Science (Faculty of)

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1-AMINOCYCLOPROPANE-1-CARBOXYLATE (ACC) DEAMINASE GENES IN RHIZOBIA: ISOLATION AND CHARACTERIZATION
(University of Waterloo, 2007-05-14T13:14:45Z) Duan, Jin
A collection of 233 putative Rhizobia strains from 30 different sites across Saskatchewan, Canada was assayed for ACC deaminase activity, with 27 of the strains displaying activity. When all 27 strains were characterized based on 16S rRNA gene sequences, it was noted that 26 strains are Rhizobium leguminosarum and one strain is Rhizobium gallicum. PCR was used to rapidly isolate ACC deaminase structural genes from the above mentioned 27 strains; 17 of them have 99% identities when compared with the previously characterized ACC deaminase structural gene (acdS) from Rhizobium leguminosarum bv. viciae 128C53K, whereas the other 10 strains are 83% identical compared to the acdS of R. leguminosarum bv. viciae 128C53K. Southern hybridization showed that each strain has only one ACC deaminase gene. Using inverse PCR, the region upstream of the ACC deaminase structural genes was characterized for all 17 strains and shown to encode a leucine responsive regulatory protein. The results are discussed in the context of a previously proposed model for the regulation of bacterial ACC deaminase and facilitates an elaboration of the role of ACC deaminase in nodulation and nitrogen fixation.
1H MAS NMR Study of Water on Pd-MCM-41
(University of Waterloo, 2015-06-18) Crone, Joshua
Hydrogen spillover represents one of the most promising avenues to achieve hydrogen storage at the density required for transportation applications. The spillover phenomenon, however, is a topic of much debate, with many conflicting results existing in the literature. The goal of this work is to thoroughly study and understand a system where spillover has been reported, palladium loaded MCM-41 (Pd-MCM-41), thus laying a groundwork favorable to accurate, conclusive work on the spillover phenomenon in the future. Specifically, the nature of the material and how water (an important factor in certain spillover systems) interacts with it are investigated. This information would not only benefit the study of spillover, but also any other application of Pd-MCM-41 where water is involved. 1H MAS NMR measurements were carried out on three mesoporous silica samples at a range of water hydration levels. The materials were unmodified (pristine) MCM-41, Pd-MCM-41 and reduced (ie. treated with H2 gas) Pd-MCM-41. The spectra from these samples were fit using a previously published model for water on pristine MCM-41, which was extended to account for differences in the current samples. The model was applied first to the pristine MCM-41 spectra. In the hydration range from 0.0 to 0.2 monolayers (ML) of water adsorbed on the pore surface, the results were similar enough to those from Walia's publication that they were used to aid and assess the fitting results of the Pd loaded samples. Additional features observed in the results for pristine MCM-41 were the appearance of a new peak at 0.5 ML, attributed to water condensing and filling sections of the pore volume, and the development of water-water interactions, which are typically absent at lower hydration levels. Two additional peaks, designated Pd Water Groups 1 and 2, are observed in the spectra of the palladized samples. Once these were added to the fitting model, the spectra were determined to be adequately fit by the model; features of the remaining peaks matched those in the pristine sample. Two models, labeled A and B, are presented to explain the differences between the results from pristine MCM-41 and Pd-MCM-41. In Model A, water dissociatively and preferentially adsorbs onto the Pd, causing water to condense around the metal clusters. This multilayer water phase exchanges with water on the pore surface, resulting in Pd Water Group 1. Pd Water Group 2 is attributed to the first layers of water molecules strongly bound to Pd. Model B, which relies on Pd causing nearby water to have a large chemical shift, is shown to be unlikely. The main reason is that the chemical shift of this Pd shifted water is required to increase with increasing water hydration level in order to reproduce the observed chemical shift of Pd Water Group 1. For this and other reasons, Model A is concluded to be the most probable description for the behavior of water on Pd-MCM-41, based on the results presented.
2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver
(Elsevier, 2017-01-15) Zhou, Wenhu; Ding, Jinsong; Liu, Juewen
Heavy metal detection is a key topic in analytical chemistry. DNA-based metal recognition has advanced significantly producing many specific metal ligands, such as thymine for Hg2+ and cytosine for Ag+. For practical applications, however, robust sensors that can work in a diverse range of salt concentrations need to be developed, while most current sensing strategies cannot meet this requirement. In this work, 2-aminopurine (2AP) is used as a fluorescence label embedded in the middle of four 10-mer DNA homopolymers. 2AP can be quenched up to 98% in these DNA without an external quencher. The interaction between 2AP and all common metal ions is studied systematically for both free 2AP base and 2AP embedded DNA homopolymers. With such low background, Hg2+ induces up to 14-fold signal enhancement for the poly-T DNA, and Ag+ enhances up to 10-fold for the poly-C DNA. A detection limit of 3 nM is achieved for both metals. With these four probes, silver and mercury can be readily discriminated from the rest. A comparison with other signaling methods was made using fluorescence resonance energy transfer, graphene oxide, and SYBR Green I staining, respectively, confirming the robustness of the 2AP label. Detection of Hg2+ in Lake Huron water was also achieved with a similar sensitivity. This work has provided a comprehensive fundamental understanding of using 2AP as a label for metal detection, and has achieved the highest fluorescence enhancement for non-protein targets. (C) 2016 Elsevier B.V. All rights reserved.
