Sustainability Science BS
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From basic commercial systems to the research field, vacuum technology and engineering are an essential element of scientific development. For high-precision applications, such as those being applied in the nuclear physics research at Montclair State University, the level of vacuum required is in the high to ultra-high vacuum range, which has pressure values of between 10-3 to 10-5 Pa. In recent years, there has been a migration to so-called “dry” pumping systems, which reduces the risk of oil contamination. However, these dry vacuum systems have the trade-off of producing dust contamination at the pump. If the power switches off and an appropriate isolation valve between the pump and vacuum chamber is not closed, then dust can be sucked back into the vacuum chamber. The primary objection of my research is to mitigate this issue in the case of power failure with an appropriate device using a latching-relay based system. The device is designed so that the isolation valve remains closed even after the power comes back on, and that user intervention is required to reopen the isolation valve only after the experimental environment and pump has reached stability again. We packaged this entire mechanism in a small enclosure that not only prevents any misuse but provides a compact form factor for proper integration into the lab environment. The device has been put through several bench tests.
Co-Author(s): Maryum Bhatti, Sarah Cho, Davis W. Konas, Nina M. Goodey
Mycobacterium tuberculosis is the bacterium that causes the disease tuberculosis. There are antibiotic currently available to treat TB, this disease has started to show signs of antibiotic resistance. For M. Tuberculosis to survive in the human body, it needs access to tryptophan. The human body does not produce tryptophan, but fortunately for tuberculosis, the bacterium that causes it can create its own tryptophan. Idole-3-glycerol phosphate synthase is an enzyme that catalyzes a key step in the tryptophan biosynthetic pathway. The enzyme IGP synthase catalysis with CdRP to make IGP. IGP is a necessary molecule for M. tuberculosis and is a precursor for the synthesis of tryptophan. IGP synthase is believed to be an essential enzyme in M. tuberculosis and that it could perhaps be targeted by inhibitors to inhibit the bacteria’s ability to create tryptophan. The goal of the project is to understand the roles of the residues in the active site by creating single point mutations. By preforming pH profiles, comparing pka’s, Km, and Kcat from kinetic assays between the Wildtype and the mutant, we can identify the role of the residue has in the active site. Understanding how these enzyme works, the better our chances are in finding a way to combating the dilemma of drug resistance we are facing. We created a single point mutation, known as E57Q, where we replaced the glutamic acid (E), a negatively charged amino acid, with glutamine (Q), a polar amino acid. In the wildtype, we hypothesize that the glutamic acid acts as a catalytic base. With better insight to these residues, potential inhibitors can be made for M. tuberculosis IGP synthase.
With all the outbreak of viruses, it is becoming increasingly important to have contact tracing and infection tracing methods. For example, acute respiratory syndrome Coronavirus 2 (SARS-CoV2) has spread across many nations, sending billions of people into lockdown. Due to the nature of contact tracing, there is a public concern on privacy issues that has been a bottleneck to existing solutions. The problem that we are facing is Privacy-Preserving Contact Tracing for COVID-19. There are several different solutions that have been proposed over the past few years. For this research, our goal is to find a more effective and secure solution for contact tracing. The key to a privacy-preserving contact tracing system is to protect the location information of not only the patient /user but also along with the ability to check for proximity. In order to achieve these goals, we utilized a homomorphic encryption technique in a discrete grid system to develop a new and secure proximity computation method. We have proposed two different proposed solutions, which are homomorphic based encryption and Grid based solution. Our first solution is more secure but less efficient than the second solution; thereby providing a trade-off to suit different application requirements.
Clean air has always been an integral part of life that is essential for people’s well-being. Exposure to considerable amounts of air pollution for even short periods of time can significantly reduce life expectancy as well as cause various health problems. With the rise of the COVID-19 pandemic, the focus on air quality has been heightened as people became more cognizant of the air they breathe. As HEPA filters are known for their effectiveness in reducing particulate matter in the air, they have been particularly useful in reducing the spread of the COVID-19 virus (contained in aerosolized droplets) in places at which large amounts of people congregate indoors based on leading studies of COVID-19. The purpose of this research is to determine whether the levels of particulate matter in the air are affected by the age of the HEPA filters being used.
Our first study involved benchmarking a household indoor air quality monitor against a higher-quality model to check whether the former can accurately measure and categorize particles by size in the range of 0.3 -10 microns (e.g. PM0.3, PM1.0, PM2.5, PM5.0, PM10). We accomplished this by using the cleanroom laboratory in the Center of Environmental and Life Sciences building as a controlled environment. Then we measure the efficacy of HEPA-filter equipped fans in a real classroom environment. First, we will test the air for particulate matter with no active HEPA filters, which will then be compared against air quality measurements in the same room under similar conditions first using old HEPA filters, and then brand new HEPA filters.
We live in a world full of technology, where a large amount of the population has access to electronic devices, increasing by the day. Most children use such devices for entertainment purposes but due to the broad knowledge containment, they have access to content that may be inappropriate for their age. To address this situation, parental controls can be placed on their devices. Parental controls are software services that allow people to monitor and restrict what another person does online. In this project, the differences and effectiveness of various parental control software systems are investigated. While parental control applications have included a variety of online interactions (such as web browsing, social network activity, etc.) the project focused on controls for video streaming service applications (such as YouTube, Netflix, Prime video and Disney +). The controls were evaluated from two points of view. First, the technology behind the controls and their ease of use were studied. Next, the user’s perception of such controls and their effectiveness was investigated. Human Computer Interaction (HCI) is an active area within Computer Science. How easy it is to use features in an interface has significant implications on the success of deploying a new tool. The study seeks to understand both the user’s perception on available parental control technology as well as the ease of use of such technology. By doing so the study contributes to HCI and can inform future parental control interface design.
In recent years, the world has seen a quick progression in technological advancements. As cars drive on their own and handheld phones become smartphones, higher education institutions struggle to keep up with the quick pace of advancements. Recently, especially in times of the COVID-19 Pandemic, the higher education sector has taken on and become more reliant on remote learning and other new information technology-based services. Consequently, proper cybersecurity measures have become more important as higher education institutions have been experiencing ransomware attacks more than ever. To understand how vulnerable higher education institutions are in the face of cyberattacks we pursued two directions. First, quantitative data from public repositories, and state district attorney public postings were collected and aggregated into a larger repository, allowing researchers to extract statistical insights into the recent cybersecurity incident trends (in terms of number, type, and scope). Second, an in-depth interview was conducted with a university’s Information Technology professionals. The data show that over the past several years, ransomware attacks have changed from system hacking to social engineering. This means that cybersecurity incidents are best prevented through human factors. As phishing scams are one of the most common reasons ransomware attacks are successful, it is best for the institution to educate their community on the awareness of cybersecurity. Higher education institutions can suffer severe financial, reputational, and operational consequences which can be defended through easy remedies. In conclusion, our analysis shows that there has been an increasing trend in which higher education institutions are easy targets for cybersecurity breaches, thus, protocols, procedures, and simply the awareness of ransomware attacks and how they impact not just the institutions but the students and staff themselves.
Trifluoromethyl compounds are widely used in the pharmaceutical and agricultural industries. As a result, the synthesis of these compounds has become of interest in recent research. In a recent work, Ye and Sanford proposed a mechanism for the trifluoromethylation of boronic acids using both photocatalysis and copper catalysis. The goal of this study is to use computational methods in order to gain a more detailed understanding of the mechanism proposed by Ye and Sanford. Computational chemistry can determine whether the proposed mechanism is thermodynamically reasonable through calculations of the transition state energy barriers. Further analysis on the effects of using various different reactant functional groups can also be performed. Understanding the true nature of this reaction mechanism can be beneficial to the ongoing optimization of the synthesis of trifluoromethyl substituents.
Co-Author(s): Raisa Da Silva
Six bacteria: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter aerogenes abbreviated as ESKAPE are the leading cause of nosocomial infections due to their multidrug resistance. Polyphenols extracted from the leaves of Camellia sinensis contain antibacterial properties with epigallocatechin-3-gallate (EGCG) being the main polyphenol. EGCG is not naturally stable so epigallocatechin-3-gallate-stearate (EGCG-S) and palmitoyl-epigallocatechin-3-gallate (P-EGCG) were synthesized. Epigallocatechin-palmitate-based formulations cF1 and cF2 were made to study the efficiency of inhibition on growth and biofilm on ESKAPE bacteria Staphylococcus aureus and Klebsiella pneumoniae. Antibiotics tetracycline and erythromycin were used alone, and in combination with EGCG-S to observe efficiency of treatments. A time-course study and a colony-forming unit assay were conducted evaluated effectiveness of treatments and optimal killing time. Congo Red and Crystal Violet assays were conducted to observe inhibition percentage via biofilm formations. LIVE/DEAD Bactlight TM Bacterial Viability test was conducted to evaluate the efficiency of the treatments via fluorescent microscope. The results showed that cF1 and cF2 can inhibit the growth of S. aureus and K. pneumoniae at a near 100% rate. EGCG-S inhibits and reverses the formation of biofilms of these two bacteria from the Congo red assay. Crystal violet study indicated the percent of inhibition for cf1 was 62.46% and 81.93% for Staphylococcus aureus and Klebsiella pneumoniae while cF2 was 61.08% and 79.52% respectively. The results of this study show EGCG-S has promise to be an alternative treatment method that can work alone or in combination with antibiotics. Formulations cF1 and cF2 can be potential antibacterial agents against ESKAPE bacteria.
Antibiotic-resistance is one of the major causes of the spread of bacterial infections. Generally, there are two ways that bacteria can develop resistance. One is by having undergone a mutation that is beneficial in that it allows them to survive in the presence of antibiotics and the other is by being equipped with a plasmid that contains an antibiotic-resistant gene. Plasmids are circular pieces of DNA that replicate independently of the genetic material found in bacterial cells. The ability to easily engineer them has made them popular vectors that aid bacteria in surviving harsh environmental conditions, such as exposure to antibiotics that halt the bacterial growth cycle and, thus, prevent them from multiplying. In this study, HB101 competent cells were exposed to the bacteriostatic antibiotic Ampicillin over five consecutive generations with the goal of checking plasmid retention for each generation. Cells were transformed with either PGreen or PGLO plasmids. Both plasmids contain the GFP gene and the Ampicillin-resistance gene and this co-expression was exploited to mark the presence of plasmids in competent cells by measuring the fluorescence in each bacterial generation. The fifth-generation bacteria were plated in LB media with and without Ampicillin and the plates were placed under UV light to determine if the genes in the plasmid were expressed by the bacteria. From the data, we have evidence that there is no clear pattern of plasmid retention over generations among the bacterial samples grown in the presence and in the absence of Ampicillin. Even though some of the samples show a gradual decline in plasmid gene expression over generations, there are outliers that tell a different story. They exhibit a mixture of declines and spikes in gene expression among generations. We suspect that these results can be explained by a combination of several factors including the disruption of promoters in the plasmids, the inhibition of factors that guide the RNA polymerase to the transcription site, the incorporation of the Ampicillin resistance gene in the bacterial genome, and even increased levels of GFP toxicity in the cell.
Co-Author(s): Ariella Hernandez
Gravitational waves are novel astronomical tools for observing the dynamic side of the Universe. Unlike light-based telescopes that observe stars and galaxies in electromagnetic waves or light, gravitational-wave detectors such as the Laser Interferometer Gravitational-wave Observatory (LIGO), are 4 km-long Michelson interferometers that use infrared lasers and light interference to sense gravitational waves from merging black holes, or colliding neutron stars. Detected for the first time in September 2015, gravitational waves carry information that cannot be obtained in any other way, helping our understanding of their origins, and of the Universe. With very sensitive detectors, we could observe gravitational waves from even further sources – as far as the edge of our Universe itself, and upgrading the current detectors to increase their sensitivity just brings us closer. Our research is focused on the development of one key device that contributes to improving the sensitivity of these detectors – a Faraday isolator. This device operates based on a magneto-optical material which helps control the polarization of light by applying an external magnetic field. Improved Faraday isolators require high transparency, effective polarization control, and minimal distortion of the transmitted beam. Cerium Fluoride (CeF3) is one promising magneto-optical candidate, and we will be addressing these aspects in our study.
Co-Author(s): Mariam Mchedlidze
The next generation of gravitational-wave detectors would be very sensitive to wide-open the window to the Universe’s farthest edge, and let us get a glimpse on the formation of the earliest black holes, and of the Universe itself. Faraday isolators are devices that directly help improve the sensitivity of the gravitational-wave detectors, by protecting them from scatter light that would build noise in the detectors. At the core of Faraday isolators are magneto-optical materials, which rotate the polarization of light when they are immerse in a magnetic field along the beam propagation. One of the very promising materials in the wavelength range of interest of 1-2.4 microns is Bismuth-substituted Yttrium Iron Garnet (BiYIG), which shows extremely high effectiveness of producing Faraday rotation, high transparency around 2 microns wavelength, and good beam quality when magnetically saturated.
Co-Author(s): Vladislav Snitsarev
In contrast to normal cells, cancer cells grow uncontrollably and produce a local chemical environment that supports this growth. When found to be in a hypoxic state, a condition seen in rapidly growing cells, for example, enzymes in the glycolytic pathway are upregulated. One side effect seen from this switch however is a decrease in pH leading to a more acidic environment. Although the impact pH can have on growth rates is not yet clearly understood, it is thought to involve transcriptional changes in genes involving pH regulation and metabolic processes. Our previous results demonstrate a complex effect of acidic pH on Jurkat T-cell growth. In our research we are analyzing transcription of genes involved in these pathways in order to determine if there is a change in response to varied pH conditions. Specifically, RNA was isolated from Jurkat cells grown in either pH 7.2 or 7.4 media. Following this isolation, qPCR was performed to evaluate changes in specific gene expression. Using primers against Hexokinase 2, Phosphomutase and GAPDH as an internal control, we were able to get amplification of these genes in a template specific manner. Primer design and results will be explained more in depth later in the results section.
