VictorJuiz/thesis huggingface dataset:
Development of an Organotellurium Tag Compatible with Mass Cytometry to Probe Senescence-associated beta-Galactosidase Activity
Keywords: aging
beta-galactosidase
cancer
chemical biology
senescence
tellurium

Fluoresence-based flow cytometry has found great use in investigating biomarker composition in cell samples. Its reliance on fluorophores, however, restricts the technology from comfortably performing multiparametric experiments. Mass cytometry (MC) has emerged as an alternative, capable of simultaneous quantification of multiple parameters over zero background. However, the antibody-conjugated mass tags commonly used as probes can only detect presence of analyte, and do not provide direct information regarding activity of enzyme targets. Therefore, we developed an activity-based small molecule probe compatible with MC, with senescence-associated beta-galactosidase as a target and tellurium as the mass tag. The stabilities of various organotellurium functionalities were compared to determine the most optimal candidate for incorporation into probes compatible with MC, with the tellurophene exhibiting the best characteristics. Various generations of the senescence probe were evaluated in vitro, with the tellurophene-containing derivatives showing the most promise. Preliminary studies in senescent cell culture have yielded encouraging results.
The Role of Nutritional Factors in Acute Respiratory Tract Infections
Keywords: anthropometry
diet quality
nutritional risk factors
respiratory tract infection
vitamin D

Children 1-17 years with laboratory-confirmed influenza were recruited in a multi-center setting over two consecutive influenza seasons. Influenza was more severe among underweight (n=9), stunted (n=4), and wasted (n=4) children compared to normal counterparts (P
Anemia Mediated by an Anti-erythrocyte Antibody is Not Closely Linked to the Amelioration of Murine Passive Immune Thrombocytopenia (ITP)
Keywords: anemia
Anti-D
erythrocytes
Immune thrombocytopenia
platelets
TER-119

Immune thrombocytopenia (ITP) is an autoimmune disease characterized by platelet destruction. A first line therapy for ITP is Rh immune globulin (anti-D) which reacts with erythrocytes and can cause anemia. Nine antibodies reactive with murine erythrocytes were evaluated for their ability to induce anemia and ameliorate murine ITP. Several anemia-inducing antibodies did not ameliorate the ITP and no antibody which did not induce anemia ameliorated ITP. The glycophorin A specific antibody (TER-119) was found to be able to induce anemia and ameliorate ITP. TER-119 was able to ameliorate ITP before it could induce significant anemia, and had no therapeutic effect 4 days after its administration when it induced maximal anemia. This work demonstrates that while the ability of an antibody to induce anemia could be an important attribute of an effective antibody, it seems unlikely that the anemia itself is necessary for therapeutic activity in murine ITP.
Serotonin Receptor Electrophysiology in Cortical Neurons Critical for the Response to Antidepressants
Keywords: Electrophysiology
Fluoxetine
Motor Cortex
Pyramidal Neuron
S100a10
Serotonin

The gold standard for treating depression is a class of medicines known as selective serotonin reuptake inhibitors (SSRIs). Recent research identified a subgroup of layer V pyramidal neurons in the cerebral cortex important for the antidepressant action of SSRIs. Using transgenic mice that have these p11-expressing neurons labeled with GFP, I characterized these neurons and their neighbours under control conditions and after chronic treatment with the SSRI fluoxetine (FLX). Experiments were conducted with a particular focus on serotonin (5-HT) responses, using whole-cell recording in acute brain slices of motor and prefrontal cortex. Further investigation explored the effects of chronic FLX treatment in a mouse model of stress. I found that chronic FLX treatment has significant effects on neurons in both motor and prefrontal cortices, that p11-expressing neurons differ subtly in their response to 5-HT, and that there is evidence of an interaction between stress and FLX treatment in p11-expressing neurons.
Leukemic Stem Cell-targeting Auger Electron Radioimmunotherapeutic Agent for Acute Myeloid Leukemia
Keywords: Auger electron
Cancer
Leukemia
Radioimmunotherapy
Stem cell

