Master's Theses

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An Evaluation of a Northern Bobwhite (Colinus virginianus) Parent-reared Release in South Carolina
Haley, Ryan
Northern bobwhites (Colinus virginianus) have experienced large, range-wide declines mainly attributed to the loss of early-successional habitat. Bobwhite population recovery is predicated on sound habitat management. Even when adequate habitat exists, low bobwhite densities and limited dispersal capabilities may limit population recovery. Restocking techniques, including release of pen-reared birds, wild bobwhite translocation, and the use of wild-strained, parent-reared captive-raised bobwhites have been explored as surrogates to natural recolonization. In this study, I evaluated survival and reproduction of parent-reared bobwhites, compared to resident bobwhites, on a private property in South Carolina from April 2009-April 2013. I used a sequential modeling approach to evaluate adult survival and nest survival using Program MARK. Bobwhite survival was best explained by temporal (annual and weekly) effects and group (parent-reared vs. resident) effects. Weekly bobwhite survival for both parent-reared and resident bobwhites was too low to produce a stable population. Parent-reared bobwhite survival was lower than resident bobwhites during the first 3 weeks post-release but similar during later weeks. Parent-reared bobwhites released in August had higher survival (S = 0.884, 95% CI = 0.862, 0.903) than birds released in early fall (S = 0.707, 95% CI = 0.621, 0.782). Nest survival and other reproductive parameters for parent-reared and resident bobwhite were similar. The viability of the parent-reared release system as a restocking technique is limited as currently constructed and future modification is needed if it is to produce a viable bobwhite population
Germanium silicon tin oxide thin films for uncooled infrared detectors
Cardona, Jaime
Microbolometer is a class of infrared detector whose resistance changes when the temperature changes. In this work, we deposited and characterized Germanium Silicon Oxide thin films mixed with Tin (Ge-Si-Sn-O) for uncooled infrared detection. Ge-Sn-O was deposited by co-sputtering of Sn and Ge-Si targets in an Ar+O environment using a radio frequency (RF) and direct current (DC) sputtering system. The electrical and optical properties of the thin films were tested to verify whether Ge-Si-Sn-O could be used as a sensing material in a microbolometer. From this testing, it was shown that with the an atomic composition consisting of Ge0.36Si0.04Sn0.11O0.43 the Ge-Si-Sn-O alloy could have a temperature coefficient of resistance (TCR) greater than -3.5 %/K, optical band gap of around 1 eV, and noise value of 300 μV/√Hz at 10Hz. With these values, besides the slightly high noise value, it has been determined that Ge-Si-Sn-O alloy is a viable candidate for use in microbolometer development.
In vitro Assessment of Phytoconstituents, Efficacy and Cytotoxicity of Extracts from Medicinal Plants on Prostate Cancer C4-2 Cells
Asuzu, Peace Chiamaka
Phenolic compounds are products of secondary plant metabolism known for their biological activity including their antimicrobial, antioxidant, analgesic, stimulant, anti-carcinogenic, and aphrodisiac properties. The main objective of this study was to assess the content and properties of bioactive phytochemicals in the extracts of Prunus africana, Pausinystalia yohimbe, Moringa oleifera, Momordica charantia and Orthero spp and determine their potency/cytotoxic effects. Total phenolics (TPC), carotenoids, anthocyanins, and flavonoids and their antioxidant properties in water, ethanol, methanol, acetone, and dichloromethane extracts of the different plant parts of these five plants were measured using the Folin-Ciocalteu, 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH), ferric reducing antioxidant power (FRAP), and 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) radical scavenging (ABTS) assays. For most of the plant samples, extraction yields were highest in ethanol or methanol extraction solvents. The highest total phenolic content (1397.33 mg GAE/g) was seen in the methanol extract of P. africana bark from Cameroon, while the acetone extract of M. charantia leaves yielded the highest total flavonoid content (217.33 mg RU/g). The FRAP values in this study ranged from 7.09 in the DCM extract of P. africana bark (Kenya) to 131.57 mM Fe2+/g in ACE extract of M. charantia leaf. The EC50 values for the acetone and methanol extracts of P. africana bark (Cameroon), methanol and ethanol extracts of P. yohimbe leaf and the methanol extract of P. yohimbe root were comparable to ascorbic acid (0.18 mg/mL). TPC showed a strong positive correlation with TFC of acetone extracts of P. yohimbe and Orthero roots, FRAP of ethanol and methanol extracts of P. africana (Cameroon) root, acetone and methanol extracts of P. africana (Cameroon) leaf, methanol extracts of P. yohimbe leaf, M. charantia leaf and the TEAC of P. africana (Cameroon) bark water extract, ethanol extracts of P. yohimbe leaf and Orthero root. Using high performance liquid chromatography (HPLC), seven phenolic acids, namely methyl 4-hydroxybenzoate, protocatechuic acid ethyl ester, trans-sinapic acid, vanillic acid, trans-ferulic acid, p-coumaric acid and caffeic acid were isolated from nine extracts of P. africana and P. yohimbe. The most abundant phenolic acids were vanillic acid (116.41 mg/g dry extract in methanol extract of P. yohimbe leaf) and trans-sinapic acid (102.22 mg/g dry extract in water extract of P. africana bark). On gas chromatographic phytosterol analysis, stigmasterol, β-sitosterol and campesterol were present in all plant parts of P. africana and P. yohimbe except for P. africana root and bark, where campesterol was not detected. β-sitosterol showed the highest concentration and variation between plant parts, ranging from 0.55-2.26 in the bark and leaf and 0.35-0.46 mg/g in the root and leaf of P. africana and P. yohimbe, respectively. Using different concentrations of P. africana extracts, prostate cancer C4-2 cells, a hormonally insensitive subline of LNCaP cells, were treated in a proliferation assay. A concentration dependent inhibition of cell growth in cells treated with P. africana bark and root extracts was present from days 1 through 3 of incubation, with the methanol extract of the bark showing the strongest effect. Compared to other plant parts, leaf extracts were significantly less cytotoxic at the same concentrations. All plant part extracts contained significant amounts of phenolic compounds and pigments with potent antioxidant activity comparable to that of ascorbic acid, in the case of P. africana, demonstrated in vitro cytotoxicity.
