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Vesicles are a type of biological or biomimetic particle consisting of one or more often spherical bilayers made up of amphipathic molecules, creating a closed system. They can function as an encapsulating device, holding hydrophilic molecules on the inside of the bilayer membrane(s) or hydrophobic molecules in the non-polar interstitial space in the middle of the bilayers. Because of this capacity to carry molecules, vesicles are a premier system for drug delivery and even theranostics in vivo. A peptide-based approach to release of encapsulated molecules has previously been developed but since drug delivery vesicles are in the size range of nanometers, the mechanisms have not been visualized. This project aims to produce giant unilamellar vesicles as a model system used to visualize membrane interactions vital to the understanding and further development of smaller vesicle-based systems for drug delivery. Giant unilamellar vesicles were produced successfully and a preparation protocol was established. Additionally, some membrane interactions were investigated using fluorescence microscopy.

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<p>This article-based dissertation provides a review on the broad subject of magnetars-their characteristics, giant flares (GFs) and associated observations of X-ray, gamma-ray, and radio emissions and their proposed physical mechanisms. The primary purpose of this dissertation is to provide an extensive description of the two research projects I undertook during my tenure as a Graduate Research Assistant, under the guidance of my advisor. Broadly, my research was focused on building analytical models and running three-dimensional (3-D), high-resolution magnetohydrodynamic (MHD) simulations using the astrophysical PLUTO code to investigate the physical mechanisms behind high-energy (X-ray and gamma-ray) and radio emissions associated with magnetar GFs using observational constraints. This, in turn, aided in either validating or disfavoring existing theories behind such energetic explosions.</p><p>Chapter 1 provides a review on magnetars, their GFs and associated high-energy and radio emissions, largely based on excellent reviews by [1]–[5]. I summarize interesting observational features of magnetars, specifically those of soft gamma-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs), along with known aspects of their X-ray and gamma-ray activity. I focus on the December 27, 2004 GF emitted by SGR 1806-20, the most energetic GF out of the three that occurred to date, describe its energetics and summarize existing theories behind the physical mechanisms that give rise to two emission characteristics associated with the GF - (i) quasi-periodic oscillations (QPOs) seen in the tail, and (ii) a radio afterglow detected a week after the GF. Lastly, I describe the methods I used to hypothesize the physical mechanisms behind QPOs and the radio emission and compare and contrast them with those suggested previously.</p><p>In chapter 2, I present a version of the research article in preparation and pending publication in the Monthly Notices of the Royal Astronomical Society. The work titled “Radio afterglow of magnetars’ giant flares”, undertaken under the supervision of Dr. Maxim Lyutikov and in collaboration with Dr. Maxim Barkov, explores the possible physical mechanisms behind the radio afterglow associated with the SGR 1806-20 GF using high-resolution 3-D MHD simulations.</p><p>In chapter 3, I present a version of the research article previously published by the Journal of Plasma Physics. The work titled “Tilting instability of magnetically confined spheromaks”, undertaken under the supervision of Dr. Maxim Lyutikov, in collaboration with Dr. Lorenzo Sironi and Dr. Maxim Barkov, investigates the tilting instability of a magnetically confined spheromak using 3-D MHD and relativistic particle-in-cell (PIC) simulations with an application to astrophysical plasmas, specifically to explain the QPOs arising in the tail of the SGR 1806-20 GF.</p><p>I summarize the main results and conclusions of the two research projects and describe future prospects in chapter 4, followed by appendices A and B which describe additional theoretical concepts and simulation results for a better understanding of the nature of radio afterglows associated with GFs, and structure of spheromaks. References are compiled after the appendices in order that they are first cited, followed by a brief autobiographical sketch, and a list of publications.<br></p>

Fossils of the giant short-faced bear, Arctodus simus (Cope, 1879), have been recovered from over 100 localities in North America, extending from Mexico to Alaska and California to Virginia. Despite this large range, the species has never been recorded from the southeastern United States. The lesser short-faced bear, Arctodus pristinus Leidy, 1854 is well represented from this region, particularly Florida, but all known occurrences are late Pliocene middle Pleistocene in age (about 2.5 to 0.3 Ma). Differentiating A. simus from A. pristinus can be difficult because large individuals of A. pristinus overlap in size with small individuals of A. simus, and there are few morphological differences. However, these two taxa can be clearly separated based on the relative proportions of their molars and premolars. Two Pleistocene records of A. simus representing a minimum of three individuals from the Withlacoochee River drainage of central Florida are reported here, substantially extending the distribution of this massive bear into southeastern North America. A late Pleistocene age for these occurrences is corroborated by an associated Rancholabrean fauna and rare earth elemental analyses. One of the reported individuals is quite large, supporting the hypothesis of extreme sexual dimorphism in A. simus and rejecting a hypothesis of two subspecies.

