VictorJuiz/thesis huggingface dataset:
BRCA1 Modulation of Glucocorticoid Receptor Signal Signaling in High-grade Serous Ovarian Cancer Cells
Keywords: BRCA1
Breast Cancer
1
Glucocorticoids
Ovarian Cancer

Germline BRCA1 mutations increase a woman’s risk of developing high-grade serous ovarian cancer (HGSOC) up to 43-fold. Lifetime ovulatory events also associate with increased risk. Studies suggest the post-ovulatory pro-inflammatory milieu persists longer in BRCA1 mutation carriers compared to control women. Slowed remediation of pro-inflammatory signaling leads to increased reactive oxygen species levels that potentiate DNA damage accumulation, which may ultimately promote malignant transformation. Preliminary evidence suggests BRCA1 may modulate glucocorticoid receptor (GR) activity, a major anti-inflammatory mediator. Impairment of GR signaling by BRCA1 mutation may contribute to increased HGSOC risk. My objective was to determine if BRCA1 deficiency affects GR signaling in HGSOC cells. My results indicate BRCA1 enhances GR levels and GR transcriptional activity independent of its effect on GR levels. BRCA1 expression also correlates with diminished pro-inflammatory cytokine mRNA levels at baseline. Overall, BRCA1 has a dynamic role in modulating inflammatory signaling through GR in HGSOC cells.
The effect of Lactobacillus rhamnosus GR-1 supernatant on endotoxin-induced cytokine secretion in human myometrial cells
Keywords: Cytokines
Lactobacillus rhamnosus GR-1
Myometrium
Preterm Birth
Probiotics

Prophylactic administration of probiotic Lactobacillus rhamnosus GR-1 supernatant (GR1SN) was shown to prevent lipopolysaccharide (LPS)-induced preterm birth (PTB) in mice by suppressing pro-inflammatory cytokine expression in uterine tissues in vivo. The aim of this thesis is to elucidate the effects of GR1SN in human myometrial cells in vitro, where I hypothesize it will suppress LPS-induced cytokine secretion. Here I demonstrate that PBS-based GR1SN contains protein moieties that induce endotoxin tolerance-like phenotypes in myometrial cells to suppress secretion of pro-inflammatory factors following LPS stimulus. The observed effects are unique to a GR1SN-myometrial cell interaction, and cannot be replicated using supernatant derived from non-GR-1 lactobacilli species. However, in vivo, GR1SN-PBS does not delay the onset of LPS-induced PTB in pregnant CD-1 mice under the experimental conditions used. Through this project, I have highlighted the unique capacity of protein moieties secreted by L. rhamnosus GR-1 to inhibit inflammatory signals in human myometrial cells.
The Circulating Furan Fatty Acid Metabolite CMPF Directly Enhances Hepatic FGF21 Secretion and Lipid Metabolism
Keywords: ACC Inhibition
CMPF
FGF21
Lipid metabolism
NAFLD
Steatosis

Elevation of the fish oil metabolite 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) induces metabolic remodeling within the -cell to a preferential use of fatty acids. Although detrimental to -cell function, this energetic switch could benefit metabolic tissues like the liver, where obesity increases hepatic fat accumulation. CMPF primarily utilizes the Organic Anion Transporter (OAT) family, with OAT2 expressed in the liver. Following treatment, CMPF enters the hepatocyte. To determine a direct effect on liver function, isolated murine hepatocytes were treated for 24-hours with CMPF. CMPF significantly increased hepatic fatty acid oxidation and lipogenesis, without altering fatty acid uptake or gluconeogenesis. CMPF improved hepatic insulin signaling following lipid overload and enhanced FGF21 expression. Enhanced lipid oxidation occurred without ACC/AMPK phosphorylation, CMPF impaired enzymatic activity of isolated ACC, and direct ACC inhibition similarly increased FGF21 expression, suggesting an ACC inhibitor like effect of CMPF. These results demonstrate a potential therapeutic target to prevent hepatic steatosis.
PKCδ Regulates the Behavior of Migrating Cells in the Drosophila ovary
Keywords: Drosophila
migration
ovary
PKCδ

