VictorJuiz/thesis huggingface dataset:
Exploiting Caenorhabditis elegans as a Discovery Platform to Identify Nematode Parasiticides that Act Through Neuromuscular Disruption

Nematodes that parasitize humans, non-human animals and plants are an underappreciated burden to human health, food security and economic development. The compounds that rid animals and plants of parasitic nematode infections, termed nematode parasiticides, are tremendously important for human development. The emergence of genetic resistance and warranted restriction on the use of toxic parasiticides beckon the development of a new generation of effective compounds to combat nematode parasites. Most nematode parasiticides developed to date act through neuromuscular disruption. this is an effective strategy as several behaviours that are essential for maintaining a state of parasitism including feeding, reproduction, and attachment to host tissues rely on neuromuscular function. The non-parasitic nematode Caenorhabditis elegans has emerged as a powerful biological study model. The neuromuscular biology of C. elegans is well conserved with nematode parasites of plants and animals. Here, I describe my efforts towards identifying and characterizing novel parasiticidal compounds using Caenorhabditis elegans as a discovery model. I first exploited C. elegans egg-laying behaviour to identify small-molecules that disrupt C. elegans neuromuscular function. I identified two scaffolds that disrupt C. elegans neuromuscular function that also demonstrate potent activity against nematode parasites of animals and plants. The first scaffold that I describe, wact-55, disrupts nematode motor behaviours by eliciting the release of neurotransmitter containing vesicles through yet uncovered mechanisms. Wact-55 demonstrates a strong synergistic interaction with inhibitors of acetylcholinesterase, an established class of nematode parasiticides. The second scaffold that I describe, wact-45, is an inhibitor of the vesicular acetylcholine transporter that flaccidly paralyzed nematodes. Wact-45 synergistically kills C. elegans with the most commercially successful nematode parasiticide ivermectin. Thus, I have identified two novel parasiticide scaffolds that may prove useful for combatting nematode parasites that plague humans.

Keywords: anthelmintic
antiparasitic
caenorhabditis elegans
egg laying
nematicide
parasiticide
Advisor: Roy, Peter J
Identification of Novel Regulators of the Hippo Pathway using Positive Selection Genome Wide CRISPR Screens

The Hippo pathway is established as a master regulator of tissue growth and organ size and its dysregulation can lead to cancer. The core pathway consists of the kinases MST1/2 and LATS1/2, their adaptor proteins, SAV1 and MOB1A/1B, respectively, and the transcriptional module YAP and TAZ. Multiple upstream signals such as mechanotransduction, GPCRs and metabolic pathways activate MST1/2 which along with SAV phosphorylates and activates LATS1/2 together with MOB proteins which phosphorylate and sequester YAP/TAZ in the cytoplasm leading to their subsequent degradation. The core pathway is well studied, however, many upstream pathway regulators are ill-defined/unknown. To identify novel Hippo pathway regulators, I undertook two positive selection genome-wide CRISPR screens. I generated clonal cell lines of T24 bladder and MDA-MB-231 breast cancer cells expressing two proteins, Cas9 which enabled gene deletion and a FKBPiCaspase9 fusion protein under YAP/TAZ transcriptional control, which when expressed causes cell death upon addition of chemical dimerizer, AP20187. CRISPR-mediated loss of genes promoting YAP/TAZ activity, allows cell survival by downregulating the FKBPiCaspase9 protein. The first screen, in T24 bladder cancer cells identified the phosphatase adaptor protein PPFIA1 as a positive regulator of YAP/TAZ. I demonstrated that loss of PPFIA1 leads to decreased YAP/TAZ protein levels, increased YAP/TAZ phosphorylation, enhanced cytoplasmic localization and iii decreased YAP/TAZ target gene expression. Immunoprecipitation analysis demonstrated that PPFIA1 interacts with YAP. These data suggest a model in which PPFIA1 plays a role in maintaining YAP in a dephosphorylated state, possibly by recruiting a phosphatase. To identify novel regulators that might be relevant to multiple cell lines I performed a second screen in the MDA-MB-231 cells and identified the Gα protein chaperone RIC8A, which also functions as a Guanine Nucleotide Exchange Factor (GEF), as another putative regulator of the Hippo pathway. I showed that abrogation of RIC8A expression mediated a decrease in total YAP /TAZ protein levels, a decrease in YAP /TAZ target gene expression and increased cytoplasmic localization of YAP/TAZ in both bladder and breast cancer cells. Overall, my thesis introduces a novel method to interrogate the Hippo pathway in multiple cancer types and identifies new regulators of YAP and TAZ.

