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Phenotypic Characterization of Wild-Type and Food-Associated Aspergillus
No full textAspergillus is a genus of filamentous fungi comprising approximately 250 unique species found in a variety of niches within human food environments, ranging from beneficial fermentation to detrimental mycotoxin production. The genus is wide ranging and amenable to growth on various carbon sources, finding niches within many ecosystems in critical biodeterioration roles. Aspergillus oryzae and Aspergillus flavus exhibit strong genetic similarity up to 99.5% yet diverge remarkably in their phenotypic expression. This thesis explores the phenotypic markers of closely related dyads of food-associated and wild Aspergillus species, focusing on enzymatic activities, growth patterns and organoleptic quality characteristics. In evaluating these characteristics, distinct phenotypic profiles emerged.
Aspergillus oryzae strains exhibit significant alpha-amylase activity, indicative of adaptation to starch-rich environments such as those found in sake production. Aspergillus flavus displays weak enzymatic activity but strong growth across substrates. While there is broad overlap in the volatolome of both Aspergillus species, A. oryzae exhibits significantly more variety and greater quantity of unique volatile organic compounds, many of which can engender favorable sensory characteristics to fermented foods. These phenotypic specializations underscore the adaptive responses of Aspergillus species to human foodways. Moreover, the findings suggest potential implications for industrial applications and offer insights into the adaptation of fungal species into unique human food environments.Master of Science (M.S.
Development of Automated Infrastructures in Microfluidics for Site-Specific Labeling of RNA (PLOR)
No full textPosition‐specific labeling of RNA (PLOR) is a technique that enables incorporation of modified nucleotides at defined positions within an RNA transcript. However, traditional PLOR workflows rely on manual sequential reagent delivery, leading to significant time consumption and reagent waste when labeling large RNA strands. In this study, we developed an automated, multiplexed pneumatic peristaltic pumping platform integrated into a multilayer PDMS microfluidic chip that enables precise, low‐dead‐volume reagent delivery for PLOR. We first studied how membrane thickness, valve geometry, and channel dimensions influence single‐channel peristaltic flow and optimized a metering module that achieves a volumetric flow rate of approximately 370 nL/min at 1.67 Hz. We then conducted simulated reagent routing using colored dyes to evaluate an eight‐channel multiplexing architecture—demonstrating how combinations of reagents could be driven by the pneumatic peristaltic pumps and routed through multiplexed valves into designated channels. During RNA transcription and specific labeling these streams would include different NTP mixes, modified nucleotides, and buffer solutions. In parallel, we implemented an on‐chip PLOR platform in which reagents are driven by constant‐pressure pumps and delivered into reaction chambers via pneumatic valves. This system is capable of PLOR on any DNA template by pausing transcription at defined positions and incorporating user‐selected modified nucleotides. In this study, 5‐aminoallyl‐UTP was incorporated and subsequently fluorescently tagged, as demonstrated by pausing a custom 69‐nt RNA at positions 11 and 12 for site‐specific labeling. By eliminating manual pipetting, reducing dead volume, and enabling high‐throughput operation, our platform provides a robust, scalable solution for reproducible RNA synthesis and labeling, paving the way for integrated biosensing, single‐molecule fluorescence, and advanced structural studies.NIH R01HG013861Master of Science in Chemical Engineering (MSChE)2026-09-0
FABRICATION REIMAGINED: TRANSFORMING FAST FASHION INTO SUSTAINABLE BUILDING MATERIAL
No full textFast fashion is the mass production of clothes that represent the latest trends at high speeds and low costs to maximize profits. The fashion industry, particularly the fast fashion sector, has become a symbol of environmental degradation, contributing significantly to pollution and waste. However, these challenges present a unique opportunity for innovation. This project explores the potential of repurposing fast fashion textile waste into sustainable building materials, addressing the environmental concerns associated with the fashion industry while meeting the growing demand for eco-friendly construction solutions. By adopting an interdisciplinary approach, this study seeks to establish a connection between the construction and fashion industries by converting waste from fast fashion into long-lasting building materials like interior finishes, acoustic panels, and insulation.