3-Phenylpyrazino[1,2-a]indol-1(2H)-ones as dual cholinesterase and amyloid aggregation inhibitors
(University of Waterloo, 2017-05-10) Gujral, Sarbjeet Singh
The year 2017, marks the 110th anniversary of the discovery of Alzheimer’s disease (AD)- a devastating neurodegenerative disease. Regardless of the significant advances made in the past century on the pathology of AD, the current pharmacotherapy options for AD remains woefully low and provide symptomatic relief only. Inhibitors of cholinesterase enzymes such as donepezil (Aricept®), rivastigmine (Exelon®) and galantamine (Razadyne®) which represents the primary class of agents used in the management of AD targets one of the many pathological routes of AD. Our study aims at discovering novel small hybrid molecules based on 3-phenylpyrazino[1,2-a]indol-1(2H)-one (PPI) ring system which can potentially exhibit multiple activities toward various factors involved in AD pathophysiology including (i) the inhibition of cholinesterase enzymes such as acetyl (AChE) and butyrylcholinesterases (BuChE); (ii) preventing the aggregation of the neurotoxic amyloid beta (Aβ) peptide and (iii) antioxidant properties. Initial modeling studies suggested that the tricyclic PPI template fits in the catalytic site of AChE and the C3 phenyl can orient toward the peripheral anionic subsite (PAS) in the AChE enzyme. In addition, C3-position provides opportunities to incorporate Aβ binding pharmacophores. With this goal, we synthesized the PPI compound library by coupling ethyl indole-2-carboxylates esters with 2-bromoacetophenones to obtain ethyl-1-(2-oxo-2-phenylethyl)-1H-indole-2-carboxylates which underwent an intramolecular cyclization in the presence of ammonium acetate to afford PPI derivatives (5a-n). The compounds were characterized by analytical methods including NMR and LCMS. The cholinesterase inhibition was evaluated using Ellman’s protocol by UV-Vis spectroscopy. The anti-Aβ-aggregation property was evaluated by fluorescence spectroscopy using thioflavin- T (ThT) assays. Antioxidant activity of the PPI derivatives was assessed using DPPH assay method. Transmission electron microscopic imaging (TEM imaging) were also performed to support the in vitro data obtained from ThT based fluorescence assays. The Discovery Studio (DS) software, Structure-Based-Design program (4.0) from BIOVIA Inc. was used to determine the binding interactions of the PPI derivatives for SAR optimization. Our results indicate that several compounds in the series exhibit dual cholinesterase inhibition properties; one such compound is 5h (3-(2-methoxyphenyl)pyrazino[1,2-a]indol-1(2H)-one) with IC50 AChE = 7.3 μM , IC50 BuChE = 1.9 μM. Compound 5h was found to be much more potent than reference agents donepezil and rivastigmine toward BuChE inhibition. Several other compounds such as 5d ( 3-(3,4-dimethoxyphenyl)pyrazino[1,2-a]indol-1(2H)-one) and 5h (- 3-(2-methoxyphenyl)pyrazino[1,2-a]indol-1(2H)-one exhibited excellent of Aβ40/42 inhibition (% inhibition of Aβ40 = 83.3% and 67.7% at 25 µM respectively, and % inhibition of Aβ42 = 90% and 94% at 25 µM respectively). Compound 5d and 5h were found to be more potent than curcumin and resveratrol towards Aβ42 inhibition. The PPI derivatives were also found to exhibit antioxidant activities. Unsubstituted PPI compound 5a exhibited good antioxidant activity (~33% DPPH radical scavenging at 50 μM), while, compound 5k (3-(4-hydroxy-3-methoxyphenyl)pyrazino[1,2-a]indol-1(2H)-one) exhibited excellent antioxidant activity (~ 84% DPPH radical scavenging at 50 μM). This proves the multi-targeted activities of PPI derivatives. Our results indicate that the fused tricyclic phenylpyrazino[1,2-a]indo-1(2H)-ones (PPI) represent a novel class of compounds which can be modified chemically to design and develop multi-targeting agents aimed at the cholinergic, amyloid cascade and oxidative stress hypothesis of AD.
A 30-Year Study of Impacts, Recovery, and Development of Critical Effect Sizes for Endocrine Disruption in White Sucker (Catostomus commersonii) Exposed to Bleached-Kraft Pulp Mill Effluent at Jackfish Bay, Ontario, Canada
(Frontiers, 2021-04-22) Ussery, Erin J.; McMaster, Mark E.; Servos, Mark. R.; Miller, David H.; Munkittrick, Kelly R.