A leukemic stem cell (LSC)-targeting Auger electron-emitting radioimmunotherapeutic agent for acute myeloid leukemia (AML) comprising the monoclonal antibody CSL360 with high affinity for the LSC CD123+/CD131- immunophenotype modified with indium-111 and a nuclear localization sequence peptide (111In-NLS-CSL360) was constructed and evaluated. Methods: CD123 immunoreactivity of 111In-NLS-CSL360 was measured. Toxicity and anti-leukemic effectiveness of a three-dose regimen of 111In-NLS-CSL360 were assessed in a NOD/SCID mouse model of AML. Results: Immunoreactivity of 111In-NLS-CSL360 was preserved. 111In-NLS-CSL360 was found to be non-toxic. While leukemic engraftment in the bone marrow was paradoxically increased by 111In-NLS-CSL360, splenic engraftment in mice with low disease burden was significantly lower than in mice treated with a control radioimmunoconjugate. Conclusion: 111In-NLS-CSL360 remains a promising investigational therapeutic agent for targeting LSCs, but due to complications with the NOD/SCID mouse model, an alternative strain of mice is recommended for future studies.
Experience, Struggle and Change: Saudi Women Studying in a Canadian Context, under the King Abdullah Scholarship Program
Keywords: Lived experiences
Religion
Saudi students
Scholarship
Transformation
Women's studies

This study will trace the impact of the King Abdullah Scholarship Program KASP on Saudi women currently studying in Canada, as well as the academic and socio-cultural complexities that participating in this scholarship program entails. In particular, issues of religion and gender are explored, with an emphasis on the experiences, struggles and changes elicited through the educative process.
Regulation of Metabolism in Early Drosophila Embryos by the Smaug RNA-binding Protein
Keywords: drosophila
embryo
metabolism

Smaug is a RNA-binding protein that regulates translational repression and/or degradation of its targets, and is required for the elimination of a large number of maternal transcripts in early Drosophila embryos. Here, I explored a novel role of Smaug in regulation of Smaug in early embryos. Previous experiments identified mRNAs encoding glycolytic enzymes as associated with Smaug. I found that mRNAs encoding these enzymes have predicted Smaug recognition elements (SREs) and are destabilized by Smaug. Furthermore, I performed enzyme activity assays and showed increased activity of several glycolytic enzymes in smaug mutants. Experiments comparing the metabolome of wild-type and smaug mutant embryos implicated Smaug in an array of metabolic pathways including glycolysis.
Methods for the Identification of Biomarkers in Prostate and Breast Cancer
Keywords: biomarker
breast cancer
prostate cancer

Given the high incidence rate of both prostate cancer and breast cancer, it is crucial to identify early which individuals have cancer and moreover, which ones are at risk for their diseases. Currently available markers are either overly invasive or are insufficiently sensitive/specific. The goal of this project is to create effective diagnostic and prognostic biomarkers for prostate and breast cancer. Two separate but complimentary approaches have been taken. In prostate cancer, we developed a set of circulating DNA (cirDNA)-based biomarkers using a supervised machine learning approach. Using methylation patterns in cirDNA, we were able to predict whether a sample was cancer or normal with good sensitivity and specificity. Similarly, a set of prognostic candidates was derived using copy number aberrations (CNAs) in breast cancer samples.
Thermally-activated Mechanical Failure from Point Defects in Two-dimensional Material Systems
Keywords: Failure Mechanism
Graphene
h-BN
Molecular Dynamics
Point-defects
Thermal-activation

The phenomenal mechanical properties found in graphene have inspired interest in other two-dimensional materials, such as hexagonal Boron Nitride (h-BN). However, the pristine lattice that contributes to its strength is rarely manufactured in practice; instead, point defects are common. Using atomistic simulations, we analyzed defective structures to understand the failure mechanisms and determine failure properties. We analyzed the role of temperature and strain-rate on failure in point-defective graphene using molecular dynamics (MD). Activation energy barriers were obtained by Arrhenius relationships and used to predict realistic strengths. Thereafter, MD was used to evaluate thermally-activated failure from point defects in h-BN. Athermal simulations were performed with density functional theory to obtain the theoretical strength of h-BN. The overall contribution of this thesis allows us to predict realistic strengths of graphene with point defects and shows us that h-BN has the potential to exhibit phenomenal strengths that have been experimentally determined in graphene.
Airway Nucleases and Surfactant Protein D in Neutrophil Extracellular Traps Clearance
Keywords: airway nucleases
alveolar macrophages
neutrophil extracellular traps
surfactant protein d