Evaluation of Phytochemical Composition in Selected Medicinal Plants and Potential Application as Antimicrobial Agent
Smith, Jallah Chuku
Four medicinal plants native to Cameroon (C) and Kenya (K): Prunus africana (C) bark and root, P. africana (K) bark, Pausinystalia yohimbe bark, and Orthero root were screened to assess their phytochemical compositions and antioxidant activities. The plant parts were extracted using aqueous (80%) acetone, methanol, and ethanol (solvent: water, 80:20 v/v). The antioxidant capacity of the extracts was evaluated by their ability to scavenge free radicals using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and their antiradical power (ARP); trolox equivalent antioxidant capacity (TEAC) by utilizing 2,2′-azinobis-(3-ethylbenzothiaziline-6-sulfonate) (ABTS); and ferric reducing antioxidant power (FRAP). The total phenolic content (TPC) and total flavonoid content (TFC) were estimated by the Folin-Ciocalteu (FC) and aluminum-chloride (AlCl3) assays, respectively. Pigment content was determined spectrophotometrically, and phenolic acids were quantified by high performance liquid chromatography-photodiode array detector (HPLC-PAD) using eight aqueous solvent extracts with EC50 values (±0.125), in comparison with the standard (i.e., ascorbic acid). In addition, the antimicrobial activity was demonstrated using the agar disc diffusion assay followed by the measurement of the average zone of inhibition (ZOI) in which the first five aqueous solvent extracts in the order of decreasing antioxidant power were tested against two clinical foodborne bacteria (gram-negative E. coli and gram-positive S. aureus). The highest DPPH radical scavenging activity was found in P. africana (K) bark (95.77%; aqueous acetonic extract) though its aqueous methanolic extract exhibited the lowest antioxidant power with the highest effective concentration (EC50) and lowest ARP (7.298 mg/mL and 0.137), respectively; and its aqueous acetonic extracts also exhibited the lowest TPC and TFC, respectively (166.27 mg GAE/g and 9.60 mg RU/g). However, the highest EC50 and ARP (0.093 mg/mL and 10.753 respecively), and highest TPC (1131.70 mg GAE/g) were exhibited by the aqueous ethanolic extract of P. africana (C) bark while the highest ferric reducing capacity (11.33 mM Fe2+/g) and ABTS•+ radical scavenging activity (126.87 mM TE/g) was exhibited by the aqueous acetonic and aqueous methanolic extracts of P. yohimbe bark, respectively. Moreover, the highest TFC (61.33 mg RU/g) was also exhibited by the aqueous acetonic extract of P. yohimbe bark. Except for xanthophylls, the highest recorded pigment (61.92 mg/g) in this study was exhibited by the aqueous acetonic extract of Orthero root; the highest measure of all other pigments (chlorophyll a and b; total chlorophyll, lycopene, β-carotene, carotenoids, and anthocyanin) were exhibited by the aqueous acetonic extracts of P. yohimbe bark (9.16 and 22.46; 32.21, 2.78, 6.83, 20.08, and 0.53 mg/g, respectively). There was a significant positive correlation between TPC, TFC and DPPH, and a significant negative correlation between TPC and the other two antioxidant assays (FRAP and TEAC). Methyl 4-hydrocybenzoate and protocatechuic acid were detected and quantified in all the selected extracts, trans-sinapic acid (SIA) in P. africana (C) bark and root, and ferulic acid (FA) in P. africana root extract only. P. africana (C) bark and root extracts had the highest phenolic acid in all plant parts (i.e., SIA) with recorded values >100 mg/g which agrees with their spectrophotometrically determined high TPC. All aqueous solvent controls used for extraction, inhibited the growth of both E. coli and S. aureus while the sterile blank disc controls showed no inhibitory zone. Of all the tested extracts, both concentrations (50 and 100 mg/mL) of aqueous acetonic extracts of P. africana (C) bark exhibited no growth inhibiton against E. coli but an active to highly active inhibitory zone against S. aureus (8.0 to 17.33 mm). The highest growth inhibition was exhibited by the aqueous ethanolic extract of P. africana (C) bark against S. aureus (17.33 mm). These results clearly support the potential uses of these plant parts in a wide range of applications such as antimicrobials and antioxidants.
Comparative RNA-Seq Analysis of Phenotypically Different Sweetpotatoes (Ipomoea batatas [L.] Lam)
Fiedler, Elizabeth Ann Marie
Sweetpotato is arguably one of Earth’s top ten most important crops. It is relatively low maintenance, packed with essential vitamins and nutrients, and in addition to serving as an effective food crop, it has been suggested for use as a material for synthesizing plastics and as a replacement for corn as a source for bioethanol production. Sweetpotatoes are difficult to bring to seed, so most sweetpotato plants are grown from slips, which are cuttings from sweetpotato vines. This makes it very easy for sweetpotato viruses to spread from generation to generation. Currently, virus disease complexes, which are infections of two or more viruses with a synergistic interaction, pose the biggest threat to sweetpotato yields. It is therefore crucial to have a better understanding of different sweetpotato genotypes. Sweetpotato genotypes tend to be very similar, since crossing and outbreeding strategies are all but impossible to carry out on sweetpotatoes, as different genotypes tend to be very similar. Transcriptome profiling could prove to be an extremely useful method for understanding the causes of phenotypic differences in genotypes. This project details the construction of the transcriptome profiles of three phenotypically different genotypes. Illumina sequencing was carried out on the 2500HiSeq platform and the resulting reads were aligned to the sweetpotato genome constructed by the Max Planck Institute. Bioinformatics software was used to carry out alignment and analysis. The analysis techniques were used to calculate and normalize gene expression, make fold change comparisons, convert this data to log 2-fold change, determine which genes had the greatest expression differences, group these genes into functional groups, and perform other analyses.
