VictorJuiz/thesis huggingface dataset:
Mechanical and Histological Characterization of Porcine Aortic Valves under Normal and Hypercholesterolemic Conditions
Keywords: heart valve
aortic valve disease
micromechanical testing
micropipette aspiration
multilayered biomaterial
histology
porcine
animal model
hypercholesterolemia
proteoglycan
lipid
Sox9

Calcific aortic valve disease (CAVD) is associated with significant cardiovascular morbidity. While late-stage valve disease is well-described, there remains an unmet scientific need to elucidate early pathobiological processes. In CAVD, pathological differentiation of valvular interstitial cells (VICs) and lesion formation occur focally in the fibrosa layer. This VIC pathological differentiation has been shown to be influenced by matrix stiffness in vitro. However, little is known about the focal layer specific mechanical properties of the aortic valve in health and disease and how these changes in matrix moduli may influence VIC pathological differentiation in vivo. In this thesis, micropipette aspiration (MA) was shown to be capable of measuring the mechanical properties of a single layer in multilayered biomaterial or tissue such as the aortic valve, if the pipette inner diameter was less than the top layer thickness. With MA, the fibrosa of normal porcine aortic valves was significantly stiffer than the ventricularis; stiffer locations found only within the fibrosa were comparable to stiffnesses shown in vitro to be permissive to VIC pathological differentiation. Early CAVD was induced in a porcine model, which developed human-like early CAVD lesion onlays. Extracellular matrix remodeling occurred in the absence of lipid deposition, macrophages, osteoblasts, or myofibroblasts, but with significant proteoglycan-rich onlays and chondrogenic cell presence. These early onlays were softer than the collagen-rich normal fibrosa, and their proteoglycan content was positively correlated with Sox9 chondrogenic expression, suggesting that soft proteoglycan-rich matrix may be permissive to chondrogenic VIC differentiation. The findings from this thesis shed new light on early disease pathogenesis and improve the fundamental understanding of aortic valve mechanics in health and disease.
CREB-mediated Enhancement of Hippocampus-dependent Memory Consolidation and Reconsolidation
Keywords: memory
CREB
hippocampus
animal model
reconsolidation
context fear conditioning
spatial memory
viral vectors
CRTC1
transcription factor

Memory stabilization following encoding (synaptic consolidation) or memory reactivation (reconsolidation) requires gene expression and protein synthesis. Although consolidation and reconsolidation may be mediated by distinct molecular mechanisms, disrupting the function of the transcription factor CREB (cAMP responsive element binding protein) impairs both processes. We use a gain-of-function approach to show that CREB (and CREB-coactivator CRTC1) can facilitate both synaptic and systems consolidation and reconsolidation. We first examine whether acutely increasing CREB levels in the dorsal hippocampus is sufficient to enhance spatial memory formation in the watermaze. Locally and acutely increasing CREB in the dorsal hippocampus using viral vectors is sufficient to induce robust spatial memory in two conditions which do not normally support consolidation, weakly-trained wild-type (WT) mice and strongly-trained mutant mice with brain-wide disrupted CREB function. CRTCs (CREB regulated transcription co-activators) are a powerful co-activator of CREB, but their role in memory is virtually unexplored. We show, for the first time, that the novel CREB co-activator CRTC1 enhances memory consolidation. Locally increasing CRTC1 (or CREB) in the dorsal hippocampus of WT mice prior to weak context fear conditioning facilitates consolidation of precise context memory. Last, we show that CREB or CRTC1 facilitates precise and enduring memory consolidation and reconsolidation. Acute enhancement of hippocampal CREB or CRTC1 during initial synaptic consolidation can maintain precision of remote context memory, while increasing CREB or CRTC1 just prior to reactivation of a weak remote context memory enhances context memory reconsolidation. These gain-of-function manipulations indicate that increasing CRTC1 or CREB function is sufficient to enhance the strength of new, as well as reactivated established, memories without compromising memory specificity. Together with previous results, these findings indicate that CREB is both necessary and sufficient for hippocampal-dependent memory formation, and underline its pivotal role in the hippocampal molecular machinery underlying long-term memory consolidation and reconsolidation.
Influence of Crystalline Microstructure on Optical Response of Single ZnSe Nanowires
Keywords: semiconductor nanowires
optical characterization