Co-Author(s): Beth Phipps, Maham Irfan
When exposed to inhospitable environmental conditions, such as UV radiation, extreme temperatures, and chemical damage certain bacteria will initiate sporulation processes to form endospores as a self-preservation mechanism. Endospores are the dormant form of vegetative cells with a hardy proteinaceous coat that enables survival in harsh environments, until optimal conditions allow for germination. These highly resistant spores pose significant threats in the form of HAI (Hospital-Acquired Infections) such as meningitis, gastroenteritis, food poisoning, and contamination. Our research investigates three such spore-forming, rod-shaped Gram-positive bacteria; Bacillus cereus, Bacillus megaterium, and Bacillus subtilis. Previous studies have highlighted that modified EGCG (epigallocatechin-3-gallate), a polyphenol found in green tea leaves from Camellia sinesis, has antibacterial, antioxidant, anti-inflammatory and now sporicidal properties. EGCG is reported to inhibit the germination of spores from vegetative cells and is believed to be synergistic with antibiotics against bacterial growth, increasing susceptibility. In this study, EGCG-S and P-EGCG containing formulations were used to evaluate their effects on these bacterial vegetative cells and their spores. Vegetative cells were exposed to six various antibiotics alone or in combination with EGCG-S to determine the synergistic effects. The findings suggest that EGCG-S increases some antibiotic activity and improves Bacillus.spp vegetative cell susceptibility. Time course studies on both cells and spores were conducted using two formulations, CF1 and CF2. The results indicated that both formulations can inhibit vegetative cells ranging from 97% to 99% and spores ranging from 74% to 90%. The findings suggest that CF1 and CF2 are promising anti-bacterial and anti-spore agents.
Co-Author(s): Abraham Helwani, Mohamad Gacham
Prosthetic joint implantations have greatly changed orthopedic medicine by allowing people to regain their physical function with minimal side effects. However, individuals are susceptible to complications due to bacterial infections. Three significant bacteria which are responsible for bacterial infections post prosthetic joint implantations include Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis. These bacteria stick to the prosthetic joint and form biofilms as a defense mechanism and therefore become antibiotic resistant. Green tea polyphenols, extracted from the leaves of the Camellia sinensis plant have shown antibacterial, anti-inflammatory and antioxidant characteristics. Modified epigallocatechin-3-gallate-stearate (EGCG-S) and palmitoyl-epigallocatechin-3-gallate (P-EGCG) are efficient and have a synergistic effect on antibiotics indicating a positive role in the elimination of bacterial infections. In this study, the inhibitory effect of EGCG-S and P-EGCG with or without two antibiotics (Polymyxin B and Bacitracin) and wash on Pseudomonas aeruginosa individually as well as the on the three bacteria in combination was investigated. Colony-forming unit (CFU) assays were used to determine the percent of inhibition by the tea polyphenols. The results indicated that EGCG-S and P-EGCG tea polyphenols inhibited Pseudomonas aeruginosa bacterial growth by 33.12 percent and 20.13 percent respectively. Time course studies were performed using CF1 and CF2 formulations to determine the percent of inhibition. Congo Red qualitative biofilm assays were used to analyze the effect of tea polyphenols on biofilm. Combination treatments were shown to overcome the formation of biofilm. Crystal violet quantitative biofilm assays were used to analyze the effect of tea polyphenols on the percent of biofilm inhibition. P-EGCG and EGCG-S inhibited biofilm formation by 64.70 percent and 95.11 percent respectively. These results indicate that EGCG-S and P-EGCG could be used as a treatment option against bacteria that cause joint infections.
Co-Author(s): Abraham Helwani, Kavneet Chahil
Prosthetic joint implantations have reformed orthopedic medicine and have made it possible for people to regain their physical function. Unfortunately, these implantations are susceptible to post-surgical complications due to bacterial infections. Staphylococcus epidermidis can adhere to the prosthesis and form biofilms thus making it more antibiotic-resistant. The modified green tea polyphenols, Epigallocatechin-3-gallate-stearate (EGCG-S) and palmitoyl-epigallocatechin-3-gallate (P-EGCG) have shown antibacterial, antioxidant, anti-inflammatory properties, and can enhance antibiotics activities. In this study, the inhibitory effects of EGCG-S and P-EGCG with or without two generally used antibiotics (Bacitracin or Polymyxin B) on Staphylococcus epidermidis were investigated. Colony-forming unit (CFU) assay was used to determine the viability and percent of inhibition. The results indicated that EGCG-S and P-EGCG inhibit 52% and 71% of bacteria, respectively. Time course study was performed using P-EGCG containing formulations CF1 and CF2 to determine the efficacy of the formulations. The results were very promising with a percentage of inhibition up to near 100%. Congo Red assays were used to qualitatively analyze the effect of tea polyphenols on biofilm and the results suggest that P-EGCG, EGCG-S, and all other combination studies can prevent biofilm formation. Crystal Violet assay was done to quantitatively analyze the effects of the polyphenols and antibiotics with a percent inhibition for all treatments ranging from 26% to 98.5%. This study showed that EGCG-S and P-EGCG when used in combination with Bacitracin or Polymyxin B, resulted in the best antibacterial effect and could be used as a treatment against bacteria that cause joint infections. Formulated CF1 and CF2 are promising antimicrobial agents for future commercialization.
Co-Author(s): Calvin Taylor
The inappropriate use of antibiotics throughout the years has led the world to face an emergence of multidrug-resistant microorganisms that have become one of the top ten threats to global public health. Concomitantly, the development of new antimicrobial drugs has been diminished. Acinetobacter baumannii and Pseudomonas aeruginosa are two of the six antibiotic-resistant bacteria species responsible for most of the current nosocomial infections. These bacteria cause severe infections in immunocompromised patients in hospital settings. The main goal of this research was to determine the efficiency of EGCG-Stearate used alone or in combination with erythromycin and cF1/cF2 formulations against the growth and biofilm formation of A. baumannii. and P. aeruginosa. Standard serial dilutions were performed to determine the optimal dilution factor for these bacteria. Congo Red Assay was conducted to study the effectiveness of 250 ug/mL of EGCG-S used alone and in combination with Erythromycin, and cF1/cF2 against biofilm formation. EGCG-S presented 99.650% of inhibition and a 2.46 log reduction of A. baumannii and 50% of inhibition of P. aeruginosa when used on its own after one hour of treatment. In the Congo Red Biofilm Assay, EGCG-S showed to inhibit the formation of biofilm when used on its own and in tangent with the antibiotic Erythromycin. In the formulation study, 30 seconds was enough to inhibit nearly 100% of both bacteria. These results indicate that EGCG-S is a potential therapeutic agent to be used against P. aeruginosa and A. baumannii.
Co-Author(s): Mohamad Gacham, Kavneet Chahil
In medical microbiology there are constant challenges that are being faced. One of these challenges revolves around prosthetic joint bacterial infections. Staphylococcus aureus (S. aureus) is a predominant microorganism that is responsible for biofilm formation on the prosthetic joint and has the ability to become antibiotic resistant. An alternative to combat the antibiotic resistance of S. aureus is through polyphenols extracted from the leaves of Camellia sinensis plant. These polyphenols have been reported to have notable anti-inflammatory, antioxidant, and antibacterial properties. Epigallocatechin gallate (EGCG) is the most abundant polyphenol in this plant that is responsible for the cellular benefits and inhibitory properties of intrusive microorganisms. Modified versions, epigallocatechin-3-gallate-stearate (EGCG-S) and palmitoyl-epigallocatechin-3-gallate (P-EGCG) have shown to be more stable and effective on inhibition of microorganisms. In this study, common antibiotics used to treat S. aureus (Polymyxin B and Bacitracin) for joint infection were tested alone or in combination with the modified polyphenols to compare the efficacy of different treatments. These various tests include a colony-forming unit assay (CFU) and time course studies using P-EGCG containing CF1 and CF2 formulations to test bacterial viability. Congo Red qualitative biofilm assay and Crystal Violet quantitative biofilm assays were carried out to test biofilm formation and percent inhibition. The results indicated that EGCG-S and P-EGCG enhance the antibiotics treatment; CF1 and CF2 can efficiently inhibit the growth of cells to near 100% in 30 seconds. Congo Red and Crystal Violet assays indicated treatments preventing biofilm formation. The studies concluded that EGCG-S and P-EGCG have a promising inhibitory effect on the growth of S. aureus. CF1 and CF2 are promising anti S. aureus agents.
Co-Author(s): Angadh Singh, Laura Lepore, Taylor Isles, Istiaque Chowdhury, Charles Du
Retrotransposons, exclusive to eukaryotes, are genomic elements which can copy and insert themselves to other loci within a genome. These RNA-based elements, also referred to as Class I transposable elements, can be categorized as short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINE), terminal-repeat retrotransposons in-miniature (TRIMs), or long terminal repeats (LTRs). Of these categories, LTR retrotransposons constitute approximately 65% of the total genomic sequence of maize. An LTR retrotransposon may be considered recently active and able to undergo reverse transcription if it has not seen differential mutations between its 5’ and 3’ LTR sequence. Here, we describe a computational biology method to analyze whole-genome sequencing data from maize and locate candidates of potentially active LTR retrotransposons. This method uses a freely accessible tool as a base for locating LTRs in genomic sequences known as “LtrDetector”. Once candidate LTR sequences are presented by LtrDetector, the results can be filtered by size (e.g. 5,000 basepairs) and by chromosome. Active LTR retrotransposon candidates are further filtered for identical 5’ and 3’ LTRs. A defining feature of these elements known as a polypurine trace (a sequence of purine residues immediately upstream of the 3’ LTR) is utilized to further filter potential candidates. 5 basepair target site duplications (TSDs) which flank on the outside of the 5’ and 3’ LTRs must also be identical. Finally, a primer binding site is identified and used in filtering active retrotransposon candidates. Our results show that from a pool of 29 maize genomes, and an original list of 3,771,936 candidates from LtrDetector, we were able to identify fewer than 2,000 possible active retrotransposons.
Co-Author(s): Rayan Murtada, Ray Stanton, Teuta Hida, Wilthon Gilles, Nathalia Letrari
Elucidation of glycans, or oligosaccharides, is a rapidly evolving field of research that seeks extraordinary potential to serve as early biomarkers for diseases involving or including cancer metastases, autoimmune diseases, pathogen-host interactions, inherited diseases, and Alzheimer’s disease, among others. Much attention in recent decades have therefore shifted heavily towards the accurate characterization, discrimination, and highly-sensitive detection of glycans via liquid chromatography-mass spectrometry (LC-MS). To aid in this endeavor, glycans can be derivatized with reagents that are strategically synthesized with functional groups that significantly improve their analysis. Herein, four different reagents were synthesized with (1) an amino group for covalent attachments at the reducing termini of glycans, (2) a free radical precursor for the induction of systematic, predictable, and efficient fragmentations for glycan characterization and discrimination, and (3) a fluorophore base that allows for highly-sensitive fluorescence-based detection. The capabilities of each reagent were analyzed and compared in terms of their (a) glycan fragmentation quality via mass spectrometry, (b) methylation turnover for fixed charge development to aid in mass spectrometric analysis, (c) glycan coupling efficiency, and (d) detection sensitivity via fluorescence.
Solar flares are powerful events that rapidly move large quantities of energy and charged particles from the surface of the sun to space. When directed at the Earth, these events can potentially knock out operational satellites and even Earth-based IT infrastructure. In this study, data gathered from flares by NASA’s Solar Dynamics Observatory (SDO) is first used to visualize patterns among solar flares and then to train a machine learning classifier to ascertain if these events can be confidently predicted. After the classifier is trained, it is tested and used to predict the magnitudes of future flare events.
The UMAP algorithm scales and reduces the dimensions of the dataset and provides a more comprehensive visualization of the raw data. In the second part, the scaled dataset is fitted to a support vector machine (SVM) to train it. The results from UMAP show visual clustering patterns inside the higher dimension dataset while still keeping the overall structures, which indicates the possibility of distinguishing certain classes of flares from raw data. This is supported by the confident results from the trained SVM and gives insight into the unrealized potential of using machine learning to predict new instances of events as important as solar flares.
In our effort to set up a laboratory for undergraduate students with the tentative title ”Studying enzymatic activity of Carbonic Anhydrase (CA)”, we successfully determined CA activity and demonstrated its inhibition by acetazolamide, a potent CA inhibitor, using the electrometric Wilbur-Anderson assay (WAA).
WAA hinges upon determining the time T (in seconds) required for 4 mL of saturated with carbon dioxide (CO2) water to lower pH from 8.3 to 6.3 of the mixture when added to 6 mL of 0.02M Tris buffer at 0°C without (T0) and with enzyme (TE). Activity (A) is defined as A = 2*(T0/TE-1) assay units (AU). In n = 16 blank trials, T0 = 75.0±10.7s (Mean±Standard deviation), and with 0.001mg of CA in n = 12 trials, TE = 50.2±8.1s, A = 0.99±0.66 AU (p < 0.001). When for a test we used EDTA, a carboxylic high-affinity metal ion chelator, to inactivate this Zn2+-containing enzyme, we unexpectedly encountered that in the presence of the sodium salt of EDTA (Na2EDTA): 1) T was significantly slowed in a concentration-dependent manner: for 5µM, 50µM, and 500µM, T was 84.3±7.9s (n = 10, p < 0.05), 108.5±.6s (n = 7, p < 0.001), and 130.8±22.7s (n = 10, p < 0.001), respectively; and 2) unexpectedly, in the context of the previous finding, Na2EDTA significantly enhanced CA activity (TE = 38.5±4.0s, A = 1.84 AU, n = 10, p < 0.001) in the presence of 5µM Na2EDTA that was abrogated by 10µM Acetazolamide, a potent CA inhibitor (T =138.3±10.4s, n = 7, p < 0.001). TPEN, a pyridinic metal ion chelator, significantly slowed T0 (99.5±15.9s, n = 4) similar to Na2EDTA, and significantly enhance CA activity (TE = 41.1±3.8, n = 4, p < 0.05) with equal potency.
This indicates that principally chemically different metal ion chelators EDTA and TPEN interfere with the determination of CA activity in the context of WAA.
Cytochrome P450 is a heme protein essential in the metabolization of drugs. In this experiment we are studying the role of E267 in Cytochrome P450 BM-3. We hypothesize that mutations to E267 will alter the kinetics of Cytochrome P450 by interfering with proton transfer in the mechanism. Acidic residue E267 was mutated to valine (hydrophobic), aspartic acid (smaller acidic), and lysine (basic). Deuterium buffer was used to further examine whether E267 is involved in proton transfer. The findings showed that the Vmax, the point where the enzyme is over-saturated with substrate, for E267D mutant was about 3 times slower in deuterium than in the phosphate buffer. These results signify that E267D has a dependency on deuterium and thus perhaps proton transfer is dependent on the size of the residue and not just the charge at position 267. Future experiments are essential to understand the role of E267D in proton transfer.