The border cell cluster (BCC) in the Drosophila ovary allows us to study the molecular mechanisms that regulate cell migration in vivo. Our lab previously showed that PKCδ, a member of the protein kinase C family, affects BCC motility. My goal was to determine the expression pattern and the function of PKCδ in BCCs. I generated antibodies that target PKCδ to examine BCCs with increased expression of PKCδ. PKCδ seemed to be enriched in the cortical region and some cellular protrusions, and appears to be complementary to Myosin II. An analysis of BCCs with mosaic overexpression of PKCδ revealed that rosette cells with increased PKCδ expression have a decreased tendency to reside at the leading edge of the BCC during migration. Further examination showed that PKCδ-overexpressing rosette cells extend less major protrusions than wild-type cells, and are less compact as a group than a group of wild-type cells.
Engineering of Actively Targeted Block Copolymer Micelles for Delivery of Doxorubicin to Breast Cancer Cells Overexpressing HER2 and EGFR
Keywords: block copolymer micelles
breast cancer
doxorubicin
EGFR
HER2

Tumour heterogeneity remains one of the hallmark challenges in nanomedicine. Heterogeneous cell receptor expression presents a need for personalized therapeutic treatment options. In the case of human epidermal receptor 2-positive (HER2+) metastatic breast cancer (MBC), trastuzumab often results in the acquisition of trastuzumab resistance (TR). The implementation of dual-targeted nanoparticles is proposed as a strategy to overcome tumour heterogeneity and TR. A BCM delivery system was designed to deliver doxorubicin to HER2 and EGFR-overexpressing MBC cells through dual active targeting with peptides. Physico-chemical characterization of the BCM and its components was performed and in vitro cytotoxicity was evaluated in order to determine the effects of dual-targeting. Only minor targeting activity was observed during EGFR-targeting, although HER2-targeting was effective. The dual-targeted formulation was effectively able to enhance the cytotoxicity of the DOX-loaded BCMs and there is evidence that dual-targeting may provide therapeutic response to multiple cell lines with variable receptor phenotypes.
Microfluidics for Fluid Analysis in Oil Sands and Tight Oils
Keywords: Bitumen
Hydraulic fracturing
Imbibition
Microfluidics
Oil sands
Shale oil

Unconventional oil recovery has advanced over the decades as conventional oil supply declines. In North America, unconventional oil has been commercialized in the oil sands and shale formations. However, as oil prices collapse and emission concerns associated with hydrocarbon recovery increases, producers are seeking cost-effective methods to improve economic and environmental performance. Steam-Assisted Gravity Drainage (SAGD) and hydraulic fracturing methods are hindered by massive water demands for stimulating formations. Microfluidics, a fluid analysis tool benefiting from small sample volumes and precise quantification, has emerged as a useful platform for hydrocarbon analysis, particularly for demanding, reservoir-relevant conditions (high temperatures and pressures). In this vein, the presented work demonstrates two microfluidic applications. The first method is a tube-based viscometer with in-line mixing relevant to solvent-based recovery of oil sands. The second method is a physical model of nanopores relevant to hydraulic fracturing with the aim to show fluid interactions at the pore-scale.
Development and Alpha Testing of a Fertility Decision Aid for Young Canadians Diagnosed with Breast Cancer at Risk of Infertility Following Cancer Treatment
Keywords: Breast Cancer
Decision-Making
Decision Support Tools
Fertility
Qualitative
Young Adults

Young women (45 years of age or younger) diagnosed with breast cancer are at risk of treatment-related infertility. Even with established fertility preservation options available in Canada, women feel as though they have limited support and access to resources. This thesis aimed to develop a Canadian decision aid to assist young women in making value-based fertility preservation decisions prior to breast cancer treatment. The development process was guided by the Ottawa Decision Support Framework and International Patient Decision Aids Standards criteria including an evaluation of existing decision support resources, initial paper prototype development and content expert review, end user engagement at a one-day meeting, development of an online decision aid, and alpha testing. The final paper and online decision aid will be pilot tested and disseminated across Canada to help young breast cancer patients make informed fertility decisions in partnership with their health care providers prior to treatment.
The Evolution of Sexual Dimorphism: Resource Investment in Anura and a Case of Sexual Selection in a Scramble Breeder (Lithobates sylvaticus)
Keywords: allometry
anura
evolution
resource investment
sexual dimorphism
sexual selection