Semiconductor nanowires (NWs) are anticipated to play a crucial role in future electronic and optoelectronic devices. Their practical applications remain hindered by an urging need for feasible strategies to tailor their optical and electronic properties. Strategies based on strain and alloying are limited by issues such as defects, interface broadening and alloy scattering. In this thesis, a novel method to engineer the optoelectronic properties based on strain-free periodic structural modulations in chemically homogeneous Nanowire Twinning Superlattices (NTSLs) is experimentally demonstrated. NTSLs are an emerging new class of nanoscale material, composed of periodically arranged rotation twin-planes along the length of NWs. The main objective of this thesis is to establish the relationship between the electronic energy band gap (Eg) and the twin-plane spacing (d) in NTSLs, quantified using a periodicity parameter, based on ZnSe. ZnSe was chosen because of its excellent luminescence properties, and potential in fabrication of optoelectronic devices in the near-UV and blue region of the spectrum. A prerequisite to establishing this correspondence is a prior knowledge of the photoluminescence (PL) response and the nature of fundamental optical transitions in defect-free single crystal ZnSe NWs with zinc-blende (ZB) and wurtzite (WZ) crystal structures. There has been no systematic work done yet on understanding these fundamental optical processes, particularly on single NWs and in relation to their crystalline microstructure. Therefore, the secondary objective of this thesis is to study the influence of native point defects on the optical response of single ZnSe NWs in direct relation to their crystalline microstructure. The PL response from single ZB and WZ NWs was determined unambiguously, and excitonic emission linewidths close to 1 meV were observed, which are the narrowest reported linewidths thus far on ZnSe NWs. Based on this and extensive optical and structural characterization on individual NTSLs, a linear variation in Eg is shown through a monotonic shift in PL peak position from ZnSe NTSLs as a function of d, with Eg's that lie between those of ZB and WZ crystal structures. This linear variation in Eg was also validated by ab Initio electronic structure calculations. This establishes NTSLs as new nanoscale polytypes advantageous for applications requiring tunable band gaps.
Molecular Characterization Reveals Novel Genes Implicated in Aetiology and Progression of Osteosarcoma
Keywords: osteosarcoma
copy-number change
oncogene
tumour-suppressor gene

Osteosarcoma is the most common bone malignancy in children and adolescents with poorly understood aetiology. Recently, disease susceptibility and aetiology in several cancers have been associated with genomic copy-number (CN) change. We therefore studied the contribution of CN change in osteosarcoma. We report that individuals with osteosarcoma have increased germline structural variation compared to controls. These CN variants (CNVs) preferentially localize to genes implicated in control of osteoblast differentiation, bone mineralization and ossification. We propose that germline CNVs contribute to osteosarcoma susceptibility through deregulation of developmental processes controlled by genes contained within CNVs. Further supporting the notion that germline CNVs in individuals with osteosarcoma are pathogenic, we demonstrate that CNVs are associated with poor patient survival. Finally, we characterize two germline CNVs, at chromosome 1q43 and 2p11.2, which are overrepresented in osteosarcoma patients and propose that they contribute to osteosarcoma susceptibility through effect on neighbouring genes, which could be involved in control of microtubule dynamics and tumour suppression. We further characterize two regions in the tumour genome of osteosarcoma patients that harbour recurrent CN alterations (CNAs). These include deletions at chromosome 3q13.31 and vi ii amplifications at chromosome 7p14.1, which are the most altered regions in osteosarcoma and contest the view that CNAs in osteosarcoma are non-recurrent. Both chromosome 3q13.31 and 7p14.1 CNAs involve genes implicated in carcinogenesis, including LASMP at 3q13.31 and TARP at 7p14.1, while 3q13.31 CNAs also involve two non-coding RNAs. We further show that expression of 3q13.31 genes correlates with the presence of 3q13.31 CNAs. We report that chromosome 3q13.31 and 7p14.1 CNAs are also common in other cancers, identifying these loci as candidates with a global role in carcinogenesis. Supporting the notion that 3q13.31 deletions play a role in osteosarcomagenesis, we find that depletion of 3q13.31 genes promotes proliferation of osteoblasts by regulation of apoptotic and cell-cycle transcripts and also VEGF receptor 1 and that genetic deletions of 3q13.31 are associated with poor survival of osteosarcoma patients. In summary, our study implicates germline and somatic CN changes in osteosarcoma and represents a model approach for elucidation of elements contributing to disease susceptibility and aetiology in human cancer.
Characterizing the Roles of PilF and PilQ in Pseudomonas aeruginosa Type IV Pilus Biogenesis
Keywords: Pseudomonas aeruginosa
PilF
PilQ
protein-protein interactions
pilotin
secretin
bacterial virulence
pilus biogenesis
X-ray crystallography
lipoprotein
type IV pilus
PilF-PilQ interactions