Jackfish Bay is an isolated bay on the north shore of Lake Superior, Canada that has received effluent from a large bleached-kraft pulp mill since the 1940s. Studies conducted in the late 1980s found evidence of reductions in sex steroid hormone levels in multiple fish species living in the Bay, and increased growth, condition and relative liver weights, with a reduction in internal fat storage, reduced gonadal sizes, delayed sexual maturation, and altered levels of circulating sex steroid hormones in white sucker (Catostomus commersonii). These early studies provided some of the first pieces of evidence of endocrine disruption in wild animals. Studies on white sucker have continued at Jackfish Bay, monitoring fish health after the installation of secondary waste treatment (1989), changes in the pulp bleaching process (1990s), during facility maintenance shutdowns and during a series of facility closures associated with changing ownership (2000s), and were carried through to 2019 resulting in a 30-year study of fish health impacts, endocrine disruption, chemical exposure, and ecosystem recovery. The objective of the present study was to summarize and understand more than 75 physiological, endocrine, chemical and whole organism endpoints that have been studied providing important context for the complexity of endocrine responses, species differences, and challenges with extrapolation. Differences in body size, liver size, gonad size and condition persist, although changes in liver and gonad indices are much smaller than in the early years. Population modeling of the initial reproductive alterations predicted a 30% reduction in the population size, however with improvements over the last couple of decades those population impacts improved considerably. Reflection on these 30 years of detailed studies, on environmental conditions, physiological, and whole organism endpoints, gives insight into the complexity of endocrine responses to environmental change and mitigation.
3D bioprinting of liver-mimetic construct with alginate/cellulose nanocrystal hybrid bioink
(Elsevier, 2018-03-01) Wu, Yun; Lin, Zhi Yuan (William); Wenger, Andrew; Tam, Kam C.; Tang, Xiaowu (Shirley)
3D bioprinting is a novel platform for engineering complex, three-dimensional (3D) tissues that mimic real ones. The development of hybrid bioinks is a viable strategy that integrates the desirable properties of the constituents. In this work, we present a hybrid bioink composed of alginate and cellulose nanocrystals (CNCs) and explore its suitability for extrusion-based bioprinting. This bioink possesses excellent shear-thinning property, can be easily extruded through the nozzle, and provides good initial shape fidelity. It has been demonstrated that the viscosities during extrusion were at least two orders of magnitude lower than those at small shear rates, enabling the bioinks to be extruded through the nozzle (100µm inner diameter) readily without clogging. This bioink was then used to print a liver-mimetic honeycomb 3D structure containing fibroblast and hepatoma cells. The structures were crosslinked with CaCl2 and incubated and cultured for 3 days. It was found that the bioprinting process resulted in minimal cell damage making the alginate/CNC hybrid bioink an attractive bioprinting material.
3D N-doped hybrid architectures assembled from 0D T-Nb2O5 embedded in carbon microtubes toward high-rate Li-ion capacitors
(Elsevier, 2019-02) Tolami Hemmati, Sahar; Li, Ge; Wang, Xiaolei; Ding, Yuanli; Pei, Yu; Yu, Aiping; Chen, Zhongwei
Herein, a unique nitrogen-doped T-Nb2O5/tubular carbon hybrid structure in which T-Nb2O5 nanoparticles are homogeneously embedded in an in-situ formed nitrogen-doped microtubular carbon is synthesized, utilizing a facile and innovative synthesis strategy. This structure addresses the poor electron conductivity and rate capability that hinder T-Nb2O5's promise as an anode for Li-ion devices. Such a distinctive structure possesses a robust framework that has ultrasmall active nanocomponents encapsulated in highly conductive carbon scaffold with hollow interior and abundant voids, enabling fast electron/ion transport and electrolyte penetration. Moreover, nitrogen-doping not only ameliorates the electronic conductivity of the heterostructure, but also induces pseudocapacitance mechanism. When evaluated in a half-cell, the as-prepared material delivers a specific capacitance of 370 F g−1 at 0.1 A g−1 within 1–3 V vs. Li/Li+ and excellent cyclability over 1100 cycles. A high energy density of 86.6 W h kg−1 and high power density of 6.09 kW kg−1 are realized. Additionally, a capacitance retention as high as 81% after 3500 cycles is achieved in an Li-ion Capacitor (LIC) with activated carbon as the cathode and nitrogen-doped T-Nb2O5/tubular carbon as the anode.