Fast fashion has a well-documented negative impact on the environment, with resource depletion, water pollution, and overflowing landfills being the main concerns. Most garments take over 200 years to decompose in landfills, yet only 15% of textile waste is currently recycled. (Cho, 2021; Noble, 2024) highlighting the urgent need for better waste management strategies. Despite the awareness of these issues, there is a noticeable gap in practical solutions that recycle or upcycle textile waste effectively. This study proposes a fabric recycling plant that transforms textile waste into architectural materials. Using a fluid, fabric-based system designed for integration into buildings with an emphasis on reuse and adaptability.
I approach this challenge with a dual perspective, having been a fast fashion consumer, as most people are, as well as an advocate for sustainable building materials. This allows me to fully grasp the opportunities and challenges facing both industries. The transformation of fast fashion waste into building materials represents a modern solution to the contemporary problems of waste and environmental degradation. This research holds the promise of not only reducing textile waste but also reshaping industries, fostering a more sustainable future, and turning the byproducts of consumerism into the building blocks of tomorrow.Master of Architecture (MArch
PARAMETRIC PRAGMATISM: TRANSFORMING BUILDING USE AND FACADE FOR SUSTAINABLE REUSE
No full textThe urgency of addressing climate change has become increasingly apparent, driven by the excessive amounts of carbon dioxide (CO2) that directly impact both the natural and built environments (Sijakovic and Peric 2021). The pressing evidence of climate change compels architects and engineers to rethink conventional approaches, positioning computational modelling and simulation approaches as a transformative solution that balances aesthetic innovation with environmental responsibility (Kabošová, Katunský, and Kmet 2020). In response, this thesis explores the concept of Parametric Pragmatism as a solution-oriented approach to sustainable architecture. In this thesis, I intend to utilize parametric design methods, specifically in optimizing building facades, to create environmentally responsive architectural solutions that significantly reduce carbon emissions and enhance energy efficiency and improve aesthetics of the building. In response, this thesis explores the concept of Parametric Pragmatism as a solution-oriented approach to sustainable architecture.
Retrofitting existing downtown buildings plays a critical role in reducing embodied carbon—the carbon emissions associated with material extraction, manufacturing, and construction—by extending the life of existing structures rather than demolishing and rebuilding. Many buildings constructed during the 1960s–1980s have inefficient facade systems that not only lead to high operational carbon emissions but also limit interior flexibility by enforcing deep floor plates with poor daylighting and ventilation, constraining opportunities for diverse programmatic uses. Instead of demolishing these structures and triggering the carbon-intensive processes required to construct new buildings, retrofitting facades and reusing existing structural systems can significantly reduce embodied carbon while revitalizing urban areas. Facade retrofitting not only improves thermal performance but also redefines a building’s interface with its environment by balancing key parameters such as solar radiation control, daylight access, building reprogramming in response to solar and daylight simulations, and the variation of monotonous facades. This process requires navigating tradeoffs between operational energy reductions and the embodied carbon of new materials, ensuring that performance gains justify the retrofit’s environmental and structural costs. Additionally, the post-COVID rise in commercial real estate vacancies offers an opportunity to repurpose underutilized buildings for mixed-use development, addressing both the commercial crisis and urban housing shortages.