Type IV pili (T4P) are bacterial biomolecular machines that mediate interactions with the environment. Bacterial pathogens such as Pseudomonas aeruginosa require T4P for virulence. Significant progress has been made in recent years towards our understanding of how the proteins in the T4P system interact and function. While over 50 different proteins are involved in T4P biogenesis, the two outer membrane components, PilF and PilQ, are the focus of the work presented in this thesis. PilF was found to be required for assembly of PilQ into secretins, the outer membrane channels through which T4P fibers exit the cell. The functions of PilF are consistent with a family of lipoproteins called pilotins, to which the roles of secretin assembly and/or localization are attributed. Structure determination by X-ray crystallography revealed that PilF is composed of six tetratricopeptide (TPR) protein-protein interaction motifs. Functional mapping of PilF indicated that a hydrophobic groove on the first TPR is involved in secretin assembly. Secretin localization correlated directly with that of PilF. The effects of pilF mutations and the structural data led to the hypothesis that PilF and PilQ interact directly. We propose that PilF and PilQ interact at the inner membrane and are co-transported to the outer membrane by the Lol lipoprotein sorting system. PilQ multimerizes into secretins upon outer membrane insertion and aligns with inner membrane T4P proteins to form a complete molecular machine. PilQ mutagenesis mapping showed that: the N-terminal “system specific” domain is important but not essential for secretin function; the central “multimerization” domain is critical for secretin assembly and function; and the C-terminal tail implicated in secretin-pilotin interactions is dispensable for PilQ function. Purified PilQ enabled copurification of PilF from cell lysates, providing the first evidence for their interaction. These data provide a framework for future exploration of T4P assembly in P. aeruginosa.
Endocrine Regulation of Stem Cells and the Niche in Adult Mammopoiesis
Keywords: stem cells
mammary gland
hormones

Adult mammopoiesis occurs in close synchronization with reproductive development when the hypothalamic-pituitary-ovarian axis delivers integral systemic hormone cues to propel mammary morphogenesis during puberty, remodeling during reproductive cycles and functional differentiation following pregnancy. While hormones remain the driving force behind normal glandular development, increased life-time hormone exposure is a strong risk factor for breast cancer. Breast cancer heterogeneity has been attributed to different cells of origin and/or different mutation repertoires. Stem/progenitor cells are intensely investigated as cells of origin given their regenerative and self-renewal properties that provide conceivable advantage in cancer. Although hormones have a fundamental influence in breast cancer, their capacity to regulate stem/progenitor cells was unknown, and presents the central directive in this thesis. Employing mouse models, we show that mammary epithelial subpopulations and in particular, stem cells, are highly responsive to ovarian hormones and depend on key molecular events. A progesterone peak during the luteal phase of reproductive cycles results in a significant increase in stem cell-enriched basal cells and an expansion of stem cells measured by in vivo transplantation assays, with rapid development of lobuloalveoli. Progesterone was found to stimulate expression of mitogenic ligands, RANKL and Wnt4, in ER+PR+ luminal epithelial niche cells concomitant with increased expression of their receptors and target genes in the ER-PR- basal stem cell population, suggesting a cross-talk between luminal and basal cells that elicits stem cell expansion within the niche. The requirement of RANKL signaling for hormone-induced mammary stem cell dynamics was further explored utilizing mice deficient for its receptor, RANK, and by pharmacological inhibition of RANKL. Disruption of RANKL/RANK signaling resulted in abrogated activation of the basal stem cell-enriched population and alveolar progenitor cells in response to progesterone. This was accompanied by a marked reduction in cell proliferation, cell cycle regulators, alveolar lineage determinants and notably, in epithelial Wnt responsiveness. Thus, progesterone orchestrates a series of molecular events in the mammary stem cell niche where RANK is effectively positioned to deliver instructive signals to stem cells, culminating in stem cell recruitment and alveolar regeneration, processes which when deregulated have considerable potential to promote breast cancer pathogenesis.
Comparative Interactome Investigation of γ-secretase Complex in Alzheimer’s Disease
Keywords: Alzheimer's Disease
Gamma-secretase
Amyloid beta peptide
Proteomics

