VictorJuiz/thesis huggingface dataset:
Chromatin Looping and Cell Type-specific Regulation of Sox2 Expression
Keywords: embryonic stem cells
chromatin looping
enhancer
transcriptional regulation
Sox2

The Sox2 gene encodes a HMG box transcription factor that plays a critical role in maintaining the self-renewal of embryonic stem (ES) cells and regulating neuroectodermal differentiation. Although Sox2 is expressed in ES cells and embryonic brain, cell-type specific regulation of Sox2 transcription remains unclear. In this thesis, I found that the chromatin architecture surrounding the Sox2 locus is highly cell type specific. The Sox2 promoter and proximal enhancers interacted with a cluster of putative enhancer candidates located 80-120 kilobases (kb) downstream to Sox2 in ES cells but not in embryonic brain, whereas in embryonic brain the Sox2 proximal region adopted a more compact chromatin conformation than ES cells. Also, the distal enhancer cluster showed higher enhancer activities than the Sox2 proximal enhancers in ES cells. Together, these results suggest that the novel enhancer cluster downstream to Sox2 plays an important role in ES cell specific regulation of Sox2 transcription.
The Effect of Insulin on Atherosclerosis and Restenosis
Keywords: insulin
atherosclerosis
restenosis
NPH
neointima
plaque

Diabetes mellitus and metabolic syndrome, which are states of insulin resistance, are both well-known to increase the risk of atherosclerosis and restenosis. We present evidence that insulin itself is anti-atherogenic and anti-restenotic. Systemic insulin treatment decreases atherosclerosis independent of its effects on glycemia. Insulin-treated ApoE -/- mice showed a 42% decrease in plaque burden in the descending aorta and an increase in markers of plaque stability in the aortic sinus. We have previously shown that systemic insulin treatment decreases neointima area after arterial injury. However, systemic insulin treatment has the risk of hypoglycemia. Therefore we explored an alternative local route of application of insulin around the vessel via Pluronic gel in rats. We found that regular insulin and neutral protamine Hagedorn (NPH) insulin significantly decrease neointima area by 24% and 17% respectively at 28 days. These studies suggest that insulin is vasculoprotective.
Characterization of the N-terminal Region of the RNA-Binding Protein Smaug in Post-transcriptional Regulation During Drosophila Embryogenesis
Keywords: Smaug
post-transcriptional regulation
Drosophila
RNA

The Drosophila sequence-specific RNA-binding protein Smaug (Smg) regulates the expression of mRNAs in the early fly embryo. It is the founding member of a conserved family of post-transcriptional regulators defined by an RNA-binding sterile alpha motif (SAM) domain. Smg regulates gene expression through its ability to repress the translation, and/or induce degradation of target mRNAs. Through a structure-function analysis using smg truncation mutants, I show that sequences N- and C-terminal to the Smg SAM domain are involved, and have partially redundant roles in mRNA decay. Moreover, another conserved region of Smg modulates the mRNA decay function of the N-terminal sequences in a transcript-specific manner. Finally, sequences within the Smg N- and C-terminal regions are also required for the degradation of Smg protein.
Preference and Acceptability of Alternative Delivery Vehicles for Prenatal Calcium Supplementation among Pregnant Women in Bangladesh
Keywords: preference
acceptability
calcium
supplementation
preeclampsia
pregnancy
Bangladesh
nutrition

In populations with low dietary calcium intake, prenatal calcium supplementation is recommended by the WHO to decrease the risk of hypertensive diseases of pregnancy. This study evaluated preference and acceptability for four different calcium delivery vehicles (conventional tablets, chewable tablets, unflavoured powder, and flavoured powder) among pregnant women in urban Bangladesh. Participants (n=132) completed a 4-day run-in period in which each vehicle was sampled once, followed by a 21-day selection period during which participants were free to select a vehicle of their choice on each day. The probability that participants selected the conventional tablets was greatest (62%), followed by chewable tablets (19%), flavoured powder (12%), unflavoured powder (5%), and no delivery vehicle (2%). The present assessment of participants’ actual supplement use and expressed perceptions of acceptability suggested that a tablet formulation is likely to be the most appropriate calcium delivery vehicle for future use in field studies and scale-up planning.
Ants as Flower Visitors and their Effects on Pollinator Behavior and Plant Reproduction
Keywords: Pollination
Ants
Bees
Behavior