3D printing of soft hydrogels incorporating functional nanomaterials
(University of Waterloo, 2017-01-10) Wu, Yun
Tissue engineering (TE) scaffolds are required to closely mimic the human body environment to enable the study of cell behavior in vitro and allow the fabrication of artificial tissue constructs. The scaffolds should possess controlled structural and mechanical properties, such as stiffness and porosity. In addition, its physical and chemical properties, such as electrical conductivity, should be able to promote cell differentiation and growth. In the search of developing an ideal scaffold, hydrogels that incorporate functional nanomaterials scaffolds are being explored. This study, as a fulfillment for a master’s degree, investigates the ability of cells to survive in a three-dimensional (3D) printed soft hydrogels incorporated with functional materials. In this work, alginate, a natural polymer, was used as the main hydrogel material. It can physically crosslink by adding CaCl2 or chemically crosslink after methacrylation, by introducing carbon-carbon double bonds. However, pure alginate hydrogel is mechanically and rheologically weak. Previous mechanical tests indicated that cellulose nanocrystals (CNC)-incorporated alginate-based hydrogels increased the mechanical strength of the scaffolds, which can contribute to the interactions between CNC and polymeric networks. Rheological tests showed that the incorporation of cellulose nanocrystals into the alginate matrix introduced strong shear thinning behavior and improved shear modulus. The enhancement of rheological properties improved the printability and fidelity of the hybrid pre-gel solution. Finally, cell viability was explored by suspending 3T3 fibroblasts in the bioink. It was shown that the hybrid bioink was nontoxic and the cell viability remained high over a 7-days period. This master’s thesis demonstrates the feasibility of 3D printing of soft hydrogels for the fabrication of 3D scaffolds that mimic real tissues. It is anticipated that a broad array of ink compositions with suitable viscosity can be printed and multiple cell lines can grow in the same scaffold. This research provides a platform for the fabrication of biocompatible polymers and stretchable biosensors within an engineered scaffold.
400 kHz Spectral Domain Optical Coherence Tomography for Corneal Imaging
(University of Waterloo, 2021-12-23) Chen, Lin Kun
The cornea is the transparent, outermost layer of the human eye that contributes approximately 70% of the refractive power of the eye in air. It is composed of five major tissue layers: the epithelium, the Bowman’s membrane, the stroma, the Descemet’s membrane, and the endothelium. Corneal diseases such as Keratoconus and Fuchs’ dystrophy can change the morphology of some or all of the corneal layers, which can lead to vision impairment and eventually blindness. For example, Keratoconus causes localizes thinning and thickening of the corneal epithelium, damage to the collagen structure of the corneal stroma (scarring) and alteration of the corneal curvature. All of these changes result in blurred and double vision, and in severe cases can lead to corneal blindness that would require corneal replacement surgery. Fuchs’ dystrophy is a genetic disease that damages the endothelium cell. Since the endothelial cells are responsible for maintaining the fluid level in the stroma, impairment or death of the endothelial cells leads to dehydration or edema of the cornea that results in partial or full corneal blindness. Systemic diseases such as diabetes also affect the physiology and morphology of the cornea. Diabetes affects all the corneal cells and leads to abnormalities such as neuropathy, keratopathy, stromal edema, decrease in endothelial cell density, low tear secretion etc. Although there have been many clinical studies of these diseases, knowledge of the early-stage changes in the corneal morphology at the cellular level remains unclear. Understanding the early stage of disease development with the help of high speed and ultra-high resolution optical coherence tomography (UHR-OCT) corneal imaging can improve the early diagnostics of corneal diseases and well as monitoring the effectiveness of different therapies such as surgical intervention or administration of pharmaceutical drugs. The main objectives of my research project were: a) to upgrade the 34 kHz OCT system with a new camera that offered a 400 kHz data acquisition rate and 8192-pixel linear array sensor, b) test the performance of the 400 kHz OCT system for ex-vivo and in-vivo corneal imaging, and c) develop pre-processing for the interferogram and post-processing algorithms for the images. Implementing a camera with a faster acquisition rate will help to reduce the motion artifact caused by involuntary eye motions. Also, compared to 4500 pixels used in the 34 kHz camera, the new system utilizes approximately 7500 pixels, resulting in a larger scanning range. Although new camera has smaller sensor size (30% smaller), vertical binning is applied to ensure the light signal is all captured. However, due to the faster acquisition rate (~11 times faster), about 10 dB of SNR will suffers from the reduced integration time. Doubling the sample arm power while keep all other conditions the same can boost the SNR by about 3 dB. Therefore, incident power at the sample arm will be raised carefully according to the maximum permissible exposure calculated using the American National Standard for Ophthalmics – Light Hazard Protection for Ophthalmics instruments provided by ANSI. The result from the technical tests shows that the 400 kHz SD-OCT system offers 1 µm axial resolution in biological tissue with an extended scanning range of 2.8 mm (compared to 1.2 mm of the 34 kHz system). It has a lateral resolution of 1.04 μm/pix and can resolve group 7 element 6 of the USAF target with a 20x objective. It can provide 83 dB SNR with 0.95 mW of incident power at a 400 kHz image acquisition rate which should be sufficient to image semi-transparent biological tissues such as the human retina and cornea. However, given the much higher image acquisition rate (> 10x higher), the imaging power can be increased safely to ~ 4 mW, which will increase the system’s SNR to ~ 90 dB. So far, the performance of the 400 kHz OCT system has been tested by imaging plant tissues (cucumber) and ex-vivo pig corneas, due to the cancellation of all in-vivo human and animal studies imposed by COVID-19.
