VictorJuiz/thesis huggingface dataset:
The Molecular Ecology of Hyporheic Zones: Characterization of Dissolved Organic Matter and Bacterial Communities in Contrasting Stream Ecosystems
Keywords: 0329
0425
0793
0307

The aims of this thesis were to characterize the molecular ecology of the hyporheic zone – between dissolved organic matter (DOM) and microbes – and to test whether seasonal and spatial patterns existed in correlation with seasonal ecosystem processes. The hyporheic zone is an area of vertical integration between groundwater and surface water, and lateral integration between terrestrial and stream ecosystems. Colonization corers were used to collect in situ DOM and bacterial communities from the hyporheic sediments of two streams that varied in hydroperiod (i.e., permanent vs. intermittent). DOM was collected using passive samplers and analyzed using 1H NMR and fluorescence spectroscopy; bacteria were characterized using terminal-restriction fragment length polymorphism. At the permanent site, bacteria correlated significantly with seasonal environmental factors including: fall communities with DOM concentration; spring and winter communities with nitrate concentrations; and summer communities with temperature. Bacterial communities at the intermittent site were significantly correlated with flooding as a function of hydrologic connectivity. Sediment communities were discriminated between hyporheic sediments and interstitial porewaters, and shared several operational taxonomic units (OTUs). Sediment communities were more distinct when hydrologic connectivity was low, and porewater communities changed dramatically upon flooding. Fifteen out of 259 OTUs were shared across aquatic sediments, interstitial porewater and watershed soil samples. DOM was spatially and seasonally dynamic in both sites. Five key DOM groups described using 1H NMR spectroscopy revealed spatial differences between the permanent and intermittent sites. EEM-PARAFAC models confirmed that despite significantly different molecular components, the relative sources of DOM at both sites were similar, including humic-like terrestrial sources and tyrosine (microbial) sources. This study provides new knowledge on both organic matter dynamics and bacterial communities in a dynamic aquatic ecotone, and also confirmed the hypothesis that bacterial communities correlated significantly with ecosystem processes within a watershed.
Modeling Dust Formation in Lime Kilns
Keywords: Lime Kiln
Dust

Dusting is one of the major problems in the operation of lime kilns because dust particles interfere with kiln operation and reduce its efficiency. A numerical model is developed to predict the rate of dust formation in rotary lime kilns. The model consists of four major components: 1) a 3D model for the kiln gas, solving fluid flow, heat transfer, and combustion in the gas region; 2) a 1D model for the kiln bed, solving for variation of the solids composition, including moisture content, along the kiln; 3) a 3D model to predict the motion of the solids in the bed, and to estimate the reaction rates; 4) a mathematical model to predict the rate of particle pickup from the bed. Additionally, motion of dust particles was modeled, for the first time, using Stochastic Separated Flow model (a Lagrangian approach). The developed model of particle tracking enables the user to predict distribution of dust particles in the gas section of the kiln. Different components of the model were validated using experimental data published in the literature. The developed model was used to simulate operation of a full-scale lime kiln at typical operating conditions, i.e. at different fuel and air flow-rates. Dusting signatures were also estimated for each setting to determine the effect each operating condition has on dusting. The results presented in this thesis indicate that dust formation is mainly affected by the kiln gas velocity. Effect of other operating conditions was found to be negligible within the ranges studied. The results presented here suggest that dust formation can be controlled by minimizing the input gas flow rate.
Chip-based Sensors for Disease Diagnosis
Keywords: Sensors
Diagnosis
Eletrochemistry
Nanotechnology

