title: Identification of PEA3 Target Genes in Human Cells

contributor:
Hassell, John
Biology

subject: PEA3 target genes, human cells

abstract: Mouse PEA3 is the founding member of the PEA3 subfamily of ETS transcription factors that includes ERM and ER81. Numerous studies implicate PEA3 subfamily members in a diversity of human cancers, especially breast cancer. Dominant-negative PEA3 (L1NPEA3En) effectively represses activated transcription by all three PEA3 subfamily members. When expressed under control of the MMTV promoter, L1NPEA3En significantly delays the appearance of mammary tumors and reduces their number and size in mouse models of HER2 mediated breast cancer. In addition, L1NPEA3En is not expressed in the mammary tumors that do develop in these mice. These findings strongly suggest a required role for PEA3 subfamily members or other ETS proteins with similar DNA binding specificity in HER2-mediated oncogenesis. The primary objective of this research was to identify the PEA3 subfamily target genes that could play a role in the initiation and progression of tumors, specifically in the breast. To achieve this, a recombinant adenovirus carrying L1NPEA3En was constructed to express L1NPEA3En in three human mammary tumor cell lines: MDA-MB-468, BT-549 and MDA-MB-361. Gene expression analysis using Affymetrix® GeneChip® technology identified a common set of 39 downregulated and 2 upregulated genes in cells expressing L1NPEA3En compared to control cells in all three tumor cell lines. Differentially expressed genes included some that have been shown to play key roles in tumorigenesis such as activating transcriptionfactor 3, heat shock 70kD protein lA and interleukin-8. In addition one colon carcinoma cell line, SW620, was used for gene expression analysis and 7 genes identified in the mammary tumor cell lines were also identified in the colon carcinoma cell line. The results suggest a role for PEA3 subfamily genes in a multiple human cancers mediated through a small subset of common target genes. The genes identified as being differentially expressed by ~NPEA3En hold potential value not only as targets for therapeautic drug discovery, but also as diagnostic or prognostic markers for human cancers, specifically breast cancer.

abstract: Thesis

abstract: Master of Biological Science (MBioSci)


title: Two techniques for symmetric multiple description coding with reduced storage space decoder

contributor:
Dumitrescu, Sorina
Electrical and Computer Engineering

subject: storage space decoder

abstract: In this work we propose two techniques for symmetric multiple description coding with reduced storage space decoder. The first technique is multiple description scalar quantizer with linear joint de-coders. We propose an optimal design algorithm similar to Vaishampayan's algo-rithm, to which we add an index assignment optimization step. We also solve an additional challenge in the decoder optimization, by proving that the problem is a convex quadratic optimization problem with a closed form solution (under some mild conditions). Our tests show that the new method has very good performance when the probability of description loss is sufficiently low. The other technique is an improvement to the traditional multiple description coding scheme based on uneven erasure protection. We evaluate the asymptotical performance of both schemes for a Gaussian memoryless source. The analysis reveals that the improvement reaches over 1 dB for up to ten descriptions and low probability of description loss. From our experiments we observe that the improved scheme is very competitive comparing to other multiple description techniques as well.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Methodology for Screening Office Buildings for Energy Retrofit Measures

contributor:
Chidiac, Samir E.
Civil Engineering

subject: retrofit office energy

abstract: Both private and public sectors own and operate an array of office buildings that consume energy and contribute to the emission of greenhouse gases. In an attempt to reduce energy demands, an analysis into the cost/benefit relationship of incorporating energy retrofit measures (ERMs) was carried out. The main objective was to develop a methodology for screening office buildings for both their current level of energy efficiency and their potential for retrofit applications. Optimal retrofit options can be determined by examining how different building characteristics affect the benefits received from improving various components. By characterizing the office building stock into a manageable set of representative models, it was possible to make estimations on energy consumption for lights, computers, pumps, fans, hot water supply, cooling and heating loads. Employing EnergyPlus, an energy modelling software package, these representative building models were analyzed using three different climate regions for the specific effects that altering building components have on energy consumption. Using a statistical regression analysis, a set of equations was derived for determining the energy consumption based on building-specific variable values. A life cycle cost analysis was used to obtain the net present value associated with the implementation of various retrofit ERMs. Payback period was adopted to quantify the cost effectiveness of ERMs.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Actin Gene Expression During Myogenic Differentiation of BC^3H1 Cells

contributor:
Lee, Raymond W. H.
Biology

subject:
actin
myogenic differentiation
BC^3H1

abstract: Myogenic differentiation of muscle cells in culture is characterized by changes in morphology and in pattern of gene expression. When the myoblasts in culture are induced to diffrentiate either by cell to cell contact or by serum-starvation, a vast array of muscle tissue-specific genes including α-actin, are activated and is accompanied by a concomitant down-regulation of non-muscle genes such as, β- and γ-actins, tubulins etc.. The coordinate activation of muscle-specific genes is suggested to be mediated by cis-acting regulatory sequences in the muscle gene-promoters and muscle-tissue-specific DNA-binding proteins belonging to the MyoD class of regulators. But the mechanism behind the repression of non-muscle gene expression during differentiation has not yet been well understood. To date, no consensus has been achieved on the mechanism governing the down-regulation of β- actin gene, and no information is available on the regulation of -y-actin gene during muscle differentiation. The results from the present study showed that during differentiation of BC^3H1 cells the β- and γ-actins genes were down-regulated to ≈25% of their initial levels in undifferentiated cells. Measurement of half-life during differentiation indicated that the half-lives of both β- and γ-actins decreased to ≈25% of their original levels in myoblasts. These results suggest that changes in mRNA stability play an important role in the down-regulation of non-muscle actin genes. Second messengers and oncogenes are known to block the differentiation program of muscle cells. In the present study cAMP and ElA were observed to inhibit the down-regulation of β- and γ-actin  genes in BC^3H1 cells. In both cAMP-and E1A- treated cells the β- and γ-actin  mRNAs were found to have a higher half-life than the untreated differentiated BC^3H1 cells. This observation also suggests that mRNA stability might play an important role in the regulation of β- and γ-actin gene expression. The muscle-specific α-actin is activated by cell-cell contact and serum-starvation. Results in the present study suggested that cAMP was able to inhibit the activation of α-actin expression mediated by serum-starvation while it had no significant effect on the signal mediated by cell-cell contact. It is hypothesized that the two signals mediating a-actin activation might follow different intracellular signalling pathways. The effects of cAMP and E1A on the expression of muscle-specific and non-muscle actins could be a direct primary event or might be an indirect secondary event, mediated by other intracellular factors such as myogenin. The results showed that cAMP did not block the transcription of the myogenin while secondary evidences suggested that cAMP might negatively-regulate myogenin at a point downstream of transcription. E1A was observed to block the expression of myogenin gene suggesting that E1A might be mediating its effect through myogenin. Because the muscle-specific(α) and non-muscle(β- and γ-) isoforms were expressed both in the presence and in the absence of myogenin, myogenin's role in the regulation of actin genes is unclear.

abstract: Thesis

abstract: Master of Science (MS)


title: CHARACTERIZATION OF THE METAL-DEPENDENT KDO8P SYNTHASE FROM CAMPYLOBACTER JEJUNI AND INHIBITION BY KDO8P OXIME, A NOVEL SLOW-BINDING INHIBITOR

title: CAMPYLOBACTER JEJUNI KDO8PS: A METAL-DEPENDENT KDO8PS

contributor:
Berti, Paul J.
Chemistry and Chemical Biology

subject: Campylobacter jejuni KDO8PS Kinetics

subject: KDO8P oxime inhibitor, novel slow-binding inhibitor, residence time

abstract: Antibiotic resistance is a worldwide threat to human health yet fewer new antibiotics are being approved. New antimicrobial drugs are urgently required. 3 Deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) is a target for antimicrobial drug design. KDO8PS catalyzes the condensation of D-arabinose-5 phosphate (A5P) with phosphoenolpyruvate (PEP) to produce KDO8P. KDO8PS catalyzes the first committed step in the lipopolysaccharides (LPS) biosynthesis pathway in Gram-negative bacteria and is critical for bacterial pathogenicity/virulence. We have characterized KDO8PS from Campylobacter jejuni (cjKDO8PS), a new metal-dependent KDO8P synthase (KDO8PS). cjKDO8PS is a tetramer in solution and optimally active at pH 7.5 and 60 °C. We have kinetically established that cjKDO8PS follows a rapid equilibrium sequential ordered ter ter kinetic mechanism, where Mn2+ binds first, followed by PEP, then A5P.  Pi dissociates first, before KDO8P, then Mn2+. cjKDO8PS was inhibited by KDO8P oxime, a novel slow tight-binding inhibitor. KDO8P oxime is a competitive inhibitor with respect to PEP and A5P, but uncompetitive with respect to Mn2+, with Ki = 10 ± 1 μM and an ultimate Ki* = 0.28 ± 0.10 μM. KDO8P oxime has a residence time (tR) of 5 days on the enzyme, a parameter that is highly correlated to in vivo efficacy. Crystallization conditions for the cjKDO8PS‧Mn2+‧KDO8P oxime complex have been found and can be optimized to obtain a crystal structure that shows how KDO8P oxime interacts with the active sites.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: The relentless increase in global antibiotic resistance is, regrettably, not matched with an increase in new effective antibiotics. New antimicrobial drug discovery strategies are desperately needed. Enzymes are key targets for drug design because they catalyze the majority of biological processes. In this project we sought to study and inhibit the activity of KDO8P synthase (KDO8PS) from Campylobacter jejuni, a common cause of food poisoning. KDO8P synthase is a critical enzyme involved in the lipopolysaccharide (LPS) biosynthesis in Gram-negative bacteria. The LPS acts as a permeability barrier and is crucial for bacterial pathogenicity/virulence. We found that C. jejuni KDO8PS is potently inhibited by KDO8P oxime, a novel inhibitor of KDO8PS. This inhibitor presents a unique opportunity to study these enzymes and a platform from which antibiotics against Gram-negative bacteria can be developed.