Co-Author(s): Renad Abdalla, Sandra D Adams, George Arteaga Lopez Jr, Raegan Bailey, Nicole Benjamin, Kevin Bilyk, Mena Botros, Frank Brigati, Lloyd Brown, Nancy Bull, Emily Cabrera, Sevval Cakir, Erick Campoverde, Nicolas Cano, Mike Cauterucci, Anthony Chapman, Zaire Monee’ Durham, Sandra Duszkiewicz, Nick Frank, Ed Fraser, Jess Gallo, John Gallo, Virginia Garcia, Camila Gavilanes, Alejandro Gili Olivares, Hrisa Goga, Eliette Gomez, Denzel Griffith, Alina Guerrero, Adriana Guzman, Safwan Hassan, Kaylee Helwig, Jenna Horowitz, Sophia Ibrahim, Alexis Ignacio, Elyse Ippolito, Trish Kelman, Ansha Khokhar, Veronica Lach, Michael Lapczynski, Jonathan Lartey, Tom Mabey, Emily Manrique, Ethan Martinez, Shantae Mcleod, Karina Mejias, Kevin Millman, Rahma Mohsin, Kirsten Monsen-Collar, Kate Montero, Mohamed Musbah, Wesline Noel, Tiffany Okungbowa, Lucynda Oppong-Kyekyeku, Karielyz Ortiz, Chris Paccione, Melissa Palacios, Camila Pedroza, Flora Pierre-Louis, Bre Pifano, Asmaa Ramadan, Anushka Rana, Isha Rana, Bradly Raphael, Yadira Reyes Gomez, Jose Rivera, Emil Sanchez, Tiffany Santos, Julia Scirica, Edoardo Severino, Arej Shaabneh, Erin Tyll, Steven Valencia, Quinn Vega, Nicole Wich, Jedidiah Worrell, Edward Wynman
To date, students at Montclair State University have isolated 217 phage using Mycobacterium smegmatis, and Arthrobacter sp. as hosts. Of these 217 phage, 22 have been sequenced and 17 have been deposited in GenBank (with two currently in review). During the spring of 2022, MSU students are working to annotate the genomes of three novel Arthrobacter phage: BenitoAntonio, Hankly, and Inked. BenitoAntonio is a cluster AM phage with approximately 98 coding genes, Hankly is a cluster AM phage with approximately 102 coding genes, and Inked is a cluster AU phage with approximately 91 coding genes. Pairwise alignments between genomes shows a 51% identity between BenitoAntonio and Inked, a 49.7% identity between Hankly and Inked, and an 85.7% identity between BenitoAntonio and Hankly. The results of the pairwise alignments are not surprising given BenitoAntonio and Hankly are both in cluster AM and Inked is in cluster AU. Work on these annotations is ongoing and the students at MSU anticipate their annotations to be complete by May 1, 2022.
Given the recent 2021 H.R.3684 – Infrastructure Investment and Jobs Act enacted will ensure that 55 billion dollars are spent on water and wastewater infrastructure, there is an imperative to analyze local water systems for overall water quality. Considering the health and wellbeing of water management and securing water resources safety is paramount for New Jersey State Government oversight. However, few can discern the overall health and contamination levels through values recorded alone. For Essex County, comprehending the levels of frequently tested contaminants is significant for the livelihood of Essex County municipalities, and local government officials to discern. To accomplish the intended thesis’s purpose, data of 20 of the most sampled contaminants shall be compilated from the data files of each municipality of Essex County NJDEP Water Watch Websites. Each contaminant’s data will be averaged to best represent the municipality it originated from, and then mapped through ARC GIS to visually display contamination level results. The purpose of this research is to display 20 contaminant levels in Essex County to assess the county’s overall water quality. The current intended results of the research are in their preliminary phase and are intended to be fully actualized with the completion of the final project.
We investigate the dynamics of inertial and non-inertial particles in a double-gyre flow model. The underlying structure of the flow field is determined by the Lagrangian coherent structures (LCS) which are found by computing finite-time Lyapunov exponents (FTLE). Maximal FTLE ridges correspond to repelling coherent structures in forward time or to attracting coherent structures in backwards time. The behavior of massless non-inertial particles are investigated using the fluid velocity fields from the double-gyre model. For inertial particles with finite size and mass, we use the Maxey-Riley equation to describe the particle’s motion. Within this framework, we explore the preferential aggregation of inertial particles for varying Stokes numbers and density ratios. We show that inertial particles which are heavier than non-inertial passive tracer particles aggregate toward the maximal FTLE ridges, while inertial particles which are lighter than non-inertial passive tracer particles are repelled from the maximal FTLE ridges and instead form clusters in the center of the gyres.
Co-Author(s): Hussein I. Abdel-Shafy
This project aimed to evaluate ferrate(VI) for the treatment of secondary effluent from municipal wastewater treatment plants, i.e., biologically treated municipal wastewater, for reuse in agricultural irrigation. Ferrate(VI), the oxyanion FeO42-, is an emerging and safe water treatment agent with little formation of disinfection byproducts and multiple treatment mechanisms, including chemical oxidation, disinfection, in-situ coagulation, precipitation, and adsorption. In this study, laboratory-scale experiments were first carried out to evaluate the variation of water quality over ferrate(VI) treatment of secondary effluent at varied experimental conditions. Assessments were made in terms of effluent organic matter (EfOM), bacterial indicators, phosphorus (P), nitrogen (N), and emerging contaminants in treated wastewater. Special attention was paid to wastewater nutrients. Results showed that ferrate(VI) could efficiently alleviate total P (TP), including the majority of orthophosphate and part of organic P. The P removal was favored by higher chemical dose and lower pH (6.0-7.5). In contrast, it poorly mitigated total N in all the studied conditions. Of interest, though total N remained nearly constant, organic N declined with the increasing ferrate(VI) dose accompanied by the growth of inorganic N. The N retention in reclaimed water would benefit ensuing water reuse in agriculture due to reduced demand for fertilizers. Moreover, the reuse of iron sludge (i.e., iron (hydr)oxides) produced from ferrate(VI) reduction was carefully assessed in ferrate(VI) treatment of secondary effluent. The sludge reuse could lessen loadings of certain wastewater pollutants (e.g., EfOM and TP) for ferrate(VI) treatment, thereby decreasing ferrate(VI) dose and saving the treatment costs. These findings validate that ferrate(VI)-based technology represents a promising water reclamation alternative for agricultural sustainability and resilience.
Rising sea water poses a serious threat for many coastal environments. The gradual increase of saltwater moving into coastal soils can negatively impact soil function, leading to reduced seed germination and plant health. Cheesequake State Park, a coastal park located near Raritan Bay in Matawan, NJ, has seen a salt concentration increase within its cedar swamp area since 2012 and further increases in salinity are expected. Previous research at Montclair State University has examined the impact of artificial root exudates on metal contaminated soil. Root exudates are compounds released by plants into soil; they nourish microorganisms and promote healthy soil function. It has been shown that artificial root exudates can revitalize metal contaminated soils, there is no research on how they may influence saline soils. The goal of this experiment is to determine how two factors (salinity and root exudates) can impact soil function, and if artificial root exudates can offset the negative consequences of increasing soil salinity. Soil collected from Cheesequake State Park will be treated with specific artificial root exudate and various salt solutions. An experimental matrix will be constructed in which salt and exudate concentrations will be given to each pot depends on where it fits. This 4×4 matrix will have three salt/exudate concentrations and one Milli-Q control: increasing salt concentration moving right and increasing exudate concentrations moving phosphatase activity, soil salinity, pH, and moisture will be measured in each pot. The results will provide a greater understanding of how salt influx can impact soil, whether the addition of artificial root exudates can offset the negative effects of salinity, and whether there is a ‘threshold’ salinity level for cedar trees to survive. The results of this experiment will help ecologists to protect coastal plant species from rising sea water.
The warming of Earth associated with the mass extinction at the end of the Permian Period (~252 Ma) was likely triggered by a rapid CO2 emission from the eruption of the Siberian Traps volcanism, eliminating more than 90% of marine and 70% of terrestrial species. However, the links between volcanism, carbon isotope excursions, chemical weathering, oceanic anoxia, and biotic turnover remain poorly understood. Here we assess the biogeochemical perturbations during the crisis through analysis of chemical weathering, redox condition, and productivity based on major and trace elements. Results show an increasing trend of chemical weathering indices (chemical index of alteration [CIA], plagioclase index of alteration [PIA], and chemical index of weathering (CIW)) across the extinction event indicate enhancement of chemical weathering. The end-Permian mass extinction was also characterized by negative shifts of geochemical proxies (U/Th, Cr/V, and Ni/Co), indicating an expansion of oceanic anoxia. At the same time, primary productivity appears to increase abruptly, presumably due to an increased riverine flux of nutrients (Ni, Fe, and P) that stimulated marine productivity. The ecosystem stresses imposed by elevated nutrient fluxes and anoxia expansion are likely amplified by simultaneously intensified chemical weathering, highlighting the importance of integrating geochemical proxies in tracking the environmental responses to climate changes.
Co-Author(s): Adi Ackerman
Auxin (indole acetic acid) is a phytohormone with a conserved history going back ~470,000,000 years to the first simple, terrestrial plants, the bryophytes. Auxin is stored in plants conjugated to other molecules such as amino acids and sugars. These inactive auxin conjugates are accumulated in plants and hydrolyzed to recover phytohormone action. The orthologues have been conserved to help regulate auxin homeostatic levels during growth and development. Recent research demonstrated that this hydrolase family could be evolutionarily traced back to liverwort, the most ancient extant land plant lineage. Liverwort’s auxin hydrolase has little activity against auxin conjugate substrates and does not appear to actively regulate auxin. Because of the low concentrations of auxin in liverwort tissue and the lack of hydrolase activity, it was hypothesized that the Marchantia polymorpha enzyme (MpILR) may not be physiologically required by liverwort for auxin regulation. It may be that background degradation of auxin conjugates is sufficient to provide enough phytohormone for the plant to grow normally. In order to test this hypothesis, we have designed a CRISPR-Cas9 expression construct targeted at MpILR mRNA. We have transformed this construct into Agrobacterium tumefaciens. We are presently transforming liverwort tissue with the A. tumefaciens in an attempt to knock-out the MpILR gene activity. Our goal is to test liverwort transformants against untransformed plants to determine if their free auxins and conjugated auxins have altered.
Co-Author(s): Jennifer Krumins
Soil is the largest organic carbon (C) pool in terrestrial ecosystems, but its ability to retain and store C varies. Here, we constructed a meta-analysis focusing on 30 cm soil depth by collecting data from over 191 prior studies measuring soil organic carbon (SOC) stocks across natural, urban green space, and urban intensive habitats. We then compared the SOC data between different climatic zones, vegetation types, and anthropogenic influences with the human footprint index. The result indicates that SOC stocks in natural habitats (98.22 ± 49.10 Mg ha-1) are significantly higher than those of urban green spaces (54.61 ± 22.02 Mg ha-1) and urban intensive habitats (65.88 ± 35.27 Mg ha-1). We find a significant and negative relationship between the human footprint and SOC stocks only in natural habitats, not for the urban habitats. Nevertheless, when compared across climatic zones or vegetation types, the capacity of natural soils to store C is variable and vulnerable to the human footprint. Carbon storage in urban soils is likely limited by persistent and stable anthropogenic influences keeping variability low. This is most pronounced in urban green spaces where human management is likely high and SOC is low. A comprehensive understanding of C storage in soils is essential to land management and climate mitigation measures.
Effects of amines on carbon dioxide (CO2) escape from water to the atmosphere
The carbon dioxide (CO2) concentration in the atmosphere is at the highest level recorded in history, with a peak of 0.042% at Mauna Loa observatory. These concentrations continue to increase with the historically highest rate due to anthropogenic industrial activity. This atmospheric CO2 is the cause of acid rain that has a pH of 5.6. The atmospheric CO2 equilibrates with aqueous CO2 in open reservoirs of water such as oceans and lakes, this leading to the acidification of these waters. Studying the exchange of CO2 between water and air is important for developing carbon offset systems through CO2 capture and sequestration. Therefore, we set up a system that electrochemically monitors the escape of CO2 from water to the atmosphere. The set-up consists of a data logging pH meter, a magnetic stirring plate, and a 50mL beaker of 3.9mm internal diameter. When the pH electrode (1.2mm external diameter) is placed in 50mL of solution in the beaker, the exposed to the atmosphere aqueous area is p*(3.9 ± 0.05)2 mm2 – p*(1.2 ± 0.05)2 mm2 = 43 ± 3 mm2 ~ 4.3*10-5 m2.
To obtain the control measurements of the rate with which CO2 escapes from pure water at room temperature and atmospheric pressure; 50mL of the saturated with CO2 water was added to the beaker, the pH electrode was placed in the water, and data logging was initiated with the 2 minute resolution. The initial pH was 3.94 ± 0.06 (n = 4), and the dependence of pH on time was linear for about 150 minutes with the slope of 0.0126 ± 0.0004 pH units/min followed by a plateau that leveled at pH = 6.8 ± 0.2.
In the presence of 1 mM of NH4Cl, the initial pH was 3.78 ± 0.04 (n = 7), the rate of the pH increase significantly decreased to 0.0069 ± 0.0004 as compared to the control, and pH plateaued at 5.5 ±0.1.
In the presence of 1mM of Glycine, the initial pH was 3.88 ± 0.04 (n = 6), the rate of the pH increase significantly decreased to 0.0061 ± 0.0003 as compared to the control, and pH plateaued at 4.67 ±0.04.
In the presence of 50µM of Na2EDTA, the initial pH was 3.97 ± 0.02 (n = 6), the rate of the pH increase significantly decreased to 0.0069 ± 0.0003 as compared to the control, and pH plateaued at 6.43 ±0.02.
We conclude that the amino groups slow down the rate at which CO2 escapes from saturated with 100% CO2 water solution to the atmosphere (~0.042% of CO2).
Data visualization is turning raw data into an arrangement that is more digestible, easier to interpret and understand, and easier to manipulate a view of the data for specific use cases. An efficient way to visualize data is a key component of communicating the significance of the data found in any given study.
There have been many attempts to engage those viewing data in a more captivating and immersive way. In the past, there was the breakthrough of CAVE systems. CAVE systems consisted of an empty room of variable size with projections laid over the walls, ceiling, and floor of the room. These projections were shown to completely immerse the sole person standing inside the CAVE system into the data visualization experience. The CAVE system would have the ability to adapt the view of data by tracking the location of the person to create another degree of immersion.