This work addresses the mechanism of cell cycle specific actin reorganization in Drosophila syncytial blastoderm embryos. During mitosis in typical animal cells after chromosome segregation is complete, daughter cells are separated in a process called cytokinesis. Cytokinesis is ordinarily driven by constriction of an actin ring that physically pinches the cell in two. The early Drosophila embryo is a syncytium; nuclei divide in a single cell without intervening cytokinesis. During the later syncytial divisions, nuclei are arranged in a monolayer at the cortex of the embryo. This stage of embryogenesis is characterized by cycles of actin reorganization that are coordinated with the nuclear division cycles. Since several components of typical cleavage furrows function in this cell cycle driven actin reorganization, the syncytial blastoderm has been used as a model system to better understand cell cycle driven actin reorganization in typical cells. The syncytial Drosophila embryo is easily manipulated genetically, cytoskeletal structures can be visualized in both fixed and living embryos, and large quantities of embryos are attainable for biochemical analysis. We have therefore chosen this model system to study actin reorganization. We show that actin reorganization in syncytial embryos is coordinated by cell cycle cues similar to those utilized in typical cells. Drosophila embryo actin reorganization has several unique features, however. For instance, actin reorganization appears to be associated with centrosomes in a process that does not require microtubules. In addition, the driving force for formation of Drosophila cleavage structures may be actin filament polymerization, rather than contraction of an acto-myosin ring. Whether these characteristics of Drosophila embryo actin reorganization typifies actin reorganization in other cells remains to be seen.

Les tests « in vitro » permettent d’établir près de 70% des diagnostics et leur développement pour une utilisation au plus près du patient apparaît donc comme un enjeu majeur de santé publique. Dans ce contexte, les critères ASSURED (« Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable to end-users ») a été défini par l’organisation mondiale de la santé pour que les chercheurs développent des outils de diagnostic dits « Point of Care » utilisables par le plus grand nombre. Avec l’essor de la microfluidique, la gamme des dispositifs possibles s'est élargie et des biocapteurs intégrés ont été développés, transformant le signal biologique d’une reconnaissance d’un biomarqueur par une sonde biologique en un signal optique, électrochimique, mécanique ou encore magnétique. Comme les milieux biologiques sont en grande majorité amagnétiques, les capteurs magnétiques ne sont pas affectés par l’utilisation de matrices biologiques complexes comme peuvent l’être les mesures optiques ou électrochimiques. De plus ces capteurs sont faciles à produire et intégrables dans les puces microfluidiques. Cette thèse a pour objectifs de concevoir un outil de diagnostic in vitro basé sur des capteurs à magnétorésistance géante et de tester ses performances. Cette étude a été réalisée en utilisant une lignée cellulaire de myélome murin. Les cellules sont marquées spécifiquement par des particules magnétiques fonctionnalisées par des anticorps dirigés contre un de leurs antigènes et sont passées dans le canal microfluidique au-dessus des capteurs. Cette méthode de détection dynamique permet de compter les objets magnétiques un par un. La difficulté réside dans la distinction des signaux spécifiques provenant des cellules marquées des signaux faux positifs induits par les billes restant en solution. Deux types de dispositifs ont été conçus dans cette thèse pour lever ce verrou. Le premier possède une couche inerte de séparation de quelques micromètres entre les capteurs GMR et le canal qui permet de supprimer les signaux des billes isolées. Le second dispositif, qui a des capteurs à la fois au-dessus et au-dessous du canal microfluidique, permet une double détection simultanée de chaque objet magnétique. Il est ainsi possible de connaître le nombre de billes qui les marquent et de déterminer s’il s’agit d’un agrégat de billes ou d’un objet biologique. / The « in vitro » tests are requested for the establishment of nearly 70% of diagnoses and their development for on-site detection therefore appears to be a major public health issue. In this context, the ASSURED criterion (« Affordable, Sensitive, Specific, User-friendly, User-friendly, Rapid and robust, Equipment-free and Deliverable to end-users ») has been defined by the World Health Organization to encourage researchers to develop diagnostic tools called « Point of Care » that can be widely used.With the rise of microfluidics, the range of possible devices has broadened and integrated biosensors have been developed, transforming the biological signal from a biomarker recognition by a biological probe into an optical, electrochemical, mechanical or magnetic signal. As biological environments are largely non-magnetic, magnetic sensors are not affected by the use of complex biological matrices as are optical or electrochemical measurements. In addition, these sensors are easy to produce and can be integrated into microfluidic chips. The objectives of this thesis are to design a diagnostic tool in vitro based on giant magnetoresistance sensors and to test its performance. Its development was carried out using a murine myeloma cell line. The cells are specifically labeled by magnetic particles functionalized by antibodies directed against one of their antigens and flown in the microfluidic channel above the sensors. This dynamic detection method allows magnetic objects to be counted one by one. The challenge is to distinguish the signals coming from the labeled cells from those of the beads remaining in solution. In order to address this problem, two labs on chips are developed in this thesis. In a first device, an inner layer of a few micrometers separates the sensors from the channel which allows to suppress the signals of the isolated beads. The second device has sensors both above and below the microfluidic channel and can measure the number of beads corresponding to each doubly detected object which can thus be identified (aggregates or biological objects).