title: INVESTIGATION OF CADMIUM ZINC TELLURIDE DETECTOR FOR MEDICAL IMAGING APPLICATIONS

contributor:
Deen, M. Jamal
Electrical and Computer Engineering

subject:
CZT
Medical Imaging

abstract:
The wide band gap semiconductor Cadmium Zinc Telluride (CZT) is of recent
interest for medical imaging at room temperature. A number of properties, including
superior energy resolution, 3D photon position sensitivity, compact size, direct
photon conversion and energy-resolving capability, make CZT a promising candidate
for positron emission tomography (PET) and photon-counting X-ray imaging systems.
Despite these advantages, drawbacks, such as low mobility of holes, hole trapping,
charge sharing effect and characteristic X-ray escape degrade the performance of
large volume CZT detectors.
In this research, characterization and evaluation of single-crystal CZT photon
detector using simulation and experimental studies were done. First, a comprehensive
analytical model was developed and implemented by using Monte Carlo simulation
and finite element analyses. This model includes the generation and transportation of
charge carries within CZT detectors, and it provides useful guidance in optimizing the
electrode design and associated readout circuits.
Second, the performance of a 20×20×5mm3
 CZT crystal with 8×8 pixel anodes
and a planar cathode was integrated with readout electronics that can be used to build
a PET system was studied. The experiments demonstrate an energy resolution of
~2.26±0.84% full width half maximum (FWHM) at 662 keV and 19±3 ns
coincidence time resolution with planar parallel field configuration. A novel
algorithm based on charge sharing effect and transient signal analysis targeting the
improvement of spatial resolution, was proposed. The sub-pitch spatial resolution is
found to be ~30 µm and ~250 µm under signal-to-noise ratio of ~17, for inside and
outside the valid range of charge sharing, respectively.
Finally, the feasibility of CZT in photon-counting Computed Tomography (CT)
was studied by using monoenergetic sources, with a special attention paid to energy
degradation due to characteristic X-ray escape and the charge sharing effect. The
effects of detector configuration and incident beam location were also investigated.
The results show that the pixel size can be reduced to 500 µm without significant
count loss (~5%) and charge loss (~15%) for the photo-counting X-ray applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A General Platform for Aptamer Mediated Capture of Specific Targets

contributor:
Filipe, Carlos
Pelton, Robert H.
Chemical Engineering

subject: Aptamer mediated capture, specific targets, platform, general, DNA, RNA, polymer, phase transition

abstract:
 The purpose of this research is to develop a general method for capturing and separating specific targets. Nucleic acid aptamers are short sequences of single-stranded DNA or RNA which have the ability to bind to the small organic or inorganic molecules such as protein and metal ions with high binding affinity. In this study, a bioconjugate re-usable system was developed. It can reversibly load or unload DNA aptamers.

 To allow separation, a thermally responsive polymer (N-isopropylacrylamide, PNIPAM) is used. This polymer can undergo a reversible phase transition upon adding NaCl and/or increasing temperature. A short sequence of single stranded DNA (ssDNA) was coupled to PNIPAM. The ssDNA will experience a reversible phase transition because of the PNIPAM.

 The DNA sequence for an aptamer can be extended to contain a sequence that is complementary to that of the ssDNA coupled to PNIPAM. Adding this extended aptamer to the conjugate will result in spontaneous hybridization of the two strands of DNA. These strands can be separated using an agent (e.g. urea) that destroys hydrogen bonding. The conjugate can be recovered using a reversible inverse phase transition.

 The same PNIPAM-ssDNA conjugate can be used reversibly for coupling different aptamers. The aptamers did not lose their binding ability when coupled with PNIPAM-ssDNA conjugates. In the process of precipitation separation targets, the PNIPAM-ssDNA conjugate showed little loss with applied phase transition. Moreover, the coupling efficiency of the ssDNA to PNIPAM conjugates was determined. The
binding ability of the ATP aptamers to ATP was also investigated.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Measurement of Brown Adipose Tissue Using MRI in Adult Humans

contributor:
Morrison, Katherine Mary
Medical Sciences

subject:
brown adipose tissue
non-alcoholic fatty liver disease
magnetic resonance imaging

abstract:
BACKGROUND: There has been renewed interest in the study of brown adipose tissue (BAT) as a potential therapeutic target for obesity, diabetes and non-alcoholic fatty liver disease (NAFLD). There is now much evidence to suggest that BAT is not only important in thermogenesis but also plays an important role in metabolism. In adults, cold-induced BAT activation has led to a significant increase in insulin sensitivity and energy expenditure as well as decreased blood sugar levels. Thus, it is important to identify factors associated with these metabolic disorders such as the presence and activity of BAT to better understand if and how BAT can be targeted to treat these disorders. However, as a potential therapeutic target, it is important to develop accurate, precise, robust and reproducible non-invasive modalities to measure BAT.
PROJECT OBJECTIVES:
1) Develop and assess protocols for the use of MRI in measuring BAT characteristics and activity
2) Examine the relationship between BAT MR outcomes and known covariates such as age, sex, body fat percentage and outdoor temperature in adult humans
3) Determine if there is any association between BAT outcomes and liver fat in adult humans, before and after adjusting for potential covariates of liver fat such as age, sex and body fat percentage
METHODS: In total, 36 healthy participants (i.e. no conditions or medications that could influence BAT metabolism and/or liver disease) aged 18 to 60 years were recruited to this cross-sectional study. There were two study visits. In visit 1, anthropometrics (i.e. height, weight and waist circumference), blood pressure and body composition (via dual x-ray energy absorptiometry) were measured. Additionally, fasting bloodwork was collected and a 75-g oral glucose tolerance test (OGTT) was administered. During visit 2, participants were exposed to a standardized cold exposure set at 18°C for 3 hours using a water-perfused suit. MRI scans were acquired to evaluate changes in fat-fraction (FF%) and T2* relaxation (T2*) (BAT MR outcomes), liver fat and abdominal fat after a cold exposure. During the cold exposure protocol, mean skin temperature (MST) was monitored using 12 wireless temperature loggers placed at different sites of the body while electromyography (EMG) was used to measure shivering intensity.
RESULTS: In the current study, an MRI protocol capable of detecting BAT in the supraclavicular (SCV) region was developed. This protocol included the use of FF and T2* masks to more accurately characterize BAT in the SCV region. Additionally, the MR segmentation protocol was found to be very reliable, as demonstrated by excellent ICC values (i.e. ICCagreement and ICCconsistency ≥ 0.90) for all BAT MR outcomes irrespective of cold exposure. As expected, FF% (mean difference = -2.97; p < 0.0001*) and T2* (mean difference = -0.84; p < 0.0001*) values in the SCV significantly decreased after cold exposure, consistent with BAT activation. Furthermore, the decline in both FF% and T2* after cooling was specific to the SCV region, as these changes did not occur in the posterior neck fat. In examining the relationship between BAT MR outcomes and known covariates of BAT (i.e. age, sex, body fat percentage and outdoor temperature), it is important to note that lower FF% or T2* values are reflective of a browner phenotype while a greater reduction in FF% is indicative of higher BAT activity. BAT characteristics (A: pre-cold FF%; B: pre-cold T2*) and BAT activity (C: FF% reduction) were correlated with age (A: r = 0.54; p = 0.0007*; B: r = 0.42; p = 0.0112*; C: r = -0.39; p = 0.0213*) and body fat percentage (A: r = 0.83; p < 0.0001*; B: r = 0.58; p = 0.0002*; C: r = -0.64; p < 0.0001*). That is, higher age and body fat were associated with a less brown phenotype prior to cold exposure and with less BAT activity (i.e. lower FF% decline) in response to cold exposure. However, no associations were found between BAT MR outcomes and sex or outdoor temperature. Lastly, liver fat was associated with higher values of pre-cold FF% (r = 0.60; p < 0.0001*) and pre-cold T2* (r = 0.47; p = 0.0040*) while FF% reduction was inversely correlated with liver fat (r = -0.38; p = 0.0295*). Additionally, the relationship between BAT MR outcomes and liver fat still existed after adjusting for age and sex while its effects were mediated by adiposity.
CONCLUSION: In this study, a highly reliable MR segmentation protocol was developed that is capable of measuring BAT characteristics and activity irrespective of cold exposure. Additionally, the cold exposure protocol used was sufficient to elicit changes in BAT MR outcomes, as demonstrated by significant changes in FF% and T2* after cooling. Consistent with previous studies, BAT outcomes (as measured by MRI) were associated with age and body fat percentage. Lastly, findings in this thesis provide strong supporting data that BAT may regulate liver lipid content, however, the extent and mechanisms remain to be determined.

abstract: Thesis

abstract: Master of Science (MSc)


title: Secretion of Marker Proteins from Alginate-Poly-L-Alginate Microcapsules and Hydroxythely Methacrylate-Methyl Methacrylate Capsules

contributor:
Chang, P. L.
Biology

subject: marker proteins

subject: hydroxyethyl methacrylate-methyl methacrylate

abstract:
The objective of this study was to encapsulate cell lines that secrete marker proteins that cover a large molecular weight range (M^r from 45,000 to 300,000) and monitor the secretion of the marker proteins from alginate-poly-L-lysine-alginate (APA) microcapsules and hydroxyethyl methacrylatemethyl methacrylate (HEMA-MMA) thermoplastic capsules. Different parameters for the APA microcapsules, such as the duration of poly-L-lysine (PLL) and sodium citrate treatment, the initial cell density for encapsulation was studied, and their effects on secretion rate and cell proliferation were closely examined. Cell lines used for encapsulation secreted human growth hormone (hGH) (M^r 45,000), β-hexosaminidase (β-hexo.) (M^r 120,000) and β-glucuronidase (β-gluc.) (M^r 300,000). Monitoring the secretion rates, as well as the distribution of the marker proteins within the microcapsules following encapsulation enabled the permeability of the membrane to be assessed over one month in culture. Encapsulation of cell lines in both types of capsules was effective in producing viable cells capable of proliferating within a semi-permeable membrane. Encapsulating cells in single-coated APA microcapsules at 4°C, treated with 10 minutes PLL, 20 minutes sodium citrate and at a cell density of 2x10^6 cells/ml alginate was found to provide the most optimal conditions for prolonged viability of and stable secretion by the recombinant cells. Human growth hormone diffused readily across the capsule membrane into the culture media from both APA and HEMA-MMA capsules, at rates similar to the non-encapsulated cells. Human growth hormone did not accumulate in the intracapsular space in significant quantities.
β-glucuronidase and β-hexosaminidase could diffuse across APA capsule membrane, but not across HEMA-MMA capsule membrane into surrounding media. β-glucuronidase secretion from APA microcapsules was 8-fold lower than non-encapsulated cells. β-hexosaminidase secretion from APA microcapsules was 4.5-fold lower than non-encapsulated cells. Slight retention of both β-glucuronidase and β-hexosaminidase was observed in the intracapsular space of APA capsules. HEMA-MMA capsules completely blocked the secretion of both β-glucuronidase and β-hexosaminidase out of the capsule. Massive accumulation of both kinds of secretory enzymes was found in the intracapsular space of HEMA-MMA capsules. This indicated APA microcapsules have a molecular weight cut-off of >300,000 whereas HEMA-MMA microcapsules have a molecular weight cut-off of <120,000.