With these CAVE systems came innovation. However, there also came some drawbacks when pertaining to its use. The cost of creating a CAVE system was high, with the need for an empty space, multiple projectors, proper lighting, and tracking cameras. Once a CAVE system was set up, it was no simple task to take down and relocate the system. There also came the issue of having more than one person at a time within a CAVE system. The tracking cameras would not work for more than one person at a time and therefore immersion was broken for anyone other than the person being tracked.
This work, conducted over the course of Spring 2022 and supervised by Dr. Stefan Robila, shows the possibilities of a three-dimensional visualization of data in a portable, multi-person experience.
Ponds across a landscape often house unique species, resulting in high species diversity at broad landscape levels. However, biotic homogenization due to flooding can make each pond compositionally similar and reduce the number of species supported at broader landscape scales. The focus of this project is to understand if flooding events alter the long-term taxonomic diversity of zooplankton communities in ponds by homogenizing the egg banks in soils. Homogenized egg banks across a broad landscape could result in reduced species diversity at broad landscape scales for many years, potentially negatively affecting water quality. To investigate these processes, we collected data at Walker Avenue Wetlands, which is an important freshwater wetland in Wayne, NJ. The site consists of one main wetland body and twenty small satellite ponds along the Pompton River. The satellite ponds and wetland are environmentally heterogeneous with highly variable concentrations of important nutrients. Additionally, each pond contained unique zooplankton communities in August, 2021. However, intense storm events in late 2021 caused the Pompton River to overflow and flood the main wetland and satellite ponds. These flooding events have resulted in high rates of sedimentation, which washed in resting eggs of zooplankton taxa, potentially resulting in long-term biotic homogenization of the zooplankton community. Egg banks of most zooplankton species are viable for many years, even if they are in extreme heat or dry conditions. Therefore, homogenized egg banks across the entire wetland complex might result in reduced species turnover among each unique satellite pond, and reduced species diversity in the wetland. In order to understand if the zooplankton egg banks were homogenized by flooding, soil samples were collected from each of the 20 ponds, the main wetland, and the Pompton River (23 sites) at Walker Avenue Wetlands. Additionally, water samples were collected to understand abiotic heterogeneity at each of the 23 sites. We allowed the resting eggs to hatch by adding low-nutrient water to each soil sample. We then quantified the zooplankton taxa from each soil sample, along with the chemistry from each pond. Those data will then be co5mpared to samples from the summer of 2021 to understand how biotic and abiotic homogenization has altered the pond communities following intense flooding events.
Co-Author(s): Paula Hernandez, Mihal Grinberg, James Reilly
Vertebrate reproduction has attracted a great amount of attention considering 20% of couples are infertile worldwide; consequently, much research has been dedicated to using model organisms to gain an understanding of the reproductive mechanisms of vertebrates and the elements involved in this process. For a further analysis of these elements, Enhanced Green Fluorescent Protein (EGFP) was used to ensure successful insertion and expression of promoter sequences into ovarian specific cells in a zebrafish model. By measuring EGFP levels across different tissues, it was determined that the CYP19a promoter is ovarian specific. Now that we have identified the promoter we can utilize molecular cloning to produce a plasmid vector expressing ICER (Inducible cAMP Early Repressor) under the control of the cyp19a1 promoter region effectively creating an ovarian specific inducible ICER gene. This ovarian specific inducible ICER would be combined with Tol2 transgenesis to generate a transposable element capable of incorporating this gene into the genomes of zebrafish creating transgenic organisms.
Co-Author(s): Jennifer Smith
Over the years students have been struggling with completing assessments under a specified time. Many students find it difficult to answer assessment questions correctly due to time constraints. Students are put under pressure to quickly recall information that they may not have even retained or understand. Timed math assessments have been popular for years in the United States and with state Common Core Standards pushing for timed tests, teachers are left with no option but to “teach to the test”.
With this research project, we hope to shine some light on the effects of time assessments on individual student development, students’ emotional health, and student learning. For the project, we collected data from one a middle school mathematics classroom in New Jersey. Using surveys, and timed versus. untimed tests, we compared how well different groups of students did on assessments based on overall numerical scores. We also share more qualitative reactions and insights from students regarding timed assessments. This research can help parents and teachers understand the problems students are facing with timed assessments and the anxiety that time constraints can build into students’ math experiences.
This research focuses on the Diophantine equation that sums three cubes into one modulo a prime number. Every solution to the equation belongs to one of the two types, Type I and Type II. More specifically, Type I solutions have two identical components while Type II solutions have three distinct parts. For each prime number, we calculate the number of solutions of Type I and Type II. The software Python is the computational tool in checking and finding solutions to the equation. For infinite prime numbers, we provide explicit formulas for the solutions of each type. For the rest of the prime numbers we give a lower bound for the number of solutions.
Tuberculosis (TB) is a disease that is caused by a bacteria called Mycobacterium tuberculosis and primarily attacks the lungs but can spread to other areas of the body as well. TB can develop resistance to drugs that may be used to cure the disease. Multi-drug resistant TB, for example, does not respond to the two most powerful anti-TB drugs, which are isoniazid and rifampicin. For this reason, finding new ways to target TB are highly needed. One possible way to do this is to target the enzymes in the tryptophan biosynthetic pathway of M. tuberculosis. Studies have suggested that the enzyme indole-3-glycerol phosphate synthase (IGPS) in M. tuberculosis (MtIGPS) coded for by the trpC gene could be a target (Shen et al. 2009). The interactions between ligands and MtIGPS were thus investigated by introducing mutations to residues that had been proposed to play a role in catalysis or binding. Specifically, E168 was mutated to glutamine, Q and K119 was mutated to arginine, R. Predictions for these mutations were that K119 is a catalytic acid and that E168 plays a role in substrate binding. We investigated the impact of these mutations on steady state kinetics and rate-pH profiles to obtain insights into the roles of these two residues in substrate binding and catalysis. These findings will facilitate the design of MtIGPS inhibitor candidates.
Co-Author(s): Dante Maida, Stephanie Avalos
DNA photolyases are enzymes that use blue light to repair DNA that is damaged by UV light. Class I photolyases bind two cofactors – flavin adenine dinucleotide (FAD) and 5,10-methenyltetrahydrofolate polyglutamate (MTHF) – which are important for catalytic and light-harvesting activity, respectively. In our hypothesis, we propose that MTHF provides photoprotection to FAD from photodamage under continuous light-induced stress. After excitation with light to a singlet excited state, flavin molecules can form triplet states from which they can undergo electron transfer and other chemical reactions that can potentially result in photodegradation. The goals of our research include the determination of the possible interactions between MTHF and FAD in solution and the potential involvement of the FAD triplet state in these interactions. To test our hypothesis, we have done long time-scale absorption experiments in solution to investigate whether there is an effect of MTHF on the rate of flavin degradation. The results indicate that the presence of MTHF influences the rate of degradation of oxidized FAD at low concentrations. Additional kinetic photodegradation studies with potassium bromide – a singlet excited state quencher – show that FAD stability is improved by the presence of Br– Furthermore, purging the FAD solution to remove O2, a triplet state quencher, accelerates the FAD photodegradation. Our current results support the hypothesis that MTHF may provide photoprotection to FAD in solution and, possibly, in DNA photolyase, and that the triplet states may play a role in the photodegradation of FAD and that deactivation of the FAD triplet state provides photoprotection. Observation of a signal at 632.8 nm during steady-state irradiation suggests the possible formation of a neutral flavin radical. Experimental approaches by mass spectrometry will be taken to determine the photoproducts of FAD and MTHF formed during steady-state irradiation. These experiments will expand our understanding of a possible photoprotective interaction mechanism between MTHF and FAD.
Metal contamination of soils resulting from anthropogenic interference is a pervasive issue globally and can result in low soil function. However, not all metal-contaminated soils behave the same. At Liberty State Park (LSP), a New Jersey brownfield site, there is a section of the park that is closed to the public because of elevated levels of metal contaminants. Despite the presence of metals in the soil, much of the area supports plant life and only a few areas are barren. In a previous study at LSP, we found no statistical difference along depth in metal concentration in the vegetated site (25F) but an accumulation of metals at the surface of the baren site (25R). For example, Pb concentrations were significantly higher in the top 0-2 cm cross-section (16,200 ± 5,575 ppm) compared to the bottom cross-section (301 ± 114 ppm). Do the metal-soil complexes play a role in metal accumulation at the surface of site 25R? The goal of this project is to understand metal soil interactions along depth in barren contaminated soils. To do this, 10 cm deep core samples will be collected from LSP and divided into 2 cm cross sections. The top 0-2 cm cross section and the lower 8-10 cm cross section will be analyzed. We will use selective sequential extraction (SSE) and X-ray dispersion spectroscopy (XRD) to identify metal species in the soil samples. These data can provide information about the relationship between metal-soil complexes and the ability for contaminated soils to support plant life.
Co-Author(s): Sarah Krisak, Jennifer Krumins, Nina Goodey
When contaminated areas remain unvegetated, also known as industrial barrens, they cannot provide ecosystem services. Industrial barrens may be non-point pollution sources in severe rain and storm events. Since there are no plant roots to maintain soil structure and trap contaminants, high contamination and low soil nutrients limit plant and soil microbial growth at such sites. A preliminary analysis of the soils from our study site, a brownfield within Liberty State Park (LSP), Jersey City, New Jersey, has shown high peroxidase activity and high metal concentrations in the barren soil. We hypothesized that vegetated soils would display high ligninase activity due to lignin-degrading bacteria and fungi, while barren soils may not. That said, ligninase activities have been reported in soils contaminated with polycyclic aromatic hydrocarbons and studied to assess the degradation of these contaminants. We optimized the enzyme and substrate concentrations to detect ligninase activities in the LSP soils from previously developed kinetic spectroscopy enzyme catalysis protocols. To change the concentration of enzyme molecules, we varied the soil quantity while preparing the soil slurry. We found that 0.1 g soil in a 50 mL buffer solution gave the optimal enzyme concentration to determine phenol oxidase and manganese peroxidase activities in LSP soils. Then, by varying the substrate – 2,2’-azino-bis(3-ethyl benzothiazoline-6-sulfonic acid) (ABTS) – concentration, we narrowed it down to that substrate concentration at which half the active sites on the enzyme molecules get filled, confirming the occurrence of significant catalytic activity. Remediation enzymes such as peroxidase and phenol oxidase degrade soil contaminants to nourish the unique contaminant-tolerant soil microbiota. Thus, contaminated soils exhibiting ligninase activities provide a measure of soil quality that can help design bioremediation strategies to restore brownfield soils.
Co-Author(s): Ying Cui, Shijun Jiang
The Paleocene-Eocene Thermal Maximum (PETM; ~56 million years ago) is a time where global temperatures increased greatly from rapid carbon emissions, making it one of the best comparisons to anthropogenic climate change. However, there is much debate on the pattern, amount, rate, and source of carbon emitted during this time. Although previous studies investigated ocean acidification (OA) in the deep ocean or sites in the polar regions, limited studies have explored low latitude and shallow marine environments. We use the Earth system model cGENIE to create “double-inversion” experiments that force d13Ccarb collected from the eastern Tethys and d11B, a proxy for pH, onto the surface ocean. The results show two distinct carbon emission pulses with varying d13C values, suggesting the North Atlantic Igneous Province could have initiated the PETM and carbon cycle feedbacks associated with a second, more 13C-depleted source. Specifically, the eastern Tethys lags in response to OA compared to the rest of the global ocean. Understanding the differences between deep and shallow sea responses can help infer the carbon emission history and evaluate the carbon release mechanism that drives the initiation and recovery of the PETM, providing insight on how modern oceans will respond to OA.
Co-Author(s): Ying Cui, Shijun Jiang, Stefanie Brachfeld, Maurizia De Palma
The PETM (Paleocene-Eocene Thermal Maximum) is a rapid global warming event that occurred 55.9 Ma (Westerhold et al. 2018) and is notable as the most analogous hyperthermal event to the contemporary climate crisis. While the PETM is well documented, the smaller rapid warming event prior to the PETM, known as the POE (Pre-Onset Excursion) remains poorly documented and understood. Many of the sites studied previously are from deep sea locations, where dissolution, bioturbation and sediment mixing can impact the fidelity of the records. In this study we reconstruct paleoclimate conditions from the eastern Tethys, the precursor to the modern day Mediterranean, a unique site that has not been studied previously. This region was an important source of heat and moisture at a low latitude shallow marine basin during the PETM and the POE, and holds critical information regarding the Earth system feedbacks related to rapid warming and climate recovery. The samples recovered were analyzed for magnetic susceptibility, elemental composition, and stable isotopes. Utilizing the information gathered we have laid the groundwork for filling in a significant research gap, as we make interpretations on the oceans redox state, increased weathering of material, and injection of carbon dioxide into the atmosphere. These details being among many other under-reported factors related to the event such as vegetation changes, mineral formations and paleoproductivity in shallow waters.
Geological records reveal five mass extinction events during the last 541 million years. Earth witnessed the loss of 80-90% of marine species and 70% land species during the largest mass extinction of all time, known as the end-Permian mass extinction (EPME) occurred at about 252Ma. The Siberian Traps volcanism (ST) is postulated to be the trigger of this event via the release of massive amount of CO2 from the huge volumes of magma outpoured. The impact of the volcanic event on the EPME and the subsequent recovery of life is still poorly understood. The lithium isotopes (7Li) can be used as a weathering tracer to detect weathering changes on climate-change events. The silicate weathering which removes CO2 is the only process that affects lithium. Here, we use 7Li of marine carbonates and clay to test the idea that voluminous fresh flood basalt were rapidly weathered, and sequestered large quantities of CO2. We use the silicate weathering flux derived from an independent carbon cycle modeling based on marine algae biomarker data from the Finnmark Platform that span across the EPME, along with a Li cycle box modeling coded in Python and R programming language to quantify the role of silicate weathering in driving negative excursion of 7Li. Future research will focus on isotope inversion in an Earth system model of intermediate complexity (cGENIE) with 7Li data from the Finnmark Platform and South China to better understand the link between silicate weathering and biotic recovery in the Early Triassic lithium cycle-box-model.
