VictorJuiz/thesis huggingface dataset:
Mechanical force sensing drives extrusion of Enterovirus-A71-infected cells from colonic epithelial organoids

Enterovirus A71 (EV-A71) can cause severe disease upon systemic infection, sometimes leading to severe neurological dysfunction. However, in most cases infection is limited to the gastrointestinal tract, where virus is amplified for transmission. In this work described in this thesis, we sought to utilize three-dimensional epithelial organoids generated from crypt stem cells of healthy patient colon tissue (colonoids) to investigate viral spread through the gastrointestinal epithelium, the tissue most relevant for viral transmission. Chapter 1 introduces the reader to the viral and tissue model systems relevant for this work. In Chapter 2, the generation and characterization of an apical-out, differentiated colonoid model for EV-A71 infection is described. Chapter 3 details the surprising phenomenon of whole-cell extrusion of virus-infected cells from intact colonoids, including the timing and frequencies of these events. Poliovirus-infected cells were also readily observed extruding from gastrointestinal organoids, suggesting this phenomenon occurs during infection with multiple Enterovirus species. Chapter 4 explores the mechanism for extrusion of EV-A71-infected cells and the identification of mechanical force-sensing ion channels as required for the removal of infected cells from organoids. Finally, in Chapter 5 we explore the potential benefits of extruding a virus-infected cell for both the virus and the host. We find the extruded cells themselves are infectious, capable of initiating new infections in both monolayers and colonoid cultures. These results suggest a novel mechanism for extrusion of live, virus-infected cells through mechanical cell compression forces. In the gastrointestinal tract, apically extruded cells are released into the lumen of the gut and eventually excreted in feces; therefore, extruded infected cells likely contribute to virus spread both throughout an infected host and between hosts

Keywords: Microbiology and Immunology.
Advisor: Kirkegaard Karla
Amieva Manuel
Carette Jan
Li Jin (Billy)
Mechanics of epithelial cell division

Epithelial cells undergo striking morphological changes during division to ensure proper segregation of genetic and cytoplasmic materials. These morphological changes occur despite dividing cells being mechanically restricted by neighboring cells, indicating the need for extracellular force generation. Beyond driving cell division itself, forces associated with division have been implicated in tissue-scale processes, including development, tissue growth, migration, and epidermal stratification. In this dissertation, I focus on understanding how dividing cells generate forces to drive the morphological changes necessary for cell division, in epithelial tissues and single-cell contexts. While forces generated by mitotic rounding are well understood, forces generated after rounding remain unknown. I identify two distinct stages of division force generation that follow rounding: (1) Protrusive forces along the division axis that drive division elongation, and (2) outward forces that facilitate postdivision spreading. Cytokinetic ring contraction of the dividing cell, but not activity of neighboring cells, generates extracellular forces that propel division elongation and contribute to chromosome segregation. Forces from division elongation are observed in epithelia across many model organisms. In the second part of my dissertation, I discuss improvements made to a custom-built atomic force microscope with side- and bottom-view imaging paths. I use this instrument to measure the mechanical properties of dividing cells. In summary, we find that cells generate extracellular forces to drive cell division, and this represents a universal mechanism in confining environments

Keywords: Mechanical Engineering.
Advisor: Chaudhuri Ovijit
Dunn Alexander Robert
Levenston Marc Elliot
A mechanism design perspective on firms and market power

Each chapter of this PhD dissertation develops new mechanism design techniques to study the following three economic problems relating to firms with market power: (i) optimal pricing and product design (Loertscher and Muir, 2021), (ii) optimal wage-setting and employment decisions (Loertscher and Muir, 2022), and (iii) optimal contracting by an input supplier and the decision of whether or not to offer a competing downstream product (Kang and Muir, 2022). The first chapter (Loertscher and Muir, 2021) considers the welfare implications of underpricing and rationing by a monopoly seller. These practices are considered something of a puzzle among economists. They are frequently observed in markets for perishable goods and often give rise to resale markets. This chapter develops a coherent model of these phenomena and deepens our understanding of the likely impact of policies such as the BOTS (Better Online Ticket Sales) Act, which reduces the efficiency of resale markets without banning them entirely. The second chapter of this dissertation (Loertscher and Muir, 2022) studies the implications of minimum wage policies when employers have market power. While the textbook model of a perfectly competitive market suggests that introducing a minimum wage can only reduce employment, it is well-known that imposing a minimum wage on a monopsony employer can increase employment. This chapter seeks to provide regulators with clearer guidance by showing how measures such as wage dispersion, efficiency wages and involuntary unemployment can be used to predict the implications of an increase in the minimum wage for employment. The third chapter (Kang and Muir, 2022) of this dissertation focuses on the antitrust implications of platforms that use their own marketplaces to sell in-house products. A natural example of such a platform is Amazon, which sells e-commerce and distribution services upstream, as well as its own private-label products downstream. In this chapter we adopt a mechanism design approach to characterize the optimal menu of contracts that dominant platform offer in upstream markets. Our main result then shows that consumers always benefit from the platform's decision to offer a competing product downstream. Consequently, antitrust laws prohibiting platforms from selling their own private-label products, such as those recently implemented in India, can harm consumers

