VictorJuiz/thesis huggingface dataset:
Investigation of the Immunologic Changes that Discriminate Asymptomatic Antinuclear Antibody Positive Individuals from Systemic Autoimmune Rheumatic Disease Patients
Keywords: Antinuclear Antibody
Autoimmune

The Systemic Autoimmune Rheumatic Diseases (SARD) are a class of chronic autoimmune diseases with widespread inflammation leading to heterogenous clinical manifestations and significant morbidity. Antinuclear antibodies (ANA) are the hallmark of SARD but are also detected in healthy individuals. Some immune abnormalities associated with SARD have also been identified in asymptomatic ANA+ individuals. Here, we demonstrate that asymptomatic ANA+ individuals have significant immune activation as compared to ANA- healthy controls, which is intensified in individuals who will progress to SARD. Furthermore, elevated monocyte levels and trends to decreased regulatory T cells were observed in SARD patients compared to asymptomatic ANA+ individuals indicating that the balance of proinflammatory to regulatory factors is central to SARD progression. These findings enhance our understanding of the immune mechanisms involved in SARD pathogenesis and suggests that ANA+ individuals with the highest immune activation have an increased risk of progression.
Investigating the Molecular Role of Tubby in Subcellular Localization of RNAs
Keywords: RNA localization
Tubby
Tulp3

Mice and humans deficient in the Tubby (Tub) protein, which contains a nucleic acid-binding TUB domain, exhibit maturity-onset obesity, insulin resistance, and sensorineural deficits. We found that Tub has roles in RNA localization. As seen for many RNA binding proteins governing subcellular mRNA localization, I demonstrated that nuclear localization of Tub is essential for its regulation of localization of its target Neuropeptide Y and that Tub-bound sequences can repress translation. To investigate the shared roles of Tub and the related Tulp3 in ciliary trafficking, I showed that disruption of the phosphoinositide PI(4,5)P2 binding motif did not affect their ciliary localization, and induced nuclear localization of Tub but surprisingly not Tulp3. Using the MS2 RNA binding system, I have taken the first steps to examine Tub-dependent ciliary GPCR RNA localization. Altogether, I provide evidence that begins to explore the RNA-based mechanism of Tub in regulating subcellular mRNA localization.
Seasonality and the Immune System during Pregnancy: Impact of Seasonal Affective Disorder
Keywords: Inflammation
Pregnancy
Seasonal Affective Disorder
Seasonality

The current analysis examined whether high maternal seasonality was associated with a unique pattern of immune activity during pregnancy. Plasma C-reactive protein (CRP) was measured in 100 highly seasonal mothers and 100 matched controls in the 1st and 3rd trimester. In trimester 1, highly seasonal women had significantly lower CRP than controls. There was no effect of season on CRP for both study groups during pregnancy. In a subsample, gene expression of pro- (IL1β, IL6, TNFα) and anti-inflammatory (IL4, IL10) cytokines were measured in peripheral leukocytes. No cytokine gene expression differences between groups were detected. Multiple regressions were conducted to predict CRP using BMI, maternal seasonality group, gene expression of each cytokine, and cytokine by seasonality group interaction. Significant predictor variables were IL1β by group interaction and IL10 gene expression. These findings suggest highly seasonal pregnant women have a different immune profile than control women in early gestation.
Characterization of the Role of Downstream Regulatory Element Antagonist Modulator (DREAM) in the Murine Circadian Clock
Keywords: Calcium binding protein
Calcium Signaling
Circadian rhythm
Light Entrainment
Suprachiasmatic Nucleus
Transcription Repressor

DREAM is a multifunctional Ca2+ binding protein with diverse functions both inside and outside the nucleus. However, no study to date has examined the role of DREAM within the suprachiasmatic nucleus (SCN), even though DREAM is present in high abundance in the SCN. Here, we find that DREAM ablation results in a shorter period of wheel-running activity and impaired entrainment to environmental light cycles. However, at the molecular level, the absence of DREAM established no significant change in the expression of pERK, immediate early genes and clock genes. At the transcriptome level, RNA-seq analysis suggests that DREAM may be involved in or impact cellular stress mechanisms, cell excitability, and structural remodelling of neurons. These findings identify DREAM as a potential regulator of circadian clock speed and photic entrainment. However, further experiments are needed to find the precise role and mechanism of action of DREAM within the SCN.
Information Effects on Parental Preferences for Regulatory Types of Early Childhood Education and Care
Keywords: Conjoint Analysis
ECEC
Information Effects
Parental Preferences

