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Distribution of Radiation-Induced Defects in Quartz at the ACKIO Uranium Prospect, Athabasca Basin, Saskatchewan: Tracing Uranium-Bearing Fluids
Get PDFThis thesis presents the results of an electron paramagnetic resonance (EPR) spectroscopic study of quartz from the Baselode Energy Corp.’s ACKIO uranium prospect in the Athabasca Basin, northern Saskatchewan. The study included samples taken from both the Athabasca Supergroup sandstones and basement rocks from 16 diamond drillholes. Detailed EPR analyses revealed that quartz from both sandstones and basement rocks host a suite of silicon-vacancy hole centers, formed by the bombardment of alpha particles emitted from the radioactive decay of uranium, thorium, and their unstable daughter isotopes. The differences in EPR signal intensities of these hole centers indicate that quartz grains received different accumulative doses of alpha-particle irradiation in different locations within the ACKIO prospect. A three-dimensional distribution model of the EPR signal intensities of these radiation-induced defects in quartz has been constructed. This model shows that quartz in a mineralized sample has the highest EPR signal intensity due to the presence of disseminated uraninite. For quartz sampled away from uranium mineralization, the elevated EPR intensities of the silicon-vacancy hole centers most likely indicate a temporary source of radiation, such as ancient uranium-bearing fluids.
Along the sandstone-basement contact at the ACKIO project, the EPR signal intensities vary greatly and differ by approximately two orders of magnitude. Anomalously high EPR intensities recorded in fault gouges and brecciated areas suggest that these fractures served as the conduits for the migration of ancient uranium-bearing fluids and that there was limited migration of uranium-bearing fluids along the sandstone-basement contact at the ACKIO prospect. Moreover, the defined conduits for the migration of uranium-bearing fluids potentially point to new targets toward the south of the ACKIO area for further exploration. This thesis demonstrates the power of the systematic study of radiation-induced defects in quartz to reveal ancient pathways of uranium-bearing fluid vectors to explore potential mineralization targets
Contrasting Nitrogen Fertilization and Brassica napus (Canola) Variety Development Impact Recruitment of the Root-Associated Microbiome
Get PDF© 2023 The American Phytopathological SocietyPlant Phenotyping and Imaging Research Centre; the Canola Council of Canada, Alberta Canola, SaskCanola and Manitoba Canola Growers Association; and the Government of Canada under the Canadian Agricultural Partnership's AgriScience Program, a federal, provincial, territorial initiativePeer ReviewedCanola (Brassica napus) is an important broadacre crop, produced under high nitrogen (N) fertilizer application. Modern canola varieties are developed under high N rates but the impacts on root-associated microbiomes of different varieties are unknown. We studied eight canola varieties spanning historical Canadian spring canola development at two sites under high and low N fertility and characterized bacterial and fungal microbiomes in the root and rhizosphere using amplicon sequencing. Environmental conditions and the resulting canola varietal responses strongly affected the root-associated bacterial and fungal microbiomes. Microbes regulated by N fertility in each canola variety were mainly Gammaproteobacteria, Bacteroidia, Actinobacteria, Sordariomycetes, Dothideomycetes, and Agaricomycetes classes. Differentially abundant (DA) microbial taxa showed that N more strongly enriched bacteria in the roots and fungi in the rhizosphere. Each variety had its specific pattern of DA amplicon sequence variants (ASVs) responding to soil N availability, and the profile of DA-ASVs in paired canola varieties were also altered by soil N availability, especially bacteria in the rhizosphere. The yield was strongly associated with a subset of microbial taxa, mainly from Proteobacteria, Actinobacteriota, and Ascomycota. These variety-dependent responses to N and links to yield performance make the root-associated microbiome a promising target for improving the agronomic performance of canola by manipulating microorganisms tailored to soil fertility and plant genotype
Impacts of Short-Term Cover Cropping on Soil Microbial Communities and Biogeochemical Functions in Prairie Canada
Get PDFCover crops have the potential to confer numerous benefits to agricultural soils. Many ecosystem services derived from cover crops are underpinned by activities of soil microorganisms, while the cover crop acts as a catalyst. While the biological impacts of cover crops are relatively well understood in temperate agroecosystems, research in semi-arid environments is limited. My research addressed this knowledge gap by focusing on the impacts of cover cropping on biological indicators of soil health in semi-arid agroecosystems. I analyzed phospholipid fatty acid (PLFA) abundance and composition, and extracellular enzyme activity (EEA) in soils at three locations in the Canadian prairies: Saskatoon, Saskatchewan; and Carman and Glenlea, Manitoba. The study had eleven treatments at each site, comprising four-year rotations with and without cover crops, two-year rotations without cover crops, and a perennial alfalfa check, arranged in a randomized complete block design with four replicates per site. Cover crops were first grown in Saskatoon and Carman in 2018, and in 2019 in Glenlea. Surface soils were sampled in fall 2020, spring 2021, and summer 2021. I hypothesized that cover cropping would support a more active, abundant soil microbial community and impose changes in microbial community composition, leading to improved soil health compared to non-cover cropped treatments. The perennial alfalfa had higher fungal PLFA abundance and lower stress indicators compared to rotation treatments. Sampling time affected total PLFA abundance (p < 0.05) at all locations, and EEA measurements at nearly all sampling times and locations. However, specific impacts of seasonality differed between sites. The inclusion of cover crops did not affect PLFA abundance, microbial community composition, nor EEA activity. These findings suggest that biological indicators of soil health in the short-term are more impacted by factors aside from cover cropping, such as soil properties or climatic differences, and do not support the use of cover crops to enhance biological soil health in the short-term. These results may be partly due to the limited time cover crops had to establish sufficient biomass to induce effects on soil microbial communities. Longer-term studies may use these findings as a benchmark and should track changes attributable to cover cropping over a longer timeframe
