University of Saskatchewan Research Archive
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Making chemical sense of phase in soft X-ray spectroptychography
Get PDFNSERCPeer ReviewedSpectroptychography is being used to realize a significant improvement in the spatial resolution of x-ray spectromicroscopy, allowing chemical microanalysis at finer spatial scales. The chemical sensitivity of near edge X-ray absorption fine structure (NEXAFS) is familiar to most researchers who use x-ray spectromicroscopy for chemical microanalysis. However, the additional phase information available through ptychography provides additional and tantalizing data, and potentially additional chemical information. This paper explores the chemical information available in phase for a system of silicon dioxide nanospheres
TelA Promoted Telomere Resolution Features an Underwound Pre-cleavage Intermediate
Get PDFAgrobacterium tumefaciens and Borrelia species are two examples of prokaryotic organisms that have linear replicons, in contrast to most prokaryotes that have circular genomes. These organisms can replicate the lagging strand end of linear (deoxyribonucleic acid) DNAs without the loss of the DNA’s information due to the covalently closed DNA hairpin telomeres at the termini of the DNA. Replication of DNAs with hairpin telomeres produces a circular inverted repeat dimer with replicated telomere junctions. This intermediate cannot be segregated into two daughter cells without a two-step DNA breakage and rejoining process known as telomere resolution. Specialized enzymes known as telomere resolvases create hairpin telomeres from a dimeric replication intermediate through telomere resolution. Telomere resolvases share a similar mechanism to that of topoisomerase-IB and tyrosine recombinase enzymes. The proposed models for telomere resolution include a pre-cleavage intermediate where the base pairing between the scissile phosphates is broken helping to propel the reaction forwards. A class of variants was examined in previous studies on the borrelial telomere resolvase, ResT. These variants were inactive on parental substrates but were rescued by substrate alterations that mimicked DNA unwinding between the cleavage sites. In ResT, the catalytic domain and the hairpin-binding module cooperate to stabilize an underwound pre-cleavage intermediate. The idea that the telomere resolvase from Agrobacterium tumefaciens, TelA, and ResT follow the same reaction pathway was generated from the crystal-structure data of TelA, and the homology between ResT and TelA. We generated TelA variants homologous to those in ResT that stabilize the pre-cleavage intermediate. We also generated TelA variants of sidechains that were shown to interact with the hairpin turnarounds in TelA structures. Reaction analysis showed that the central two basepairs of the replicated telomere (rTel) junction are likely to be underwound and stabilized by TelA in a pre-cleavage intermediate. We also have evidence that the next two basepairs are also broken and likely have a base flipped out of the helix in the pre and post-cleavage intermediate. It is predicted that an underwound pre-cleavage intermediate drives the reaction forward and ensures reaction completion
Linking Soil Nitrogen Cycling and Plant Biotic Traits to Nitrogen Use Efficiency Parameters Among Diverse Canola (Brassica napus) Genotypes
Get PDFCanola (Brassica napus) is a dominant oilseed crop grown globally, second only to soybean. It requires relatively large amounts of nitrogen (N) fertilizer input compared to other oilseeds or cereal crops, but global estimates suggest that less than 50% of applied nitrogen (N) is recovered in canola seed harvest, indicating significant N-use inefficiencies. These inefficiencies contribute to resource overuse and waste, that can negatively impact the environment. There is significant variation in N-use efficiency (NUE) between crop genotypes, across different soil types and regions, and between different crop management systems. These factors make it challenging to implement strategies to improve NUE. Therefore, to create strategies to improve NUE, researchers must examine genotype (G) x environment (E) x crop management practices (M). Three studies employing varying combinations and degrees of G x E x M highlighted below-ground interactions (between soil properties, root phenology, and rhizosphere and root endosphere microbiomes) and above-ground plant traits (N uptake, N utilization, N partitioning, and seed protein) to determine relevant factors that contribute to canola productivity. This dissertation aims to link below-ground soil–plant–bacterial interactions to plant N uptake, remobilization, and partitioning that can improve canola harvest parameters such as yield, partial factor productivity (PFP), and NUE. Sixteen canola genotypes were grown on a Dark Brown Chernozem in Saskatchewan, Canada, with soil and plants sampled five times from 32-81 days after sowing (DAS), and seeds sampled at 81 DAS. Canola genotypes in this thesis exhibited different concentrations of below-ground soil parameters like moisture and NO3- -N; and genotypes with higher NUE and PFP were linked greater absorption of these soil parameters. Root morphology and rhizosphere and root microbiomes did not correlate with NUE or PFP. However, root surface area negatively correlated with soil NO3--N concentrations, suggesting that genotypes with larger absorptive surfaces acquired more soil mineral N. Rhizosphere bacterial diversity and community structure varied with changes in soil NH4+-N and pH, respectively, while root bacterial diversity and community structure varied with changes soil moisture and pH, and soil NO3--N, respectively. Plant-bacterial interactions likely shaped these microbiomes, making them distinct between genotypes
Wakefield Damping in a Distributed Coupling Linear Accelerator for the Compact Linear Collider