Advisor: Attisano, Liliana
Collusive Critique: Paranoid Reading and Contemporary American Literature

My dissertation argues that recent deployments of paranoia in American literature enable new paradigms for paranoid reading and epistemology. With the advent of Trumpism and the public visibility of conspiracy theory groups like QAnon, what Richard Hofstadter called “the paranoid style” has once again taken centre stage in the American political theatre. At the same time, inspired by Eve Sedgwick’s “Paranoid Reading and Reparative Reading,” the current methodological debates in literary studies continue to negotiate the merits of paranoid practices of critical reading in the forms of critique and the hermeneutics of suspicion. The dissertation argues that paranoia’s unique conceptual lexicon and discursive force makes it a powerful tool for conceptualizing and contesting some of the most pressing problematics of our time: the structures of anti-Black racism, climate change denial, repressive surveillance apparatuses, and nascent forms of late capitalist commodification. My first chapter argues that the Black protagonist of Colson Whitehead’s The Intuitionist rejuvenates older forms of paranoid detection to mobilize a roster of racialized styles of paranoia that contain the tools for perceiving and dismantling the structures of anti-Black racism. Chapter Two argues that, whereas Don DeLillo’s Libra uses conspiracy thinking to ascribe cosmic significance to an embattled and precarious white male hegemony, Suzan-Lori Parks’s Topdog/Underdog represents anti-Black violence as a form of political assassination that must be understood as conspiratorial. In the third chapter, I argue that Karen Tei Yamashita’s Tropic of Orange deploys the precepts of paranoid thought to give readers a unique purchase on the ongoing anthropogenic eco-apocalypse. The dissertation’s final chapter interrogates how two novels about consumer capitalism—William Gibson’s Pattern Recognition and Colson Whitehead’s Apex Hides the Hurt—counteract hegemonic and racializing forms of surveillance capitalism by undermining the visual logic of commodification. In the dissertation’s coda, I contemplate the simultaneous difficulty and necessity of rejuvenating paranoia in the wake of the Trump presidency, asserting that a kind of collusive critique between reader and text might enable the dismantling of the types of discursive and coercive forms of violence that Trump fomented. Paranoia, I ultimately assert, is itself in need of reparation.

Keywords: Contemporary American Literature
Ecocriticism
Genre
Paranoia
Race and Ethnicity
Theories of Reading
Advisor: Downes, Paul
Characterization of Immunity-related GTPase Q (IRGQ) as a Novel ATG8 Family Interactor

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.

Keywords: ATG8
Fertility
Immunity-related GTPase
Innate immunity
IRGQ
Macroautophagy
Advisor: Brumell, John
Political Friendship: Liberal Notables, Networks, and the Pursuit of the German Nation-State, 1848-1866

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.

Keywords: Friendship
German History
German Unification
Liberalism
Nationalism
Political Friendship
Advisor: Retallack, James N
Intersections of Voluntary and Involuntary Poverty: The Friars and the Lay Indigent in Late Medieval England, 1221–c.1430

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.

Keywords: Charity
England
Medieval
Mendicant
Poverty
Advisor: Ghosh, Shami
Cochelin, Isabelle
What Polypharmacy Is and Does

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.

Keywords: ethnography
long-term care
polypharmacy
power
practice theory
sociomaterial
Advisor: Thompson, Alison
Novel Molecular Templates Targeting Histone Deacetylase 6 - Promising Strategy Towards Clinical Translation

Histone deacetylase 6 (HDAC6) is a maverick member of the lysine deacetylase family of proteins collectively known as histone deacetylases (HDACs). HDAC6 is structurally unique with peculiar, non-conserved domains that differentiates it in terms of location and function. Functionally, HDAC6 deacetylates non-histone substrates and regulates protein function, cytoskeletal dynamics, and cell migration. These roles are essential to cellular function and survival and have disease implicating consequences in several cancers and neurodegeneration. Interestingly, loss of HDAC6 function by inhibition, degradation, or deletion is well tolerated and HDAC6-knockout mice develop identically as wildtype mice. These combined attributes have made HDAC6 highly attractive to medicinal chemists and clinicians as an effective therapeutic target. Six ‘HDAC6-selective’ drugs are currently in clinical studies, however, a rational molecular design strategy for selectively inhibiting HDAC6 is not well defined, and several of these inhibitors achieved selectivity stochastically. This thesis describes a rational, iterative, and structural engineering strategy that identified through multiple x-ray crystallography structures, a unique molecular template to reliably target HDA6 selectively. Inspired by this chemical template, newer analogous with picomolar binding affinities and outstanding selectivity for HDAC6 were designed. These new analogues have desirable pharmacokinetic profiles and brain bioavailability, affording their use in the in vivo investigation of HDAC6-relevant diseases such as melanoma, multiple myeloma, and Alzheimer’s disease. Additionally, chimeric degraders of HDAC6 known as PROteolysis TArgeting ChimeraS, PROTACS inspired by initially reported targeted motifs were designed. These HDAC6 PROTACS potently and selectively degraded HDAC6, demonstrating >95% HDAC6 degradation with sub-nanomolar. In conclusion, this thesis encompasses a body of work with significant impact. Firstly, it provides a structural template with a unique binding modality that can be harnessed by medicinal chemists and drug discovery teams interested in the selective targeting of HDAC6. Secondly, the structural engineering strategy described herein can provide a blueprint for optimizing lead HDAC6 candidates for pharmacokinetic improvements and advanced preclinical studies. Finally, developing a HDAC6 degrader technology from this structural template provides a complementary approach that can afford superior efficacy. Collectively, this thesis provides and validates a unique and robust binding modality that can be harnessed by future HDAC6 drug programs.

Advisor: Gunning, Patrick T
Modelling Multilineage Human Heart Field Development with Pluripotent Stem Cells

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.

Keywords: embryonic cardiogenesis
heart field development
lineage specification
scRNA-seq
stem cell
Advisor: Keller, Gordon M