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Subgenome Inference in polyploids: Insights from Synteny-based Linkage
No full textPolyploidy is a common occurrence in flowering plants, where whole genome duplication or triplication
events result in additional sets of chromosomes (or subgenomes). Almost all flowering plants have undergone at
least one polyploid event, with some experiencing multiple events since their ancestral angiosperm. Polyploidy
leads to subgenomes with redundant gene copies that are rapidly lost through gene fractionation. Synteny
blocks can aid in inferring the evolutionary footprint of the genomes. However, assigning synteny blocks
to different subgenomes representing subsets of the organism’s genome is challenging due to recurring
polyploidization and fractionation events. These events complicate the situation by scrambling gene order on
a background of evolutionary processes such as gene family expansion, gene loss, and genome rearrangement.
Existing methods for subgenome identification require manually organizing genes into subgenomes, which is
laborious, prone to error, and requires expertise. To the best of our knowledge, an automated subgenome
reconstruction method does not exist. To address this challenge, we developed the SyntenyLink algorithm
that automatically reconstructs subgenomes from synteny blocks. The algorithm considers differences shown
in substitution and fractionation patterns in synteny blocks, as well as continuity of conserved order of
genes to reconstruct the most parsimonious subgenomes. The algorithm first utilizes the BLASTP and
DAGchainer programs to identify synteny blocks across different chromosomes of two related genomes. It then
organizes the blocks into subgenomes using depth-first search on a weighted graph where the vertices in the
graph represent super synteny blocks identified by translocation breakpoints. The graph edges are weighted
using the combined information of percent identity, block chain, and gene density between the two vertices
connected by the edge. The algorithm then minimizes the number of translocation events by using a maximum
neighborhood method. The SyntenyLink algorithm was validated using published subgenomes of Brassica
rapa, Brassica oleracea, Brassica nigra and manually curated subgenomes of Brassica napus, and Sinapis
alba. The results provide compelling evidence for the efficacy of the SyntenyLink algorithm in accurately
reconstructing subgenomes. The algorithm demonstrated favorable accuracy in placing genes to subgenomes
overall, especially with subgenome1, which achieved accuracy of 87% in B. rapa, 80% in B. oleracea, 79% in
B. nigra, 83% in B. napus and 86% in S. alba. The results revealed relatively lower accuracy (60% to 85%)
for subgenome2 and subgenome3 in all five species, largely due to the highly similar fractionation patterns
exhibited in these two subgenomes and the wide-spread segmental gene duplications, posing a challenge in
accurately distinguishing genes belonging to each. SyntenyLink was then applied to separate the subgenomes
of two Brassica species, Brassica juncea and Brassica carinata. This algorithm represents a promising tool for
reconstructing subgenomes from complex polyploid genomes, with far-reaching implications for the study of
the evolutionary history of flowering plants and other polyploid organisms
Development of Flax- and Hemp-based Polylactic Acid Films for Bioplastic Applications
No full textPlastic, widely used for packaging fresh food, poses environmental risks. It threatens marine and terrestrial ecosystems, while also contributing to global greenhouse gas emissions. To tackle this problem, bioplastics has emerged as a promising alternative to traditional plastics. Bioplastics, such as polylactic acid (PLA), offer advantages like wide availability, cost- effectiveness, and non-reliance on petroleum. PLA is non-toxic, biodegradable, strong, and has excellent film-forming properties, making it suitable for single-use applications like food packaging. Bioplastics holds promise, but sustainable raw material sources are necessary. Saskatchewan's crop production yields agricultural biomass, like flax straw, which can enhance the province's agriculture industry. While hemp is increasingly grown in Saskatchewan, its biomass quality may not meet high-quality fiber production standards. The utilization of excess agricultural by-products in composites remains unexplored, with limited studies on agricultural waste utilization for composite creation.