A 4d Lorentzian Spin Foam Model With Timelike Surfaces
(University of Waterloo, 2010-10-07T18:19:40Z) Hnybida, Jeffrey
We construct a 4d Lorentzian spin foam model capable of describing both spacelike and timelike surfaces. To do so we use a coherent state approach inspired by the Riemannian FK model. Using the coherent state method we reproduce the results of the EPRL model for Euclidean tetrahedra and extend the model to include Lorentzian tetrahedra. The coherent states of spacelike/timelike triangles are found to correspond to elements of the discrete/continuous series of SU(1,1). It is found that the area spectrum of both spacelike and timelike surfaces is quantized. A path integral for the quantum theory is defined as a product of vertex amplitudes. The states corresponding to timelike triangles are constructed in a basis diagonalised with respect to a noncompact generator. A derivation of the matrix elements of the generators of SL(2,C) in this basis is provided.
5-HT7 Receptor Neuroprotection against Excitotoxicity in the Hippocampus
(University of Waterloo, 2014-04-11) Vasefi, Seyedeh Maryam
Introduction and Objectives: The PDGFβ receptor and its ligand, PDGF-BB, are expressed throughout the central nervous system (CNS), including the hippocampas. Several reports confirm that PDGFβ receptors are neuroprotective against N-methyl-D-asparate (NMDA)-induced cell death in hippocampal neurons. NMDA receptor dysfunction is important for the expression of many symptoms of mental health disorders such as schizophrenia. The serotonin (5-HT) type 7 receptor was the most recent of the 5-HT receptor family to be identified and cloned. 5-HT receptors interact with several signaling systems in the CNS including receptors activated by the excitatory neurotransmitter glutamate such as the NMDA receptor. Although there is extensive interest in targeting the 5-HT7 receptor with novel therapeutic compounds, the function and signaling properties of 5-HT7 receptors in neurons remains poorly characterized. Methods: The SH-SY5Y neuroblastoma cell line, primary hippocampal cultures, and hippocampal slices were treated with 5-HT7 receptor agonists and antagonists. Western blotting was used to measure PDGFß receptor expression and phosphorylation as well as NMDA receptor subunit expression and phosphorylation levels. Real-time RT-PCR was used to measure mRNA level of PDGFß receptor in neuronal cultures. Cell death assays (MAP2, MTT) were used to measure the neuroprotective effects of 5-HT7 and PDGFß receptor activation. Results: My research involved elucidating the molecular mechanisms of neuroprotection after 5-HT7-induced PDGFß receptor upregulation. I demonstrated that 24 h treatment with the selective 5-HT7 receptor agonist, LP 12, increased not only the expression but also the activation of PDGFß receptors as measured by the phosphorylation of tyrosine 1021, the phospholipase Cγ binding site. Activation of the 5-HT7 receptor also selectively changed the expression and phosphorylation state of the NR2B subunit of the NMDA receptor. Activation of 5-HT7 receptors was neuroprotective against NMDA-induced toxicity in primary hippocampal neurons and this effect required PDGFß receptor kinase activity. Thus, long-term (24 h) activation of 5-HT7 receptors was neuroprotective via increasing the expression of a negative regulator of NMDA activity, the PDGFß receptor. In contrast, acute activation (5-30 min) of 5-HT7 receptor increased NMDA evoked current and altered NMDA receptor subunit phosphorylation in hippocampal neurons in a manner that was different from what we observed in our 24 h experiments. Conclusions: I identified two 5-HT7 receptor to NMDA receptor pathways: acute activation of the receptor increased NMDA-evoked currents whereas long-term 5-HT7 agonist treatment prevented NMDA-induced excitotoxicity in a PDGFß receptor-dependent manner. This research is significant in the ongoing advances for the treatment of mental heath disorders, such as schizophrenia and depression, that involve the 5-HT, glutamate, and neuronal growth factor systems.
