VictorJuiz/thesis huggingface dataset:
The Tansmembrane Associations of HIV-1 Vpu and its Human Targets
Keywords: FRET
HIV-1
transmembrane
Vpu

Many viruses evade the innate immune response through the expression of accessory proteins that modulate the activity of immune system proteins. The HIV-1 protein Vpu functions to downregulate a number of host cell surface proteins within infected cells. For several target proteins, including the NTB-A and PVR receptors and the restriction factor tetherin, downregulation occurs through direct interaction of the proteins’ transmembrane (TM) domains. The mechanism through which a single TM domain can interact with a wide range of targets that share no obvious interaction motifs is poorly understood. In this thesis we characterize the TM domain homo and heterooligomerization of Vpu and its human targets, tetherin, NTB-A and PVR. By using a series of fluorophore labeled TM domain peptides we used Förster resonance energy transfer (FRET) to characterize the interactions of Vpu with itself as well as its human targets. Our data show target TM domains compete for interaction with Vpu, suggesting that all targets bind the same helical face, also that formation of each heterooligomer has a similar free energy of association to the Vpu homooligomer. This leads to a model in which Vpu monomers, Vpu homooligomers and Vpu-target heterooligomers coexist and suggests that the binding surface of the Vpu TM domain has been selected for weak binding to multiple targets. We also document the role of the lipid bilayer, specifically lipid phase and hydrophobic thickness, on TM domain assembly within the Vpu-target system. We show that thicker membranes and gel phase lipids non-specifically promote associations of Vpu and its targets without affecting secondary structure. The properties of the lipid bilayer are an important factor in Vpu-target oligomerization and may explain differences in Vpu-target oligomerization in different subcellular compartments. This work provides new insight into the molecular mechanism of Vpu and furthers our knowledge of membrane protein assembly
Plk4 Regulates Cell Motility through Arhgef1 and Rho GTPase Activation
Keywords: Arhgef1
GEFs
migration
motility
Plk4
Rho GTPases

Cell migration is a fundamental process essential for embryogenesis, immune cell function and maintenance of homeostasis. It is driven primarily by polymerization of the actin cytoskeleton, which is regulated by a family of small Rho GTPases. Rho GTPases Rac1 and Cdc42 are known as the major regulators of actin polymerization and RhoA is mostly thought of as the regulator of actin stress fiber formation and actomyosin contraction. Rho GTPases are activated by GEFs and deactivated by GAPs. Polo-like kinase 4 (Plk4) is well-acknowledged as the master regulator of centriole duplication. Nevertheless, our laboratory has shown that Plk4 activates RhoA during cytokinesis to ensure proper cleavage furrow positioning. We also identified a novel role for Plk4 in regulation of spreading, migration and invasion of normal and cancer cells. However, the mechanisms through which Plk4 regulates these processes are not completely understood. I hypothesized that Plk4 regulates the activation of RhoA and possibly other Rho GTPases to indice cell migration and spreading. In support of this hypothesis, I show here that Plk4 acts as an activator of Rho GTPases RhoA and Rac1 in cycling cells. I also identify 12 GEFs that possess Plk4 consensus phosphorylation motif and show that Plk4 physically interacts with the GEFs Arhgef1 and P-Rex2. Plk4 functionally interacted with Arhgef1 to affect cell migration, showing at least partial dependence of Plk4 migration phenotype on Arhgef1. Further delineation of their interaction showed that Plk4 binds the DH/PH domains and phosphorylates the L-DH/PH fragment of Arhgef1, and that Plk4 enhances Arhgef1 GEF activity. Finally, I show that Plk4 is not likely to activate Arhgef1-RhoA pathway to enhance cell spreading but may act through P-Rex2-Rac1. These results identify a novel mechanism through which Plk4 regulates cell migration. Plk4 has emerged as a potential oncogene, promoter of tumour progression and metastasis formation, prompting the creation of Plk4 inhibitors for therapeutic purposes. The data presented here deepen our understanding of the pathways that may be affected by the Plk4-targeted therapy.
Microfluidic Devices for High-resolution Cellular Profiling
Keywords: Cancer
Cell sorting
Circulating tumour cells
CRISPR
Microfluidics