A wide variety of waste biomass feedstocks such as wet, solid, and gaseous waste streams can be used to generate renewable energy. Biologically derived semi-solid and gaseous waste biomass such as food waste and biogas can produce dispatchable energy such as heat, electricity, and transportation fuels. Previous studies have reported several energy conversion methods to reduce waste volume. These methods transform food waste and biogas into usable energy by the processes known as waste-to-energy (WTE). WTE-based electricity production helps reduce waste volume besides reducing energy dependence on fossil fuels that contributes to greenhouse gases (GHGs) and climate change. New Jersey (NJ) State, due to its coastal location and population density, is most vulnerable to the adverse effects of climate change and waste generation. Using food waste and biogas for electricity production could minimize climate change risks and waste volume in NJ. However, the economic feasibility of the collection, conversion, and distribution of WTE-based electricity need to be ascertained. This study will determine the economic competitiveness of WTE technologies using the value-cost ratio of the WTE-based electricity to the electricity available on the grid. Additionally, sensitivity and uncertainty analyses will be conducted to assess the cost parameters. Moreover, the study will synthesize potential drivers and barriers that impact the provision of the recovered energy into the existing distribution system.
Co-Author(s): Danlin Yu
Increases in the severity and frequency of natural disasters in recent years have intensified the need to understand social and physical vulnerabilities as they relate to environmental hazards. Similarly, the onset of the COVID-19 pandemic has resulted in restrictions on indoor activities, reaffirming the importance of providing access to outdoor spaces to improve both physical and mental health. Environmental justice explores the relationship between these types of environmental hazards and resources, providing an opportunity to understand and mitigate existing inequities that could otherwise lead to disproportionate levels of harm. To this end, this project seeks to provide insight into trends in modern environmental justice studies through an in-depth review of relevant research articles published since 2015. Studies were carefully categorized based on their subject matter, methodology, and conclusions to identify trends in the literature. Results showed studies continue to analyze environmental justice by measuring access to resources or distribution of harm regarding three distinct categories: distribution justice, recognition justice, and representation justice. Distribution forms of justice were most common among the studies reviewed, often employing quantitative methodologies that relied on spatial characteristics to measure exposure and access based on socio-economic characteristics. Recognition and representation justice research utilized surveys, interviews, focus groups, and document reviews to understand the mechanisms behind cultural and procedural impacts on environmental justice topics. Overall, studies in the realm of environmental justice are moving toward expanding measures of vulnerability, employing emerging technologies and techniques, and incorporating larger quantities of data to capture environmental injustices.
Co-Author(s): Huan Feng, Jing Nie
Oluwafemi Soetan, Huan Feng*, Jing Nie
Department of Earth and Environmental Studies, Montclair State University, Montclair, NJ, USA
Remedial sediment dredging involves the removal of sediment, which has been widely used as a means of environmental remediation in order to reduce contaminant concentrations in aquatic systems. Several studies have reported the efficiency of sediment dredging in mitigating heavy metal pollution. However, recent studies have suggested that the long-term impacts of dredging may constitute more harm than good for the aquatic environment. While studies investigating the short-term effects of dredging have addressed the negative immediate impacts and the subsequent positive impacts over a stabilization period, only a few studies have evaluated the long-term impacts on metal concentrations and the subsequent ecological effects. Metal concentration data for sediment and water samples from the LPR were collected for the pre-dredging and post-dredging periods. The data were statistically analyzed to determine the immediate to long-term impact oN metal pollution and also measure the dredging effectiveness. The ecological and environmental status of the river is also evaluated using different indices. The seasonal variations in dredging efficiency reported in long-term studies as reflected in the water samples were further investigated. The broad goal of this study is to contribute to the existing knowledge about the reliability of sediment dredging as a sustainable and effective remedial method.
Co-Author(s): Huan Feng
The purpose of this study is to examine the impact, theory, and environmental management implications of the decisions using the Dugong cases as an example. The Okinawa Dugong was found to be protected as living cultural property. In the early 2000’s a proposed plan the US Department of Defense to relocate a U.S. Air Station in Okinawa, Japan by threatened to eliminate several feeding grounds of the Okinawa Dugong (dugong dugong), a species listed as threatened according to the Endangered Species Act of 1972 (ESA). A series of cases were heard by the Northern District of California, which ultimately came to the decision that the Okinawa Dugong would be protected under the National Register of Historic Places Act of 1966 (NHPA) as cultural property. This study reviewed the (1) development of cultural property law to include natural cultural property and heritage; (2) the differences in jurisdiction and protection afforded by ESA and NHPA; (3) and how this decision exemplifies the application of alternative approaches to environmental management.
We consider an extended Hodgkin-Huxley conductance model which includes additional ion channel dynamics. The model consists of a set of nonlinear ordinary differential equations which are numerically solved using an adaptive Runge-Kutta solver in the Python programming language. The results show that the model is capable of accurately describing experimental results, including duration and form of action potentials, amplitude of the spike, oscillations, and ionic changes. This enables one to study the effects of A-type nodose sensory neurons as well the effects of known ion channel blockers, such as tetrodotoxin (TTX) which is found in pufferfish.
The emergence of the novel coronavirus (SARS-CoV-2) in late 2019 has led to a global pandemic (COVID-19) which continues to cause enormous public health and economic challenges around the world. It is therefore important to improve our understanding of the outbreak and spread of COVID-19 as well as to investigate how one might contain or stop the spread of COVID-19 via different control measures. We consider a COVID-19 model based on an SEIR compartmental model. The model includes susceptible, vaccinated, exposed, pre-symptomatic, symptomatic infectious, asymptomatic infectious, hospitalized, recovered, and deceased compartments, each of which is sub-divided into 17 age groups. Furthermore, we incorporate contact structure which accounts for the number of contacts between individuals experience at school, work, home, and other environments. The model is parameterized based on New Jersey data, and we consider the effect of a hypothetical vaccine of varying efficacy that is introduced at the start of the epidemic outbreak in New Jersey. The results demonstrate how different control measures, including vaccine and lockdown, interact with each other and lead to different epidemic outcomes.
Load forecasting is an important tool for both the energy and environmental sectors. It has progressed hand-in-hand with machine learning innovation, where recurrent neural networks, a type of artificial neural network, is primarily used. This thesis compares progressively complex, feed-forward artificial neural networks using a mix of weather and temporal data. We demonstrate that electrical load in New Jersey can be reliably predicted using memory-less algorithms with minimal predictors drawn from preexisting public data sources. The methods used in this thesis could be used to build competitive load forecasting models in other states, and if included in diverse model ensembles, may generate significant improvements.
Conditions of a reaction can have a drastic impact on the rate of a reaction, especially on enzymes. IGPS is an enzyme in Mycobacterium tuberculosis that catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose 5’-phosphate (CdRP) into indole-glycerol-phosphate (IGP). To gain insight on how IGPS interacts with ligands, a variety of mutations were made to amino acid residues in IGPS. These mutants are purified through a nickel column with a His-tag using PBS buffer. The PBS buffer was replaced with Tris buffer to determine if the mutants would have a higher rate of reaction when studied through steady state kinetic experiments. It is hypothesized that PBS buffer might interact with the phosphate group in the active site of IGPS, so a variety of other buffers were tested to determine which one has the highest rate of reaction. After purification, the mutants are studied through steady state kinetic experiments to obtain Km and kcat values using [100 uM] PIPES buffer. [50 mM] Tris, [50 mM] HEPPS, and [100 mM] PIPES were tested with a variety of sodium chloride and EDTA concentrations to determine which set of conditions yield the greatest reaction rates. From these results, it can be determined if different conditions result in different catalytic activity. With these optimized conditions, our group can more efficiently study low activity mutants.
Co-Author(s): Sandra Passchier
As atmospheric CO2 continues to rise higher than experienced in the recent past, the importance of researching geological periods of great paleoclimate variability becomes highly critical. The greenhouse to icehouse transition at the Eocene-Oligocene boundary (34 Ma) marks the appearance of continental scale glaciation in Antarctica. The material recovered from the Ocean Drilling Program site 696 is the only record spanning this major climatic shift in the Weddell Sea region. Using quartz microtextural analysis, thirteen samples spanning the EOT were analyzed to understand the transportation history of coarse sand material. The grains were visually grouped into five types and characterized by grain outline, relief and surface microtextures. Glacial textures are present throughout the entire interval (33.2-34.4 Ma) with the frequency of these textures decreasing into the early Oligocene. Mass accumulation rates of glacial grains reveal that glacially and iceberg transported material does increase following 33.6 Ma but is also accompanied by an increase in eolian and sea-ice rafted grains, which explains the relative decrease in glacial textures. These findings confirm the existence of the West Antarctic Ice Sheet in the Weddell Sea region at the E-O boundary with expansion in the early Oligocene under decreasing atmospheric CO2 concentrations. Understanding the sensitivity of the West Antarctic ice sheet under this shift in climate state provides context for the ice mass loss and sea level rise observed today, and for which only short instrumental records exist.
Road salt application is a primary factor leading to the salinization of freshwater rivers and streams throughout the Northeastern United States and globally. Rising salinization within fresh water bodies is problematic because it can modify community structure and detritus processing within freshwater ecosystems, induce mortality among macroinvertebrates and other aquatic life, and mobilize metals that can pose harm to human health. Road salts also threaten surface and underground drinking water supplies, kill riparian vegetation, and corrode infrastructure, such as bridges and roads. This research examines 4 ½ years of continuous water quality monitoring data collected from two sensor stations along the Paulins Kill River in Newton, New Jersey to assess the seasonal impact that road salt is having on the river. Specific conductance and depth were examined during each season. The data showed that if precipitation fell when air temperatures were above freezing, conductivity and depth exhibited an inverse relationship. The additional freshwater from rainwater diluted the concentration of ions in the river, causing conductivity measurements to decrease as the river depth rose. When precipitation occurred when air temperatures were below freezing, however, conductivity levels rose along with the river’s depth because road departments were applying road salt to Newton’s streets. This research provides important implications for winter road management by public works departments and their impacts on local rivers.
Co-Author(s): Anuradha Singh
With an urgent need to decarbonize transportation, ride-sharing companies are moving fast to adopt electric vehicles (EVs). However, the use of electric vehicles for ride-sharing services needs to be managed based on their battery demand, EV charging station’s location, their availability, and charging time among other factors. In addition, ride-sharing EVs need to maximize their profits by increasing the number of passengers and the number of rides. This study explores two artificial intelligence algorithms which explore these EV ride-sharing optimization issues through the game theory perspective. The first algorithm is built on a MinMax algorithm, where one player (representing an EV-ride sharing company) chooses its next move within a matrix based on the passenger’s total travel distance (the longer the passenger’s travel distance, the larger the profit), while another player (representing a second EV-ride sharing company) chooses its next move on electric battery consumption based on a ratio between the passenger’s travel distance and the distance to the passenger (with the idea that a more optimum ratio will allow the car to go further without recharging, and thus save on recharging time). In the second algorithm, we explore the optimal order of passengers to be picked up with the shortest route possible to save the battery life of an electric vehicle. The results show that increasing passenger numbers over time, results in the highest battery savings (comparable to the initiation of a rush hour or the ending of a major event), followed by stable passenger numbers and falling passenger numbers. Furthermore, our MinMax algorithm indicates that if an EV decision to select close proximity passengers with a potential large travel distance increases by just 4%, rather than basing its decisions entirely on random passengers with the largest travel distances, it can reduce the battery usage by 40%, while only losing 1% of the potential profit. Decarbonizing the transportation using EVs and autonomous vehicles is progressing effectively and optimizing their energy use using such algorithms will make them more effective by reducing energy needs and greenhouse gases emissions. In addition, such algorithms increase the cost-effectiveness of ride-sharing services, increase consumer participation, and passenger per mile. This work makes a broader impact on Smart Mobility and Smart Cities.
The classic N-queens problem in chess posits whether it is possible to place N number of queens on an N x N chessboard such that no queen can kill another. While this is mainly related to the realm of AI in Games, it has wider applications, e.g. in defense strategizing where potential sources of threat can be placed at locations such that they do not attack each other. It has been shown using AI that there are several ways to place N queens on a chessboard greater than size 3 x 3. After building upon existing heuristics regarding how the queens can be placed on the same board, this project finds 4 interesting solutions to the 8-Queens problem without using brute force methods. This is achieved by developing heuristics using the AI concepts of Constraint Satisfaction and Forward Checking. The solutions proposed herewith can be applicable to finding solutions on larger chess boards, indicating the extendibility of the idea. Likewise, in applications such as defense strategizing, scalability can be obtained on similar lines. Other potential applications of this work can be market competition and network routing, in scenarios where forestalling threat is important using appropriate planning.
The design of new molecules that function as fluorescent sensors for cations is an area of current interest. Some of these sensors are based on a chromophore-spacer-receptor design and use photoinduced electron transfer (PET) to generate or quench a fluorescence signal. We have developed a fluorescent sensor that uses a tertiary nitrogen as a part of the receptor and it will generate a fluorescence signal with proton binding as well as zinc ion binding. Our goal is to modify this sensor so that it will generate a fluorescence signal for zinc ions and not for protons. This is based on our observation that an additional aromatic ring can generate a new PET when the tertiary nitrogen is protonated. Our progress in the synthesis of this new sensor will be presented.
A non-zero matrix A is called a zero divisor if there is a non-zero matrix B such that AB = 0. The zero-divisor graph of certain matrices represents the zero divisors as its vertices and its edges between two zero divisors A and B if and only if AB = 0. Such a graph is applied to describe coloring of an algebraic structure and it became a hot area of research which involves both theoretical algebra and graph theory. The focus of this research is to classify the zero-divisor graph G that arises from a set of the special type of “Tri-Diagonal Matrices”. The graph G has 170 vertices and more than 2640 edges. The vertices are divided into 7 classes and a class graph is developed to better describe the total graph G. The class graph provides a more general picture of the graph G. Guided by the class graph, the entire structure of G is provided.
This study investigated how problem-solving videos can be used in video-mediated professional learning to support secondary preservice mathematics teachers (PMTs) in developing teacher knowledge for noticing student thinking in the context of the derivative concept in calculus. A model of the trajectory of PMTs’ noticing was constructed as six PMTs viewed and analyzed videos of students’ problem solving. At the same time, the nature of video-mediated interactions that were found to be productive in supporting this knowledge development was examined. A design experiment was used as the research methodology. Data was collected from video recordings of eight semi-structured teaching episodes and analyzed through a grounded theory approach. Considering that the knowledge was video-mediated, developed collaboratively, and assessed in action, the study was grounded in situated and sociocultural perspectives, and the conceptual framework of professional teacher noticing guided the analysis. The constructed model that emerged from the experiment is composed of the following processes: describing, interpreting, contrasting, and responding. This model represents an approach to an ambitious professional vision that can support calculus educators in continually and iteratively improving their practice through readily accessible, video-mediated professional learning. These findings contribute to research in calculus education, with implications for the design of learning experiences for mathematics teacher preparation.
