VictorJuiz/thesis huggingface dataset:
Nanomechanics of Barnacle Proteins and Multicomponent Lipid Bilayers Studied by Atomic Force Microscopy

Owing to atomic force microscopy’s (AFM) high-resolution in both imaging and force spectroscopy, it is very successful in probing not only structures, but also nanomechanics of biological samples in solution. In this thesis, the nanomechanical properties of lipid bilayers of biological relevance and proteins of the barnacle adhesive were examined using AFM indentation, AFM-based force mapping, and single-molecule pulling experiments. Through high-resolution AFM-based force mapping, the self-organized structures exhibited in phase-segregated supported lipid bilayers consisting of dioleoylphosphatidylcholine / egg sphingomyelin / cholesterol (DEC) in the absence and presence of ceramide (DEC-Ceramide) were directly correlated with their breakthrough forces, elastic moduli, adhesion, and bilayer thickness. Results were presented as two-dimensional visual maps. The highly stable ceramide-enriched domains in DEC-Ceramide bilayers and the effect of different levels of cholesterol as well as of diblock copolymers, on the nanomechanical stability of the model systems studied were further examined. For the proteins of the barnacle adhesive, scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and chemical staining with amyloid-selective dyes, in addition to AFM imaging, indentation, and pulling experiments were performed to study the structure and nanomechanics of the polymerized barnacle glue. Nanoscale structures exhibiting rod-shaped, globular, and irregularly shaped morphologies were observed in the bulk barnacle cement by AFM. SEM coupled with energy dispersive x-ray (EDX) makes evident the organic nature of the rod-shaped nanoscale structures while FTIR spectroscopy on the bulk cement gave signatures of β-sheet and random coil conformations. Indentation data yielded higher elastic moduli for the rod-shaped structures as compared to the other structures in the bulk cement. Single molecule AFM force-extension curves on the matrix of the bulk cement often exhibited a periodic sawtooth-like profile, observed in both extend and retract portions of the force curve. Rod-shaped structures stained with amyloid protein-selective dyes (Congo Red and Thioflavin-T) revealed that about 5% of the bulk cement are amyloids.

Keywords: multicomponent lipid bilayers
barnacle proteins
nanomechanics
force mapping
AFM force spectroscopy
raft mimics
Advisor: Walker, Gilbert C.
Theory of Mind and Pretend Play in Children with Specific Language Impairment

The ability to represent the mental states of others (i.e., Theory of Mind, ToM) is vital for social interaction. There is limited information on ToM knowledge in children with specific language impairment (SLI). These children have deficient language abilities that cannot be explained by hearing, cognitive, or neurological problems. Furthermore, children with SLI experience difficulty in initiating and maintaining social pretend play. Language, pretend play, and ToM typically develop in concert, which may indicate that they share an underlying capacity for representation. Given that language is deficient in children with SLI, these children may have problems with ToM, which might be related to their social behaviors during pretend play. This study was the first to investigate the association between ToM and pretend play in children with and without SLI. Twenty-two children with SLI and 22 with typical development (TD), between 48-71 months of age, participated in this study. Children engaged in a variety of ToM tasks and participated in two pretend play assessments: a standardized pretend play assessment and a role play activity. Children with SLI scored significantly lower on ToM tasks and engaged less often in some sophisticated forms of pretend play than their age-matched peers with TD. After controlling for language and SES, there were no significant associations between ToM and pretend play in children with and without SLI. When language groups were analyzed individually, different patterns of associations emerged for children with and without SLI. ToM was positively associated with pretend play in children with TD but negatively associated in children with SLI. Moreover, inconsistent patterns of associations were observed for some children with SLI (i.e., poor ToM understanding but sophisticated pretend play or vice versa). This study demonstrated that children with SLI may also have concomitant problems in ToM and pretend play, which may have implications for clinical assessment and intervention. The study contributes to the literature by investigating the link between ToM and different forms of sophisticated pretend play in children with and without SLI. Given the different patterns of partial correlations, future investigation of the relationship between ToM and pretend play relationship is warranted.