DETERMINANTS OF COVID-19 SEVERITY AND OUTCOME AMONG NORTHERN SASKATCHEWAN FIRST NATIONS
Get PDFBackground: Severe acute respiratory syndrome due to Coronavirus-2 (SARS-CoV-2) remains a global public health concern. Demographic and medical factors like vaccination status have been reported to influence the disease burden and outcome. Indigenous populations have been reported to be disproportionately affected by COVID -19; however, the impact of COVID-19 on Indigenous people in Canada remains understudied. The objectives of the study are to: 1) describe the characteristics of COVID-19 cases among on-reserve northern Saskatchewan First Nations people for the period March 2020 to December 2022; and 2) determine the association of demographic and medical factors with various indicators of COVID-19 severity and outcomes.
Methods: We accessed de-identified data of 8,428 laboratory-confirmed COVID-19 cases during the period March 2020–December 2022. We conducted univariate, bivariate, and multivariate analyses to describe COVID-19 in this population and to determine the of association between various characteristics and COVID-19 severity. Characteristics of interest were demographic, clinical, and vaccine related. Three indicators of severity were included: hospitalization, admittance to an intensive care unit, and death.
Results: Even though they account for 12 months before onset of infection. Like in other studies, the presence of symptoms, and co-existing medical conditions were significantly associated with increased odds of hospitalization. The risk of dying from COVID-19 was higher in people >65 years, males, and those with co-existing medical conditions. The risk of dying from COVID-19
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was lowered following vaccination with two or more doses of COVID-19 vaccine when compared to those who received one dose of the vaccine or those who were not vaccinated.
Conclusion: The implication of this study finding is that prioritizing vulnerable populations during COVID-19 and in subsequent public health emergencies and providing them with relevant interventions will reduce the burden of disease among these groups of individuals
Twisted Higgs Bundles, Topological Recursion, and Quantum Curves
Get PDFThe focus of this thesis is on the interplay between Higgs bundles and topological recursion. Our interests lie in the relationship between quantum curves and the quantization of Hitchin spectral curves, and also the relationship between Eynard-Orantin differentials and the geometry of the Hitchin moduli space.
We give an overview of existing results in the literature on quantum curves, covering the necessary material to construct a quantum curve from a meromorphic SL(2, C)-Hitchin spectral curve. Starting from the quantum curve, we offer a new perspective on the quantization that includes the spectral correspondence and C∗-action. We view the quantization as a procedure that happens on the spectral curve, rather than the base. This idea frames quantization around the tautological section, rather than the Higgs field.
Previous works relating meromorphic Higgs bundles to topological recursion have considered non-singular models to allow the recursion to be done on a smooth Riemann surface. In this thesis, we start from an L-twisted Higgs bundle. By studying the deformation theory of the L-twisted moduli space, we interpret L as meromorphic data on a subbundle of an ordinary Higgs bundle. We encode this meromorphic data as a b-structure on the base Riemann surface and spectral curve. We then propose a so-called twisted recursion on the spectral curve, where the Eynard-Orantin differentials live in the twisted cotangent bundle. We show that the g = 0 twisted Eynard-Orantin differentials compute the Taylor expansion of the period matrix of a Hitchin spectral curve, mirroring a result for ordinary Higgs bundles and topological recursion. In particular, this shows that the geometry of the spectral curve is independent of the ambient space in which it resides
Future-proofing B.C.'s highways : climate scientists and engineers building relationships
No full textCanada First Research Excellence FundNon-Peer ReviewedExperience of a Global Water Futures researcher in collaborating in climate research with practitioners
Development of new IRE-activated pro-drug triggers for the treatment of pancreatic cancer, and new aza-BODIPY dyes
No full textThe abstract of this item is unavailable due to an embargo
Transparent Injection into Electron and Positron Accelerator Rings
No full textParticle accelerator rings utilize high energy particles for a broad range of scientific purposes. Synchrotron
light source facilities such as the Canadian Light Source (CLS) utilize radiation emitted by the acceleration
of electrons in an electromagnetic trap called a storage ring to investigate many topics including agricultural,
biomedical, and materials science problems. Particle colliders like the planned Future Circular Collider
electron-positron machine (FCC-ee) also store a beam of accelerated particles in a collider ring. The difference
is that the FCC-ee will also have a second beam traveling in the opposite direction. The two beams collide
at interaction points (IPs) which are observed using very precise detectors. Colliders study the fundamental
particles’ structure and test the standard model, one goal of FCC-ee is to intensely study the Higg’s boson[1].