abstract: Thesis

abstract: Master of Science (MS)


title: Waveform Shaping for Directly Modulated Laser Diode

contributor:
Huang, Weiping
Electrical and Computer Engineering

subject: waveform shaping, directly modulated, laser diodes, nonlinearities, Volterra series model

abstract:
The objective of this thesis is to study the dynamic properties of laser diodes and the compensation for the nonlinearities of laser diodes based on the theory of Volterra series. In the first part of this thesis, an analytical expression in Volterra series is discussed to depict the nonlinear distortion of laser diodes up to the third order. The simulation results of this analytical method show that Volterra series model improves the accuracy of the description of the nonlinearity of laser diodes in comparison with small-signal analysis model. In the second part, the p^th-order inverse theory is introduced to
compensate the lasers' nonlinear distortion. The compensation scheme is constructed and the simulation of the system is conducted in this thesis. The result shows that the laser nonlinear distortion can be compensated by using this technique.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Neural and kinematic assessment of dance partnering as an ecological model of haptic mutual entrainment

contributor:
Brown, Steven
Psychology

subject:
rhythmic entrainment
joint action
haptic interaction
leading
following
neuro-imaging
motion capture
dance partnering

abstract: Entrainment is the rhythmic coordination of movement with a signal or other person. Most studies on entrainment have looked at synchronization with auditory or visual signals, whereas much less is known about how entrainment emerges mutually between individuals, especially when they are in physical contact with one another. In this dissertation, I empirically explored dance partnering as an ecological model for understanding interpersonal entrainment through haptic interaction. I began by performing a statistical meta-analysis of functional neuroimaging articles devoted to the most common experimental paradigm for entrainment, namely externally-paced finger tapping to an acoustic rhythmic stimulus (Chapter 2). The results showed that the cerebellar vermis was a strong neural marker of entrainment, as it was more activated by externally-paced tapping than by self-paced tapping, whereas the basal ganglia was activated by both types of rhythmic movements. Next, I used functional magnetic resonance imaging (fMRI) with a group of participants trained at couple dancing in order to explore the neural basis of haptic mutual entrainment, with a focus on the dynamics of leading and following (Chapter 3). While mutual interaction overall engaged brain networks involved in somatosensation, internal-body sensation and social cognition, leading showed enhanced activity principally in areas for motor control and self-initiated action, whereas following showed enhanced activity mainly in sensory and social-cognition areas. Finally, I used 3D motion capture to explore multisensory coupling for mutual entrainment at the group level during folk dancing (Chapter 4). The results showed that dancers relied most extensively on haptic coupling to synchronize as a group, whereas auditory and visual coupling were dependent on the spatiotemporal context. These studies advance our understanding of the neural and behavioural mechanisms underlying joint actions in which entrainment emerges mutually through haptic interaction.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Entrainment is the rhythmic coordination of movement with a signal or other person. Most studies on entrainment have looked at synchronization with auditory or visual signals, whereas much less is known about how entrainment emerges mutually between individuals, especially when they are in physical contact with one another. I began my research by performing a statistical analysis of the literature examining the brain basis of synchronization with auditory signals, identifying a key brain area for entrainment. Next, using a group of participants trained at couple dancing, I explored the brain areas engaged when two individuals in physical contact improvised movement together, focusing on who is leading or following the interaction. Finally, I explored how folk dancers use multiple sensory signals (auditory, visual and tactile) to synchronize as a group. These studies advance our understanding of the neural and behavioural mechanisms by which people mutually entrain through physical interaction.


title: Inter-Bar Currents In Rotating Stator Induction Machines

subject: inter-bar currents, machine efficiency, rotating stator induction machines

abstract: This work pioneers the experimental acquisition of data relating to the heating effects of inter-bar currents and the frequency components of the main field rotating flux. Previous research in the field of inter-bar currents is reliant on theory and mathematical modeling. Yet, with the growing need for increasing machine efficiency; experimental application of conceptualized theoretical models of machine losses is paramount. Focusing specifically on inter-bar currents in a rotating stator induction machine revealed a correlation between the heat generated in the iron core and the presence of inter-bar currents. Using temperature sensing instrumentation, experimental data was gathered to determine the inter-bar current distribution along the length of the rotor bars during acceleration. Additionally, custom current transducers were implemented to directly measure the main field rotating flux. The results present a solid foundation for direct and indirect measurement of inter-bar currents.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Fault Daignosis and Fault Tolerant Control of Complex Process Systems

contributor:
Mhaskar, Prashant
Chemical Engineering

subject:
Complex Process Systems
Fault Diagnosis
Fault Tolerant Control
High-gain observers
Uncertainty
Nonlinear Systems
Networked Systems
HVAC systems

abstract:
Automatic control techniques have been widely employed in industry to increase efficiency and profitability of the processes. However, reliability on automation increases the susceptibility of the system to faults in major control equipment such as actuators and sensors. This realization has motivated design of frameworks for fault detection and isolation (FDI) and fault tolerant control (FTC). The success of these FDI and FTC mechanisms is contingent on their ability to handle complexities associated with process systems such as nonlinearity, uncertainty, high dimensionality and the resulting effects of the existence of complexity in system structure such as faults that cannot be isolated. Motivated by the above considerations, this thesis considers the problem of fault diagnosis and fault tolerant control for complex process systems.

First, an FDI framework is designed that can detect and confine possible locations for faults that cannot be isolated. Next, the problem of simultaneous actuator and sensor fault diagnosis for nonlinear uncertain systems. The key idea is to design FDI filters in a way they account for the impact of uncertainty explicitly. This work then considers the problem of simultaneous fault diagnosis in nonlinear uncertain networked systems. FDI is achieved using a distributed architecture, comprised of a bank of local FDI (LFDI) schemes that communicate with each other. The efficacy of the proposed FDI methodologies is shown via application to a number of chemical process examples.

Finally, an integrated framework is proposed for fault diagnosis and fault tolerant control of variable air volume (VAV) boxes, a common component of heating, ventilation and air conditioning (HVAC) systems as an industrial case study of complex systems. The advantages of the proposed framework are diagnosing multiple faults and handling faults in stuck dampers using a safe parking strategy with energy saving capability.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Automation is the key to increase efficiency and profitability of the processes. However, as the level of automation increases, major control equipment are more prone to faults. Thus, fault detection and isolation (FDI) and fault tolerant control (FTC) frameworks are required for fault handling.  Fault handling, however, can only be efficiently achieved if the designed FDI and FTC frameworks are able to deal with complexities arising in process systems such as nonlinearity, uncertainty, high dimensionality and the resulting effects of the existence of complexity in system structure such as faults that cannot be isolated.

This motivates design of FDI and FTC frameworks for complex process systems. First, FDI frameworks are presented that can diagnose faults in the presence of complexities mentioned above. Then, an integrated framework is designed for diagnosing and handling faults of heating, ventilation and air conditioning (HVAC) systems as an industrial case study of complex process systems.


title: Nanowire Quantum Dot Photodetectors

contributor:
LaPierre, Ray
Engineering Physics

subject:
nanowires
photodetector
quantum dot
III-V
silicon
molecular beam epitaxy

abstract:
InAs/GaAs quantum dots (QDs) embedded within InP/GaP nanowires (NWs)
were grown on Si substrates by Au-assisted and self-assisted vapor-liquid-solid
(VLS) growth using molecular beam epitaxy (MBE). The morphology and
structure of the NWs was characterized using scanning electron microscopy
(SEM) and transmission electron microscopy (TEM). The samples were analysed
using photoluminescence (PL) and photocurrent measurements to study the
properties of NW-based QDs.
The composition of InAs x P 1-x QDs embedded within InP NWs was varied
from x = 0.25 to x = 1, demonstrating the tuning of quantum confined energy
levels. PL measurements demonstrated an emission peak that shifted towards
lower energy levels as the As composition was increased. This result was also
observed for QD absorption peaks through wavelength-dependent room
temperature photocurrent measurements. InP NWs were successfully passivated
with an AlInP shell, which was demonstrated through PL analysis.
The growth mechanism of patterned self-assisted GaP NWs on Si was studied
through SEM and TEM analysis. It was found that for large V/III flux ratios the
Ga seed particle reduced in volume throughout growth, which led to a smaller
NW diameter. Conversely, for small V/III flux ratios the Ga seed particle
increased in volume throughout growth, resulting in larger NW diameters. The
dependence of V/III flux ratio on NW growth was characterized, allowing the
tuning of NW diameter.
iv
GaP NWs with p-i-n junctions were fabricated on a Si substrate with GaAs
QDs embedded within the intrinsic region. To the author’s knowledge, this is the
first time such a device was demonstrated. The device demonstrated diode
characteristics as expected for a p-n junction. Wavelength-dependent photocurrent
measurements demonstrated the absorption of light within GaAs QDs, which was
collected through electric field dependent tunneling and thermionic emission. The
absorption of light extended beyond the bandgap of GaP due to the GaAs QDs.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: DISCOVERY AND FUNCTIONAL CHARACTERIZATIONS OF PLAG1 IN HUMAN HEMATOPOEITIC STEM AND PROGENITOR CELLS