Ramsey Theory is a field that studies the mathematical phenomenon that sufficiently large objects unavoidably contain structured sub-objects. In this research, we study the multicolored bipartite Ramsey number of double stars. That is, we attempt to answer the following question. How large does an edge-colored complete bipartite graph have to be in order to guarantee the existence of a double star such that all of its edges are the same color? We use mathematical techniques as well as computing to improve the best-known bounds and find exact values in some cases.
Liberty State Park (LSP), New Jersey’s largest state park, is a former industrial railyard site sitting on a coastal estuary adjacent to the Hudson River Bay and Manhattan, NY. The rail yard was a major shipping hub and source of anthropogenic soil pollution, with the facility closing in 1969. An area within the park has remained closed to the public and undisturbed since that time. The natural attenuation of the soil since this time period has provided a unique opportunity to study this industrial brownfield site. Previous studies have collected data from four study areas within LSP and compared it to a site at Hutchenson Memorial Forest (HMF) in Franklin, NJ. HMF provides a unique, unpolluted reference site to LSP as it is of the same chrono sequence and geological makeup. Soil data collected include characterization of organic and inorganic contaminants, pH, nutrient levels, and bulk organic matter.
Our efforts hope to determine concentrations of poly-cyclic aromatic hydrocarbon (PAH) contaminants such as pyrene and chrysene at the study site. Using Soxhlet extraction and gas chromatography-mass spectrometry (GCMS), we will gain a more thorough knowledge of contaminant concentration gradients and understanding of relationships between soil contamination and soil-plant interactions at this site. Combining this data with that of detailed enzymatic activity will provide valuable insights to contaminant-microbe-plant feedback loops at brownfield sites. This knowledge may be used to reduce remediation costs and help stakeholders make more informed decisions on future land development of brownfield sites.
Smart grid technologies have numerous benefits like reliability, efficiency, self-monitoring that represents an unprecedented opportunity to move the energy industry into a new era of intelligent power grid system. The focus of our project is the prevention of power outage issue in a smart grid environment. Power outages occur when electricity demand exceeds supply, more specifically consider a utility company which sets a threshold on the total power usage of households in a neighborhood. Whenever total power usage from the neighborhood exceeds the threshold, some of the households must reduce the power consumption to avoid the power outage issue. This problem is referred as Threshold-Based Power Usage Control (TPUC). The two-way communication between the smart grids and meters reflects how we use electricity which is sent to the utility company helping to resolve the power outages issues. However, solving the TPUC problem raises the privacy concerns since the utility company can profile the daily activities of a user based on the energy consumption patterns. We emphasize that the existing privacy- preserving TPUC algorithms are either insecure or inefficient. Therefore, to preserve the privacy of the households in a neighborhood, we proposed a novel secure and distributed threshold-based power usage control protocol. The initial evaluation of the proposed protocol demonstrates that it is very practical.
Co-Author(s): Joseph Affinito
The New Jersey Meadowlands wetland complex contains many historically contaminated reclaimed grassland and wetland sites noted for their avian biodiversity. As natural areas surrounded by urban sprawl, these sites attract many species of birds as habitat for migratory stopover and breeding. In this project, two sites in the Meadowlands, Harrier Meadow and the adjacent Erie Landfill in North Arlington, New Jersey, were assessed to determine how many individuals and species of passerines and near-passerines utilized these habitats. Avian diversity was sampled using mist nets ~2 times per week during migration and breeding seasons from 2019 – 2021; netted birds were banded to identify individuals over time. In total, 4346 individuals of 90 species were banded with 246 of these birds recaptured 321 times. Forty-five species utilized the areas for stopover during spring migration while 62 species stopped over during fall migration. Fifty-six species were banded during breeding season, of which 22 had physiological evidence of active breeding. At least 24 species successfully fledged young locally and hatch-year birds represented 37% of individuals banded during the breeding season. The relatively high recapture rate across seasons (~6%) demonstrates that individuals using these sites survive over time, a testament to the quality of the locations. Two birds recaptured in 2021 were originally banded on site in 2014 demonstrating long-term site fidelity and considerable longevity of at least some individuals utilizing these locations.
Co-Author(s): Bhagyashree Vaidya
Brownfield sites are areas that were contaminated by anthropogenic activities. Our study site, an abandoned rail yard, is located within Liberty State Park in Jersey City, New Jersey. The contaminated section of the park has been closed off and left undisturbed since 1969. Previous studies have reported polycyclic aromatic hydrocarbons (PAHs) and heavy metals in high concentrations at the site. While some areas of the park yield natural plant growth despite high contaminant levels, others remain barren. The roots of plants in vegetated areas naturally secrete root exudates into the soil, which include a variety of sugars, amino acids, and organic acids. These compounds nourish microbes within the soil thus promoting their function and improving the health and quality of the soil. In an attempt to revitalize barren, contaminated soils, we used an artificial root exudate solution prepared in our lab. By measuring carbon dioxide emission rates and phosphatase activity–markers of microbial function and soil health–over a period of 150 days, we were able to examine if the effects of a single addition and repeated additions of artificial exudates differ, and if the effects depend on soil type. Both the single addition and repeated additions of artificial root exudates stimulated soil microbes, resulting in higher CO2 emission values and soil phosphatase activity than the control even after ceasing exudate additions. Studying plant-soil-microbial interactions exclusive to this site may be relevant for the development of “green” remediation strategies to clean up barren brownfield sites.
Cell membranes are a vital part of all cells, and the lipid bilayer composed of hydrophilic heads and hydrophobic tails, provides a key defense for its cell against the environment and foreign invaders, while also responsible for signaling responses and other cell-cell interactions like gap junctions. In order to propagate itself, viruses invade and utilize its host’s own membrane against it via membrane reorganization spurred by protein binding. In particular, viral binding is known to cause “raft partitioning proteins” to be organized around the virus. How a phase-separating vesicle organizes its domain in response to protein-binding interactions is a topic of interest. In this research, we examined the spatial organization of lipid domains at the intermembrane junction between two protein-bound lipid membranes using a model membrane reconstitution. Artificial membrane vesicles, specifically giant uniamellar vesicle (GUVs) and supported lipid bilayers (SLBs) were engineered to anchor model binding pair proteins, and were examined after establishing the intermembrane interaction with confocal laser scanning fluorescence microscopy. Results show an established relationship between the reorganization of phase-separating GUVs as a result of protein-protein interactions, specifically a strong preference for the polarization of one domain at the intermembrane junction.
Co-Author(s): David Konas, Nina M. Goodey
Tuberculosis (TB), an infectious disease, is caused by M. tuberculosis. It is the second leading cause of death globally. Indole-3-glycerol phosphate synthase (IGP synthase) catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose 5’-phosphate (CdRP) into indole-glycerol-phosphate (IGP). Research suggested that IGP synthase could be a new potential TB drug target. The goal of our study is to predict the binding conformation and energies of selected ligands to M. tuberculosis IGP synthase. Molecular docking can be used to predict the orientation of a particular ligand binding within the active site of a protein. We used AutoDock Vina 1.5.6 and Chimera 1.16 softwares to perform docking. From the protein data bank (PDB), 3T44 (M. tuberculosis IGP Synthase) was fetched and optimized (determine charge) using Chimera. The ligands (rCdRP, IGP) were optimized and fetched in the same way. Grid box was made around the active site of the protein. Grid box’s coordinate values were entered and AutoDock Vina predicted the conformation and binding affinities of IGP and rCdRP with 3T44. Our docked IGP with 3T44 matches with an experimental structure that was already available. Our results with rCdRP showed nine different conformations with binding affinities ranging from -8.4kcal/mol (1st pose) to -6.6 kcal/mol (last pose). This result indicated that rCdRP binds to M. tuberculosis IGP synthase and validating M. tuberculosis as a drug target. Now, more ligands will be docked and shortlisted for experimental testing from data provided by docking.
Co-Author(s): Robert O’Hagan
In the O’Hagan Lab, we use the nematode C. elegans to study the Tubulin Code, Microtubule-associated proteins (MAPs), and cilia, and how they affect the function of neurons. The Tubulin Code hypothesis suggests that different tubulin isotypes, as well as post-translational modification of tubulins, can specialize and regulate the MT cytoskeleton. MAPs are believed to play an important role in the regulation and stability of microtubules (MTs). MAPs bind to various sites along the MT tracks. However, how these MAPs affect neuronal function in vivo is mostly unknown.
Most non-dividing cells in humans, including neurons in the adult brain, have a non-motile primary cilium, which acts as a cellular antenna to detect signals from the environment or from other cells. Defects in primary cilia in mouse brains result in neurodegeneration, but the influence of primary cilia in neurodegenerative diseases such as Alzheimer’s disease has not been extensively studied.
PTL-1 is a C. elegans homolog of Tau, a MAP involved in neurodegenerative diseases in humans. TBA-9 encodes a neuronal alpha-tubulin. PTL-1 localizes to cilia in dopaminergic CEP neurons in a TBA-9 dependent manner in C. elegans. However, it is currently unknown how the loss of PTL-1 or TBA-9 affects the function of the CEP neurons, which mediate behavior in which animals slow their locomotory rate in response to the detection of food. To test how the loss of PTL-1 or TBA-9 affects the function of the CEP neurons, we are recording videos of behavioral assays and using automated computer vision analysis of animal behavior to measure the basal slowing response. Our results suggest that TBA-9 and PTL-1 are not essential for dopaminergic basal slowing, but do regulate the fraction of time animals spent moving backward. Our results may illuminate how the Tubulin Code, the MAP Tau, and cilia are involved in the function of neurons in the human brain.
Co-Author(s): Dileep K. Birur, Pankaj Lal
Nepal has been a part of trade liberalization, starting in 1992, and was the first least developed country to join the WTO in 2004. Being an agrarian country with more than 66% of its population directly engaged in farming, agriculture and livestock play a significant role in the nation’s economy. Thus, the main objective of this research is to quantify and analyze the economy wide impact of free trade agreements with 100% tariff and 50% non-tariff measures (NTMs) removal for agricultural sectors. Computable General Equilibrium (CGE) models are extensively used for analyzing the economic impacts of trade barriers and captures the interactions between different policy scenarios in various economic perspectives. As a result, this study had constructed a CGE model using a Global Trade Analysis Project (GTAP-10) database for Nepal. For the South Asian Free Trade Area (SAFTA), 100% elimination of tariffs and 50% NTMs removal resulted in decreased imports of commodities by $28.15 million (0.31%) and created an increase of exports by $231.21 million (11.92%), when compared to the baseline year 2020. Similarly, for the Bay of Bengal Initiative for Multi-Sectoral Technical and Economic Cooperation (BIMSTEC), 100% tariff and 50% NTMs removal also resulted in a decrease of imports by $28.75 million (0.32%) and an export of the commodities increased by $234.42 million (12.09%) in comparison to the baseline year 2020. The GDP change was positive for all three scenarios with an astonishing average figure of $205.66 million, which is a 1.04% increase in GDP when compared to 2020. These findings prove that Nepal could benefit economically by removing the tariffs and non-tariffs. The findings from this study could provide policy makers with support for understanding strategic issues, revising current tariffs, and imposing appropriate changes so that Nepal can experience greater economic strength.
Co-Author(s): Maurizia De Palma, Samantha Benjamin, Ying Cui
The Paleocene-Eocene Thermal Maximum (PETM, ~56Ma) was a period characterized by a significant carbon cycle perturbation, high global temperatures, and is commonly cited as the most analogous case study to contemporary global warming. There is significant evidence that suggests that large amounts of carbon emissions can impact global climate. The use of black carbon isotopes (d13C) could help shed light on carbon emissions present during the PETM. Black Carbon (BC) samples from the Kuzigongsu section in the Tarim Basin of the eastern Tethys Ocean indicate incomplete combustion of organic matter in the study area, which was the expected consequence of global warming throughout the PETM. While some believe the incomplete combustions occurred in the form of wildfires, there is not enough evidence to fully support the theory. The BC isotope data that we produced show that the combustion events before the PETM would have been influenced by an older source of organic matter rather than wildfires. The pattern of BC isotopes during the PETM suggests that the main source of BC found in the samples was a combustion of living biomass, which would have occurred as a result of climate change. BC isotopes can help determine the extent of climate change that occurred throughout the PETM, which can then be compared to the factors driving the present contemporary climate crisis.
Moore EA, Kurtz AC. Black carbon in Paleocene–Eocene boundary sediments: A test of biomass combustion as the PETM trigger. Palaeogeography, Palaeoclimatology, Palaeoecology 2008, 267(1-2): 147-152.
Co-Author(s): Katherine Margolin, Dr. David Konas, Dr. Nina Goodey
Indole-3-glycerol phosphate synthase (IGPS) catalyzes the indole-forming reaction in the multi-step bacterial tryptophan biosynthetic pathway. This pathway appears to be necessary for bacterial growth and it could represent a target for potential new anti-infective agents in the future. In order to realize this possibility, more detailed information about IGPS enzyme-substrate interactions and its catalytic mechanism would be valuable. Reduction of the natural IGPS substrate results in a compound (rCDRP) that cannot turn over due to loss of a key reactive ketone carbonyl group. This presentation will describe our synthesis, purification, and characterization of rCDRP along with plans for its application to studying the IGPS protein from the M. tuberculosis bacterium.
Co-Author(s): Dani Alves, Uchechi Desouza, Jaclyn Catalano
Cytochromes P450 (CYP) are enzymes that metabolize endogenous and exogenous compounds, including drugs and toxins, and involved in the synthesis of steroids and vitamins. 2-aminofluorene is an exogenous substrate of a bacterial CYP102A (BM-3) and a procarcinogen upon metabolism by cytochrome P450 is turned into a carcinogen. Other cytochrome P450s such as CYP2S1 can catalyze the reverse reaction turning a carcinogen into a noncarcinogen. To fully understand this reaction, we studied the secondary structure of BM-3 by circular dichroism spectroscopy and enzymatic activity as a function of pH. Our results show that the enzyme can catalyze the substrate at both pH 3 and pH 7 and unfolds around pH=5. The CD spectroscopy at pH 3 shows the enzyme folded in a metastable state.