Modern buildings have evolved into complex entities where advanced technologies and diverse programmatic requirements must seamlessly integrate to fulfil various functions, from energy efficiency and structural integrity to accommodating multiple uses within a single space. To meet these demands, new computational techniques have been developed to facilitate the design of such intricate structures, establishing a quantitative relationship between the environment and the building envelope (Eltaweel and Su 2017). This thesis draws from studies on parametric design and contemporary building envelope technologies to explore how data-informed strategies can optimize performance, enhance adaptability, and address the evolving challenges of sustainable architectural retrofits
By focusing on retrofitting structurally sound, late 20th-century buildings, this research demonstrates how the innovative application of energy conversion materials and other technological advancements can significantly reduce embodied carbon emissions, improve energy efficiency, and elevate aesthetic appeal beyond the limitations of current "glass box" commercial buildings. These buildings often present a monotonous, sterile appearance, lacking in visual engagement and contributing to heat gain and energy inefficiency. Through parametric design, retrofitted buildings not only enhance environmental performance but also bring a renewed aesthetic that engages the public and integrates with diverse urban settings. Integrating adaptive and responsive facade strategies into retrofitting enhances public engagement with sustainability efforts by visibly demonstrating environmental performance. Such approaches break down the homogeneity of glass-box towers, allowing the building envelope to respond dynamically to environmental conditions, contextual cues, and diverse programmatic needs fostering a more vibrant, functional, and resilient urban fabric.Master of Architecture (MArch
He Kura Tūroa Film
No full textIn February 2025, our Huliauapaʻa ʻohana and community partners from across the pae ʻāina of Hawaiʻi and Micronesia participated in a wānanga (traditional learning hui) hosted by our Māori whanau and partners of Mātangireia Waka Trust.
This material is based upon work supported by the U.S. National Science Foundation Center for Braiding Indigenous Knowledges and Science under Award No. 2243258. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundation.This material is based upon work supported by the U.S. National Science Foundation Center for Braiding Indigenous Knowledges and Science under Award No. 2243258. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundatio
Metabolic Contributions to Primate Brain Evolution: Insights from Molecular and Functional Analyses
No full textThe goal of this dissertation work is to characterize the metabolic evolution of the primate brain and to further understand how metabolism has contributed to broader phenotypic divergence among primates. It is well understood that the human brain is larger and more metabolically expensive than the non-human primate brain. However, critical gaps in knowledge persist in the understanding of how particular metabolic pathways, cell types, and gene regulatory networks may have evolved to support the unique development, plasticity, and cognitive capacity of the human brain. Additionally, limited sampling and comparative data from a broad range of non-human primates hinders our ability to distinguish human-specific changes from more general primate patterns in brain evolution.
The data presented in this dissertation address several of these gaps in knowledge: we examine gene expression differences across eighteen primate species in four major brain regions and further discuss the expanded role of the cerebellum in the evolution of uniquely human cognition. We also analyze primate brain evolution at the level of different cell types using iPSC-based models, identifying specific metabolic pathways that vary across neural cell types and species.
Together, these studies reveal specific metabolic mechanisms that contribute to species-specific features of the primate brain. More broadly, this work underscores the value of integrating evolutionary perspectives into neurobiology and highlights how these metabolic divergences may offer new insights into the unique vulnerability of humans to neurodevelopmental disorders and neurodegenerative disease.Doctor of Philosophy (Ph.D.)2026-09-0
AI-ACCELERATED OPERATOR LEARNING FRAMEWORK FOR RAREFIED MICROFLOWS
No full textThe high computational cost of kinetic solvers such as DSMC remains a major challenge in rarefied flow simulations. This work presents a unified framework combining deep neural networks and neural operators to accelerate kinetic and hybrid solvers while preserving physical fidelity. GPU-native DNN surrogates eliminate costly moment-closure operations in Fokker–Planck methods, achieving significant speedups without accuracy loss, while physics-guided and shock-aware DeepONet architectures enable accurate, data-efficient modeling of multi-regime micro-nozzle, micro-step, and hypersonic flows. Extensions including ensemble uncertainty quantification and family-of-experts strategies further enhance robustness across wide Mach and Knudsen number ranges. Together, these results demonstrate a scalable and physics-consistent pathway toward real-time surrogate modeling in rarefied gas dynamics