abstract: Part I – I analyze a database of Smoothed Particle Hydrodynamics (SPH) simulations of collisions between planetary bodies and use the data to define semi-empirical models that reproduce remant masses. These models may be leveraged when detailed, time-dependent aspects of the collision are not paramount, but analytical intuition or a rapid solution is required, e.g. in ‘N-body simulations’. I find that the stratification of the planet is a non-negligible control on accretion efficiency. I also show that the absolute scale (total mass) of the collision may affect the accretion efficiency, with larger bodies more efficiently disrupting, as a function of gravitational binding energy. This is potentially due to impact velocities above the sound speed. The interplay of these dependencies implies that planet formation, depending on the dynamical environment, may be separated into stages marked by differentiation and the growth of planets more massive than the Moon. Part II – I examine time-resolved neutron data from the Dynamic Albedo of Neutrons (DAN) instrument on the Mars Science Laboratory (MSL) Curiosity rover. I personally and independently developed a data analysis routine (described in the supplementary material in Chapter 2) that utilizes spectra from Monte Carlo N-Particle Transport models of the experiment and the Markov-chain Monte Carlo method to estimate bulk soil/rock properties. The method also identifies cross-correlation and degeneracies. I use data from two measurement campaigns that I targeted during remote operations at ASU. I find that alteration zones of a sandstone unit in Gale crater are markedly elevated in H content from the parent rock, consistent with the presence of amorphous silica. I posit that these deposits were formed by the most recent aqueous alteration events in the crater, since subsequent events would have produced matured forms of silica that were not observed. I also find that active dunes in Gale crater contain minimal water and I developed a Monte Carlo phase analysis routine to understand the amorphous materials in the dunes. / Dissertation/Thesis / Table 1: Giant impact SPH results for Chapter 1 / Table 2: Giant impact SPH results for Chapter 1 / Table 3: Giant impact SPH results for Chapter 1 / Doctoral Dissertation Geological Sciences 2019

Primary open-angle glaucoma (POAG) is one of the leading causes of blindness worldwide. The only modifiable risk factor for POAG is elevated intraocular pressure, resulting from increased aqueous humor production or decreased drainage. Resistance to drainage in the aqueous outflow pathway is believed to reside in the juxtacanalicular connective tissue (JCT) and to be modulated by the inner wall (IW) endothelium of Schlemm’s canal (SC); however, the mechanisms that increase resistance in POAG remain unclear. To cross the IW, aqueous humor passes through I-pores on giant vacuoles (GVs) or B-pores between adjacent endothelial cells. Additionally, outflow around the circumference of the eye is segmental, or non-uniform, and fluorescent tracers can be used to label areas of high-flow and non-flow. The morphological differences in the endothelial cells of SC and their GVs in high- vs. non-flow areas have not been fully elucidated. In this project, we investigated the role of GVs and pores in the IW endothelial cells of SC in regulating segmental outflow in human eyes. We used serial block-face scanning electron microscopy to generate thousands of serial images and visualize these structures in 3D at the ultrastructural level. First, we 3D-reconstructed 45 individual IW cells and their GVs and quantified the number of connections each cell makes with the underlying JCT matrix/cells. We found that cells in high-flow areas made significantly fewer connections to JCT matrix/cells compared to cells in non-flow areas. Secondly, we analyzed 3,302 GVs for I-pores and basal openings and found a significantly greater percentage of GVs with both basal openings and I-pores in high-flow area compared to non-flow area, suggesting this type of GVs form a channel through which aqueous humor passes from JCT to SC. We also found that GVs with I-pores were significantly larger than those without I-pores. Our results suggest that decreasing number of cellular connections and increasing number of GVs with pores may be potential strategies to increase the amount of high-flow area and aqueous outflow for glaucoma treatment. Together, these studies add to our understanding of the role of GVs and pores in regulating segmental flow around the eye.

The invasion of riparian habitats by the exotic plant, Arundo donax L., commonly known as the giant reed is one of the greatest threats to ecosystems in Central and Southern California. There have been several efforts to eradicate this plant with varying control methods. This study evaluated some previously known techniques of controlling the giant reed in addition to some novel methodologies to determine the most effective approach. The study site is a section of the Lower Calaveras River that transects University of the Pacific's campus and is a prime example of the devastation caused by the giant reed. The project site was cut and cleared over a period of eight months and divided into fourteen plots. Seven different techniques including a control were selected and each treatment was randomly applied to two plots. The methods chosen were: "cut, resprout and spray", "cut-stem, spray", "chip and compost", "chip and tarp", "compost" and "compost and tarp". The response variables were the "mean regrowth height", "mean circumference of stalks" and the "number of resprouted stalks". A repeated measures ANOVA was used to analyze the response variables. The "compost and tarp" method had the lowest number of resprouted stalks and was also significantly different from the control treatment. None of the other techniques were significantly different from the control but the "compost" method showed some promise. Based on this study, the "compost and tarp" technique is the most effective treatment. The data collection for this study was limited and future experiments should be conducted on a longer time scale to assess the effectiveness of these methods. Further research should also be conducted to evaluate the effectiveness of various biotic factors on the growth of A. donax, which could enhance the efficacy of methodologies currently used to control this introduced invasive plant.