Multicellular tumor spheroid cultures (MCTS), have a wide variety of uses in the field of cancer treatment. Current methods, however, do not provide spheroids adequate large for therapy testing. In order to circumvent this problem, a bioreactor made using Polydimethylsiloxane (PDMS) was constructed to allow the adequate growth of spheroid clusters. Liver Hepatic Carcinoma cells (Hep G2) and Anaplastic Thyroid Carcinoma (SW 1736) were cultured and isolated. They were then further matured using the “hanging drop” method, involving spheroid formation using gravity. The optimal growth time for hanging drop cultures was determined to be 72 hours. PDMS wells of different diameter were then constructed using a 24-well plate as a base, and clusters of cells were transferred into them for MCTS formation. The wells were fabricated using PDMS as a mold, then carving out wells for cell growth. Development of the spheroids in the bioreactor was monitored using microscopy paired with various staining techniques, and measurements and media changes were done daily. Cell cluster volume and height were analyzed as a function of PDMS well diameter. Optimum spheroid formation occurred in 5mm diameter wells, with peaking growth around 10 days. Further research was done regarding cancer cells and HIFU (High Intensity Focused Ultrasound) and Ethanol treatments, as tests of combination cancer therapies. Cells were first treated as cell pellets, then using the spheroid method above. The use of combination therapies proved more effective than either therapy alone. Chemo-ablation is also an upcoming therapy method to be used in combination therapies. This research can be used as a starting point for larger spheroid formation, and eventually in vivo testing of cancer therapies. Further analysis can be done to compare these models for comparison of shape, viability, and the effects of anti-cancer treatments. / acase@tulane.edu

To clarify the role of ab initio molecular dynamics (AIMD) simulation, this study organizes the McMillan-Mayer (MM) theorem, the potential distribution theorem, and quasi-chemical approach to provide theory for the thermodynamic effects associated with long-length scales. This multi-scale statistical mechanical (MSSM) theory implements quasi-chemical theory after utilizing the MM theorem to integrate-out the solvent degrees of freedom. The MSSM theory treats composition fluctuations which would be accessed by larger-scale calculations, and also long-ranged interactions of special interest for electrolyte solutions. The theory is applied to a primitive electrolyte solution model proposed to investigate ion pairing in the context of tetraethyammonium tetrafluoroborate in propylene carbonate. A Gaussian statistical model is shown to be an effective physical approximation for outer-shell contributions, and they are conclusive for the free energies within the quasi-chemical formulation. Gaussian statistical theory can be more effective than the Bennett numerically exact method when exhaustive sampling is not available, i.e., for finite samples. These results lead to the analysis of the asymptotical behavior of a relative information entropy and thus a new formula for the ion excess free energies. This asymptotic perspective completely avoids the computationally limiting evaluation of the outer-shell contributions. In addition, we use AIMD to obtain the charges on tetramethylammonium and tetrafluoroborate ions contacting neutral and charge carbon nanotube electrodes, and also charges tetraethyammonium and tetrafluoroborate ions in propylene carbonate solution. / acase@tulane.edu

A spatiotemporal system of partial differential equations is implemented for describing a marine predator-prey system of shark and prey fish. The model is developed to account for predator migration and for harvesting of both predator and prey animals. The Finite Difference Method is employed to develop a numerical model to describe the behavior of the system in space over time. The dynamics of the system for different initial conditions for predator and prey populations and harvesting rates of both predators and prey using the numerical scheme. The resulting dynamics of the system from adding a predator sanctuary (an area within which the predator cannot be harvested) are also examined. It is hoped that this paper will illustrate that model behaves as a predator-prey system is expected to behave under the tested conditions. / acase@tulane.edu

A numerical method for computing three-dimensional Stokes flow driven by a doubly-periodic array of regularized forces is presented. In the non-periodic direction either a free boundary or a homogeneous Dirichlet condition is enforced. The method consists of finding a regularized Green's function in Fourier space analytically. Then only an inverse fast Fourier transform (inverse FFT) has to be computed. Accuracy is verified by comparing numerical results to a solution that is independent of the method. In an Ewald splitting, the FFT method can be used to compute the smooth component of the flow, which allows for a splitting parameter as small as a few grid cells. This selection makes the sum in physical space converge extremely fast. Numerical examples demonstrate that fact. Since the forces are regularized, in some cases splitting is not even needed, depending on the relative sizes of the numerical parameters. The method is applied to model the flow created by carpets of nodal cilia based on cilium shape. / acase@tulane.edu

