title: A Multiscale Study of the Role of Environmental Variability on the Diversity and Abundance of Rock Pool Communities

title: The Role of Environmental Variability on Diversity

contributor:
Kolasa, Dr. Jurek
Biology

subject:
rock pool communities
environmental variability
multiscale study

abstract: One of the main goals of ecological research is to understand the factors that determine how communities are structured over both space and time. However, our understanding of any system is largely a function of the scale at which we make our observations. Thus, the mechanisms that determine patterns in community structure are likely to change depending on the scale of observation. This thesis explores how environmental variability affects community structure and species performance, and how the resulting patterns change as a function of scale. Specifically, I asses the role of variability in temperature, oxygen, pH, and chloride, on species richness, abundance, diversity, and species performance, at three observational scales: micro-spatial, local temporal, and landscape-temporal scales, in 49 natural erosional rock pool microcosms, located on the northern coast of Jamaica. I found that while environmental variability was not a primary determinant of species richness or abundance, it did play a role in determining species compositions in the pools. I also show that community patterns are strongly affected by the scale of observation. Recognizing scale-dependent changes in community patterns is a prerequisite for predicting the consequences of changes in ecological systems induced by variability in abiotic factors.

abstract: Thesis

abstract: Master of Science (MS)


title: PREDICTORS OF PHYSICAL FUNCTIONING FOLLOWING INTRAMEDULLARY NAILING OF TIBIAL SHAFT FRACTURES

contributor:
Bhandari, Mohit
Lonn, Eva
Busse, Jason
Schemitsch, Emil
Farrokhyar, Forough
Health Research Methodology

subject:
Tibial Fractures
Health-Related Quality of Life
Intramedullary Nailing

abstract:
Background: Tibial fractures are associated with prolonged recovery. The aim of this study was to identify predictors of long-term physical functioning after tibial shaft fracture.
Methods: We used data from the Trial to Re-evaluate Ultrasound in the Treatment of Tibial Fractures (TRUST) to determine, in patients with unilateral, open or closed tibial shaft fracture, the association between baseline factors and physical functioning at 1-year. All fractures were fixed using intramedullary nails. Physical functioning was measured using the 100-point Short Form-36 (SF-36) Physical Component Summary (PCS) score; higher is better; minimally important difference is 2 to 5 points.
Results: There were 299 tibial fracture patients with complete data available for analysis. In an adjusted analysis, the factors associated with lower physical functioning at 1-year were: (1) current smokers (mean difference [MD] -2.55, 95% confidence interval [95%CI] -4.63 to -0.46, p=0.017), (2) body mass index >30 kg/m² (MD -2.57, 95% CI -4.86, -0.27, p = 0.029), and (3) patients who were receiving disability benefits or involved in litigation, or planned to be (MD -2.65, 95% CI -4.58 to -0.72, p = 0.007). Patients who were employed at the time of their fracture reported significantly higher physical functioning at 1-year (MD 4.56, 95% CI 2.32 to 6.80, p= <0.001) and those who were allowed to partial or full weight-bear post-operatively (MD 1.98, 95% CI 0.13 to 3.82, p=0.036). Neither age, sex, fracture severity or receipt of physical therapy were associated with long-term physical functioning.
Conclusions: Among patients undergoing surgical repair of tibial fractures, partial or full weight-bearing post-operatively and employment at the time of injury predict better long-term functioning, whereas smoking, obesity, and receipt of disability benefits or involvement in litigation (or plans to be) predict worse long-term functioning.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterizing G-quadruplexes, a novel regulatory element, in Streptomyces bacteria

contributor:
Elliot, Marie
Biology

abstract: Less is known about the mechanisms that govern gene regulation in GC-rich bacteria than in the more AT-rich model organisms like Escherichia coli and Bacillus subtilis. G-quadruplexes (GQs) are stable structures that form in G-rich nucleic acid sequences, and have the potential to be important regulators of gene expression – particularly in GC-rich organisms. Streptomyces are extremely GC-rich bacteria with the capacity to produce a vast range of antibiotic compounds. There are still many gaps in our understanding of gene regulation in these bacteria, and yet GQ sequences have never been investigated for their regulatory potential in Streptomyces, even though they are known to play important roles in various eukaryotic systems. Here, we performed an in-depth in silico analysis of the S. venezuelae genome and found an abundance of GQ sequences in these genomes. We discovered that these sequences were enriched in putative regulatory regions and in antibiotic biosynthetic clusters. We followed up this in silico analysis with reporter assays that demonstrated that GQ sequences affected gene expression in Streptomyces. We also took steps towards elucidating the mechanism of action for an observed increase in reporter activity in the presence of the GQ sequence. Finally, we discovered two proteins, SVEN_2656 and SVEN_3866, with the potential to interact with GQ sequences and may function in preventing adverse effects of GQ structures. These results indicate that GQs have the potential to act as important regulators of gene expression in Streptomyces bacteria, and future work on these systems could lead to a broader understanding of gene regulation in all bacteria, and in Streptomyces specifically, could be employed to stimulate antibiotic production.

abstract: Thesis

abstract: Master of Science (MSc)


title: Ecological Determinants of Foraging and Caching Behaviour in Sympatric Heteromyid Rodents

title: Determinants of Foraging and Caching in Heteromyids

contributor:
Daly, Martin
Psychology

subject:
foraging
caching
sympatric
heteromyid rodents

abstract: A series of studies was carried out in order to ascertain some of the ecological determinants of the foraging and caching behaviour of heteromyid rodents (kangaroo rats, Dipodomys, and pocket mice, Chaetodipus). The results show that heteromyids are sensitive to cues of predation while they are foraging. They put more effort into foraging under the safety of cover and in the dark of the new moon, when risk of predation from visually hunting predators is low. They also modulate their selectivity in relation to cues of predation risk, requiring a better pay-off(a more valuable food) as risk increases. The kangaroo rats and pocket mice compete for resources, and the pocket mice are at an aggressive disadvantage to the kangaroo rats at primary resource patches. However, the pocket mice compensate at least partially for their loss by engaging in cache pilferage. Finally, a study of the scatter caching decisions made by kangaroo rats demonstrates that they adaptively modulate cache spacing by placing more valuable seeds into caches that are more widely spaGed. This differential spacing leads to decreased probability that pilferers conducting area-localised search after encountering one cache will be able to locate further caches. The results are discussed in relation to current theory and empirical findings.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: An Assessment of the Importance of Terrestrial Primary Productivity to an Arctic and a Temperate Estuarine Tidal Flat Using Stable Isotope Ratios of Carbon and Nitrogen

subject:
terrestrial primary productivity
arctic estuarine
temperate estuarine
tidal flat
carbon
nitrogen
isotope ratios

abstract:
The isotopic composition of the organic components of an animal's body, with respect to carbon and nitrogen, reflect the weighted average of the isotopic compositions of the animal's food sources, with a certain degree of enrichment in the heavier isotopes. Thus, by comparing the
isotopic compositions of the animal and all the potential food sources, it is possible to ascertain the relative proportions of each availible food source in its diet, if the various food sources are sufficiently isotopically distinct.
This approach is particularly usefull in estuarine communities where food-webs tend to be complex and where there are several sources of primary productivity. In this study it was used on two types of claw in
an arctic and a temperate estuarine tidal flat in order to assess the
importance of terrestrially fixed organic matter to each community. The results indicated that while marine and terrestrial organics were important food sources in the arctic tidal flat, the clams in the temperate site depended mostly on marine organics.

abstract: Thesis

abstract: Bachelor of Science (BSc)


title: Investigation of Thermal Buffer Zone Effectiveness in Real Buildings

contributor:
Hamed, Mohamed
Mechanical Engineering

subject:
Passive air heat
Buffer zone

abstract: Global warming is caused by Greenhouse Gas (GHG) emissions produced from the use of fossil fuel-based energy sources. Buildings consume about 30%-35% of the global energy use, which makes buildings a major contributor to the global warming problem. A long-term plan has been established at the Thermal Processing Laboratory (TPL) at McMaster University to investigate the use of various renewable energy-based technologies to achieve Net-Zero Energy Buildings (NZEB) in Canada. This paper presents results of an investigation of the effectiveness of using a thermal buffer zone (TBZ) in real buildings. A TBZ is a closed passage built around the building that allows air to passively re-distribute heat energy from solar radiation received on the south side throughout the building. A TBZ offers an effective solution of the overheating problem usually experienced on the south side of the building and, at the same time, it helps in reducing the heating load of the north side of the building. An experimental setup employing TBZ in a model of a typical building floor has been built. An analytical model of the TBZ has been developed. The experimental data has been used to validate the developed analytical model, which then was used to simulate the performance of a TBZ implemented in a real building floor. Results showed that the effectiveness of TBZ could reach 117% in the winter (cold climate countries). Moreover, the study considered the effect of integrating the TBZ with a fan. Results showed that the use of the fan is beneficial for a certain gap width, beyond which the use of the fan is not recommended. In conclusion, results of this study confirm that the TBZ can offer an effective means of replacing parry of building consumption of fossil fuel-based energy using solar energy.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Joint Nesting in the Pukeko Porphyrio Porphyrio

contributor:
Quinn, Dr. James
Biology

subject:
joint nesting
pukeko
porphyrio porphyrio

abstract:
The primary objective of the study was to determine why established females tolerate new females that join their breeding group and lay eggs in their nest. Previous work on this population has shown that females suffer a cost of joint-nesting in the form of lowered hatching success. Therefore, we would expect female pukeko to attempt to disrupt the reproductive efforts of their co-nesters by ejecting their eggs from the joint nest.
Two hypotheses might explain why this does not happen. The "peace incentive" hypothesis states that females would forego egg destruction to avoid retaliatory behaviour by the other female. Alternatively, females might not destroy the eggs of co-nesters because they cannot discriminate between their own and another female's eggs. To test between these, we experimentally removed the eggs of one of the females from a number of joint nests. In all S(Wen cases for which we have data on the post-removal behaviour of the females, the robbed female showed no response to the disappearance of her eggs and continued to incubate the clutch.
In addition, we added eggs to eight single female nests. Again, the single females showed no sign that they could distinguish between the foreign eggs and their own. The foreign eggs were not buried, ejected, or destroyed, nor were they moved preferentially to the outer perimeter of the clutch.
To perform the egg removal experiments, I needed to correctly group joint clutches of eggs into maternal sib-groups. I evaluated two methods of doing this, one relying on qualitative observer assessment and the other on statistical techniques. I determined genetic maternity using DNA fingerprinting. Qualitative assessment was more effective than statistical techniques for identifying the maternity of eggs. Such an approach may be a useful alternative to expensive and time-consuming molecular genetic techniques for measuring reproductive skew in joint-nesting birds.
Predation rates on pukeko nests at our study site during the 1998/99 nesting season were significantly higher than they had been in previous years (1990-1995). In the intervening years, the local rabbit population crashed as the result of two rabbit control measures: poisoning and rabbit haemorrhagic disease (RHD). We hypothesised that the increase in predation rates was due to rabbit specialist predators seeking out alternative prey after the crash in rabbit populations. Such a scenario is of grave concern to wildlife managers in many areas of New Zealand where rabbits are abundant and threatened native bird species are already under extreme pressure from introduced predators.