Keywords: preschool
children
language impairment
pretend play
Theory of Mind
Advisor: Johnson, Carla J.
Design, Synthesis, and Characterization of a Novel Class of Mitochondrial Delivery Vectors: Mitochondria-penetrating Peptides

Mitochondria have evolved to play a vital role in both the life and death of a eukaryotic cell, through involvement in numerous cellular functions, such as the proficient production of energy from ATP biosynthesis and the regulation of programmed cell death. As a result, dysfunction in the biochemical processes housed within this organelle is implicated in diverse diseases, including cancer, diabetes, and neurodegenerative disorders. Advancing mitochondrial medicine by probing the subcellular biochemistry or targeting therapeutics into this organelle has motivated the development of effective mitochondrial delivery vectors. Thus, the rational design of novel mitochondrial-specific molecules, inspired by the success of cell-penetrating peptides, is described, whereby short synthetic peptides that retain the ability to traverse the plasma membrane, yet with mitochondrial-specificity were engineered. By modulating the overall physicochemical properties, through substitutions with both natural and synthetic amino acids, and monitoring the intracellular localization by confocal fluorescence microscopy, the requisite thresholds for achieving mitochondrial accumulation with a cationic peptide were elucidated. These systematic studies led to the development of a novel class of cationic yet lipophilic peptides, referred to as mitochondria-penetrating peptides (MPPs), which are readily cell permeable and preferentially localize into the mitochondria of living mammalian cells. The mechanisms of cellular uptake and mitochondrial matrix accumulation were investigated and the results from these studies suggest that MPPs utilize the negative membrane potential across these biological membranes to drive translocation. In addition, the effects of various chemical perturbations on the cellular and mitochondrial uptake, such as sequence, structure of the cation moiety, and chirality, were examined. The information obtained from these studies provided insight into the important features of these peptides and led to the design of an optimized molecule displaying pyridinium salt side chains. Moreover, MPPs were shown to be effective mitochondrial delivery vectors for diverse and bioactive small molecule cargo. In conclusion, the extensive biological and chemical characterization of MPPs revealed the importance of balancing the opposing characteristics of positive charge and lipophilicity to attain preferential sequestration into mitochondria, as well as provided evidence that these peptides will be suitable as mitochondrial delivery vectors.

Keywords: mitochondria
targeting
delivery
peptide
Advisor: Kelley, Shana O.
Robust Power Control of Optical Networks with Time-delays

We study the stability of power control algorithms applied to optical networks in the presence of both time-delays and uncertainties. The objective of power control algorithms acting on optical networks is to ensure each signal channel attains an optimal optical signal-to-noise ratio (OSNR) value such that transmission errors are minimized. The inputs to the optical network are the transmitter powers and the outputs of the optical network are the OSNR values. The primal control algorithms adjust the channel powers at the transmitters using the channel OSNR values as feedbacks to attain OSNR optimality. We also present the dual control algorithm located at the links which transmits a channel price as an additional feedback to the primal control algorithms. Together, these are called primal-dual control algorithms. We present robust OSNR models for optical networks with multiple time-delays. Specifically, we consider additive system uncertainties, input multiplicative uncertainties on the signal powers, and transmitter noise uncertainties, all within a norm-bounded uncertainty framework. We analyze and modify both central cost based algorithms and game-theoretic based algorithms, with an emphasis on the latter, to ensure the stability of the closed-loop system. We apply time-delay stability analyses to exploit the structures of the closed-loop systems for each type of control algorithm. These techniques include frequency analyses, Lyapunov-Razumikhin techniques, and Lyapunov-Krasovskii techniques. Due to nonlinearities in the closed-loop system models, and their time-scale separated dynamics, we apply singular perturbation theory modified to handle either Lyapunov-Razumikhin theory or Lyapunov-Krasovskii theory. Singular perturbation theory, modified for time-delays, allows us to decouple complicated closed-loop systems into two simpler subsystems, one on a "slow" time-scale, and the other on a "fast" time-scale. We develop stability conditions for primal algorithms applied to arbitrary networks with delays. We also develop stability conditions for primal-dual algorithms applied to single-links, single-sink networks, two channel networks, and multi-link networks with both time-delays and uncertainties. The main results are presented as either LMI conditions and algebraic criteria. Simulations verify the stability of the closed-loop systems in the presence of time-delays. In addition, the simulations show the stabilization of perturbed systems at the expense of transient convergence time.