In this work, the effects of particle size, loading and treatment (alkali and acetylation) of biomass fillers on the mechanical, moisture absorption, vapor barrier, and surface wettability characteristics of the flax and hemp-based PLA films have been studied. The study emphasizes the importance of optimizing the particle size, treatment, and loading of fillers to achieve desirable properties for specific applications. This study has explored the addition of alkali and acetylation treated fillers of particle sizes <75 μm and 149-210 μm to the PLA films and compared the properties of the treated films with untreated ones. The addition of untreated flax fillers did not improve the tensile strength and elongation at break of flax bioplastic, and Young's modulus decreased as the filler loading increased. However, alkali-treated flax fillers showed an improvement in tensile strength at 2.5% and 5% loading. Acetylation treatment improved elongation at break at lower loading percentages but became less effective as the percentage of filler loading increased. The addition of flax fillers, whether untreated or alkali- treated, resulted in a decrease in tensile strength and Young's modulus. However, at 2.5% and 5% filler loadings, both untreated and alkali-treated fillers increased the elongation at break of the films. For hemp fillers, the tensile strength and elongation at break decreased with an increase in filler content for particle sizes smaller than 75 μm. However, Young's modulus increased by 10% loading and then started decreasing. For hemp fillers of particle size 149- 210 μm, the tensile strength and Young's modulus decreased at all filler loadings, while the elongation at break increased until 5% loading and then started reducing. These trends can beattributed to factors such as changes in crystallinity, interfacial adhesion, and the presence of defects. The addition of fillers to bioplastics increased moisture absorption and water vapor permeability (WVP), with a more pronounced effect observed in untreated fillers compared to treated ones. The water contact angle of the films decreased as the filler content increased for both particle sizes. However, the decrease in water contact angle was more prominent for untreated fillers compared to treated ones.
The balance between the ability of the filler particles to fill gaps between polymer chains and the formation of a more porous structure as loading percentage increases should be carefully considered when selecting bioplastics for specific applications. Therefore, it is essential to consider several factors such as particle size, treatment, and loading of the filler and their interaction while designing bioplastics with tailored properties for various applications
The EphB4 receptor tyrosine kinase: a comparative study of the expression and function in canine and human osteosarcoma
No full textThe abstract of this item is unavailable due to an embargo
On His Majesty’s Honour: The Nature of the Crown in Indigenous Relations
Get PDFThe Crown is an essential component in our constitutional order and without understanding its honour the project of reconciliation will falter. Political considerations around a rights-based dialogue have proven to be less effective than hoped. A return to the duty-based and orthodox discourse of the honour of the Crown can provide important insights to strengthen the relationship between the Crown and Indigenous peoples.
The modern doctrine of the honour of the Crown is marked by a revitalization of a feudal conception of the Crown. This conception has been employed to execute the constitutional imperative of reconciliation with Indigenous peoples in Canada through the judicial process. This doctrine forms the core of the judicial system’s effort to resolve issues with the integration of Indigenous peoples and cultures into a liberal society, but it has been misunderstood in problematic ways such as with the creation of sui generis rights for a specific subset of the population based on ethnicity. A fulsome understanding of the honour of the Crown yields the conclusion that such sui generis rights should be abandoned entirely.
The honour of the Crown provides insight to the Court’s duty to balance the interests of Indigenous people—as guaranteed through the enactment of s. 35 of the 1982 Constitution Act—and the interests of not only non-Aboriginal persons, but also the Crown-as-state. With a greater appreciation and exploration, the honour of the Crown can serve as a bedrock of Crown-Indigenous relations into the future and provide a lens based on historical doctrine to change the perspective of actors and further the project of reconciliation
HYDROGEOLOGY OF THE INTERMEDIATE ZONE BETWEEN DEEPER ANTHROPOGENIC ACTIVITIES AND SHALLOW AQUIFERS IN SASKATCHEWAN
Get PDFLarge volumes of often saline formation water are both produced from and injected into sedimentary basins as a by-product of oil and gas production. In Saskatchewan the prominent disposal zone is the Mannville Group and despite this, the distribution and interactions of these waters have not been studied in detail, and the effects of long-term water injection on reservoir pressures and groundwater quality remain uncertain. Even where injection and production volumes are equal at the basin scale, local changes in hydraulic head can occur due to the distribution of production and injection wells.