Nucleic acid analysis is one of the most important disease diagnostic approaches in medical practice, and has been commonly used in cancer biomarker detection, bacterial speciation and many other fields in laboratory. Currently, the application of powerful research methods for genetic analysis, including the polymerase chain reaction (PCR), DNA sequencing, and gene expression profiling using fluorescence microarrays, are not widely used in hospitals and extended-care units due to high-cost, long detection times, and extensive sample preparation. Bioassays, especially chip-based electrochemical sensors, may be suitable for the next generation of rapid, sensitive, and multiplexed detection tools. Herein, we report three different microelectrode platforms with capabilities enabled by nano- and microtechnology: nanoelectrode ensembles (NEEs), nanostructured microelectrodes (NMEs), and hierarchical nanostructured microelectrodes (HNMEs), all of which are able to directly detect unpurified RNA in clinical samples without enzymatic amplification. Biomarkers that are cancer and infectious disease relevant to clinical medicine were chosen to be the targets. Markers were successfully detected with clinically-relevant sensitivity. Using peptide nucleic acids (PNAs) as probes and an electrocatalytic reporter system, NEEs were able to detect prostate cancer-related gene fusions in tumor tissue samples with 100 ng of RNA. The development of NMEs improved the sensitivity of the assay further to 10 aM of DNA target, and multiplexed detection of RNA sequences of different prostate cancer-related gene fusion types was achieved on the chip-based NMEs platform. An HNMEs chip integrated with a bacterial lysis device was able to detect as few as 25 cfu bacteria in 30 minutes and monitor the detection in real time. Bacterial detection could also be performed in neat urine samples. The development of these versatile clinical diagnostic tools could be extended to the detection of various cancers, genetic, and infectious diseases.
Conductive Anodic Filament (CAF) Formation
Keywords: solder flux
printed wiring boards
conductive anodic filament

Conductive anodic filament (CAF) is a failure mode in printed wiring boards (PWBs) which occurs under high humidity and high voltage gradient conditions. The filament, a copper salt, grows from anode to cathode along the epoxy-glass interface. Ready and Turbini (2000) identified this copper salt as the Cu2(OH)3Cl, atacamite compound. This work has investigated the influence of polyethylene glycol (PEG) and polyethylene propylene glycol (PEPG) fluxing agents on the chemical nature of CAF. For coupons processed with PEPG flux, with and without chloride, a copper-chloride containing compound was formed in the polymer matrix. This compound was characterized using x-ray photoelectron spectroscopy (XPS) as CuCl and an electrochemical mechanism for the formation of the chloride-containing CAF has been proposed. For PEG flux, with and without chloride, it has been shown that CAF only formed, but no copper containing compound formed in the matrix. It appears for PEG fluxed coupons, a PEG-Cu-Cl complex forms, binds the available Cu and acts as a barrier to the formation of CuCl in the polymer matrix. Meeker and Lu Valle (1995) have previously proposed that CAF failure is best represented by two competing reactions – the formation of a copper chloride corrosion compound (now identified as Cu2(OH)3Cl) and the formation of innocuous trapped chlorine compounds. Since no evidence of any trapped chloride compounds has been found, we propose that the formation of CAF is best represented by a single non-reversible reaction. For coupons processed with a high bromide-containing flux, bromide containing CAF was created and characterized using transmission electron microscopy (TEM) to be Cu2(OH)3Br. In addition, a copper-containing compound was formed in the polymer matrix and characterized using XPS as CuBr. An electrochemical mechanism for the formation of bromide-containing CAF has been proposed based on the XPS data. .
New Icelandic Ethnoscapes: Material, Visual, and Oral Terrains of Cultural Expression in Icelandic-Canadian history, 1875 - Present
Keywords: Icelandic Canadians
Material culture
Immigration and ethnicity
Scandinavian migration
Manitoba history