Sustainable Agriculture Practice: Quantifying the Effects of Cover Crop Planting Dates and Seeding Rates on Coverage Rates and Biomass Yields in Delaware
Challandes, Jason Paul
Cover crops have been proven to have many potential environmental and financial benefits if they are managed properly. However, proper management is dependent on the unique soil and climatic conditions in the immediate area. Management techniques that are effective in one geographical area may not be sufficient to support cover crops in other nearby conditions. While several cover crop research projects have been conducted locally, Delaware is still lacking important knowledge to provide effective recommendations to farmers growing cover crops. Specifically, the evaluation of planting dates and seeding rates is needed in order to maximize the environmental and agricultural benefits of the most commonly used varieties of cover crops. Currently, the Delaware Natural Resources Conservation Service (NRCS) offers financial subsidies to farmers who grow cover crops according to their regulations through the Environmental Quality Incentives Program (EQIP). It has been brought to their attention by farmers that their planting date deadlines may be earlier and seeding rates higher than necessary to produce sufficient groundcover and biomass. However, without research data in Delaware to legally justify changes to these requirements, farmers will have to continue following nationally established methods for planting dates and seeding rates, in order to receive subsidies. Primary objective of my research focused on investigating cover crop planting dates and seeding rates for optimum cover crop density. Ground coverage, spring aboveground biomass, nitrogen (N) removal, and total soil N at termination as affected by species, planting date, seeding rate, planting method, and their interactions within agricultural systems including no-till corn and soybean fields were evaluated. Cereal rye, barley, wheat, and rye/clover mixes were planted with three seeding rates, up to three planting dates, and two planting methods per site: broadcasted vs. drilled or incorporated with a light disk. Trials were administered at four sites during the 2015-2016 season and three sites during the 2017-2018 season. Results showed no benefit in seeding rates that exceeded 94, 101, and 101 kg/ha (84, 90 and 90 lbs/ac) for monocultures of rye, barley, and wheat, respectively and 45 kg/ha of rye and 17 kg/ha of crimson clover for mixes (40 and 15 lbs/ac). Even lower rates performed similarly for many treatments and outperformed high rates in some. Rye at any date prior to November 1 and rye/clover mixes prior to October 1 are recommended over barley and wheat for better groundcover, biomass, and N removal. Drilled plots produced greater biomass and N removal than broadcasted sites at equal seeding rates, but generally produced similar groundcover. Broadcasted plots seeded at 30% higher rates produced similar biomass as incorporated plots for some treatments, but incorporating seeds is recommended over broadcasting at later dates and for increased groundcover. The most consistent result of this study is that cover crops planted at early dates, prior to October 1, performed better than crops planted at standard dates, prior to October 15, which outperformed the late planted cover crops prior to November 1. For some treatments, cover crops planted at the standard dates performed comparably to early dates, but the late date plots consistently had lower groundcover, biomass, and N removal, regardless of crop, rate, or method.
Trophic Ecology of Juvenile Weakfish (cynoscion Regalis) in The Delaware Bay Using Stomach Content and Stable Isotope Analyses
Galvez, Brian
The Weakfish (Cynoscion regalis) is a commercially and recreationally valuable fish species that inhabits the Atlantic Coast of North America, where it primarily occurs from North Carolina to New York. The Weakfish fishery is depleted and has not rebounded despite fishing mortality decreases since 2011. The failure of the fishery to recover is currently attributed to elevated rates of natural mortality, the causes of which are not fully understood. Natural mortality is known to occur at higher rates in juvenile fish compared to adults. Because the diet of juvenile fishes is a factor of natural mortality and recruitment success, I studied the foraging habits of juvenile Weakfish in one of their primary spawning and nursery habitats, the Delaware Bay, in order to increase and update the understanding of their feeding habits prior to their emigration to offshore overwintering grounds. To answer questions regarding sources of organic matter, prey availability, prey importance, and prey origin (marsh or pelagic derived), I applied stomach content and stable isotope analyses to juvenile Weakfish in 2017 and 2018 throughout most of their Delaware Bay residency (July through October), along both coasts of the Delaware Bay (Delaware and New Jersey nearshore areas), and along the salinity gradient (lower, middle, and upper bay). These methods were used to elucidate the mechanisms and factors controlling stable isotope values of juvenile Weakfish and to determine the prey species responsible for their tissue production and growth. Juvenile Weakfish were caught from nearshore sampling stations sampled by Delaware and New Jersey Fish and Wildlife state agencies. The fish were separated into three size classes that represent a known ontogenetic shift in diet. Small Weakfish (0-60 mm SL) are mysid specialists, medium Weakfish (61-100 mm SL) begin to incorporate more forage fish into their diet, and large Weakfish (101-137 mm SL) are known to eat roughly equal proportions of forage fish and crustaceans by weight. Commonly consumed prey items, including mysid shrimp, gammarid amphipods, polychaete worms, isopods, sand shrimp, and Bay Anchovy, were also collected in 2018 for stable isotope analysis use in a Bayesian mixing model to infer the proportional contributions of individual prey items to juvenile Weakfish productivity. Generalized linear models (GLMs) were employed to analyze the relationships between carbon, nitrogen, and sulfur (CNS) stable isotopes and the factors of state (DE and NJ), bay location (lower, middle, and upper), and season (spring, summer, and fall). Results from stomach content analysis (SCA) were used as a measure of short-term diet and were also used as prior distributions in the Bayesian isotope mixing models using C and N stable isotopes. Generalized linear models illuminated that CNS