The changes in hydraulic head caused by this injection of fluids are important in understanding the potential to act as a driver of saline fluid flow, possibly leading to contamination of overlying potable groundwater resources where high permeability pathways or leaky abandoned wells are present. Across the Western Canada Sedimentary Basin's (WCSBs) Mannville Group, approximately 250,000,000 m3 of excess water has been injected into the Group. This study evaluates the effects of injection wells on deep groundwater resources by examining wells within the Intermediate Zone of the WCSB. Hydraulic head maps were created for each aquifer within the Intermediate Zone, as well as maps of the difference between aquifer hydraulic heads. By comparing maps detailing the difference in hydraulic head, it was possible to locate areas where there is the potential for waters to migrate upwards through natural pathways or leaky wells. The potential for significant upward migration through natural pathways was deemed low due to the presence of low permeability shales in the Intermediate Zone of the study area, but leaky wells pose a bigger problem. As the leaky well becomes further away from the injection well this problem is not as severe but still poses a problem for freshwater aquifers
What Emergency Sales Tell Us About Home-Based Businesses
No full textHome-Based Businesses (HBBs) represent an emerging but understudied area of e-commerce and entrepreneurship. HBBs in this study’s context design and/or create the products that they sell and make their online business distinct by capitalizing on the “real” person behind the social media posts. HBBs further depart from traditional small businesses in their use of “emergency sales” which are designed to cover unexpected personal expenses (i.e. vet bills, car repairs, etc.) and are transparently advertised as such. Using grounded theory, this qualitative study aims to explore the unique operations of HBBs and what leads them to engage in emergency sales in order to create a foundational theory for future research in this area of study
The school food environment and elementary students’ food and nutrition-related knowledge, attitudes, and practices in Saskatoon, Saskatchewan
Get PDFBackground: Globally, close to three-quarters of children get lunch at school. In Canada, regional or provincial systems exist to provide some school snack and meal programs, although there is little consistency among them. Research indicates that home-packed foods are likely to be lower in nutritional value than school-provided meals.
Purpose: The purpose of this study is to assess the school food environment and the frequency of consumption of different food and drinks by children during school hours, as well as the knowledge, attitudes, and practices of school children on food and nutrition.
Methods: Four elementary schools were selected for this study by the Saskatoon Public School Division from among those that currently have small lunch programs. A self-administered online questionnaire was used to collect data during class time with students in grades 4-6, with teachers and research personnel on hand to address any questions. A total of 185 elementary school children participated in the survey. In addition, 94 staff surveys were collected to supplement the children’s information to examine aspects of the food environment available in the schools.
Results: Among the students, 54.5% declared their gender as male and 74.7% reported being born in Canada. Approximately 46.7% and 46.2% of students reported school-day daily consumption of fruits and vegetables and dairy products/dairy alternatives, respectively. Thirty-four percent of respondents reported daily school hours consumption of sweets and sweetened beverages, and 31% consumed meat and meat alternatives. Results show that 38.2% of the student participants reported food insecurity. Children who self-reported as Asian, Arab, and African consumed 7.16 times more often meat and meat alternatives than First Nations, Inuit, and Métis children (CI: 1.33-38.60). Students who reported being born outside Canada consumed snack foods and desserts more frequently than those born in Canada (OR: 2.81, CI:1.05-7.55). Male students were significantly less likely to report school hours sugar and sweetened beverages consumption compared to females (OR: 0.42, CI: 0.18-0.98), and food-secure children consumed unhealthy beverages less frequently compared to food-insecure children (OR: 0.40, CI: 0.17-0.94). From the staff surveys, results showed that “healthy food support” was the most developed food environment domain in the two schools, while composting was the least developed domain.
Conclusion: Implementation of a universal, curriculum-integrated, healthy school lunch program may enhance the school food environment and the school hours diet quality of children. In addition, it may improve elementary students’ food and nutrition-related knowledge, attitudes, and practices
Influence of Chronic Adenosine A1 Receptor Stimulation on α-Synucleinopathy and Neurodegeneration Studied with In Vitro, In Silico, and In Vivo Approaches
No full textThe abstract of this item is unavailable due to an embargo
Study of the electron density in the high latitude ionosphere with incoherent scatter radars and Swarm satellites
Get PDFDespite century-long efforts in assessing the electron density distribution in the Earth’s ionosphere
and significant progress in identification of its major features, there are still many uncertainties
with respect to the solar cycle’s seasonal and diurnal trends at various latitudes. Knowledge of
these variations is needed for robust forecasting of the state of the ionosphere for the operation of
practical radio systems, for example communication via high frequency radio waves.
