increasing levels of disease, introduced invasive species). This projects aims to explore ecological research and conservation opportunities for reptiles and amphibians in New Jersey and represents an interesting opportunity to study how reptiles and amphibian populations persist alongside high human density populations. This project will survey reptile and amphibian communities in urbanized ecosystems of New Jersey with an emphasis on the following taxa:

  1. The Red-backed salamander (RBS; Plethodon cinereus) is among the most common (i.e. wide distribution and locally abundant) species of amphibian in the eastern U.S., yet we know little about the status of this species across its range (i.e. demographic variability across the range, state of populations). This species is the focus of a geographically and intellectually distributed, collaborative network called SPARCnet (Salamander Population and Adaptation Research Collaborative network), which has the following scientific objectives:
  • Understand impacts of land use and climate change on salamander population dynamics.
  • Develop models to describe local and regional drivers of population dynamics by creating a versatile, statistically and methodologically efficient monitoring protocol.
  • Understand the adaptive capacity of salamanders to ensuing environmental changes.
  1. Freshwater and brackish turtles (Genera Chelydra, Chrystemys, Pseudomys, Sternotherus, Malaclemys) are among the most threatened vertebrate groups in the world. New Jersey harbors both common and rare species of turtles in a variety of habitats (e.g. streams, reservoirs, natural lakes, tidal creeks, salt marshes), including species listed as threatened in New Jersey. Turtles are robust vertebrates that continue to exist in urban systems, yet the full impacts of urbanization on turtle populations has yet to be resolved. Nuanced effects of urbanization (i.e. sublethal, physiological) on turtle population dynamics have yet to be studied. Several newly developed techniques (spatial capture recapture and point counts) will be employed in New Jersey to learn about turtle populations.


Dr. Davis Jose

Assistant Professor, Chemistry and Physics


Project Title: A Spectroscopic Evaluation of the Significance of Non-Canonical DNA Conformations in Cancer and Aging.

Project Description:

The non-canonical conformations of DNA double helices play major roles in biological process such as DNA replication, recombination and transcription. In our lab, we are focusing on the structural complexities of DNA duplexes during B to A conformational transition and the unusual DNA conformations in G-quadruplexes and T-loops at single base resolution. The B-A conformational transition of duplex DNA is known to be essential for processing of genetic information, e.g. during transcription. DNA G-quadruplexes and T-loops are unusual nucleic acid structures found mainly at telomeres, the multiple repeats of guanine rich sequences found at the linear eukaryotic chromosome ends. G-quadruplex (the four stranded nucleic acid secondary structures) formation can affect chromatin architecture and regulation of replication, transcription and recombination and has been associated with genomic instability, genetic diseases and cancer progression.

We are using fluorescent base analogues to study the local conformations of individual bases at specific locations and cyanine dyes inserted into the sugar-phosphate backbone to monitor the backbone motions of different G-quadruplex structures as well as B and A form DNA duplexes. Using these approaches, we will be able to compare the structure and stability of these non-canonical nucleic acid structures under various conditions.

Dr. Yana Kosenkov

Lecturer, Chemistry and Physics


Project Title: Oxazole- and Thiazole-Based Macrocycles as Potential Anticancer Agents: A Computational Study of Conformational Equilibrium

Project Description:

Toxicity of anti-cancer drugs is an urgent problem in the field of cancer research. Inhibition of cancer cell growth can be achieved with binding of small organic ligands to DNA macromolecules in telomeres. Such ligands have been suggested as potential anti-cancer drugs. Cytotoxicity of those potential drugs can be estimated based on the selectivity of their binding to specific DNA conformations.

The current research is focused on computationally-aimed selection of small organic molecules – ligands – that have shown a potential as anti-cancer drugs with low toxicity. Specifically, various oxazole-based macrocycles will be considered. Different molecules of this class, depending on their structure and substituents, bind highly selectively to certain DNA forms (e.g., double-helix, parallel, anti–parallel, G-quadruplex and mixed–type hybrid structures). Therefore, such oxazole-based macrocycles can be selected for optimal binding to specific DNA forms, and subsequent targeted inhibition of telomerase in cancer cells. Computational chemistry tool will be utilized to study conformational equilibrium in a selected set of oxazole- and thiazole-based macrocycles and the effect of the surroundings.