While empirical studies suggest that sexually dimorphic traits are characterized by positive allometry, theoretical work suggests that this pattern may be restricted to exceptionally extravagant traits. I examine fourteen diverse traits to test this hypothesis. While I find a positive relationship between trait sexual dimorphism and allometric slope in L. clamitans, L. sylvaticus shows no relationship. I also find an overarching effect of sex on allometry, with more positive allometry than expected by theory in all four species. Secondly, I test for strength of sexual selection in the explosive breeding L. sylvaticus. I find sexual selection on forearm, body size, and hind limb shapes, with males possessing wider forearm shapes tending to mate with larger females. A preliminary literature review of sexual selection estimates reveals comparable estimates between lekking and scramble mating systems, challenging the view that sexual selection is particularly week in explosive breeders with apparent scramble competition.
Proteomic Analysis of PP2A Mutants and PP2A-related Tumor Virus Proteins
Keywords: mass spectromestry
PP2A mutations
Protein phosphatase 2A (PP2A)
tumor virus proteins

Protein phosphatase 2A (PP2A) is a tumor suppressor, whose function and activity is influenced by mutations of PP2A subunits and PP2A-related tumor virus proteins. In this work, protein-protein interaction changes in the normal PP2A interaction network caused by mutations of PP2A scaffolding A (PPP2R1A) and catalytic C (PPP2CA) subunits have been characterized by AP-SWATH. The results show that the normal function and activity of PP2A holoenzyme may be significantly altered and influenced by these mutations. This study also characterizes the interactomes of several PP2A-related tumor viral oncoproteins, including E4orf4. It is revealed for the first time that ASPP-PP1 complex subunits are among the major interactors of E4orf4, suggesting the involvement of E4orf4 in the regulation of Hippo signaling pathway. The results gained in my M.Sc. work provide a deeper understanding of the consequences of PP2A subunits mutations and the PP2A-dependent and PP2A-independent functions of the PP2A-related tumor virus proteins.
Analysis of Alpha-catenin Mediated Intercellular Adhesion in Drosophila
Keywords: alpha-catenin
Beta-catenin
catenin
cell adhesion
Drosophila
E-Cadherin

Dynamic linkage between the cadherin-catenin complex (CCC) and the actin cytoskeleton at Adherens Junctions is essential for cell-cell adhesion in epithelial cells. Alpha-catenin is a core component of the CCC that is responsible for maintaining the linkage between the actin cytoskeleton and the CCC. As part of my project, I generated an alpha-Catenin (alpha-Cat) RNAi line that was used to knockdown maternal alpha-Cat in Drosophila embryos. Knockdown of alpha-Cat in the female germline produced embryonic lethality that was characterized by severe defects throughout the embryo which suggests that the maternal contribution of alpha-Cat is indispensable for embryonic development. I also investigated if alpha-catenin function is conserved among metazoans and Dictyostelium discoideum. I generated rescue constructs using mouse, zebrafish, worm and slime mold alpha-catenin proteins and attempted to rescue alpha-Cat1 mutant embryos. The results of my analysis suggest that alpha-catenin function is conserved among metazoans but not between Dictyostelium and metazoans.
On Cryoloading: A Novel Technique used for the Functional Analysis of CAV2.2 - Synaptic Vesicle Tethering
Keywords: Assay
Calcium channel
Cryoloading
Functional
Synaptic vesicle
Tether

Temporal synchronization between quantal release and Ca2+ influx through single CaVs led to the prediction that SVs are attached by a molecular tether to channels. It has been proposed that tethering is mediated by RIM binding to channels via the C-terminal tip PDZ-ligand domain, and indirectly via a proximal SH3 domain. We hypothesized that if SV binding to the channel C-terminal was blocked by competing peptides then SV recycling should be compromised. We developed a novel method, termed cryoloading, to introduce alien compounds into synaptosomes and assayed SV recycling by a standard styryl dye uptake and release method. Neither mimetic peptide blocker, cryoloaded alone or in combination, had any effect on SV turnover. Lack of functional deficit together with complementary biochemical SV binding studies led us to conclude that SVs tether to CaV C-terminals by an alternative mechanism. Here, we propose the novel HQARRVPNGY region as a candidate tethering site.
E3 Ubiquitin Ligase Huwe1/Mule Regulates Oocyte Survival through p63 Activity
Keywords: Apoptosis
infertility
Mule/Huwe1
Oocyte
p63
Premature Ovarian Failure