abstract: Thesis

abstract: Master of Science (MS)


title: Microsatellite Variation in Human Populations of the Indian Subcontinent

title: Microsatellite Variation in Human Populations of India

contributor:
Singh, R.S
Biology

subject:
microsatellite variation
human populations
indian
subcontinent

abstract: An analysis of microsatellite variation among individuals of Indian origin was performed to compare the genetic diversity between different regions within India that are divided by spoken language and geographical distance. In addition, the relationship between the Indian and other human populations was examined. Six microsatellite loci -CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA were amplified and typed in a total of 149 individuals representing a broad geographical distribution within the Indian subcontinent. Contingency analyses of allele frequency distributions between North and South Indian populations revealed a significant difference at the vWA locus. The lack of significant differences at the other five loci may indicate a considerable amount of gene flow between these two populations or that these polymorphisms existed before the split between Northern and Southern populations. The South Indian population (n = 37) revealed the presence of an allele at the vWA locus that was not detected in either the North Indian (n = 103) or Caucasian (n = 212) populations. The absence of this allele in the North and the presence in the South may indicate a population specific allele and gives support to the hypothesis that India was occupied by an earlier Dravidian population before the more recent arrival of the Aryans who lacked this allele. Genetic distance failed to reveal any significant distances between North and South Indian populations. Phylogenetic analyses, although not significant, indicated that the two populations were not monophyletic. A correlation between genetic and geographic distance between the Northeast, Northcentral, Southeast and Southwest regions of India revealed a correlation coefficient of r = -0.53 which was not significant. The negative correlation is solely due to the fact that the two most geographically closest populations, Salem and Cochin, show the greatest genetic distance (0.442) between them. This is consistent with the fact that social factors play an important role in the genetic structuring of Indian populations. Genetic distance analyses revealed significant distance values between the Indian, Caucasian and African populations and showed the Indian population to be genetically closer to the Caucasian population. These results are consistent with earlier studies using gene frequency data and mitochondrial DNA. Overall, the results of the genetic distance and phylogenetic analyses showed that six microsatellite loci were able to distinguish between African and non-African populations, but more loci need to be utilized to differentiate between non-African populations.

abstract: Thesis

abstract: Master of Science (MS)


title: On the Stability Regions of Nonlinear Control Systems

contributor:
Mhaskar, Prashant
Chemical Engineering

abstract:
In this thesis, we report advances to the theory of stabilization of control systems. A
first contribution of this thesis is to utilize the concept of stability regions to derive
control laws to stabilize nonlinear systems with stochastic disturbances and subject
to lack of availability of state measurements. In this direction, the probability of
destabilizing behavior is approximated that incorporates the effect of the observation
error. In a second contribution, we determine, for any given input-constrained
nonlinear control system, the largest region from which stabilization can be achieved,
termed the null controllable region (NCR). Indeed, a key result of this thesis is to propose
a control law that induces stabilization from the entire NCR. In this direction,
two methods to construct NCRs are proposed using completely different principles.
In one major contribution, the NCR is given by special smooth optimal trajectories
integrated in reverse-time using Pontryagin's Maximum Principle. In another major
contribution, this same region is given by iteratively expanding an initial Lyapunov-based
stability region by applying a reachability test to boundary cells. A further
contribution of this thesis is to use the geometry of a collection of NCRs, corresponding
to modulated input constraints, to construct a control law that guarantees the
stabilization of the closed-loop system. In this direction, special modifications are
introduced in order to apply this technique to a chemical reactor example. In a final contribution, knowledge of the NCR is used to enable the formulation of a simple finite
difference scheme to solve otherwise intractable Hamilton-Jacobi-Bellman equations
in order to generate Lyapunov functions with maximal regions of attraction.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
In this thesis, advances in the theory of stabilization of control systems are reported. A
control system explains how a physical system evolves in time and how this evolution
can be influenced through the use of manipulable inputs. Accordingly, we consider
the problem of determining what sequence of inputs must be used in order for the
system to converge to a desired state. The first contribution provides a controller
design for systems that contain states that cannot be directly measured and must be
actively inferred from the changes in measurable states: a situation which is occurs
frequently in practice. In this work, theoretical arguments about the region in which
stability can be guaranteed are used to establish the odds of stabilizing certain systems
afflicted by unpredictable random disturbances, even in the presence of uncertainty
caused by estimation of the unmeasured states. The second contribution to this
problem is to efficiently determine all of the states of a system that can be stabilized
to any given setpoint, termed the null controllable region (NCR). In this direction,
two solutions are brought fourth based on completely different principles. The third
contribution is to use the geometry of the NCR to indicate the input that must be used
to induce stabilization. In this direction, several examples are used to illustrate the
efficacy of the technique, including a chemical reactor example. These are the main
contributions of the thesis. A final contribution considers optimal control problems: steering systems in a lowest cost manner with respect to a given metric. The article
explains how knowledge of the boundary of the NCR simplifies the procedure for
solving optimal control problems and how this solution reveals how to stabilize the
system.


title: TOWARDS VIABLE METHODS TO COMPUTE NONLINEAR OPTICAL PROPERTIES FOR BIOCHEMICAL SYSTEMS

contributor:
Ayers, Paul
Chemistry and Chemical Biology

subject: Computational Chemistry, Theoretical Chemistry, Nonlinear Optical Properties

abstract: Nonlinear optics is a field with new applications being regularly discovered, which leads to a growing interest in computing these properties. In this work, we attempt to determine new methods of computationally determining the properties of biologically relevant systems. We do so through testing a novel finite-field method to compute these properties. To facilitate the computation of molecular energies required for finite-field calculations, we tested a hypergeometric resummation scheme. Together, these projects form a strong step into being able to compute the nonlinear optical properties for larger systems of biological relevance.

abstract: Thesis

abstract: Master of Science (MSc)


title: Working memory and referential communication: An investigation of the cognitive factors affecting the production of overspecified referring expressions

contributor:
Humphreys, Karin
Psychology

subject:
language production
referential communication
overspecification
working memory
cognitive load
speech planning

abstract: Language production often requires speakers to convey information to a conversational partner about objects in their environment. According to Grice’s Maxim of Quantity (1975), speakers should provide only the precise amount of information needed to identify an object. However, it is frequently observed that speakers will include redundant adjectives in their referring expressions, rendering their descriptions overspecified. The majority of the research investigating overspecification has focused on how scene characteristics influence the likelihood of this behaviour. To date, less is known about the internal characteristics of the speaker that may play a role in the production of overspecified descriptions, and in referential communication more generally. The current experiment investigates the role of working memory in the generation of referential descriptions and examines how this interacts with manipulations of scene characteristics and cognitive load. Participants were asked to provide instructions to a confederate about which object to select from an array of either three or six unrelated objects while they simultaneously remembered a series of either zero, three, or five numbers. Participants also completed an operation span task to measure their individual working memory capacity (WMC). Results showed a main effect of array size for speech onset times, confirming that speakers are faster to initiate their speech when there are fewer objects in the display. Further, there was a significant three-way interaction between array size, cognitive load, and operation span scores, indicating that speakers with lower WMC are more likely to use redundant adjectives for three object arrays under low levels of load. Finally, there was a significant, negative correlation between speech rate and adjective use, indicating that speakers adjust their rate of speech depending on their choice of referring expression. The results of this research suggest a potential role for individual WMC in the production of overspecified descriptions.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Interactive communication often involves speakers relaying information to a conversational partner about objects in the environment, a phenomenon typically referred to as referential communication. A significant focus of previous research in this area is on how speakers chose to identify objects for a conversational partner. The focus of the current research is to examine the underlying cognitive mechanisms that support this behaviour. Participants were asked to communicate with a partner about objects on a computer screen while completing a secondary memory task. The findings of this research suggest that individual working memory capacity influences the amount of information speakers choose to include in their referential descriptions. Further, we show that including unnecessary information in object descriptions (i.e., referring to object attributes in the absence of contrastive objects) leads to a reduced speech rate, likely because of increased demands on speech planning.