Ants regularly visit flowers, but they may decrease plant reproductive success by competing with pollinators or damaging reproductive structures. However, how ants may exert these costs needs further clarification. In Chapter 1, I review the literature, finding that flower-visiting ants often have neutral effects on plant fitness. In Chapter 2, using artificial flowers with male and female function, I investigate how interference competition between flower-visiting Myrmica rubra ants and Bombus impatiens bumblebees changes pollen analogue movement patterns. Ant presence and scent significantly reduced pollen analogue donation and reception because bees avoided flowers with ant cues. In Chapter 3, to assess the frequency of palynivory among ants, I conducted an acetolysis survey of 75 neo- and paleo-tropical ant species. Ants consistently contained low numbers of pollen grains, suggesting opportunistic pollen consumption may be widespread. Altogether, ant visitation may be costly, but the mechanism depends on the plant, pollinator and ant identities.
SERS using Plasmonic Nanoparticles and J-aggregate Dyes
Keywords: Plasmonics
J-aggregates
SERS
Surface Enhanced Raman Spectroscopy

Semiconductor-metal composite nanoparticles offer optical properties that are superior to those of pure materials. In this study, we exploit the epsilon near zero (ENZ) phenomenon using gold and silver nanoparticles functionalized with cyanine dyes, which form distinct J-aggregates on the surface of the particle. These J-aggregates show a distinct nonlinear optical response, and a wavelength matching approach was used to couple the plasmonic particle to the J-aggregate. When the appropriate wavelength is utilized, these particles showed an enhanced SERS signal as a result of the excitonic resonance of the J-aggregate species. The theoretical properties of the particles were simulated using FDTD techniques, and these were experimentally verified by varying the dye/particle distance and testing different molecular and plasmonic resonators. Experimental SERS spectra had excellent agreement with simulations. These composite particles were then encapsulated in a lipid bilayer, forming a multi-shell structure with properties suitable for biosensing and other detection applications.
p38 Mitogen Activated Protein Kinase Mediates Free Fatty Acid Induced Hepatic Insulin Resistance In Vivo
Keywords: hepatic insulin resistance
free fatty acids
hyperinsulinemic euglycemic clamp
p38 MAPK

Elevated free fatty acids (FFA) contribute to the development of insulin resistance but the mechanisms are not completely understood. We have shown that p38 mitogen activated protein kinase (p38 MAPK) is activated in the liver by lipid infusion and we wished to determine whether it plays a causal role in hepatic insulin resistance after prolonged lipid exposure as shown in isolated hepatocytes. Intralipid and heparin (IH) infusion for 48 hours impaired insulin’s ability to suppress glucose production and tended to impair glucose utilization. Co-infusion of p38 MAPK inhibitor SB239063 with IH restored the insulin-induced suppression of glucose production but did not improve peripheral glucose utilization. IH-induced hepatic insulin resistance was accompanied by increased phosphorylated activating transcription factor 2 (ATF2), a p38 MAPK substrate and this was prevented by co-infusion of SB239063. Our results suggest that p38 MAPK activation mediates hepatic insulin resistance induced by prolonged exposure to FFA in vivo.
A Novel Approach Toward Branched Peptide Synthesis
Keywords: Organic Chemistry

Branched peptides are peptides featuring side chain-linked linear peptides which branch off from the main chain. Branched peptides have previously been employed in the development of small molecular carriers for drug delivery systems as well as in biodegradable materials and artificial enzymes. In our own efforts toward the synthesis of branched peptides, we have optimized reaction conditions adopted from Native Chemical Ligation (NCL) to prepare ligated peptides in a convergent synthesis. Herein we present the synthesis of N-terminal aziridine and C-terminal thioacid-functionalized peptides, followed by their ligation and subsequent transthioesterification with a C-terminal thioester to yield a tri-branched pentadecapeptide.
Understanding the Molecular Mechanism of Elasticity in Elastin from a Solvation Perspective
Keywords: Elastin
Molecular dynamics
Solvent effect
Methanol

