UC San Diego

We investigated phytoplankton growth and micro- and mesozooplankton grazing patterns in the California Current Ecosystem (CCE) during summer 2021. Two water parcels, followed over a duration of 4-5 days using satellite-tracked drogued drifter for quasi- Lagrangian experimental cycles were investigated for inshore and offshore differences. Phytoplankton growth rates and microzooplankton grazing rates were determined using the two-point dilution method, and daily Bongo tows were deployed for mesozooplankton collection, for biomass and grazing estimates based on gut fluorescence. Instantaneous rates of growth and grazing between the two cycles were µ = 0.45 (± 0.13) d-1 for Cycle 2 (inshore) and 0.60 (± 0.1) d-1 for Cycle 3 (offshore), and microzooplankton grazing rates were 0.36 (± 0.21) d-1 for Cycle 2 and 0.37 (± 0.11) d-1 for Cycle 3. Mesozooplankton contributed much less to grazing for both cycles, grazing 0.05 (± 0.02) d-1 inshore and 0.025 (± 0.006) d-1 offshore, removing 4% and 2% of phytoplankton standing stock, respectively. In both cycles, the net calculated phytoplankton growth was positive, but this was only statistically significant for the offshore region. The dominant grazers within the mesozooplankton community were not consistent between the two regions of the CCE: the three smallest size classes (0.2-2 mm) contributed the most to grazing in Cycle 2, while in Cycle 3, the dominant grazers were the two smallest size classes (0.2-1 mm). Mesozooplankton grazing showed changes related to diel vertical migration. These analyses contribute to our understanding of growth and grazing dynamics in plankton food webs, and to understanding carbon cycling in the CCE.

The development of cortical inhibitory interneurons (cINs) has been fine-tuned to produce a highly specialized population that serves as the substrate for cortical circuit formation. Understanding the developmental programs responsible for the precise distribution and diversification of cINs is key to unlocking the principles of building and evolving brain circuits, yet much remains unknown about their key regulators and molecular mechanisms. MicroRNAs (miRNAs) are a class of non-coding RNAs that are necessary for cIN development, as genetic ablation of miRNAs in developing cINs causes a severe decrease in cIN abundance, migration defects, and a failure to express the mature cell type markers parvalbumin (PV) and somatostatin (SST). However, due to the coarse temporal resolution of genetic knockouts over the protracted developmental period of cINs, it is unclear how or when miRNAs directly regulate cIN specification, migration, and maturation. Further, the miRNA-mediated mechanisms necessary for cIN maturation and migration are unknown, in part because the miRNA-target network specific to embryonic cINs is poorly understood.

We engineered an innovative miRNA toolbox with vastly improved temporal resolution and molecular precision to unlock mechanistic insight on miRNA regulation of cIN development. Using a novel method for rapidly and reversibly blocking miRNA function in neurons, we showed that miRNAs are necessary for cIN developmental progression and fate specification. Transiently blocking miRNAs only during late embryonic development abrogated cell death to reveal an irreversible alteration in the ratio of PV and SST cINs, suggesting that there is an embryonic critical period during which cIN fate decisions require miRNA regulation. To identify specific miRNA-mediated mechanisms of cIN development, we profiled miRNA-target interactions in cINs at two timepoints representing neurogenesis and migration, overcoming the technical challenges of targetome profiling in low abundance cell types via complementary use of two variants of AGO2 CLIPseq. We performed an unbiased analysis of gene-level miRNA load, identified putative nodes in the miRNA-target network that we term “miRNA hotspots”, and screened the top miRNA hotspots for roles in cIN migration. By manipulating the hit gene Ist1 via overexpression or whole 3’UTR gene editing to precisely mutate miRNA recognition elements (MREs), we showed that derepression of Ist1 leads to altered cellular morphology during migration, impaired dispersion across cortical regions, and increased cortical invasion, and further discovered a novel mechanism by which miR-125b preferentially represses Ist1 expression within the migratory streams.