isotopic values varied between states, bay locations, seasons, and some sampling stations. Contrarily, GLMs also found that certain sample groups of Weakfish appeared to exhibit a degree of site fidelity, as isotopic values of Weakfish collected in individual sampling stations occasionally remained stable from summer to fall, demonstrated by slow and rapid turnover tissues of muscle and liver, respectively. SCA and mixing model results revealed seasonal, locational, and state relationships for both individual prey species and groups of prey species. During the summer, Weakfish of all size classes from the middle bay consistently consumed higher frequencies of the same prey items (using percent frequency as the SCA method) compared to Weakfish from the lower and upper bays as revealed by stomach content analysis and stable isotope mixing models. Mixing model results also found that Weakfish consistently relied on gammarid amphipods (mainly Ampelisca sp.) as the most important prey item (>60% assimilation in many cases) throughout their estuarine residency, contradictory to the findings of previous studies that found mysid shrimp to be the most important prey item of small and medium size classes (by weight). The stomach content and stable isotope analyses applied to juvenile Weakfish indicate the overall variability in diet and organic matter sources over different spatiotemporal scales throughout the nearshore areas of the Delaware Bay. This variability highlights the importance of small-scale and locational (lower, middle, upper bay) primary and secondary productivity contributing to Weakfish production. Based on the findings presented in this study, future land-management decisions should consider the importance of small-scale and locational variability of optimal nursery habitats of juvenile Weakfish in the Delaware Bay.
Extracting Fuzzy Rules to Compare Genetic Algorithm-Generated Motoneuron Models
Wilt, Eric
Spinal motoneurons that have been active for prolonged periods of time exhibit different electrical properties than their less active counterparts, suggesting that prolonged neuronal activity may change how electrical signals are transmitted through the neuron. Understanding how these spinal motoneurons integrate their input signals and modulate their output is important, with implications for rehabilitation, advanced prosthetics, brain-machine interfaces, humanoid robotics, and other biologically-inspired systems. To investigate what changes may take place within a spinal motoneuron following prolonged activity, a genetic algorithm was employed to generate two distinct groups of spinal motoneuron computational models. The first group (control) simulated less active neurons while the second group simulated neurons treated with high K+, which mimics persistent activation. The models had nine variable parameters, each a conductance related to a specific ion channel present in the motoneuron. To evaluate fitness for each computational model, fuzzy logic was used to assign membership in fuzzy sets corresponding to two separate objectives: current threshold and input resistance. To mine rules from the generated data, correlations were looked at between each fuzzy set and each parameter. While no rules were successfully mined in this research, some interesting results were produced. Some relationships that exist between parameters within the control (less active) models, do not seem to exist in the treated models. Relationships were also found between parameters that exist in both groups of models, suggesting a possible co-regulation of the genes which express those traits.
Development of A High-Power Pulsed Laser via Sum-Frequency Generation for Sodium Lidar Applications
Ebongue, Christiane A.
We present the development of a nanosecond pulsed laser system resonating at sodium wavelength (589 nm) by means of sum frequency generation (SFG) with Nd:YAG lasers at 1064 nm and 1319 nm. This research is aimed to perform lidar measurements at mesospheric altitude, using sodium atoms as the tracer. These measurements include the determination of the sodium density, temperature and radial velocity. Two high power lasers at 1064 nm and 1319 nm are constructed using commercially available Nd:YAG gain modules as building blocks. The radiations emitted by the diode pumped Nd:YAG gain modules are picked up by two respective hemispherical optical cavities designed with high reﬂective mirrors at 1064 nm and 1319 nm, to produce stimulated emission at each wavelength. The 589 nm laser radiation is obtained by the sum frequency generation (SFG) of the two Nd:YAG pump laser outputs in a nonlinear crystal. Perfect mode matching, beam overlap, as well as temporal overlap of Q-switched pump laser pulses are ensured to achieve optimum frequency conversion in the SFG crystal. Precise tuning of the laser wavelength to the sodium D2 line is achieved by injection seeding of the 1064 nm pump laser with a single-frequency DFB laser. We have studied the performance of this laser for sodium lidar applications.
Bat Activity on Golf Courses in Delaware
Wallrichs, Megan
Due to landscape modifications and chemical use, golf courses have earned a negative reputation among some environmental groups, but their park-like landscapes may offer habitat for some wildlife species, especially over other land use types. In this study, I monitored bat activity using ultrasonic acoustic detectors in different small-scale habitats found on golf courses on the Delmarva Peninsula. My objective was to evaluate if and how bats are using course landscapes. I found differences in overall activity levels at the habitat level but not on different golf courses. Areas with closed canopy and open understory that were managed had significantly higher activity than other four habitats that reflected more natural habitats (open grass, dense canopy forest fragment, and open canopy forest fragment). The open understory managed areas also had significantly higher foraging activity than the other four habitats. Six of the eight bat species thought to occur on the Delmarva Peninsula were recorded, but Eptesicus fuscus and Lasiurus borealis dominated bat activity across all golf courses and habitats and had highest activity in open understory managed habitat. These findings indicate that bats are using golf courses on the Peninsula regularly as flyways and foraging grounds, and even substantially disturbed areas are used extensively. This study adds to the growing body of literature that positive partnerships can be created between wildlife and golf courses.
