VictorJuiz/thesis huggingface dataset:
Isolation of Cellulose Nanofibres: Elucidation of a Novel Approach Utilizing Fungal Pretreatment

In plant cell wall, cellulose chains are organized into perfect stereoregular configuration called microfibrils through a regular network of inter and intramolecular hydrogen bonds. The cellulose microfibril along with hemicellulose chains that tether to the cellulose microfibrils and other polysaccharides through hydrogen bonding forms the cell wall structural framework. Isolation and application of cellulose nanofibres is expanding rapidly due to their environmental benefits and specific strength properties, especially in nano-biocomposite area. Currently, cellulose nanofibres are isolated from natural fibres through a combination of high energy refining and high pressure homogenization or through a combination of biological and mechanical process that involves fibre treatment with hydrolytic enzymes followed by high pressure homogenization and all of these processes are very energy intensive. In this research, a fungal pre-treatment for wood fibres is investigated which can bring about internal defibrillation in the fibres through reduction of hydrogen bonds and cleavage of hemicellulose chains tethering the cellulose microfibrils together. The pre-treatment of wood fibres with Ophiostoma Ulmi, a causative agent of Dutch elm disease in Elm trees, has found to reduce the energy requirement to isolate cellulose nanofibres. The treatment has found to bring about internal defibrillation in the fibres by disrupting the hydrogen bonding that holds the hemicellulose - cellulose microfibril network and the cellulose chain in the cellulose microfibrils together. The effect of bio-treatment on hydrogen bonding density and their nature in the fibre cell wall was investigated using FT-IR and 13C NMR and its effect on cellulose structure using FT-IR and X-ray crystallography. The treated fibres showed a decrease in the intra-molecular hydrogen bonding density and crystallinity and also a decrease in the hemicellulose content. The net energy required to isolate cellulose nanofibres from bio-treated fibres was estimated at 2,000 kWh/T compared to 16,000 kWh/T required for isolating nanofibres from untreated fibres. The isolation of cellulose nanofibres from treated and untreated fibres by refining in disk refiner tends to obey the Rittinger’s law. These observations confirm the fact that Ophiostoma ulmi treatment of fibres can significantly reduce the energy required to isolate cellulose nanofibres from wood pulp fibres.

Keywords: Cellulose
Nanofibres
Ophiostoma Ulmi
Internal defibrillation
Hydrogen bond
FTIR spectroscopy
NMR spectroscopy
Cellulose nanofibre isolation
Advisor: Sain, Mohini
Using Chemogenomic Screens to Study the Mechanism of Action of an Antifungal Agent and Competitive Fitness in Yeast

Using chemogenomic fitness assays in S cerevisiae, I examined the mechanism of action of an antifungal agent and whether the loss of specific genes confers a competitive fitness advantage during long term culture. Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is presumed to act by disrupting the cell membranes of microorgansims. Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP) and multicopy suppression (MSP) profiling, were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to COS. The fitness assays identified deletion strains sensitive to COS and overexpression strains that suppress COS inhibition. The genes associated with these strains are involved in processes such as: transcription, translation, membrane signaling, trafficking and structure, cell division, and proteasome processes. Transcriptome analysis of wild type and 5 suppressors of COS in the presence and absence of COS revealed up-regulated transcripts in the suppressor strains involved in processes such as transcription, cell cycle, and Ras signaling. Down-regulated transcripts included genes related to protein folding and oxidative respiration. Overexpression of the ARL1 gene, a Ras-related protein involved in membrane trafficking, provided protection against COS-induced cell membrane permeability and damage. The ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and, when COS and Fluconazole were used in combination they acted in a synergistic fashion. These results indicate that COS’ mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide against drug-resistant fungal pathogens. To identify deletion strains that have better competitive fitness when grown in culture, I evaluated the homozygous and heterozygous deletion collections in a long term evolution experiment. After 600 generations, less than 1 % of the strains in each deletion collection were still present. 2-D differential gel electrophoresis protein analysis revealed that the selected populations are enriched for ribosome components. The known functions of the deleted genes in the selected strains provide insight into possible mechanisms that make these strains more fit; further experiments will help confirm these mechanisms.