Dr. Dmitri Kosenkov

Assistant Professor, Chemistry and Physics


Project Title: Modeling Energy Transfer in Light Harvesting Proteins: The Role of Molecular Vibrations

Project Description:

Mechanisms of energy transfer in biological molecules will be investigated to find new efficient ways of solar energy conversion into electricity and environmentally friendly fuels. Molecular modeling software based on novel quantum-mechanical methods will be used to obtain detailed molecular-level knowledge of the key mechanisms of light capture by biological and organic molecules—chromophores. High performance/supercomputing systems will be employed to carry out the simulations.

Project Title: Modeling Impact of Intermolecular Interactions of LPG—Alcohol Mixtures on Stability of Phyllosilicates: Towards Improvement of Drilling Fluids

Project Description:

A recently introduced technology of waterless fracking that employs liquefied petroleum gas (LPG) Alcohol Mixtures as drilling fluids (DF) is advantageous over traditional water-based DFs that cause borehole failures due to shales instability. The proposed project focuses on proving the concept that the stability of shale minerals is preserved by using drilling fluids (DF) with the certain balance between polar (e.g. Coulomb, polarization, etc.) and non-polar (e.g. dispersion) intermolecular interactions of DF components (e.g. LPG and polyhydroxyl alcohols) with shale minerals (e.g. phyllosilicates). The main goal of the proposed project is to develop a computational strategy to reveal the key intermolecular interactions for various DF formulations and therefore to facilitate the development of waterless drilling fluids that minimize negative effects of waterless fracking.


Dr. Jonathan Ouellet

Assistant Professor, Department of Chemistry and Physics


Project Title:

  1. Development of RNA aptamer binding glucose
  2. Development of RNA aptamer binding 2-hydroxyglutarate
  3. Ratiometric fluorescence measurements to monitor riboswitch activity in bacteria
  4. Kinetics of DNA-cleaving Zn-dependent DNA

Project Description:

Project #1: Development of RNA aptamer for small ligands

Diabetes is constant struggle for people afflicted by this disease. Among many other problems, regular blood-sugar monitoring, injection of insulin, strict diet and fear of coma are common place for the million Americans suffering from diabetes. A low-tech and common practice is to puncture a finger to obtain a drop of blood which is spread over a thin layer containing peroxidase enzymes that will oxidize a substrate only in presence of glucose. This process must be done several times a day; anytime when the patient feels tired, is fasting or just ate, so that the proper quantity of insulin can be injected (with a needle) to allow the cells to absorb the glucose to proceed into normal metabolism.

This research project aims to lay the foundations for an automated synthetic biology solution to diabetes, where the glucose levels are measured by an RNA Aptamer.


Project #2: Development of RNA aptamer binding 2-hydroxyglutarate

Glioblastoma and AML (Acute Myelogenous Leukemia) are aggressive brain cancers with median survival of 11-15 months. This cancer is caused by a mutation within an enzyme involved with the Krebs Cycle – the Isocitrate Dehydrogenase (IDH). Such enzyme mutation does not inactivates the enzymatic activity but rather provides gain of function where the substrate isocitrate is now converted to 2-hydroxyglutarate (2-HG) rather than the ususal alpha-ketoglutarate. The presence of 2-HG is therefore a confirmation of a glioblastoma (or AML) in formation. This research project aims to lay the foundations for the detection and eventually the treatment of glioblastoma and AML via the detection of the oncometabolite 2-HG by an aptamer.


Project #3:  Ratiometric fluorescence measurements to monitor riboswitch activity in bacteria

Gene regulation is crucial and central in biochemistry. To turn gene expression ON and OFF at the right time is fined-tuned at the level of DNA, RNA protein as well as ligand concentrations. Riboswitches, which are commonly found in bacteria, are composed of an RNA aptamer coupled to a gene expression system where, for example, the presence of a ligand can bind the aptamer portion of the riboswitch at high concentration and thereby turning OFF the gene expression of the metabolic genes. Once the concentration of the ligand lowers, it detaches from the aptamer and the riboswitch is turned ON by expressing the genes.

Such system is very clear on paper, but gets blurry when in cells. There are leakages of gene expression, and the gene expression in not 100% ON or OFF but somewhere between 0 and 100%. Studying gene expression in living system is therefore more complicated.