The Use of Probiotics in Pacific White Shrimp (litopenaeus Vannamei) Aquaculture to Increase Growth and Survival and To Reduce Gene Expression of Heat Shock Protein 70 While Subjected to Acute Thermal Stress
Smalls, Jasmine
THE USE OF PROBIOTICS IN PACIFIC WHITE SHRIMP (LITOPENAEUS VANNAMEI) AQUACULTURE TO INCREASE GROWTH AND SURVIVAL AND TO REDUCE GENE EXPRESSION OF HEAT SHOCK PROTEIN 70 WHILE SUBJECTED TO ACUTE THERMAL STRESS Jasmine Smalls Faculty Advisor: Dr. Dennis McIntosh Abstract Shrimp farmers face numerous challenges associated with the vulnerability of shrimp to disease and environmental stress. Pacific white shrimp (Litopenaeus vannamei) is one of the most commonly produced and high yielding cultured shrimp species. Growth and survival are two factors that dictate the overall production; probiotics which are ‘beneficial bacteria,’ can help improve both. Moreover, extreme temperatures are also a concern for shrimp production and can negatively impact growth and survival. Elevated temperatures can trigger the expression of Heat Shock Proteins (HSPs) in shrimp, which aid in repairing denatured proteins. To assess the impact of probiotics on shrimp, two experiments were conducted. The first experiment, which consisted of three trials, analyzed the effect of probiotics on growth and survival of post-larvae (PL) shrimp. Initially, only one trial was intended, however, because there were setbacks, two additional trials were conducted. After multiple weeks, the remaining PL shrimp from each group were counted to ascertain survival, and group weighed to calculate growth. For trial one, the Media Control (MC) appeared to produce the fastest growth followed by ISO 11 and ISO 12. PL in the MC also appeared to have the highest survival at harvest. However, a mortality event was experienced during the first trial due to various confounding factors including excessive temperatures, feeding rates, and stocking density, which prompted the initiation of trial two. For trial two, ISO 5 seemed to have the fastest growth followed by the MC and ISO 11. Survival for the Negative Control (NC), along with ISO 11 and ISO 12 were higher at the time of harvest compared to the MC and ISO 5. However, system design and sample size, in addition to other limiting factors, which influenced shrimp performance undermine the validity of the findings from trial two, so a third trial was planned. During the third trial, probiotics did not affect growth. At the time of harvest, it was found that nearly all containers contained the same number of shrimp, as nearly half of the shrimp from all experimental containers died during the first few days of the study. Due to the errors and issues experienced during all three trials, a definitive conclusion cannot be made regarding the true effectiveness of the applied probiotics on shrimp performance. In the second experiment, the objective was to determine if any of the selected probiotics effect gene expression of HSPs in juvenile shrimp. Shrimp were divided into groups and assigned to one of 12 ((3 probiotics + 1 control) x 3 temperatures)) treatments. Shrimp were pre-exposed to assigned probiotics for six days prior to the planned temperature stress event. Shrimp were sampled in two phases, exposure and recovery, to measure HSP expression with reverse transcriptase PCR. Results were compared across treatments to determine which probiotic had the greatest effect on shrimp. During this study, the intention was to collect the hepatopancreas, because it is this organ which highly expresses and regulates gene function in shrimp. However, due to a mistake in organ identification, the foregut was extracted instead. In addition to the foregut, a section of the abdominal muscle was also collected. Also, due to improper handling, and contamination of tissue samples, there was a statistically significant difference found in the quality of RNA between the NC and ISO 11 treatments at different temperatures across all sampling periods. Similarly, there was a statistically significant difference found in the expression of the HSP 70 between the NC and ISO 11 treatment at different temperatures across all sampling periods, as a possible result of thermal stress and high level of contamination. Due to the high level of contamination that was experienced during this study, a definitive conclusion cannot be made regarding the true effectiveness of the applied probiotics on mitigating shrimp stress.
Interdigitated Microelectrodes for Bio-sensing Applications
WANG, DU
According to the data from Centers for Disease Control and Prevention, Salmonella (S. typhimurium), a common food borne pathogen, is responsible for more than one million illnesses each year in the United States alone. It is one of the top most pathogens contributing to domestically acquired foodborne illnesses resulting in 19,336 hospitalizations and 386 deaths per year. The annual cost, directly and indirectly, associated with food-borne illness, is estimated to be around $77 billion a year. Most food poisoning is caused by the toxins produced by the bacteria or by the bacteria themselves. Once the food is placed in a humid and warm environment, certain bacteria can grow from one to millions in a very short periodic. Identification and detection of this food-borne pathogen is one of the keys to reduce the outbreak caused by this. Most of the conventional methods available for separation and detection of salmonella use specific agar media to separate and count bacterial cells in particular samples. These detection techniques consist of multiple steps and sub-processes which are often time consuming and take 3-4 days for initial results and up to 6-7 days for confirmation. Though these methods provide reliable data, they are not suitable for scenarios where rapid detection is the key. This work presents the design and simulation of an alternating current-DEP (Dieletrophoresis) field flow fractionation (DEP-FFF) type microfluidic chip which will detach the target cells of S. typhimurium from complex mixed culture solution with high efficiency. For design and simulation of the device, microfluidic channels were created on Silicon wafer and interdigitated electrodes were built in to apply the electric field (and DEP force) on the target cells. In addition to S. typhimurium, other unknown cells (two bacteria) were added to from the mixed solution. The design and simulation process was done by using various modules of finite analysis software - COMSOL Multiphysics. The physical dimensions of the microfluidic chip (length, depth and width) was varied to see the effect of these on cell separation efficiency. For target cells of S. typhimurium the cell separation efficiency was found to be ranging between 80.5% to 95.1%. Electroporation is one of the most efficient ways to transfect primary cells with minimum adverse effects compared to all other available technologies. As part of this work, electroporation of the cells for DNA transfer was done without damaging the cells. For this purpose, an in situ nanofiber-electroporation chip was developed to deliver DNA into hard-to-transfect cells, especially primary neuronal cells. The in-situ electroporation chip was composed of interdigitated metal electrodes lines and a biocompatible nanofiber membrane on a cover glass substrate. Metal electrodes made of Au were fabricated using liftoff technique on the cover glass substrate in the cleanroom. PCL nanofiber membrane was electropun and was aligned with the electrodes. The chip system provided conducive cell growth environment, and enabled the cells get transfected while the cells adhered during the electroporation. The transferred cells were inspected under the fluorescence microscope after electroporation is done.
Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) Behavioral Responses to Vessel Traffic and Habitat Use in the Delaware River, USA
DiJohnson, Alexander
The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus), a large, long-lived, anadromous species, experienced rapid population declines in later part of the 19th century due to overfishing and habitat loss. The Atlantic Sturgeon was listed under the U.S. Endangered Species Act (ESA) in 2012. Vessel strikes and habitat destruction, along with water quality degradation and bycatch mortality, were listed as major threats to the recovery of the species in the ESA determination. My study was conducted to further understand behavioral responses of Atlantic Sturgeon to vessel traffic and to indicate habitat preferences within an area of presumed spawning and foraging within the Delaware River. During the spring and summer of 2013 and 2015, I used a VEMCO Positioning System to monitor fine-scale movements of telemetered adult and subadult Atlantic Sturgeon. I used sturgeon spatiotemporal positions together with, commercial vessel traffic tracking data to observe possible differences between movement types, defined by using trajectory analyses for my first objective. Telemetered adult Atlantic Sturgeon exhibited several behavior types although I found no evidence that these behaviors were influenced by commercial shipping. For my second objective, I modeled habitat use of Atlantic Sturgeon in relation to Delaware River sediment types to observe whether sturgeons selected different proportions of the sediment than available. While subadults were shown to avoid muddy and sandy sediment, adults preferred course grain sediments (e.g., gravel) and avoided soft sediments (mud and sand). These results support the findings of previous studies which proposed that the study area was likely used for spawning/staging by adults during the early summer months. My findings suggest that Atlantic Sturgeon exhibit no behavioral responses to vessel presence and that individuals select areas of occupancy based on available sediments. This has direct implications in species conservation due to the continued alteration of sediments to support an increasing vessel traffic through maintenance dredging and channel deepening. If vessel avoidance is not occurring, managers must consider alternative ways of avoiding vessel strikes (e.g., seasonal restrictions such as limits to speed, draft depth, and passing zones) while also considering issues of continued sediment (i.e., habitat) alteration in critical areas of the river.
Magnetic Noise due to Interactions Between Bulk Impurities and Electrons in Nitrogen Vacancy Center Diamonds
Barrios, Bruce
Nitrogen vacancy centers (NV) diamonds present great interest as robust atomic-scale magnetic field sensors. One of the serious problems of NV-center diamond devices is electric and magnetic field noise. The noise can be verified by the optically detected magnetic resonance (ODMR) line-broadening; the noise reduce sensitivity of the devices. In this work we theoretically study the magnetic field noise caused by the magnetic dipole-dipole interactions between the bulk impurities of 13C, 14N and the electron in the NV-center. We use the cluster correlation expansion method to calculate the magnetic field fluctuations, and then, obtain the noise spectrum. The noise spectra is greater at lower frequencies but decrease at higher frequencies.
The Neuroprotective Effects of Sumo Conjugase, Ubc9, in Dopaminergic Cells and Neurons
Williams, Dionne
Parkinson’s disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and related to alpha-synuclein mediated protein aggregation. These protein aggregates are known as Lewy bodies. The Small Ubiquitin Modifier (SUMO) is a form of post-translational modification that regulates protein function and stability. Although SUMOylation may increase the solubility of alpha-synuclein, the role of SUMOylation in dopaminergic neurons remains unclear for PD pathology. Our preliminary studies show that the SUMO conjugase, Ubc9, protects rat dopaminergic cells against 1-methyl-4-phenylpyridinium (MPP+) toxicity and prevents the protein degradation of dopamine transporter (DAT) (Cartier et al., manuscript under review). We hypothesize that the overexpression of Ubc9 protects dopaminergic neurons against oxidative stress. For in vitro studies, N27 rat dopaminergic cells overexpressing Ubc9-EGFP showed higher cell viability and lower cytotoxicity against MPP+ induced toxicity, compared to EGFP only cells. In vitro studies include cell viability (MTT) and cytotoxicity assay (LDH), reactive oxygen species (ROS) detection, and mitochondrial respiration, to determine the protective role of Ubc9 in dopaminergic cells against oxidative stress (MPP+). We also established transgenic C57Bl/6 mice overexpressing Ubc9 or wildtype C57Bl/6 mice in the lab. Chronic intraperitoneal injection of the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) has been utilized to induce parkinsonism for both transgenic and wildtype C57BL/6 mice. Using immunhistological staining of tyrosine hydroxylase (TH) as a marker for dopaminergic neurons. We found that the pan-Ubc9 overexpression protected dopaminergic neurons in the striatum and the Substantia Nigra from MPTP-toxicities, compared to wildtype littermate mice. Our study supports that SUMOylation can be a potential therapeutic target to prevent oxidative stress-induced PD pathology. Currently we are assessing the neuroprotective mechanisms of Ubc9-mediated SUMOylation in PD models.