title: Three Essays in Financial Reporting

contributor:
Nainar, Khalid
Business Administration

abstract:
This thesis investigates three important topics on financial reporting and information environment: 1) the timing of patent disclosure and its effect on the cost of equity capital; 2) how CEO mobility affects innovation through changes in firm information environment and incentive structure, and 3) how variability of tort law at the state level affects financial reporting opacity.
In a natural experiment setting, the first essay shows that early disclosure of patent information reduces firms’ cost of equity capital. A notable feature of the American Inventors Protection Act (AIPA) is used, which separates the patent publication date from its grant or issue date. Using this feature as an exogenous shock, it is posited that patent disclosure choice in the patent application influences firms’ information environment by signaling firm’s proprietary information. Consistent with extant disclosure literature, this essay finds that early patent disclosure around the exogenous shock of regulatory change is associated with reduction in implied cost of equity capital. In light of scant prior literature on timing of patent disclosure, this essay offers empirical evidence that benefits of early patent disclosure outweigh the costs. This is the case even after adjusting for a real option to delay inherent in the AIPA.  To exclude alternative explanations, I run a battery of robustness and sensitivity tests and the results of early patent disclosure still hold. This essay provides new evidence on the timing of proprietary disclosure that is of practical significance and importance to investors, policy makers, and regulators. Using Inevitable Disclosure Doctrine (IDD) as an exogenous shock, the second essay provides direct evidence of how external CEOs increase technology spillover and spur innovation. In particular, two channels which have received theoretical support from extant literature are examined. The first channel is technology spillover and the second one is income inequality. My results show that external CEOs, relative to internal CEOs, increase both technology spillover and income inequality. Moreover, I find direct causal evidence linking the technology spillover with innovation. On the other hand, I do not find similar evidence for income inequality. My results remain substantially unchanged for alternative measures of technology spillover and identification strategies. I also find that CEO’s industry origin is an important factor. Specifically, CEOs from the same or similar industries drive the results. In the third essay, I examine how the changes in U.S. state-level liability regimes affect the firm-level financial reporting opacity in the US banking industry. Using tort reform as an exogenous shock, it is found that banks located in states adopting tort reforms have more opacity (greater earnings management) than those located in non-adopting states. Further analyses suggest that banks in the adopting states also smooth earnings more than those in the non-adopting states. I conduct additional analyses to test for the exogeneity of tort reform and test alternative proxies for earnings management. The results from these tests further reinforce the main results. Given the scarcity of evidence on the effects of state-level laws, this study adds to our understanding in this area and informs the stakeholders such as bank regulators and legislators.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Echoes of Entrapment: Aesthetic Representation and Responsibility in Mavis Gallant's "The Pegnitz Junction"

contributor:
Hyman, Roger
English and Cultural Studies

subject:
Canadian Holocaust literature
Mavis Gallant
Holocaust literature

abstract:
Over seventy years after the fallout of the Nazi genocide, depicting the Shoah continues to serve as a subject of widespread debate. Balancing the aesthetics of representation with historical accountability poses unique challenges to both readers and writers of Holocaust literature. In its extensive considerations of time and place, in its troubling of the conventional limitations of the Canadian novel, and in its suggestive possibilities both inside and outside of the ethnic mainstream, the genre is one of ample opportunity — a prospect that entails enormous responsibility.

The difficulty of finding the appropriate language to represent the horrors of the Shoah is the central subject of this thesis, which focuses on interpretive responsibility in Mavis Gallant’s “The Pegnitz Junction” (1973). It situates the novella in both a theoretical and Canadian literary context, examines Gallant’s understanding of the ethics of aestheticizing the event, provides a full-length study of the story, and attempts to fill some of the gaps in critical scholarship by drawing attention to the multidimensionality of the text’s portrayal of a post-Auschwitz world. I look closely at how Gallant’s work prompts a suspension of logic and normalcy, and in turn reconceptualizes the novella insofar as its indirection causes her readership to contemplate whether Holocaust responsibility is, in the words of D.G. Myers, “to be shared by [readers], despite the fact that they are not to blame” (270). I suggest that the novella is a medium in which refusal to provide logical explanations for the Holocaust through aesthetic representation not only allows audiences to ponder the implications of humanity’s capacity to preserve and erase historical memory, but also causes them to consider how human beings ought to respond responsibly to the ramifications of historical trauma.

abstract: Thesis

abstract: Master of Arts (MA)


title: Coupled Luminescence Centres in Erbium-Doped Silicon Rich Silicon Oxide Thin Films Deposited by ECR-PECVD

contributor:
Mascher, Dr. Peter
Knights, Dr. Andrew

subject:
silicon rich
oxide thin films
ECR-PECVD
coupled luminescence
erbium

abstract:
Silicon has been the mainstay of the microelectroncs industry for over four
decades. There is no material which can match the balance it affords between
cost-benefit, mass consumability, process versatility, and nano-scale electron
device performance. It is, therefore, the logical (and perhaps inevitable) platform
for the development of integrated opto-electronics - a technology that is being
aggressively developed to meet the next generation of bandwidth demands that
are already beginning to strain interconnect architectures all the way down to the
intra-chip level. While silicon-based materials already provide a variety of
passive optical functionalities, the success of a genuine silicon-based optoelectronics
will depend upon the ability of engineers to overcome those
limitations in the optical properties of bulk silicon that occur at critical junctions
in device requirements (eg. modulator and laser). Such solutions must not render
the device processing incompatible with CMOS, for then the "silicon advantage"
is lost. Achieving reliable and efficient electroluminescence in silicon remains
the most intractable of these problems to date.
Reliability problems in recently developed light emitting devices operating
near a wavelength of 1.54 f..Lm, based on the thermally induced formation of
silicon nano-clusters in erbium-doped silicon rich silicon oxide thin films, has reinforced
the need for a further understanding of the luminescence mechanisms in
this material. Indeed, the efficient and stable sensitized photoluminescence from
Er3+ ions (near the telecom wavelength), embedded in an oxide matrix, based on a
quasi-resonant energy transfer from nanostructured silicon, has the potential to
make possible compact waveguide amplifiers and thin film electroluminescence.
This thesis represents a study into the luminescence mechanisms in
erbium-doped silicon oxide (SiOx, x~2) thin films grown by electron cyclotron
resonance plasma enhanced chemical vapour deposition. Importantly, the film
growth relies on in-situ erbium doping through the cracking of a volatile organalanthanide
Er(tmhd)3 source. Rutherford backscattering spectroscopy has been
used to map the film composition space generated from an ECR-PECVD
parameter subspace consisting of precursor gas flow rates and the erbium
precursor temperature. The response of the film photoluminescence spectra in
both visible and infrared bands consistenly reveals three classes of luminescence
centres, whose relative ability to emit light is shown in this study to exhibit a
considerable degree of variability through the control of the film composition,
subsequent thermal anneal temperature, duration, and process ambient. These
three classes consist of optically active Er3
+ ions, silicon nano-clusters phase
separated during thermal annealing, and oxide-based defects (which may
additionally include organic chromophores). The latter two of these species show
the ability to sensitize the Er3 + luminescence. In fact, sensitization by intrinsically
luminescent defects is a rarely studied phenomenon, which seems to be an
important phenomenon in the present films owing to a potentially unique Er
incorporation complex. To further investigate the ability of the oxide defects in
this regard, an optimally luminescent film has been subject to a damaging ion
irradiation to induce a photoluminescence quenching. The subsequent recovery
of this luminescence with stepwise isochronous annealing has been correlated
with Doppler broadening positron annihilation spectroscopy measurements made
with a slow positron beam. Irradiation to a sufficiently high fluence has
demonstrated a unique ability to de-couple luminescent sensitizers and Er3+ ions,
producing enhanced blue and violet emissions.

abstract: Thesis

abstract: Master of Science (MS)


title: Ballistic Elbow Extension Actions in Karate-Trained and Control Subjects: Agonist Premovement Depression (PMD) and Movement Performance

contributor:
Sale, Dr. D.G.
Human Biodynamics

subject:
ballistic elbow extension
karate-trained
agonist premovement depression
movement
performance

abstract: Ballistic movements have been shown to be controlled differently by the central nervous system than slow, ramp actions. It has been suggested that the cerebellum is involved primarily with ballistic actions, while the basal ganglia primarily control slower movements. These command and control differences have been shown to manifest in unique ways at the neuromuscular level. Ballistic actions evidence high firing rates, brief contraction times, and high rates of force development. A characteristic triphasic agonistantagonist-agonist burst pattern presents itself during ballistic movement, wherein the amount and intensity of antagonist co-activation is variable. In conditions of low-grade tonic muscular activity, a premovement depression (P:MD; or silent period, PMS) can occur in both agonist and antagonist muscles prior to ballistic contraction. The agonist P:MD period may serve to potentiate the force and velocity of the following contraction A selective activation of fast twitch motor units may occur in ballistic contractions under certain movement conditions. Finally, high velocity, ballistic training induces specific neuromuscular adaptations that are representative of the underlying neurophysiological mechanisms that sub serve ballistic movement.

abstract: Thesis

abstract: Master of Science (MS)


title: HEALTHCARE INEQUITY IN CANADA: EXAMINING THE FEASIBILITY OF THE PUBLIC PRODUCTION OF MEDICINES

contributor:
Longo, Christopher J.
Global Health

subject:
Pharmaceutical R&D
Public Production of Medicine

abstract:
Background: As the global pharmaceutical industry continues to generate significant wealth, the demand for equitable access to medicine remains at the forefront of political and grassroots agendas. In recent years, poor drug coverage coupled with unaffordable drug prices have contributed to access issues for a growing number of Canadians (Morgan et al, 2015). Although the industry cites various reasons for an increase in cost, such as high-risk research, lengthy clinical trials and significant advances in technology (DiMasi et al., 2016; Ridley, 2005), there is a growing body of research that is contradictory to the industry’s reasoning for higher drug costs (Kohler et al., 2016; Siddiqui & Rajkumar, 2012; Light & Warburton, 2011).
Whereas other initiatives to date focus on drug coverage, this work proposes the Canadian Government investigate the feasibility of the public production and distribution of pharmaceuticals. Thus, the research question addresses whether successful publicly funded pharmaceutical research and development initiatives, including production and distribution, could be applicable in the Canadian pharmaceutical sector where inequity is an issue. A scoping review was conducted to draw in all relevant literature on publicly funded research models pertaining to the research and development of pharmaceuticals.
Methods: The research undertaken for this thesis is exploratory and comprised of qualitative work that is guided by the Arksey & O’Malley (2005) scoping review methodological framework. The data collected for the scoping review was analyzed with the thematic analysis method.
Findings: Following the thematic analysis, three key themes were identified: Local Production, Public Private Sector and National Production. Although there have been some successes in low to middle income countries with regard to the local production of medicine, the likelihood of success is contingent on whether there is a need to import active pharmaceutical ingredients (API). With regard to the public and private sector, the pre-competitive sphere serves as the typical space for collaboration. The public sector typically conducts research, whereas the private sector oversees drug development. The national production of medicine is underpinned by government intervention, which is evidenced by the varied measures taken to increase access to medicine. The preliminary literature review revealed that an Advisory Council was created to assess the viability of Pharmacare 2020. This council may be used to conduct the necessary research to assess the feasibility and strategy of publicly producing pharmaceuticals in Canada.
Conclusions: Healthcare inequity that is linked to unaffordable medicine is exacerbated by poor drug coverage. The findings revealed that considerable investment into infrastructure, a strong civil society that pressures the government to act, and a pharmaceutical sector characterized by high prices may encourage a government to produce medicine when faced with a health crisis. Further findings revealed that API production may prevent a country from feasibly producing medicine. Considering Canada’s standing as an industrialized and developed nation with access to state-of-the-art public infrastructure, in addition to a pharmaceutical market characterized by high drug prices and a strong civil society sector, the Canadian Government is in a likely position to produce medicine. However, the necessary research must be conducted to assess whether such an endeavour is feasible.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Effects of Molecular Structure and Design on the Plasticizer Performance Through Coarse-Grained Molecular Simulation

