VictorJuiz/thesis huggingface dataset:
Characterization of Immunity-related GTPase Q (IRGQ) as a Novel ATG8 Family Interactor
Keywords: ATG8
Fertility
Immunity-related GTPase
Innate immunity
IRGQ
Macroautophagy

Macroautophagy is a highly conserved catabolic process in eukaryotes in which cellular components are sequestered into autophagosomes for lysosomal degradation. My lab applied biotin identification (BioID) to known autophagy-related (ATG) proteins and identified IRGQ as a novel interactor of the ATG8 family, which are ubiquitin-like proteins required for autophagosome formation. IRGQ belongs to the immunity-related GTPase (IRG) family, which are interferon-inducible resistance factors against several intracellular pathogens such as Toxoplasma gondii. IRGQ is highly conserved in mammals, but its function remains unknown. My analysis revealed that IRGQ contains 5 potential ATG8 family-interacting motifs (AIMs). I showed that IRGQ interacts most strongly with the ATG8 family member γ-aminobutyric acid receptor-associated protein-like 2 (GABARAPL2) through its AIM1, while it interacts with the remainder of the ATG8s through AIM5. Localization studies demonstrated that IRGQ can colocalize with GABARAPL2 and, to a lesser extent, microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B). Although having strong interactions with multiple ATG8s, I showed that IRGQ doesn’t regulate basal or starvation-induced conjugation of ATG8 family members and autophagosome formation. Furthermore, I showed that IRGQ doesn’t play roles in three types of selective autophagy: xenophagy (Salmonella), aggrephagy (protein aggregates) and mitophagy (mitochondria). Recently, macroautophagy-independent functions have been described for ATG8s such as controlling exosome composition and biogenesis. I showed that IRGQ is secreted through exosomes in an ATG8-independent manner, but knockout of IRGQ doesn’t affect exosome biogenesis or exosomal sequestration of MAP1LC3B. I concluded that IRGQ is an exosomal cargo and may impact the composition of exosomes. I also examined the role of IRGQ in vivo using Irgq-/- mice. I tested the role of IRGQ in anti-bacterial immunity by using two infection models: Listeria monocytogenes and Citrobacter rodentium and found that Irgq-/- mice have normal resistance to these two bacteria. However, I discovered that Irgq-/- female mice have reduced fertility caused by defective activation of ovarian follicles accompanied by delayed clearance of corpus luteum. Furthermore, Irgq-/- male mice also display deficiencies in fear learning and memory. Thus, IRGQ may play important roles in animal behavior and female fertility that are worthy of future investigation.
Political Friendship: Liberal Notables, Networks, and the Pursuit of the German Nation-State, 1848-1866
Keywords: Friendship
German History
German Unification
Liberalism
Nationalism
Political Friendship

From the 1840s through the mid 1860s, a network of liberal academics, journalists, and artists across the German Confederation (1815-1866) formed close personal relationships with one another and with monarchs and state ministers. The resulting network rested on what contemporaries often called “political friendship.” My dissertation assesses how pro-Prussian liberals formed, maintained, and used these relationships in part to cultivate influence over leaders in Baden, Coburg, and Prussia. They sought to advance liberal policies and kleindeutsch national unification, largely parallel to such well-studied organizations as the Nationalverein. In the process, members of the liberal network shaped accommodations with conservative officials while demonstrating the centrality of political friendship to German political culture in the nineteenth century. Analyzing the debates and actions of this network, this dissertation argues that German liberals “thought with their friends” to reconcile liberalism’s ideals with everyday personal, professional, and political realities in an era marked by crisis. The Revolutions of 1848/49 and the First Schleswig War (1848-1851) accelerated the interweaving of individual political friendships into an informal network of mutual support. The end of the Revolutions and the conclusion of the war in Holstein in 1851 drove most members into internal exile. In this post-Revolutionary context, the political friends expressed emotions—particularly in their correspondence—to build trust, check political non-conformity, and ensure the reciprocation of professional favors. The opening of German political society around 1860 offered the political friends new opportunities to develop their views outside the network: in civic associations, state legislatures, and monarchical courts. Although they never questioned the merits of forming a unified kleindeutsch state, members of the network did differ on how to reach this goal. Because the political friendships they had cultivated in the 1840s and 1850s equated political consensus with emotional wellbeing and professional advancement, their policy debates became increasingly adversarial in the 1860s. Failing to unify around a set of policies and political tactics, the network finally dissolved with the Seven Weeks War of 1866. The historical dynamics of political friendship in this network illuminate previously neglected aspects of nineteenth-century liberalism and the uncertain path to a German nation-state.
Intersections of Voluntary and Involuntary Poverty: The Friars and the Lay Indigent in Late Medieval England, 1221–c.1430
Keywords: Charity
England
Medieval
Mendicant
Poverty