Identifying regulatory targets in parkinson’s disease pathology and screening potential therapeutics
Viana, Juan Pablo
Parkinson’s disease is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the Substantia Nigra pars compacta (SNpc). There are currently only treatments for relieving the symptoms of Parkinson’s disease with no cure. All of the treatments currently available vary in efficacy and usually cause irreversible side-effects including dyskinesia after long term use (PD Med Collaborative Group, 2014). The main cause of the loss of the dopaminergic neurons is the aggregation of proteins called Lewy bodies. The formation of the Lewy bodies is mainly mediated by alpha-synuclein. Most Parkinson’s disease cases are idiopathic. This has made scientists look at other reasons for the formation of Lewy bodies other than genetics such as post-translational modifications (PTM) on proteins. One such post-translational modification that has been looked at as having an important role in PD pathology is the small ubiquitin-like modifier (SUMO). SUMO is a post-translational modification that may be involved in the aggregation and toxicity of alpha-synuclein (Krumova et al., 2011; Zhu et al., 2018) In this study we assess the role of SUMOylation on alpha-synuclein in vivo and in vitro. Our main hypothesis is that the over-expression of SUMO conjugase, Ubc9, protects dopaminergic neurons in the striatum. We used the Ubc9 overexpressing C57Bl/6 mouse model from the John Hallenbeck lab at NINDS (Lee et al., 2012) and injecting them with the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) chronically. We then quantified the levels of alpha-synuclein in the striatum through confocal microscopy. We also generated stable N27 cell lines over-expressing wild-type alpha-synuclein-HA and the K96R:K102R mutant alpha-synuclein-HA to assess different protein-protein interactions potentially. After confirming the expression of wild-type and the SUMOless alpha-synuclein mutant, the proteins were immunoprecipitated, run on a gel, and sent out for mass spectrometry. The immunoprecipitation samples were unable to be read, but the inputs were able to be read. The most interesting observation when comparing the two inputs is the difference in ubiquitin. There is more ubiquitin in the wild-type than the mutant input, which supports our hypothesis that SUMO competes with Ubiquitin for binding to lysines in target proteins. Since the current treatment options for PD only involve treating the symptoms and do not focus on the neuroprotection or neurorecovery, we looked at a pharmacological approach to develop novel compounds that could have potential therapeutic effects. In collaboration with AurimMed Pharma Inc., we screened 31 novel small compounds supplied by AurimMed Pharmaceuticals and tested for neuroprotective effects against 1-methyl-4-phenylpyridinium (MPP+) and measured in MTT and LDH assay (courtesy of Dinesh Verma). The screening of the novel compounds resulted in the identification of a few promising compounds that showed neurorecovery effects at all the concentrations used in both MTT and LDH assays. Neurorecovery is the recovery of cells from MPP+ damage. These studies may help elucidate possible biological neuroprotective targets as well as novel compounds that do not simply target the symptoms of PD, but prevent the loss of dopaminergic neurons.
Genetics and monitoring of the eastern oyster Crassostrea Virginica within Delaware inland bays
Borsum, John Scott
Oyster enhancement to recover ecological benefits has been occurring since the late 1990s within the Delaware Inland Bays (DIBs) using a disease resistant line. Locally recruited oysters have been observed along hardened shorelines but limited quantitative information exists on the status of past or present DIBs sub-population. The goals of this study were to 1) assess the current genetic diversity of local DIBs oysters, 2) identify possible larval sources via genetic profiles, and 3) establish baseline measurements of oyster density along the selected rip-rap locations. Genetic diversity was assessed using eleven microsatellites markers to determine allele frequencies between two groups of spat collected from within the DIBs. Genetic profiles from the DIB groups were compared with a hatchery bred oysters used in local restoration and local wild Delaware Bay oysters, to determine possible source populations. Genetic results show similar allele frequencies among the two DIB groups which are more similar to local wild oysters than hatchery strains. Surveys among intertidal rip-rap habitats documented the current density and size frequency of oysters to evaluate future demographic changes. Oyster densities were generally low at the sites monitored in my study but the highest densities were observed within mid Indian River Bay. Monitoring oyster genetics and density needs to continue and expand throughout the DIBs to better understand local population dynamics and enhancement effects, as restoration continues and commercial scale shellfish aquaculture develops in the region.
Probiotics and their use in Commercially Important Aquaculture Species in the Northeastern United States
Myer, Jacqueline
Probiotics have shown to be beneficial to aquatic farming in aspects such as growth and development. This study, using three commercial aquaculture species, intends to ascertain if certain strains of Bacillus and Shewanella bacteria could possibly be used in aquaculture to improve finfish growth and survival, and be classified as true probiotics. Trials run at the DSU ARDF dose Nile tilapia (Oreochromis niloticus), rainbow trout (Oncorhynchus mykiss) and hybrid striped bass (Morone chrysops x M. saxatilis) with three probiotics Bacillus spp. (Iso 5 and Iso 11) and Shewanella spp. (Iso 12). Mortality was observed in three finfish trials over a 56-day trial or until one tank in the trial attained 10% survival. Ammonia, nitrite and nitrate were monitored throughout the trial. Feed conversion ratios, specific growth rates, weight gains and mortality were assessed at the end of the study. During the Nile tilapia experiment control tanks lost a total of 42 of 75 fish. ISO 12 (60/75), ISO 5 (56/75), and ISO 11 (58/75), treated tanks had statistically higher survival rates then the control tanks. Significant differences were also seen in survival during the hybrid striped bass experiment between the control tanks (16/30), ISO 12 (24/30) and ISO 11 (30/30). No significant differences were seen in survival for the rainbow trout experiment, but no treatment lost more than 10 finfish during the entirety of the experiment. Significant differences were observed for nitrite concentrations among tanks with probiotic treatments in the hybrid striped bass as well as with the rainbow trout experiment. ISO 5 treated tanks had a significantly lower concentration (0.107 ± 0.027 mg/l) of nitrite when compared to control tanks (0.231 ± 0.027 mg/l) during the rainbow trout experiment. Tanks treated with ISO 12 were significantly higher in nitrite concentration (0.038 ± 0.002 mg/l) than tanks treated with ISO 5 (0.030 ± 0.002 mg/l), and significantly higher than those treated with ISO 11 (0.029 ± 0.002 mg/l) during the hybrid striped bass experiment. The difference in ISO 5 and ISO 12 nitrite concentrations could be attributed to the ability of Bacillus spp. bacteria to metabolize ammonia into nitrate and nitrite, jumpstarting the nitrogen cycle. ISO 12 treated tanks very high nitrite concentration in comparison, might also be due to Shewanella spp. ability to denitrify nitrate into nitrite. If the experiment had lasted longer, perhaps an eventual decrease in nitrite would have been seen as the nitrite was converted into ammonium, a benign gaseous output. All three tested bacteria have the potential to be probiotics and used in aquaculture. Higher survival of finfish in the probiotic treatment tanks and the control tanks suggest that all three probiotics have the ability to increase survival in warm water (24 ºC) conditions, though no significant results were observed for cooler water (19 ºC). ISO 5, Bacillus cereus, and ISO 12, Shewanella spp., were both shown to have an effect on the concentrations of nitrite, but ISO 5 decreased the nitrite concentration while ISO 12 increased the concentrations when compared to ISO 5 and ISO 11, not the control. Further testing is required for ISO 12 to see if it could possibly lower the nitrite over a longer time period. Further testing is required for all three probiotic strains, and different systems as well as temperatures and salinities should be used to better understand the functions of these bacteria.