contributor:
Xi, Li
Chemical Engineering

subject:
molecular simulation
coarse-grained modelling
plasticizer
poly(vinyl chloride)
PVC
migration
size effect
design

abstract: Plasticizers are a commonly used additive used in the polymer industry to make the plastic more pliable by reducing the glass transition temperature, Tg and Young's modulus, Y. As the plasticizer aids in polymer process-ability and making it suitable for applications from industrial cables to sensitive medical equipment, the mechanism of plasticization is not fully understood. There are three theories used to explain plasticization: lubricity theory, gel theory, and free volume theory. The latter is a fundamental concept of polymer science that is used to calculate many polymer properties, but they all do not give a clear picture on plasticization. With molecular dynamics (MD) simulation, a coarse-grained (CG) model - which consist of a simple bead-spring model that generalizes particles as a bead and connects them via a finite spring – is used to explore the impact of plasticizer size throughout the polymer system. The interaction characteristics of the plasticizer is explored by representing the plasticizer molecules as a single bead of varying size. This gives better control on the variability of the mixture and pinpoint the significant contributions to plasticization. A path to understanding the the mechanism of plasticization will give insight in glass formation, and can later be used to find an optimal plasticizer architecture to minimize the migration of the additive by tuning the compatibility. Current results show a decoupling between the Tg and Y of the polymer-additive system. The overall understanding of finite-size effects shows: as additive of increasing size is added, the polymer free volume increases which in-turn would decrease the Y, but Tg is shown to increase because the polymer and additive are not as mobile to reduce caging effect of monomeric units.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Ooh What's This Button Do?

title: The Physical Requirements of Video Gaming

contributor:
Carette, Jacques
Computing and Software

subject:
video games
challenges
motor movements
motor skills
game design

abstract:
Video games as a system are composed of two component systems: the player and
the game. The interaction between these two create specific gameplay
experiences which can be described mechanically by player actions and gameplay
challenges. We systematically look at potential player actions (as defined by
basic cognitive and motor abilities) and gameplay challenges to understand how
they relate to each other. We quantify these relationships by the importance of
each action to the completion of a challenge. We summarize these relationships
in several tables, separated by controller context. From these tables we draw
conclusions about areas for novel gameplay, game analysis, and the impact of
challenge design on people of differing abilities by examining trends in the
data. We end by exploring ways to improve our methodology, refine our data, and
other avenues to explore in the future.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The derivation and utility of in vitro organoids from human pluripotent stem cells

contributor:
Draper, Jonathan S.
Biochemistry and Biomedical Sciences

subject:
Human pluripotent stem cells
In vitro differentiation
Organoids
Intestinal organoids
Enterospheres
Lung organoids
Intestinal maturation

abstract:
Human pluripotent stem cells (hPSCs) have the ability to self-renew and differentiate into all specialized body cells, providing material suitable for studying basic biology, modeling disease, and for regenerative medicine. The differentiation of hPSCs into functional cell types has been further enhanced by the production of organoids, miniature 3D organ-like structures that mimic the architecture and function of their in vivo counterparts, representing more physiologically relevant models of native tissues than monolayer cultures. Our initial aim was to differentiate hPSCs into lung epithelial organoids in vitro, and we hypothesized that applying knowledge of signaling cues during embryonic development to the dish would produce lineage-specific tissue. Using a multi-stage differentiation strategy, we derived organoids sharing properties with the developing lung as well as intestine. From this work, we learned the importance of purification, selection, and using singularized precursor cells to produce populations of bona fide lineage-restricted organoids.
Upon developing a type of intestinal organoid technology from hPSCs not reported before, we shifted our focus to the intestine. We generated cystic intestinal epithelial organoids called enterospheres (hEnS) in vitro from hPSCs, which mimic structural and cell type properties of the native small intestinal epithelium. hEnS growth, differentiation, and long-term culture can be controlled by modulating media conditions. Importantly, hEnS are functional in that they elicit an innate immune response upon treatment with enteric pathogens. We established hEnS as an attractive in vitro model system for studying human gastrointestinal biology.
We then developed an automated hEnS imaging assay to measure responses to growth factors, bacterial products, and enteric bacteria themselves. In doing so, we demonstrated the utility of hEnS as a germ-free system for studying host-microbe interactions and intestinal maturation. Finally, we investigated the expression of protein markers of intestinal maturation in tissue sections of primary human intestine spanning gestation, and made observations that are different from those reported in mice. Overall, our work provides new and important insights into hPSC differentiation, organoid technologies, and intestinal development in humans.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Analytical Approaches to Risk Assessment and Management for Railroad Transportation of Hazardous Materials

contributor:
Verma, Manish
Business

abstract:
Hazardous materials (hazmat), such as crude oil and gasoline, are harmful to humans and the environment because of their toxic ingredients, but their transportation is integral to sustain our industrial lifestyle.  In North America, a significant portion of hazmat shipments is moved via the railroad network. Rail hazmat incidents are rare though the consequences could be catastrophic. The low probability–high consequence nature of such events mandate that a risk-averse plan be implemented for routing hazmat shipments.
We propose a value-at-risk (VaR) and conditional value-at-risk (CVaR) methodology to route rail hazmat shipments, using the best train configuration, over a given railroad network with limited number of train services, such that the transport risk is minimized. Freight train derailment records of the Federal Railroad Administration (FRA) were analyzed to model the behavior of railroad accidents, and to estimate their conditional probabilities. The proposed methodologies were used to study several problem instances generated using the realistic network of a railroad operator in Midwest United States, and to demonstrate that they are superior to the existing risk measures in the literature in regard to providing risk-averse routing of hazmat shipments and being versatile enough to yield various routes based on the risk preferences of decision makers.
Next, we propose a CVaR model, as a risk-averse routing plan for multiple rail hazmat shipments and multiple origin-destinations pairs, such that the total transport risk in the railroad network as measured by CVaR is minimized. However, it may happen that certain links and yards of the railroad network tend to be overloaded with hazmat traffic and risk. To overcome this issue, we also promote equity in the spatial distribution of risk. Therefore, the main problem is to find minimum risk routes, while limiting and equitably spreading the risk in any zone where the railroad network is embedded. The problem is mathematically formulated, and a heuristic algorithm is proposed for its solution, which takes into consideration the risk load limits on arcs and transferring yards and spreads the risk equitably throughout the network. Moreover, a lower bound based on a Lagrangian relaxation of the mathematical formulation is also provided. Finally, several computational experiments are developed using the above realistic railroad network.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Differences in the Time Allocation Strategy Between Transgenic "Supermice" and Normal Controls and Their Relevance to the Principle of Allocation

title: A Time Budget for the Transgenic Supermouse

contributor:
Rollo, C. D.
Biology

subject:
time allocation
supermice
normal control
principle of allocation
transgenic mice
time budget
growth hormone
activity
behaviour
evolution
genetic engineering

abstract: This study represents the behavioural component of a larger project investigating the life history tactics, physiological resource allocation and behavioural time budgeting of a genetically engineered animal. The "supermouse" is a transgenic strain (mMT-1/rGH) that has one chromosome genetically engineered with extra copies of rat growth hormone genes, each fused to a metallothionein-1 promoter. The GH transgenes are permanently incorporated into the genome of the mouse and are inherited as a block, in a Mendelian manner. "Supermice" exhibit an accelerated growth rate and reach body weights twice that of their normal siblings: both transgenic mice and normal mice are obtained by crossing transgenic males to normal females. Although there must be increased costs associated with achieving their higher growth rate, these: mice show no increases in their specific feeding rates. Consequently there must be a reallocation of resources among various physiological and behavioural demands. The reality of such tradeoffs is known as the Principle of Allocation and predicts that reductions in behavioural activities might be one avenue for realizing extra growth. To test this, six components of the behavioural time budget (resting, locomotion, wheel running, feeding, drinking and grooming) were compared between transgenic and normal mice. Infra-red videocameras recorded the activities of individual male mice in artificial enclosures over 24 hours. The time spent in each bout of activity was recorded and compared. Transgenic mice out-slept their normal counterparts by 126% (an increase of 3.4 h) and were only 53.83% as active in terms of locomotion and wheel running as normal mice. Pooling the data revealed that on average, large mice spent more time at rest and less time engaged in locomotion. Slight but significant decreases in time spent drinking and grooming were also found. Transgenic mice spent only 77.01% as much time drinking, and 69.01% as much time grooming as normal mice. No difference in the amount of time spent feeding was found.

abstract: Thesis

abstract: Master of Science (MS)


title: A Functional Genomics Approach to Identify Novel Therapeutic Targets OF Mammary Tumour-Initiating Cells

title: An Approach to Identify Targets of Breast Cancer Stem Cells

contributor:
Hassell, John
Biochemistry and Biomedical Sciences

subject:
therapeutic target
mammary tumour-initiating cell
mammary tumour
functional genomics approach

abstract:
Much interest has recently accumulated of the role of adult stem cells in both normal tissue homeostasis and carcinogenesis. Whereas normal and cancerous mammary epithelial stem cells have been identified and isolated from bulk primary tissue, little remains known about their regulation in vivo. Here we describe the molecular profile of mammary epithelial stem cells cultured in vitro and that of their tumourigenic counterparts, breast cancer stem cells. Our studies of gene transcription reveal potential mechanisms that may cooperate in the regulation of normal and cancer stem cells in vitro, and may also reflect their in vivo behaviour. These data bear consequences for the design of novel breast cancer therapeutics, as cancer stem cells are thought to resist conventional treatments and persist thereafter, causing disease relapse and seeding metastases. To address this issue we have devised a functional genomics approach to screen for novel biomarkers and therapeutic targets of breast cancer modeled in vitro; this culture system is centered on bona fide stem cells and may therefore offer improved
relevance to human disease when compared with breast cancer cell lines.

