Summer Research Program 2020
Projects listed with an asterisk (*) below are accepting rising senior high school students.
Endowed Associate Professor of Marine Science
Project Title: Harmful Algal Blooms in Monmouth County Coastal Lakes, Estuaries, and Ocean
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 due to a combination of nutrient pollution and climate change, 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 in 2018, including the Navesink / Shrewsbury river estuaries; the Hudson-Raritan Estuary; and Monmouth County’s coastal lakes. 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.
Assistant Professor, Biology
Worldwide, 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 fish species including sturgeons and coastal sharks. 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. Through the use of acoustic telemetry we can answer many of these questions. This years, SRP will primarily focus on 1) understanding the population demographics and survival of shark species captured in the lad-based recreational fishery and 2) examining the spatial and temporal habitat use of the endangered Atlantic sturgeon in Raritan and Sandy Hook Bay. Specifically:
Sharks and Rays
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. This project builds on previous years collaborations with the recreational community. 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.
Using acoustic receivers (and previously tagged fish) over the last 2 years, we have been able to detect numerous Atlantic sturgeons within Sandy Hook and Raritan Bay. This project builds 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.
Dr. Martin Hicks
Assistant Professor, Biology
Project Title: Gene Therapy for the Treatment of Brain Tumors
The Hicks Lab Summer Research Program focuses on the design and testing of AAV gene therapy vectors 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. We are developing a novel approach using direct administration of AAV vectors that encode RNA therapeutics to deliver treatment to the tumor within the central nervous system (CNS). The proliferation of GBM is often linked to the overexpression of tyrosine kinase receptors (TKRs), a cell-surface receptor. When TKR binds to its cognate ligand, it stimulates a signal cascade that leads to cell growth, migration and tumor angiogenesis. To downregulate overexpressed TKRs in GBM, we have designed RNA therapies that reduce the expression of these oncogenic genes in GBM. To this end, we have demonstrated efficacy of multiple therapies to reduce expression of various TKR oncogenic genes in the GBM tissue culture model.
To further test these therapies, the Lab is developing a mouse model of GBM here at the Monmouth University vivarium during the summer program, we will be testing therapies directed against specific TKRs in the mouse model. We expect that the AAV gene delivery system of RNA antisense therapies will decrease expression of oncogenic genes, reduce tumor growth and increase survival in a mouse model of GBM. Furthermore, with the advancement of nanopore sequencing technology, the Lab is 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 our RNA anti-sense directed therapy platform. Students in the lab will be introduced to techniques in molecular biology, tissue culture and research animal methods and welfare to better understand human health and disease.
Project Title: 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 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 research the inhibitory effects of specific pure essential oils (Arborvitae, Cassia, Cinnamon Bark, Clove, Cypress, Oregano, Thyme, and Manuka Oil) and Methylglyoxal on the growth of multidrug resistant bacteria including: Acinetobacter baumannii, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. We will research the inhibitory effects of these essential oils alone and in combination with the currently used antibiotics used to treat these multidrug resistant bacteria. Multidrug resistant bacterial infections are a very serious global health problem.
Dr. Megan Phifer-Rixey
Assistant Professor, Biology
Project Title: Evolutionary Genetics in the Wild
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. To better understand local marine and estuarine communities, my lab will also be part of collaborative projects using eDNA (environmental DNA) to survey the lower Hudson-Raritan estuary 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, laying the foundation for ongoing collaborative research.
Assistant Professor, Biology
Project Title: Reptile and Amphibian Ecology and Conservation in Urbanized and Suburbanized Ecosystems
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, climate change). This projects aims to explore ecological research and conservation opportunities for reptiles and amphibians in New Jersey and represents an opportunity to study how reptiles and amphibian populations persist alongside high human density populations using several specific study systems.
The coastal lakes of Monmouth County, New Jersey represent urban habitats that have been used for a variety of recreational activities, including fishing, boating and swimming. Coastal lakes are also among the only remaining habitats for wildlife species that are able to persist in highly developed, urban areas. First, we will continue sampling freshwater turtles that inhabit coastal lakes and man made canals in New Jersey. For this study, we will use baited traps and capture mark recapture to collect data to estimate population such as density and annual survival.
Additionally, we will begin a basking survey of turtles which are distributed throughout the Delaware Raritan Canal in an occupancy framework to estimate the distribution of two rare species; the red-bellied cooter (Pseudemys rubriventris) and Northern map turtle (Graptemys geographica). Amphibians are another wildlife group that may use coastal lakes. Most frogs are seasonal breeders which are very challenging to observe because they breed quickly during rainy nights. We will use “frog loggers”, which are automated acoustic monitoring systems to sample for frogs in five coastal lakes.