Ablation loading and qudit measurements with barium ions
(University of Waterloo, 2023-08-31) Bramman, Brendan
Barium is one of the best ions for performing quantum information in a trapped-ion system. Its long-lived metastable D5/2 state allows for some interesting quantum operations, including the current best state preparation and measurement fidelity in qubits. This metastable state also opens up the possibility of implementing higher-dimensional qudits instead of qubits. However, installing a barium metal source in a vacuum chamber has shown to be somewhat of a challenge. Here, we present a loading technique which uses a barium chloride source instead, making it much easier to install. Laser ablation with a high-energy pulsed laser is used to generate neutral atoms, and a two-step photoionization technique is used to selectively load different isotopes of barium in our ion trap. The process of laser ablation and the plume of atoms it generates are characterized, informing us on how to best load ions. Loading is achieved, and selectivity of our method is demonstrated, giving us a reliable way to load 138Ba+ and 137Ba+ ions. The quadrupole transition into the metastable D5/2 state is investigated, with all of the individual transitions successfully found and characterized for 138Ba+ and 137Ba+. Coherent operations are performed on these transitions, allowing us to use them to define a 13-level qudit, on which we perform a state preparation and measurement experiment. The main error source in operations using this transition is identified to be magnetic field noise, and so we present attempts at mitigating this noise. An ac-line noise compensation method is used, which marginally improved the coherence time of the quadrupole transitions, and an additional method of using permanent magnets is proposed for future work. These efforts will help to make trapping barium more reliable, making it an even more attractive option for trapped ion systems. The state preparation and measurement results using the quadrupole transition to the long-lived metastable D5/2 state establish barium as an interesting platform for performing high-dimensional qudit quantum computing.
Above Bandgap Hyperpolarization Mechanism in Isotopically Purified Silicon and Optimal Bayesian Experiment Design for $T_1$ Estimation
(University of Waterloo, 2018-05-24) Alexander, Thomas
This thesis is concerned with the mechanism underlying the above bandgap illumination Dynamic Nuclear Polarization (DNP) of phosphorus donors in isotopically purified silicon-28. Two proposed DNP models are introduced and compared. A series of NMR saturation experiments are performed in which modified buildup dynamics are observed when the saturation tone is applied at the bare phosphorus resonance. This effect is attributed to the phosphorus donor being ionized via the Auger process resulting in dynamics which are modelled as a set of coupled Bloch equations. The donor bound exciton capture and neutralization rates are extracted, and a paramagnetic shift of the bare phosphorus resonance is observed. These observed dynamics strongly imply the DNP mechanism is due to phononic modulation of the donor electron spatial wavefunction inducing cross-relaxation between the hyperfine coupled electron and nuclear spins. The framework of Bayesian parameter estimation and its Sequential Monte Carlo(SMC) numerical implementation for continuous outcome probability distributions are introduced. Next, an introduction to Bayesian experiment design and its incorporation within the SMC framework is provided. A discussion of the computational challenges for continuous outcome distributions is given. To resolve these difficulties Monte Carlo Maximum Importance Sampling(MIS) numerical methods are developed which allow the evaluation of Bayesian experimental design heuristics such as the Bayes risk. These design strategies are applied to the problem of $T_1$ relaxation rate estimation with inversion recovery experiments. Experiments are optimized both respect to per-experiment performance and total experiment time. These techniques are shown to have substantial improvements over baseline methods. Furthermore, they compare favourably with previous frequentist experimental designs for IR experiments and demonstrate significant improvements.
Abundance Matching with the Galaxies of the Virgo Cluster and the Stellar-to-Halo Mass Relation
(University of Waterloo, 2012-09-27T21:17:19Z) Grossauer, Jonathan
Using data from the Next Generation Virgo Cluster Survey and high-resolution simulations of Virgo cluster-like halos, we determine the stellar-to-halo mass relation (SHMR) for subhalos, using the technique of abundance matching. The subhalo SHMR differs markedly from its field galaxy counterpart, regardless of how the subhalo mass is defined (mass at z = 0, mass at infall, or maximum mass while in the field). The slope of the relation at low mass (M⋆<10^10 Msun) is in all cases steeper than the same for the field. We find conflicting indicators of whether this difference in slope indicates an increasing or decreasing dark-to-stellar ratio; further modelling is required to reach a definitive conclusion. We also find evidence for the existence of a measurable age gradient in velocity, such that older subhalos have lower velocities than their younger peers. This opens the possibility that good quality redshifts of the lower mass galaxies of the Virgo cluster might provide additional constraints on the SHMR at high redshift and its evolution. Finally, we investigate the degree to which mergers, particularly major mergers, cause mixing of old and new material in halos, which has implications for the robustness of any implied radial age gradient. We find only a slight increase in mixing for major mergers over minor mergers, and little evidence for any large amount of mixing being induced by mergers of any ratio.
Accelerating peroxidase mimicking nanozymes using DNA
(Royal Society of Chemistry, 2015-09-07) Liu, Biwu; Liu, Juewen
DNA-capped iron oxide nanoparticles are nearly 10-fold more active as a peroxidase mimic for TMB oxidation than naked nanoparticles. To understand the mechanism, the effect of DNA length and sequence is systematically studied, and other types of polymers are also compared. This rate enhancement is more obvious with longer DNA and, in particular, poly-cytosine. Among the various polymer coatings tested, DNA offers the highest rate enhancement. A similar acceleration is also observed for nanoceria. On the other hand, when the positively charged TMB substrate is replaced by the negatively charged ABTS, DNA inhibits oxidation. Therefore, the negatively charged phosphate backbone and bases of DNA can increase TMB binding by the iron oxide nanoparticles, thus facilitating the oxidation reaction in the presence of hydrogen peroxide.