abstract: Thesis

abstract: Master of Science (MS)


title: Restoration and its impact on methane dynamics in a cutover peatland

title: Restoration and CH4 dynamics in a cutover peatland

contributor:
Waddington, J.M.
Geography

subject:
restoration
methane dynamics
peatland
cutover peatland
methane emissions
vegetation succession

abstract: Peatlands cover 3% of the earth's surface, with approximately 110 to 130 million hectares in Canada and are important in terms of the long-term sequestration of atmospheric carbon. In contrast to their removal of CO2 from the atmosphere, peatlands represent 15 to 30% of the total methane emissions to the atmosphere with Canadian wetlands emitting approximately 0.1 to 1 x 1010 g yr^-1. Drainage and harvesting of peatlands generally reduces CH4 emissions to the atmosphere and increases CO2 emissions by up to 400%. However, recent studies have suggested that drained peatlands may represent a larger source of atmospheric CH4 than undisturbed peatlands. In the first part of this study, potential CH4 production and oxidation was determined from natural, harvested and recently restored peat. Total depth integrated CH4 production decreased with time post harvest where CH4 production at 2-yr > 7-yr > 20-yr cutover peat. This decrease in CH4 production was a result of a decreased source of labile carbon, a decrease in the methanogenic population, and an increase in the concentration of alternative electron acceptors. Restoration has altered CH4 production processes so that total depth integrated CH4 production was 2-yr > 7-yr >RESTORED> 20-yr cutover peat. Depth dependent trends in potential CH4 oxidation and production from each peat were dependent on the water table position while substrate quality was the main difference production values between the Lac St. Jean and Bois-des-Bel peat. Comparison of CH4 fluxes over the four field seasons showed restored site bare peat and mosses did not play a significant role in CH4 emissions from the peatland. However, the overall CH4 function of the peatland was directly related to the increase in CH4 emissions from vascular vegetation, remnant ditches and newly constructed ponds which were directly attributed to an increase in labile carbon for methanogenesis provided by vegetation. CH4 fluxes from ditches and ponds suggest that these features are the largest sources of CH4 from the peatland. However, when weighting the fluxes to the areal extent of each feature, ditches become secondary to vascular vegetation in total CH4 emissions while the ponds had a minimal impact on the amount of CH4 emitted from the peatland. Furthermore, ebullition from ditches and ponds was insignificant in comparison to the diffusive fluxes. When comparing CH4 emissions from this site to natural peatland systems (~10 g CH4 m^-2 a^-1), it is evident that the site is still a much smaller source of CH4 and that the carbon and CH4 process are still changing as the pool of labile carbon increases (develops). Vegetation succession is still occurring and more time and monitoring is needed in order to determine if this site will return to similar CH4 functions as natural peatlands.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Study of Fish Collection Techniques and Zooplankton Community Structure of the Laurentian Great Lake Coastal Wetlands

contributor:
Chow-Fraser, Patricia
Biology

subject: Fish collection techniques, zooplankton, zooplankton community, zooplankton community structure, coastal wetlands, laurentian great lake coastal wetlands

abstract:
GENERAL ABSTRACT
The Laurentian Great Lake wetlands are highly productive and complex systems. The net loss of wetlands since European settlement has been dramatic. The remaining coastal wetlands continue to be threatened with obliteration or severe environmental degradation. Therefore, the overall objective of this study was to provide information on the ecology of the remaining coastal wetlands within the lower Great Lakes.
This study describes a coastal wetland fish community along the north shore of Lake Erie within Long Point Marsh complex over a 24-h period and catch characteristics of three common fishing techniques. The fish community was sampled at two hour intervals over a 24-h period in June, and used three types of gear to determine possible sampling biases from the different collection techniques. A total of 497 fish encompassing 11 taxa were collected. A 2-h interval, four hours prior to sunset, netted the largest number of taxa (including 3 functional feeding groups: ornmvores, planktivores, and piscivores ), as well as highest abundance and biomass values. Seine netting demonstrated a biased towards sampling the smaller planktivores, while fyke nets were biased towards larger omnivorous fish, and boat electrofishing was biased towards the large piscivores. These results will assist scientists and lake managers to develop standardized fish sampling protocol in order to accurately assess differences in wetland fish communities.
Seven coastal wetlands within Lake Erie and Ontario along both the Canadian and United States shorelines were studied to verify predicted relationships from the literature and determine the relative influences of various habitat features on zooplankton
community structure. Water quality, aquatic macrophyte, zooplankton, and fish community information were collected from the wetlands between July 4th and August 2nd of 2001. The predicted relationships from the literature concerning water quality and macrophyte species richness were verified by the results of this work. Water quality and macrophyte species richness were the most accurate predictors of wetland zooplankton community structure. Identifying the wetland characteristics that play primary roles in structuring zooplankton communities will also assist lake managers to make informed decisions of how to most effectively improve zooplankton habitat, to foster larger-bodied zooplankton populations, making the habitat more suitable for larger populations of larval and juvenile fish.

abstract: Thesis

abstract: Master of Science (MS)


title: Reduction-Respecting Parameters for Lattice-Based Cryptosystems

contributor:
Stebila, Douglas
Mathematics and Statistics

subject:
Post-Quantum Cryptography
Lattices
Learning With Errors
Security Reduction

abstract: One attractive feature of lattice-based cryptosystems is the existence of security reductions relating the difficulty of breaking the cryptosystem to the difficulty of solving variants of the shortest vector problem (Regev, STOC 2005; Peikert, ePrint 2008). As there are no known polynomial-time algorithms which solve these lattice problems, this implies the asymptotic security of the cryptosystem. However, current lattice-based cryptosystems using the learning with errors (LWE) problem select parameters for which the reduction to the underlying lattice problem gives no meaningful assurance of concrete security. We analyze the runtime of the algorithm constructed in the reductions and select parameters for a cryptosystem under which the reductions give 128-bit security. While the resulting LWE-based cryptosystem is somewhat cumbersome, requiring a dimension of n = 1460, this is less than 2 times the dimension in the recently proposed Frodo cryptosystem (Bos et al., ACM CCS 2016), and could be implemented without catastrophic damage to communication times. We also investigate the runtime necessary for a reduction to give meaningful security assurances for current cryptosystems.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The advent of quantum computing poses a serious threat to modern cryptography, as most cryptosystems in use today are vulnerable to attacks by quantum algorithms. Recently proposed cryptosystems based on lattices are conjectured to be resistant to attacks by quantum computers. These cryptosystems also have a conditional security guarantee: if the cryptosystem can be broken by an attack, then a reduction exists which uses that attack to solve variants of the shortest vector problem (Regev, STOC 2005; Peikert, ePrint 2008). As these problems have no known efficient solutions, breaking the cryptosystem should be hard. However this guarantee only holds if the cryptosystem is constructed using parameters which satisfy conditions given in the reduction. Current proposals do not do this, and so cannot claim even a conditional security guarantee. We analyze two reductions and select parameters for a cryptosystem which satisfy these conditions. We also investigate the runtime necessary for a reduction to give meaningful security assurances for current cryptosystems.


title: Probiotic modulation of mast cells in vitro

contributor:
Forsythe, Paul
Medical Sciences

subject:
Mast Cell
Probiotics
Immunology
Inflammation

abstract:
N/A, thesis is written in chapters.
Thesis
Master of Science (MSc)


title: Predictions Concerning Internal Phosphorus Release in Cootes Paradise Marsh and Implications for Restoration

contributor:
Chow-Fraser, Dr. Patricia
Biology

subject:
internal phosphorus release
cootes paradise
restoration

abstract:
To assess the relative contribution of phosphorus release from sediment in Cootes Paradise Marsh, I first examined spatial and temporal variability of laboratory-measured release rates from sediment samples collected from 12 sites within the wetland (Chapter 1 ). The microbial communities from these 12 sites were characterized on the basis of sole-carbon-source utilization using BIOLOG GN plates containing 95 substrates. Results from these experiments were entered into a principal component analysis and the release rates for all sites were regressed against corresponding PC 1 and PC2 scores (Chapter 2). Differences in microbial physiology as defined by PC 1 and PC2 scores accounted for 49% and 53%, respectively of the variation in phosphorus release rates. Using stepwise multiple regression, I concluded that the key determinants of laboratory-derived release rates from West Pond sediment (a highly eutrophic site within Cootes Paradise Marsh) are oxic state, ambient temperature and time of sediment collection (Chapter 3). Using this information I developed a multivariate model to predict release rates. This model, along with 2 alternative approaches, was used to estimate the extent of internal loading (kg d-1) in Cootes Paradise Marsh (Chapter 4). Method 1 was a highly controlled, static approach and resulted in an internal load of 11 .6 kg d-1, which was
attributed to diffusion. The remaining two methods were more dynamic in nature as they
took into account temporal variation, ambient temperature and the development of
anoxia. Using Method 2, I estimated an internal load of 7.8 to 8.5 kgd-1, which was based on empirically-derived laboratory release rates. Method 3 consisted of the predictive model from which I estimated an internal load of 6.7 kgd-1• I attributed the release from the latter two methods to microbial mineralization processes. Based on this work and a previous estimate of internal loading in Cootes Paradise Marsh (Prescott & Tsanis 1997), I concluded that mineralization accounts for 22.3% of total phosphorus loading to the system, preceded only by urban runoff ( 41% ).

abstract: Thesis

abstract: Master of Science (MS)


title: A Multiscale Study of the Role of Environmental Variability on the Diversity and Abundance of Rock Pool Communities

title: The Role of Environmental Variability on Diversity

subject:
multiscale study
environmental variability
rock pool communities
environmental diversity

abstract: One of the main goals of ecological research is to understand the factors that determine how communities are structured over both space and time. However, our understanding of any system is largely a function of the scale at which we make our observations. Thus, the mechanisms that determine patterns in community structure are likely to change depending on the scale of observation. This thesis explores how environmental variability affects community structure and species performance, and how the resulting patterns change as a function of scale. Specifically, I asses the role of variability in temperature, oxygen, pH, and chloride, on species richness, abundance, diversity, and species performance, at three observational scales: micro-spatial, local-temporal, and landscape-temporal scales, in 49 natural erosional rock pool microcosms, located on the northern. coast of Jamaica. I found that while environmental variability was not a primary determinant of species richness or abundance, it did play a role in determining species compositions in the pools. I also show that community patterns are strongly affected by the scale of observation. Recognizing scale-dependent changes in community patterns is a prerequisite for predicting the consequences of changes in ecological systems induced by variability in abiotic factors.