Keywords: Optical Networks
Power Control
Time-Delays
Advisor: Pavel, Lacra
Inhibitory Control and Reward Processes in Children and Adolescents with Traumatic Brain Injury and Secondary Attention-deficit/Hyperactivity Disorder

Children with traumatic brain injury (TBI) often experience difficulties with inhibitory control (IC), manifest in both neurocognitive function (poor performance on the stop signal task, SST) and behavior (emergence of de novo attention-deficit/hyperactivity disorder, or secondary ADHD, S-ADHD). IC allows for the regulation of thought and action, and interacts with reward to modify behaviour adaptively as environments change. Children with developmental or primary ADHD (P-ADHD) exhibit poor IC and abnormalities when responding to rewards, yet the extent to which S-ADHD is similar to and different from P-ADHD in terms of these behaviours is not well-characterized. The cancellation and restraint versions of the SST were used to examine the effects of rewards on 2 distinct forms of IC in children and adolescents divided into 4 groups (control, TBI, S-ADHD, and P-ADHD). The SST requires participants to respond to a “go signal” and inhibit their responses when encountering a “stop signal”. Rewards improved performance similarly across groups, ages, and cancellation and restraint IC tasks. Adolescents exhibited better IC and faster and less variable response execution relative to children. Significant IC deficits were found in both tasks in the P-ADHD group, with participants with S-ADHD exhibiting intermediate cancellation performance relative to the other groups. Participants with TBI without S-ADHD were not impaired on either task. The relationship between neurocognitive and behavioral IC was examined by comparing multi-informant ratings of IC across groups, and examining the relationship between ratings and IC performance on the SST. Participants in the control and TBI groups were rated within the typical range, and exhibited fewer problems than either of the ADHD groups, who differed from each other (the P-ADHD group was rated as more inattentive than the S-ADHD group). Moderate to high concordance was found between parent and teacher reports, each of which was poorly concordant with self-reports. The P-ADHD and S-ADHD groups were unaware of their own deficits. Poorer IC predicted parent and teacher classification of participants into ADHD subtypes, although IC did not predict rating concordance. Despite similar clinical presentations, S-ADHD and P-ADHD differ in the phenotypic expression of behaviour and manifestation of IC across contexts.

Keywords: traumatic brain injury
ADHD
inhibitory control
reward
children
adolescents
Advisor: Dennis, Maureen
Functions of Ubiquitin Specific Protease 7 (USP7) in Epstein-Barr Virus Infection and Associated Cancers

The Epstein-Barr virus (EBV) infects over 90% of the human population and is associated with several human malignancies. The EBNA1 protein of EBV binds recognition sites in the latent origin of replication (oriP) and is important for the replication and segregation of EBV genomes in latently-infected cells. EBNA1 is also directly implicated in malignant transformation and immortalization of the host cell. EBNA1 does not have any known enzymatic activity and it employs cellular proteins to mediate its functions. One such protein is the ubiquitin specific protease, USP7, which is a key regulator of the p53 tumor suppressor. The aim of this thesis was to functionally characterize the interaction between EBNA1 and USP7. Here I show that USP7 promotes the DNA-binding activity of EBNA1 and is recruited along with an accessory protein, GMPS, to the oriP. The USP7-GMPS complex can deubiquitinate histone H2B and may enable epigenetic regulation of latent viral infection. Additionally, I present evidence for a direct role of EBNA1 in EBV-mediated carcinogenesis. EBNA1 prevents stabilization of p53 by USP7 and abrogates p53 activation by disrupting promyelocytic leukemia nuclear bodies (PML-NBs) that acetylate p53. This interferes with p53-activated gene expression and inhibits apoptosis. EBNA1-expressing cells also have impaired ability to repair DNA, but survive as well as or better than control cells. Thus EBNA1 creates a cellular environment conducive to transformation and immortalization. These studies have also allowed me to learn more about and expand on the known functions of USP7. I provide biochemical evidence suggesting that a P/A/ExxS motif is a preferred sequence for binding the USP7 N-terminal domain. Furthermore, I show USP7 is a negative regulator of PML proteins and PML-NBs and promotes p53 DNA-binding activity. Surprisingly, neither function required the deubiquitinase activity of USP7.