This dissertation uses the Icelandic-Canadian community to discuss alternate media and the production of “ethnoscapes,” or landscapes of ethnic identity, on the prairies from 1875 to the present. Drawing from larger historiographies of food, gender, material culture, oral history, and commemoration, it offers an investigation into power, acculturation, and representation using often-marginalized terrains of Canadian ethnic expression. Each of the project’s five chapters examines the cultural history of the community through a different medium. The first chapter uses clothing, one of the most intimate and immediate ways that migrants experienced transition in North America, to explore the impact of poverty, marginalization, disease, climate, and eventual access to Anglo commercial goods on migrant culture. Chapter two analyses the role of food and drink, specifically coffee, alcohol, and vínarterta (a festive layered torte) in everyday life and the development of migrant identity. The third chapter analyses the growth of conservatism and depictions of women in the Icelandic-Canadian community in the twentieth century, with a focus on the decline of radical Icelandic language publications and the rise of ethnic spectacles. Chapter four analyses the impact of centennial and multicultural heritage campaigns on Icelandic-Canadian life, popular narrative, and domestic space by tracing the emergence of the koffort (immigrant trunk) in intergenerational family commemorative practices. Chapter five continues the discussion of popular memory with an examination of the compelling hjátru (superstitious) narrative tradition in the community. It illustrates that Icelandic migrants imported and adapted this tradition to the North American context in a way that also reflected their understanding of colonial violence as an unresolved, disruptive, and damaging intergenerational inheritance. Providing an alternate view of the community beyond either cultural endurance or assimilation, this dissertation argues that the multiple material, visual, and oral conduits through which members have experienced life in the New World have been crucial to the construction of Icelandic-Canadian identity. It is through these terrains that community members have continually engaged with public expectations and demands for both ethnic performance and suppression. The fluidity of these forms and forums and their facilitation of members’ engagement with, adaptations to, and contestation of images of ethnicity and history have enabled the continual construction of Icelandic identities in North America 135 years after departure.
Identifying Targets of ERA1 Involved in Plant Development and Abiotic Stress Signaling
Keywords: farnesylation
Arabidopsis

In Arabidopsis thaliana (Arabidopsis), by screening for the inability to germinate on low concentrations of exogenous abscisic acid (ABA), loss-of-function mutations in the β-subunit of a protein farnesyltransferase (FTase) were identified (Cutler et al., 1996). Designated era1-2, these mutants are pleiotropic and show a hypersensitive ABA response at the level of germination and stomatal closure, thereby conferring drought resistance, besides having particular developmental phenotypes (Pei et al., 1998; Bonetta et al., 2000). Although a number of proteins have been shown to be farnesylated in plants, which has provided some insight into how farnesylation regulates various processes, there is still no clear understanding of how loss of farnesylation can confer ABA hypersensitivity, for example. The simplest interpretation is that farnesylation acts as a negative regulator of ABA signal transduction. The primary goal of this thesis is to carry out several reverse genetic screens using a Arabidopsis homozygous T-DNA knockout collection to discover potential targets of farnesylation as well as to determine the overall function of these farnesylated targets in plant growth and development. This included screening for morphological changes related to era1-2, altered responses to ABA at the level of germination, and altered drought responses. In total, 15 unique mutants were identified from the aforementioned reverse genetic screens. A knockout in the gene At3g30180 became particularly interesting for further study since it exhibited several phenotypes that resemble era1-2, including ABA hypersensitivity in germination, drought resistance, protruding carpels, reduced fertility, and round and broadened leaves. At3g30180, otherwise known as CYP85A2, is a cytochrome P450 that mediates the final step in the biosynthesis of brassinolide (BL), a brassinosteroid (Kim et al., 2005). At3g30180 was also identified through a bioinformatic screen (Brady and Provart, 2009; Usadel et al., 2009). Overall, ERA1 positively regulates CYP85A2 function through farnesylation, and therefore BL production, which negatively regulates ABA signaling.
The Effect of Lactobacillus rhamnosus GR-1 Supernatant on Cytokine Production and Prostaglandins in Gestational Tissues
Keywords: Preterm Birth
L. rhamnosus GR-1
Cytokines
Prostaglandins
Bacterial Vaginosis
Fetal Sex