Objective: To determine the role of Mule in early oocyte development and explore ovarian phenotypes of Mule deficient mice. Methods: Ovaries from floxed wildtype (Mule fl/fl), conditional knockout (Mule-cKO), and Mule+/+ wildtype (ICR) mice were collected for follicle counts, immunocytochemistry, real time PCR, western blotting, and co-immunoprecipitation. Results: Oocyte specific disruption of Mule causes lack of ovulation by 7 weeks of age with severely compromised ovarian reserve. Conditional knockout mice show decreased numbers of follicles at all stages of development compared to Mulefl/fl animals, particularly at the primordial stage. Mule interacts with the transcription factor p63, causing its mono-ubiquitination, and lack of Mule results in increased expression of the p63 target Noxa, but not Puma. Conclusion: lack of Mule results in the inappropriate activation of p63 in oocytes, leading to the accumulation of downstream pro-apoptotic factors such as Noxa, and premature depletion of the ovarian reserve.
Stromal Lysyl Oxidase-Like 1 Increases Extracellular Matrix Stiffness and Enhances Collagen Fibre Alignment in Non-Small Cell Lung Cancer
Keywords: Cancer associated fibroblasts
Collagen
Integrin alpha 11
Lysyl oxidase-like 1
Non-small cell lung cancer
Stroma

Cancer associated fibroblasts (CAFs) represent a large portion of non-small cell lung cancer (NSCLC) stroma where they mediate extracellular matrix (ECM) remodelling and its interactions with neoplastic cells. A recognized NSCLC CAF marker, fibrillar collagen-binding receptor integrin alpha11 (11), known to promote lung tumour growth and metastasis, was highly correlated with stromal lysyl oxidase-like 1 (LOXL1) in two NSCLC patient cohorts. Both genes were up-regulated in tumour stroma compared to normal lung tissue and were associated with desmoplasia status in patient tumour samples. Over-expression of 11 resulted in up-regulation of LOXL1 in three in vitro models. When cultured within three-dimensional collagen matrices, cells with over-expressed 11 caused linearization, alignment and contraction of collagen fibres. In the absence of 11 expression, over-expression of LOXL1 rescued this phenotype. LOXL1 expression was directly proportional to tissue stiffness; degree of gel contraction; and collagen fibre linearization in in vitro and xenograft tumour models.
Development and Calibration of a 3-component Force Sensor for Meso-milling
Keywords: Cutting forces
Meso-milling applications
Piezoelectric force sensor
Prototype development
Sensor calibration
Sensor design

In the Autonomous Systems and Biomechatronics Laboratory (ASBLab), a concept of a novel three-component piezoelectric force sensor has been designed in order to achieve the requirements for meso-milling applications. The sensor is designed to have a minimum resolution of 10 mN, an operational frequency bandwidth of 8.3 kHz and a measuring range of up to 10-15 N. This thesis focuses on the development of a prototype of the force sensor design, including the design for physical development of the force sensor, the development of its amplification system and its calibration methodology. The result from the calibration test demonstrates that the prototype sensor developed has the required specifications for the meso-milling applications.
Novel Framework for Reduced Order Modeling of Aero-engine Components
Keywords: Finite Element Analysis
Mesh Convergence
Modal Analysis
Model Reduction

The present study focuses on the popular dynamic reduction methods used in design of complex assemblies (millions of Degrees of Freedom) where numerous iterations are involved to achieve the final design. Aerospace manufacturers such as Rolls Royce and Pratt Whitney are actively seeking techniques that reduce computational time while maintaining accuracy of the models. This involves modal analysis of components with complex geometries to determine the dynamic behavior due to non-linearity and complicated loading conditions. In such a case the sub-structuring and dynamic reduction techniques prove to be an efficient tool to reduce design cycle time. The components whose designs are finalized can be dynamically reduced to mass and stiffness matrices at the boundary nodes in the assembly. These matrices conserve the dynamics of the component in the assembly, and thus avoid repeated calculations during the analysis runs for design modification of other components. This thesis presents a novel framework in terms of modeling and meshing of any complex structure, in this case an aero-engine casing. In this study the affect of meshing techniques on the run time are highlighted. The modal analysis is carried out using an extremely fine mesh to ensure all minor details in the structure are captured correctly in the Finite Element (FE) model. This is used as the reference model, to compare against the results of the reduced model. The study also shows the conditions/criteria under which dynamic reduction can be implemented effectively, proving the accuracy of Criag-Bampton (C.B.) method and limitations of Static Condensation. The study highlights the longer runtime needed to produce the reduced matrices of components compared to the overall runtime of the complete unreduced model. Although once the components are reduced, the assembly run is significantly. Hence the decision to use Component Mode Synthesis (CMS) is to be taken judiciously considering the number of iterations that may be required during the design cycle.
Polarization Dependence of Stimulated Brillouin Gain in a Spun Fiber
Keywords: Brillouin Gain
Spectral Dip
Spun Fiber

