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Open Access Publications from the University of California

UC San Diego Electronic Theses and Dissertations

Cover page of A Lot of the Training is Not The Training

A Lot of the Training is Not The Training

(2019)

A lot of the training is not the training. At times that means buttressing one’s self against the forces of negativity that may be encountered when entering a rehearsal space. At times it means appreciating those moments you walk into a space in which the company as a whole – from the actors, to the company management, the director and playwright – finds a way to fall into a space of trust, constantly buoying each other in a harmonious process of realizing a play.

The willingness to release one’s self of any pre-determined expectations of how those amongst you will perform in their assigned roles/tasks – replacing it with only a personal expectation of how you as an individual will perform your own assigned role/task – is most beneficial in realizing a work of art in concert with others.

SERE was a room absent of ego and full of hunger. There was a hunger in each person to do/be/deliver their best in realizing this plays visions. No artist looked beyond themselves and their own performance and in doing so subconsciously entered into a metaphorical trust fall amongst a community ready and willing to catch each other.

A lot of the training is not the training. Of all the training, I believe the most valuable that is more implicitly rather than overtly taught is that of teaching actors to prepare themselves to fall with trust within any space/process they may encounter. No process could have highlighted the benefit of such an approach more than SERE.

  • 4 supplemental images

Insights Into the Mechanism of Signal-Induced IKK Activation

(2019)

NF-κB transcription factors are essential for inflammation, proliferation, survival, growth and differentiation. The exact mechanism for NF-κB activation by IKK phosphorylation is not well understood. However, it is well known that the partners IKK1/α, IKK2/β, NEMO and Linear Ubn chains are essential for IKK activity. Moreover, phosphorylation of serines 177/181 is a key event in IKK activation, which can be performed by upstream kinases or trans-autophosphorylation by IKK2/β. We confirmed previous results which showed that IKK2/β-NEMO will form a higher molecular weight complex in size exclusion chromatography and we show that Ub4 can bind sub-stoichiometrically to this complex. In addition to an established IKK2/β-ΝΕΜΟ interacting domain we discovered a secondary site of interaction between IKK2/β and the 339 to C-terminal region of NEMO that is Ub4 dependent. We propose that IKK complex oligomerizes and this higher order structure requires both IKK2/β and NEMO to oligomerize. Moreover, since Ub4 is essential for trans-autophosphorylation, (IKK activation), the binding of Ub4 to oligomerized NEMO-IKK2/β may induce a conformational change which allows for IKK trans-autophosphorylation. IKK2/β-NEMO interaction through a secondary site, mediated by Ub4, may have a pivotal role in trans-autophosphorylation.

Cover page of Control Methods for a Modal Disturbance Experiment with Structured Uncertainty

Control Methods for a Modal Disturbance Experiment with Structured Uncertainty

(2019)

The purpose of this thesis is to establish an experimental process by which a structural system may be characterized through modal analysis in an effort to develop and implement disturbance rejection control designs. Throughout this report, a structural test article representing a simplified aircraft model will be the subject of study, referred to as the "Iron Bird." This report discusses how the article was modeled using finite element analysis for the purpose of control design. Then, the report establishes a "dry" wind tunnel testing approach by utilizing readily available testing equipment and hardware as a means of testing aerodynamic control systems as opposed to requiring a wind tunnel facility for the purposes of experimental validation. Reviewing both the experimental setup and design environment, this thesis aims to establish a comprehensive account of how this system was analyzed, designed, and tested. Finally, with the inclusion of plant uncertainty this report analyzes a suite of control design approaches in order to establish methods of implementing more robust controller designs for modal disturbance rejection on this particular system.

Cover page of When I Was King

When I Was King

(2019)

My performance of Basilio in Life is a Dream by Pedro Calderón de la Barca was a culmination of my training here at UCSD. This role demanded a depth of heart, vocal tenacity, dynamic physicality, and facility with heightened text—all skills I’ve developed over the past three years.

The comprehensive vocal training has armed me with a voice expressible in a myriad of colors, textures, and sizes. The speech work has freed me from my habits and colloquialisms so that I can intentionally cater my vocal choices to the specific character I’m playing. The classical training has not only given me a technical command of Shakespeare and heightened text, but keystones like sustained and living thought have refined my approach to all text regardless of period or style. And our diverse movement training revealed valuable information about my physical habits, gave me different techniques to break them, and challenged me to stretch my physical imagination.