Advisor: Frappier, Lori
Innovative Systems for Arch Bridges using Ultra High-performance Fibre-reinforced Concrete

In this thesis, new design concepts for arch bridges using ultra high-performance fibre-reinforced concrete are developed for spans of 50 to 400 m. These concepts are light-weight and efficient, and thus have the potential to significantly reduce the cost of construction. Lightness is achieved by the thinning of structural components and the efficient use of precompression in the arch, rather than by the decrease of bending stiffness. Using the advanced properties of the material, the design concepts were shown to reduce the consumption of concrete in arch bridges by more than 50% relative to arches built using conventional concrete technology. In addition to span length, other design parameters including span-to-rise ratio and deck-stiffening were considered, resulting in a total of seventy-two design concepts. Other important contributions made in this thesis include: (1) the development of a simple analytical model that describes the transition of shallow arches between pure arch behaviour and pure beam behaviour, (2) a comprehensive comparative study of 58 existing concrete arch bridges that characterizes the current state-of-the-art and serves as a valuable reference design tool, and (3) the development and experimental validation of general and simplified methods for calculating the capacity of slender ultra high-performance fibre-reinforced concrete members under compression and bending. The research presented in this thesis provides a means for designers to take full advantage of the high compressive and tensile strengths of the concrete and hence to exploit the economic potential offered by the material.

Keywords: arches
concrete arch bridges
ultra high-performance fibre-reinforced concrete
slender members
second-order effects
shallow arches
arch analysis
bridge design
Advisor: Gauvreau, Douglas Paul
Molecular Mechanisms of Intracellular Apolipoprotein B100 Degradation

Apolipoprotein B100 (apoB), a necessary component of very low density lipoproteins, is overproduced in metabolic disorders such as type II diabetes, increasing the risk of atherosclerosis. ApoB production is regulated by intracellular degradation of the protein by proteasomes, ER-60-dependent degradation, or post-endoplasmic reticulum (ER) pre-secretory proteolysis (PERPP)/autophagy. The first aim of the present study was to understand how apoB is delivered from the ER to cytosolic proteasomes. We investigated the roles of cellular factors BiP, Derlin-1, VIMP, Hrd1, and p97 in targeting apoB to proteasomes. Co-immunoprecipitation experiments indicated that these factors associate with apoB. Use of dominant negative p97 adenoviruses led to ER accumulation of apoB, demonstrating that p97 is required to extract apoB from the ER. Therefore, these factors appear to be important for proteasomal degradation of apoB. ER-60, an ER protein with chaperone and cysteine protease activities, promotes apoB degradation through an unclear mechanism. To determine which property of ER-60 is involved, we used adenoviruses encoding wild-type ER-60 or a mutant form that lacked cysteine protease activity. Overexpression of wild-type, but not mutant, ER-60 induced apoB degradation, suggesting that ER-60 may function as a cysteine protease in apoB degradation. We then investigated post-translational degradation of apoB in cells undergoing ER stress induced by glucosamine treatment. Treatment of hepatocytes with glucosamine induced a significant loss of cellular apoB. We speculated that oxidative stress and subsequent degradation by PERPP might be responsible. Glucosamine treatment appeared to cause only a slight increase in oxidative stress, but treatment with the antioxidants desferrioxamine or vitamin E blocked glucosamine-induced apoB degradation, suggesting involvement of PERPP/autophagy. Overall, these studies have increased our understanding of the molecular mechanisms of intracellular apoB degradation and led to identification of critical factors and pathways that may be explored in the future to control hepatic apoB production in metabolic disease.

