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Open Access Publications from the University of California

UC San Diego Electronic Theses and Dissertations

O-GlcNAcylation dynamics in the brain

(2021)

The role of post-translational modifications in the brain such as phosphorylation

and ubiquitination have been well studied. However, the role of O-GlcNAcylation in

distinct subpopulations of neurons remains unknown. This post-translational

modification is an addition of single sugar moiety O-GlcNAc, derived from glucose

metabolism, to serine or threonine residue of proteins. O-GlcNAcylation is catalyzed by

O-GlcNAc transferase (OGT), a highly expressed metabolic sensor enzyme in the brain,

shown to be a gatekeeper for neuronal function and health. Here, we investigated the role

of OGT and O-GlcNAc dynamics in the brain. First, we demonstrated under the fasted

state, brain regions such as the paraventricular nucleus of hypothalamus, cortex and

cerebellum, have significant reduction in O-GlcNAc levels. While the hippocampus

regions, CA3 and dentate gyrus, have increased levels of O-GlcNAcylation. Then in order

to investigate the role of O-GlcNAcylation in Parvalbumin-positive inhibitory

interneurons (PV), we generated a PV-specific-OGT knockout mouse line (PV.OGTKO).

Our detailed behavioral and histological analysis indicated that loss of OGT in PV

neurons leads to lower survival rates, motor defects, and loss of PV neurons. Overall, our

results suggest the OGT plays crucial role in PV neuronal health and survival.

Cover page of Metadata Models and Methods for Smart Buildings

Metadata Models and Methods for Smart Buildings

(2020)

Applications in smart buildings have shown potential for improving energy efficiency, automated operation, and for creating better living conditions for occupants. To achieve these goals requires effective collection and use of sensing data and collaboration among different subsystems such as Heating, Ventilation, Air-condition (HVAC), security, lighting and sensing subsystems. Data generated and used by these subsystems are heterogeneous and often contextualized to real-time conditions. Contextual information is often provided by subsystem vendors as "metadata", that is, the data about data. The multiplicity of vendors makes most metadata idiosyncratic without any consistent meaning or usage that can be directly inferred from such metadata. This makes them difficult to be useful. Vendors and building operators have to often "guess" based on the unstructured text of metadata written by different engineers. Converting building metadata to a machine-readable format usually involves significant manual effort. We envision building systems that are able to seamlessly exchange data across subsystems as well as across various building services in a programming framework. Such information exchange is mediated by timely sensor information, its automated organization and navigation, thus creating a technical basis for future `smart buildings'.

Methods and tools for automated handling of metadata are crucial to this vision. Second, we present an application programming framework comprised of machine learning algorithms to help organize the current unstructured metadata information from existing buildings into a structured format such as Brick+. Third, we propose an application workflow that relies only on a standard information model for unified and secure application deployment. Using Brick+, Scrabble and Plaster programming support tools, we have built an end-to-end applications and services framework for smart buildings. Using buildings on the UC San Diego campus, we describe and demonstrate the effectiveness of the proposed methods. We demonstrate several new applications, such as a personal thermostat application called Genie and an energy dashboard, that can be built and deployed with minimal human effort. In addition to the demonstrated value of metadata models and methods in building portable applications for smart buildings in this dissertation, we continue to pursue building a community of system builders for the smart building environments.

Characterizing and Controlling the Interface of Metal-Organic Framework and Polymer Components in Mixed-Matrix Membranes

(2020)

Metal-organic frameworks (MOFs) are a class of materials that combine the chemical tunability of organic molecular chemistry with the porosity of zeolites. The crystallinity, porosity, and chemical versatility of MOFs has led to their study for applications including storage and delivery of gases, catalysis, and separations. In order to utilize MOFs for industrial applications, however, they must be processed into other forms. Previous work showed that small amounts of flexible polymers can be combined with different MOFs to form ‘sheets’ of MOF, termed mixed-matrix membranes (MMMs), that display useful MOF porosity and chemical accessibility in a flexible, stable form factor.

To build on this previous work, MMMs using three polystyrene-based polymers that are similar in chemical structure but provide a range of flexibility are developed in Chapter 2. MOF accessibility and MMM cohesion at up to 90 wt% MOF in styrene/butadiene copolymers is demonstrated, and it is shown that the starting flexibility of the polymer affects the utility of the resulting MMM.

To assess the factors that influence MMM cohesion, computational experiments predicting the microscopic interfacial structures of MOF-polymer MMMs are performed in Chapter 3. This computational modeling is then correlated with experimental findings to elucidate the structure-compatibility relationship of the MOF-polymer pairs studied, and two examples of MOF-polymer MMMs are found to contain both a flexible MOF-polymer interface and strong MOF-polymer hydrogen bonding interactions.