Keywords: Chemogenomics
Yeast
Saccharomyces cerevisiae
chitosan oligosaccharide
Chitosan
chitooligosaccharide
antifungal
membrane
Sytox
Fluconazole
Amphotericin B
Terbinafine
haploinsufficiency profiling
homozygous profiling
multicopy suppression profiling
membrane permeabilization
ADP ribosylation factor–like
ARL1
heterozygous deletion strains
suppressor strains
fitness
ergosterol biosynthesis
genome-wide assay
Selection
Competitive fitness
Experimental evolution
Advisor: Westwood, J. Timothy
Lopez-Llorca, Luis Vicente
Nislow, Corey
Regulation of Multidrug Resistance at the Developing Blood-brain Barrier

P-glycopotein (P-gp) plays an important role in the protection of the fetal brain from foreign compounds. The studies described in this thesis have demonstrated that blood-brain barrier (BBB) P-gp protein and activity levels increase in concert with rising levels of fetal plasma glucocorticoids. Brain endothelial cells (which form the primary BBB) become increasingly responsive to the upregulatory effects of glucocorticoids with advancing gestation. These data provide strong evidence that fetal BBB drug resistance likely increases due to rising fetal glucocorticoid levels. The rise in BBB P-gp protection is subsequent to a decline in global fetal protection provided by placental P-gp. The decline in placental P-gp protection suggests that a “window” during development exists in which the fetus and fetal brain are susceptible to teratogens that may be in maternal circulation. Many women take prescription medications during pregnancy, a large number of which are potentially teratogenic with many of these being P-gp substrates. The susceptibility of the developing fetus to circulating teratogens may be further increased in pregnancies complicated by infection. Infections are common during pregnancy and result in the release of pro-inflammatory cytokines - potent inhibitors of P-gp. This thesis describes how pro-inflammatory cytokines released during infection inhibit fetal BBB drug resistance, particularly as the cells become more responsive to cytokines near term. Infection also accounts for ~40% of preterm births. These women often receive synthetic glucocorticoids (a potent modulator of P-gp) to mature the fetal lungs. Prenatal exposure to synthetic glucocorticoids can potentially further enhance the responsiveness of the developing BBB to pro-inflammatory cytokines, widening the “window” in which the fetal brain is susceptible to teratogens - putting the fetal brain at even more risk. The understanding of fetal multidrug resistance regulation and alteration has improved through the studies presented in this thesis. Understanding how events during gestation can negatively affect the drug susceptibility of the offspring will be critical in the development of future therapies to counteract these effects.

Keywords: Multidrug Resistance
P-glycoprotein
Breast Cancer Resistance Protein
Glucocorticoid
Cytokine
Brain
Endothelial
Guinea Pig
Development
Advisor: Matthews, Stephen G
Genomic Causes and Consequences of the Evolution of Self-fertilization in the Flowering Plant Genera Capsella and Collinsia

The shift in mating system from outcrossing to selfing is associated with many evolutionary changes including reduced flower size and changes in sex allocation, leading to a suite of morphological characteristics known as the selfing syndrome. Furthermore, the evolution of selfing is expected to have important effects on genetic variation and the efficacy of natural selection. However, the underlying genomic causes of morphological evolution and the extent of relaxed selection remain unresolved. In this thesis I use new genomic approaches to investigate the genetic basis of floral evolution as well as the consequences of the evolution of selfing in the genus Capsella (Brassicaceae), in which the highly selfing C. rubella evolved recently from the self-incompatible, obligately outcrossing C. grandiflora. Quantitative trait locus (QTL) mapping results suggest that few loci with major effects on multiple floral phenotypes underlie the evolution of the selfing syndrome. Patterns of neutral diversity in QTL regions from both resequencing and next-generation transcriptome sequencing suggest an important role for positive directional selection in the evolution of the selfing syndrome. Combined with the identification of differentially expressed genes, the signals of positive selection provide candidate regions for identifying the causal evolutionary changes. Analysis of whole-transcriptome polymorphism patterns shows a significant increase in the ratio of unique nonsynonymous to synonymous polymorphism in C. rubella, consistent with a genome-wide relaxation of selection. To investigate the evolution of selfing in the genus Collinsia, I combined transcriptome sequencing with Sanger resequencing of multiple populations of the large-flowered Collinsia linearis with its small flowered, more highly selfing sister species Collinsia rattanii. Patterns of nucleotide diversity suggest the recent divergence of C. rattanii associated with a severe population bottleneck. C. rattanii showed an increased proportion of nonsynonymous polymorphism, consistent with a relaxation of natural selection following the population bottleneck and shift to selfing. In general, my results using combined genome-wide polymorphism, QTL mapping and gene expression data allow for a powerful approach to investigate the targets of adaptive evolution following the shift to selfing, and highlight the potential for relaxation of selection associated with this transition