Co-Author(s): Corbin Hudson, Maria Fahmy, Evelyn Visan, Allyssa Angel, Dr. Nina Goodey, Dr. Lisa Hazard, Dr. Ueli Gubler
The current molecular diagnostic methods for detection of deadly pathogens within a population can require various steps of experimentation that are time consuming. When surveying a population for the presence of a disease time is a valuable resource, therefore, the need for a rapid pathogen test to use in the field will allow for faster detection of disease that can lead to determining a course of action for conservation of a species. Ranavirus is a double stranded DNA virus that can cause severe mass mortality events in amphibian, reptile and fish populations. The disease can have the potential to wipe out entire species if not controlled, having a 90-100% mortality rate. Recent methods of development for a rapid pathogen test have involved target detection probes using aptamers, or short single stranded DNA, as molecular probes. Studies have shown that molecular probes are more stable and cost-efficient than antibodies, and are also easier to modify. Using an existing starting library of 10(subscript 14) non-specific aptamers that have been previously enriched to bind to Ranavirus via SELEX, our objective is to determine the binding affinities of the selected aptamers to the major capsid protein (MCP) Ranavirus target using electrophoretic mobility shift assays (EMSA). The results of this research will provide a better understanding of the aptamers high affinity and specificity for MCP, and the selected aptamers can therefore be used for the development of a rapid pathogen test that can be used in real-time in the field.
This research aims to identify the urbanization of different areas in New Jersey and see how it affects the prevalence of microplastics. Samples will be collected from local rivers and streams using sieves and will be examined visually for results. By using filter paper with a 7µm pore size, I anticipate filtering out polluted water to trap tiny particles found in water. Of these particles using a microscope, I will determine the average quantity/concentration of microplastics in three 1000 ml of sample water at each site. This study also takes into account the urbanization of the areas that the samples were taken from, and aims to identify a correlation between the urbanizations around the sample site of the river and the number of found microplastics. It was concluded that there are microplastics found in these local rivers.
Co-Author(s): Britney Ferdetta, Johannes P. M. Schelvis
DNA damage is an ongoing issue that living organisms experience on Earth due to ultraviolet radiation from the Sun. When UV radiation comes in contact with DNA in cells, the structure of DNA can change into the cyclobutane pyrimidine dimer (CPD) and the pyrimidine-(6-4)-pyrimidone dimer (6-4 PP). These dimers in DNA are linked to skin cancer. It is vital to understand the mechanism organisms can repair these lesions and ultimately find a way to prevent skin cancer. The class of enzymes that can repair specific DNA lesions, such as CPD and (6-4)-PP are known as photolyases. With that said, photolyase is not present in humans. The goal of this project is to test the mechanism of DNA binding to photolyase using two model systems. The first model proposed is the facilitated diffusion mechanism by which CPD photolyase searches along the damaged DNA site to form an ES complex and initiates monomerization of the lesion. The second mechanism proposed uses diffusion of the enzyme with nonspecific or random binding to DNA to find the specific DNA damage site. This model depends on the CPD flipping in and out of the dsDNA. The rate of DNA binding will be studied closely as a higher or lower rate constant will be affected by the flipping of CPD and affects its recognition by the enzyme. The DNA used for this experiment was an 11-mer that contains 2-AP, a fluorescent base. The 11-mer DNA was damaged with UV radiation to form DNA with the CPD lesion and then purified using HPLC. The fluorescence intensity data for the 11-mer 2-AP and complementary strands with and without CPD were used to give information about the base stacking stability at the CPD lesion by titration experiments and computer analysis to fit the data. This project aims to identify dsDNA strands with different CPD flipping rates to find how CPD photolyase recognizes and binds to specific damaged DNA bases in a sequence.
Co-Author(s): Dr. Xiaona Li
Climatic changes may increase the frequency of forest fires in temperate forests of the Eastern United States. An understanding of the impact of forest fires on biogeochemical cycles will give better insight into a post-fire biome and hydrology. Our previous studies investigated the major, minor, and trace element composition of soils following fires (including prescribed and wildfire) in the mixed oak hardwood forest of the Pocono Mountains (Appalachians) of Northeast Pennsylvania, USA. An additional field experiment ascertained the composition of the contributing ash component from burned wood of different tree species. These studies identified post-fire soil enrichment in Fe, Mn, and Ca (as expected) as well as trace elements Cu and Ba. In addition, there was a post-fire soil depletion of almost all rare earth elements (REEs) despite the potential enrichment of REEs found in wood ash. The study presented here attempts to address, by lab experimentation, previously uninvestigated factors that may impact the retention, or volatility, of these signature elements.
Samples of natural forest soil from the area were obtained, including O, A, incipient E, and B horizons. The soil samples were dried (and moisture content recorded), then carbon content estimated using the loss on ignition method. Element composition of major, minor, and trace elements, in mass percent or parts per million, was determined using ICP-MS, with the sample solutions prepared by the fusion method, and calibrated against USGS rock standards. Using separates of the same soil sample, an unburned control sample was compared to samples heated to 350? or 550? in an oven or furnace then cooled (simulating forest fire burn and smolder), as well as with soils devoid of organic carbon (after loss on ignition). The hypotheses are: 1) REEs may volatilize more with higher temperatures, and may change with varying cooling rates; 2) signature element sequestration may depend on the amount of clay or remaining carbon (a factor of colloids and surface area).
Multispectral cameras collect image data within specific wavelength ranges across the electromagnetic spectrum. Since collecting data in such way allows differentiation of materials with improved accuracy than monochrome or color camera produced data, multispectral cameras have found their way in most of the science and technology fields, including life and health sciences, agriculture, earth and environmental science, food science, industrial quality control, etc. Pre-built multispectral cameras can be very expensive and thus most educational institutions could not afford to purchase them and use them as part of their research and educational programs.
This project describes efforts to develop a low-cost multispectral camera using mostly off the shelf components. The camera is built as a monochrome system with different lighting configurations that emit within specific spectral wavelengths. For this, different Light Emitting Diode (LED) solutions were compared with respect to the wavelengths, ranging from ultraviolet (400nm) to red (680nm), luminosity, and diffusion. In parallel, high definition monochrome cameras and lenses were also evaluated with respect to shutter speed, sensitivity and ultimately price.The proposed solution included diffused LEDs from Jameco Electronics, an Alvium USB 3.1 Allied Vision monochrome camera, an EO Edmund 25mm UC series fixed focal length lens, and a 4PC 400 point solderless breadboard. Once all the parts were in house research was done to properly connect them in order to make a working multispectral camera. This included researching how LEDs work with breadboards, identifying the proper resistors, and the Arduino based software components to activate the LEDs on set intervals. Next, the camera software set up was completed through downloading vimba SDK and drivers to interact with the camera to take pictures. Testing is currently ongoing and will be followed by research on the assembly of the LEDs into a more secure casing. This can be done with a circuit board. The project resulted in a successful prototyping of a multispectral camera at significant cost reduction compared to a pre-built one. To date we are also in the process of sorting out projects to test such as mineral measurements in soil, measuring graphite behind an oil painting, and measuring fluid in petri dishes.
Global amphibian populations have been declining since the 20th century; one of the most significant contributors to these declines is a genus of viral pathogens known as Ranavirus (Rv). Frog virus 3 is one of these viral agents and is currently found affecting frog populations throughout NJ, MD, PA, DE, and VA. Having no cure, it is imperative to be able to detect and monitor the virus in the wild, but current testing methods require extensive training, expensive equipment, and time investments. To combat these issues with detection and develop a rapid field test that provides real time, in field results, we propose the development of a novel aptamer discovery technique to generate short single-stranded DNA sequences that specifically bind to the virus’s major capsid protein (MCP). This technique would use Systematic Evolution of Ligands by Exponential Enrichment (SELEX), a polymerase chain reaction (PCR) based method that narrows a large library of random DNA sequences into a smaller library of targeted sequences. Previous SELEX using a dual target system alternating between whole virus Rv and Rv MCP yielded an enriched library that was used to develop electrophoretic mobility shift assays (EMSA) to assess binding affinity. Our new SELEX approach alternates between two differently tagged Rv MCP targets, and we expect it to enrich a library for high affinity binding to Rv MCP. The enriched library will then be screened using EMSA to assess binding affinity and find aptamers for use in the proposed rapid field tests.
The understanding of cellular communication is the foundation to understanding various disorders and diseases in the human body. Cells communicate with one another by sending and receiving signals; neurons are able to send a signal via the release of a chemical or neurotransmitter when it binds to the receptor of the receiving neuron. Current tools are either able to measure these quick reactions but do not have high spatial resolution or are not fast enough but have a high spatial resolution. Light addressable electrochemical sensors are able to detect low concentrations of neurotransmitters as well as capture these quick reactions. These sensors use light to activate an electrochemical reaction and control where the reaction is taking place. Using metals makes them an even more ideal tool because metals are widely understood reactions, especially the electron transfer that takes place, hence they are ideally used for Schottky junctions for LAES. This is because the reaction takes place on the metal instead of the semiconductor. Previously, this has been tested by depositing gold nanoparticles onto the silicon surfaces of the samples where a Schottky junction has formed, yielding promising results. However, some limitations of gold have been detected which have propelled our group to try depositing another metal, platinum. Here we discover the advantages of using Pt instead and can even possibly apply it to understanding the cell communication among cancer cells and the role hydrogen peroxide may play in it.
Co-Author(s): Jaclyn Catalano
Cytochrome P450 is a heme protein essential in the metabolization of drugs. CYPs have been investigated as drug targets for anticancer prodrugs (to be activated by P450 only in cancer cells). We are using a bacterial model of cytochrome P450 to mimic the active site of CYP2S1, which is overexpressed in breast cancer cells, by creating single mutations at residue 267 and a hexamutant. We are using a bacterial model since they are easier to work with because they are soluble, easy to express, and easy to purify. First, we studied the role of E267 in Cytochrome P450 BM-3. We hypothesize that mutations to E267 will alter the kinetics of Cytochrome P450 by interfering with proton transfer in the mechanism and/or be involved in expanding the binding pocket to incorporate bulkier substrates. Acidic residue E267 was mutated to valine (hydrophobic), methionine (hydrophobic), aspartic acid (smaller acidic), and lysine (basic). Michaelis Menten kinetics and the effect on the kinetics as a function of pH was studied. The findings show that all three mutants have a similar pH profile compared to the wild-type and there is no activity for the methionine mutant. Second, we have successfully created the hexamutant mimic to incorporate bulkier non-natural substrates. We are working to express and purify the hexamutant and find out if the active site has widened to catalyze large substrates.
Co-Author(s): Megan Klutts
The Motus Wildlife Tracking System is a network of automated receivers that uses radio telemetry to track the movements of birds, bats, and insects across vast distances. Radio transmitters were affixed to seven Gray Catbirds (Dumetella carolinensis) and twelve Song Sparrows (Melospiza melodia) in September – October 2021 to track their southern migration from the New Jersey Meadowlands along the east coast of the United States. Twelve of the birds were successfully detected by the Motus network: all seven catbirds and five of the sparrows. Catbirds tagged earlier in the season migrated further with final detections on the coasts of South Carolina and Georgia. Catbirds tagged later in the season migrated to Delaware and Maryland. The five sparrows detected also migrated to Delaware and Maryland; there was no difference in migration route or distance based on date tagged. It is likely that the undetected sparrows did not migrate, as many Song Sparrows overwinter in New Jersey. For this reason, future migration studies will focus on another species of sparrow with a stronger migratory character. However, as all catbirds in the study were successfully tracked, this species will continue to be used in future research.
Co-Author(s): Edgar Medina, Adi Ackerman, Julia Kopell, Nicole Rodriguez Ortiz, Mya Theodore
Hurricane Sandy struck the New York metropolitan region on October 29, 2012. The storm severely impacted the physical state of Barnegat Bay, New Jersey, with its heavy storm surge which scoured the sea bottom, effecting many forms of benthiclife and ripping up extensive beds of Zostera marina. Previous studies of the genetic status of Z. marina in Barnegat Baysuggested low levels of heterozygosity and high levels of inbreeding. We are presently examining the long-term effects of Hurricane Sandy on the eelgrass beds of New Jersey. Preliminary data among all population sites studied (Oyster Creek, Ham Island, Connective Sedge, Rt.72 South, and Barnegat Inlet) suggest that present observed levels of heterozygosity are low compared to expected levels (mean Ho =0.499+0.089 and He=0.560+0.060), suggesting worsening diversity. Overall mean inbreeding levels (Fis = 0.202+0.102) indicate little outbreeding within grass beds and the fixation index (mean Fst = 0.175+0.106) suggests low connectivity between populations with a “medium” level of differentiation. Phylogenetic cladograms generated using Chord and Delta Mu distances coincide with Fst values and indicate differentiation among these populations. This data suggests that the genetic health of grass beds in Barnegat Bay have declined in the last decade. Thirteen polymorphic microsatellite alleles were employed in this study giving a high degree of resolution.
Co-Author(s): Kingsley Maduka
Lead (Pb) can be found in air, soil, leaded gasoline, lead-based paints, and various manufacturing products. Lead toxicity has been a serious issue for the past years, occurring at higher incidence rates in the human population than other heavy metals. In general, lead toxicity has diminished in the United States since the 1970s. More recently, there have been concerns in cities in New Jersey due to old and corroding pipes in our household water supply. Developing bones absorb lead quickly. As a result, young, developing children exposed to toxic lead are more susceptible to stunted skeletal growth and osteoporosis in old age. Moreover, during pregnancy and lactation, lead exposure causes premature births, malformation of bones, neurological and cognitive defects, and soft tissue damage to the kidneys and reproductive organs. In a growing fetus, cartilage is converted to bone. During this process, the osteocytes in the lacunae of long bones deposit calcium. Since lead and calcium compete in the mineralization process, damage from lead is modified by simultaneous exposure to both lead and calcium, and adversely influences proper mineralization. Our ongoing research experiment is testing to identify the effects of different lead concentrations on bone cultures obtained from 9-day old chick embryos. The experimental mechanisms used will determine and reveal the role of the physiological stress of lead exposure on normal bone development. The samples being tested were a control media of MEM with 10% fetal calf serum, 250ppm of lead, and 62.25ppm of lead. Daily monitoring of each experiment for growth, development, differentiation, deterioration, or malformations of bones was done. Bone growth or loss was expressed as a percentage of the total number of millimeters gained or lost throughout the study. Lastly, a parallel study was followed to determine the effects of lead on the growth of chick embryo tissue grown from 4-5 mm. biopsy cultures. The effects of lead on cell proliferation were correlated with bone growth observations.