Elastin is an extracellular matrix protein that provides tissues with elasticity. In this thesis, we studied three aspects of elastin-based peptides by performing molecular dynamics (MD) simulations in explicit solvents: aggregation, solvent quality & mechanical property. First, by simulating the peptides in water and methanol, we found that methanol stabilizes the secondary structure of amyloid-like peptides, based on which we hypothesized that the reduction of solvophobic effect in methanol compared to that in water prevents their formation of amyloid-like fibrils. Second, we studied the solvent effects of various solvents with different polarities on the peptides, and found that they exhibit different solvent qualities. Third, we developed a model to predict the Young’s modulus of elastin-like material using data from MD simulations. This model produces consistent results with experimental measurements, hence provides a way to evaluate the solvent effects on elasticity. We conclude that hydrophobic effect plays an important role in generating elasticity.
Preparation of Novel Soybean Oil Based Polymers and Investigation of their Application in the Delivery of Anticancer Drugs
Keywords: nanoparticle
anticancer drugs

Previously our group has developed a polymer-lipid hybrid nanoparticle (PLN) system that can effectively deliver the anticancer drugs. However, the polymer, hydrolyzed polymer of epoxide soybean oil (HPESO), used in this system, has low water solubility at neutral pH, which complicates the process of making the PLNs. Therefore, this thesis focuses on the synthesis of new soybean oil based polymers that exhibit better water-solubility and investigation of their application in the delivery of the anticancer drug cisplatin. Three new polymers were synthesized: a) alcohol-based polymer; b) aspartic acid-based and c) taurine-based polymers. These polymers had similar molecular weights, but had higher aqueous solubility and better pH-dependent solubility profile as compared to HPESO. The loading cisplatin into the polymer was likely via covalent conjugation between the polymers and the platinum atom. Platinum drug-loaded PLNs were prepared using lipid and taurine-based polymer and showed a sustained drug release profile similar to Miriplatin.
The Generation of Synthetic Antibody Reagents for Clostridium difficile Toxins
Keywords: phage display
C. difficile toxins
antibodies
toxin A
toxin B
CDT

The symptoms of C. difficile infection are primarily caused by two toxins, toxin A and toxin B. Some strains produce a third known toxin, C. difficile transferase (CDT) toxin; however, its role in virulence remains unclear. I aimed to develop synthetic antibodies using phage display technology to block toxin entry by binding to the receptor-binding domain (RBD) of the toxins. I first described the generation of anti-toxin A and anti-toxin B Fabs. I presented Fab A3, which bound to the full-length toxin, but did not functionally inhibit toxin entry. In chapter 2, I described the generation of novel anti-CDTb antibodies. I further demonstrated that five of the anti-CDTb antibodies could functionally inhibit CDTb binding in an ELISA-based assay and on cultured cells. These antibodies can be used as tools to understand the toxins’ role in human disease and potentially be used as therapeutics.
The Effect of Scyllo-inositol on Adult Hippocampal Neurogenesis in the TgCRND8 Model of Alzheimer's Disease
Keywords: Alzheimer's disease
Neurogenesis

I hypothesize that scyllo-inositol treatment, through the reduction of amyloid-beta peptide (Abeta) pathology, increases neurogenesis in the hippocampus of TgCRND8 mice. Adult hippocampal neurogenesis in the dentate gyrus is altered in both young (100/121-day old) TgCRND8 mice and old (200/221-day old) TgCRND8 mice. Treatment of young TgCRND8 mice with the anti-Abeta aggregation compound, scyllo-inositol, rescues alterations in cell proliferation, increases the survival and neuronal differentiation of newborn cells while reducing hippocampal Abeta pathology. scyllo-Inositol treatment of old TgCRND8 mice also reduces hippocampal Abeta pathology, but has no effect on the deficits in cell proliferation and neuronal differentiation. Reduction of hippocampal Abeta pathology in young TgCRND8 mice is sufficient to rescue alterations in neurogenesis. In contrast, the reduction of hippocampal Abeta pathology in the old TgCRND8 mice is not sufficient to rescue neurogenesis, suggesting that the neurogenic niche may be dysfunctional or damaged.
The Impact of VEPH1 on Ovarian Cancer Tumour Progression in a Xenograft Mouse Model
Keywords: Veph1
ovarian cancer
xenograft
tumour