Choosing early childhood education and care (ECEC) services is a complex process and research has shown that parents are poorly informed consumers of these services. Experimental studies show that when participants are informed on the importance of a specific decision, they engage in a more complex decision-making process. In this paper, we test whether providing parents with information about the regulatory stringency of ECEC options available to them would influence their ECEC preferences. A conjoint survey capturing quasi-behavioural preferences of ECEC services was completed by 682 parents. Prior to engaging with the survey, participants were randomly assigned to a treatment that informs them about the stringency of oversight of ECEC options available in the province of Ontario or a control group. Receiving information did not meaningfully change the preferences of the entire sample. However, subgroup analysis of parents identified as lower-resourced indicates an important information effect for parent decisions.
Physical and Mechanical Properties of a Dental Resin Covalently Attached to Epigallocatechin-3-gallate
Keywords: EGCG
epigallocatechin-3-gallate
green tea
mechanical properties

Background: Epigallocatechin-3-gallate (EGCG) is an antibacterial green tea polyphenol that can inhibit dentinal protease activity and help preserve dentin-bond strength. However, current methods of EGCG delivery involve passive inclusion of EGCG into methacrylates, leading todiffusion of EGCG and rapid depletion of its bioactive properties. Objectives: To evaluate the physico-mechanical properties of a novel resin based on methacrylate copolymer covalently attached with EGCG. Methods: Resins were formulated with EGCG functionalized at varying degrees (E33, E67, and E100) and varying concentrations (0.5, 1, 2, 5, 10%), and compared to passively incorporated EGCG (E0) and the control group (TEGDMA). Degree of conversion (n=3), flexural strength, modulus of elasticity, modulus of resilience, and microhardness were tested (n=8). Results: EGCG-methacrylate groups had statistically similar physico-mechanical properties to control group except 10% E33. Conclusions: Functionalized EGCG-methacrylate groups except 10% E33 possess adequate physico-mechanical characteristics to progress with further testing in an innate dentin matrix model.
Deciphering the Molecular Actions of Suppressor of Fused in Hedgehog Signaling and Sonic Hedgehog Medulloblastoma
Keywords: Hedgehog signaling
Medulloblastoma
Sufu

Suppressor of Fused (SUFU) is a key regulator of the Hedgehog (Hh) pathway and is implicated in a subset of Sonic Hedgehog medulloblastoma (SHH MB). Although extensively studied, characterization of the molecular actions and protein interactions of SUFU in SHH MB are still limited. My project focused on further elucidating the SUFU interactome and its molecular actions in Hh signaling and SHH MB. I performed pilot proteomic-based experiments to explore the SUFU interactome in a SHH MB context under near physiological conditions. I also prepared CRISPR reagents to generate Halo/HalomAID-tagged Sufu mouse lines and showed that these tags do not appear to affect the negative regulatory function of SUFU in vitro. Together, my project provides useful reagents that will allow our lab to study the physiological SUFU interactome and for the generation of useful mouse models to elucidate the molecular actions of SUFU in Hh signaling and SHH MB.
Investigating Sialic Acid Deficiency on Promoting Renal Thrombosis
Keywords: Endothelial
Glomerulus
Glycan
Kidney
Platelet
Sialic Acid

Atypical Hemolytic Uremic Syndrome (aHUS) is a rare condition which causes thrombosis in the renal microvasculature. Pneumococcal aHUS (P-aHUS) is a rare subtype resulting from severe Streptococcus pneumoniae infections. Although the pathophysiology of P-aHUS remains unknown, patients often present with high blood levels of sialidase, enzymes which remove terminal sialic acids from cell surface glycans. Recently, recessive mutations resulting in loss-of-function in the sialyltransferase ST3GAL1 were identified in three siblings with aHUS. To determine how sialic acid-deficiency promotes thrombosis in the renal microvasculature, the desialylated glycoproteins expressed on sialic acid-deficient endothelial cells were identified and the renal phenotypes of sialic acid-deficient rats were characterized. In total, 5 desialylated glycoproteins of interest were identified by mass spectrometry proteomics, while sialic acid-deficient rats were revealed to have significant renal microvasculature injury. The data collected provides evidence for sialic acid-deficiency as a mechanism for promoting renal thrombosis, and potentially novel targets for future study.
Functional Characterization of Proximity-dependent Degraders
Keywords: E3 Ligase
FACS-Based Screening
ORFeome
Targeted-Degradation Therapeutics
Ubiquitin Proteasome System