Get PDFParticle accelerators are made of series of metal coupled pillbox cavities. The dimensions of the cavities are tuned to resonate at a particular frequency when excited by radio frequency (RF) waves. This thesis studies a new accelerator design for the Compact Linear Collider (CLIC). The number of cells in a -mode standing wave (SW) accelerating structure for the CLIC project is limited by mode overlap with nearby modes. The distributed coupling scheme avoids mode overlap by treating each cell as independent. Designs of cells suitable for distributed coupling with strong wakefield damping have not previously been studied. In this thesis we develop a SW cell to be used in a distributed coupling structure that can satisfy the CLIC transverse wake potential limit. From the middle cell of the CLIC-G* travelling wave (TW) structure, we design a SW cell. We match the cell with a power coupler so the cell to be suitable for distributed coupling. To increase the wakefield damping of the cell in an ideal case where all extracted wakefields are damped outside the cell, we adjust the higher order mode (HOM) waveguide dimensions. We evaluate the effect of total wakefield reflections at the distribution network. We find a coupling power from a distribution network to the cell through the side of one of the HOM waveguides reduces the reflected wakefields to levels similar to the open boundary case. To increase the efficiency of a distributed coupling structure for CLIC, we add nose cones to the cell design and evaluate its high-gradient performance and wakefield damping properties. We evaluate the wakefield damping performance of combinations of coupler cells and normal cells which take advantage of cell-to-cell coupling. We find the wakefield damping performance of distributed coupling structures can be improved by forming triplet modules consisting of a coupler cell flanked by two normal cells. To account for the longer filling time of a SW structure, we calculate the RF pulsed heating of a structure made of our designed cell. We compare the performance of distributed coupling structures operating at room and cryogenic temperatures when fed by different power sources
Translating hydrology research into practice: A Canadian Perspective
Get PDFEGU23-4485
https://doi.org/10.5194/egusphere-egu23-4485
EGU General Assembly 2023
© Author(s) 2023. This work is distributed under the Creative Commons Attribution 4.0 License.Peer ReviewedHydrology research is regarded as vital for advancing human development and environmental conservation through improved hydrological process understanding and by devising solutions to address water management challenges. This is particularly acute in a time of global change and the need to find pathways to water sustainability. Success for research in hydrology is often measured through quantitative research outputs, such as the number of journal publications, citation indices, number of students trained, patents, and external research funding. User involvement in the research and development process is rarely considered a metric for success in hydrology. Despite successful scientific or engineering advancements, a greater scientific understanding of hydrology and ever-increasing publications, much of the research has limited uptake by practitioners and implementation into practice, leading to a growing gap between research and practice. This lack of utilisation is not due to a lack of need by users, but rather is a symptom of the disconnect between these advances and research that would most add value to practitioners and their application needs. We explore some outstanding challenges in translating academic research into practice and make some recommendations to bridge the increasing gaps between research and practice through a transdisciplinary approach, user engagement metrics in funded research and strong knowledge mobilization. We also discuss the success and challenges of these approaches in the Global Water Futures program along with lessons learned
Density-dependent habitat selection of plains bison in Grasslands National Park
Get PDFHabitat selection models are commonly used to inform species conservation and management decisions; however, such models are context dependent, and results may vary depending on how close a population is to the carrying capacity. Despite acknowledgment that habitat selection is density dependent, relatively few researchers account in their analyses for changes in population density over time. Using a long-term dataset (11 years) for GPS-tracked Plains Bison (Bison bison) at Grasslands National Park, Saskatchewan, Canada (n = 22), I examined seasonal habitat selection during a period of natural population growth following reintroduction and a period of population size manipulations. I used resource selection function (RSF) and latent selection difference function (LSD) analyses to model interactions between selection for vegetation productivity and distance from roads and population density. Bison showed decreased avoidance of roads as density increased and increased avoidance of roads following reductions in population density at most spatio-temporal scales examined. The relationship between selection for vegetation productivity and density was highly seasonally variable: bison selected for abundant forage when density was low and became less selective at high density during and immediately after calving. Consistent with predictions of density-dependent habitat selection, bison were free to select for abundant forage in areas far from human activity when density was low and were required to become less selective as density increased during seasons when the herd is most vulnerable and nutritional requirements are high. My study highlights the importance of considering changes in population density when using habitat selection models to inform decisions on wildlife population management
Biochar and Ash Amendments to Improve Soil Phosphorus Fertility, Water Relations and Retention