Rapid and accurate detection, quantification and analysis of rare cells in biological samples is of critical importance for a variety of clinical applications. These cells, which can be outnumbered a billion to one by non-target background cells, can have important implications in cancer diagnostics, diagnosis of viral infections and regenerative medicine. Microfluidics allows the processing of large sample volumes quickly while maintaining rigorous control over dynamical and chemical conditions at the microscale. Though many technologies have been developed to identify bulk populations of rare cells, some applications require higher resolution detection methods, increased throughput, or improved purity to advance current research and clinical practices. This thesis reports the design and application of a novel, high-resolution cell sorter incorporating a high-performance ferromagnetic alloy. Incubating biological samples with magnetic nanoparticles specifically bound to a cell surface marker of interest yields cell subpopulations exhibiting differential magnetic loading. These cells are then deflected laterally by rows of cobalt-based ribbons and directed to one of several outlets corresponding to their level of magnetic loading. Using integrated graphene Hall sensors, we demonstrate for the first time concurrent automated profiling of single cells and CTC clusters. We demonstrate the utility of our approach by profiling cancer cells derived from a mouse xenograft model. We then modify our approach with an eye towards maximizing throughput, and develop a modified design capable of sorting 30 million target cells per hour. With multiple devices running in parallel, we sort hundreds of millions of cells in a genome-wide CRISPR-Cas9 loss-of-function screen to identify genetic regulators of CD47, a clinically relevant protein overexpressed on the surface of many tumour cells. Our screen hits were then validated by side-by-side comparative screens run with the two most widespread cell sorting technologies, FACS and MACS. Overlapping hits between the three distinct methods reveal as many as five heretofore unexplored potential targets for cancer immunotherapy.
Relational Speculation: Rereading Inheritance in Victorian Fiction
Keywords: Inheritance
Novel
Speculation
Victorian

My dissertation offers a new entry point into Victorian fiction’s well-documented concern with the credit economy by calling attention to inheritance as a mode of capitalist exchange and subject formation that, although pervasive, has been under-examined. I argue that Victorian novels interrogate the assumption that intergenerational succession is a timeless, natural institution that remains aloof from the psychic and moral dangers commonly associated with financial speculation. My detailed readings of Dickens’s Our Mutual Friend (1864-5), Collins’s Armadale (1866), and Eliot’s Middlemarch (1871-2) demonstrate how their juxtapositions of stockjobbers and gamblers with expectant heirs and testators not only figure inheritance’s alliances with finance but also uncover its intrinsically speculative logic. Through this recurring comparison, which I call “relational speculation,” these novels imbricate the abstracting logics of credit, risk, and contract with the morally and affectively imbued structures of family, marriage, and property. In focusing on relational speculation, I complicate critical tendencies to view the persistence of inheritance plots in nineteenth-century novels as mere “convention” or as a kind of infrastructural holdover. Instead, I illuminate this persistence by tracing tensions in eighteenth- and nineteenth-century popular, legal, and political accounts of succession and bequest, showing how they struggle to redefine these models of intergenerational transmission both through and against the precepts of capitalism, contractual individualism, and corporate personhood. I suggest that Dickens, Collins, and Eliot foreground the paradoxes implicit in these efforts via the trope of relational speculation, which pervades their plots, figures, and modes of narration. Their novels question the speculative and corporate-like relationship these models of inheritance construct between testators and would-be heirs by depicting identity mistakes and impersonations, fantasies of posthumous ownership, fears of inherited liability, and constraining dead hands. Relational speculation thus reveals the substitutive and proleptic structures of identity, ownership, and responsibility latent to speculation and inheritance alike. Insofar as it prompts these novels both to ironize some of inheritance’s key narrative conventions and to seek ways of controlling their own implicitly speculative dynamics, relational speculation ultimately plays an important role in shaping their formal as well as thematic concerns.
Pirandello's Dramaturgy of Time
Keywords: Bergson
Einstein
Heidegger
Husserl
Pirandello
Luigi
Time