Neutrophils release neutrophil extracellular traps (NETs) to trap and kill invading pathogens. However, NETs can damage host cells. A mechanism of NET clearance in the airways has not been established. We investigated whether NETs are cleaved by airway nucleases. Our study showed that nucleases are present in murine airways and that genomic DNA and NETs are cleaved in a magnesium/calcium- and calcium-dependent manner, respectively. We also found that these nucleases function optimally at specific pH ranges, such as near neutral pH and acidic pH. We also assessed the role of SP-D in NET clearance. We found that SP-D-deficient mice are defective in NET clearance compared to WT mice. SP-D supplemented to NET-alveolar macrophage (AM) cultures had fewer remaining NETs. Thus, we conclude that SP-D enhances the clearance of NETs by AMs. Overall, we conclude that nuclease digestion and SP-D are involved in the clearance of NETs in the airways.
Identifying Molecular Mechanisms of Progesterone-responsive Mammary Stem Cell Expansion
Keywords: Bioinformatics
Hormones
Mammary Gland
Microarray
Stem Cells

Progesterone is a key mediator of cellular changes in the mammary gland. These changes occur naturally during the reproductive cycle and likely underlie the correlation between ovarian hormone exposure and breast cancer risk. This study utilizes microarray gene expression profiling to study the effects of progesterone on distinct mammary epithelial subsets, under defined hormone conditions. Through these transcriptomic analyses, we yield critical information that enables us to better understand molecular mechanisms underpinning progesterone-driven actions in the mammary gland. In this study, we combined bioinformatics approaches ranging from pre-processing to functional analyses, with wet lab techniques such as clonogenic assays and
Effects of Filtering Visual Short Wavelengths on Circadian Photic Phase Resetting
Keywords: circadian rhythms
light
masking
short-wavelength light
suprachiasmatic nucleus

The mammalian circadian system relies on retinal photoreceptors to entrain the master circadian pacemaker in the suprachiasmatic nucleus (SCN) to environmental light-dark cycles. Non-visual light responses, including acute physiological changes and circadian phase resetting, demonstrate a spectral sensitivity to visual short wavelengths (450-480 nm). In this thesis, I examine the effects of filtering visual short-wavelengths from polychromatic white light(~100µW/cm
Binding, Activation and Cellular Actions of Teneurin C-terminal Associated Peptide (TCAP)-1 with its Putative Receptor, Latrophilin-1 (ADGRL1), in Immortalized Cell Lines
Keywords: Latrophilin
Peptides
Receptor-ligand interaction
TCAP
Teneurin

Teneurins are multifunctional type II transmembrane proteins that bind the Adhesion G-protein coupled receptor subfamily L/Latrophilin (ADGRL) in the only intermolecular synaptic adhesion unit conserved between invertebrates and vertebrates. However, the specific interaction between teneurin and ADGRL is not well understood. The distal extracellular region of teneurin possesses a potentially cleavable bioactive peptide termed the ‘teneurin C-terminal associated peptide’ (TCAP). A synthetic version of TCAP-1 is highly active in cells, causing increased expression of cytoskeletal components and actin re-arrangement. Yet the mechanism by which TCAP-1 induces these effects remains unclear. HCT116 cells over-expressing ADGRL1 have increased uptake of TCAP-1 compared to wild-type cells. ADGRL1 expression causes increased adhesion between cells and reduces their expression of f-actin. TCAP-1 treatment induces f-actin polymerization and modulation of cellular morphology only in ADGRL1-expressing cells. These data are the first to establish TCAP-1 as an endogenous ADGRL1 ligand, and further elucidate its mode of action.
Wnt/ β-catenin: A Novel Candidate Pathway for Bone Repair in Neurofibromatosis Type 1
Keywords: CPT
Fracture repair
Neurofibromatosis
NF1
Pseudarthrosis
tibia