Get PDFBiochar and ash, both as separate products and including ash as a component of biochar, are produced as by-products from thermochemical decomposition and bio-energy generation processes such as combustion, gasification, or pyrolysis. The addition of biochar to improve nutrient uptake and retention has been studied in various settings and with a variety of crops. However, biochar, when applied without other treatments, has often been found to have limited impact on crop yields in Canadian prairie soils. This study aimed to determine the effects of biochar amendments, with and without added phosphorus fertilizer, on soils and crops in the Canadian prairies as related to crop yield, phosphorus uptake and recovery, soil phosphorus retention, water dynamics and phosphorus loss in leachate and runoff. This thesis reports on studies undertaken in 2022 with biochar and phosphorus fertilizer amendments on nutrient poor soils from the brown and black soil zones in southern Saskatchewan (controlled environment study) and from the brown soil zone at a site near Central Butte, Saskatchewan (field study). Under optimal conditions of the growth chamber, biochar derived from canola hull, manure and willow feedstocks were shown to contribute some available P for plant uptake, with observed recovery of applied biochar P being at best about 50% of Triple Superphosphate fertilizer. The biochars increased residual P in soil in both chamber and field depending on feedstock, with manure and willow biochars as well as the meat and bonemeal ash being the most effective, but the effects of biochar amendments on crop yield were variable, leading to the conclusion that the effects are at least partly related to the biochar feedstock and production conditions, as has been shown in many other studies on biochar. An important benefit of biochar amendment observed in the study was increased phosphorus retention in soil that contributed to increased post-harvest labile P as well as reduced leaching and snowmelt runoff export. To a lesser extent the biochars contributed to increased water holding capacity and water infiltration. The results of this study indicate that biochars and ash can potentially benefit canola and wheat production, by enhancing P nutrition and recovery, and that a balance may be obtained between biochar supplying P during the growing season while at the end of the season reducing P loss in the spring snowmelt runoff or during leaching events. Biochar added at 10 tonnes per ha showed the best performance in terms of agricultural improvement potential under both controlled environment and field conditions when applied to brown and black chernozem soils from southern Saskatchewan
Probing Matter with Photons, Electrons and Neutrons: A Study of Water and Flax
No full textScattering is a vital mechanism through which we interact with the world. This thesis utilizes various
scattering methods to probe the formation of ice structures and interactions between flax based peptides
and gold nanoparticles. The topics covered in this work differ greatly, however the approaches taken to
investigate the respective systems employ the same concepts of scattering. Scattering provides a basis for
the investigation of both water and the flax based semiconducting material. Structural investigations of ice
employing primarily elastic scattering methods supplemented by inelastic scattering methods. Electronic
structure investigations of the flax based semiconductor employed in elastic scattering methods, with the
absorption of visible light also interpreted through the lens of inelastic scattering.
Crystalline phases are typically plotted in phase diagrams with pressure and temperature dependence,
to denote the stability regions of the different structures. Meta-stable regions relating to transformation
and nucleation require further investigation and are often overlooked in these diagrams. Transformation
between adjacent phases portrayed in two dimensions depends on the path taken to achieve the transition.
This is evident in the recent discourse on ice Ih transformations where one can either observe crystal-crystal
transitions, or an intermediate amorphous phase in ice Ih transformation. Dependence on compression rate
and temperature play an important role in the mechanism of ice transformation. Standard clathrate hydrate
stability relations, between pressure and temperature, imply various clathrates are unlikely to form under
high vacuum. However, with appropriate mixtures and heating rates, several improbable hydrates have been
formed. Understanding the mechanism of formation is vital to the study of water mixtures in interstellar
environments.
Solar power is a possible solution to the growing problem of pollution. Conventional solar cells rely
on crystalline inorganic materials to absorb sunlight. Advances in organic semiconducting technology and
nano-fabrication open new avenues for energy production. Here, bio-organic molecules (Linusorbs) derived
from flax seed oil are combined with plasmonic photon absorption in an effort to convert light to electrical
power. Devices fabricated exhibited light absorbing properties however power conversion was limited, with
hysteresis observed while testing under illumination. Further investigation probed the binding interaction of
the peptides and nanoparticles, through insights into the binding angle of the peptide and gold surface.
Employing a combination of elastic and inelastic scattering methods structural transformations in water
and electronic structure of flax based semiconductor were investigated. These studies have very different
applications but are tied together through the methods employed for investigation. Scattering methods can
be used to investigate a wide range of parameters in a variety of systems. This thesis shows a small subset
of possible scattering methods available
An Underlying Perplexity
Get PDFAn underlying perplexity is a celebration of human beings’ inability to comprehend reality, a celebratory gesture for our confusion. Whether in this text or the two parts of my exhibition, I have humbly tried to position myself where I need to be. If I were to seek an affect within the pieces of my show, it would be nothing but showing empathy and care for those who are lost, marginalized, isolated, or sick.1 This show and this text are my way of communicating with the outside world, including layers of depression and social anxiety. Through wondering around human beings’ existential struggles, I have hoped to address social, political, inter/intrapersonal miscommunication, mental health issues, and the mechanisms of power and justice. While much of my research focuses on drawing attention to these problems in detail, my creative practice aims to demonstrate my significant care for and empathy towards those who have been suppressed by these notions, in hopes to ultimately create simple pathways for micro- solutions. That being said, this body of works also contain a certain level of the ugly truth, an honest and exposing gesture for those who are ignorant of reality, invoking inner conversations and a critical view of their beguiling experiences
Blackberry Dreams : Modelling water vapour’s role in climate change
Get PDFCanada First Research Excellence FundA group of young modelers collaborate to simulate an alternate Planet Earth