Significant differences in MOF pore accessibility between these two MMMs prompted further study and comparison, and NMR experiments detailed in Chapter 4 suggest the polymer component infiltrates into MOF pores to differing extents depending on the nature of the polymer used. This differing polymer infiltration behavior directly affects the utility of the composite as assessed through other experiments.

Chapter 5 describes the fabrication of new MMMs from an inexpensive commodity polymer, poly(ethylene-co-vinyl acetate) (EVA). These MMMs are then used in liquid-phase applications including sorption and removal of harmful perfluoroalkane substances and catalytic breakdown of a chemical warfare agent simulant. When EVA-based MMMs are compared with MMMs prepared using different polymers discussed in previous chapters, polymer-dependent differences in MMM performance are observed.

Cover page of Dynamics of Tidally-Driven Flows in Coral Reef Shelves: Observations from Autonomous and Fixed Instruments

Dynamics of Tidally-Driven Flows in Coral Reef Shelves: Observations from Autonomous and Fixed Instruments

(2020)

The present work examines the hydrodynamics of the inner-shelf region, focusing on tidally-driven alongshore flows over coral reef shelves. This study draws on field data collected in O’ahu, Hawai’i using fixed and mobile assets to develop new modes of observational research.

First, a theoretical model is developed to describe how autonomous underwater vehicle (AUV)-based water velocity measurements are influenced by a surface wave field. The model quantifies a quasi-Lagrangian, wave-induced velocity bias as a function of the local wave conditions, and the vehicle’s depth and velocity using a first-order correction to the linear wave solution. The theoretical bias is verified via field experiments over a range of wave and current conditions. The analysis considers velocity measurements made using a REMUS-100 AUV, but the findings apply to any small AUV (vehicle size ≪ wavelength) immersed in a wave field. The observed wave-induced biases [O(1–5) cm/s] can be significant, and can be comparable to steady flow velocities for inner-shelf regions.

Second, a new approach to estimate lateral turbulent Reynolds stresses (u′v′) in wavy coastal environments using acoustic Doppler current profilers (ADCPs) is described. The performance of the proposed method is evaluated via comparisons with independent acoustic Doppler velocimeter (ADV)-based stress estimates at two sites, and the vertical structure of the tidally-averaged turbulent Reynolds stresses is examined for an unstratified, tidally-driven flow over a rough coral reef seabed in weak waves. Observations and analysis indicate that lateral stresses are sustained by the cross-shore gradient of the mean alongshore flow, and driven by bottom-generated turbulence. Scaling considerations suggest that cross-shore transport by lateral turbulent mixing could be relevant to coral reef shelves with steep cross-reef slopes and rough bottoms.

Finally, a tidally-driven alongshore flow over a forereef shelf is examined using AUV-based spatial velocity measurements along with time series data of the alongshore pressure gradient. Ensemble phase averages of AUV-based velocities reveal characteristics akin to an oscillatory boundary layer, with the nearshore flow leading the offshore flow in phase and with a corresponding velocity magnitude attenuation near the shallower regions of the reef. Analysis of the depth-averaged alongshore momentum equation indicates that the cross-shore structure and evolution of the alongshore flow is well described by a balance between local acceleration, barotropic pressure gradient, and bottom drag. This primary balance allows the estimation of a spatially-averaged drag coefficient as a function of cross-shore distance over depths spanning from 24 to 6 m. Seabed roughness data suggest that larger scales, with wavelengths of O(10 m), are more relevant than smaller meter-scale roughness for drag.

Photodetection in Disordered Materials

(2020)

This dissertation offers two different mechanisms for photodetection in disordered materials. Photodetectors made of amorphous materials enable low cost optical imaging and communications over non-semiconductor platforms. The key challenges are to improve efficiency, sensitivity, and frequency response. Using the localized surface plasmon resonance (LSPR) effect and an efficient carrier multiplication process, cycling excitation process (CEP), the plasmonically enhanced amorphous silicon photodetector (PEASP) with a thin (60 nm) absorption layer achieves a high external quantum efficiency with a record fast impulse response of 170 ps (FWHM). This approach offers the possibility of making detectors out of amorphous material for high frame rate imaging and optical communications in spite of the material’s low carrier mobility.