contributor:
Hope, Kristin
Biochemistry and Biomedical Sciences

subject: PLAG1

subject: HSC

abstract:
Discovery and functional characterization of self-renewal regulatory factors constitute one of the central themes in the field of human hematopoietic stem and progenitor cell (HSPC) biology both for advancing the fundamental science as well as harnessing the knowledge to expand hematopoietic stem cells (HSCs) for regenerative therapeutics purposes.
Musashi-2 (MSI2) is a marker and essential positive regulator of HSCs but knowledge of the transcription factors (TFs) that ensure its appropriate HSC-specific expression is lacking. I believed that uncovering the transcriptional circuitry of MSI2 could also offer opportunities for the discovery of candidate TFs with similar or superior functions in human HSPCs. To that end, initial investigations were set out to identify a conserved minimal promoter region bound by TFs upstream of the translation start site of human MSI2. In silico analysis of the minimal promoter region and series of TF binding-site mutagenesis biochemical assays identified USF2 and PLAG1 as key co-regulators of MSI2 expression and function in the model K562 cell line and cord blood HSPCs. The approach identified PLAG1 as a candidate TF whose function in HSPCs was not previously reported.
I have characterized PLAG1 as an important regulator of HSPCs self-renewal using in vitro and xenotransplantation functional genomics coupled with RNA sequencing and downstream pathway analysis. In vitro, overexpression of PLAG1 (PLAG1OE) imparts sustained pro-survival advantage to progenitors and produces significantly more CD34+ cells compared to control culture. PLAG1OE enhances BFU-E and total  colony forming unit (CFU) output. Complementary in vitro assays using shRNA-mediated knockdown (PLAG1KD) elucidated impaired CFU output, increased apoptosis and significantly reduced CD34+ cell counts. In vivo transplantation of PLAG1OE CD34+ cells into NSG mice at limiting doses robustly enhances the frequency and absolute number of HSCs by a magnitude of 24.1-fold compared to control. Serial transplantation of bone marrow cells into secondary recipients demonstrated enhanced self-renewal of HSCs compared to control. Mechanistically, transcriptome-wide gene-set enrichment and network analysis revealed that ribosome biogenesis and proteostasis pathways are significantly attenuated. PLAG1OE up-regulates expression of H19 and MEG3 imprinted long non-coding RNA (lncRNA)-derived miR-675 and miR-127 species respectively. In silico overlap analysis with experimentally validated targets of both miR-127 and miR-675 revealed ribosome biogenesis and proteins synthesis pathways components as prime targets. PLAG1 also represses the pan-ribosome biogenesis transcriptional regulator MYC. Down regulation of MYC demonstrates another layer of PLAG1-mediated transcriptional attenuation of protein synthesis. Additionally, we observed dampening of IGF1R/PI3K/AKT/mTOR signaling pathway. Conversely, PLAG1KD down regulated H19 and MEG3 expression and reverses global gene-set enrichment observed by PLAG1OE in reciprocal fashion. Taken together, our study presents PLAG1 as master regulator of ribosome biogenesis and protein synthesis from multiple checkpoints to enhance clonogenicity, survival and long-term self-renewal capacity of HSCs.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Analog Computability with Differential Equations

contributor:
Zucker, Jeffery
Mathematics and Statistics

subject: Analog Computability, Differential Equations

abstract: In this dissertation we study a pioneering model of analog computation called General Purpose Analog Computer (GPAC), introduced by Shannon in 1941. The GPAC is capable of manipulating real-valued data streams. Its power is characterized by the class of differentially algebraic functions, which includes the solutions of initial value problems for ordinary differential equations. We address two limitations of this model. The  first is its fundamental inability to reason about functions of more than one independent variable (the `time' variable). In particular, the Shannon GPAC cannot be used to specify solutions of partial differential equations. The second concerns the notion of approximability, a desirable property in computation over continuous spaces that is however absent in the GPAC. To overcome these limitations, we extend the class of data types by taking channels carrying information on a general complete metric space X; for example the class of continuous functions of one real variable. We consider the original modules in Shannon's construction (constants, adders, multipliers, integrators) and add two new modules: a differential module which computes spatial derivatives; and a continuous limit module which computes limits. We then build networks using X-stream channels and the abovementioned modules. This leads us to a framework in which the speci cations of such analog systems are given by fi xed points of certain operators on continuous data streams, as considered by Tucker and Zucker. We study the properties of these analog systems and their associated operators. We present a characterization which generalizes Shannon's results. We show that some non-differentially algebraic functions such as the gamma function are generable by our model. Finally, we attempt to relate our model of computation to the notion of tracking computability as studied by Tucker and Zucker.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Emergency Governance in Liberal Democracies

contributor:
Waluchow, Wil
Philosophy

subject: emergency, constitutional law, judicial deference

abstract: This dissertation explores conceptual, normative, and institutional dimensions of the emergency problematic and defends judicial participation in emergency governance. I develop my arguments on the basis of Posner and Vermeule’s discussion in their book Terror in the Balance. I reject their institutional account of emergency governance captured in their deference thesis by showing its incompatibility with fundamental liberal democratic commitments. As I argue, Posner and Vermeule’s call for across-the-board judicial deference to the executive during emergencies is unwarranted in a number of cases, most notably those involving conflicts of constitutional rights. I also reject Posner and Vermeule’s account of emergency policymaking captured in their tradeoff thesis by showing that it does not provide a suitable criterion by means of which the legitimacy of emergency policies could be determined. My arguments against the tradeoff and deference theses are based in part on my critique of Posner and Vermeule’s conception of emergency situations. In fleshing out my conception of emergency, I present and defend a methodological approach to studying the emergency problematic and offer an extensive discussion of exceptionality associated with emergencies. My conclusion is that it is necessary to take in account liberal democratic commitments in the process of emergency policymaking and that judicial review of the executive during periods of emergency is conducive to legitimate emergency governance.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Some national security crises pose serious challenges to western liberal democracies. On the one hand, because such crises threaten individual lives and the welfare of the political community, there is a strong case in favor of demanding that the government do everything in its power to quash such threats by any means necessary. On the other hand, a number of constitutional commitments seem to prevent liberal democracies from using some means in addressing national security crises. In particular, emergency measures such as coercive interrogation and indefinite detention seem to undermine a number of values and commitments that are fundamental to liberal democratic regimes. In addition, there is a controversy surrounding the role of the judiciary during emergencies. Should judges review executive action to ensure its legitimacy during emergencies or should the executive be the final authority on the legitimacy of its policies? My dissertation develops answers to these questions. I begin by exploring conceptual issues surrounding emergencies. On the basis of this exploration, I provide an account of the role of fundamental liberal democratic commitments in the project of emergency governance and argue in favor of judicial participation in governing liberal democratic communities during periods of emergency.


title: A Hybrid Method for Lattice Basis Reduction and Applications

contributor:
Qiao, Sanzheng
Computing and Software

subject:
Lattice
Lattice reduction
LLL algorithm
Jacobi method
MIMO
Cryptography
BKZ 2.0

abstract:
Lattice reduction aided techniques have been successfully applied to a wide range of applications. Efficient and robust lattice basis reduction algorithms are valuable. In this thesis, we present an O(n^4 logB) hybrid Jacobi method for lattice basis reduction, where n is the dimension of the lattice and B is the maximum length of the input lattice basis vectors. Building upon a generic Jacobi method for lattice basis reduction, we integrate the size reduction into the algorithm to improve its performance. To ensure the convergence and the efficiency of the algorithm, we introduce a parameter to the Lagrange reduction. To improve the quality of the computed bases, we impose a condition on the size reduction, delay the structure restoration, and include a postprocessing in the hybrid method.

Our experiments on random matrices show that the proposed algorithm produces better reduced bases than the well-known LLL algorithm and BKZ 2.0 algorithm, measured by both the orthogonality defect and the condition number of the basis matrix. Moreover, our hybrid method consistently runs faster than the LLL algorithm, although they have the same theoretical complexity. We have also investigated two potential applications of the hybrid method. The application simulations show that the hybrid method can improve the stability of the communication channels for Multi-Input Multi-Output systems, and can partially discover the plain text when attacking the GGH cryptosystem.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Lattice reduction aided techniques have been successfully applied to a wide range of applications. Efficient and robust lattice basis reduction algorithms are valuable. In this thesis, we present an O(n^4 logB) hybrid Jacobi method for lattice basis reduction, where n is the dimension of the lattice and B is the maximum length of the input lattice basis vectors. Our experiments on random matrices show that the proposed algorithm produces better reduced bases than the well-known LLL algorithm and BKZ 2.0 algorithm, measured by both the orthogonality defect and the condition number of the basis matrix. We have also investigated two potential applications in MIMO systems and cryptosystems.


title: Depth Dependent Roles of Methane, Ammonia and Hydrogen Sulfide in the Oxygen Consumption of Base Mine Lake, the pilot Athabasca Oil Sands Pit Lake

contributor:
Warren, Lesley
Geography and Earth Sciences

abstract:
Extraction processes in the Athabasca Oil Sands Region of Canada (AOSRC) produce large volumes of tailings waste that require management and reclamation. Water capped tailings technology (WCTT) is currently being assessed as a reclamation strategy by Syncrude Canada Limited in the form of Base Mine Lake (BML), as it is the first AOSRC demonstration WCTT project (Fort McMurray, AB). BML is a pit lake (PL) consisting of a ~40 m layer of fluid fine tailings (FFT) that is capped with a ~10 m mixture of fresh and oil sands process waters. For BML to be considered a reclamation success, it should be able to support macrofauna; i.e. an oxic zone must develop and persist within the water cap. It is important to identify redox biogeochemical processes that influence oxygen concentrations in this pilot PL demonstration system to inform the design of the ~30 pit lakes (PL) that are currently planned across the AOSRC to ensure reclamation success.
To identify the oxygen consuming constituents (OCC) and the biogeochemical processes impacting BML oxygen concentrations, this study comprehensively characterized the water cap geochemistry using standard aquatic sampling methods over the summer of 2016, as well as using a specialized sampling device capable of capturing simultaneous samples every 10 cm over a 2-meter zone (n=20). The Fixed-Interval Sampler (FIS) was used to retrieve simultaneous samples in identified biogeochemically active zones of the metalimnion and hypolimnion- FFT-water interface (FWI) during the summer of 2016.
	Seasonal results identified depth dependent concentration trends consistent with the FFT acting as a source of oxygen consuming constituents (OCC) to the overlying water cap. Characterized concentrations of CH4, NH4+ and ΣH2S were highest in the surface FFT pore water at ~450µM, ~250µM and ~25µM, respectively, subsequently decreasing by the metalimnetic region to concentrations <20% of their respective hypolimnion-FWI concentrations, consistent with redox biogeochemical cycling and the observed profile of decreasing oxygen concentrations with increasing depth. Characterization of FIS samples provided greater resolution of trends specifically within the FWI region and the metalimnion. Results show that ΣH2S extinguishes rapidly above the FFT, reaching non-detectable concentrations by 1m above the FWI. Methane concentrations also decreased rapidly from ~450µM in the FFT to ~100µM by 0.3m above the FWI, consistent with methanotrophy. Characterization of FIS samples for nitrogen species concentrations within both the FWI and metalimnetic regions identified a near 1:1 conversion from NH4+ to NO3- by the metalimnion consistent with microbial nitrification. This process has not been shown to occur in oil sands tailings ponds, indicating that WCTT conditions can enable divergent biogeochemical cycling from that occurring in active tailings ponds. Evidence suggests that the relative concentrations of CH4 and O2 in the lower BML hypolimnion limit the ability of ammonia oxidizing microbes to carry out the full two-step nitrification process. This study has revealed the key oxygen consuming processes within the metalimnion and hypolimnion of BML and provides evidence that BML exhibits a difference in the relevance and magnitude of biogeochemical processes than those observed in tailings ponds. As such, tailings pond research cannot be solely relied upon to determine the viability of PL as a successful reclamation strategy and further PL research is required to develop robust WCTT reclamation strategies.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Operators in the Athabasca Oil Sands Region of Canada (AOSR) produce millions of m3 of waste known as fluid fine tailings (FFT). A wet reclamation strategy currently being piloted by Syncrude Canada Ltd. to deal with these large volumes of tailings is water capped tailings technology (WCTT) in the form of a pit lake (PL), Base Mine Lake (BML). BML was built in an exhausted open pit mine, covering a layer (~40m) of FFT with a ~10m freshwater cap. For WCTT to be successful, a freshwater ecosystem capable of supporting life must develop within the water cap. As FFT contains compounds which can consume oxygen if mobilized into the water cap, there is uncertainty as to whether WCTT will be a successful FFT reclamation strategy. This thesis aimed to characterize oxygen consuming processes occurring throughout the water cap and revealed depth dependent importance of methane, ammonia and hydrogen sulfide in determining water cap oxygen concentrations.