Acceptance of Commercially Available Wearable Activity Trackers Among Adults Aged Over 50 and With Chronic Illness: A Mixed-Methods Evaluation
(JMIR Mhealth Uhealth., 2016-01-27) Mercer, Kathryn; Grindrod, Kelly; Schneider, Eric; Li, Melissa; Chilana, Parmit; Giangregorio, Lora M.
Background: Physical inactivity and sedentary behavior increase the risk of chronic illness and death. The newest generation of “wearable” activity trackers offers potential as a multifaceted intervention to help people become more active. Objective: To examine the usability and usefulness of wearable activity trackers for older adults living with chronic illness. Methods: We recruited a purposive sample of 32 participants over the age of 50, who had been previously diagnosed with a chronic illness, including vascular disease, diabetes, arthritis, and osteoporosis. Participants were between 52 and 84 years of age (mean 64); among the study participants, 23 (72%) were women and the mean body mass index was 31 kg/m2 . Participants tested 5 trackers, including a simple pedometer (Sportline or Mio) followed by 4 wearable activity trackers (Fitbit Zip, Misfit Shine, Jawbone Up 24, and Withings Pulse) in random order. Selected devices represented the range of wearable products and features available on the Canadian market in 2014. Participants wore each device for at least 3 days and evaluated it using a questionnaire developed from the Technology Acceptance Model. We used focus groups to explore participant experiences and a thematic analysis approach to data collection and analysis. Results: Our study resulted in 4 themes: (1) adoption within a comfort zone; (2) self-awareness and goal setting; (3) purposes of data tracking; and (4) future of wearable activity trackers as health care devices. Prior to enrolling, few participants were aware of wearable activity trackers. Most also had been asked by a physician to exercise more and cited this as a motivation for testing the devices. None of the participants planned to purchase the simple pedometer after the study, citing poor accuracy and data loss, whereas 73% (N=32) planned to purchase a wearable activity tracker. Preferences varied but 50% felt they would buy a Fitbit and 42% felt they would buy a Misfit, Jawbone, or Withings. The simple pedometer had a mean acceptance score of 56/95 compared with 63 for the Withings, 65 for the Misfit and Jawbone, and 68 for the Fitbit. To improve usability, older users may benefit from devices that have better compatibility with personal computers or less-expensive Android mobile phones and tablets, and have comprehensive paper-based user manuals and apps that interpret user data. Conclusions: For older adults living with chronic illness, wearable activity trackers are perceived as useful and acceptable. New users may need support to both set up the device and learn how to interpret their data.
Accurate Determination of the Diffusion Coefficient of Proteins by Fourier Analysis with Whole Column Imaging Detection
(American Chemical Society, 2015-01-21) Zarabadi, Atefeh; Pawliszyn, Janusz
Analysis in the frequency domain is considered a powerful tool to elicit precise information from spectroscopic signals. In this study, the Fourier transformation technique is employed to determine the diffusion coefficient (D) of a number of proteins in the frequency domain. Analytical approaches are investigated for determination of D from both experimental and data treatment viewpoints. The diffusion process is modeled to calculate diffusion coefficients based on the Fourier transformation solution to Fick’s law equation, and its results are compared to time domain results. The simulations characterize optimum spatial and temporal conditions and demonstrate the noise tolerance of the method. The proposed model is validated by its application for the electropherograms from the diffusion path of a set of proteins. Real-time dynamic scanning is conducted to monitor dispersion by employing whole column imaging detection technology in combination with capillary isoelectric focusing (CIEF) and the imaging plug flow (iPF) experiment. These experimental techniques provide different peak shapes, which are utilized to demonstrate the Fourier transformation ability in extracting diffusion coefficients out of irregular shape signals. Experimental results confirmed that the Fourier transformation procedure substantially enhanced the accuracy of the determined values compared to those obtained in the time domain.
Acetic and Acrylic Acid Molecular Imprinted Model Silicone Hydrogel Materials for Ciprofloxacin-HCl Delivery
(Multidisciplinary Digital Publishing Institute, 2012-01-02) Hui, Alex; Sheardown, Heather; Jones, Lyndon W.