In this project, the goal is to monitor the potential change in secondary structure of Vibrio Cholerae Cryptochrome 1 (VcCry-1), which undergoes a switch in function from DNA repair to signaling with an approximate pKa of 7. The pH values that we are focusing on are pH 6 and pH 8 to test if the secondary structure of the protein is affected by changing from a higher pH to lower pH. The secondary structure has mainly contributions from a-helix and ß-sheet in the protein structure. We use FTIR-transmission spectroscopy with a liquid cell consisting of two CaF2 IR windows with a customized cell holder and plates. Using this method makes the removal of unwanted contributions of any solution molecules easy and the results of the samples were very consistent working with FTIR-transmission spectroscopy. The purpose of using the FTIR-transmission is to measure the Amide I band (1600-1700cm-1) of the protein to show potential changes in the secondary structure of the protein that could be due to the change from low to high pH. When analyzing the Amide I band with Gaussian line shapes that can be assigned to different secondary structure elements, secondary structural changes for the VcCry-1 at different pH values may be observed. This will allow us to test the overall hypothesis of a potential change in protein secondary structure when the function of the protein changes with pH.
Co-Author(s): Dr. Joan Bennett
Sick building syndrome (SBS) is a diagnosis in which multiple symptoms are associated with time spent in a particular building, rather than a specific illness. In some cases, SBS is caused by toxins, (i.e., lead or chemical vapors). Contamination of buildings with molds or fungi may also be an important cause of SBS. While the chemicals emitted from fungi or molds have been biochemically identified, the effects of these chemicals on animals are unknown.
We used C. elegans as an animal model in order to rapidly discover how animals are affected by fungal volatile chemicals, and elucidate their possible roles in SBS. Use of C. elegans provides many benefits for this study due to their short life cycle, simple nervous system, fully sequenced diploid genome and their large population size on a single petri dish after 3-5 days. We exposed C. elegans to four different fungal volatiles to see if there was an effect on their 1) growth and size, 2) viability or reproduction, and 3) locomotion. Our findings indicate that several of the fungal volatiles do in fact have a strong effect on the viability, growth, and size of C. elegans, as well as the rate of reproduction of new worms. In future studies, we will determine the genes involved in the toxicity of the fungal volatiles to better understand the impacts these toxic volatiles have on C. elegans, as well as any potential effects these volatiles can have on humans who suffer from SBS.
Zooplankton play an integral role in marine ecosystems acting as the dispersal phase of many species, as well as vital trophic transfer links to higher predators that directly or indirectly feed on them. However, food webs can be disrupted when the growth of one species changes the community. In New Jersey’s coastal lagoons, increased human development has led to the increase in the jellyfish, Chrysaora chesapeakei. This apex predator reduces the abundance and diversity of many taxonomic groups as it exerts top-down control of these communities. Four lagoon communities were sampled for zooplankton in Barnegat Bay in June, July, and August 2021 using lift nets and plankton tow nets to characterize the larger gelatinous zooplankton and the smaller zooplankton they prey upon. Results showed a direct top-down predation of C. chesapeakei on most taxon in the system, including the comb jelly, Mnemiopsis leidyi. As C. chesapeakei increased in abundance by mid-summer, other taxa such as calanoid copepods, shrimp larvae, and crab larvae declined. By the end of the summer, some taxa rebounded with the decline of C. chesapeakei in August including shrimp and crab larvae, but this may have also reflected the reproduction pattern of different crustacean species.
Co-Author(s): Charles Ezenwanne, Ann Marie DiLorenzo
Clinical and epidemiological studies have shown a correlation between inflammation and lung cancer. Methylsulfonylmethane (MSM) has been used for years as a dietary supplement and clinical studies have shown the benefits of MSM as an anti-inflammatory substance also active in the prevention of stress of immune cells. In particular, these studies have shown that MSM potentially induces apoptosis in cancer cell lines and prevents the spread of cancer cells. However, the specific molecular control role that MSM plays has yet to be investigated. Experiments are in progress to determine if specific microRNA (miRNA) can be identified and shown to be significantly altered in the presence of MSM. Identification and observation of miRNA have been of interest to our lab because of its key role in the regulation of gene expression. These small non-coding RNAs are known to post-transcriptionally fine-tune up to 30% of genes and are currently implemented in cancer-based therapy. Specific miRNAs have been found to be up-regulated or down-regulated when cells start metastasis. Our lab is exploring the possible role that MSM plays in cell growth inhibition, apoptosis and MSM regulated molecular pathways in A549 human lung cancer cells. Our preliminary studies show that low doses of MSM (100 – 200 mM) may be effective in apoptosis induction and proliferation inhibition of A549 cells without toxicity. We have also begun to analyze expression patterns of several miRNAs that have been previously shown to be involved in the regulation of apoptosis.
The invasive clinging jellyfish (Gonionemus vertens) was first documented in New Jersey in 2016 and has been expanding and increasing in abundance ever since. This species has a complex life history which includes the adult medusa and an extremely small polyp stage. Both life stages live in shallow water attached to seagrass and algae. The medusa life stage creates public health concerns due to its harmful sting. In this experiment, the clinging jellyfish polyps were monitored on individual etched glass slides for 11 weeks to evaluate colonization, growth rates, and asexual reproduction. Polyps colonized plates in 3 weeks and showed a large spike in asexual reproduction at 5 weeks. A significant regression showed that new polyps took about 2 weeks to reach fully mature sizes capable of generating more asexual clones of themselves, as well as being able to produce medusa to complete their life cycle. This new information may help explain the sudden increases of this invasive species in New Jersey and help figure out how to control the spread to ensure the safety of the general public using these areas for recreation.
Co-Author(s): Julian, Andres, Hernandez Suarez
Ecologists have long been concerned with understanding the behavior of complex communities and how they evolve over time. While significant research has been performed to capture and quantify the interaction links between species of different ecological communities, much less work has been done to understand the dynamics of these food webs. We consider the deterministic and stochastic dynamics of the cascade model, a type of synthetic food web, and study primary extinction and the resulting secondary extinction cascade. With these results, we lay the groundwork for the dynamical analysis of the Southern Ocean food web.
Co-Author(s): Eric Forgoston, Vladislav Snitsarev
The electrophysiology of nodose ganglia neurons is of great interest in the analysis of cell membrane currents and action potential behavior. This behavior was initially outlined in the Hodgkin-Huxley conductance model using a system of nonlinear differential equations. One significant shortcoming of this original model, however, was that it provided an incomplete description of ion channels involved in neuronal action potential activity. This project extends the Hodgkin-Huxley model to account for additional ion channel dynamics via coupling with a Ca²? fluid compartment model in an effort to integrate more information about the electrical signatures of A-type and C-type nodose neurons. An expanded set of solutions to nonlinear differential equations were numerically computed to match observational data. This updated model successfully characterizes the electrical behavior of A-type and C-type nodose neurons and broadens the predictive range of the Hodgkin-Huxley system.
Co-Author(s): Daniel Chioffi, Maya Glenn, Stefan O. Nita, Vlad N. Nita, Dr. Bogdan G. Nita
In this paper we study the mathematical connection between the shape of a 36-string harp tuned in the equal temperament scale to develop a formula that models the neck’s harmonic curve. This model of the neck of the classical harp is based on the length of the strings, their tension, and density. Through this analysis we were able to find a model that closely resembled that of the classical harp while deepening our understanding of mathematical concepts. Using this model, we created new harp designs by modifying the soundboard and keeping all other parameters the same. By examining these existing connections between mathematics and music we created an exercise that takes advantage of both creative and analytical skills to develop a mathematical model.
Co-Author(s): Martha Mahady, Dirk Vanderklein
The purpose of this study is to compare the effect of vernalization of seeds on the growth of purple loosestrife (Lythrum salicaria) compared to native winged loosestrife (Lythrum alatum). Purple loosestrife is a wetland plant that is invasive in North American and can have serious impacts on wetland ecosystems. In this study, purple loosestrife from Sussex County, New Jersey and United Kingdom seeds and native North American winged loosestrife seeds were grown in simulated wetland conditions outside on the roof of the Science Building at Montclair State University. Each type of seed was sown in sterilized wetland soil from Sussex County NJ, USA. Seeds to be vernalized were sown in January, while seeds to be non-vernalized were sown in May. There was no significant difference in height and mass between plants grown from vernalized and non-vernalized seeds for purple loosestrife from Sussex County NJ, USA, purple loosestrife from the UK, and winged loosestrife. This indicates that there is the potential for the range of purple loosestrife to expand into areas without the cold winter temperatures required for vernalization.
Co-Author(s): Adriana LaVarco, Angela Chemidlin, Anthony Minervini, Ray Nunez Castaneda
White-Cheeked Gibbons are Lesser Apes that live mainly in South East Asia. Gibbons are understudied when compared to other apes and their social interactions are not well understood. Four Gibbons (2F,2M) were observed at the Turtle Back Zoo located in West Orange, New Jersey. To determine the degree of social interaction, self-stimulation and self-play was compared to other-stimulation and other-play. Both grooming (stimulation) and play behavior was compared across a 2-month period. It was found that there was a significant difference between self-stimulation (14 bouts) and other-stimulation (124 bouts) such that other-stimulation was significantly greater than self-stimulation (X2=87.68, p<.00001). Furthermore, other-play (141 bouts) was also significantly greater than self-play (9 bouts; X2=116.16, p<.00001). These data indicate Gibbons have a high degree of social affinity.
New Jersey has several different species of mosquito that as larvae live in relatively small bodies of water (“container mosquitoes”). Mosquito larvae are often the largest and most dominant species in these small bodies of water. In New Jersey, it is predicted that the average summer temperatures will continue to increase. Higher temperatures cause the pH of a solution to decrease as water ionizes and forms more hydrogen ions. The pH of aquatic environments is important to the many species that live in them. Because of rising temperatures, the pH levels of the environments in which mosquito larvae live may fluctuate significantly. However, the reciprocal relationships between mosquito density and pH are poorly understood, especially across distinct taxa. Here we test out how pH fluctuates depending on which species of container mosquito live in them, using the mosquito species Aedes albopictus, A. triseriatus, and Culex pipiens. We predict that the presence of mosquito larvae will affect the pH of their habits and that different species of mosquito differ in the degree to which these changes occur.
Co-Author(s): Maurizia De Palma, Anthony Gachetti, Emily Cepin, Ying Cui, Stefanie Brachfeld, Shijun Jiang
The Paleocene-Eocene Thermal Maximum (PETM) was the last great global warming event that took place ~56 million years ago. The PETM is most analogous to modern climate change, considering global temperatures rose between 5-9 Co as a result of rapid release of carbon emissions. During this time wildfires occurred in some regions of the world, producing black carbon (BC), a product of incomplete combustion of organic matter. We study the Kuzigongsu section within the Tarim Basin in the eastern Tethys and modern-day northwestern China, to investigate how subtropical, shallow marine environments responded to the PETM. Magnetic susceptibility (MS) is directly related to the amount of Fe-oxide-bearing terrigenous material present in the sedimentary rock samples, and was measured using an AGICO MFK2A Kappabridge. We aim to determine if BC isotopes (d13CBC) and MS values are correlated to inform us of the drivers of environmental changes that occurred at the Tarim Basin during the PETM. Our results show higher MS values and more negative d13CBC values during the PETM, suggesting higher terrigenous content and a shift in vegetation from gymnosperms to angiosperms. These shifts can be interpreted as increased continental weathering, potentially driven by precipitation and increased runoff in the region due to warmer temperatures during the PETM. Overall, understanding how environments may have responded during the PETM enables us to improve future projections of how modern ecosystems may shift looking forward.
Co-Author(s): MORGAN, Joanna V., GLASS, Billy P., DE PALMA, Maurizia, WU, Tina, NSINGI, Joseph Mayala, CUI, Ying
The discovery of a Cretaceous/Paleogene (K/Pg) marine bathyal section on Gorgonilla Island, Pacific of Colombia, has revealed the presence of a virtually unaltered 2-cm-thick spherule-rich bed separating the Maastrichtian from the Danian. This bed represents Chicxulub asteroid impact ejecta deposits based on detailed mineralogical, geochemical, and stratigraphic studies. The Chicxulub impact is thought to be responsible for the mass extinction at the K/Pg boundary. Although there have been many studies of ejecta deposits around the globe, relatively few have focused on spherule morphology. Taking advantage of the exquisite preservation of the spherules (up to 90% of are pure glass) from Gorgonilla Island, a detailed morphological analysis of 1000 individual spherules has been carried out. Our results indicate all spherules correspond to spin or spin-induced forms with no evidence of ablation-form spherules. The spin-induced spherule morphology can be subdivided into four main categories: I) Splash-forms (the most abundant type); II) Fused-forms (that includes any combination of 2 or more splash-forms); III) Deformed-forms (that includes splash-forms with evidence of deformation by rotation or impact), and IV) Irregular forms (undefined morphologies including ground impact effects). Regarding the splash-forms (Category I), we propose a novel classi?cation scheme based on the axial ratios of ellipsoids, which include a diverse array of shapes ranging from spheres, rods, ovoids, ovoid disks, spherical disks, dumbbells, bowties, oval bowls, circular bowls, teardrops, teardrop bars, ovoid teardrops, and teardrop disks. These different shapes are interpreted as a result of spinning while cooling and solidifying, which indicates that surface tension and centrifugal forces associated with the rotation of fluid droplets are the main factors determining the shapes of this type of Chicxulub’s spherules. While a fraction of the spherical shapes may correspond to condensed droplets of the vapor plume, it is also possible that they correspond to advanced stages of other splash forms or to droplets too small to be deformed during spinning. All other shapes clearly correspond to splash forms (fluid – non-condensed droplets).These results represent the first morphological classification of the type of ejecta produced during the Chicxulub asteroid impact and provide direct evidence of glass spherules formation mechanisms during asteroid impacts.
Co-Author(s): Jiayin Wang, Chunguang Du
The research focuses on an interdisciplinary topic of both Computer Science and Biology. Helitrons represent a new class of transposable elements (TE) recently uncovered in animals and plants. One remarkable feature of Helitrons is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, Helitrons are hard to detect computationally given their lack of classical transposon structural features. In this research experience, we created a deep-learning algorithm based on the Long-Short Term Memory (LSTMs), which is a Recurrent Neural Network architecture, to develop a tool to identify Helitron sequences. We applied the model in predicting Helitrons in maize and achieved an accuracy of over 99%.