Each year, more than 185,000 people in the U.S. lose a limb to injury or pathological conditions. Currently, the only replacement for amputated limbs is the fitting of a prosthetic device. While artificial limbs greatly enhance the lives of amputees, these devices have their limitations. Prosthetics tend to have reduced (or no) function and limited sensation. These devices require charging and maintenance, are expensive, and have a shorter life than a natural limb. Additionally, artificial limbs are not able to completely replace the biological roles of natural bone such as calcium-ion exchange and hematopoiesis. To overcome the limitations of prosthetics, the ideal replacement for an amputated limb would be the regrowth of a patient's own biological limb. Mammals have the ability to regenerate the distal portion of the third phalangeal element (P3). This regeneration response progresses through several distinct phases which are defined in this thesis. The initial phases - inflammation, histolysis, and epidermal closure - are not unique to the P3 amputation response, but are seen following injury to almost every tissue. For mammals, the most common response to injury is a repair process that starts with inflammation, histolysis and wound closure, but produces aberrant collagen deposition and loss of original structure. A mammalian P3 amputation is exceptional in that the initial stages following injury lead to a regeneration event. We aim to understand the initial stages of P3 regeneration and to determine if these stages play a role in creating (or inhibiting) a regeneration-permissive environment. We also examine what factors comprise a regeneration-permissive environment, specifically, how tissue oxygen tensions influence regeneration. We find that regeneration is dependent upon both temporal oxygen fluctuations and the initial influx of inflammatory cells. Future goals, based on this work, are to determine how we can manipulate both oxygen tensions and inflammation to augment the regeneration capabilities of the body. / acase@tulane.edu

Conserving avian populations requires understanding how they are limited by density-independent factors and regulated by density-dependent processes. To better understand the relative importance of limiting factors and regulatory processes in wintering American Redstarts (Setophaga ruticilla), I carried out two related studies. First, to determine how food availability affects space use, body composition, and migration timing, I experimentally decreased food availability in high-quality mangrove habitat. Using an insecticide, I reduced food by ~80%, which mimicked natural losses in nearby scrub habitats. I found that food-reduced redstarts deposited fat and lost muscle compared to control birds. Subsequently, food-reduced redstarts experienced on average a one-week delay in departure on spring migration. Previous work has demonstrated that for each day delayed after the first male arrival on the breeding grounds, redstarts experience an 11% decrease in the chance of successfully reproducing. Thus, my results demonstrate experimentally, for the first time, that fluctuations in winter food-availability can lead to fitness costs for migratory birds, and that the mechanism involves a fat-muscle trade-off. Second, to understand how limiting factors and density-dependence interact to drive population dynamics, I used four years of data on redstarts wintering in Jamaican scrub and mangrove forests. In a dry and food-limiting year in scrub, I found that individuals on territories surrounded by a high density of conspecifics experienced large losses in food availability, suggesting a density-dependent depletion of resources. These losses in food were correlated with poor body condition, and individuals on high -density territories delayed departure on spring migration. In two wetter and less food-limiting years in scrub, and in all years in high-quality mangrove habitat, no effects of neighbor density were evident and density-independent factors alone appeared to determine body condition and departure date. Previous research has shown that poor body condition reduces annual survival and that delayed departure has carry-over effects into the breeding season, resulting in lower fecundity. Thus, both food limitation and neighbor density appear to drive population dynamics, but density-independent factors may override the negative effects of density when weather conditions are favorable. / acase@tulane.edu