Luigi Pirandello’s drama, at its heart, deals with the problems of being and becoming, identity, and creativity. His works are centered upon the nature of personal experience and the ways in which we perceive and interact with the world and its inhabitants. But often overlooked is the role that time plays in those dramas’ already complicated and divisive subject matter. While concepts and themes related to time—e.g., memory and narrative—are often at the core of Pirandello’s drama, a cohesive approach to the topic of time and temporality in his work is lacking. This thesis, using three of Pirandello’s majors plays as case studies, will offer an analysis of the playwright’s dramaturgical management of time as a textual theme, as the basis of dramatic narrative, and—in the guise of memory and anticipation—as the ontological foundation of the concept of dramatic character. These plays, written in the midst of the general discourse on time and temporality at work in the early part of the 20th-century, lend themselves to be read in dialogue with 1) the philosophical exploration of the concept of time, memory, and duration developed by Bergson, 2) the phenomenology of internal time consciousness advanced by Husserl, 3) Heidegger’s idea of temporality as the underlying structure of both being and meaning, and 4) Einstein’s consideration of the relativity of mankind’s perception of events in the space-time continuum. In this thesis, I will demonstrate that Pirandello was working at the intersection of trends deriving from each of these philosophical premises, creating a theory of dramatic form that is structured by the very concept it illustrates thematically, namely the relativity of time in man’s experience of the world and the notion of temporality as the foundation of all consciousness.
Paratextual Reading in the Romantic Period
Keywords: annotation
British Romanticism
Maria Edgeworth
paratext
Robert Southey
Walter Scott

Paratextual Reading in the Romantic Period demonstrates that Maria Edgeworth, Robert Southey, and Walter Scott used paratext as a formal strategy to disrupt established relationships among readers, texts, and an increasingly global sense of context. Referring to this interrupted reading process as “paratextual reading,” this study shifts its attention towards paratext’s use as a tool to discipline the public’s reading habits for a new information age. As British imperial expansion brought distant cultural and geographical spaces closer to metropolitan readers, Romantic writers developed new genres – such as the “footnote novel” and the annotated long poem – to make representations of these spaces accessible to the British reading public. By grafting the knowledge produced by antiquarian and Orientalist scholarship onto popular narrative forms, these annotated texts reframe pleasure reading as an opportunity to gather information about the expanding world beyond the book. Alongside their newly referential paratexts, however, Edgeworth, Southey, and Scott also adapt eighteenth-century traditions of metafictional annotation, calling deliberate attention to their notes’ disruption of readers’ progress through their fictional narratives. Beginning with Edgeworth’s use of paratext to improve her “lazy” English readers’ capacity for intellectual labour in time for Ireland’s imminent Union with Britain, Paratextual Reading then turns its attention to Southey’s and Samuel Henley’s various efforts to use Orientalist annotation to discipline the perversities of readerly desire. Finally, focusing on Scott’s paratextual incorporation of his anecdotal source materials into his Magnum Opus edition of the wildly popular Waverley novels, this thesis concludes by considering the commercial impact of paratextual strategies of rereading. By documenting paratext’s participation in efforts to reform lazy, curious, or otherwise unauthorized readers, Paratextual Reading shows how Romantic writers worked to cultivate a reading public fit to cope with information overload in a new age of British imperial expansion.
Les Figures de Parias et de Marginaux dans la transcréation québécoise
Keywords: Hétérochronotopie
Marginal
Paria
Transcréation