The present dissertation examines the coexistent phenomena of voluntary and involuntary poverty in England from 1221 to c.1430, seeking to determine whether the introduction and subsequent rise of the friars in England had a discernible effect on the perception and treatment of the realm’s indigent. The friars’ impact on the lay poor has elicited drastically different conclusions from scholars who have approached this relationship from different angles, a chasm that this dissertation seeks to bridge by adopting a holistic approach. It explores the discursive and pragmatic interaction between these two groups of “poor” through the lenses of rhetoric and practice, drawing upon religious polemic, vernacular literature, sermons, and testamentary evidence. The first three chapters survey contemporary understandings of the interplay in question, focusing particularly on the charges leveled against the mendicant orders regarding their interactions with and exploitation of the poor, and the courses of action encouraged by these critics that might have had an effect on lay support for both groups. These chapters examine responses from various religious communities, Wycliffite criticism, and literary conceptions respectively, exploring how the discursive treatment of poverty in each set of texts both reflected contemporary perceptions and shaped actions through the perpetual reframing of poverty and the invocation of social contracts, charitable duty, and consent to sin. The fourth chapter shifts focus to examine the social messaging of the friars by situating the involuntary poor in mendicant preaching materials. This analysis questions whether there was a conscious differentiation between these two manifestations of poverty, how the lay poor were framed by the friars, and how the latter conceived of their duties towards the lay indigent. The final chapter probes the real effects of the coexistence of voluntary and involuntary poverty within the same charitable landscape. At its centre is an analysis of wills enrolled at the Court of Husting in London from 1252 to 1430, in which the number of bequests to the lay poor, secular charitable institutions, and the mendicant orders are charted over the period of the friars’ rising popularity in England so as to identify any correlated changes in charitable sentiment.
What Polypharmacy Is and Does
Keywords: ethnography
long-term care
polypharmacy
power
practice theory
sociomaterial

This dissertation is a study in rethinking the phenomenon of polypharmacy, reconceptualizing it as practice. Conventional research in polypharmacy and medication work has failed to consider conceptions of power, situated and collective knowing, and key roles of the body, materials, and discursive practices. Drawing on ethnographic research in a Canadian long term care facility, I trace everyday organizational routines that are integral to the prefigurative practice-arrangement of the work of doing polypharmacy. My observational research, focussing on the bi-annual medication review and the medication reconciliation process, illustrates how practitioners and residents engaged in the broad range of medication work, talk and act in ways that are dissimilar to the conventional literature.The practice of polypharmacy has intended and unintended impacts and power effects on practitioners and residents. I illustrate how sociomaterial elements such as bodily sayings and doings, space, and objects pattern the world of the long-term care organization. I explore the tangled work on residential floors and show how humans and non-humans are relationally implicated in the production and reproduction of maintaining the organizational flow of medications. I describe the work of polypharmacy that keeps residents and practitioners dependent on each other as the residents require medications and practitioners engage in paid medico-legal work. One significant effect is that vulnerable residents are largely excluded from polypharmacy related decision-making while, at the same time, accepted routines impose on them a significant burden of treatment. My research challenges and then extends our real-world understanding of polypharmacy. It exemplifies how everyone, and everything is engaged in doing the institutional work of polypharmacy. My work argues for recognizing polypharmacy as practice. In so doing, I recast polypharmacy from an individual, cognitive, and decontextualized activity to one that recognizes it as a sociomaterial, distributed, and complex routinized institutional practice. The work of polypharmacy is a ‘boring’ yet powerful routine. This new understanding comes with a fresh vocabulary, novel ways of thinking and brand-new questions to be asked. I propose that this new way of understanding the institutional work of polypharmacy and medication work has significant consequences for research, medical practice and education programs.
Modelling Multilineage Human Heart Field Development with Pluripotent Stem Cells
Keywords: embryonic cardiogenesis
heart field development
lineage specification
scRNA-seq
stem cell