All of these combined empowered me to rise to the true size and transformational needs of Basilio rather than pulling him down to a pedestrian level. I found a unique vocal and physical quality that embodied his status, age, and mental state, I navigated his large heightened speeches with deftness and specificity, and I employed these techniques to deepen my investment in the given circumstances and emotional landscape of the play. This was the true revelation of my training at UCSD: Rather than being distracted by the more cerebral and practical techniques, they integrated seamlessly into my performance without interfering with my sense of authenticity.

  • 3 supplemental PDFs

Y-Box Binding Proteins regulate CD8+ T cell differentiation and function

(2019)

CD8+ T cells are important for pathogen clearance and have many intrinsic and extrinsic factors that can determine how they differentiate into effector and memory cells. The Y-box binding protein (YBX) family of genes have been identified as potential regulators of CD8+ T cell differentiation as early as the first division (Kakaradov et al. 2017). Previous studies have shown that YBX1 and YBX3 affect various cellular pathways and functions; however, none have focused on YBX genes affecting CD8+ T cell differentiation and function. To address this gap in knowledge, this thesis investigated the effects on CD8+ T cell differentiation at early and late time points in an acute infection model using a shRNA approach. To do this, we validated retroviral shRNAs that knocked down YBX1 and YBX3, and a control non-targeting retroviral construct. Activated P14 CD45.1 and CD45.1.2 CD8+ T cells were transduced with targeting and non-targeting retroviruses, respectively, and adoptively transferred into recipient mice that were subsequently infected with Lymphocytic Choriomeningitis Virus (LCMV) Armstrong. Seven days and thirty days after infection, mice were sacrificed, and spleen and small intestine tissue were analyzed using flow cytometry. Relative to the non targeting control-transduced cells, cells knocked down for YBX1 and YBX3 expression exhibited reduced CD8+ TE and CD8+ TCM populations. Knock down of YBX1 and YBX3 expression also resulted in an increase of CD8+ TRM cells within the small intestine, and an increase of circulating TEM cells and cytokine-producing cells.

Alignment Methods for Optical Maps

(2019)

Optical mapping is a DNA physical mapping technique that can measure large-scale structural variation in genomes and enables more accurate completion of genome assemblies. Particularly, we focus on the case where optical mapping is used to complete genome assembly on pre-identified segments such as may be found in a breakpoint graph. In this work we study methods for aligning optical map contigs with reference genome segments. This work introduces a novel method for optical map alignment that outperforms existing methods for aligning breakpoint graph reference segments to assembled optical map contigs. Also discussed are some additional modifications that can be made to the method.

Structure, chemical dynamics and electron localization in the mineral and surface interface

(2019)

Reactions in the mineral surface/reservoir fluid interface control geochemical processes such as the dissolution and growth of minerals. In this dissertation we present properties of hematite bulk, AIMD simulation of structures and reactions (Fe2+ absorption) in the hematite–water interfaces region with intension of interpreting the structure of the reactive interface region, the dynamics of the water, solute molecules and atoms in this region and the electronic structure associated with hydrogen and covalent bond formations.

We also study symmetry breaking in the mean field solutions to the 2 electron hydrogen molecule within Kohn Sham (KS) local spin density function theory with Dirac exchange (the XLDA model). This simplified model shows behavior related to that of the (KS) spin density functional theory (SDFT) predictions in condensed and molecular systems. The Kohn Sham solutions to the constrained SDFT variation problem undergo spontaneous symmetry breaking as the relative strength of the non-convex exchange term increases. This results in the change of the molecular ground state from a paramagnetic state to an antiferromagnetic ground states and a stationary symmetric delocalized 1st excited state. We further characterize the limiting behavior of the minimizer when the strength of the exchange term goes to infinity. The stability of the various solution classes is demonstrated by Hessian analysis. Finite element numerical results provide support for the formal conjectures.

In Chapter 1 experimental and theoretical backgrounds and progress are introduced. In Chapter 2 computational methods including first principle methods and AIMD are briefly introduced. %In Chapter 3 the properties of hematite bulk are calculated and analyzed.