Keywords: Economics.
Advisor: Milgrom Paul R. (Paul Robert)
Akbarpour Mohammad
Segal Ilya
Mechanisms of dendrite morphogenesis

Dendrite morphogenesis is a critical developmental process that establishes the architecture and function of neural circuits. Outgrowing neurites are guided by a variety of extracellular cues that are recognized by guidance receptors on the surface of the cell, which in turn modulate intracellular signaling pathways and cytoskeletal regulators to mediate changes in cell morphology. The regulation of these guidance receptors allows for correct pathfinding and efficient outgrowth. However, the precise mechanisms linking guidance receptor-ligand interactions to changes in the cytoskeleton, and their regulation, are not fully understood. Using the highly branched dendritic arbor of the PVD neuron in C. elegans as a model system, we identified a proteolytic cleavage event that regulates guidance receptor localization to promote dendrite outgrowth. We showed that the Furin homolog KPC-1 cleaves the co-receptor HPO-30, previously shown to form a complex with the guidance receptor DMA-1. This cleavage event is necessary for formation of higher order dendrites in PVD. Furthermore, we show that this cleavage event promotes the internalization of DMA-1 from the plasma membrane into RAB-10-positive recycling endosomes, and that excess DMA-1 on the membrane is associated with overstabilization of dendrites and reduced outgrowth. Our work reveals a mechanism by which guidance receptor localization is controlled in order to promote dendrite outgrowth. In addition, during development, neurons must coordinate various cytoskeletal regulators that work together to create structured actin networks during dendrite morphogenesis. Here, we showed that outgrowth of the PVD neuron occurs through localized expansions in the dendrite (termed "swellings") at branch initiation sites, followed by the rapid extension of thin filopodia from these swelling sites. The formation of filopodia required UNC-115/abLIM, an actin-binding LIM protein, and UNC-34/Ena/VASP, which promotes the extension of linear actin bundles. On the other hand, the formation of both swellings and filopodia depends on the WAVE Regulatory Complex (WRC), which promotes the formation of branched actin networks. We therefore propose that, following guidance receptor activation, WRC creates local branched actin networks at swellings that stochastically specify sites of new dendritic branches. UNC-34 and UNC-115 are then recruited to bundle actin filaments and create filopodia that initiate these new dendritic branches. In summary, dendrite morphogenesis requires regulation of guidance receptors and their down-stream signaling pathways. We have identified a co-receptor cleavage event that regulates guidance receptor localization to allow both dendrite outgrowth and stabilization, as well as a mechanism that coordinates cytoskeletal changes downstream of guidance receptor signaling

Advisor: Shen Kang
Luo Liqun
Shah Nirao
Südhof Thomas C.
Mechanisms of mutant huntingtin quality control and the impact on cellular proteostasis in Huntington's disease

Huntington's Disease is a neurodegenerative disorder characterized by a genetic mutation that expands a CAG trinucleotide repeat in exon 1 of the huntingtin gene resulting in a lengthened polyglutamine stretch. Importantly, the genetic neurodegenerative disorder Huntington's Disease shares key characteristics with other neurodegenerative diseases, including misfolded protein pathology and aberrant endolysosomal pathway function. While Huntington's Disease genetics pinpoints the underlying cause of disease, mechanisms of neurodegeneration and disease biology remain unclear. Many studies have highlighted a loss-of-function or gain-of-function caused by the mutant huntingtin protein, which has diverse cellular roles. However, rarely are both loss-of-function and gain-of-function aspects considered together. In this work, we aim to investigate altered huntingtin functions by comparing the in-cell protein-protein interactions of an exon 1 mutant huntingtin to exon 1 of the wild-type protein. We discover a gene set involved in the endolysosomal pathway that is highly specific to mutant huntingtin. We map endosomal interaction back to full-length huntingtin function, and show wild-type huntingtin and mutant huntingtin have fundamentally different interactions with endosomal membranes. These interactions highlight a novel VPS4 mediated protein quality control pathway we propose for regulating mutant huntingtin. Importantly, mutant huntingtin's altered endosomal interaction can be described by both a loss-of-wild-type-function and gain-of-mutant-function, which we correlate with widespread defects in endolysosomal pathway function. Ultimately, we propose a link between endolysosomal defects and the Huntington's Disease mutation, which provide mechanistic insight to disease relevant biology and inform potential therapeutic avenues