Cette thèse explore l’aspect protéiforme des parias et marginaux à travers deux médias, la littérature et le cinéma. Notre étude s’éloigne des questionnements généraux sur l’altérité et des théories sociologiques et anthropologiques qui ne distinguent pas ces différentes formes d’exclusion. À travers des micro-analyses instituées par les champs de l’éthique et de l’histoire, nous proposons de distinguer les termes, de rendre compte du rapport qu’ils entretiennent avec la société et d’examiner leur évolution, à travers les siècles et les formes d’expression artistique. Après une réflexion visant à dégager les complexités critiques du champ de l’adaptation cinématographique, nous proposons le terme de « transcréation » et définissons un cadre d’analyse précis, basé sur la narratologie du film qui permet d’appréhender efficacement les figures concernées. Cette thèse interroge une grande variété de récits, datant de la première moitié du XXe siècle (Un Homme et son péché, Grignon (1933) ; Gury (1949) et Binamé (2002)) jusqu’au tournant du XXIe siècle (Littoral, Mouawad (1999) adapté par l’auteur en 2004), et de genres variés : roman fantastique (Sur le seuil de Senécal (1998) ; Tessier (2004)), autofiction (Borderline et La Brèche de Labrèche (2000 ; 2002) ; Charlebois (2008)), nouvelle (Le Torrent d’Hébert (1950) ; Lavoie (2012)) et théâtre (Matroni et moi de Martin (1998) ; Duval (1999) ; et Les Feluettes de Bouchard (1987) ; Greyson (1996)), afin d’exploiter de manière efficace et convaincante les formes que prennent les parias et les marginaux et de proposer une typologie des esthétiques associées au thème de l’exclusion. Plusieurs études comparées d’un vaste corpus québécois laissent, dans un deuxième temps, place à des analyses détaillées, construisant au cours des chapitres une critique du sujet. Nous réfléchissons d’abord à la violence intrinsèque à la société et aux diverses manières de stigmatiser et punir, pour ensuite nous tourner vers des thématiques morales (le Mal), esthétiques (la mort et l’animalité) et philosophiques (l’abjection). Progressivement, nous verrons que, loin d’être essentiellement négatives, ces figures développent une part de positivité, que ce soit par une caractéristique exceptionnelle du protagoniste ou par un traitement particulier des récits appréhendés.
Metabolomics analysis reveals novel aspects of 2-hydroxyglutarate homeostasis and links citramalate to branched chain amino acid metabolism
Keywords: Branched Chain Amino Acids
Cancer
Genetics
Metabolomics
Saccharomyces cerevisiae

Cells produce a wide variety of metabolic products. Many of these metabolites have annotated functions in supporting the life of a cell or organism, but many others whose functions are unknown or unclear are considered errors in metabolism. It is well established that cell metabolism changes based on the type and quantity of the nutrients available. The work presented herein explores how growth on different nutrient types affects the metabolism of two compounds with incompletely defined roles: citramalate and 2-hydroxyglutarate (2-HG). I leverage the genetic and metabolic tools available for the yeast Saccharomyces cerevisiae to examine the metabolism of these two isomeric compounds. I demonstrate that citramalate is a product of pyruvate and acetyl-CoA whose synthesis is catalyzed by leucine biosynthesis enzyme Leu4. I show that citramalate is produced when cells adapt to mitochondrial dysfunction and propose that citramalate synthesis is an alternate, energetically conservative path to isoleucine biosynthesis. The findings described here expand our understanding of branched chain amino acid biosynthesis. The oncometabolite D-2-HG is believed to be the product of metabolic error because it is produced from the readily available compound α-ketoglutarate by a variety of enzymes with other, already well established functions. In the yeast Saccharomyces cerevisiae D-2-HG is produced by the first enzyme in serine biosynthesis, phosphoglycerate dehydrogenase. I show that D-2-HG metabolism may contribute to mitochondrial electron transport and is also regulated by mitochondrial health. I show there are two metabolic pathways in yeast for the turnover of D-2-HG that occur in different sub-cellular compartments. The work presented in this thesis shows that "off-target" catalysis by metabolic enzymes can be means for cells to adapt to changing nutrient availability.
Body Size Evolution and Diversity of Fishes using the Neotropical Cichlids (Cichlinae) as a Model System
Keywords: Allometry
Cichlids
Geometric Morphometrics
Ontogeny

