Transcription is tightly regulated to ensure genes are appropriately expressed both temporally and spatially. This tight regulation governs various processes within the cell, such as differentiation and cell identity, cellular maintenance, and dynamic responses to external signals. Transcription factors (TFs) coordinate these various gene programs and in particular, are key...
This dissertation presents two projects with the goal of understanding how to quantitatively describe biological data, particularly data that is highly dynamic. The first study presents an improved quantitative tool for the analysis of particulate trajectories. Particulate trajectory data appears in several different biological contexts, and the majority of analyses...
Endothelial cells (ECs) require glycolysis for proliferation and migration during angiogenesis; however, the necessity for the mitochondrial respiratory chain during angiogenesis is not known. In this study, we report that inhibition of respiratory chain complex III impairs proliferation, but not migration of ECs in vitro by decreasing the NAD+/NADH ratio....
Herpes simplex encephalitis (HSE) is a rare and severely debilitating life-threatening disease caused by herpes simplex virus type 1 (HSV-1) infection of the human central nervous system (CNS). The severe and often fatal outcomes of HSE contrast starkly with the more frequent and largely benign consequences of herpes labialis. Whole...
Rhythmic oscillations in the brain are widespread. Extracellular recordings of local field potentials (LFPs) using methods ranging from microelectrodes to scalp electroencephalography (EEG) have demonstrated that oscillatory dynamics play a vital role in operations such as network synchronization, sensory tuning and information packaging. Empirical and computational evidence suggest that these...
Biomass has the potential to be our country’s leading renewable source of energy. Specifically, fast pyrolysis is a promising method for the conversion of biomass to valuable fuels and chemicals. Given that fast pyrolysis has a residence time of about two seconds, computational methods are particularly useful in obtaining product...
Quantum technologies have the capability of greatly increasing the security of communication systems. Many components are required for a full quantum network including memory, repeaters, routers, and detectors. The efficiencies of quantum communication technologies suffer greatly due to their inherent sensitivity to loss. Low-loss propagation and high detection efficiency can...
Newcomers, or new members to organizations or professions, bring insights that are critical to the advancement of society. Yet newcomers often have low self-efficacy, or low beliefs in their abilities to achieve a task, which can impact performance and retention. Research suggests that self-efficacy can be developed through in-person social...
Economic and political processes are heavily intertwined. Political processes put constraints on economic activity while economic development influences the way the political system operates. This interconnection is especially tight in developing countries and transition economies with less secure property rights, less stable political institutions, and more rapid economic changes. In...
Cancer progression is a complex process, leading to metastatic spread of primary tumor cells that colonize distant vital organs and mortality if not stopped. Since clinical strategies to stem this progression are still being developed, it is of great importance to detect this end stage metastatic spread as early as...
End-stage renal disease, or kidney failure, can result from acute kidney injury or sustained kidney damage in the form of chronic kidney disease. As the prevalence of end-stage renal disease continues to rise, the gold-standard treatment—kidney transplantation—is increasingly restricted by the shortage of transplantable donor kidneys. Bioengineered kidney tissues may...
The structural aspects of biological systems are tightly paired with their functions. This understanding has been demonstrated over a broad range of length scales, spanning the ultrastructure of a cell to the macroscopic architecture of organs. Connecting structure and function relies on the integration of physical and biological sciences to...
Organic semiconductors are an active area of research with great promise for delivering next generation electronics and clean energy technologies. As the field matures, understanding the connection between molecular structure, materials’ properties, and device performance will be critical in finding the right material for an intended application. An effective strategy...
Supported transition metal oxides are an important class of catalysts with a wide range of industrially relevant applications. However, commonly used synthesis techniques to prepare these catalysts often result in a complex mixture of surface species. This inhomogeneity makes it difficult to understand what specific structures might be responsible for...
This dissertation combines perspectives from social networks and teams research to advance understanding of team self-assembly. Across three substantive chapters, I explore team member search behaviors and invitation patterns in contexts where individuals exercise agency to select team members. First, I consider the search for team members in a social...
Frontotemporal dementia (FTD) encompasses a group of neurodegenerative disorders characterized by cognitive and behavioral impairments. Heterozygous mutations in progranulin (PGRN) cause familial FTD and result in decreased PGRN expression, while homozygous mutations result in complete loss of PGRN expression and lead to the neurodegenerative lysosomal storage disorder neuronal ceroid lipofuscinosis...
Responsiveness -- the time it takes for a message recipient to respond to a message -- has long been of interest to scholars in the fields of computer-mediated communication and human-computer interaction. It has been hypothesized that responsiveness is used to signal emotional information, and many empirical studies have demonstrated...