Over the past two decades, research efforts have aimed to develop event-based therapeutics for targeted protein degradation (TPDs). In recent years, TPDs were developed to hijack E3 ligases for the targeted degradation of proteins of interest. E3 ligases are components of the ubiquitin proteasome system that determine the target specificity of ubiquitylation reactions. The development of novel TPDs is currently limited by a reliance on a few E3 ligases. I established a large-scale forced-proximity screen for identifying potent degraders. I identified UBE2B as a highly potent degrader that outperformed E3 ligases currently recruited by TDPs, suggesting it as a prime candidate for TPD development. Analysis of uncharacterized protein PRR20A suggested wider screen versatility with putative identification of a degron sequence capable of protein degradation both in cis and in trans. Together, my results suggest my novel screening platform can facilitate functional characterization of mammalian quality control and degradation systems and identify novel candidates for TPD development.
Salvianolic Acid B Inhibits Platelet Aggregation and Blood Coagulation
Keywords: Cardiovascular Disease
Coagulation
Hemostasis
Platelet
Thrombin
Thrombosis

Dan Shen extracts have been reported for centuries to control cardiovascular diseases in Chinese medicine, and its depside salts are approved in China to treat chronic angina. As the most abundant active compound of Dan Shen, salvianolic acid B (SAB) has been shown to exhibit anti-thrombotic properties in animal models. However, its mechanism of action has not been adequately explored. Interestingly, we found SAB bears structural similarities to dabigatran. SAB reduced clot weight, delayed coagulation determined by PT, aPTT, and TEG. Confocal and scanning electron microscopy revealed SAB also reduced fibrin network density. We demonstrated SAB attenuates ADP- and collagen-induced platelet aggregation. Remarkably, SAB inhibits thrombin-induced platelet aggregation more potently than other agonists. Ex vivo perfusion chamber studies showed SAB reduced platelet adhesion/aggregation under flow conditions. These data establish a novel mechanism of SAB in the inhibition of platelet aggregation and blood coagulation, likely partially through direct thrombin inhibition.
A Molecular-level Investigation of Soil Organic Matter Responses to Climate Change in Two Temperate Forests
Keywords: cutin
lignin
nuclear magnetic resonance spectroscopy
organic matter biomarkers
soil organic matter
suberin

Climate change is expected to alter the amount and type of carbon (C) stored in forests as soil organic matter (SOM). To better understand the response of forest SOM to warmer temperatures and enhanced nitrogen (N) deposition, samples were collected from the Detrital Input and Removal Treatment plots at University of Michigan Biological Station and the Soil Warming and Nitrogen experimental plots at Harvard Forest after 10 years of manipulation. Molecular-level analytical techniques were used to understand the composition and degradation state of SOM from these plots. Results indicated that although neither site showed changes in the amount of C or N stored after 10 years, there were changes in the composition and decomposition state of SOM. The results of this thesis have demonstrated that forest SOM cycling and storage are sensitive to environmental change, and also highlight the importance of long-term forest manipulation studies.
Estrogens, Inflammation, and Cognition: Does Inflammation Mediate Verbal Memory Deficits Observed in Surgically Menopausal Women?
Keywords: cognitive decline
cytokines
estradiol
inflammation
memory
oophorectomy