Advisor: Adeli, Khosrow
Landscape Structure and Watershed Mercury Sensitivity in Boreal Headwater Regions

Aquatic mercury (Hg) contamination caused by industrial Hg emissions, atmospheric transport and deposition to sensitive ecosystems is an ongoing concern in many parts of the world. Boreal ecosystems are particularly sensitive to Hg deposition, and large soil-Hg burdens in these regions may prolong recovery of Hg impacted surface waters for many decades. Four studies were undertaken to examine interactions between watershed characteristics, hydro-climatic variability and terrestrial-aquatic export of key chemical parameters linked to watershed Hg sensitivity. Two new quantitative techniques, hydrogeomorphic edge detection and characteristic morphology analysis, were developed to explicitly map and characterize the spatial distribution, geomorphic form and hydro-biogeochemical function of forested wetlands using airborne Light Detection and Ranging (LiDAR) surveys. The results demonstrate the critical contribution of forested wetlands and upland-wetland interactions to the production and mobilization of dissolved organic carbon (DOC) and methyl-mercury (MeHg) - respectively - to downstream surface waters. Results of strategic, event-based hydrochemical sampling also demonstrate the critical contribution of summer high-flow periods to terrestrial-aquatic MeHg export. Finally, an analysis of historical monitoring databases of streamflow volume, hydrochemistry and Hg concentrations in yearling perch in two contrasting headwater lake basins was conducted. The results indicate strong potential for short-term, hydrologically-driven shifts in terrestrial-aquatic coupling and watershed Hg sensitivity, but only for the wetland-dominated, humic lake that exhibited consistent, summertime hypolimnetic anoxia. These various findings suggest that accurate characterization of watershed structure can help researchers identify first-order limitations on whole-watershed methylation efficiency, particularly in relation to hydro-climatic drivers of terrestrial-aquatic coupling in Boreal headwater regions.

Keywords: hydrology
mercury
LiDAR
wetlands
methyl-mercury
GIS
Advisor: Branfireun, Brian
Investigation of the Effect of n3-Polyunsaturated Fatty Acids on Vulnerability to Atrial Fibrillation in Cardiomyopathy

Atrial fibrillation (AF) is a common and serious arrhythmia. Current treatments are of limited efficacy, and most do not treat the atrial structural remodeling (hypertrophy and fibrosis) that underlies most clinical AF. Our group has created an experimental dog model of atrial mechanical stretch called the simultaneous atrial and ventricular pacing (SAVP) model (which results in atrial fibrosis and susceptibility to AF) in order to study novel treatments for structural remodeling induced AF. Omega-3 polyunsaturated fatty acids (n3 PUFAs), particularly the marine derived forms eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have been shown to be effective in treating arrhythmias (including AF) in some animal studies and clinical trials. The mechanism for this effect of n3 PUFAs is not well understood. In this study we sought to characterize the n3 PUFA effect on AF vulnerability, atrial electrophysiology, histology, and gene expression, and determine relevant mechanisms. Dogs were paced for 0, 2, 7 or 14 days and given n3 PUFAs, olive oil or nothing. Prophylactic n3 PUFAs significantly reduced both AF vulnerability and conduction slowing in SAVP dogs (%AF inducibility: 9.2±8.8 vs. 4.7±6.3; global atrial conduction time: 75±11ms vs. 65±6ms [SAVP 14 days vs. SAVP 14 days with n3 PUFAs, P<0.05 for both comparisons]). Prophylactic n3 PUFAs also reduced inflammation (mean CD18 grade: 2.1±0.8 vs. 1.3±0.6 [SAVP 2 days vs. SAVP 2 days with n3 PUFAs, P=0.055]), hypertrophy (myocyte cross-sectional area: 498±64µm2 vs. 322±111µm2 [SAVP 14 days vs. SAVP 14 days with n3 PUFAs, P<0.05]), and fibrosis (%collagen area vs. unpaced dogs: 178±58 vs. 127±37 [SAVP 14 days vs. SAVP 14 days with n3 PUFAs, P<0.05]). N3 PUFAs were also found to reduce the expression of structural remodeling related molecules such as TGF-β, EGF, ERK and Akt. N3 PUFAs given after some pacing had already occurred were found to be less effective at reducing AF vulnerability and structural remodeling. The results of this study suggest that, in the SAVP model, n3 PUFAs reduce vulnerability to AF by attenuation of adverse structural remodeling at the genetic level.

Keywords: heart
omega
fibrillation
fish
atria
fat
cardiovascular
diet
Advisor: Dorian, Paul