Animal populations are limited by their environment and interactions with one another, the latter proportional to density. How density-dependent mechanisms regulate populations is poorly understood, particularly for migratory animals. Winter, or non-breeding, mechanisms remain particularly poorly understood for almost all migratory bird species. This dissertation tested the hypothesis that American Redstarts (Setophaga ruticilla) are regulated both within and between habitats in the winter by two mechanisms, a crowding effect and a buffer effect. As population size increases, crowding increases competition for space and resources and more individuals are relegated to lower quality habitats and forced into a transient behavioral strategy, which buffers high quality habitats from negative feedback of density. My study was carried out in Jamaica, where redstarts occupy diverse habitats. I found that population size varied among habitats, but accounting for both territorial and transient individuals was critical for accurate assessment of this variation. Ecological conditions drive differences in habitat suitability and redstart density at multiple spatial scales. Regionally, redstart survival, density, and numbers of transient individuals distinguish inland from coastal populations, consistent with differences in ecological conditions (e.g. rainfall). Locally, timing of spring departure, as well as age and sex structure distinguish neighboring habitats, consistent with increased competition for food. When population size increased over the years of this study, changes in local density were similar among habitats, and thus not the result of a buffer effect. However, increasing densities decreased food availability, which corresponded with negative feedback on departure timing and territorial behavior, i.e. more transients, in poorer habitats. This supported a crowding effect on spatial behavior (territoriality) and late-winter condition of individuals relegated to low suitability habitats. High quality inland habitats appear to buffer individuals from the effects of changing population abundance, as well as ecological conditions, evidence of a regional buffer effect. / acase@tulane.edu

The stress and trauma exposure associated with disasters can lead to mental health problems. Studies have indicated a high prevalence of mental health problems among Hurricane Katrina survivors, in general, with worse mental health outcomes among survivors located in the New Orleans Metropolitan area as compared to those in other affected areas. Furthermore, in comparison to previous disaster research that typically shows decreases in mental health problems two years following disaster, the Katrina literature indicates continually elevated levels of mental health problems for this time frame. The proposed study examines the long-term mental health outcomes among Hurricane Katrina adult survivors residing in the metropolitan New Orleans area, two years after the storm. Specifically, the present study explores whether evacuation status and other hurricane-related stressors (length of displacement, neighborhood damage, and property damage) are related to symptoms of anxiety, depression, and hostility. The present study advances current knowledge by examining exposure to hurricane-related stressors, a broader range of mental health outcomes, and whether the relationship between the hurricane-related variables and mental health outcomes are moderated by income. The findings suggest that while evacuation status and hurricane-related stressors are not directly related to increased mental health symptoms, evacuation status is related to increased symptoms for those of low-income. Additionally, both age and gender predicted poor mental health outcomes. / acase@tulane.edu

This thesis examines the Euler equations of gas dynamics and develops a new adaption indicator, which is based on the weak local residual measured for the non- conservative pressure variable. We demonstrate that the proposed indicator is capable of automatically detecting discontinuities and distinguishing between the shock and contact waves when they are isolated from each other. We use the developed indi- cator to design a scheme adaption algorithm, according to which nonlinear limiters are used only in the vicinity of shocks. The new adaption algorithm is realized using a second-order limited scheme and a high-order nonlimited central-upwind scheme. Robustness and high resolution of the designed method is shown on a number of one- and two-dimensional numerical examples. / acase@tulane.edu

Methicillin-resistant Staphylococcus aureus (MRSA) is a Gram-positive bacterium which poses a substantial threat to public health due to its high virulence and multi-drug resistance. Membrane vesicles (MVs) are naturally-derived nanoparticles which have been shown to provide protection against bacterial infections. In this study, MVs were investigated as a potential vaccination strategy against MRSA infection. MVs were extracted from a USA300 strain of MRSA and visualized with transmission electron microscopy. Antisolvent crystallization was found to be a more efficient extraction method than ultrafiltration, and MVs were successfully purified from solution using ammonium sulfate precipitation. Protein content, particle size, and dispersity in solution were studied using gel electrophoresis and dynamic light scattering. MV samples were found to be within 20-200 nm in diameter and to aggregate substantially in solution. MV preparations were tested for toxicity in vitro with RAW 264.7 murine macrophages and in vivo with a Galleria mellonella model. MRSA-derived MVs demonstrated lower toxicity than E. coli MVs, even at higher concentrations. G. mellonella treated with MRSA MVs had a 70% survival rate through 5 days, compared to a 10% survival rate in the E. coli MV group. Protection against infection was investigated in BALB/c mice, which showed IgG responses specific for MRSA after two intranasal immunizations. Mice were challenged intranasally with 1x108 CFU of MRSA and monitored for morbidity and mortality. Mice immunized with MVs displayed significantly lower bacterial burdens in their lungs compared to naïve mice. The results of these experiments indicate that MRSA MVs may represent a novel vaccine strategy for preventing MRSA infection. / acase@tulane.edu