The mammalian heart contains molecularly and functionally distinct cardiomyocytes which derive from first the heart field (FHF), anterior second heart field (aSHF), and posterior second heart field (pSHF) lineages. Genetic lineage tracing and retrospective clonal analyses in model organisms have demonstrated that the specification of these cardiac lineages takes place during gastrulation. To access different types of human cardiomyocytes and study the early lineage decisions of the human cardiogenic program, we established an hPSC-based platform that models multi-lineage human cardiogenesis from mesoderm specification to terminal myocyte differentiation and delineated these processes using single-cell RNA sequencing (scRNA-seq). Analyses of hPSC-derived and published mouse mesoderm transcriptomic data identified human FHF, aSHF, and pSHF mesoderm subtypes that share similarities with their mouse counterparts. These mesoderm subsets could be isolated based on their expression of GYPB, CXCR4, ALDH1A2, and CD1D and when cultured further gave rise to respective progenitor populations which in turn generated specific cardiomyocyte derivatives. The development of these human cardiomyocyte subtypes recapitulated the developmental trajectory described in the mouse, reflecting a highly conserved cardiac program. Overall, the findings from this study provide a comprehensive landscape of human embryonic cardiogenesis, which can be used to model a broad spectrum of congenital heart diseases and chamber-specific cardiomyopathies.
Pustaka Pūjā: A Study of Sūtra Worship in Mahāyāna Buddhism
Keywords: Books
Buddhism
Mahayana
Nepal
Newar
Paratexts

This study deals with the questions of why Mahāyāna texts advocate book worship, what forms of worship they advocate, and what their worship was like historically and in the present day. In answering these questions, it first employs a textual study of Mahāyāna Buddhist, non-Mahāyāna Buddhist, and Brahmanical textual references to book worship or the agency of speech. Secondly, it engages with contemporary Newar Buddhist texts and practices related to Buddhist book wor-ship in the Kathmandu Valley of Nepal. The methodological approach of this study is based in the fields of the study of orality, paratexts, materiality, and book history. Going beyond the bounds of the disciplinary silos of Buddhist studies and South Asian studies, it shows how a trans-sectarian understanding of agency and orality is necessary to explain trends in the development of Buddhist and Brahmanical manuscript culture and worship. On that basis, this study suggests that while South Asian religions view divine speech as imbued with ritual agency, Mahāyāna Buddhist book worship used the same logic with the physical book in advocating their worship. Furthermore, while not renouncing orality, Mahāyāna Buddhist literature hardwired self-referential prescriptions for their worship within the body of their texts to promote themselves in physical form in a way that freed it from reliance upon the system of oral transmission upon which the non-Mahāyāna nikāya and āgama literature relied. Tracing the form of that worship throughout the first millennium, this thesis shows how it became increasingly tantricised, resulting in the incorporation of the Mahāyāna sūtras within maṇḍalas. A continuity of ancient forms of book worship and recitation, as well as a continually evolving and adapting tradition, is explored in the case of Newar Buddhist book worship and recitation in the Kathmandu Valley of Nepal, revealing the continued effects of the agency of these books as texts, objects, and deities.
Molecular, Cellular and Circuit Mechanisms that Underlie a Two-pore Potassium Channel’s Regulation of Membrane Potential, Synaptic Activity and Locomotion
Keywords: circuits
K2P
locomotion
premotor interneurons
TWK-40

Two-pore potassium channels (K2Ps) establish the resting membrane potential (RMP) and regulate membrane excitability. Little is known about the physiological roles of K2Ps in the context of intact neural circuits and behaviors.I have identified and functionally characterized a C. elegans K2P, TWK-40. First, through molecular genetic studies, I discovered that the functional increase and decrease of TWK-40 activity drastically alter motor activities and motor patterns through a pair of descending premotor interneurons, AVA. Second, AVA is commonly thought to mainly govern only the backward motor state, antagonizing the forward state. But through the cell and genetic ablation, optogenetics, and calcium imaging, I discovered that AVA is not only critical for backward movement but also promotes forward movement by maintaining an unusually depolarized, ~ -22mV RMP through at least one K2P, TWK-40, and sodium leak channels. Third, I address circuit mechanisms through which AVA regulates the forward state. I discovered that both classic neurotransmitter and neuropeptide signaling from AVA contribute to its promotion of forward movement. In addition, AVB, another pair of premotor interneurons, is a necessary mediator of AVA’s role in the forward circuit. Lastly, AVA’s regulation of the forward state may involve other circuit components, such as the AS motor neurons. These findings offer new physiological insight into how K2Ps regulate RMP and synaptic activity. They shed light on how a professedly simple circuit drives complex motor behaviors.
Liquid Guanxi: Chinese Social Networks in an Age of Digitalization
Keywords: China
digitalization
social networks