title: Peroxisome Assembly in Yarrowia Lipolytica

contributor:
Rachubinski, R. A.
Biochemistry

subject:
peroxisome assembly
Yarrowia Lipolytica

abstract: The primary goal of the research presented in this thesis has been to establish the yeast Yarrowia lipolytica as a model genetic system for the study of peroxisome biogenesis. To facilitate this, three steps were necessary. First, mutant strains of Y. lipolytica that manifested peroxisomal defects were generated; second, a genomic DNA library was created to rescue the mutants and, hence, clone the gene(s) involved; and third, the parameters governing high efficiency DNA transformation of Y. lipolytica were defined to make complementation of mutants with the genomic library feasible. This work culminated in the cloning, sequencing and characterization of a gene, dubbed PAY 4, that is required for peroxisomal assembly in Y. lipolytica. Two of the mutant strains of Y. lipolytica isolated, ole 2 and ole 4, were identified as peroxisome assembly mutants as they; (i) grew in acetate medium but failed to grow on oleic acid medium, and thus were peroxisomal as opposed to mitochondrial mutants; (ii) lacked recognizable peroxisomal structures when observed by immunofluorescence using a polyclonal serum that recognized a number of peroxisomal proteins and; (iii) had several peroxisomal enzyme activities localized to the cytosol, i.e. they manifested mistargeting of otherwise lumenal peroxisomal proteins. These were complemented with a genomic library, which represented at least 19 000 independent recombinants (insert size ~5-7 kilobases) cloned into a vector (piNA445) capable of autonomous replication in Y. lipolytica. Estimations of the size of the Y. lipolytica genome indicate that probability of this library containing a given portion of the genome is .999. To utilize the library effectively, an electro-poration protocol was developed that could transform Y. lipolytica at high efficiency (>5·10^4 transformants·μg-^1 of DNA). Using these resources, the gene complementing the ole 4 mutation was cloned and sequenced. It encodes Pay4p, a protein of ~112 kDa, containing two putative ATPase modules. Preliminary studies indicate that expression of Pay4p is induced slightly by growth on oleic acid.

abstract: Thesis

abstract: Master of Science (MSc)


title: Caloxins: New Class of Plasma Membrane Ca^2+Pump Inhibitors

contributor:
Grover, A. K.
Biology

subject:
plasma membrane
Ca^2+ pump

abstract:
Caloxin2A 1 is a novel peptide that inhibits the activity of Plasma Membrane Calcium ATPase (PMCA). PMCA is known to play a role in homeostasis of cytosolic calcium and cell signaling. There are 4 genes (PMCA1-4) that code for the various isoforms of the calcium pump. Based on hydropathy plots, PMCA proteins have 5 putative extracellular domains. We screened combinatorial peptide phage display library for binding to specific extracellular targets.
Caloxin 2A1 was obtained as a peptide sequence that would bind to the 2nd putative extracellular domain of PMCA 1 isoform. Caloxin2A1 selectively inhibited the Ca2+-Mg2+ ATPase activity in human erythrocyte leaky ghosts that express mainly PMCA 4 isoform. It produced 50% inhibition of the pump activity at 0.4 mM. Caloxin2A1 inhibited the formation of the acid stable 140 kDa acyl phosphate in the reaction cycle of the calcium pump in the human erythrocyte leaky ghosts. It also produced endothelium dependent relaxation in the pig coronary artery. The random peptide phage display library was screened again with higher stringency to obtain caloxin with higher affinity in order to be cost effective and with greater therapeutic potential. This time, the targets were the 2nd putative extracellular domain of PMCA 1 and 2nd and 3rd putative domains of PMCA 4. The peptides selected for binding to the 2nd putative extracellular domain of PMCA 4 selectively inhibited the Ca2^+-Mg^2+ ATPase activity in human erythrocyte leaky ghosts but with a similar affinity as Caloxin2A1. The peptide selected for binding to the 3rd putative extracellular domain of PMCA 4 was hydrophobic and water insoluble. Substitution of its C-terminus amino acid with lysine residue made the peptide water-soluble and it did inhibit the Ca^2 +-Mg^2 + ATPase with slightly higher affinity. However, the inhibition was due to hydrophobicity of the peptide as the randomized version of the peptide also produced inhibition. We have obtained the first selective inhibitor of PMCA and shown that perturbing extracellular targets can affect protein activity even though most of the functional groups of this protein are in the cytosol.

abstract: Thesis

abstract: Master of Science (MS)


title: Bicistronic vectors for animal models of breast and prostate cancer

contributor:
Muller, W.J
Biology

subject: Bicistronic vectors, animal models, breast,prostate cancer

abstract:
The improving of our understanding of cancer development still depends
on cancer research at the molecular level. In his project, bigenic vectors for
animal models of breast and prostate cancer are created.
Bigenic constructs are useful because they create animals expressing two
genes of interest at a time, with one injection step and no need for crossings. In
order to produce these vectors, previous animal models have been analyzed, and
the elements that worked successfully in previous models were gathered in a new
arrangement for the creation of an improved model. In order to create a bigenic
vector, the viral internal ribosomal entry site was utilized, as a means of obtaining
two protein products from one transcript.
One vector, the MMTV-Neu1842-IRES-Cre was successful in generating
a line of transgenic mice. Female founders of this line already express the
expected phenotype, tumors of the mammary tissue. Once this line is established,
it can be crossed with the Rosa26 line, to determine the pattern of Cre expression.
Other vectors were created for models of prostate cancer, using the
probasin promoter and the MT oncogene. While transgenic mice were attempted,
there were no phenotype differences between wild type and transgenic mice.
All created vectors were tested for expression ofthe two genes carried in
tissue culture experiments. All the experiments were successful, indicating a
working oncogene (by means of a focus assay) and Cre activity (by excission
assay).
The new breast cancer animal model carrying the MMTV-Neu1842-IRESCre
construct is promising and can be used in combination with existing models
to answer some of the remaining questions regarding breast cancer signaling
pathways.

abstract: Thesis

abstract: Master of Science (MSc)


title: Search for Cell Cycle Control Genes and the Characterization of CLN3^+ in Saccharomyces Cerevisiae

contributor:
Futcher, A. B.
Biochemistry

subject:
sacchromyces cerevisiae
cell cycle
CLN3^+

abstract: Cell cycle control genes in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have been studied in detail in the past few years. The cdc25+ and wee1+ genes of S. pombe play key roles in the commitment to division. Genes homologous to the mitotic inducer cdc25+ and the mitotic inhibitor wee1+ of Schizosaccharomyces pombe were searched for in Saccharomyces cerevisiae using DNA cross-hybridization as the method of detection. Such homologs were not found in Saccharomyces cerevisiae by this method. Attention was therefore turned towards sequencing and partially characterizing a previously cloned gene, WHI1+, and its mutant form WHI1-1 (now call CLN3+ and CLN3-1 respectively). Sequence analysis showed that CLN3+ is a cyclin homolog. Cyclins are probably present in all eukaryotes and play an important role in controlling the onset of mitosis. However, unlike these mitotic cyclins, CLN3+ functions in G1. CLN3-1 cells enter a new round of the cell cycle at an aberrantly small cell size and are α-factor resistant. Sequence analysis showed that the CLN3-1 protein was a truncated form of CLN3+ caused by a nonsense mutation in the CLN3+ gene. Cells overexpressing CLN3+ had the same phenotype as CLN3-1 cells, suggesting that the truncated CLN3-l protein was a hyperactive form ofthe wild-type protein. CLN3+ and CLN3-1 were placed downstream of the yeast GAL1 promoter in a shuttle plasmid. Cells transformed with these plasmids and grown in the presence of galactose and the absence of glucose produced CLN3+ or CLN3-1 in large amounts. Cell size was reduced in such cells. These cells were also α-factor resistant.