This thesis utilizes data from the incoherent scatter radar (ISR) at Poker Flat (Alaska, USA)
to assess the diurnal and seasonal variations of three parameters of the ionospheric F2 region, the
peak density, the height of the peak, and the thickness of the layer. These parameters are assessed
for relatively high solar activity in 2014, and relatively low solar activity in 2016. Daytime electron
densities were found to be largest during winter and spring and nighttime electron densities were
found to be smallest in winter. Electron densities during the higher solar activity year were found
to be greater than those during the lower solar activity year by a factor of 2-5, depending on the
time of day, as expected. Details of the diurnal variations in electron density for various seasons
are further discussed.
ISR electron density data are also used for the validation of electron density measurements
from Langmuir probes onboard the Swarm satellites in the topside ionosphere (~500 km). This
work is an expansion of previous studies that use a different mode of ISR operation and a different
approach to both ISR and Swarm satellite data handling. In addition to observations over Poker
Flat (geographic latitude of ~60° N), observations over Resolute Bay, Canada at extreme high
latitudes of ~80° are also considered. It is shown that, overall, the ratio of Swarm electron density
measurements to those measured by ISRs is ~0.5-0.6 and that smaller ratios are observed at larger
electron densities, usually during the daytime. At low electron densities less than 3∙1010 m-3
, the
ratios are typically greater than 1, indicating an overestimation effect. The overestimation effect is
stronger at night and at higher altitude. It is also more evident during lower solar activity when the
electron density in the topside ionosphere is smaller. The conclusions on the electron density
underestimation and overestimation by the Swarm Langmuir probes are overall consistent with
previous reports, but this thesis confirms that these effects also occur at high latitudes
Epidemiology of Hoof-Related Lameness in Western Canadian Feedlot Cattle
Get PDFThe research objectives were to: 1.) To describe the epidemiology of hoof-related lameness (HRL) in western Canadian feedlots (Chapter 2) with additional focus on digital dermatitis (DD) (Chapter 3), and 2.) To analyze risk factors, at the animal-level (Chapters 2 and 3) and feedlot-level (Chapter 3) for associations with HRL and DD, and 3.) To inform recommendations for future research on the control and prevention of HRL (Chapter 2) and DD (Chapter 3). The indi-vidual animal health data included records for 1,772,565 cattle from 28 western Canadian feed-lots (2014-2018, inclusive). The case-control study in Chapter 3 segregated those same 28 feed-lots into DD case (n = 14) or DD control feedlots (n = 14), based on one or more DD cases being diagnosed (2014-2018). All data were accessed through a proprietary feedlot animal health data-base and analyzed using commercially available software.
In chapter 2, lameness accounted for 28.52% of disease diagnoses, 71.80% of which were HRL cases, representing 20.64% of disease diagnoses. The incidence risk of first lifetime HRL diagnoses ranged from 1.94% to 3.07% of the population, annually. The HRL diseases focused on were foot rot (FR); DD; and toe tip necrosis syndrome (TTNS), accounting for 90.40%, 7.52% and 2.08% of HRL cases, respectively. Foot rot occurred at a constant rate throughout the feeding period by days on feed (DOF), with some variability in cases coinciding with season. Less than 10% of DD occurred before 80 DOF with 90% cases occurring by 300 DOF. Over 50% of TTNS cases occurred within the first 50 DOF and coincided with seasonal feedlot popu-lation increases during the fall placement season.
For the individual animal-level analysis of chapter 2, cattle placed in small capacity feedlots (SCF), regardless of age class or acquisition source, were higher risk for HRL development than cattle placed in large capacity feedlots (LCF). The largest effect was observed in ranch-direct (RD) yearlings whose HRL risk was 4.23 times (95% CI 1.48 to 12.07, P = 0.007) higher when placed in SCF versus placement in LCF. This may be related to increased pull rates in SCF due to smaller populations and increased time allotment for identifying and treating cattle, however, the identification of the risk factors driving this difference still need to be identified.