The enabling and constraining properties of guanxi networking culture, its networking mechanisms, and network-level consequences in personal networks in modern China has been extensively studied in a large and growing literature since Fei Xiaotong’s celebrated From the Soil. Although guanxi continues to be the glue that lubricates transactions in China’s economic, labor market, military, political, scientific, and school systems in China, researchers of guanxi have overlooked the rise of social networking sites (SNSs) in everyday networking in China, which is now home to the largest and fastest population of SNS users worldwide and nearly universal adoption in everyday networking. This dissertation empirically investigates how the widespread uptake of SNSs is transforming the cultural and psychological principles of interpersonal networking in guanxi, Chinese networks. This dissertation argues that the digitalization of interactions on SNSs is rendering guanxi networks in China more liquid and theorizes the expressions of this liquidity across three networking mechanisms (tie-creation, tie-maintenance, and tie-activation) and two networking conditions (proximity and information openness) in guanxi. This dissertation consists of seven standalone papers that examine each of these facets. This dissertation theorizes the liquefying transformations to guanxi culture as refractions of a changing Chinese modernity based in the arrangements of a new social space emerging within SNSs: a digital agora, where public and private spheres come together in an intermediary space that marshals within the individual a compulsion and ability to be communal without abrogating the comforts of the private; a synergy essential to social survival in China. Among the first systematic studies to examine how SNSs fundamentally transform the ways that people in China think about and carry out their networking on an everyday level, this dissertation contributes to the study of guanxi, social networks, and Chinese modernity in general by articulating a sociological account of the changing nature of Chinese social relations in an age of digitalization.
Cell-Cell Adhesion Dynamics and Cortical Tensions in Embryonic Tissue Structure and Mechanics
Keywords: cell-cell adhesion
cortical tension
cytoskeleton
interstitial networks
modeling
Xenopus laevis

The mechanics and dynamics of cell-cell adhesions are fundamental to morphogenesis, the shaping of tissues during development. Modern biophysical approaches model adhesion between cells with surface tensions that arise from cortical actomyosin contractility and adhesion molecule binding, similar to the adhesion of a water droplet to a surface. Collections of adherent cells form tissues, which are modeled as space-filling foams, where each constituent bubble is a cell with a tension along each cell-cell boundary. These tissues are permeated by interstitial networks (“gaps”) and during development can stretch, bend, and flow, resulting in cell rearrangements and changes in interstitial network structure. How cell-level cortical tensions contribute to the structure of gaps and the dynamics of tissues is still unclear. To further our understanding, I investigated how the preexisting surface tension model of cell-cell adhesion can explain the presence of gaps within tissues and if this model quantitatively predicts the behavior of newly forming cell-cell contacts. Through computational analysis in the first part of this work I found that the structure of gaps depends on the ratio of tension at cell-cell contacts relative to cell-gap interfaces, which was supported by accompanying experimental work done by Barua et al. (2017). In the second part of this work, I combined experimental, mathematical, and computational approaches to show that cortical tension from the actomyosin cortex alone is insufficient to explain the dynamic behavior of cell-cell adhesions, which can rapidly grow to a Ca2+-independent low adhesion state before more slowly proceeding in a logistic-like fashion to their Ca2+-dependent high adhesion state. To accommodate these empirical findings, I further develop our surface tension model to show that a combination of adhesion energy, cytoskeletal elasticity, and cytoskeleton network turnover can explain the observed adhesion dynamics. Therefore, cytoskeletal mechanics and dynamics are essential factors regulating cortical tensions, the relative values of which determine gap structure and contact growth, and thus tissue structure and dynamics.
Sequencing Protein Interaction Dynamics at Proteome Scale
Keywords: Barcode Fusion Genetics
interactome
protein-protein interaction
recombinatorial multiplexing
sequencing
Yeast Two-Hybrid

Protein interactions link genotypes to phenotypes. Although phenotypes are known to depend on environmental context, the response of protein interactions to environmental change has not yet been explored at the scale of proteome. Here, I engineered and validated the fluorescence Barcode Fusion Genetics Yeast-Two Hybrid (fBFG-Y2H) technology, which enables multi-environment proteome-scale interaction measurements via recombinatorial barcode sequencing. I demonstrate two proteome-scale applications of fBFG-Y2H: First, I describe the use of fBFG-Y2H to generate the first binary protein interaction map connecting SARS-CoV-2 and human proteins. The identified human protein targets are enriched for interactors of proteins in severe COVID-19-associated loci, suggesting mechanistic connections involving vesicle trafficking and TNF-signaling. Second, I describe the application of fBFG-Y2H to generate an interaction map amongst ~30 million yeast protein pairs under baseline, DNA damage, carbon starvation, and oxidative stress environments, yielding the first proteome-scale atlas of dynamic protein interactions for any organism. Integrating the dynamic interactome map with transcriptome and phosphoproteome measurements in matching conditions reveals both local mechanisms underlying individual pathways and global patterns of cellular response to changing environments. Finally, I provide proof-of-principle results for a messenger BFG-Y2H (mBFG-Y2H) technology, which counts transcripts bearing recombinatorial barcode loci and has the potential to capture global protein interaction dynamics at an unprecedented 10-minute resolution.