Third, we will be designing and completing an experiment to understand the influence of hovering height and environmental conditions on the detection of 3D-printed diamondback terrapins (Malaclemys terrapin) by unmanned aerial systems (e.g., drones). This drone research is attempting to demonstrate proof of concept for wildlife managers to estimate population parameters using drones.
Chemistry and Physics
Assistant Professor, Chemistry and Physics
Project Title: Cell Motility through Torque Spectroscopy and High Speed Video Analysis
Motile flagella and cilia of swimming microorganisms at low Reynolds number have been under scrutiny due to their multi-functional roles such as sensing extracellular signals, nutrient uptake, and exerting propulsive force and torque for locomotion.
1) The bacterial flagellar motor (BFM) in Escherichia coli (E. coli), a tiny rotary engine (~ 40 nm) that powers microorganisms, is one of the most complex and the largest biological motors. Its components such as a rotor, stators, a flexible hook, and filaments consist of ~ 25 different proteins. In particular, the complex of rotor and stators constitutes a torque generating unit. In the model bacterium E. coli, for example, the rotor is connected to a hook and surrounded by approximately 11 stators, and the estimated maximum torque when fully loaded is ~ 1260 pN·nm. However, much remains to be investigated, in particular, the torque generating mechanism of the BFM. In this study, we will investigate the torque generating mechanism of the BFM in E. coli using innovative instrumentation, Magnetic Tweezers (MT).
2) Paramecium is a unicellular protozoan covered by thousands of cilia. It is commonly studied in biology as representative of the ciliates due to its being widespread in nature and its relatively large size. Moreover, it shows clear quantifiable responses to environmental stimuli such as magnetic field, electric field, temperature, light, and chemical gradients. Of particular interest has been its response to gravity and viscosity that play important roles in cell life. In spite of its importance and many studies of responses to those environmental stimulations, some crucial properties such as ciliary motor characteristics have not been clearly elucidated. This project will investigate a detailed ciliary behavior of swimming paramecia and their response to gravity and varying viscosity.
Lecturer, Chemistry and Physics
Project Title: Modeling Energy Transfer in Light Harvesting Proteins: The Role of Molecular Vibrations
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.
Associate Professor, Chemistry and Physics
Project Title: Synthesis of Novel Cationic Ligands as Potential Telomerase Inhibitors
In recent years the reverse transcriptase enzyme telomerase has become an attractive target for the development of novel anticancer therapeutics, due to its overexpression in more than 85% of tumors. Several strategies have been developed to inhibit telomerase and, among these, folding of the telomeric DNA sequence (G-Quadruplex) induced by small organic molecules has shown some promising results. In this project we will be synthesizing novel small cationic molecules (ligands) that have been designed to bind effectively to the DNA G-Quadruplex sequence. Successful binding and stabilization of the G-Quadruplex can lead to the development of a novel class of anticancer drugs.”
Associate Professor, Chemistry and Physics
Project Title: Preparation and Physical Studies of NHC-Stabilized Rhenium Polyhydride Complexes
Nitrogen heterocyclic carbene (NHC) groups are rings of, typically, carbon and nitrogen atoms supported by hydrogen atoms and/or alkyl or aryl fragments. NHCs also include a carbon atom with a lone pair of electrons that can serve as a Lewis base. NHCs have become common ligands for transition metal complexes where the Lewis base carbon center donates its pair of electrons into an empty metal orbital to form a dative bond between carbon and the metal atom. Olefin metathesis reactions, an important synthetic step in many syntheses of organic molecules, became much more useful when Grubbs et al. found that the catalysts used in such reactions were more effective when supported by NHC ligands rather than by tertiary phosphine ligands.
Several rhenium polyhydride complexes are known to catalytically transform small organic molecules. Nearly all known rhenium polyhydride complexes are supported by tertiary phosphine ligands. Recently, however, the first report of rhenium polyhydride complexes supported by NHC ligands appeared in the literature. Because of the more stable bonds in NHC ligands we suspect that NHC-stabilized rhenium polyhydride complexes should be more durable catalysts for small molecule transformations. We have had considerable recent success in determining the fluxional rearrangement modes for eight-coordinate rhenium polyhydride centers that are stabilized by tertiary phosphine ligands by preparing such complexes, measuring their NMR spectra at a variety of temperatures, simulating the experimentally measured spectra and then using the simulation models and resultant data to explain the fluxional processes in the molecules. In this project we plan use the same techniques to examine the fluxional nature of eight-coordinate rhenium polyhydride complexes supported by NHC ligands.