In Chapter 3 simulations of surface and aqueous fluid interfaces of hematite (001) and (012) are carried out. Projected density of states for interfacial atoms, water adsorption process on surface, hydrogen bond analysis, electron density profiles and etc are investigated. In Chapter 4 symmetry breaking in density functional theory due to Dirac exchange for a Hydrogen molecule is studied. In Chapter 5 Dynamic Mean Field Theory method and applications are presented. In Chapter 6 summary and future work are discussed.

Cover page of Dadum : The Self in Data through Somatic Immersive Memory

Dadum : The Self in Data through Somatic Immersive Memory

(2019)

Dadum investigates new ways of recreating memories using digital tools. Exploring

re-creations of those lost, object reminiscences, and how these structures translate into digital becomings. The theories here look toward conversations on data, particularly as we grow ever-tethered to our digital self. Exploring how the next-generation interface with this digital self is becoming immersive. The ideas and research written focus on ways data is handled and the role immersion will play in our growing social digital self with expanded notions of somatic integration. I explore this relationship through the development of my artwork which memorializes my memory of my deceased father through digital reconstruction and transcription of artifacts he left behind.

An Examination of Intestinal Microbiota of Mesopelagic Fish Reveals Microbial Community Diversity Across Fish Families

(2019)

Mesopelagic fishes are of utmost importance to the health of global oceanic ecosystems. These fishes comprise the largest known marine biomass, and are a vital source of food many economically important fish and marine mammals. Further, they serve as a major component of the biological carbon pump, moving food items through the water column via diel migration. Though significant effort has gone into understanding species diversity, and positioning in marine food webs, the microbial component of these animals remains poorly characterized. Symbiotic microbial populations associated with the gastrointestinal (GI) tract assist the host with nutrient uptake, digestion, defense against pathogenic microbes, but can also be detrimental to host health as parasites or pathogens. This study investigates the normal intestinal microbiota of wild mesopelagic fish to determine community diversity and distribution across multiple host families with varying migratory and dietary lifestyles. The results presented here indicate that midwater fish have unique microbial communities from fish of other pelagic zones, where, for example, mesopelagic hosts show enrichment in Betaproteobacteria and Gammaproteobacteria microbial classes. Within mesopelagic fish families, major differences were seen: Gonostomatidae are enriched in three Mycoplasma taxa, Stomiidae had highest alpha diversity, Melamphaidae had the highest abundance of Planctomycetes, and Myctophidae gut communities were enriched in Betaproteobacteria. This study brings new understanding to the microbial ecology of the mesopelagic, and demonstrates that despite sharing space in the water column, mesopelagic fishes contain different microbial communities. Clearly, life history traits must be considered in addition to environment in order to better understand the mesopelagic ecosystem.

Mesopelagic fishes are of utmost importance to the health of global oceanic ecosystems. These fishes comprise the largest known marine biomass, and are a vital source of food many economically important fish and marine mammals. Further, they serve as a major component of the biological carbon pump, moving food items through the water column via diel migration. Though significant effort has gone into understanding species diversity, and positioning in marine food webs, the microbial component of these animals remains poorly characterized. Symbiotic microbial populations associated with the gastrointestinal (GI) tract assist the host with nutrient uptake, digestion, defense against pathogenic microbes, but can also be detrimental to host health as parasites or pathogens. This study investigates the normal intestinal microbiota of wild mesopelagic fish to determine community diversity and distribution across multiple host families with varying migratory and dietary lifestyles. The results presented here indicate that midwater fish have unique microbial communities from fish of other pelagic zones, where, for example, mesopelagic hosts show enrichment in Betaproteobacteria and Gammaproteobacteria microbial classes. Within mesopelagic fish families, major differences were seen: Gonostomatidae are enriched in three Mycoplasma taxa, Stomiidae had highest alpha diversity, Melamphaidae had the highest abundance of Planctomycetes, and Myctophidae gut communities were enriched in Betaproteobacteria. This study brings new understanding to the microbial ecology of the mesopelagic, and demonstrates that despite sharing space in the water column, mesopelagic fishes contain different microbial communities. Clearly, life history traits must be considered in addition to environment in order to better understand the mesopelagic ecosystem.