abstract: Thesis

abstract: Master of Science (MS)


title: Beneficial Effects of Nutraceutical Cofactor Therapy in Patients with Mitochondrial Disorders

title: Nutraceutical Cofactor Therapy in Mitochondrial Disease

contributor:
Tarnopolsky, Dr. Mark A.
Kinesiology

subject:
nutraceutical
cofactor
therapy
mitochondrial disorders

abstract:
Mitochondrial diseases are a group of heterogenous disorders that share common cellular consequences resulting from mitochondrial dysfunction: (i) decreased ATP production;
(ii) increased reliance on alternative anaerobic energy sources; and (iii) increased production of reactive oxygen species. Objective: We evaluated the effect of a combination (COMB) therapy comprising creatine monohydrate, coenzyme Q1 and lipoic acid to target the above mentioned consequences using a randomized, double-blind, placebo-controlled, crossover study design in patients with mitochondrial cytopathies. Results: Compared with placebo, the COMB therapy resulted in lower resting plasma lactate concentrations, lower urinary 8-isoprostane excretion and attenuated the decline of peak dorsiflexion strength in all patient groups. Improved body composition was only observed in patients in the MELAS group. Interpretation: These results suggest that combination therapies targeting multiple final common pathways of mitochondrial dysfunction favorably influence surrogate markers of cellular energy dysfunction. Future therapies should be designed to target specific mitochondrial diseases to provide the greatest therapeutic benefits for those patients. In addition, future studies employing larger sample sizes in homogeneous groups of patients will be required to determine whether such combination therapies will influence function and quality of life.

abstract: Thesis

abstract: Master of Science (MS)


title: Host-Cell Reactivation of a UV-Damaged Reporter Gene in Unirradiated and Pre-UV-Irradiated Rodent Cells

title: Inducible Repair of a UV-Damaged DNA in Rodent Cells

contributor:
Rainbow, Dr. A.J.
Biology

subject:
host cell
uv-damaged
pre-uv-irradiated
reporter gene
rodent cells

abstract:
A non-replicating recombinant adenovirus, Ad5MCMVlacZ, which expresses the 13-galactosidase (l3-gal) reporter gene, was used to examine both constitutive and inducible repair of UVC-damaged DNA in Chinese hamster ovary (CHO) cells. Host cell reactivation (HCR) of 13-gal activity for UVC-irradiated Ad5MCMVlacZ was examined in non-irradiated and UVC-irradiated nucleotide excision repair (NER) proficient parental CHO-AA8 and m mutant CHO-UV61 cells which are deficient in the transcription-coupled repair (TCR) pathway of NER. Cells were infected with either UVC-irradiated or non-irradiated Ad5MCMVlacZ and scored for 13-gal activity 24 h later. HCR of 13-gal activity for UVC-irradiated Ad5MCMVlacZ was significantly reduced in non-irradiated CHO-.UV61 cells compared to that in non-irradiated CHO-AA8 cells suggesting that repair in the transcribed strand of the UVC-damaged reporter gene in untreated CHO-AA8 cells utilizes TCR. Prior UVC-irradiation of cells with low UV fluences resulted in a transient enhancement of HCR for expression of the UVC-damaged reporter gene in CHO-AA8 cells but not m TCR deficient CHO-UV61 cells. Pre-UVC-treatment of cells resulted also in an enhanced expression of 13 -gal for unirradiated Ad5MCMVlacZ in both CHO-AA8 and CHO-UV61 cells. However, compared to CHO-AA8 cells, the CHO-UV61 cells exhibited comparable levels of enhanced 13-gal activity following significantly lower UVC exposures to cells suggesting that persistent damage in active genes plays a direct role in enhancing 13-gal activity driven by the MCMV promoter in CHO cells. These results suggest that prior UVC treatment results in a transient enhancement in repair of UVC-damage DNA in the transcribed strand of the active reporter gene in CHO-AA8 cells through an enhancement of TCR or a mechanism that involves the TCR pathway and that the upregulation of reporter gene expression alone is not sufficient for enhanced repair of the reporter gene in CHO-UV61 cells.
The HCR assay was used also to examine both constitutive and inducible repair of UVC-damaged DNA in mouse embryonic fibroblast (MEF) cells. HCR of B-gal activity for UVC-irradiated Ad5MCMVlacZ was examined in non-irradiated and UVC-irradiated NER proficient parental wild type MEF cells and in MEF cells with specific knockouts in the p53 (p53-/-), pRb (pRb-/-), and p107 (p107-/-) genes. Cells were infected with either UVC-irradiated or non-irradiated Ad5MCMVlacZ and scored for ~-gal activity 24 h later. HCR of ~-gal activity for UVC-irradiated Ad5MCMVlacZ did not show a significant difference in non-irradiated cells for any of the MEF knockouts cells compared to the parental strain suggesting that p53, pRb and p107 does not play a role in repair of the UV -damaged reporter gene in untreated MEF cells. Prior UVC-irradiation of cells with low UVC fluences resulted in an enhancement of HCR for expression of the UV C-damaged reporter gene in MEF wild type cells, low passage pRb-/-and p 1 07 -I-MEF cells but not in p53-/-MEF cells or in high passage pRb-/-and p107-/-MEF cells. These results suggest that prior UVC treatment MEF cells results in an induced repair of UVC-damaged DNA that is dependent on p53. The presence of an enhancement of HCR for the UVC-damaged reporter gene in pre-UVC treated cells in low passage, but not in high passage, pRb-/-and p 1 07-I-cells suggests that the lack of pRb or pI 07 expression per-se does not result in a deficiency in inducible DNA repair. However, these results suggest that the lack of pRb or p 1 07 expression results in alterations in MEF cells at high passage number that abrogate inducible repair of UVC-damaged DNA.
UVA produces predominantly single base damage that is repaired through base excision repair (BER), whereas UVC and UVB produce predominantly cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PP) that are repaired through NER. The colony survival following exposure to various UV sources was examined in cells proficient and deficient in (NER). The UV sources were a UVC source from a germicidal lamp emitting predominantly at 254 nm. and a UVA source from a lKW Hg-Xe arc lamp using either a Band pass filter (BPF) or a 335 Cut-off-filter (335COF). NER deficient CHO-UV5 and CHO-UV61 cells were more sensitive to UVC exposure compared to NER proficient CHO-AA8 cells, consistent with the production of UVC-induced DNA damage predominantly in the form of CPDs and 6-4PPs which are repaired through the NER pathway. NER deficient xeroderma pigmentosum cells from complementation group D (XPD) were more sensitive compared to NER proficient normal human cells following exposure to the UVA-BPF source. In addition XPDdenV cells, which express the denY gene from bacteriophage T4, were more resistant than XPD cells following exposure to the UVA-BPF source. Since the denY protein is specific for excision ofCPDs these results indicate a substantial proportion of the induced DNA damage resulting from the UV A-BPF is in the form of CPDs, presumably due to a significant UVB component in the beam. In contrast, the NER deficient CHO-UV5 and CHO-UV61 cells showed a similar sensitivity compared to the NER proficient CHO-AA8 cell line following UVA-335COF exposures up to 60 KJ/m2• However, for UVA-335COF exposures greater than 60 KJ/m2 the NER deficient cells were more sensitive compared to the NER proficient CHO-AA8 cells, although the difference in sensitivity between NER deficient and NER proficient cells was less than that detected following UV A-BPF exposure. These results suggest that the UVA-335COF exposure produces predominantly DNA damage of the single base type for exposures less 60 KJ/m2. This is consistent with the calculated spectral distribution, which showed a 5.62% UVB component for the UVA-BPF, but only 0.14% UVB component for the UVA-335COF.

abstract: Thesis

abstract: Master of Science (MS)


title: Toxicity of Cd, Cu, Pb, Ni, and Zn to Chironomids, and Trophic Transfer of Cd from Chironomids to Zebrafish

title: Toxicity of Metals to Chironomids, Cd Trophic Transfer from Chironomids to Zebrafish

contributor:
Gillis, P.L.
Wood, C.M.
Biology

subject:
toxicity
metals
chironomids
trophic transfer
cd
zebrafish

abstract:
The toxicity of the metals: Cd, Cu, Pb, Ni, and Zn to the freshwater aquatic larvae of the midge fly Chironomus riparius was investigated using 24 h waterborne exposures. Even at the most sensitive life stage, first instar, the chironomids were extremely metal tolerant, with LC50 values for all metals being orders of magnitudes above both the CCME Canadian water quality guidelines for the protection of aquatic life, and the USEP A Water Quality Criteria. This high tolerance of C. riparius to metal toxicity, combined with an exceptional ability to accumulate and tolerate high internal metal burdens makes the chironomid an ideal organism to use in studies on factors affecting the trophic transfer of Cd.
Zebrafish were fed with Cd-contaminated chironomids for 7 days, followed by 3 days of gut clearance with clean chironomids. Chironomids loaded with Cd by exposure to Cd-contaminated sediments exhibited a significantly higher trophic transfer efficiency (TTE) than did zebrafish 1 fed chironomids contaminated with Cd by waterborne exposure, although in both cases the TTE's were low (<2%). The majority ofCd transferred to zebrafish was stored in the gut and carcass, irrespective of ingestion of a natural diet (chironomids loaded with Cd), or a manufactured pellet diet of identical Cd concentrations. On a tissue concentration basis, the highest tissue accumulations in zebrafish were (in decreasing order): kidney> gut> liver> gill> carcass; this accumulation pattern w;ls also independent of concentration of Cd in the diet or of prey exposure route.
Subcellular fractionation of chironomids found most of the Cd in the metal rich
granule fraction followed by the organelle fraction. It also revealed that sediment exposed chironomids had significantly more Cd in the metallothionein-like protein fraction, and significantly less Cd in the cellular debris fraction than water-borne exposed chironomids, although these fractions accounted for only a small percent (~7%) of the total accumulated Cd. Despite this difference in prey subcellular fractionation, the subcellular storage of Cd in zebrafish fed on sediment-exposed chironomids and zebrafish fed on water-borne exposed chironomids was the same, with the highest accumulations in the organelles, enzymes, and metal rich granules fractions. Main areas of subcellular storage in zebrafish fed on a manufactured pellet food were identical to those ofzebrafish fed on chironomids. However, zebrafish fed on chironomids had significantly more Cd in the metallothionein-like protein fraction (5-10%) than did zebrafish fed on pellets :o%).
Overall, TTE's were independent of concentration, but were dependent on route of prey exposure. Tissue-specific accumulations and tissue-specific distributions in zebrafish were independent of both concentration and route of prey exposure, and the gut consistently accounted for the highest proportion of overall body burden, and had the highest accumulation of all tissues; verifying its importance in preventing the internalization of Cd. Subcellular distributions were also independent of concentration, although zebrafish fed a biological food (chironomids) had more Cd in the metallothionein-like protein fraction than zebrafish fed a manufactured food. This has biological implications for Cd detoxification.