Contact lenses, as an alternative drug delivery vehicle for the eye compared to eye drops, are desirable due to potential advantages in dosing regimen, bioavailability and patient tolerance/compliance. The challenge has been to engineer and develop these materials to sustain drug delivery to the eye for a long period of time. In this study, model silicone hydrogel materials were created using a molecular imprinting strategy to deliver the antibiotic ciprofloxacin. Acetic and acrylic acid were used as the functional monomers, to interact with the ciprofloxacin template to efficiently create recognition cavities within the final polymerized material. Synthesized materials were loaded with 9.06 mM, 0.10 mM and 0.025 mM solutions of ciprofloxacin, and the release of ciprofloxacin into an artificial tear solution was monitored over time. The materials were shown to release for periods varying from 3 to 14 days, dependent on the loading solution, functional monomer concentration and functional monomer:template ratio, with materials with greater monomer:template ratio (8:1 and 16:1 imprinted) tending to release for longer periods of time. Materials with a lower monomer:template ratio (4:1 imprinted) tended to release comparatively greater amounts of ciprofloxacin into solution, but the release was somewhat shorter. The total amount of drug released from the imprinted materials was sufficient to reach levels relevant to inhibit the growth of common ocular isolates of bacteria. This work is one of the first to demonstrate the feasibility of molecular imprinting in model silicone hydrogel-type materials.
Achievable Polarization for Heat-Bath Algorithmic Cooling
(University of Waterloo, 2015-08-17) Rodríguez Briones, Nayeli Azucena
Highly pure quantum states play a central role in applications of quantum information science, both as initial states for quantum algorithms and as resources for quantum error correction. Controlled preparation of pure enough quantum states that satisfy the threshold for quantum error correction remains a challenge, not only for ensemble implementations like nuclear magnetic resonance (NMR) or electron spin resonance (ESR) but also for other technologies. Heat-bath algorithmic cooling (HBAC) is a promising method to increase the purity of a set of qubits coupled to a bath. In this thesis, we investigated the achievable polarization of this technique by analyzing the limit when no more entropy can be extracted from the system. In particular, we give an analytic form of the maximum polarization achievable for the case when the initial state is totally mixed, and the corresponding steady state of the whole system. Furthermore, we give the number of steps needed to get a specific required polarization (the exact number for the two qubit case and an upper bound for more general cases).
Action Mechanism and Structural Studies on the Lipopeptide Antibiotic Daptomycin
(University of Waterloo, 2019-07-02) Beriashvili, David
Daptomycin (dap) is calcium-dependent lipopeptide antibiotic that is used clinically to treat systemic infections caused by Gram-positive pathogens. It is thought that dap brings about its antimicrobial effect by binding cytoplasmic bacterial membranes, via a calcium meditated interaction with the lipid phosphatidylglycerol (PG), and subsequent oligomerization. There is consensus that dap oligomerization is required for bactericidal activity, but the exact mechanism by which dap oligomers cause cell death is contested. Significant experimental evidence suggests that dap oligomers form cation-selective pores that cause membrane depolarization halting metabolite transport and resulting in cell death. Other proposed action modes include dap-induced non-selective membrane permeabilization, lipid extraction, and dislodgement of membrane-associated biosynthetic enzymes. The effect of phospholipids acyl tails on dap cation-selective pore formation has not been studied. In this thesis, fluorescence spectroscopy experiments on large unilamellar vesicles were used to study the effects of phospholipid acyl tails on dap cation-selective pore formation in a systematic fashion. It was observed that dap could permeabilize membranes composed of equal parts PC and PG with myristoyl acyl tails, but not those containing palmitoyl and oleoyl acyl tails. Oleoyl lipid acyl tails were found to render membranes insusceptible to dap pore formation regardless of the headgroup they were ligated to and at low concentrations in the membrane (10 mol%). Further studies showed that inhibition of dap pore formation by phospholipid acyl tails is correlated with increased acyl tail length rather than lipid unsaturation. Oleoyl acyl tails were found to restrict dap pore formation by disrupting the final stage of oligomer assembly. Attempts to permeabilize oleoyl lipid acyl tail containing membranes by branching and increasing the length of dap’s acyl tail moiety were unsuccessful. Overall, these findings suggest that lipid acyls affect dap’s action mode and should be a major consideration when designing model membrane systems for future dap action mode studies. Determining dap’s membrane-bound structure at an atomic level would help resolve the debate in literature regarding its action mode and establish dap’s structure-activity relationship. Previous attempts to determine the membrane-bound structure by solution-state nuclear magnetic resonance have failed because no suitable membrane mimetic existed. The latter portion of this thesis investigated the suitability of novel styrene-maleic acid (SMA) co-polymers to create membrane nanodisc suitable for determining dap’s membrane-bound structure. Through dynamic light scattering, fluorescence spectroscopy, and solution-state NMR it was found that this polymer can form membrane nanodiscs, with a diameter small enough for structural studies by solution-state NMR, in the presence of PG (50 mol%) and 3 mM calcium. Further, these PG containing nanodiscs allow for partially dap oligomerization, and are stable on the timescale of NMR experiments. Overall, while the SMA polymer used in this study did not allow for full dap oligomerization, the partial structure of membrane-bound dap could be obtained with this system by solution-state NMR.

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