Epithelial ovarian cancer has the greatest death to incidence ratio of all gynecological cancers in Canada. The FoxO, TGF-β, and Hippo signalling pathways are implicated in ovarian tumourigenesis; ventricular zone-expressed PH domain protein (Veph1) may be a novel modulator of these pathways. This thesis addresses the objectives of determining the physiological murine tissue expression of Veph1A/B isoforms, and establishing the effect of Veph1 expression on ovarian tumourigenesis. Veph1A and Veph1B transcripts were identified in whole embryos; whereas, only Veph1A transcripts were present in adult tissues. Veph1 expression significantly reduced tumour growth rate in a xenograft mouse model. This was associated with reduced microvessel density and increased necrotic tumour area with no effect on proliferation index. This study suggests that Veph1 may be involved in angiogenesis. Future investigation regarding the effect of Veph1 expression on metastases and ascites formation will be necessary to establish its role in ovarian tumourigenesis and survival.
Effects of Transcranial Focused Ultrasound on Hippocampal Neurogenesis and Astrogenesis
Keywords: Alzheimer's Disease
Focused Ultrasound

As a therapy for Alzheimer’s disease (AD), focused ultrasound (FUS) can increase blood-brain barrier permeability and enhance delivery of commercial and endogenous antibodies targeting amyloid-β peptides (Aβ). Here, the long-term effects of treatment on hippocampal cell proliferation, differentiation and Aβ load were examined at 18 days. In non-transgenic mice, FUS application significantly increased cell proliferation, neurogenesis and the differentiation of unidentified cells, without affecting the proportion of cell populations intrinsic to the hippocampus. In the TgCRND8 mouse model of AD, neither FUS nor FUS with the anti-Aβ antibody BAM10 significantly increased proliferation or differentiation but increased the percentage of unknown cells. FUS + BAM10 was found to significantly reduce Aβ load by 18 days. Overall, this study demonstrates that FUS increases hippocampal proliferation and neurogenesis in non-transgenic mice and reduces Aβ load in TgCRND8 mice, suggesting its long-term, multifaceted treatment potential.
RGD-conjugated Nanoparticles for Targeted Inhibition of Metastasis of Integrin αvβ3-overexpressing Breast Cancer Cells
Keywords: nanoparticle
RGD
metastasis
αvβ3 integrin receptor

The use of actively targeted nanoparticles as a delivery system for both the diagnosis and treatment of cancer has been explored extensively. However, selective tumor accumulation is not guaranteed. The objectives of this thesis were 1) to optimize the nanoparticle surface content of cyclic arginyl-glycyl-aspartic acid (cRGD) decorated solid lipid nanoparticles (RGD-SLN) in targeting αvβ3 integrin receptor, and 2) to evaluate the potential of RGD-SLN in inhibition of metastasis. Nanoparticles of cRGD content ranging from 0 – 10% mol were synthesized. They showed enhanced binding for αvβ3 integrin receptors and increased cellular uptake in the breast cancer cells. In vitro treatment with RGD-SLNs reduced tumor cell adhesion and invasion. Maximum tumor accumulation was demonstrated in 1% mol of RGD on the nanoparticle surface among all formulations tested in vivo. This work has laid a foundation for further development of anticancer drug-loaded cRGD-nanoparticle formulations useful for the treatment of breast cancer metastasis.
Long-term Outcomes in Lung Transplant Patients Who Required Prolonged Mechanical Ventilation and their Family Caregivers
Keywords: lung transplant
caregivers
mechanical ventilation
functional ability
mental health
quality of life

Lung transplant literature has focused on patient survival, hindering its ability to characterize long-term morbidity in patients requiring prolonged mechanical ventilation (PMV) after transplant, and the health of their caregivers. ICU research has evaluated PMV and suggests that patients and caregivers may be at risk for increased morbidity. This study examined: 1) patient functional ability, quality of life (QOL) and mental health, and 2) caregiver QOL and mental health. Patients (N=44) and caregivers (N=33) completed standardized instruments approximately four years after transplant. Using regression modeling, patient functional ability was associated with older age and lower respiratory function. Fewer patient depressive symptoms were associated with better caregiver psychological well-being. Caregiver depression was associated with poor functional and mental health in patients, and caregiver factors including male gender, reduced support and increased assistance. Interventions may be of most benefit to older patients with reduced respiratory function, and caregivers who lack social support. (Limit: 150 words)
The Role of Sodium-coupled Neutral Amino Acid Transporters in Alveolar Fluid Homeostasis
Keywords: SNAT
alveolar fluid clearance
ENaC
SGLT1
alveolar fluid secretion
pulmonary edema