Skeletal abnormalities occur in half of the individuals with neurofibromatosis type-1 (NF1), the most difficult to manage is congenital pseudarthrosis of tibia (CPT). High levels of β-catenin result in a phenotype similar to CPT in mice fractures. β -catenin in CPT samples was up-regulated, therefore we hypothesized that Wnt/ β-catenin pathway partially mediates the effect of NF1 mutation on bone by altering the differentiation of MSCs into osteoblasts. Conditional knock-out Nf1 mice were crossed with conditional β-catenin over-expressing and knock-out models. Adenovirus expressing Cre recombinase was injected at the fracture site to activate the conditional alleles. Fracture healing was evaluated by radiological, histological and biomechanical tests. Nf1 deficient tibial fractures were associated with higher cellular β-catenin levels and delayed healing, exhibiting a fibro-cartilaginous phenotype with abundant undifferentiated MSCs. Down-regulating and stabilizing β-catenin, improved and exacerbated Nf1 deficient fracture healing respectively. These data indicate that the level of β-catenin in NF1 patients and Nf1 deficient fractures is abnormally elevated, and this level inhibits osteoblastogenesis and bone repair. Since pharmacologic agents to inhibit β-catenin are under developemt, this data also suggests a novel therapeutic approach to improve bone healing in patients with NF1.
Integrin Activation and Focal Adhesion Kinase in the Survival and Regeneration of Injured Adult Rat CNS Neurons
Keywords: Apoptosis
CNS
focal adhesion kinase
integrins
Retina

The retina develops as an outpouching of the diencephalon, and retinal ganglion cells (RGCs) are central nervous system (CNS) neurons whose axons form the optic nerve and extend into the brain. The retina provides an excellent model to study diseases affecting both RGCs and other CNS neurons. Integrin attachment to the extra-cellular matrix (ECM) provides developmental, survival, differentiation and axon extension cues to RGCs which are suspected to be dependent on focal adhesion kinase (FAK) activation. Damage to the optic nerve induces RGC apoptosis and release matrix metallo-proteinases (MMPs) to degrade the ECM and arrest pro-survival signals. This work demonstrates that MMP activation and reduced FAK activity occur early in the apoptotic process and that by respectively reducing and increasing their activity we are able to rescue significant amounts of RGCs, and increase the number of regenerating axons following optic nerve transection.
Characterizing Novel PPAR Agonists Derived from Cashew Nut Shell Liquid for the Treatment of Metabolic Disease
Keywords: CNSL
diabetes
DIO
dyslipidemia
fatty acids
PPAR

The peroxisome proliferator-activated receptors (PPARα,γ,β) are important druggable targets to treat patients with type 2 diabetes and dyslipidemia. However, current PPAR agonists lead to serious adverse effects, including edema, cardiovascular disease, weight gain, and bone fractures. We hypothesized that PPAR agonists with properties similar to their endogenous ligands may be therapeutically desirable for treatment of metabolic disease while limiting the adverse effects. Using in vitro models, we found that a number of LDT compounds derived from cashew nut shell liquid acted on the PPAR receptors. Specifically, we identified LDT409 that showed partial agonistic activity and equal binding affinities to PPARα and PPARγ receptors with reduced affinity for PPARβ. Using diet-induced obese mice, we determined that LDT409 was protective from high fat diet-induced weight gain, fatty liver disease, and insulin resistance without increasing markers of edema, bone loss, and heart failure. Together, these studies suggest that LDT compounds will be efficacious to treat metabolic disease and may have fewer adverse effects compared to traditional PPAR agonists.
Engineering the Refugee Crisis- Governmentality through humanitarianism in the evolving context of Turkey
Keywords: Govermentality
Humanitarianism
Migration management
Turkey

This study explores the dynamics of forced migration and refugee management in the context of Turkey through an examination of the evolving legal framework between 2013 and 2016. Weaving together a policy discourse analysis with the narratives of refugees in Turkey and their agency, I seek to challenge conventional discourses of victimhood and the use of humanitarian rhetoric to further political interests and manage flows using a critique of governmentality through humanitarianism. Particular attention is paid to the shift from an open door policy to the implementation of the New Law on Foreigners and Temporary International Protection, the provision of works permits and the Turkey-EU deal. This paper compares and contrasts the differing experiences of non-Syrian asylum-seekers and Syrians under guest status. In addition, I contemplate the discourse of crisis and management and interrogate the rhetoric of vulnerability and humanitarianism in the context of the migration-foreign policy nexus and Turkey-EU relations.
Harnessing Neuronal-glial Interactions to Prevent Postanesthetic Cognitive Deficit
Keywords: Astrocytes
Dexmedetomidine
Electrohpysiology
General Anethetics
Postoperative Cognitive Disorders
Treatment mechanisms