Women who have had an oophorectomy prior to spontaneous menopause experience a decline in E2 production and are more susceptible to dementia (Sherwin, 1988; Farrag et al., 2002; Gervais et al., 2020). Women with Alzheimer’s disease (AD) display elevated levels of inflammation compared to age-matched controls (Trollor et al., 2001; Lee et al., 2018). This study investigated the role of inflammation in mediating verbal memory deficits observed in surgically menopausal women. Our analyses revealed that women with a bilateral salpingo oophorectomy (BSO) experienced significantly greater verbal memory decay in the Logical Memory task and had significantly higher levels of CRP, IL-1????, IL-8, IL-18, and MCP-1 compared to pre-menopausal age-matched controls and/or women with a BSO taking E2 related hormone therapy (BSO + E2). Furthermore, MCP-1 mediated the difference in verbal memory decay between the BSO and BSO + E2 groups.
The Potential Role of Cyclooxygenase-2 as a Folding Factor of Vascular Endothelial Growth Factor
Keywords: Cancer
Cyclooxygenase-2
Disulfide Bonds
Hypoxia
Vascular Endothelial Growth Factor

Secreted proteins contain disulfide bonds to support the structural three-dimensional fold. Known pathways for disulfide bond formation are dependent on oxygen, but vascular endothelial growth factor (VEGF) is among proteins that fold and function under hypoxia. We previously identified the oxidoreductase cyclooxygenase 2 (COX2) as a potential interactor with VEGF in the secretory pathway, and we propose that COX2 supports VEGF folding. Here we established models to address this, including a CRISPR-Cas9 mediated COX2 knockout cell line. Preliminary data suggest that COX2 is required for efficient disulfide bond formation and secretion of VEGF both under normoxic and hypoxic conditions. This research aims to discover a novel protein folding pathway that will give insight into protein assembly in the ER in normoxia and hypoxia.
Characterization of Inter-neuronal Communication by Material Exchange between Primary Photoreceptors In Vitro
Keywords: cell communication
material exchange
photoreceptors
retina
tunnelling nanotubes

Recent discoveries in retinal transplantation have reframed our understanding of photoreceptor communication. The presence of pre-labelled donor cells in recipient retinas was assumed to be synaptic integration of transplanted cells but is now reinterpreted as intercellular material exchange (ME) between donor and recipient cells. The transfer of cytosolic material via membranous protrusions is known to occur in a number of cell types; however, the mechanisms and functional relevance are unclear. In this study, we established an in vitro model of primary retinal neurons to investigate the mechanisms behind ME. We observed intercellular transfer of proteins and mitochondria via neurite-like protrusions between primary photoreceptors. We propose that ME occurs through a mechanism involving cytoplasmic continuity and membrane fusion and is modulated by Rho GTPase cytoskeletal remodelling. The findings of this study contribute to expanding our understanding of inter-neuronal communication between retinal cells and its implications in retinal function and pathology.
Design of Optical based Pressure Transducer for use in Harsh Environments
Keywords: Demodulation
Fabry Perot
Fringe counting

In this thesis, a prototype of a low cost optical pressure transducer for use in harsh environments (temperatures up to 350◦C and pressures up to 10,000 PSI) was developed. Minimizing changes to the transducer body design, a setup replacing the previous strain-gauge based system with an optical interferometer and a low cost external signal demodulator that converts the light signal into a pressure reading, a ferrule that holds the optical system inside the transducer and aligns the fiber optic cable at the center of the diaphragm at a specified cavity distance. The thesis explores the use of the fringe-counting algorithm to detect cavity depth change, which changes as a response to applied pressure. A novel bi- directional fringe counting algorithm utilizing the mean voltage signal for direction determination was introduced and evaluated for use.
Exploring Cell-free Synthetic Biology Tools for De-centralized Diagnostics and Protein Manufacturing
Keywords: Automated protein expression
Biosensors
Cell-Free Protein Synthesis
Diagnostics
Synthetic Biology

Food security and disease prevention are of utmost importance in maintaining societal welfare. This work outlines some strategies to tackle these issues through the use of cell-free technologies. These include development of sensors for detecting Classical Swine Fever and colistin resistance genes, as well as advancement of capabilities for manufacturing of therapeutics and lab reagents. Classical Swine Fever poses a major threat to global food supply and trade. In this work, construction of low-cost and portable sensors for detection of Classical Swine Fever is demonstrated with the ultimate goal of field deployment. Furthermore, building and screening of gene circuits for tracking of colistin resistance genes is showcased. This thesis also explores several parameters relating to cell-free expression and purification of protein-based therapeutics and laboratory reagents. By canvassing these applications, this work aims to help bring the power of genetically-encoded tools outside of the laboratory.
Development and Application of a Cell Competition Assay
Keywords: Apoptosis
Cell Competition
CRISPR
Genetic Screening
Myc