Abstract The work presented in this dissertation addresses three broad areas of video signal processing: video transmission, motion estimation and error concealment. In the first category, focused on the source-side, we present two machine learning models for efficient content-aware resource allocation and packet prioritization for video transmission over shared/constrained, lossy...
Glioblastoma (GBM) is a highly malignant brain tumor that accounts for the most commonly diagnosed type of primary brain tumors in adults. It has a poor prognosis of only 15 months from the time of diagnosis. The gold standard therapy regimen consists of radiotherapy and the chemotherapeutic temozolomide. Both of...
This dissertation focuses on two topics: macroeconomic implications of consumer inertia, and sovereign debt. In Chapter 1, I explore the role of consumer inertia---persistence in households' consumption choices---as a driver of the rise in corporate profits and decline in the share of young firms in the US economy during the...
Microfluidic technologies enable multi-tissue culture and precise control of media exchange and therefore have significant potential to create more complex in vitro models of reproductive systems, including endocrine cycles. However, microfluidic technologies have largely been applied to gamete-level culture in reproductive biology, with very little progress in organ-level culture. Herein...
Pathogenic bacteria scavenge essential nutrients including metals, amino acids and peptides to survive within the hostile host environment. Bacteria utilize ATP-binding cassette (ABC) transporters, powered by the energy of ATP hydrolysis, to move substrates across cellular membranes. The substrate-binding protein (SBP) shuttles substrate in the periplasm and directs the substrate...
A functional democratic society rests on the premise that the mass public holds clear preferences for policies, candidates, and more. To arrive at these preferences, many citizens rely on their social identities, making political decisions based on what they see as benefitting the groups to which they belong. They may...
In an 18-month ethnographic and interview-based study of Afghan Americans in the greater Bay Area, California, I explore the relationship of culture and religion amongst this refugee community. As a majority of refugees in the past decade have been Muslim, it is important to understand what their process of integration...
Methylation of histone 3 lysine 4 (H3K4) catalyzed by the COMPASS family of lysine methyltransferases is universally associated with eukaryotic transcription. However, despite thousands of published studies examining the deposition, dynamics, and genomic positions of this chromatin modification, there is no clear consensus as to the molecular function or biological...
Oocyte meiosis is a specialized, but error prone, form of cell division that is poorly understood. Errors during meiosis often result in aneuploidy, or abnormal chromosome number, that impacts human health and fertility. Aneuploidy is the leading cause of miscarriages and birth defects, such as Down's syndrome in which cells...
Visual matching is an important and fruitful research topic in computer vision area. Starting from the early face recognition, super-resolution, object tracking to the most recent person re-identification, cross-model retrieval, visual matching plays an important role as the core component in these tasks. The quality of visual matching directly and...
Emotion perception is multisensory and involves decoding and integrating input from both visual and auditory modalities. This dissertation investigates the influence of cultural and linguistic experience on multisensory perception of emotion. Experiment 1 examines the effect of cultural background on modality bias (i.e., the amount of influence a modality exerts...
The study of the translucent interstellar medium (ISM) is important for understanding the behavior of the ISM as it transitions from hot, tenuous gas to dense, star-forming regions. This regime is know to be associated with the initial formation of persistent molecular material, and thus represents the first stages of...
The rapid development of flexible electronics enables a huge amount of bio-integrated applications with advantages of the mechanical compliance, stretchability and comformability of the devices. My dissertation further advances this area by a series of projects, which include designing and optimizing novel compliant structures, proposing novel elastomer encapsulation process for...
Successfully grappling with the widespread linguistic variation of daily life requires speakers to adapt to systematic variation in the environment while discarding incidental variation, based on their prior experience. In the case of phonotactics, speakers’ prior experience is that talkers who differ in their language background are likely to vary...
Wastewater and bioreactors in wastewater treatment plants (WWTPs) are reservoirs for antibiotic resistance genes (ARGs), which can pass through treatment processes and migrate into the environment as they are released in effluent. WWTPs harbor a variety of ARGs that can be spread by horizontal gene transfer facilitated by mobile genetic...
Store-operated Ca2+ entry through Orai1 channels mediate transcriptional, proliferative, and effector cell programs in many cells and are activated through a unique inside-out mechanism involving binding of the endoplasmic reticulum Ca2+ sensor, STIM1, to cytoplasmic sites on Orai1. Mutations in Orai1 that block channel activation or evoke constitutive channel activity...
This dissertation explores hip-hop as a moral philosophy in action; a set of aesthetic and ethical values that manifest in young people’s perspective about the good life. Hip-hop is an arts movement of rap, movement, and style originating among Black and Latinx youth in the South Bronx during the late...