Keywords: Mating system evolution
Genomic causes and consequences
Advisor: Wright, Stephen
Poetry and the Press: Women's Literary Publishing in Canadian Newspapers, 1850-1900

This dissertation explores the important role the nineteenth-century newspaper played as a vehicle through which literary women could participate in public life, and specifically how women poets used this textual space as a forum for the exercise of rhetorical power. The newspaper was a space where women writers could speak with authority on the issues that concerned and affected them – a space where they could contribute to the dialogue in which the newspaper participated and, in doing so, claim a place for themselves as authors. The poetry sections of the daily newspapers in Canada were thus far from politically neutral, and they are deserving of attention, I argue, because they illustrate the extent and complexity of women’s involvement in nineteenth-century literary culture in Canada. In each of my three chapters I consider the rhetorical strategies women used to assert themselves in the political – and the literary – worlds. Chapter One focuses on the Halifax Acadian Recorder between 1850 and 1870 and the ways women used sentimentality in their writing as a pedagogical tool, in terms of content and form, to teach their readers appropriate modes of compassionate response to the world around them. I suggest that sentimentalism’s seeming indulgence in emotion proved a method by which women could extend themselves beyond the confines of the domestic spaces that were their ostensible focus. Chapter Two focuses on the Montreal Star’s Sunday Reading section between 1871 and 1888 to show how women co-opted the language of religion, and specifically the language used to describe Christ, in order to link feminine moral authority to God’s spiritual authority, thereby suggesting the female poet’s message was sanctioned by God. Finally, Chapter Three focuses on the Toronto Evening Telegram between 1880 and 1900 and writers’ significant shift away from earlier models of feminine morality as they embraced the persona of the poet as spokesperson for the city, taking on municipal politics and urban affairs more explicitly towards the end of the nineteenth century than ever before. As they reached beyond the subjects that had previously defined their work, these authors also reached beyond definitions of authorship that reinforced those boundaries. Although we can see significant change over the course of the fifty years that shape my project, throughout this period the newspaper remained an essential part not just of how women accessed their audiences but how they inserted themselves into Canadian life broadly as interested and invested participants, and as authors.

Advisor: Murray, Heather
The Order of St John of Jerusalem in London, Middlesex, and Surrey, c.1128–c.1442: A Social and Economic Study Based on The Hospitaller Cartulary, British Library Cotton MS Nero E vi

This dissertation is a socio-economic analysis of the Knights Hospitallers’ estate management in London, Middlesex, and Surrey. It is based on the examination of 372 charters that trace the social, legal, administrative, and economic history of the Order in England between c.1128 and c.1442. The Hospitallers’ involvement in London’s property market is placed within the larger social and economic context of the city. The evolution of the Order’s administrative policy from serving largely as an absentee landlord, to one entangled in litigation to recover rents in arrears, allowed the Order to more than double its income from urban and suburban possessions between the twelfth and fifteenth centuries. Regarding the rural Middlesex estates, it is argued that the Hospitallers tailored their administrative tactics to suit local social and economic conditions. They developed new estates with aggressive solicitation of properties and manorial assets, and expanded pre-existing manors by purchasing scattered properties and quit-claims from the descendants and widows of tenants. In response to fourteenth-century population decline and rising prices and wages, the Order shifted to long-term leasehold tenancies, removing themselves ii from the direct management of the properties. Social tensions after 1381, moreover, resulted in shorter leases, and the emergence of copyhold tenancies in the early fifteenth century. A comparative analysis of the Templars’ urban and rural possessions, and of the Hospitallers’ administration thereof following the dissolution of the Templars in 1312, is included in this dissertation. It is argued that the Hospitallers’ acquisition of Templar possessions increased not only their economic standing in England, but also positively impacted the spiritual profile of the priory church at Clerkenwell, London. This dissertation is the first of its kind to examine the corpus of charters pertaining to the Hospitallers’ estate management in London, Middlesex, and Surrey. It is a valuable contribution to our understanding of one of the most important medieval military orders in Europe, and its relationship with London. It is also of interest to scholars of the social and economic history of England. The charters that serve as the basis for this dissertation have been edited, and are included here as an appendix.