Preterm birth remains a major challenge in obstetrics. It complicates up to 13% of all pregnancies and accounts for approximately 80% of neonatal mortality and morbidity. Bacterial Vaginosis (BV) is associated with a 1.4-fold increased risk of preterm birth. Due to ineffectiveness of antibiotics in preventing preterm labour, probiotics have been proposed to serve as an alternative for treatment of BV and prevention of preterm birth. The objectives of this thesis were to determine 1) the effect of Lactobacillus rhamnosus GR-1 (L. rhamnosus GR-1) supernatant on cytokine profile and prostaglandin (PG)-regulating enzyme expression in lipopolysaccharide (LPS)-stimulated human chorion and placental trophoblast cells from human placentae, 2) the potential signaling pathways through which lactobacilli act and 3) the potential role of immune and placental trophoblast cells in initiating a response to LPS and L. rhamnosus GR-1 treatments. Primary cultures of human placental trophoblast cells were pre-treated with lactobacilli supernatant and then with LPS. In addition, immune cells were removed from cell suspensions using a magnetic purification technique to determine their role in modulating cytokine levels. The expression of pro- and anti-inflammatory cytokines and prostaglandin-regulating enzymes was then determined. We found sex-specific differences in the ability of LPS to increase the output of TNF-α, IL-10, and PTGS2. We also showed that L. rhamnosus GR-1 is able to act through the JAK/STAT and MAPK pathways to increase IL-10 and G-CSF, and independently down-regulates PTGS2 and TNF-α and up-regulates PGDH. The increase in G-CSF and PGDH were only observed in women carrying a female fetus. L. rhamnosus GR-1 may serve as an alternative to antibiotics in preventing some infection/inflammation-mediated cases of preterm birth.
Encounters with the Real: A Zizekian Approach to the Sublime and the Fantastic in Contemporary Drama
Keywords: drama
Slavoj Zizek
theatre
psychoanalysis
Caryl Churchill
Peter Shaffer
S. An-sky
Tony Kushner
Jacques Lacan
John Mighton
Eric-Emmanuel Schmitt
The Dybbuk
Equus
The Skriker
Possible Worlds
The Illusion
Enigma Variations
sublime
fantastic

This study brings the insights of Slavoj Žižek’s Lacan-inspired approach to bear upon a series of influential 20th century plays and their engagement with what Lacan calls the Real. The plays to be explored share a focus on experiences, events or encounters which transcend, exceed, disrupt, and in some cases shatter characters’ normal, familiar realities. Examined through the lens of Žižek, these confrontations with the sublime and the fantastic reveal a crucial relation to the plays’ contemporary contexts, prompting us to “look awry” upon the dynamics of our own symbolically-regulated reality and the ever-changing and precarious nature of our relation to it. Similarly crucial is the relation of the Lacanian Real to our theatrical forms and modes of perception in the theatre. In staging “encounters with the Real,” these plays prompt us simultaneously to explore the ways in which the Real operates —and “appears” — in our own theatrical experience, ensnaring our gaze and the force of our desire. The study offers a Žižekian approach to works including Peter Shaffer’s Equus, John Mighton’s Possible Worlds, S. An-sky’s The Dybbuk, or Between Two Worlds, Caryl Churchill’s The Skriker, Tony Kushner’s The Illusion, and Eric-Emmanuel Schmitt’s Enigma Variations.
Structural and Functional Characterization of Leukocyte-type Core 2 {beta}1,6-N-acetylglucosaminyltransferase
Keywords: glycosyltransferase
crystallography
C2GnT