γ-Secretase plays a pivotal role in the production of neurotoxic amyloid β-peptide (Aβ), the principal component of amyloid plaques present in Alzheimer’s disease. It consists of a core complex of presenilin (PS), nicastrin, anterior pharynx-defective 1 (Aph-1), and presenilin enhancer 2 (Pen-2) proteins. PS harbors the catalytic aspartates required for regulated intramembrane proteolysis and the paralogs (PS1 and PS2) contribute to the assembly of distinct subpopulations of γ-secretases that may fulfill distinct roles. To characterize the molecular environments of distinct γ-secretases complexes in-depth quantitative comparisons were performed on 1) wild-type PS1 and its derivative carrying point mutations known to cause heritable early-onset AD in mice, and 2) PS1- or PS2-containing γ-secretase complexes equipped with N-terminal tandem-affinity purification (TAP) tags on PS paralogs in HEK293 cells. Isobaric labeling of co-purifying peptides for quantitative mass spectrometry revealed that γ-secretase complexes interact with other protein networks, including the cellular catenin-cadherin network, the molecular machinery that targets and fuses synaptic vesicles to cellular membranes, and the H+-transporting lysosomal ATPase macro-complex. The study revealed mature γ-secretase complexes containing PS1 or mutant PS1 to be indistinguishable in their protein composition, confirmed several previously proposed γ-secretase interactors, identified many novel interactors and uncovered a subset of proteins which can engage in robust interactions with γ-secretase complexes in individual cell types but may escape detection when whole brains are used as biological source materials. Interestingly, signal peptide peptidase (SPP), a Type II TM cleaving aspartyl protease, was pre-dominantly found to co-purify with PS2-containing γ-secretase complexes and could be shown not to influence their maturation but to affect cleavage or release of cellular Aβ. A model emerged from this work that suggests PS1 and PS2 paralogs may divide up the task of handling a broad range of membrane stubs at least in part by associating with different molecular environments.
Thucydides on the Outbreak of War
Keywords: Thucydides
War

This project illuminates Thucydides’ political thought through a novel interpretation of the first book of the History of the Peloponnesian War. It explores how Thucydides reveals the human causes of war through the outbreak of a particular war, the Peloponnesian war. The primary claim is that Thucydides intends the breakdown of the Thirty Years’ Peace between Athens and the Peloponnesians, which inaugurates the great Peloponnesian war, to be understood by grasping how the characters of the Athenian and Spartan regimes contribute to the outbreak of the war and, crucially, how Athens and Sparta differently express human nature. In broad outline, the History’s first book reveals how the regime characters of Athens and Sparta inform their respective foreign policies, but also how the interaction between the two cities—informed by the distinctive necessities pressing upon them—causes the Hellenic status quo to tremble and fall. Throughout the first book, while never obscuring the specific events triggering war, Thucydides progressively develops and expands his original statement that it was Spartan fear of Athenian power that compelled the fighting. The study argues that necessity (or compulsion) is the bright thread that Thucydides uses to guide his reader through the episodes of the first book, from the immediate causes of the Peloponnesian war to the human causes of war, from the particular events to the History’s universal themes.
Constitutional Possibilities: An Inquiry Concerning Constitutionalism in British Columbia
Keywords: constitutionalism
constitutional law
constitutional theory
Aboriginal rights
experimentation