Keywords: Hospitallers
Templars
Military Orders
London
Middlesex
Surrey
Southwark
Medieval England
New Temple
Indulgences
Advisor: Gervers, Michael
"Incongruent Bedfellows": Physics and Medicine in the Formation of North American and British Radiology, 1896-1930

The announcement of the discovery of x-rays in 1896 sparked great excitement among physicists who rushed to replicate Wilhelm Röntgen’s experiments, hoping to make sense of the properties of this new disturbance in the aether. The medical world was equally entranced by the x-ray pictures that circulated in the press. The diagnostic possibilities were clear, and within a few months, doctors were able to purchase equipment to begin their own x-ray investigations. Physicists and doctors asked very different kinds of questions of these new rays, and the medical and physical investigations were largely separate. There were, however, a number of points of contact between these two worlds. Physicists were members of the first x-ray societies alongside doctors, and, by the 1920s, a small number of physicists were employed in the United States and Britain in hospitals and medical schools. In this study, I trace the contributions of these few physicists in medicine in order characterise the professional relationships that developed between doctors and physicists, individuals from very different disciplinary cultures. I show that the physicists’ values of objectivity and precise measurement, along with their deep belief in regularity, often clashed with the culture of individualism in early 20th century medicine. The first doctors to use x-rays expressed faith in their own, unique clinical art, and emphasized bodies’ idiosyncratic responses to radiation. These conflicting attitudes were evident in debates surrounding the best way to measure therapeutic x-rays, and I argue that the eventual adoption of the röntgen as the international unit of x-ray measurement in 1928 represents a victory of the values of physics. I link the increasing authority awarded to physicists in the American and British x-ray communities to the particular leadership roles taken on by these individuals as physics teachers and safety inspectors.

Keywords: History of Science
History of Medicine
Advisor: Yeang, Chen-Pang
The Biased Mirror: A Functional Approach to Intergroup Motor Resonance

Similar neural circuits are activated during action and during the observation of action, and such motor resonance is said to support action understanding and could potentially facilitate affect sharing, communication, cooperation and interpersonal coordination. Here I describe a line of research that uses suppression of electroencephalographic mu-oscillations as an indicator of motor resonance to look at motor resonance in an intergroup context. In study 1 I find that group categorization and intergroup biases can restrict motor resonance to the ethnic ingroup, potentially making it unavailable during cross-group interactions. In study 2 I investigate a reduction in affect sharing as a potential consequence of group biases in motor resonance. Using EEG prefrontal asymmetry patterns as an indicator of negative affect and avoidance tendencies, I show that participants do not share the sadness of outgroup members. Finally, I present two studies that test the boundary conditions of the ingroup bias in motor resonance. Study 3 shows that when motivational relevance of the outgroup is increased, because participants are in an inclusive, perspective taking mindset, group biases in motor resonance disappear. Similarly, study 4 shows that when the situation is highly motivationally relevant, such as when the behavior poses a potential threat; people will show motor resonance in response to anyone independent of group membership.

Keywords: motor resonance
prejudice
mu-suppression
Advisor: Inzlicht, Michael
Ottoman Constructions of the Morea Rebellion, 1770s: A Comprehensive Study of Ottoman Attitudes to the Greek Uprising

The topic of our dissertation concerns the Greek uprisings against the Ottoman Empire, which took place in the context of the Ottoman-Russian struggle of 1768-1774. That is, our research focuses on the Morea Rebellion which is often claimed as not only the first crucial step on the way towards creating an independent Greek state, which came into being in 1829 with the treaty of London, but also occasionally as one of the most significant turning points both for the history of the Ottoman Empire and for the struggle of Greek independence. The meaning of the Morea Rebellion has long been under discussion among Greek historians. While we will deal with Ottoman side of the issue, this study will shed light on matters of Greek historiography which has been generally been created without taking account of the Ottoman side of the story. In the light of Ottoman archival documents as well as writings of earlier, more contemporary sources, we will argue for the complexity and intricacy of the Morea Rebellion, as reflected in the Ottoman documents, many of which have not been used before. We have tested the veracity of narratives in contemporary chronicles, many of which have been subsumed into the narratives that are current still, by comparing them in Ottoman archival documents. Accordingly, we have revisited many widely accepted assumptions, such as those describing Ottoman society of the time as being divided into homogenous groups clearly defined religion, nation or other identity. In opposition to the earlier explanations of this uprising, our primary sources lead us to see the Morea Rebellion as predominately an international issue. Our conclusions invalidate the long held assumption that the Ottomans were ignorant of Russian initiatives in the Morea. Last but not least, the Ottoman attitudes towards the rebels as well as Ottoman preoccupation with Russia long after the collapse of the rebellion are considered in greater detail. On balance, we believe that, with the help of a better analysis of the secondary literature and the major new primary sources, we have provided an original and comprehensive story of the Morea Rebellion.

Keywords: The Morea Rebellion
Ottoman
Greek
Russia
Millet
Nationalism
Advisor: Aksan, Virginia