Cell competition is a type of intercellular communication that results in the elimination of suboptimal cells and is emerging as an important biological phenomenon in a number of contexts, including embryonic development and cancer. To date, the rules that govern mammalian cell competition are still largely elusive. Here we report an optimized workflow to establish and validate a scalable, image-based, in-vitro assay to probe cell competition. Our pipeline integrates aspects of previously published studies to guide the design of assay parameters, including, but not limited to, the choice of cellular model and seeding conditions, competition metrics, and suitable experimental controls. We demonstrate the application of our workflow on a system of cancer cell competition triggered by differences in the expression levels of the proto-oncogene c-Myc. The feasibility of this workflow makes it an attractive platform for the medium- to high-throughput studying of mammalian cell competition using high-content imaging.
Development of a Perfusion Bioreactor for the Fabrication and Optimization of Bioengineered Intervertebral Discs
Keywords: Annulus fibrosus
Bioreactor
Intervertebral disc tissue engineering
Nucleus pulposus
Perfusion
Shear stress

A therapeutic approach to treating the degeneration of the intervertebral disc (IVD) would involve the tissue engineering of a biological disc replacement using a perfusion bioreactor. Such reactors have been previously shown to improve nutrient delivery, provide beneficial forces, and support the cultivation of large 3D constructs. It was hypothesized that a perfusion bioreactor system, designed to culture IVD constructs, will be capable of generating outer annulus fibrosus (oAF) and nucleus pulposus (NP) tissues comparable to established spinner reactor cultures and improve upon static culture conditions as determined by cellular viability, nutrient delivery, and tissue formation. Perfusion grown oAF and NP tissues did not show a significant difference in ECM quantity or cellular phenotype when compared to their control conditions, maintained cellular viability at their tissue cores, and received enhanced diffusion of media throughout the tissue when compared to static conditions. This study lays the groundwork for future IVD tissues to be interfaced, scaled up, and mechanically stimulated, conditions difficult or not possible to achieve in previous culture systems
Multiscale Cell-to-vehicle Thermo-electrical Modelling, Simulation and Testing of Electric Vehicles: A Case Study for Battery Pack Temperature Estimation Models
Keywords: Battery Modelling
Electric Vehicles

Advancements in modelling of electric vehicles (EVs) are needed to improve vehicle and battery thermal performance. This thesis aims to develop a multiscale cell-to-vehicle model in MATLAB Simulink to study the effects of five battery pack temperature estimation models based on two metrics: battery thermal management system (BTMS) power consumption and maximum temperature gradient. The study considers battery packs with parallel and serial cooling delivery modes in both summer and winter conditions. These estimation models include average temperature, maximum temperature, top 10 percentile, reduced maximum temperature and reduced average temperature. This study also considers temperature sensing resolution in typical commercial EV battery packs by varying the number of temperature sensors used to estimate the two metrics. The findings from this study suggest that parallel cooling delivery mode with the reduced average temperature estimation model is best suited when considering the two metrics.
Determinants of Variation in Natal Dispersal Distances amongst North American Birds
Keywords: birds
dispersal
ecomorphology
flight efficiency
wing shape

Dispersal is fundamental to many processes such as community connectivity, gene flow, and macroevolution. Natal dispersal, movement from birth site to breeding site, is usually the longest dispersal event among birds and thus the most influential to these processes. Recent work has suggested that the cost of transport may be an important factor for determining dispersal distance. I use large-scale mark-recovery data to estimate natal dispersal distances in North American birds and incorporate morphologically based flight efficiency proxies, ecological and behavioural factors into models that explain the variation of dispersal distances across species. Model inference techniques suggest that flight efficiency, population size and habitat are important for natal dispersal distance, the individual effects of which are difficult to disentangle. I suggest that since these parameters capture information about a species mobility, mobility is what determines natal dispersal distances in North American birds.