abstract: Thesis

abstract: Master of Science (MSc)


title: Peatland Carbon Accumulation Following Wildfire on the Boreal Plains: Implications for Peatland Reclamation and Wildfire Management

contributor:
Waddington, James Michael
Earth and Environmental Sciences

subject:
organic soil carbon accumulation
peatland
wildfire
Boreal Plains
resilience
recovery
ecohydrology
hydrological response area
glacial sediments
ombrotrophic bog
reclamation

abstract: Peatlands in the sub-humid Boreal Plains of Alberta exist at the limit of their climatic tolerance and are vulnerable to wildfire. This is especially true at the interface between the peatland and forestland (margins) due to water table fluctuation resulting in high peat bulk density and low moisture content during dry periods in some peatland systems. Deep burning at the margins may reduce a peatland's ability to recover to its previous state, leading to a reduction in area and/or collapse following fire, and bringing into question the long-term stability of Boreal Plains peatlands on the landscape under current and future climate predictions. Previous research has identified small peatlands located at a mid-topographic position on coarse sediments as hotspots for deep burning, as these peatlands are not regularly connected to regional groundwater flow. The ability of these peatland systems to recover lost carbon from both the interior and margin within the fire return interval, however, has not yet been investigated. This thesis further examines the relationship between surficial sediment assemblages and the impact of wildfire on overlying peatlands through assessment of organic soil carbon accumulation following wildfire across the Boreal Plains landscape. Peatland organic soil recovery along a chronosequence was assessed in the interior and margin of 26 ombrotrophic bogs located at various positions on the post-glaciation landscape of Northern Alberta using estimates of organic soil carbon accumulation calculated through loss on ignition of peat above the uppermost charcoal layer in peat cores from each site, as well as characterization of peat properties along a transect from the adjacent forestland into the peatland interior. Soil organic carbon accumulation with time since fire was greater in studied peatland interiors than margins. Underlying sediments were found to have little effect on total soil organic carbon accumulation in the interior and margins of the studied peatlands, indicating that organic soil carbon accumulation rates following wildfire estimated in this study can be extended to ombrotrophic bogs across the Boreal Plains landscape. Though total soil organic carbon accumulation following wildfire does not appear to be influenced by hydrogeological setting, the ability of a peatland to recover the quantity of carbon lost within the fire return interval will be dependent on the amount of carbon which was released through smouldering, which is influenced by hydrogeological setting for peatland margins. Based on published measurements of organic soil carbon loss during wildfire and organic soil carbon accumulation rates estimated in this thesis, peatlands located at topographic lows on coarse grained glaciofluvial outwash sediments or on low-relief, fine grained sediment deposits from glaciolacustrine or subglacial paleoenvironments are predicted to be resilient to wildfire on the Boreal Plains landscape. Peatlands which experience severe smouldering at the margins, such as ephemerally perched systems on glaciofluvial outwash sediments, will likely undergo permanent loss of legacy carbon stores. The resilience of peatlands which are perched above regional groundwater on glaciofluvial outwash or stagnant ice moraine deposits is unknown at this time; further investigation into water table dynamics, margin peat properties, and smouldering depths in these systems is required. Identification of peatland systems which are at risk of permanent carbon loss at the margins and those which are most resilient to wildfire in this thesis can be applied to wildfire management strategies and the design of peatland systems for reclamation of oil sands leases. The stability of natural and created peatlands through time on a landscape where wildfire is frequent is an important consideration in terms of both lasting ecosystem services and the potential risk to fire suppression and community safety that vulnerable systems pose.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Catenin p120^ctn Regulates Kaiso-Mediated Transcriptional Repression

contributor:
Daniel, Juliet
Biology

subject:
Catenin
Transcriptional Repression

abstract: Kaiso is a POZ-ZF transcription factor initially identified as an interaction partner for the cell adhesion co-factor p120^ctn. Kaiso-DNA binding is inhibited by p120^ctn, implicating p120^ctn in the regulation of Kaiso transcriptional activity. In this study, Kaiso repressed transcription of a luciferase reporter carrying four copies of the sequence-specific Kaiso-binding site (4xKBS) in artificial promoter assays. Mutation of the 4xKBS which is known to disrupt Kaiso-DNA binding also abrogated Kaiso-mediated transcriptional repression. Moreover, p120^ctn inhibited Kaiso-mediated transcriptional repression via the 4xKBS, yet neither the p120^ctn deletion mutant ΔR3-ll (lacking the Kaiso binding site) or p120^ctn NLS mutant (which cannot enter the nucleus) inhibited transcriptional repression. Furthermore, in NIH 3T3 cells (which do not demonstrate a Kaiso-pl20ctn interaction), pl20ctn failed to inhibit transcriptional repression. Many POZZF transcriptional repressors recruit an HDAC complex via their POZ domain to repress transcription. To investigate the mechanism of Kaiso-mediated transcriptional repression, the POZ domain of Kaiso was deleted, which abrogated transcriptional repression. Kaiso immunoprecipitates contained HDAC activity, and the HDAC co-repressor Sin3A co-immunoprecipitated with Kaiso, implying that Kaiso recruits Sin3A to repress transcription in an HDAC-dependent manner. Lastly, Kaiso repressed transcription via a human 𝑚𝑎𝑡𝑟𝑖𝑙𝑦𝑠𝑖𝑛 promoter fragment. This suggests that the KBS element is functionally relevant and implicates 𝑚𝑎𝑡𝑟𝑖𝑙𝑦𝑠𝑖𝑛 as a Kaiso target-gene. Collectively, these data establish Kaiso as a sequence-specific, HDAC-dependent transcriptional repressor that is regulated by the adhesion co-factor p120^ctn.

abstract: Thesis

abstract: Master of Science (MSc)


title: Immunoelectron Microscopy Provides Evidence for the Extramitchondrial Localization of a Number of Nuclear- and Mitochondrial- DNA Encoded Proteins

contributor:
Gupta, R. S.
Biochemistry

subject:
mitochondria
immunoelectron microscopy

abstract:
Mitochondrial proteins are presently believed to reside and function only within the mitochondria, under normal physiological conditions. However, in recent years many
examples have come to light where proteins originally identified on the basis of
 extramitochondrial functions, upon characterization were found to be bonafide mitochondrial proteins. This raises important questions concerning the cellular functions of mitochondrial proteins. To investigate this phenomenon of mitochondrial proteins being present at extramitochondrial locations, we have examined by means of immunoelectron microscopy, the subcellular localization in normal rat tissues of a number of well characterized mitochondrial proteins which are encoded either by the nucleus (chaperonin 10 (Cpn10) and mitochondrial aspartate aminotransferase (mAspAT)), or by mitochondrial DNA (Cytochrome c oxidase subunits I and II (COX I and II)), using highly specific antibodies. Both Cp10 and mAspAT have already been shown to be involved in extramitochondrial functions. Cpn10 has been shown to be identical to early pregnancy factor, which is an immunosuppressant and growth factor found in maternal serum. mAspAT is identical to fatty acid binding protein isolated from
plasma membranes of several cell types, involved in the transport of long chain free fatty
acids. Immunofluorescent labeling of BS-C-1 African monkey kidney cells with these
antibodies showed characteristic mitochondrial labeling. In all tissues examined, the
antibodies showed strong labeling of mitochondria, as was expected. In several tissues,
the binding was seen exclusively within mitochondria. However, in a variety of tissues
such as pancreas, anterior pituitary and kidney, these antibodies showed strong and
specific labeling of one or more of the following compartments- pancreatic zymogen
granules, growth hormone granules, secretory granules in islet cells, red blood cells,
condensing vacuoles in kidney and on the cell surface of different regions of the kidney.
All of the observed labeling with these antibodies, both within mitochondria and in other
compartments, was abolished upon omitting the primary antibodies or upon adsorption of
the Cpn10 antibody (in the case of Cpn10) with purified recombinant protein. The extramitochondrial localization of these proteins, particularly those encoded by mitochondrial DNA provides strong evidence that these proteins have reached these sites by exiting from mitochondria. These observations have important implications concerning the roles of
 mitochondria and mitochondrial resident proteins in different mitochondrial diseases. Also, the function of these proteins and the precise mechanism by which they reach these extramitochondrial sites is of great interest.

abstract: Thesis

abstract: Master of Science (MSc)


title: Multi-tank hybrid energy storage using water and phase change materials in a direct system

contributor:
Lightstone, M. F.
Cotton, J. S.
Mechanical Engineering

abstract:
Novel multi-tank thermal energy storage (TES) containing water and phase change materials (PCMs) was evaluated numerically. The multi-tank storage is based on the interconnection of small volume hot water storage tanks in series configuration. Water enters and exits the system directly and is used as the heat transfer fluid (HTF). PCMs are incorporated in the water tanks to investigate  their latent energy storage capability. They are cascaded in a descending order of their melt temperatures to match the operating range of the system. The system was tested for the typical Canadian weather data and demand profiles.

 An in-house FORTRAN code was developed to solve the problem computationally. PCMs are placed in vertical cylinders and water flows along them within the tank shell. This is referred to as a hybrid system hereafter. Both component and system level analysis are presented in detail in the thesis. The developed mechanistic model was thoroughly validated and verified with published data with a very good agreement (<5% deviation). The main goal of the current work is to assess the dynamic performance of the proposed system when linked with the solar collector in the Solar Domestic Hot Water system (SDHW) context. Possible storage volume reduction relative to a water only system for the same benefit to the household is  the primary objective.
Component level analysis was conducted to understand the behavior of the hybrid system under isothermal charging conditions. It aided in the choice of key parameters when the entire system was modeled. The analysis shows that in narrow temperature operating ranges (around 10oC); the energy density of the hybrid system can be significantly increased to around five times relative to a system containing water only. This is attributed to the latent energy stored during the phase change. The main hindering factor is the low thermal conductivity of the PCM, which can be overcome by encapsulating the materail in small diameter cylinders and thus decrease the imposed thermal resistance on the system.

On the system level, a hybrid single tank model was linked with the collector performance and the system was tested for typical days of Canadian weather with different demand profiles. The solar fraction of the hybrid system was compared to that of an identical system using water-only as the thermal storage medium. Solar fraction is the amount of energy delivered by the solar system relative to the total energy required by the load. The systems approach is critical since it allows for the coupled effects of SDHW components to be incorporated.  The analysis clearly shows that incorporation of PCMs into the thermal storage results in enhanced solar fraction at small tank volumes (around 200 liters).  In contrast, as the tank volume is increased, the benefit of the PCMs diminishes.  An energy balance of the system reveals that, the benefits of the PCMs in small storage volumes are due to the reduction in the collector fluid inlet temperature which increases the pump run time and thus the solar energy collected. This conclusion presented a clarification for the mixed results from the literature concerned with the incorporation of PCMs in hot water tanks.
Using the key parameters of the system level analysis for the single tank, the analysis was extended to the multi-tank system. The multi-tanks contain PCMs cascaded in a descending order of their melt temperature from the source to the load. The PCM was found to tune the bulk of the tank temperature around its melting temperature. This aided in having better sequential stratification between the tanks. Cooler water returning to collector relative to the single PCM case was maintained. Decreased collector losses and extended the pump activation time were obtained relative to the single PCM case. This resulted in an increase in the time period on the system was able to meet the load demand of hot water and hence augmented solar fraction. It was found that for a multi-residential building of three families, a 630 liter tank containing water only gives the same solar fraction provided by three cascaded 100 liters tank containing 50% PCMs by volume. The melting points of PCMs are (42oC, 32oC and 16oC) respectively. This guarantees more than 50% reduction in volume for the same benefit in the household side.