Alveolar fluid clearance (AFC) is a physiological process by which the lungs remove fluid from the alveolar space by active absorption that is driven by epithelial Na+ uptake. In isolated rat lungs, inhibition of the amiloride-sensitive apical epithelial sodium channel (ENaC) with amiloride blocks AFC, and can reverse transepithelial ion and fluid transport, inducing alveolar fluid secretion (AFS). In vivo the scenario is complicated by the potential involvement of amiloride-insensitive epithelial Na+ co-transporters. Specifically, we considered the role of Na+-glucose co-transporter 1(SGLT1) and Na+-coupled neutral amino acid transporters (SNATs) using the isolated perfused rat lung model. AFC remained unchanged under basal conditions whether SGLT1 or SNATs were stimulated (via providing respective substrates) or inhibited. However, addition of L-alanine in the alveolar space reversed amiloride-induced AFS to become AFC and this rescue was Na+-dependent. SNATs are therefore potentially a novel target for treatment of pulmonary edema.
Ontario Homeopathic Practitioner Survey: Are homeopaths prepared to be regulated?
Keywords: Regulated Health Professions
Homeopathic Practitioners
Standards of Practice
Survey Study

Ontario homeopaths are to be granted self-regulatory status under the Regulated Health Professions Act. The objectives of this study were to describe homeopaths currently practicing in Ontario and determine the proportion of practitioners that are eligible to become regulated. Questionnaires were distributed to Ontario homeopaths (n=831). The response rate was 56% (n=442/789, 43 ineligible participants). The majority of active practitioners were female (62.0%) with a mean age of 48 years. Almost two-thirds (66.3%) reported working part-time. The majority (77.5%) had at least a College/University/ diploma/certificate/degree. The majority was in favour of the regulation of homeopathy. Almost two-thirds (64.1%) appeared to be eligible for registration. Practitioners that appeared to be ineligible for registration were older, and had been in practice longer. In conclusion, only two-third of active practitioners that responded appeared eligible for registration when regulations are enacted.
Protein Tyrosine Phosphatase Sigma (PTPσ) Targets Apical junction Complex Proteins in the Intestine and Modulates Epithelial Permeability.
Keywords: Inflammatory Bowel Disease
Protein tyrosine phosphatase
Intestinal Barrier Defense
Epithelial cell signalling

Protein tyrosine phosphatase sigma (PTPsigma) was shown previously to contain SNP polymorphisms that confer susceptibility to inflammatory bowel disease (IBD). PTPsigma(-/-) mice exhibit an IBD-like phenotype and show increased susceptibility to acute models of murine colitis. The function of PTPsigma in the intestine is uncharacterized. Here, I show an intestinal epithelial barrier defect in the PTPsigma(-/-) mouse, demonstrated by a decrease in trans-epithelial resistance and increased macromolecular permeability. We identified several putative PTPsigma intestinal substrates, including ezrin. My results show that ezrin binds to and undergoes tyrosine de-phosphorylation by PTPsigma in vitro, suggesting it is a direct substrate for this PTP. The results suggest a role for PTPsigma as a positive regulator of epithelial barrier integrity in the intestine. The proteins identified in the screen, including ezrin, suggest that PTPsigma may modulate epithelial cell adhesion through the targeting of AJC-associated proteins, a process impaired in IBD.
The Role of PPAR-γ in Trophoblast Layer Dynamics Based on a Cell Model of Trophoblast Differentiation
Keywords: Pre-eclampsia
Pregnancy
Heme oxygenase-1
PPAR-gamma
Glial cell missing-1
Rosiglitazone
Placenta

Severe pre-eclampsia (sPE) is a pregnancy disorder stemming from the placenta which features abnormal trophoblast layer physiology. A transcription factor, glial cell missing-1 (GCM-1), regulates differentiation of cytotrophoblast cells into syncytiotrophoblast (SCT) within the layer. GCM-1 is regulated by PPAR-γ, a nuclear receptor controlling trophoblast differentiation in mice. We have previously shown that activation of PPAR-γ ameliorates disease features in a rat model of sPE via an upregulation of heme oxygenase-1 (HO-1), a cytoprotective enzyme. Here, we assessed how manipulating PPAR-γ influences gene expression and alters proliferation/differentiation balance in a human cell line, BeWo, which mimics SCT formation. PPAR-γ activation induced HO-1 expression and led to a transient upregulation of GCM-1 expression. Blocking PPAR-γ activity increased cell proliferation and decreased differentiation, whereas PPAR-γ stimulation did not change this balance. Since HO-1 and GCM-1 are downregulated in sPE, their upregulation via PPAR-γ offers insights into a pathway relevant to sPE management.