The influence of body size on an organism’s physiology, morphology, ecology, and life history has been considered one of the most fundamental relationships in ecology and evolution. The ray-finned fishes are a highly diverse group of vertebrates. Yet, our understanding of diversification in this group is incomplete, and the role of body size in creating this diversity is largely unknown. I examined body size in Neotropical cichlids (Cichlinae) to elucidate the large- and small-scale factors affecting body size diversity and distribution, and how body size shapes species, morphological, and ecological diversity in fishes. Characterization of body size distributions across the phylogeny of Neotropical cichlids revealed considerable overlap in body size, particularly in intermediate-sized fishes, with few, species-poor lineages exhibiting extreme body size. Three potential peaks of adaptive evolution in body size were identified within Cichlinae. I found freshwater fishes globally tend to be smaller and their distributions more diverse and right-skewed than marine counterparts, irrespective of taxonomy and clade age, with a strengthening of these trends in riverine systems. Comparisons of Neotropical cichlid body size diversity and distribution to this broader context shows that body size patterns are largely abnormal compared to most freshwater fishes, particularly those of the Neotropics. This implies that small body size is rarer in Cichlinae, despite several independent cases of body size decrease in this lineage. I found that these small-bodied lineages are miniaturized cichlids, exhibiting strong reduction in body size, as well as paedomorphic characters and ontogenetic truncation compared to their sister taxa. Further examination of ontogenies across Neotropical cichlids found considerable shape conservatism over ontogeny and phylogeny, with cichlids following similar ontogenetic trajectories. Therefore, ontogenetic pathways do not contribute considerably to morphological divergence seen in adults, with divergence likely occurring in the larval stage or perhaps during embryology. The evolution of ontogeny, body size, and shape did not correspond to a unique adaptive peak in miniatures, or three body size optima predicted from the distribution of size across the phylogeny. Rather, it is complex and, like early trait divergence previously seen, diversifies early in the phylogeny across the major lineages of Neotropical cichlids.
Henry of Ghent and John Duns Scotus on Self-Agency and Self-Motion: An Inquiry into the Medieval Metaphysics of Causal Powers
Keywords: causal powers and causation
Henry of Ghent
John Duns Scotus
medieval metaphysics
self-motion
Thomas Aquinas

In the Physics, Aristotle argues that everything that moves is moved by something else, and thus that things cannot move themselves, in the sense of self-motion that refers not just to changing location, but also more generally to causing a change in oneself. This dissertation focuses on how, working within the framework of Aristotle’s philosophy, Henry of Ghent and John Duns Scotus defend the possibility of self-motion and self-agency (in contrast to self-motion, in self-agency a thing causes a feature in itself, but there is no temporal moment to which we can assign this causal fact). To understand Henry’s and Scotus’s defences of self-motion and self-agency, I consider their views about causal powers: in any case of causation, including self-motion and self-agency, things do what they do by exercising their causal powers. I argue that Henry and Scotus think very differently about the nature of powers and their causal contribution. Henry takes powers to be without causal efficacy, a view that pushes him to assign to them only an explanatory role, and to argue that in causation, what causes the change and what undergoes the change is the whole thing that has a power. In contrast, Scotus understands powers as forms, that is, as entities that can have direct causal efficacy, and thinks that in causation, what causes the change and what undergoes the change are these forms, which are parts of things. I further explain how Henry’s and Scotus’s views about causal powers are responsible for their different understandings of self-change. Because he focuses on how the whole thing is affected in a causal interaction, Henry is forced to conclude that in created beings, no perfect self-change is possible, for what starts the change and what ends it are not strictly the same. By focusing on the causal contribution of the parts of a thing, Scotus manages to bypass Henry’s conundrum, and develops an account according to which things can change themselves in virtue of having active and passive principles by whose mutual manifestation a feature is produced by the self-agent in itself.