This dissertation combines archival research and oral histories to construct a case study of IBM’s adoption of free and open source software (FOSS) between 1998-2003, with a focus on the Linux operating system. This work makes theoretical and methodological contributions to recent scholarship that analyzes the role of fictional expectations and imagined futures in enabling action under conditions of uncertainty. Specifically, I make use of temporal comparison to examine how executives within the company overcame the uncertainty surrounding the open source development process and Linux’s viability as operating system for large-scale enterprise computing systems. I emphasize the role that a set of fictional expectations, which together formed what I call the network-centric imaginary, played in enabling executives to make sense of both Linux and FOSS more generally. While many studies have demonstrated how imaged futures enable actors to coordinate action in situations where they lack the information required to make decisions based on calculable risk, few have been able to demonstrate the mechanisms through which they take take on a performative dimension. My research fills this gap in the literature by emphasizing the material and political economic aspects of imagined futures. I demonstrate how the expectations and interests held by IBM executives regarding Linux reshaped the operating system through a set of institutions created by the company and through which employees could directly influence the operating system’s development. Through this materialist approach, I make sense of transformations to Linux that occurred during the early 2000s, which I argue were crucial for the operating system’s transformation from a hacker tool and academic curiosity into a constitutive element of modern corporate controlled cloud computing infrastructure.

The aim of this dissertation is to increase the understanding of how the cerebral vasculature (CV) becomes dysregulated in neurological disease, with a focus on the blood-brain barrier (BBB). I begin this dissertation with a literature review on the topics of the BBB in health and disease, the complex pathology of sporadic Alzheimer’s disease (AD), the importance of lipids in neuroinflammatory contexts such as AD, evidence of CV dysfunction in AD, and a brief overview of the key findings of my dissertation research establishing a connection between these topics. A large body of literature implicates CV dysfunction, including avascularity, reduced cerebral blood flow (CBF), hemorrhage, and BBB permeability, as a common feature of AD pathology; however, the molecular nature of this dysfunction had never been explored. To address this knowledge gap, I employed a multi-omic approach, leveraging both proteomics and lipidomics, to identify the molecular changes to the CV in post-mortem sporadic AD patients. This multi-omic strategy revealed a loss of sphingolipid (SL) and ceramide (CER) biosynthetic machinery at the protein level, and a distinct loss of CERs at the lipid level. To understand the functional importance of these changes to the CV, I used mouse genetics to conditionally inhibit SL biosynthesis specifically in endothelial cells (ECs), the BBB-containing cells lining the lumen of the CV. In doing so, I found that loss of EC SL biosynthesis promotes BBB permeability in healthy adult mice and inhibits angiogenesis capacity promoting hemorrhage in response to a hypoxic environment; all of which have been shown to occur in AD patients. In this process, I noticed a fatty acid (FA) elongase enzyme, Elovl7, to be downregulated in the AD CV at the protein and transcript level. Further, I found that Elovl7 is uniquely expressed in brain ECs in both humans and mice and becomes dysregulated in several mouse models of neurological disease. To clarify the role of Elovl7 in brain ECs, I used mouse genetics to conditionally delete Elovl7 from brain ECs of adult mice. In doing so, I discovered that Elovl7 generates phosphatidylcholines (PCs) and lyso-PCs (LPCs) for the CV, and its absence results in decreased levels of docosapentaenoic acid (DPA), an anti-inflammatory FA, in the brain. When confronted with a systemic inflammatory stimulus, loss of Elovl7 exacerbated hemorrhage and drove persistent reactivity in astrocytes and microglia. Together, these findings show that lipids synthesized within brain ECs are important in maintaining CV integrity and modulating neuroinflammation. This body of work reveals multiple novel targetable therapeutic avenues to fortify the brain vasculature across a broad spectrum of neurological disorders.

Recent increase in the demand for low latency and high data rate wireless links is the main reason for the rapid advancement in >100 GHz millimeter-wave systems especially D-band (110-170 GHz) communication links. Emerging applications such as virtual/augmented reality (VR/AR), high speed backhaul communication and the Internet of Things (IoT) now have greater opportunities.

The first contribution of this thesis is the development of the world’s first 140 GHz 128-element fully 2D scalable wafer-scale dual receive phased array in CMOS technology. In the first contribution, the wafer-scale beamformer chip is composed of 128 RX channels for an 8×8 dual-polarized array. RF beamforming is employed with 4-bit phase and gain controls on every element, and on-chip dual down-converters are used for an intermediate-frequency (IF) interface at 9-14 GHz. Also, a ×6 local-oscillator (LO) multiplier chain is used and two 64:1 Wilkinson combiners are employed for the RF distribution network with signal amplification within the combining network. The chip is flipped on a low loss organic interposer (RF PCB) containing the RF transitions, LO, and IF distribution networks, and which feeds an 8×8 dual-polarized microstrip antenna array with a spacing of 0.57 λ×0.57 λ (at 140 GHz) in the horizontal and vertical directions. The array scans to ±45 ◦in all planes for both polarizations, and the measured response supports 64 QAM operation with 2×55 Gb/s links, and achieving > 100 Gb/s links from a single aperture.