General anesthetics trigger memory deficits that persist long after the anesthetics have been eliminated, by increasing an extrasynaptic GABAA receptor-mediated tonic inhibitory current in the hippocampus. This increase in tonic current contributes to cognitive deficits associated with postoperative delirium, a debilitating disorder that affects 20% of elderly patients undergoing surgery. The Îą2-adrenergic receptor (Îą2R) agonist dexmedetomidine (DEX) reduces postoperative delirium in ICU patients. The mechanisms involved are unknown. Interestingly, DEX modulates astrocyte function to protect neurons in other injury models. This thesis explores the mechanism of DEX-neuroprotection from anesthetic-induced increase in tonic current, using a cell culture model. My studies show that DEX stimulates astrocytic Îą2Rs to release neuroprotective factors, possibly including BDNF and EGF, which act on hippocampal neurons to prevent the anesthetic-induced increase in tonic current. These results present a potential mechanism by which DEX reduces anesthetic-induced cognitive deficits and identifies alternative drugs that may treat postoperative delirium.
Growth in Infants Receiving Modified Fat Breast Milk for the Treatment of Chylothorax following Cardiothoracic Surgery
Keywords: Breast Milk
Chylothorax
Growth
Infant

Background: In infants diagnosed with chylothorax, breast milk provision is often discontinued and a medium chain triglyceride (MCT) formula is prescribed. Alternatively, modified fat breast milk (MFBM) can be used as treatment, however its impact on growth is unclear. Objective: To assess growth in cardiac infants receiving nutrient enriched MFBM for chylothorax treatment. Methods: In this open-label trial, infants were randomized in to one of two interventions: Target Fortification, where MFBM protein concentration was measured prior to fortification (n=3); or Higher Initial Concentration, where MFBM was fortified to a higher initial energy and nutrient level (n=2). For this thesis, analysis of the two MFBM interventions were combined. Growth was compared to infants receiving the standard MCT formula treatment (n=7). Results: No differences were found in the change of weight-for-age, length-for-age, head circumference-for-age and weight-for-length z-scores between the groups. Conclusion: Further MFBM subject recruitment is required to determine how the different nutrient enrichment methods impact growth.
Modeling and Proof of Concept of a Passive Irrigation Controller for Efficient Water Use in Low-Income Areas
Keywords: Agriculture
Human Centered Design
Irrigation Control
Soil Water Potential

Irrigation has been shown to contribute to the alleviation of poverty around the globe. However, its success is limited by water scarcity. Human Centered Design (HCD) principles were employed to address agriculture's involvement in global water scarcity from an engineering standpoint, particularly in low-income areas. An irrigation controller was developed in partnership with a low-income community in Nicaragua to regulate soil water potential (SWP). Ground research and interviews inspired the adaptation of passive technology using locally available materials such as PVC fittings. A prototype was constructed and presented to the community for feedback. A semi-empirical model of the controller was developed and experimentally verified to enable sizing of the components and evaluation of the system capabilities. The controller model was coupled to an environmental model to predict the performance. The model results show the controller has a potential water savings of up to 69%.
Investigating the interaction of AKAPs with PLN to mediate phosphorylation processes
Keywords: A-kinase associated protein (AKAP)
cardiomyocyte
cardiomyopathy
heart
phospholamban (PLN)
protein kinase A (PKA)

A common characteristic of cardiomyopathy is dysregulated Ca2+-cycling. During Ca2+-cycling, Sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) reuptakes Ca2+ into the sarcoplasmic reticulum (SR). SERCA is inhibited by Phospholamban (PLN). PLN inhibition is reversed through phosphorylation of Ser16 by protein kinase-A (PKA) when anchored to A-kinase anchoring proteins (AKAPs). Previous studies identified 3 human PLN-mutants –R9C, R14Del, and L39stop– causing cardiomyopathy. We were interested in the mechanisms by which wild-type PLN (PLN-WT) and PLN-mutants are phosphorylated through AKAPs-PLN-PKA interactions. Using publically-available RNA-seq and proteomic data we identified muscle AKAP (mAKAP) to be expressed in the heart. Immunofluorescent data showed mAKAP to be expressed in the SR and co-localizing with PLN. Immunoprecipitation in co-transfected HEKs showed pull-down of mAKAP and PLN-WT/mutants. We showed PLN-mutants exhibit altered protein phosphorylation and mAKAP-PLN interactions. In conclusion, we determined a possible link between mAKAP and PLN for the regulation of PLN phosphorylation by PKA.