Summer Research Program 2023
Biology || Chemistry and Physics || Computer Science and Software Engineering || Mathematics || Urban Coast Institute
Sean C. Sterrett
Assistant Professor of Wildlife Ecology, Biology
Project: Suburban Turtle Ecology and Conservation
Reptiles and amphibians are diverse groups of vertebrates undergoing global declines due to human activity. Urbanization and suburbanization are types of development that create challenging threats for these animals to persist (i.e. habitat loss, increasing levels of disease, collection for pet trade). This collection of projects aims to explore ecological research and conservation for reptiles and amphibians in New Jersey and represents an opportunity to how populations fare alongside high human density populations using two specific study systems; Diamond-backed terrapins living in coastal environments and Eastern box turtles living in forested habitats. Diamond-backed terrapins are a turtle species living in highly modified habitat and are among the most visible turtles in coastal marsh habitats especially during seasonal mating aggregations, making them easily visible from unmanned aerial vehicles (i.e., drones). Partnering with NJ conservation groups, and building on a previous experiment of terrapin detection using 3D-printed terrapins, we will sample real populations of terrapins to understand how this novel method of detection can be leveraged for population estimation. Specifically, we would like to learn if turtle behavior is influenced by drone use. Eastern box turtle is a wide ranging and mostly terrestrial species that has declined due to various human-related threats; habitat loss and conversion, disease and poaching. Last year, we began a new project aimed at understanding the movement ecology of this species, using radiotelemetry (i.e., attaching radio transmitters to turtles in order to track their movement, behavior, etc.), in a suburban island environment, which is surrounded by housing developments, high traffic roads and other infrastructure. In 2023, we will continue radiotracking this species, but will be adding an emphasis on habitat selection and thermal ecology with new methods.
Jeffrey H. Weisburg
Specialist Professor, Biology
Project: Use of Pomegranate Juice Extract and Apple Extract to Treat and to Inhibit Chronic Inflammation in Cancers of the Oral Cavity
Oral cancer (OC), a type of head and neck cancer, has an annual worldwide incidence of 274,000 cases. Besides tobacco and alcohol, another risk factor for OC is chronic inflammation. Chronic inflammation can genetically alter normal cells resulting in the activation of oncogenes and the inactivation tumor-suppressor genes leading to the evolution of tumor cells by inducing cell proliferation and promoting prolonged cell survival.
Nutraceuticals are any products derived from food sources with extra health benefits in addition to the basic nutritional value found in foods. Two of most powerful nutraceuticals is pomegranate juice extract (PJE) and apple extract (AE). Both PJE and AE have been shown to have anti-proliferative, pro-apoptotic, and anti-inflammatory properties in some cancers.
Previously, we have demonstrated that both PJE and AE selectively target and kill cancers of the oral cavity, using the human squamous carcinoma cells, HSC-2, as compared to normal gingival fibroblast cell, HF-1. The transcription factor NF-kB, a key element in inflammation, has been shown to upregulate gene expression of other pro-inflammatory cytokines. Increased NF-kB activation is thought to be one of the links between cancer and inflammation. Research has shown that NF-kB activation can occur in most cell types. Treating the cells with PJE and AE, we want to observe if these nutraceuticals could inhibit or decrease the activation of NF-kB, preventing the inflammatory process. Inflammatory cytokines produced by NF-kB activation are interleukin-1 beta (IL-1β), Tumor Necrosis Factor (TNF), and IL-6. Secretion of these cytokines further amplifies the immune response. We want to examine if treating the cells with the nutraceutical can also inhibit the secretion of IL-1β, TNF and IL-6. Determining receptor for these inflammatory cytokines and epidermal growth factor receptor (EGFR) expression levels on these cells will also be done as signaling through these receptors initiates and maintains inflammation.