Spin-coating thin film is another approach in obtaining disordered materials. Organometallic halide perovskites attract strong interests for their high photoresponsivity and solar cell efficiency. However, there was no systematic study of their power and frequency dependent photoresponsivity. Two different power-dependent photoresponse types in methylammonium lead iodide perovskite (MAPbI3) photodetectors were identified. In the first type, photoresponse remains constant from 5 Hz to 800 MHz. In the second type, absorption of a single photon can generate a persistent photoconductivity of 30 pA under an applied electric field of 2. 5 ×10^4 V/cm. Additional absorbed photons, up to 8, linearly increase the persistent photoconductivity, which saturates with absorption of more than 10 photons. This is different than single photon avalanche detectors (SPADs) because the single photon response is persistent as long as the device is under bias, providing unique opportunities for novel electronic and photonic devices such as analog memories for neuromorphic computing. An avalanche-like process for iodine ions was proposed, with the estimation that absorption of a single 0.38 aJ photon triggers motion of 108-9 ions, resulting in accumulations of ions and charged vacancies at the MAPbI3/electrode interfaces to cause band bending and change of material electric properties. This is the first observation that single-digit photon absorption can alter the macroscopic electric and optoelectronic properties of a perovskite thin film. DFT toy model calculations were also conducted to further support the proposed ionic impact ionization.

Conversion of Metal Chelators to Selective and Potent Inhibitors of New Delhi Metallo-beta-lactamase

(2020)

Metalloproteins are essential to a wide range of biological functions including nucleic acid modification, protein degradation, and many others. Metalloproteins that utilize a metal ion to facilitate catalysis are known as metalloenzymes. Due to their role in the proliferation of many diseases, ranging from diabetes, cancer, anxiety, and pathogenic infections, there has been an increased awareness and effort to target metalloenzymes for therapeutic intervention. This dissertation will focus on the utilization of a metal-binding pharmacophore library for the fragment-based drug discovery of novel New Delhi Metallo-β-lactamase-1 (NDM-1) inhibitors. NDM-1 is a metalloenzyme that hydrolyzes β-lactam containing antibiotics and contributes to the heightened threat of antibiotic resistance. NDM-1 Inhibitor development presented in this dissertation will focus on the conversion of traditional metal chelating fragments to compounds which form stable protein:inhibitor ternary complexes. Chapter 1 describes the current landscape of metalloenzyme inhibitors and relevant background information of NDM-1. Chapter 2 details the discovery of dipicolinic acid (DPA) as a lead fragment and the hit-to-lead development of DPA derivatives as inhibitors for NDM-1. The development of DPA isosteres and investigation in the relationship of observed inhibition value versus mechanism of action is presented in Chapter 3. The investigation of an alternative MBP, iminodiacetic acid (IDA), into a second class of novel NDM-1 inhibitors is described in Chapter 4. Chapter 5 includes a description of alternative synthesized libraries and perspective on the future of NDM inhibitor development. Together these chapters demonstrate the utility of fragment-based drug discovery and metal-binding pharmacophores for the development of novel and potent NDM-1 inhibitors.

Derivation and Analysis of Distributed Computing Algorithms in Biological Systems

(2020)

There are numerous examples of biological systems outperforming human-designed algorithms at engineering tasks. Rather than relying on one central controller, these systems rely on distributed agents following simple local interaction rules that yield complex collective behavior. My research studies these biological systems systems in order to reverse-engineer optimization algorithms, with a focus on designing robust, efficient routing networks.

Repairing broken links is a fundamental problem for human-designed routing networks, as well as trail networks used by ants to travel between nests and food sources. Many ant species have evolved methods to solve the repair problem under more restrictive constraints than those faced by human engineers. Arboreal turtle ants are especially interesting, because their movements are constrained by the branches in the vegetation. I defined a mathematical model for the unique repair problem faced by turtle ants. I demonstrated techniques for using turtle ant behavioral data to derive a distributed repair algorithm and infer critical features of turtle ant behavior. The algorithm is biologically realistic, scalable, and robust to a variety of topologies. I then analyzed data on trail networks formed by turtle ants over several days to conclude that turtle ant trail networks eschew shorter branches in favor of nodes whose physical orientations allow for quicker pheromone reinforcement.

Human-designed routing networks often seek to maximize efficiency while minimizing cost. These objectives often conflict, which necessitates manage trade-offs. Neural arbors face a similar challenge of conducting signals quickly while conserving material. I defined a mathematical framework for the multi-objective optimization problem that neural arbors face. I showed that neural arbors are significantly better at optimizing trade-offs between material cost and signal delay than would be expected by chance. I showed how this framework can be used to predict an arbor's structure based on its function. My work confirms the value of using neural arbors as inspiration for network design algorithms, and identifies promising new avenues for neuroanatomy research.

My research highlights the symbiotic relationships between biology and computer science: collecting and analyzing behavioral data can inform algorithm design, while algorithmic thinking can elucidating novel behavioral patterns.