Stimulated Brillouin Scattering (SBS) in an optical fiber is dependent on the polarization of the counter-propagating pump and probe waves. This polarization dependence changes for different types of optical fibers. In this thesis, we show the study of the SBS behaviour in a Spun fiber, which is a fiber with elliptical core whose preform has been twisted during drawing. We report here, the first time observation of polarization-dependent spectral dip within the Brillouin gain, when spun fiber is used. Through experiments and simulations, we prove that this dip is caused by a filtering effect of the Spun fiber, similar to that of a solc filter, due to a twisted elliptical core fiber being combined with the polarizing effect of SBS.
A CMOS Multi-modal Contact-imaging Scanning Microscope
Keywords: Biomedical Imaging
CMOS active pixel
Delta Sigma
Image Sensor
Microscope
Pixel

This thesis presents the design, implementation and partial experimental characterization of a multi-modality scanning-contact microscope (SCM) with application in biomedical imaging. Bench-top light microscopes are bulky and expensive and provide only one imaging modality. The resolution of most conventional lens-less (contact) microscopes is limited by their pixel size which renders them unsuitable for applications demanding high resolution such as cell imaging. The SCM's imaging component is a custom-made CMOS imager in the AMS0.35m imaging process. Six pixel types are integrated into the imager, which enable the SCM to support six imaging modalities. For sub-pixel resolution imaging, a specialized pixel layout is used which allows the system to support a super-resolution algorithm which takes multiple images with sub-pixel shifts as its input and generates a single high-resolution image. Each pixel type may generate an output voltage or current, depending on whether it is active or passive. A low-power dual-input 2nd order ADC with an SNR of 78dB is implemented to accommodate both current and voltage inputs while preserving noise-shaping characteristics for both inputs.
Development of Coupling Partners for Bioorthogonal Reactions with N-Hydroxylamines
Keywords: bioorthogonal chemistry
hydroxylamine

Bioorthogonal chemistry enables biological chemists to study the dynamics of complex biological systems. Bioorthogonal chemistry allows the selective reaction of an orthogonal tag, which is incorporated on the molecule of interest via biosynthetic or biochemical pathway, and its reactive partner without interfering with native biochemical processes. A number of reactions have been developed in the past two decades. However, there is still a need to develop new chemistries to widen the scope and power of these chemistries to elucidate the biological systems. Therefore, we developed a metal-free bioorthogonal reaction between N-hydroxylamine (orthogonal tag) and a bifunctional probe with aldehyde and alkene (reactive partner) to form a stable isoxazolidine cycloadduct. We showed that glucose could be modified with N-hydroxylamine in four steps. In addition, we designed and synthesized probes that condense then cyclize at 37 °C within 24 hours to yield the cycloadduct, thus making this reaction a viable chemistry to use in biological systems.
Respiratory Syncytial Virus Fusion Protein Interaction with its Cellular Receptor, Nucleolin
Keywords: fusion
nucleolin
respiratory
RSV
syncytial

Respiratory Syncytial virus (RSV) fusion protein (F) interacts with nucleolin during viral fusion. RNA binding domains 1 and 2 (RBDs) of nucleolin, when expressed as a complex, inhibits RSV infection in vitro. We examined the interaction between pre- vs. post-fusion F, and whole virus, with the RBDs complexed and individually. Both RSV Fs co-precipitated RBD1,2. Immobilized RBD1,2 precipitated both RSV Fs and whole viral particles. Immobilized RBD1 precipitated post-fusion but not pre-fusion RSV F. RBD1,2 inhibited infection at 20nM when co-incubated with the virus and the cells for 24 hours. RBD1 inhibited infection to a lesser extent with the same conditions. RBDs were not able to inhibit infection with coincubation with virus prior to infection. RBD1,2 interacts with RSV F, showing different preferential binding for one conformation over another depending on assay conditions, while inhibiting infection at 20nM with 24 hours of coincubation.