Dottie Lobo and Jim Mack
firstname.lastname@example.org and email@example.com
Project: Effects of Specific Essential Oils and Methylglyoxal on the Growth and Proliferation of a Variety of Human Cancer Cell Lines and Specific Multidrug Resistant Bacteria
One project to be addressed is the influence of specific essential oils and methylglyoxal on the proliferation and survival of normal and cancerous cells grown in culture. Previous research in this laboratory has indicated that kumquat essential oil treatment leads to decreased proliferation and apoptosis in a variety of human cell lines. This summer, we would like to continue to study the effects of essential oils and methylglyoxal on the regulation of apoptosis in 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, Arbor vitae, Thyme, Cinnamon bark and Melaleuca) and Methylglyoxal on the growth of the multidrug resistant bacterium Klebsiella pneumonia. We will also test 109 Essential Oils (a gift from doTerra) if time permits.
Chemistry and Physics
Assistant Professor, Chemistry and Physics
Project: Exploring the Mechanism and Catabolic Pathways of Flavonoid Degradation by Various Gut Bacterial Enzymes Using Biophysical Methods
Flavonoids are a large group of polyphenolic compounds found in fruits, vegetables, and in beverages like tea and wine that have anticancer, anti-microbial, anti-inflammatory, anti-oxidant, anti-osteoporotic, and anti-allergic actions. This project aims to understand the mechanisms by which gut bacterial enzymes convert flavonoids into secondary metabolites with health benefits. Gut microbiota modulates the biological activities of flavonoids because some bacteria can biotransform flavonoids such as quercetin into secondary metabolites with more potent biological effects. The primary site of flavonoid biotransformation is the large intestine, where the action of gut microbial enzymes converts flavonoids into different metabolites through deglycosylation, ring fission, dehydroxylation, and demethylation. However, biochemical properties and the substrate range of flavonoid biotransforming bacterial enzymes and their distribution in gut microbial species are poorly understood. The bacterial enzyme quercetin 2,3-dioxygenase identified in Bacillus subtilis is known to degrade quercetin to metabolites such as 3,4,6-trihydroxybenzoicacid, 3,4-dihydroxyphenylaceticacid (DOPAC), etc. which are with potent biological activities. The bio transforming action of quercetin 2,3-dioxygenase is believed to be broad range, and it is known to complex with several other flavonoids. Our short-term goal is to understand how dietary metal ions and sequence variation alter the binding and mechanism of enzymatic action of quercetin 2, 3-dioxygenase on different classes of flavonoids in vitro usinga combination of biochemical, spectroscopic, and biophysical methods. In the future, this will help us design and develop microbiota-targeted nutraceuticals to treat lifestyle-related diseases.
Assistant Professor, Chemistry and Physics
Project: Biochemistry of Nucleic Acids Structure/Function
The Ouellet research laboratory is focused on the biochemistry involving nucleic acid structures.
A group of projects are to study the structure/function of RNA as well as DNA, by fluorescence spectroscopy. More specifically, we have projects about the hammerhead ribozyme, the RNA spinach aptamer and the IR-3 Zn-dependent DNA-cleaving DNA enzyme (D-Zyme).
Another group of projects is to use synthetic biology to create new biosensors. In particular, we are developing by SELEX new RNA aptamers that binds specifically and tightly the ligand glucose as well as the ligand 2-hydroxyglutarate. Once discovered, those aptamers will be converted to riboswitches by an innovative method of selection that we are also developing into the laboratory. Those biosensors may provide new therapeutic tools for diabetes as well as some form of AML and gliomas.
The Green Fluorescent Protein (GFP) is often used to identify protein localization and gene expression. It is however dependent on the translational machinery, yielding substantial time delay in gene expression. Moreover, it cannot identify mRNA trafficking. Few years ago, an RNA aptamer was developed to bind a ligand to enhance its green fluorescence, the spinach aptamer. The usefulness of the spinach RNA increases constantly as researchers replaced GFP for it. The crystal structure of the spinach aptamer has been determined and the core consists of an RNA G-quadruplex and base triplet above the first tetrad to stabilize the planar fluorophore.
As a collaborative effort between an organic chemist and biophysicist, various organic ligands will be added to the spinach aptamer to find one that greatly stabilize or destabilize its structure.