The Molecular Architecture of Spore Morphogenesis in Bacillus subtilis

(2020)

Many cellular processes in bacteria transpire at a scale of ~1-2 µm that are difficult to study by optical microscopy alone due to limitations imposed by diffraction properties of light. Hence, visualization of cellular structures at a high spatial resolution in the native cellular milieu in bacteria is a poorly explored field. My thesis aims to study the process of sporulation in a Gram-positive bacterium, Bacillus subtilis. During conditions of nutrient deprivation, B. subtills undergoes a developmental pathway that culminates in the production of two cells with different sizes and fates, the smaller forespore and the larger mother cell. I have studied different stages of sporulation in B. subtilis using novel modalities in the field of cryo-electron microscopy, namely cryo-focused ion beam milling coupled with cryo-electron tomography (or cryo-FIB-ET). Cryo-FIB-ET allows visualization of macromolecules inside the cell at a resolution of a few nanometers. Using this technique, I have elucidated important principles governing the following processes during sporulation:

(1) Polar cell division: We demonstrate that FtsAZ filaments, the major orchestrator of cell division in bacteria are localized uniformly around the leading edge of the invaginating septum during vegetative growth but present only on the mother cell side during sporulation, a process mediated by a sporulation-specific protein, SpoIIE. This asymmetry in divisome localization during sporulation dictates not only the septal thickness but also the diverse fate of the two daughter cells.

(2) Engulfment: We study the role of cell wall remodeling and chromosome translocation during engulfment. We show that the mother cell membrane migrates in finger-like projections around the forespore due to uneven cell wall degradation. We also show that the turgor pressure generated by the forespore chromosome inflates the forespore and helps it maintain its well-rounded shape. These studies have thrown light on spatiotemporal regulation of important complexes dictate architectural transformations during engulfment.

Overall, our studies have added more cases to support the observation that several complex traits to regulate critical cellular processes like division, cell migration, DNA dynamics, cell shape etc. that were previously thought to be a characteristic of only eukaryotes are also present in prokaryotes and that cryo-FIB-ET will likely be the tool of the future to probe these and other processes at a molecular detail.

Electrophysiological characterization of neurons in primary auditory cortex of the awake mouse

(2020)

The cerebral cortex is a laminar neural structure which serves as a critical substrate for higher cognitive abilities in humans and other mammals. Here, I use single-neuron recordings to investigate primary auditory cortex, the first cortical area to process aural information, in the brains of awake mice. Neurons in primary auditory cortex are sensitive to sounds of certain frequencies and intensities. I explore the synaptic bases for those preferences and demonstrate that they can be modulated on a moment-by-moment basis by changes in brain state.

Cover page of Alternative Weld Details and Design for Continuity Plates and Doubler Plates for Applications in Special Moment Frames

Alternative Weld Details and Design for Continuity Plates and Doubler Plates for Applications in Special Moment Frames

(2020)

Steel Special Moment Frames (SMF) are regularly used as seismic force-resisting systems due to their excellent ductility and wide accommodation of building floor plans and heights. The current AISC Seismic Provisions require the use of reinforcing continuity plates and dictate their size based on a set of rules conservatively inferred from experimental testing. These rules often result in the unnecessary reinforcement of columns and usually require costly complete-joint-penetration (CJP) groove welds to fasten the reinforcing plates. Full-scale testing of 10 moment frames was performed to investigate the design of these continuity plates and their weldments. Six of these frames were exterior connections utilizing the prequalified Reduced Beam Section (RBS) connection, while the remaining four were interior connections utilizing the prequalified Welded Unreinforced Flange-Welded Web (WUF-W) connection. While violating the current continuity plate requirements, all 10 connections surpassed the 0.04 rad story drift requirement of SMF according to the prequalification criteria of the AISC Seismic Provisions. Experimental testing was also performed to measure, for the first time, the in situ residual stresses of a continuity plate. Detailed parametric finite element modelling and modern fracture mechanics using the Cyclic Void Growth Model for ductile fracture prediction was used to develop an amended set of limit states of reinforced columns. These amended limit states, in conjunction with a newly proposed width-to-thickness requirement, permit the design of column reinforcement based on a rational plastic approach. A fillet weld design that capacity protects the weldments based on a von Mises yield surface is included in this new plastic design method. This new experimentally verified design basis for fillet weldments of continuity plates results in significant fabrication savings. It was also found that sizing the doubler plate weldments for the average developed shear flow according to the relative doubler plate stiffness was adequate to fasten the doubler plate. This results in significant savings over current requirements which currently require welds to develop the shear strength of the doubler plate.