Assistant Professor, Department of Chemistry and Physics
Project Title: Biochemistry of the RNA 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 as well as gel kinetics. More specifically, we have projects about the hammerhead ribozyme, the spinach aptamer and the IR-3 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.
Computer Science and Software Engineering
Professor, Department of Computer Science and Software Engineering
Project Title: Hawks Code: NAO Robot Programming
* Project Description: NAO is an autonomous, programmable humanoid robot. It is a great tool to learn programming and conduct research into human-robot interactions. This project will explore the speech recognition capability of NAO robots. Students will develop a NAO-user communication system that the robot can answer questions related to Monmouth University in general and all degree programs at the CSSE department, and can make movements according to user requests. Python will be the programming language.
Professor, Department Chair, Mathematics
Project Title: Impact of Compression of Similar Signals Using Wavelets
The process of compressing an audio signal is, in part, the result of an effort to reduce the file size. This is necessary in applications related to both storage and transmission of the file. In a general sense, compression is either lossy or lossless where the former employs techniques or algorithms that approximate or discard information making it impossible to fully reverse the compression process. In other words, there is no free lunch; efficient compression comes at a cost. Of course, the consequences of the loss of information in lossy compression varies.
It is reasonable to consider that a signal may have different variations. Between studio and live versions of a song could be thought of as variations of the same signal. One may think of the studio version of a song as the (original) signal and consider live versions as the variations. In this situation, the differences exist before compression begins.
Basic wavelet compression employs a signal representation in terms of a basis. Consequent levels of decomposition based on nested subspaces and leads to a version of the signal that largely conserves the energy of the signal among other characteristics. Portions of these characteristics may be approximated or even dismissed to reduce file size and result in a lossy compression. The aim of this project is to investigate the impact of wavelet compression on different versions of the same signal. We will attempt to understand what similarities or differences exist initially and what the impact of compression has. In particular we will explore the ratio and related threshold parameters and how they relate to different versions.
Assistant Professor, Math
Project Title: confcurve: Development of an R Package for Statistical Inference with Confidence Distributions
A reproducibility crisis is brewing in the application of statistics to medicine and the social sciences. The reproducibility crisis has many causes, including P-hacking, the garden of forking paths, and the file drawer effect. Much of the blame for the reproducibility crisis has been heaped on P-values and their abuses. Confidence intervals have been proposed as a supplement or alternative to P-values. However, even confidence intervals suffer from the pre-assignment of a default coverage level, typically 95%, and thus fall into the same trap as using the standard 0.05 cutoff for statistically significant versus non-significant estimates.
Confidence distributions provide a straightforward and readily graspable way to extract all of statistical information that can be inferred from a given data set under a given model, including point estimates, confidence intervals, and P-values. The theory of confidence distributions is well-developed, and the practical aspects of their implementation with many commonly used models has reached maturity. However, without readily available and user-friendly software for generating confidence distributions from data, confidence distributions will likely remain outside the toolkit of practicing scientists who lack extensive training in mathematical statistics.
During this project, students will design statistical software in R to construct confidence distributions for a diverse set of statistical procedures. This software will be validated using real world data sets. Over the course of the summer, students will gain skills in statistical inference, numerical analysis, and software development that will serve them well in any future endeavor in the applied sciences.
Susan Fiske, former president of the Association for Psychological Science, has called advocating for methodological reform in her own field of social psychology “methodological terrorism.” One person’s terrorist is another person’s freedom fighter. Join the resistance this summer!
Associate Professor, Mathematics
Project Title: Maximal Length Divisor Cycles
A finite sequence of distinct positive integers is called a divisor chain if each term is either a divisor or a multiple of the preceding term. A divisor chain is called a divisor cycle (or loop) if the first term is also either a divisor or multiple of the last term. The chain (or cycle) is bounded by the natural number n if the terms of the sequence are all less than or equal to n. It’s natural to ask: what is the longest chain or cycle that can be constructed with a given bound n?
Erdös and Pomerance initiated the study of maximal bounded divisor chains in the 1980’s by looking at their asymptotic behavior. Our project will focus on smaller, computational problems concerning maximal bounded divisor cycles and other similar structures, as well as the structure of their graph-theoretic models. Students working on this project will have the opportunity to increase their knowledge in the areas of number theory, abstract algebra, and graph theory.