A growing field in synthetic biology is the development of RNA molecules that bind tightly and selectivity to a specific ligand. Those RNA aptamers can be coupled to a gene regulation system called riboswitch. For example, a riboswitch could be developed to turn-ON gene expression strictly in presence of the ligand, while turn-OFF without.
The laboratory has been working extensively on the development of aptamer binding two distinct small molecules. With the future aim at curing diabetes, glucose is one of the ligands, and with the aim at curing glioblastoma and AML, the small molecule 2-hydroxyglutarate have been selected.
Computer Science and Software Engineering
Specialist Professor, Computer Science and Software Engineering
Project: Develop a Deep Learning Model to Predict Grant Application Success
Each year, the National Science Foundation (NSF) and the National Institutes of Health (NIH) award tens of thousands of research grants totaling in the billions of dollars. On average, only 25% of proposals are granted funding. Why are 75% rejected? More importantly, why are 25% accepted?
This research project will comb through vast amounts of awarded grant applications to determine why they were selected for funding. By comparing these applications to the funding announcements, the goal is to come up with a deep learning model that can predict the relative success of sample applications.
Award data from both agencies will be synthesized to recognize patterns common to successful applications. A classifier with be developed using a neural network that embodies the presence or absence of these patterns. The model will be established and trained to yield a success probability of sample proposals.
Professor, Computer Science and Software Engineering
Project: Emergency Healthcare Performance Evaluation and Optimal Staffing
A health emergency is a situation that poses an immediate risk to health and life and requires urgent intervention to prevent its worsening. Emergency healthcare service is a real-time service, where timeliness is critical to mission success. Stochastic timed Petri nets have been proved to be a powerful tool in patient flow modeling and performance evaluation. The proposed work is a continuation of our previous summer research projects. This research will further explore the use of colored stochastic timed Petri nets in emergency healthcare service modeling, timing performance assessment and resource requirement analysis.
Interim Dean and Professor
Project: Modeling the Spread of Infectious Diseases by Dynamical Systems
The spread of infectious diseases and other epidemiological phenomena can be modeled and analyzed using dynamical systems. The simplest of these models includes the classic SIR (Susceptible, Infected, Recovered) compartmental model which is a set of three coupled first order differential equations. These models become increasingly complicated as more compartments, specific details, and interactions are added. While these additions are necessary to render the model more realistic, analysis of solutions becomes equally complicated. In these instances, reliable numerical techniques are needed to approximate the solutions or even understand specific properties of the solutions such as long-term behavior.
This project will initially focus on building a mathematical model related to the spread of infectious diseases where the incorporated complexities are related to the Monmouth University community, campus layout, and student body. In addition to developing the model, we will seek solutions based on power series representation of the compartments that make up the model. The focus on this second component of the project will seek to determine the radius of convergence based on a time frame for the series solutions and attempt to quantify the convergence behavior based on factors that support the coupling of the system.
Urban Coast Institute
Associate Director, Urban Coast Institute
Project: Sediment Transport Analysis for Tidal Marsh Island Restoration
Salt marshes are key coastal ecosystems that provide habitat for wildlife and vital ecosystem services for humans, such as protection from storm surge and waves. A study by NOAA examining the impacts of coastal salt marshes on flood risk to properties in Barnegat Bay, NJ found that marshes reduce annual flood risk by up to 70% over a wide range of storm characteristics. Sea level rise (SLR) is decreasing marsh acreage, reducing habitat and exposing communities to greater storm damage. Reducing the loss of marsh acreage may require the addition of sediments onto the marsh platform to increase its elevation at a pace equal to or greater than SLR. The most effective method to supplement marshes with sediment is presently subject to great debate. Natural sediment deposition on marshes occurs due to infrequent storm surge driven overwash and higher frequency estuarine overwash (that is, sediment re-suspended and moved from the estuary, tidal flats, or marsh edge and onto the marsh during storm conditions). Very little is known about the natural sediment transport in New Jersey’s coastal bays. The proposed research seeks to measure waves, tides and currents adjacent to a tidal salt marsh in Barnegat Bay to determine the potential natural sediment transport capacity available to aid marshes in keeping up with future SLR.