Parsing the Within- and Between-Therapist Positive Regard-Outcome Association in Cognitive-Behavioral Therapy for Generalized Anxiety Disorder
No full textPositive regard—rated from multiple perspectives across various psychotherapies—correlates positively with patient improvement. Yet, existing research has not parsed this total correlation into its within- and between-therapist components, which limits its interpretability. Thus, the present study explored (a) the association between patients’ experience of therapist-offered positive regard and their treatment outcome at both the within- and between-therapist levels, (b) whether between-therapist differences in positive regard moderated the within-therapist positive regard-outcome association, and (c) whether treatment condition (cognitive-behavioral therapy [CBT] versus CBT that integrated client-centered principles) moderated either level of the positive regard-outcome association. Adults with generalized anxiety disorder were randomly assigned to CBT alone (n = 43) or CBT integrated with motivational interviewing (MI-CBT; n = 42) to responsively address patient resistance (Westra et al., 2016). Twelve therapists treated patients in CBT and nine distinct therapists treated patients in MI-CBT. Patients rated therapist-offered positive regard repeatedly across 15 sessions and their worry and general distress outcomes at baseline and posttreatment. Multilevel structural equation modeling revealed a significant association between patients’ experience of higher early treatment positive regard and lower posttreatment general distress at the within-therapist level (this effect was similar for worry, though nonsignificant). There was no between-therapist association for either outcome. Additionally, neither between-therapist positive regard nor treatment condition moderated the within-therapist effect of positive regard on either outcome. Results underscore the value of therapists working to foster their patients’ felt regard irrespective of the treatment they use or the general ability they have in cultivating this relational experience.Master of Science (M.S.
Interactions of per-and-poly fluoroalkyl substances (PFAS) with the Aryl hydrocarbon receptor (AHR) pathway and larval toxicity in zebrafish (Danio rerio)
No full textPolycyclic aromatic hydrocarbons (PAHs) are a class of chemicals frequently produced by combustion and industrial processes. They are frequently present in drinking water, and many are both carcinogenic and developmentally toxic. Several interact with the aryl hydrocarbon receptor (AHR), which regulates gene expression responses to xenobiotic exposure. Increased expression of cytochrome P450 (CYP) family 1 genes contribute to clearance and metabolism of some xenobiotics. Per- and poly- fluoroalkyl substances (PFAS) are persistent environmental contaminants widely produced for uses as surfactants, nonstick coatings, and in firefighting foams. They are also often present in drinking water and are developmentally toxic. Several PFAS have been shown to interact with both CYP proteins as well as the AHR, raising the question of whether mixtures of these chemicals as seen in the environment may be more toxic than each chemical individually. However, PFAS interaction with CYPs and AHR is not well explored. This work aims to investigate the interactions between PFAS and the AHR response to xenobiotics as well as associated developmental toxicity of these substances. Transgenic, fluorescent reporter zebrafish were exposed to PFAS and beta-naphthoflavone (an AHR agonist) mixtures from 24-100 hours post fertilization; then, fish were assessed for morphology, CYP1A-like-acitivity, pancreatic and liver development, and gene expression. Co-exposures of the 8-carbon, sulfonated perflourooctane sulfonate (PFOS) and beta-naphthoflavone were found to significantly reduce fish length, increase pericardial area, and decrease CYP1A-like activity compared to the same level of beta-naphthoflavone exposure alone; expression of the related cyp1a gene was also reduced by co-exposure. In contrast, the 6-carbon perflourohexane sulfonate (PFHxS) did not significantly affect pericardial area or CYP1A-like activity in co-exposures, and cyp1a expression was instead increased. PFOS was also found to inhibit the catalytic activity of human CYP1A1 enzyme ex vivo. Many PFAS were found to have affinity for CYPs as well as nuclear receptors and other proteins related to AHR via in silico molecular docking as well as structural predictions. Thus, this study suggests PFAS and PAH mixtures may be more toxic than either individually, and provides insights into the molecular mechanism for PFAS interactions with AHR.Funding for this work was provided by the National Institutes of Heath (R01ES025748 to ATL)Master of Science (M.S.)2026-09-0