Leukocyte type core 2 {beta}1,6-N-acetylglucosaminyltransferase (C2GnT-L) is a key enzyme in the biosynthesis of branched O-glycans. It is an inverting, metal ion-independent glycosyltransferase that catalyzes the formation of the core 2 O-glycan (Gal{beta}1,3[GlcNAc{beta}1,6]GalNAc-O-Ser/Thr) from its donor and acceptor substrates, UDP-GlcNAc and the core 1 O-glycan (Gal{beta}1,3GalNAc-O-Ser/Thr), respectively. The primary objective of the work described in this thesis is to shed light on the structure, catalytic mechanism and substrate specificity of C2GnT-L. Since glycosyltransferases are membrane bound glycoproteins that possess disulphide bonds, the first challenge was to produce sufficient quantities of C2GnT-L for biochemical and structural characterization. To this end, C2GnT-L and various active site mutants were expressed and purified from stably transformed mammalian cell lines. The x-ray crystal structure of wild-type C2GnT-L was solved, in both its apo and acceptor substrate complexed forms. The structures, along with revealing the structural basis for acceptor substrate specificity, showed that C2GnT-L belongs to the GT-A glycosyltransferase fold type. This was a surprising result given that, to this day, C2GnT-L is the only GT-A glycosyltransferase that does not possess a DXD motif and does not require a divalent metal ion for catalysis. The mechanism of the metal ion-independent C2GnT-L activity, within the context of the metal ion-dependent GT-A fold, was probed further using site directed mutagenesis in conjuncition with x-ray crystallography, enzyme assays, and frontal affinity chromatography. It was found that positively charged side chains in C2GnT-L functionally replace the divalent metal ion found in other GT-A glycosyltransferases, providing evidence for a convergence of metal ion-independent activity between GT-A and GT-B glycosyltransferase fold types.
Cardiovascular, Utero- and Fetoplacental Function in Mice during Normal Pregnancy and in the Absence of Endothelial Nitric Oxide Synthase (eNOS)
Keywords: eNOS
Pregnancy
cardiovascular
uterine circulation
umbilical circulation
ultrasound
preeclampsia
IUGR
mouse
remodeling
placenta
VEGF

In pregnancy, the maternal cardiovascular and placental circulation undergoes structural and functional changes to accommodate the growing fetus, but the mechanisms involved are not fully understood. Nitric oxide (NO) increases in normal pregnancy and lack of NO has been implicated in pregnancy related complications, preeclampsia and fetal growth restriction. Thus, the objective of the thesis was to determine if cardiovascular, uteroplacental and fetoplacental changes observed in human pregnancy also occur in mice and to assess the obligatory role of eNOS in mediating these changes. I showed that like humans, mice exhibit increases in maternal cardiac output, stroke volume, plasma volume, and uterine arterial blood flow, and a transient decrease in arterial pressure during pregnancy. Importantly, I showed that endothelial nitric oxide synthase (eNOS) plays an important role in promoting the progressive increase in maternal cardiac chamber dimensions and output and the enlargement of the aorta during pregnancy in mice. Another novel finding was that eNOS plays an important role in remodeling of the uterine and umbilical vasculatures during pregnancy. The remodeling of the uterine vasculatures, including the uterine and spiral arteries, were blunted in the eNOS KO mice with ko fetuses (KO(ko)) and this likely contributed to elevated vascular resistance and reduced perfusion of the uterine circulation during pregnancy. Impaired spiral artery remodeling may be caused by a deficiency in decidual uterine natural killer cells. Fetal placental vascularization was also impaired in eNOS KO(ko) mice, which likely increased vascular resistance and thereby reduced fetoplacental perfusion. Reduced vascularization may be due to decreased VEGF mRNA and protein expression in KO(ko) placentas. Decreased perfusion in both the uterine and umbilical circulations most likely contributed to elevated placental and fetal hypoxia in the eNOS KO(ko) mice. Interestingly, despite placental hypoxia, eNOS KO(ko) mice do not show the classical signs of preeclampsia including hypertension and proteinuria nor are maternal plasma sFlt1 levels elevated. Nevertheless, eNOS KO(ko) pups are growth restricted at term, and this is mainly due to the fetal genotype. These findings suggest that eNOS plays an essential role during pregnancy in remodeling of the maternal heart, aorta, and uterine and umbilical vasculatures thereby augmenting blood flow to the maternal and fetal sides of the placenta and thereby promoting fetal growth in mice.