abstract: Thesis

abstract: Candidate in Philosophy


title: ROLE OF ATP-CITRATE LYASE AND AMP-ACTIVATED PROTEIN KINASE IN REGULATING LIVER LIPID SYNTHESIS

contributor:
Steinberg, Gregory
Medical Sciences

subject: ATP-citrate lyase, AMP-activated protein kinase, NAFLD, ASCVD, Atherosclerosis, LDL-C

abstract: Cholesterol and fatty acid homeostasis is maintained by a complex network of regulatory mechanisms that control the biosynthesis and deposition of lipids over diverse physiological conditions. However, these processes can become dysregulated and uncoupled from energy metabolism by metabolic stress such as a hyper-caloric diet and physical inactivity; eventually manifesting as risk factors associated with atherosclerotic cardiovascular disease (ASCVD), Type 2 diabetes (T2D), and/or non-alcoholic fatty liver disease (NAFLD). AMP-activated protein kinase (AMPK) is a sensor of cellular energy status that promotes metabolic homeostasis by mediating effects on multiple cellular processes including cholesterol and fatty acid synthesis biosynthesis. However, the mechanisms linking AMPK to lipid metabolism under normal and pathological conditions, remain undefined. In these studies, we identify a novel nutrient sensing mechanism whereby the coenzyme A (CoA) activated esters of long-chain fatty acids (LCFA-CoA) directly activate AMPK via specific interactions within the β1-regulatory subunit involving a Ser108 residue previously shown only with synthetic activators. We demonstrate the physiological relevance for this mechanism in an acute setting by showing that fatty acid oxidation was attenuated in mice harboring an AMPKβ1-S108A knock-in mutation compared to WT mice. We then demonstrated that β1-selctive AMPK activation is mimicked by the CoA conjugated form of bempedoic acid, a synthetic small molecule lipid synthesis inhibitor in clinical development for lowering elevated levels of low-density lipoprotein cholesterol (LDL-C). The importance of this mechanism was determined by assessing multiple disease outcomes in Ampkβ1-/-/Apoe-/- double knockout (DKO) mice fed a high fat-high cholesterol (HFHC) diet ± bempedoic acid. In these studies, bempedoic acid treatment reduced plasma LDL-C and atherosclerosis in both Apoe-/- and DKO mice, while no differences in disease outcomes was detected between the two genotypes in response to HFHC feeding. Further mechanistic investigations in rodent and primary human hepatocytes, revealed that the CoA conjugate of bempedoic acid suppressed lipid synthesis via competitive inhibition of ATP-citrate lyase (ACL), which promoted LDL receptor upregulation and associated reductions in LDL-C. We then integrate these findings with published literature in a written synthesis aimed to evaluate the role of ACL in metabolism, and its potential utility as a therapeutic target to treat ASCVD and metabolic disorders in humans. Although several questions remain regarding the metabolic role of AMPK activation by LCFA-CoAs, these studies have expanded our understanding of how cells acutely integrate lipid and energy signals to maintain lipid homeostasis, and identified ACL as a promising strategy to treat hypercholesterolemia, ASCVD, and associated metabolic disorders.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The dysregulation of cholesterol and triglyceride metabolism can manifest as risk factors for life-threating diseases such as atherosclerotic cardiovascular diseases (ASCVD), Type-2 diabetes (T2D), and nonalcoholic fatty liver disease (NAFLD). However, the underlying mechanisms controlling lipid homeoastasis in health and disease are not completely understood. ATP-citrate lyase (ACL) and AMP-activated protein kinase (AMPK) are emerging as key nodes in metabolism that integrate lipid metabolism with signals of nutrient availability and cellular energy status, respectively. These strategic positions in metabolism suggest that both these enzymes could play an important role in the underlying pathophysiology of lipid-related diseases, and are therefore, prime candidates for therapeutic intervention. In these studies, we expand our understanding of the role of AMPK in metabolism beyond energy sensing by identifying specific lipid metabolites as direct allosteric activators of kinase activity. We also evaluate the therapeutic utility of targeting both AMPK and ACL in novel models of hypercholesterolemia and metabolic disease, and demonstrate that ACL inhibition offers a promising strategy to address multiple unmet medical needs.


title: The Design, Implementation and Evaluation of the KT-MCC Strategy: A Knowledge Translation Strategy Aimed At Improving The Quality of Decision Making For Ontario Multidisciplinary Cancer Conferences

contributor:
Simunovic, Marko
Sonnadara, Ranil
McConnell, Meghan
Wright, Frances
Health Research Methodology

subject:
Knowledge Translation
Theoretical Domains Framework
COM-B
Multidisciplinary Cancer Conferences
Decision Making

abstract:
Multidisciplinary cancer conferences (MCCs) are prospective meetings to discuss diagnoses and treatment plans for patients with cancer. MCCs are typically attended by surgeons,  medical and radiation oncologists, pathologists and radiologists. To date, the quality of MCCs, specifically MCC decision making, has not been formally evaluated in a Canadian context.
We utilized progressive knowledge translation methodology, specifically the use of theory, models and an integrated knowledge translation approach, to design, implement and evaluate an intervention, titled the KT-MCC Strategy (KT-MCC). The purpose of the KT-MCC is to improve the quality of MCC decision making. This thesis is comprised of four parts. In Part 1, we completed a generalizability study to evaluate the reliability of an MCC assessment tool (MTB-MODe) in an Ontario context. In Part 2, we conducted key informant interviews using the Theoretical Domains Framework (TDF) to identify barriers and facilitators to optimal MCC decision making. In Part 3, we mapped identified TDF barriers and facilitators to the COM-B Behavioural Change Wheel to develop the KT-MCC, an intervention aimed at improving the quality of MCC decision making. In this study, we examined the validity of the key informant findings using focus groups and surveys completed by individual MCC participants. In Part 4, we conducted a before-and-after pilot study to evaluate the feasibility and impact of the KT-MCC on MCC decision making in preparation for a possible randomized controlled trial testing the efficacy of the KT-MCC.
There are few examples in the KT literature that provide a complete and detailed description of the design, implementation and evaluation of a complex KT strategy using progressive KT methods such as TDF interviews to identify barriers and facilitators to practice change; the COM-B model to identify potential interventions; and use of integrated KT with front-line workers. We describe in detail our methods to design, implement and evaluate the KT-MCC. This thesis provides a significant contribution to the knowledge translation literature and provides recommendations to improve the quality of MCCs in Ontario.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Multidisciplinary cancer conferences (MCCs) are regular meetings held by health professionals to prospectively discuss diagnoses and treatment plans for patients with cancer. The purpose of MCCs is to facilitate input from numerous experts to ensure that each patient receives an optimal treatment recommendation. To date, the quality of MCCs, specifically MCC decision making, in Ontario has not been formally evaluated. We aimed to identify gaps in Ontario MCC decision making and design an intervention to mitigate these gaps. The intervention was designed using an integrated knowledge translation approach, meaning MCC participants were involved in the design, implementation and evaluation of the intervention. The resulting intervention, called the KT-MCC Strategy, was evaluated at four Ontario MCC sites. This thesis provides a significant contribution to the knowledge translation literature and provides recommendations to improve the quality of MCCs in Ontario.


title: Assessing Migration and Demographic Change in pre-Roman and Roman Period Southern Italy Using Whole-Mitochondrial DNA and Stable Isotope Analysis

title: The Biogeographic Origins of Iron Age Peucetians and Working-Class Romans From Southern Italy

contributor:
Prowse, Tracy
Poinar, Hendrik
Schwarcz, Henry
Anthropology

subject: Ancient DNA analysis; Roman bioarchaeology; stable isotope analysis; population history; Iron Age Italy; Roman Vagnari; migration

abstract:
Assessing population diversity in southern Italy has traditionally relied on archaeological and historic evidence. Although informative, these lines of evidence do not establish specific instances of within lifetime mobility, nor track population diversity over time. In order to investigate the population structure of ancient South Italy I sequenced the mitochondrial DNA (mtDNA) from 15 Iron Age (7th – 4th c. BCE) and 30 Roman period (1st – 4th c. BCE) individuals buried at Iron Age Botromagno and Roman period Vagnari, in southern Italy, and analyzed δ18O and 87Sr/86Sr values from a subset of the Vagnari skeletal assemblage.

Phylogenetic analysis of 15 Iron Age mtDNAs together with 231 mtDNAs spanning European prehistory suggest that southern Italian Iapygians share close genetic affinities to Neolithic populations from eastern Europe and the Near East. Population pairwise analysis of Iron Age, Roman, and mtDNA datasets spanning the pan-Mediterranean region (n=357), indicate that Roman maternal genetic diversity is more similar to Neolithic and Bronze Age populations from central Europe and the eastern Mediterranean, respectively, than to Iron Age Italians. Genetic distance between population age categories imply moderate mtDNA turnover and constant population size during the Roman conquest of South Italy in the 3rd century BCE.

In order to determine the local versus non-local demographic at Vagnari, I measured the 87Sr/86Sr and 18O/16O of composition of 43 molars, and the 87Sr/86Sr composition of an additional 13 molars, and constructed a preliminary 87Sr/86Sr variation map of the Italian peninsula using disparate 87Sr/86Sr datasets. The relationship between 87Sr/86Sr and previously published δ18O data suggest a relatively low proportion of migrants lived at Vagnari (7%).