When studying gene expression, several controls are usually required to establish if a new reporter system is properly working. In order to make this system robust, we are developing a riboswitch reporter system where a single promoter would initiate the transcription of mCherry gene (fluorescent red), the riboswitch and finally GFP gene (fluorescent green).

This ratiometric fluorescent reporter will be later used when the aptamers from the previous projects will be transformed into riboswitches.


Project 4: Kinetics of DNA-cleaving Zn-dependent DNA

The gold standard tool for structure/function analysis of ribozymes cleavage by site-specific mutations is to label the substrate RNA strand with the radioactive isotope 32-P. Once the long substrate gets cleaved in two, the mixture of long and short RNA substrates are resolved on an acrylamide gel and the radioactive densities are measured to calculate the percentage of cleavage. We don’t have the permits nor the instrumentation to use this radioisotope (or any radioisotope) for research.

A few years ago, the laboratory initiated a project to monitor the DNA percent cleavage by SYBR Gold, but it failed to show a linear correlation at high DNA concentration. We are now switching to 2-aminopurine (2-AP) fluorescence and will initiate a project to cut a parvovirus causing kidney failures.


Professor Katie Gatto

Specialist Professor, Department of Computer Science and Software Engineering


Project Title: Hawks Code: Developing an Assistive Compiler to Enhance Student Learning of Java Programming

Project Description:The team will help to create/refine an online compiler designed to help students improve their Java coding skills with adaptive corrections.

Goals and Objectives

  1. Create an adaptable pedagogical online compiler for the Java language in order to help students identify errors in their code and correct those errors.
  2. Assist students in identifying patterns of errors, in order to provide extra practice in Java development and object orientated programming at the basic levels.



Dr. Cui Yu

Associate Professor, Department of Computer Science and Software Engineering



Project Title: Computer Applications Across Multiple Disciplines

In this project, students will design computer applications that exploit advanced practices or research results of other disciplines, such as psychology, education, and/or social work.


Dr. Richard Bastian and Dr. Pedram Daneshgar

Lecturer, Mathematics

Associate Professor, Biology



Project Title: Marine Ecology in the Bahamas

Project Description: Statistical design, data collection & analysis (types of tests, sample sizes, power, effect sizes, etc.) needed to answer research questions about the marine ecology in the Bahamas.

Dr. Richard Bastian and Dr. Lindsay Mehrkam

Lecturer, Mathematics

Assistant Professor, Psychology



Project Title: Analysis of Dog-Owner Behavior in Play Park (Collaboration with Dr. Lindsay Mehrkam in Psychology

Project Description: Analysis of play park data involving animal to animal and human to animal behaviors.

Dr. Richard Bastian and Dr. Alison Morgera

Lecturer, Mathematics

Veterinarian, Garden State Veterinary Hospital


Project Title: The Effect of Different Surgical Drapes on Infection Rates in Veterinary Surgeries

Project Description: Analysis of infection rates following surgery using different surgical drapes.

Dr. Francis Valiquette

Assistant Professor, Mathematics


Project Title:  SAGE implementation of the Equivariant Moving Frame Method

Project Description: Differential geometry is a branch of mathematics that uses techniques from differential calculus, integral calculus, and linear algebra to study smooth geometric objects such as curves, surfaces, and more generally submanifolds.  To understand these structures, one of the main tasks of a geometer is to compute differential invariants, which intrinsically characterize their local geometry.  There are several techniques available for computing these invariant quantities.  One of these procedures is known as the equivariant moving frame method, which is a powerful tool for studying the local geometry of submanifolds under the action of a group of transformations.  Unfortunately, for complicated group actions the computations can become overwhelming and difficult to perform by hand, thereby limiting the scope of the method.  To alleviate this issue, the aim of the proposed research project is to develop symbolic routines that will perform basic moving frame computations on a computer.


Mathematica and Maple are two popular software currently used to perform symbolic computations.  Regrettably, these software packages are expensive to purchase.  Furthermore, since they are commercially developed, their source codes are not readily available which prevents the research community from scrutinizing their code and their implementation.  As an alternative to Mathematica and Maple, the routines developed in this research project will be implemented in SageMath, which is a free open-source computer algebra system.