Numerous photophysical processes in both natural and artificial systems are dictated by the interaction between chromophores. For example, in photosynthesis, light is absorbed by an antenna complex composed of an array of chlorophyll chromophores that collectively transfer the energy to the reaction center where interactions between a series of redox...
Social comparison is a ubiquitous part of social life. People compare themselves to others to establish and maintain a sense of social hierarchy and structure, to develop and sustain interpersonal relationships, and even to help understand themselves. In this dissertation, I focus on how the referent of social comparison –...
The critical importance of alternative mRNA splicing and the RNA binding proteins that orchestrate this essential layer of post-transcriptional gene regulation is increasingly recognized in gene regulatory programs. We and others have shown that alternative splicing plays a causal role during the Epithelial-Mesenchymal transition, a cell-developmental program that is hijacked...
Viral Verses investigates the influence of social media publication on the relationship between poetry and community formation in southeastern Africa. As more artists in the global South reach wider audiences through online publication, poetic form has shifted to reflect social media’s aesthetic norms, embracing urgency, contemporaneity, and populism. Digital media...
Increasing industrialization and the resulting negative environmental impacts highlight the need to develop alternative renewable energy sources. The Sun is a massive source and organic solar cells are a growing field of study. As new materials are synthesized, the efficiencies of organic solar cells continue to grow, but without an...
Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique that can detect single molecules and simultaneously obtain structural information. When an analyte molecule binds to a nanostructured noble metal surface, the otherwise weak normal Raman signal is enhanced by as much as a factor of 108. This makes SERS the...
This work combines the use of high-throughput mass spectrometry with peptide arrays for to monitor reactions on peptides. The Mrksich lab introduced a high-throughput, label-free, biochemical assay that relies on self-assembled monolayers on gold and matrix-assisted laser desorption/ionization mass spectrometry, termed SAMDI-MS. This dissertation introduces new applications of SAMDI-MS and...
Organismal development depends upon countless cell decisions to adopt particular fates at the appropriate time and place. These decisions are executed by systems of biochemical reactions called regulatory networks. Elucidating the general principles underlying the structure and function of these networks is vital to understanding all developmental processes, as well...
This study examines how Latino migration politics developed in Chicago from the 1930s to the 1970s. Although scholars usually identify the emergence of Latino immigration activism in the 1960s and predominantly in the region of the Southwest with the farm workers movement, this study argues that immigration activism began much...
One of the grand challenges in materials chemistry and nanochemistry is the development of functional materials through ordered, hierarchical structures using synthetic building blocks. Nature has done this through evolution of molecular components such as nucleic acids, saccharides, lipids, amino acids, and inorganic crystals. The precise spatial positioning of these...
This thesis centers around the development and application of novel high throughput lithography tools. These advances help: 1) establish the field of nanocombinatorics, where massive libraries (termed megalibraries) of materials can be prepared in a positionally encoded manner and then screened for functional activity, and 2) advance stereolithographic 3D printing...
Type I interferon (IFN) is the primary antiviral cytokine establishing a broad and potent antiviral response to protect mammalian cells from virus infection. The functional repertoire of IFN extends to innate and adaptive immunity, neoplastic transformation, resistance and cancer immunotherapy. IFN functions are primarily mediated through the Janus kinase (JAK)...
This dissertation contains three empirical studies in economic history and labor economics. The first chapter discusses two sources of historical data on work stoppages in the United States: the Third Annual Report of the Commissioner of Labor (1888) and the Tenth Annual Report of the Commissioner of Labor (1896). It...
The vast majority of interactions between customers and service providers are experiences that extend over time. Service systems that deliver excellent customer experience achieve greater customer satisfaction and therefore customer loyalty, and eventually raise revenue. The temporal aspects of service delivery have not yet been analyzed as carefully as its...
Nanocarriers are nanometer-sized (1-1000 nm) structures capable of encapsulating cargo. This encapsulation can drastically alter the pharmacokinetic properties of the cargo, while also allowing for the rational design and engineering of the nanocarrier itself. Poly(ethylene glycol)-block-poly(propylene sulfide) is an amphiphilic diblock copolymer capable of self-assembling into diverse nanocarriers. The purpose...
Nanomaterials are broadly defined as materials that exhibit at least one dimension that is less than 1,000 nm. Encompassed within nanomaterials are a class of constructs known as nanocarriers, which are applied as delivery vehicles for both encapsulated and covalently bound payloads. Poly(ethylene glycol)-block-poly(propylene sulfide) (PEG-b-PPS) is an amphiphilic block...