Constitutional change is relentless. Today, states jockey with regional associations, international organizations, transnational networks and sub-state authorities to define the scope of legitimate political conduct and establish rival bases for political affiliation. Constitutional theorists must be resolute but they should not be rigid. Especially in such uncertain conditions, theories are best understood not as plans to be implemented but as hypotheses to be tested. Charles Sabel and David Dyzenhaus write separately but share this pragmatic orientation, in which doubt is indispensable and truth is the end of public inquiry. They also share a distinctive belief that constitutionalism serves a moral end: it is the project of cultivating citizens who conceive their political community in terms of the commitments revealed by its practices. Their position, which is well suited for contemporary challenges, warrants elaboration and examination. British Columbia offers an ideal constitutional laboratory for that test. During the 1970s and 1980s, doubts mounted about the legitimacy of the constitutional settlement imposed by the Crown in the westernmost province of Canada. Legal, political and constitutional decisions raised the possibility that aboriginal rights and title survived colonization and Confederation. Since 1990, their existence has been confirmed in a cascade of constitutional experiments. Those initiatives can be distilled into four procedures: litigation, negotiation, consultation and collaboration. Although they have delivered practical benefits to some indigenous peoples, these procedures have not transformed provincial politics into a moral endeavour. The constraints on constitutionalism in British Columbia are both conceptual and institutional. Despite marginal improvements, those constraints endure and constitutionalism remains for now the sporadic pursuit of a small elite. To conceive constitutionalism as a project is to set a sound but exacting standard. Although British Columbia falls short, its failure is informative: the theory is useful.
Macroinvertebrate Community Structure and Function in Seasonal, Low-land, Tropical Streams across a Pristine-rural-Urban Land-use Gradient
Keywords: Freshwater
Tropical stream
Macroinvertebrates
Human impacts

Tropical freshwater ecosystems are understudied and not well understood relative to temperate systems; however, they are becoming increasingly imperiled by escalating anthropogenic impacts. The aim of this thesis was to investigate how tropical freshwater macroinvertebrate communities changed both structurally and functionally over a pristine-rural-urban land-use gradient, in relation to different spatial and temporal scales, as well as to the availability of potential food sources. Fifteen streams in the Panama Canal Watershed were sampled during the dry and wet seasons of 2007 and 2008, for macroinvertebrate communities (benthic and leaf litter), environmental variables, and potential food sources. Along the land-use gradient, in both habitat types, taxon richness, diversity, and evenness all decreased significantly; whereas, abundance increased significantly. For the benthic macroinvertebrate community, unique variation was explained equally well by local (water chemistry and sediment type) and landscape (riparian vegetation and watershed land use) characteristics in the dry season, and landscape characteristics explained slightly more variation in the wet season. Leaf-litter macroinvertebrate community unique variation was better explained by local variables than by landscape variables in both seasons. In terms of potential food resources, fine detritus and inorganic material were the most common across all streams (increased quantities in urban streams) and seasons; whereas, the availability of diatoms and leaf material increased in the dry season. Using gut content analyses, we found that collectors (gatherers and filterers) were by far the most common functional feeding group, increasing in abundance along the land-use gradient. Predators, shredders, and scrapers were all most abundant in pristine streams and decreased along the land-use gradient. Finally, using seven community metrices, a potential biomonitoring tool was developed, the Neotropical Low-land Stream Multimetric Index (NLSMI), which distinguished well among the different levels of stream impairment. This study demonstrated that tropical communities were negatively affected by human land alteration, but that community responses depended on the habitat sampled, the influence of different spatial scales varied between the seasons, and the effect of food resources appeared to be complex. These aspects must be taken into consideration for management decisions and restoration strategies to be effective.