This research is the first to generate whole-mitochondrial DNA sequences from Iron Age and Roman period necropoleis, and demonstrates the ability to gain valuable information from the integration of aDNA, stable isotope, archaeological and historic evidence.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: With biochemical information obtained from teeth, this study examines the population structure and geographic origins in two archaeological communities located in southern Italy. Analysis of classical remains has traditionally been the subject of historical and archaeological inquiry. However, new applications evaluate these population changes with integrated stable isotope and ancient DNA techniques. Overall, the biochemical results suggest that the pre-Roman communities harbor deep maternal ancestry originating from eastern Europe and the eastern Mediterannean. These results, when compared to the genetic diversity of Roman and broader Mediterranean populations, indicate that the Romans share closer genetic similarity with ancient Stone and Bronze Age communites from Europe and the eastern Mediterranean, than with the pre-Roman community studied here. Furthermore, tooth chemistry results indicate a predominantly local population buried in the Roman period cemetery.


title: Motion Control of Under-actuated Aerial Robotic Manipulators

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

subject: Motion control, under-actuation, nonholonomic, virtual decomposition, model-based, adaptive control, kinematic redundancy, multi-body system, aerial robotic, UAV, manipulator

abstract:
This thesis presents model-based adaptive motion control algorithms for under-actuated
aerial robotic manipulators combining a conventional multi-rotor Unmanned Aerial Vehicle
(UAV) and a multi-link serial robotic arm. The resulting control problem is quite
challenging due to the complexity of the combined system dynamics, under-actuation, and
possible kinematic redundancy. The under-actuation imposes second-order nonholonomic
constraints on the system motion and prevents independent control of all system degrees
of freedom (DOFs). Desired reference trajectories can only be provided for a selected
group of independent DOFs, whereas the references for the remaining DOFs must be determined such that they are consistent with the motion constraints. This restriction prevents
the application of common model-based control methods to the problem of this thesis. Using
insights from the system under-actuated dynamics, four motion control strategies are
proposed which allow for semi-autonomous and fully-autonomous operation. The control
algorithm is fully developed and presented for two of these strategies; its development for
the other two configurations follows similar steps and hence is omitted from the thesis.
The proposed controllers incorporate the combined dynamics of the UAV base and the serial
arm, and properly account for the two degrees of under-actuation in the plane of the
propellers. The algorithms develop and employ the second-order nonholonomic constraints
to numerically determine motion references for the dependent DOFs which are consistent with the motion constraints. This is a unique feature of the motion control algorithms
in this thesis which sets them apart from all other prior work in the literature of UAVmanipulators.
The control developments follow the so-called method of virtual decomposition,
which by employing a Newtonian formulation of the UAV-Manipulator dynamics,
sidesteps the complexities associated with the derivation and parametrization of a lumped
Lagrangian dynamics model. The algorithms are guaranteed to produce feasible control
commands as the constraints associated with the under-actuation are explicitly considered
in the control calculations. A method is proposed to handle possible kinematic redundancy
in the presence of second-order motion constraints. The control design is also extended to
include the propeller dynamics, for cases that such dynamics may significantly impact the
system response. A Lyapunov analysis demonstrates the stability of the overall system and
the convergence of the motion tracking errors. Experimental results with an octo-copter integrated with a 3 DOF robotic manipulator show the effectiveness of the proposed control strategies.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Purification and Biochemical Characterization of Ethanolamine Kinase from Spinach

contributor:
Weretilnyk, Elizabeth
Biology

subject:
spinach
ethanolamine kinase

abstract:
Ethanolamine kinase (EC 2.7.1.82) catalyses the reaction of ethanolamine and Mg^2+-ATP to produce phosphoethanolamine and Mg^2+ -ADP. For spinach (Spinacia oleracea) the activity of ethanolamine kinase is increased in leaf extracts of salinized plants. A comparison of
ethanolamine kinase activity between extracts from control and salinized plants after native polyacrylamide gel electrophoresis shows that ethanolamine kinase activity migrates to the same position on a gel. This observation suggests that salinization does not induce the activity of a novel ethanolamine kinase isozyme. Ethanolamine kinase has been purified 6,537 fold to apparent homogeneity from spinach leaves by ammonium sulphate fractionation and sequential fractionation by both open-bed and HPLC chromatography, using ion-exchange and hydrophobic interaction matrices. The enzyme has an estimated molecular weight of 80,000 D by gel filtration chromatography and a subunit size of 38,000 D by sodium dodecyl sulphate polyacrylamide gel electrophoresis. Ethanolamine kinase has a broad pH optimum between pH 7 and 9 and the optimal ratio of Mg^2+:ATP for the reaction is 1: 1 at 5 mM. The apparent K^m value for the substrate ethanolamine is 16 μM and the V^max is 438 nmol • min^-1 •mg^-l protein. Monomethylethanolamine and dimethylethanolamine serve as substrates for. ethanolamine kinase but not trimethylethanolamine (ie choline). Enzyme activity is slightly stimulated by NaCl and KCl and inhibited to varying degrees by phosphate, ammonium, phosphoethanolamine and phosphodimethylethanolamine. Not surprisingly enzyme activity is also inhibited by ADP and to varying degrees by the divalent cations Mn^2+, Ca^2+, Co^2+, Ba^2+ and Ni^2+. This work is the first purification and biochemical characterization of ethanolamine kinase in spinach and is the first step towards understanding the contribution ethanolamine kinase makes towards the synthesis of choline.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Functional Investigation of the DIP1 Gene in Drosophila Melanogaster

contributor:
Campos, Ana
Biology

subject:
drosophilia melanogaster
DIP1 Gene

abstract:
Reported here is the isolation and molecular characterization of two novel alleles of the DIP 1 gene; GE89 and GE77. As well, a third deletion of the DIP 1 gene, EY*4, isolated by our collaborators in France was characterized. PCR and sequencing analysis confirms all three alleles to be molecular deletions of the DIP 1 gene. However, in none of these cases is the entire gene excised. Also, immunohistochemistry of ovaries from each of these strains does not demonstrate a complete lack of DIPl protein expression in any of the deletion strains. Thus, it appears that some protein product is being formed in each case. However, it is not clear whether this protein is functional. An assay was also conducted to investigate a function for DIPl in mechanisms of epigenetic gene silencing. Although the findings of these
experiments are incomplete, it appears that DIPl may play a functional role in heterochromatin formation and/or post-transcriptional gene silencing. Interestingly, appendage formation phenotypes were observed in the original P-element insertion line as well as a female sterility phenotype in the GE77 allele. Overall, DIP 1 is an interesting double stranded RNA binding protein. Newly isolated alleles of the DIP 1 gene will be useful tools for further investigation of the functional role of this gene.

abstract: Thesis

abstract: Master of Science (MSc)


title: Metabolite Profiling for New Advances in Biomarker Discovery, Cystic Fibrosis Screening and Drug Surveillance

contributor:
Britz-McKibbin, Philip
Chemical Biology

subject:
Capillary Electrophoresis
Mass Spectrometry
Metabolomics
Cystic Fibrosis
Biomarker
Analytical Methods
Inborn Errors of Metabolism
Drugs of Abuse
Drug Screening
Population Screening

abstract: The role of biological markers (biomarkers) in public health, pediatric medicine and clinical toxicology cannot be understated. Clinically validated biomarkers used in newborn screening (NBS) serve to detect individuals at risk for a disease in the population, pre-symptomatically diagnose affected neonates early in life and/or accurately predict disease progression and treatment responses to therapy. However, there is urgent need for the discovery of more specific biomarkers that can improve screening accuracy in a high throughput, cost-effective yet ethical manner. The major objectives of this thesis were to develop innovative nontargeted metabolite profiling methodologies based on multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) for early detection of treatable genetic diseases, as well as comprehensive surveillance of drugs of abuse (DoA) in high risk subjects. Chapter II introduces a multiplexed MSI-CE-MS strategy for confirmatory testing of known biomarkers for various inborn errors of metabolism from a dried blood spot (DBS) that was rigorously validated using proficiency test specimens from Centres for Disease Control and Prevention (CDC) and authentic neonatal samples from Newborn Screening Ontario (NSO) with quality assurance. Additionally, MSI-CE-MS together with temporal signal pattern recognition revealed for the first time a novel class of pathognomonic marker elevated in galactosemia, namely N-galactated amino acids. Chapter III describes an untargeted metabolomic study to discover biomarkers of cystic fibrosis (CF) to reduce the high false positive rate and widespread carrier identification by current two-tiered NBS algorithms that rely on genetic testing. A panel of metabolites from retrospective DBS specimens, including several amino acids, ophthalmic acid and an unknown peptide, allowed for differentiation of asymptomatic CF neonates from screen-positive yet unaffected carriers and transient hypertrypsinogenemic cases. Chapter IV develops and validates a high throughput MSI-CE-MS assay for rapid screening for DoA and their metabolites in human urine with improved specificity and broad spectrum coverage as compared to classic targeted immunoassays. This method can also applied to ensure compliance, drug efficacy and patient safety while detecting for potential substitution or adulteration when using high resolution MS/MS. In summary, this thesis contributes an innovative methodology and data workflow for biomarker discovery for improved neonatal screening of rare genetic diseases in the population, which was also applied for more effective drug surveillance strategies in public health given the alarming worldwide opioid crisis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Argos and the Spitz Group/der Pathway Function to Regulate Midline Glial Cell Numbers in Drosophila Embryos

title: Argos and Spitz Group/der Pathway Function in the MG

contributor:
Jacobs, J. R.
Biology

subject:
drosophilia
argos
glial cell

abstract: The midline glia (MG) perform an active role in the pioneering and morphogenesis ofthe commissural axons of the central nervous system (CNS) during Drosophila embryogenesis. Following the establishment of these commissural axon pathways, a subset of the MG undergoes apoptosis and the surviving MG remain to ensheath the commissures. Previous studies demonstrated that the pattern ofthis developmental apoptosis is stochastic. The surviving MG exhibit intersegment variability in their final number and position relative to the commissures. Interestingly, argos, a gene which encodes a diffusible extracellular factor with an epidermal growth factor (EGF) motif, is only expressed in MG which survive. argos expression in this subset of MG is initiated at the onset of apoptosis, reflecting the temporal pattern of cell death of the other MG. In argos loss-of-function mutants, there are extra surviving MG in each segment while ectopic over-expression of argos results in increased apoptosis among the MG. Therefore, Argos has a negative regulatory effect on MG survival. Its effects are opposite to the spitz group/Drosophila EGF receptor (DER) pathway, a cassette of genes required for MG survival. However, argos is hypostatic to the spitz group/DER pathway function and its expression requires a certain threshold of spitz group and DER pathway activity. Argos is postulated to act as an EGF receptor antagonist. It attenuates signaling of the DER pathway. Therefore, the regulation of MG survival is mediated by a balance of extracellular inductive and inhibitory signals. How can this signaling pathway be reconciled with the stochastic pattern of MG survival and the observation that only argos expressing MG survive? We propose a model in which the adherens junction along with possible accessory proteins like Rhomboid and Star mediate the close apposition of MG and promote intense Spitz mediated DER pathway signaling. The MG with the most concentrated coupling of this adhesion and signaling pathway network achieve sufficient DER signaling to express argos. These MG are in tum fated to assume a final differentiated identity and will remain to ensheathe the commissures. Argos is secreted and it mediates the apoptosis of MG with reduced levels of adhesion contacts and lower DER signaling (MG not expressing argos). The other mesectodermal cell (MEC) lineages appear to develop independently of argos function. The repercussions of HSargos elicited MG loss to the commissural axons and CNS cytoarchitecture was also examined. Removal of the MG through ectopic expression ofargos results in a loss of ensheathment and the commissural axon tracts are exposed to the haemolymph. Furthermore, the commissural axons are wider and they misexpress Fasciclin II, a phenotype reminiscent of mutations in roundabout.

abstract: Thesis

abstract: Master of Science (MSc)