Understanding the Common bean (Phaseolus vulgaris L.) Transcriptome in Response to Salinity Stress
Brown, Mariama Tricuonia
Salinity is a grave threat to agriculture as it affects crop growth globally; it is known as one of the major stressors that hinders common bean production. Common bean (Phaseolus vulgaris L.) is the main source of human dietary vegetarian protein that constitutes approximately half of the consumed grain legumes globally. Additionally, common bean is of great economic weight as it provides income for millions of small farmers; however, the crop is known to be sensitive to salinity. In this study, common bean plants were salt stressed in a hydroponic system at 0 mM, 50 mM and 150 mM of NaCl for ten days (early stress) and five weeks (prolonged-flowering stage) in an effort to identify salt responsive genes. Exposure of plants to salt for several hours to a few days induces osmotic stress genes; lengthier salt stress treatments from a few days up to several weeks will ultimately induce salt specific genes that are involved in the plant’s adaptation to, and development under stress. Therefore, we isolated root RNA from ten days and five weeks salt stressed bean tissues and sequenced their transcriptomes. RNA-Seq analysis identified more differentially expressed genes (DEGs) in roots at five weeks compared to ten days salt treatment of 0 mM, 50 mM and 150 mM of NaCl. Some early and delayed salt responsive genes were identified which includes: Salt Tolerance Homolog 2 (STH2), Sodium Hydrogen Exchanger (NHX1), Chloride Chanel A (CLC-A), Late Embryogenesis Abundant (LEA) & Proline Transporter 1 (PROT1).The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the Mitogen-Activated Protein Kinase (MAPK) signaling pathway which contained ten DEGs including protein kinase (CTR1), calmodulin 1 and WRKY33. Transcription factors (TFs) that are known to be involved in flower development and flowering time such as WRKY, MADS-box and bZIP were observed to be up-regulated both at ten days and five weeks of salt stress when compared to the control (no salt treatment). The up-regulated genes identified were functionally classified using the Protein ANalysis THrough Evolutionary Relationships (PANTHER) classification system for Gene Ontology (GO) Slim (general) categories. Additionally, PANTHER overrepresentation test was done to identify granular (specific) terms that were enriched for both upregulated and down regulated genes. This first report on common bean under prolonged salt stress of five weeks has identified potential candidate genes that are perhaps needed for acclimation to salt stress and hence will serve as a genetic resource for plant salt tolerance.
Migratory routes and stopover regions of eastern breeding veeries (turdidae: catharus fuscescens) as revealed by archival light-level geolocators
Mendez, Devin Charles
Nearctic-Neotropical migrant passerines have experienced population declines presumably largely due to habitat loss and degradation on both the wintering and breeding grounds. Only recently have these declines been attributed in part to the loss of suitable stopover sites available during migration. Stopover sites of high ecological quality are essential along an ecological barrier in order to provide areas for migrants to rest and refuel. The identification and conservation of high quality stopover sites has become a research priority; however, until recent advances in technology it was difficult to identify these sites without quantitative field surveys. Archival light-level geolocators are the only technology that allows ornithologists to recreate the daily positions of small songbirds (<50g) throughout their annual cycle. The focus of the present research was to further our knowledge of the annual movements of the Nearctic-Neotropical migratory species, the Veery (Catharus fuscescens), through the use of miniaturized tracking technology. My objectives were to (1) identify important stopover regions used by migrating Veeries, and (2) identify important migratory flyways between the Veery’s breeding and wintering grounds. I used kernel density estimations and hot spot analysis to identify important stopover regions used by two distinct eastern breeding populations and compared the results of the different analyses. I identified differences in stopover regions used during migration on the basis of age, sex, and seasons. I also identified the migratory routes taken by 58 individuals over an eight-year period and found that age and sex did not significantly affect the migratory routes taken during migration; however, I did find that the migratory routes varied greatly between years with respect to the path taken by individuals preparing to cross the Gulf of Mexico. My results highlight the importance of long-term geolocator studies to furthering our understanding of migratory connectivity. Also, through this study, I began establishing a potential framework for the identification of important stopover regions for Nearctic-Neotropical migrants in general. This research will enable conservationists to make more informed decisions regarding the stopover regions to prioritize for protection in future long-term conservation planning efforts.

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