Keywords: Biology.
Advisor: Frydman Judith
Abu-Remaileh Monther
Gozani Or Pinchas
Ting Alice Y.
Mechanisms of neural communication predicted from computational modeling of healthy and pathological brain circuits

The topics of memory processing and epilepsy are investigated through computational modeling with the overarching goal of predicting novel mechanisms that can be experimentally verified via a number of genetic, electrophysiological, and imaging methods. Specifically, we leveraged biophysically detailed and more abstract machine-learning inspired modeling approaches through the development of 1) a microcircuit model of hippocampal CA3 and 2) a novel computational pipeline that can infer and mine the higher-order organization of large-scale epileptic circuits built from single cells. Simulations from these computational models predicted a critical role for inhibitory plasticity to perform 'world inference learning' by filtering out irrelevant stimuli during circuit processes associated with spatial navigation, and predicted a novel functional cell type - the superhub cell - that preferentially emerges in the preseizure brain and can propagate excitatory activity downstream with high fidelity. Critically, as patients with epilepsy often exhibit cognitive comorbidities including memory dysfunction, deeper understanding of these topics has potential to drive more holistic strategies for intervention that include both seizure reduction and normalization of computational processes associated with memory

Keywords: Bioengineering.
Advisor: Soltesz Ivan
Druckmann Shaul
Nuyujukian Paul Herag
Mechanistic & spectroscopic studies on O2-activation and reactivity by coupled binuclear copper enzymes

Coupled binuclear copper (CBC) enzymes constitute a major family of O2-activating metalloenzymes that catalyze a wide range of oxidation and oxygenation reactions. The most predominant member of this enzyme family, tyrosinase (Ty) in its dicopper(I) reduced form (deoxy-Ty) binds O2 to form a μ-η2:η2-peroxide dicopper(II) intermediate (oxy-Ty) that can monooxygenate para-substituted monophenols to catechols, which in its native function constitutes the initial step in melanin biosynthesis in a wide range of organisms, from soil bacteria to humans. The mechanism of this important monooxygenation reaction has not been fully understood, with its key reaction intermediates remaining elusive. This thesis presents advancements in defining the monophenol monooxygenation mechanism of Ty by (i) trapping and spectroscopically characterizing key reaction intermediates, (ii) investigating their reactivity by kinetic methods, and (iii) correlating experimental results to quantum-mechanics/molecular-mechanics (QM/MM) calculations. Analysis of our experimental and computational results provides a molecular-level definition of the reaction coordinate for the monophenol monooxygenation reaction of Ty. This mechanism is different from the general paradigm based on previous model complex studies and provides new insights into how Nature employs Cu2O2 active sites to perform enzymatic catalysis

Keywords: Chemistry.
Advisor: Solomon Edward I.
Cegelski Lynette
Stack T. (T. Daniel P.)
Mediatizing terrorism : a study of audiences' construction of violent events under datafied capitalism

This dissertation studies the circulation of transnational mobile media accounts of terror attacks in order to examine the intersection of violence, liberalism, anti-Muslim racism, and authoritarianism as it is transformed in the data-driven political economy of communication. The dissertation's central question asks: how is mediatized terrorism encountered, made sense of, and responded to by mobile audiences in datafied media? To answer, I use a new method for digital observation that collects screenshots from participants' mobile devices every five seconds for longitudinal studies. Through observation of U.S. mobile media users' reception of a wave of Daesh-linked terror attacks in Europe and North Africa in the spring of 2017, I identify four mediatized rituals responding to these attacks. One ritual, specific to far-right ecosystems, assimilates attacks and unrelated social conflict into an imagined future of what liberal pluralism portends, creating the possibility for offline action stoking cycles of violence. The other observed responses constitute a limited suite of individualized responses that are habituated by the data-driven political economy of mobile media. These findings contrast with prominent critiques of social media (e.g., polarization) by highlighting the distinct threat posed by ritual action in far-right mobile media. This analysis also adds nuance to disinformation frameworks that abstract users' construction of reality from their mediatized social contexts and cultural practices. The conclusion proposes developing a decolonial global media technology ethics based on these findings that mobilizes media against persistent orientalism and far-right authoritarianism in the global political landscape emerging under datafication

Keywords: Communication.
Advisor: Glasser Theodore L.
Hamilton James
Turner Fred
Wang Ban
Memory Politics in Independent Kazakhstan: The Great Famine and National Identity

Stalin’s collectivization policies created a famine that killed around 1.5 million people in Soviet Kazakhstan from 1932 to 1933. However, the Kazakhstani state remains reluctant to incorporate the famine into official historical narratives and marginalizes public discourse about this period of history. This paper analyzes the evolution of official rhetoric about the 1932-33 famine from 1991 to today as a lens through which to understand elite-level political concerns behind national identity building in Kazakhstan. I find that an instrumental relationship to history and political expediency governs debates about the famine in Kazakhstan, including the desire to create a civic “Kazakhstani” national identity and concerns about Russia’s stake in Kazakhstan’s memory politics.