In both machines the particle beams travel in very high vacuum to minimize scattering off gas particles.
However, the beams travel near the speed of light and traverse the nearly 100 km FCC-ee ring many thousands
of times, and the much smaller 171 m CLS ring millions of times, per second. Thus, particle losses are
non-negligible and beam current decays over time. In a light source the intensity of radiation provided to
experiments is important for the quality of their measurements. In a collider the key value is luminosity, a
measure of the rate of interactions between particles. Both these values depend on the beam current stored in
the rings and each machine benefits greatly from maintaining consistently high beam current. Thus, particles
are regularly injected into the rings to prevent the beam current from decaying, called top-up injection.
In order to store new particles in an accelerator ring, pulsed magnets are used to steer the additional
particles into the machine. These magnets disturb the beam stored in the ring resulting in oscillation of the
beam after each injection. The intensity of light CLS provides modulates as the electron beam moves relative
to experimental optics, affecting researcher’s data. Similarly, misalignment of the beams in a collider will
reduce the luminosity. Ideally, injection would be transparent to the experiments, not disturbing the stored
beam. In practice transparent injection does not completely remove the disturbance but minimizes it.
This thesis presents my work on transparent top-up injection for CLS and FCC-ee. For the CLS I had the
objective of finding alternative injection schemes which could be implemented into the current CLS machine,
and minimizing the post-injection transient oscillation of the stored beam. Simulation of several approaches
achieved a reduction of the magnitude of post-injection stored beam oscillation by a factor of 50. However,
the large size of the injected beam at the CLS meant that the injection efficiency was insufficient for the
alternative injection approach to be used in normal operations.
For FCC-ee my objectives were to develop magnet settings to allow for each of four proposed injection
approaches. Further, I studied injection with the novel multipole kicker magnet design proposed for FCC-ee.
Simulation of effects of the multipole kicker on the stored beam, and its sensitivity to misalignments and
other errors showed that there is risk for instabilities of the beam potentially resulting in significant losses.
These studies led to a recommendation for the baseline injection scheme as the FCC-ee project continues
Unraveling Acr-mediated Deactivation of CRISPR-Cas Systems: A Transformer Approach
No full textClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas)
serve as a formidable defense mechanism for bacteria against foreign DNA; on the other hand, some bacterio-
phages (phages) and mobile genetic elements have evolved anti-CRISPR (Acr) proteins to counteract CRISPR-
Cas systems and ensure their own survival. Because Acr proteins provide phages with a fitness advantage
relative to the bacteria that they infect, accurately identifying Acr proteins that inhibit CRISPR-Cas systems
has the potential to significantly and positively impact our ability to harness phages to fight antimicrobial
resistance. However, Acr identification is, at present, laborious and involves costly experimental procedures.
Existing computational tools for protein-protein interaction (PPI) are not designed to predict complex inhibi-
tion, which could be the collective result of multiple complex PPIs. In this study, we developed a transformer-
based deep neural network, AcrTransAct, to predict the likelihood of Acr-mediated CRISPR-Cas inhibition.
Our model comprises two main components: 1. a feature extraction module that incorporates a pre-trained
Evolutionary Scale Modeling (ESM) protein transformer and the NetSurfP-3.0 secondary structure predic-
tion system; 2. a classification module that consists of either a convolutional or recurrent neural network.
We created an inhibition dataset compiled from two Acr databases, AcrHub [69] and Anti-CRISPRdb [13],
and several published works [21, 48, 45, 36]. The AcrTransAct model is trained and tested on this dataset.
We achieved an accuracy of 95% and an F1 score of 0.95 in predicting the inhibition of I-C, I-E, and I-F
CRISPR-Cas systems by Acrs. We evaluate our classifier’s performance by using four different feature sets:
amino acid sequences, structural features, ESM features, and a combination of ESM and structural features.
Our work provides a valuable tool for predicting interactions between Acrs and CRISPR-Cas systems and
facilitates experimental Acr activity experiments by selecting the most likely Acr from many homologous
candidate proteins. Furthermore, we provide insights into the capabilities of transformer networks in biolog-
ical sequence analysis tasks, especially in the context of protein-protein interactions. A web application of
AcrTransAct (https://acrtransact.usask.ca) is implemented with the best-performing models from this
study to predict the probability of multiple CRISPR-Cas systems inhibited by a putative Acr protein. Our
code and data are available here: https://github.com/USask-BINFO/AcrTransAct