abstract: Thesis

abstract: Candidate in Philosophy


title: Factors Affecting Macrophyte and Fish Distribution in Coastal Wetlands of Georgian Bay

title: Factors Affecting Georgian Bay Coastal Wetlands

subject:
macrophyte
fish distribution
Georgian Bay
coastal wetlands

abstract: Coastal wetlands of Georgian Bay have been virtually ignored by ecologists until recently, when these ecosystems were found to have exceptionally high biodiversity compared to other Gr,~at Lakes wetlands. To address this deficiency, we conducted a baseline survey (2002 to 2007) to determine the biotic and abiotic characteristics of 92 wetlands in 18 quatemary watersheds, using a suite of published ecological indices developed specifically for coastal wetlands (Water Quality Index (WQI); adjusted Wetland Macrophyte Index (WMiadj), and the Wetland Fish IndexBasinPAex (WFIBasinPAex)). Although a majority of the watersheds are located in remote eastern and northern parts of the Bay and therefore receive minimal human disturbance, one watershed, Sturgeon River, located in southern Georgian Bay receives relatively high urban, recreational and agricultural disturbance. Mean scores of WQI and WMiadj varied significantly across the watersheds, ranging from 0.48 to 2.15, and from 2.29 to 3.77, respectively. Mean WFIBasinPAex scores, however, were less variable and only ranged from 3.53 to 3.86. Of the 88 macrophyte species identified, the most common were hardstem bulrush. (Schoenoplectus acutus), water celery (Vallisneria americana), richardson's pondweed (Potamogeton richardsonii), slender waternymph (Najasjlexilis) and Canadian waterweed (Elodea canadensis). Six non-native macrophytes, Purple loosestrife (Lythrum wlicaria), narrow-leaf cattail (Typha angustifolia), hybrid cattail (Typha x glauca), Eurasian milfoil (Myriophyllum spicatum), curly pondweed (Potamogeton crispw) and frogbit (Hydrocharus morsus-ranae) were also recorded, the most common ofwhieh was Eurasian milfoil. Sago pondweed (Stuckenia pectinata), a native species that can be invasive, and is tolerant of poor water-quality, was present in about half of the watersheds. Ofthe 51 fish species, pumpkinseed (Lepomis gibbosus) bluntnose minnow (Pfmephales notatus), brown bullhead (Ameiurus nebulosus), rock bass (Ambloplites rupestris), and yellow perch (Percajlavescens) were the most widespread and abundant. Three non-native species, common carp (Cyprinus carpio), alewife (Alosa pesudoharengus), and round goby (Neogobius melanostomus) were present but not dominant. WMI scores were highly correlated with WQI scores, and as expected, wetlands in the most disturbed southern watershed were associated with the lowest WQI and WM[ scores, and had the greatest number of exotic species. However, WMI scores of wetlands in a few exposed sites located at the tip of the Bruce Peninsula were similarly low, even though these sites are not yet impacted by human activities. There was no significant relationship between WFIBasinPAand WQI scores, although the WFIBasin PA did not seem to be affected by exposure. We recommend that the WQI and WMiadj be used in long-term monitoring programs of Georgian Bay to track negative impacts of human disturbance on these valuable ecosystems.

abstract: Thesis

abstract: Master of Science (MS)


title: The In Vitro and In Vivo Effects of Alginate on Immune Response in Model Systems

subject:
in vitro
in vivo
alginate
immune response
model systems

abstract:
The use of polymeric biomaterials in regenerative medicine and drug delivery is a continually growing practice. Alginic acid (alginate) is widely used in these fields because of its beneficial properties from an engineering and mechanical perspective. Still, alginate has not yet been fully investigated from a biological perspective. For disciplines that anticipate in vivo use of their devices, it is crucial to understand the biological interactions between the device and the host.
In this project, the in vitro and in vivo immunological effects of alginate are examined in two model systems: one with a protein antigen and one with a xenogeneic cell antigen. The former system is used as a proof of principle study for alginate's immunological effect on simple protein-based systems, similar to those found in protein/drug deli very applications and certain types of vaccines. This model uses bovine serum albumin (BSA) as the protein antigen. The latter system is used to demonstrate alginate's effect on more complex antigens, such as whole cells. Thus, Chinese hamster ovary (CHO) cells are used as the as the cell antigen. This model represents a system that may be found in tissue engineering applications, where whole cells are delivered with a biomaterial scaffold.
Antibody production from blood serum indicated that alginate solution has adjuvant abilities while alginate microspheres do not. Thus, alginate solution possesses great potential in the field of vaccines. In addition, in vivo alginate challenges were found to have effects on second-set responses of splenocytes to in vitro alginate and antigen challenges. Splenocytes from alginate-injected mice were overall equally or less responsive to in vitro challenges than splenocytes without previous alginate immunization. Therefore, alginate solution may also have immunosuppressive effects, although the results from this project merely speculate on this possibility. Still, this ability would be helpful in overcoming current transplantation problems as well as certain tissue engineering hurdles.

abstract: Thesis

abstract: Master of Science (MS)


title: The Isotopic Composition of Sulphur in Meteorites and Sea Water Sulphates

title: Sulphur Isotopes in Meteorites and Sea Water Sulphates

contributor:
Thode, H. G.
Physics

subject:
isotopic composition
sulphur
meteorites
sea water sulphates
sulphate

abstract: The isotopic composition of meteorite sulphur and sea water sulphates was investigated by means of a simultaneous collection mass spectrometer. It was found that sixteen samples of meteorite sulphur possessed identical isotope abundances within the precision of the instrument. The sulphates from various depths in the Atlantic, Pacific and Arctic Oceans, were found to be enriched in s34 compared to the meteorite base level. The overall variation in s32/s34 content was 0.39 percent for the sea water samples.

abstract: Thesis

abstract: Master of Science (MS)


title: Molecular and Functional Characterization of the Mouse PEA3 Promoter

contributor:
Hassel, J.A.
Biochemistry

subject:
mouse pea3 promoter
molecular characterization

abstract:
PEA3 is a member of the expanding Ets family of transcription factors. In the adult mouse, PEA3 mRNA is expressed at highest levels in the brain, epididymis and at lower levels in the mammary gland, testes, ovary and uterus. PEA3 mRNA is expressed differentially during mouse embryogenesis and is down-regulated following retinoic acid induced differentiation in mouse embryonal carcinoma cell lines. PEA3 is overexpressed at the transcriptional level in 93% of all HER2/neu positive human breast tumors. The molecular basis for differential transcription of the PEA3 gene is not known. Sequence analysis revealed that the upstream region of the PEA3 gene has characteristics of a CpG island and does not possess a recognizable "TATA" element. Rapid amplification of 5' eDNA ends (5'RACE) reveals that transcription initiates from multiple sites, consistent with the absence of TATA elements. To localize cis-acting sequences required for PEA3 expression, deletions of the putative promoter were placed upstream of a luciferase reporter gene and tested for activity in the FM3A cell line. FM3A cells express substantial levels of PEA3 mRNA and protein, which suggests that all of the factors required for transcription are present in the cells. Transient transfections of 5' and 3' deletion mutants of the PEA3 promoter indicated that the efficiency of the PEA3 promoter depended on both negative and positive cis-elements, located upstream and downstream of the transcription start sites. A DNA fragment containing a region from -3 to +676, relative to the major start site of transcription, was sufficient for maximal promoter activity.
Luciferase reporter plasmids containing more 5' flanking sequence had lower activity indicating the presence of silencer elements. To aid the identification of critical sequence elements within the minimal PEA3 promoter, we cloned and sequenced the putative human PEA3 promoter. Comparison of the mouse and human PEA3 DNAs revealed that sequences required for maximal promoter activity in the mouse were highly conserved in the human gene. Furthermore, these conserved sequences corresponded to a variety of consensus binding sites: 6 Sp1, 8 c-ets-1, 3 PEA3, 3 AP-2, 3 MZF-1, 2 MyoD, 2 Ik-1, 2 c/EBPB, 2 oEF-1/USF, 2 HSFI and one of each of the following: AP-4, Ik-2, SRY, CP2, HEN-I, CREB andE47.

abstract: Thesis

abstract: Master of Science (MS)


title: Spectrochemical Analysis of the White Mountain Magma Series and Some Finnish Granites

title: Spectrochemical Analysis of White Mountain and Finnish Granitic Rocks

contributor:
Shaw, D. M.
Geology

subject:
spectrochemical analysis
white mountain
magma series
finnish granite

abstract: This paper presents the results of the spectrochemical analysis of a suite of rocks and rock minerals from the White Mountain magma series of New Hampshire and of some Finnish granites. The analysis elements are gallium, tin, lead, lithium, copper, and silver.