Keywords: Kazakhstan
Famines
Memory
Memory > Political aspects
Nazarbaev, Nursultan
Tokaev, K. K. (Kasymzhomart Kemelevich)
Central Asia
Kazakh-Russian relations
Text
Thesis
Advisor: Naimark Norman
Weiner Amir
Mesenchymal Stromal Cells Rescue Hypoxia-Induced Survival Defect in Ex Vivo Acute Myeloid Leukemia Cell Cultures

Acute myeloid leukemia (AML) is an aggressive cancer characterized by the clonal accumulation of immature blood cells. The cancer stem cell model hypothesizes that healthy hematopoietic stem cells (HSCs), which populate the entire blood compartment, acquire lesions over time and become leukemia stem cells (LSCs). These mutant cells are responsible for disease progression and act as a reservoir of cancer-forming cells following chemotherapy, causing relapse. In healthy hematopoiesis, mesenchymal stromal cells (MSCs) in the oxygen-poor bone marrow microenvironment are the niche for HSCs, providing factors to maintain and regulate self-renewal and multipotency. Current efforts seek to understand the role of the niche in aberrant hematopoiesis. While efforts to replicate human disease are aided by the in vitro study of primary AML patient sample cells (APSCs), these studies do not typically recapitulate the presence of MSCs or the hypoxic conditions of the niche. I found that hypoxia decreases APSC growth, but this defect can be rescued in a non-contact-dependent manner by co-culture of APSC with MSC or culture of APSC in MSC-conditioned media (CM). Cytokine detection analysis showed that MSC-CM contained high levels of cytokines whose transcripts are also highly expressed in primary MSCs from healthy donors. Although no singular tested cytokine was necessary for APSC survival, I determined that the expression of cytokines and receptors can independently cluster healthy and leukemic cell subsets. Therefore, cytokine combinations may contribute to APSC survival. Collectively, these results show that MSCs are sufficient to enhance APSC survival in physiologic hypoxia. The niche-like ex vivo model I established will enable the translation of laboratory findings into clinical applications.

Keywords:  Department of Biology
Biology
Acute myeloid leukemia
Cancer
Hematopoiesis
Microenvironment
Niche
Conditioned media
Cytokines
Personalized medicine
Drug discovery
Stem cells
Hypoxia
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Thesis
Advisor: Majeti Ravindra
Cyert Martha
Metabolic reprogramming during breast cancer progression

Cancer cells exhibit altered nutrient requirements and utilization compared to normal cells. A comprehensive understanding of the causes and consequences of these altered metabolic features can help inform the development of novel therapeutics aimed at impairing cancer cell proliferation and promoting differentiation, in addition to enriching our understanding of how cancer comes to be. In this thesis, we utilized breast cancer as a model to study how altered cell metabolism relates to differences in proliferative capacity and cell lineage identity. Using a targeted metabolomics approach, we discovered a metabolic signature suggestive of elevated serine and one-carbon (1C) unit metabolism in the aggressive, tissue-tropic metastatic subpopulations of triple-negative breast cancer cells. In line with previous reports, we confirmed a role for the oncogene c-Myc in driving the enhanced proliferation of the metastatic subclones compared to parental cells. Functional validation using genetic and pharmacologic inhibition approaches uncovered an exquisite dependency of metastatic cells on this mitochondrial pathway for growth in vitro and in vivo. Analyses of human breast cancer patient data further identified a significant association between high expression of mitochondrial serine and 1C unit pathway genes with patient mortality. In follow-up work, we determined that low serine levels drives a metabolic signature associated with breast cancer cell aggressiveness characterized by the transcriptional induction of genes involved in de novo serine synthesis and mitochondrial serine and 1C unit metabolism. A global transcriptome analysis uncovered serine starvation-mediated repression of estrogen receptor (ER) signaling in ER+ breast cancer cells, effectively converting them to an ER-- like state. Metabolomics, isotope tracing, and chromatin immunoprecipitation assays revealed a defect in glucose-derived central carbon flux leading to a loss of histone acetylation and silencing of ER pathway genes. Acetate supplementation rescued histone hypoacetylation and ER pathway activity, demonstrating that serine starvation influences breast cancer cell state through a metabolic and epigenetic regulatory axis

Advisor: Rankin Erinn
Ye Jiangbin 
Gozani Or Pinchas
Oro Anthony
Plevritis Sylvia