For cattle from RD-sources placed in LCF and cattle from AM-sources placed in LCF, the risk of developing HRL was 2.21 (95% CI 1.23 to 4.00, P = 0.010) and 1.45 (95% CI 1.25 to 1.68, P < 0.001) times in calves higher than yearlings, respectively. Conversely, for cattle from AM-sources placed in SCF, calves were lower risk than yearlings (RR = 0.68, 95% CI 0.52 to 0.91, P = 0.008). Future research should focus on evaluating management-level differences, such as frequency of rehandling and acquisition source, between calves and yearlings and their poten-tial associations with HRL.
Confined background (CB)-sourced yearlings, placed in LCF were 7.21 (95% CI 4.46 to 11.64, P < 0.001), 2.54 (95% CI 2.12 to 3.06, P < 0.001) and 1.79 (95% CI 1.13 to 2.85, P < 0.001) times higher risk for HRL development than yearling cattle placed in LCF and sourced from RD, AM and grass cattle (GC), respectively. It is speculated that high levels of commin-gling increase the likelihood of HRL introduction, and confinement in potentially poor pen con-ditions may predispose CB-sourced cattle to poor hoof integrity. Yearlings from GC-sources placed in LCF were 4.02 (95% CI 2.13 to 7.58; P < 0.001) times higher risk than RD-sourced yearlings placed in LCF. Ranch direct-sourced calves placed in LCF (RR = 0.54, 95% CI 0.37 to 0.79, P = 0.002) and RD-sourced yearlings placed in LCF (RR = 0.35, 95% CI 0.22 to 0.56, P = < 0.001) were lower risk for HRL versus their age class counterparts placed in LCF and sourced from AM, respectively. It is speculated, similarly to CB sources, that increased commingling of unknown cattle in GC and AM sources increases the likelihood of HRL introduction into the population.
In Chapter 3, the RR of DD in females was 4.98 (95% CI 2.97 to 8.33, P < 0.001), 2.79, (95% CI 1.54 to 5.05, P < 0.001) and 1.85 (95% CI 1.16 to 2.95, P = 0.009) times higher than males in high morbidity (HighMorb) years, medium morbidity (MediumMorb) years, and low morbidity (LowMorb) years, respectively. Future research should focus on determining if this is a result of differences in physical characteristics, or the management of males and females. Com-pared to AM cattle, the risk of developing DD was greater in cattle sourced from CB (RR = 2.63, 95% CI 1.92 to 3.59, P < 0.0001) and GC (RR = 2.00, 95% CI 1.18 to 3.39, P = 0.010), but lower in RD (RR = 0.04, 95% CI 0.01 to 0.10, P < 0.001). It is speculated here that in-creased commingling may introduce DD into the population. Cattle placed in quarter (Qtr) 1 (RR = 1.66, 95% CI 1.06 to 2.60, P = 0.027) and cattle placed in Qtr2/Qtr3 (RR = 2.28, 95% CI 1.48 to 3.52, P < 0.001) were higher risk for DD than cattle placed in Qtr4. These results are likely due to fluctuations in pen conditions during the spring and summer months.
The relative risk of DD development was lower for cattle in SCF compared to LCF (RR = 0.24, P = 0.027). At the feedlot level, SCF were at a lower risk of having a confirmed case of DD than LCF (RR = 0.24, 95% CI = 0.05 to 0.76 P = 0.027). For both results, it is speculated that LCF acquire cattle from a wider variety of sources than SCF. This increased variation in sources reflects an increase in commingling of unknown cattle and increased potential for novel diseases, such as DD, to be introduced into the population.
Acquisition source, sex, and age class at the animal-level, as well as feedlot population size, both at the animal and feedlot level, play important roles in the development and incidence risk of HRL and DD in western Canadian feedlots. Additional research is recommended to broaden the knowledge base concerning HRL and DD, and to provide insights regarding management tools for the control and prevention of lameness in feedlots