abstract: Thesis

abstract: Master of Science (MS)


title: Population Genetics of St. Lawrence Beluga Whales, Assessment of Inbreeding by DNA Fingerprinting and Assessment of Biopsy Darting Factors for Minimal Wounding and Effective Sample Retrieval

contributor:
White, Bradley N.
Biology

subject:
st. lawrence
beluga whales
interbreeding
population genetics
biopsy darting
dna fingerprinting
sample retrieval

abstract: The endangered St. Lawrence beluga (Delphinapterus leucas) population is not recovering from severe depletion despite its protected status over the past 20 years. DNA fingerprinting analysis of St. Lawrence beluga whales with three minisatellite probes (Jeffreys 33.6, 33.15 and Ml3) indicate a reduced level of genetic variability compared to Mackenzie Delta animals. The average band-sharing between individuals of the St. Lawrence beluga population for the three probes (0.534, 0.573, 0.478) was significantly higher than the average band-sharing of the Mackenzie Delta beluga population for the same probes (0.343, 0.424, 0.314). Higher levels of mean homozygosity in the isolated St. Lawrence belugas (0.33 vs 0.21) as well as a high degree of relatedness suggest that this population is inbred and that inbreeding depression is a factor in the lack of recovery of the St. Lawrence beluga population. Because sampling of some beluga populations may be biased, there is the need of alternative sampling procedures such as biopsy darting. To evaluate the impact of biopsy darting on beluga whales, different combinations of dart and stop sizes were tested on fresh beluga carcasses and the effect of different factors on the success of retrieval and the extent of wounding were evaluated. Tips with smaller diameters were more likely to retrieve a sample than those with larger diameters (p <0.05) and longer tips were also more likely to retrieve a sample than shorter tips (p < 0.10). The force of impact, a function of draw weight and distance, had a significant effect on the severity of wounding (p<0.05). The samples obtained from all biopsy darts tested yielded sufficient amounts of DNA for genetic analysis.

abstract: Thesis

abstract: Master of Science (MS)


title: The Mathematical Theory of Multicomponent Diffusion with Application to Transformations in the Iron-Rich Alloys of Iron-Manganese-Carbon

contributor:
Kirkaldy, J. S.
Physics

subject:
mathematical theory
multicomponent diffusion
transformation
application
iron-rich alloy
iron-manganese-carbon

abstract: A theoretical study reducing the general diffusion solution in a multicomponent system to an eigenvalue problem is carried out. Certain properties of the diffusion coefficient matrix are investigated. Special solutions are obtained tor a ternary finite diffusion couple and for a moving phase boundary in an infinite medium involving diffusion on both sides or the interface. The latter solution is used to study the kinetics of the growth of proeutectoid ferrite in ternary Fe-Mn-C austenite. Information on the iron-rich corner of the ternary Fe-Mn-C phase diagram in the temperature range from 725°C to 790°C has been obtained experimentally, and the diffusion coefficient of manganese in a-iron has been determined.

abstract: Thesis

abstract: Master of Science (MS)


title: The Role of Mismatched Repair in the Repair of DNA Damage Induced by Ultraviolet Radiation and Hydrogen Peroxide

title: MMR Genes in the Repair of DNA Damage Induced by UV and H2O2

contributor:
Rainbow, A.J.
Biology

subject:
mismatch repair
dna damage
ultraviolet radiation
hydrogen peroxide

abstract:
DNA mismatch repair (MMR) recognizes and repairs bases incorrectly incorporated during DNA replication. Germ line mutations in two MMR genes, namely hMSH2 and hMLHl, account for approximately 98% of hereditary non-polyposis colorectal cancers. There is conflicting evidence for the role of hMLHl and hMSH2 in the transcription-coupled repair (TCR) pathway of nucleotide excision repair (NER). Here we have examined the role of these MMR genes in NER using two reporter gene assays. AdHCMVlacZ is a replication-deficient recombinant adenovirus that expresses the B-galactosidase reporter gene under the control of the human cytomegalovirus (HCMV) immediate-early promoter. We have reported a reduced host cell reactivation (HCR) for B-galactosidase expression of UVC-irradiated AdHCMVlacZ in TCRdeficient Cockayne syndrome (CS) fibroblasts compared with normal fibroblasts, indicating that HCR depends, at least in part, on TCR. In addition, we have reported that UVC-enhanced expression of the undamaged reporter gene is induced at lower UVC fluences to cells and at higher levels after low UVC fluences in TCR-deficient compared with normal human fibroblasts, suggesting that persistent damage in active genes triggers increased activity f~om the HCMV-driven reporter construct. We have examined HCR and UV-enhanced expression of the reporter gene in hMLHl-deficient HCT116 human colon adenocarcinoma cells and HCT116-chr3 cells (the MMR-proficient counterpart of HCT116) as well as hMSH2-deficient LoVo human colon adenocarcinoma cells and their hMSH2-proficient counterpart SW 480 cells. We show a greater UV -enhanced expression of the undamaged reporter gene after low UVC exposure in HCT116 compared with HCT 116-chr3 cells ;md in Lo Vo compared with SW 480 cells. We show also a reduced HCR in HCT 116 compared with HCT 116-chr3 cells and in Lo Vo compared with SW 480 cells. However, the reduction in HCR was less or absent when cells were pretreated with UVC. These results suggest that detection of an involvement of hMLHl and hMSH2 in TCR is dependent on UVC (254 nm) fluence to cells.
We have also used these two reporter gene assays to examine the role of hMSH2 and hMLHl in the repair of oxidative DNA damage induced by UV A light (335-400 nm) and H20 2• UV A and H20 2 produce a number of oxidative lesions in DNA (such as 8hydroxyguanines and thymine glycols) that are repaired by the base excision repair (BER) pathway. \ve show a reduced HCR for B-galactosidase expression of UVAtreated AdHCMVlccZ in hMSH2-deficient LoVo human colon adenocarcinoma cells compared to their hMSH2-proficient counterpart SW480 cells, but not in hMLHl-deficient HCT116 human colon adenocarcinoma cells compared to the hMLHl-proficient HCT116-chr3 cells. We also show that pre-treatment of cells with UVA enhances reporter gene expression to higher levels and at lower UV A fluences in Lo Vo compared to SW480 cells but not in HCT116 compared to HCT116-chr3 cells. These results suggest an involvement of hMSH2 but not hMLHl in the repair of UVA-induced oxidative DNA damage. In contrast, no detectable differences were observed between SW480 and LoVo cells, as well as HCT116-chr3 compared to HCT116 cells, in both of the reporter gene assays that used H20 2 as the DNA damaging agent. Based on these results, these findings suggest that neither hMSH2 nor hMLHl play a significant role in the repair of oxidative damage induced by H202.

abstract: Thesis

abstract: Master of Science (MS)


title: Introductory Biology Laboratory Manuals

contributor:
Blizzard, A.C.
Wood, C.M.
Science

subject: introductory biology laboratory manuals, labratory manuals, introductory biology, biology laboratory, biology lab

abstract:
ABSTRACT
This project describes the development and evaluation of two
laboratory courses in First Year Biology, each of which is part of a
larger full-year course of instruction given by the Biology Department
at McMaster University. Introductory Human Physiology is prepared for
Physical Education students. Adaptation in the Biological World - a
general Biology course - is prepared for Natural Sciences students.
Design of the laboratory exercises utilizes a variety of
different educational models which are intended to stimulate the
students' interest in Biology. The exercises give students first-hand
experience with important principles and concepts related to the lecture
material.
This project stresses the role of the Teaching Assistants who
supervise activities in the laboratories and who demonstrate the basic
skills we expect students to learn.
Conclusions drawn from this project are:
1. The majority of students consider the laboratory courses to be
useful.
2. Educational goals established for the courses are being met.
3 • Change and improvement are important ongoing components of the
curriculum.
4. As funds become available, we must introduce more interesting
techniques and methodologies to the curriculum.
5. It is essential to maintain a high level of efficiency and
organization within the team of people associated with laboratories.

abstract: Thesis

abstract: Master of Science (Teaching)


title: The Half-Lives of Sr90 and Cs137

contributor:
Tomlinson, R. H.
Chemistry

subject: half lives

subject: Sr90

subject: Cs137

abstract: The half-lives of Sr90 and Cs137 were measured by the method of observing the disintegration rate rate of a known number of atoms. A 4(pi) proportional counter was designed and constructed to measure the absolute disintegration rates of the samples used. The efficiency of the counter was tested with calibrated radioactive solutions from the National Bureau of Standards. The submicrogram quantities of the carrier-free radioisotopes used for counting were determined with the mass spectrometer along with isotope dilution techniques. Independent evidence is given to support the half-lives found in this investigation.

abstract: Thesis

abstract: Master of Science (MS)


title: Egg-Laying Competition and Maternal Effects in a Plural-Breeding Joint-Nesting Bird

title: Maternal Effects in a Joint-Nesting Bird

contributor:
Quinn, James S.
Biology

subject:
egg-laying
maternal effects
plural-breeding
joint-nesting bird

abstract:
I investigated the maternal effects that take place in a joint-nesting bird: the
smooth-billed ani. Female anis were shown to respond to increasing group size by
increasing the number of eggs produced per capita, by tossing and burying more eggs per
capita, and by taking longer to reach the dedicated incubation phase. These results
support the hypothesis that females respond to increased egg laying competition by trying
to skew the contents of the final incubated clutch of eggs in their own favor.
I showed that in ani groups, yolk testosterone and estradiol deposited by females
in eggs increased from early- to late-laid eggs. Increases in yolk steroid levels over the
laying sequence may function to mitigate the disadvantage of being a later-hatched chick.
This maternal influence may not be a mere reflection of a female's hormonal status as
female plasma circulating levels of testosterone and estradiol did not vary in the same
direction as yolk hormone profiles.
I showed that yolk corticosterone levels, an indicator of maternal physiological
stress, increased with laying order in multi-female groups, but not in single-female
groups. Results suggest that laying females experience higher levels of stress in multifemale
groups. The above results suggest that communal life in anis generates
competition and egg production waste that likely reduces short-term per capita
reproductive benefits. Female anis can vary egg quality via deposition of hormones in eggs, and also lay eggs of different sizes. I showed that circulating plasma testosterone levels were higher in
nestlings with better begging abilities. Furthermore, nestlings hatched from eggs laid late
in the laying sequence had better begging abilities. These results suggest that testosterone
is an important controlling mechanism of begging behaviour, and that female testosterone
depositions in eggs rave long lasting effects on offspring development and behavior.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)