The second contribution is a scalable 8x8 transmit and receive array phased array at D-band. Its grid size is maintained close to (or equal) λ /2 at 140 GHz in both x- and y-directions, hence achieving a wide electronic scanning angle of up to 60 ◦. The measured peak effective isotropic radiated power (EIRP) of the TX array is 34-37.5 dBm at 137.5-145 GHz which is the highested reported EIRP so far for silicon technologies. Communication link measured for both TX and RX operations supports modulated 16-/64- quadrature amplitude modulation (QAM) signals with up to 16 Gb/s data rates with an rms EVM less than 7 %/6 % respectively, in a room and up to 5.2 m distance between the Tx and Rx phased-arrays.

The third contribution is the development of a 16x16 element Ka-Band reflector array. A new analysis method is presented to illustrate the effect of multiple reflections between the passive phase shifter and the antenna, and it is based on an S-parameter analysis. Simulations show that it is critical to have a well matched antenna for good operation of reflect arrays and with low phase errors. The presented design can scan to +/-70 ◦. in all planes and in both polarizations.

Time-of-day has been shown to regulate exercise capacity, with skeletal muscle function proposed to be the key regulator. Skeletal muscle plays a central role in exercise performance and systemic energy metabolism, serving as the primary site of post-prandial glucose disposal. However, as of this dissertation, no study has empirically tested intrinsic muscle function at different times-of-day. Further, the mechanisms by which skeletal muscle takes up glucose from the blood in response to contractions remain to be fully defined. We focused on the lysine acetyltransferases E1A binding protein p300 (p300) and cAMP response element binding protein binding protein (CBP) as potential regulators of contraction-stimulated (C-stim) glucose uptake because they have previously been shown to be required for insulin-stimulated glucose uptake and their activity can be regulated by various C-stim kinases. Thus, the objective of this dissertation was to determine if the intrinsic physiological properties of skeletal muscle are regulated by time-of-day and to investigate the role of p300/CBP in C-stim glucose uptake. To measure the intrinsic physiological properties of skeletal muscle, we used an ex vivo approach to control for neuromuscular interactions, temperature, and substrate availability. In Study #1, we found that time-of-day does not regulate the intrinsic contractile properties of skeletal muscle, including submaximal and maximal force production, endurance, or ability to take up glucose from the blood in response to contractions. In Study #2, we found that time-of-day does not regulate mitochondrial function at the transcript, protein, or enzymatic level in skeletal muscle. In Study #3, we demonstrate that p300 and CBP are essential for C-stim glucose uptake using both inducible, skeletal muscle-specific knockouts of p300/CBP and pharmacologic inhibitors of p300/CBP acetyltransferase activity. In summary, we demonstrate that while time-of-day does not regulate intrinsic skeletal muscle contractile function, mitochondrial function, or C-stim glucose uptake, p300/CBP are required for C-stim glucose uptake and are potentially novel fundamental regulators of C-stim glucose uptake.

Significant progress over the past decade has transformed oral drug delivery, extending gastric retention time, improving therapeutic efficacy and patient compliance. Cutting-edge innovations leveraging robotic technologies have transformed oral administration, overcoming the limitations of traditional oral delivery and paving the way for a new era of personalized medicine. Nearly 70 years ago, Richard Feynman envisioned ingestible miniaturized medical devices capable of performing surgery within the body. While remarkable advancements have been made since then, Feynman’s dream of “swallow the surgeon” concept remains only partially realized. However, the emergence of microrobotics in active drug delivery is bridging the gap between the pharmaceutical and microrobotic fields, bringing this vision closer to reality. This dissertation presents a time-tunable multi-segment capsule designed to enhance patient adherence to oral medications, particularly in cases of polypharmacy. By simplifying complex medication regimens, this system improves adherence, a crucial factor in chronic disease management and personalized medicine. The capsule enables the programmed release of multiple medications at preselected times, ensuring patient compliance and high therapeutic efficiency. By incorporating micromotors into the capsule, this system enables active drug delivery, improving absorption and bioavailability, optimizing therapeutic outcomes, and seamlessly integrating treatment into patients' daily lives. This advancement marks a major step toward precision drug delivery. Furthermore, incorporating micromotors whether synthetic (e.g., Mg- or Zn-based) or biohybrid (e.g., algae-based) into pharmaceutical carriers represents a groundbreaking approach to active drug delivery, This strategy addresses the limitations of oral drug delivery by leveraging micromotors propulsion for gastrointestinal drug delivery, as demonstrated in vivo using murine and porcine models. Chemical and biological propulsion of micromotors enables immediate disintegration and prolonged gastrointestinal retention, leading to significant dose reduction and enhanced bioavailability. These innovations maximize therapeutic efficacy while minimizing side effects, paving the way for precision therapeutics. Finally, this dissertation explores the future applications of smart robotic capsules, offering a versatile platform. These capsules serve as closed-loop oral devices for continuous monitoring, on-demand drug release, and theranostic applications. By integrating robotic capabilities with multisegment capsule designs, this work envisions a future where there is “plenty of room in a capsule”, a paradigm shifts toward personalized medicine.

The blood-brain barrier (BBB) is a specialized set of features unique to the central nervous system vasculature that tightly regulates the movement of ions, molecules, and cells between the blood and the brain, maintaining neural homeostasis. BBB dysfunction is a hallmark of many neuroinflammatory conditions, including multiple sclerosis, traumatic brain injury, and stroke. One of the least understood components of the BBB is the glycocalyx, the dense layer of glycans and glycoconjugates that coats the luminal surface of the cerebral vasculature and serves as the first point of contact between the blood and brain. Though it may prove vital to our understanding of the BBB and offer new therapeutic targets to treat neuroinflammation, research into the BBB glycocalyx has been limited.This dissertation explores the BBB glycocalyx in health and neuroinflammation. By refining existing methods, we overcame key technical challenges, which enabled the first in-depth molecular analysis of the BBB glycocalyx. Our research revealed that the BBB glycocalyx has a highly unique glycan landscape with distinct structure, molecular composition, and function compared to glycocalyces in the peripheral vasculature. Notably, we found that the BBB glycocalyx is highly resilient, showing minimal structural and molecular changes across several models of neuroinflammation. Ultimately, this work advances our understanding of the BBB glycocalyx and offers new tools and targets for future research into its role in health and disease.

Despite promising clinical responses to programmed cell death-1 (PD-1) blockade in less than 20% of head and neck squamous cell carcinoma (HNSCC) patients, advances are needed to extend these benefits to patients with resistant tumors. Resistance is attributed to immune suppression within the tumor microenvironment (TME), which restricts the intratumoral (IT) recruitment and activation of tumor-killing CD8+ T cells, CD4+ T cells, and NK cells. CXCR3, a chemokine receptor for the interferon-inducible chemokines, CXCL9, CXCL10, and CXCL11, is highly expressed on activated CD8+ and CD4+ T cells as well as NK cells and plays a critical role in directing their migration. Chapter 1 establishes the correlation with increased expression of CXCR3 and its ligands, CXCL9 and CXCL10, with early tumor stage, increased immune infiltration, inflammatory gene signatures, and improved overall outcomes in patients with HNSCC. In chapter 2, syngeneic murine models of tobacco-associated HNSCC are utilized to show that IT delivery of recombinant CXCL10 drives tumor elimination through the recruitment of CD8+ T cells, CD4+ T cells, and NK cells. Furthermore, we demonstrate that by combining IT CXCL10 treatment with PD-1/PD-L1 checkpoint blockade inhibition, we achieve further suppression of tumor growth and complete remittance. Chapter 3 highlights that T cells recruited to tumors via CXCL10 ligand display enhanced activation, decreased markers of early T cell exhaustion, and increased tumor antigen specificity, indicating that CXCL10 not only directs cell migration, but may also enhance T cell function. Finally, in chapter 4, we explore additional projects and future directions aimed at enhancing the effectiveness of CXCL10-treatment through combinational therapies and improved delivery.

In this thesis, I explore how proximity between play-texts and personal texts forms the foundation of my sound design process. I investigate how my sound design process intersects with dramatic literature, other design elements, and personal experience to create a cohesive and purposeful theatrical environment. Furthermore, I juxtapose accounts of my creative process on two case studies with biographical anecdotes and original proposals for new works.