OPUS: Open Ulethbridge Scholarship

Open ULeth Scholarship (OPUS) is the University of Lethbridge's open access research repository. It contains a collection of materials related to research and teaching produced by the academic community.

Self-archiving your research in OPUS is one way to meet Open Access policies of granting agencies. It is important to retain your final, post-peer-reviewed drafts for submission to OPUS, as this is often the only version publishers will allow to be archived. Click here for information on the U of L Open Access Policy.

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Recent Submissions

The Blood song winter count: a cycle of musical compositions interpreted through the perspective of Blackfoot ritual and Indigenous storywork
(Lethbridge, Alta. : University of Lethbridge, Dept. of Music, 2023) Day Rider, Sonny-Ray; University of Lethbridge. Faculty of Fine Arts; Schultz, Arlan
The Blood Song Winter Count, is a collection of five (5) musical works that collectively function as sonic symbols which document my personal experience of grief and loss. These works function as ritualized emotional “time capsules” of my lived experience and are interpreted through my Indigenous knowledge inheritance of Blackfoot storywork and ritual. Although this supporting paper is meant to contextualize their creation, this document also serves a relational seed to root myself in an audiences’ soil. To fully decipher the sonic symbols that make up The Blood Song Winter Count, you must fully understand their ancestral lineage, which ultimately originates with the land and with an emotional-spiritual ecosystem within me.
Exploring sulfate cycling in a mineral-soil wetland restored with wastewater
(Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, 2024) Denny, Mariya; University of Lethbridge. Faculty of Arts and Science; Bogard, Matthew J.
Sulfate (SO42-) pollution is contributing to the salinization of surface waters worldwide. Wetlands are natural filters on the landscape that remediate surface water by retaining and processing pollutants. However, the capacity for wetlands to process excess SO42- from wastewater is poorly understood, especially for natural (as opposed to constructed) wetlands. Here, I explore the SO42- remediation capacity of Frank Lake, a restored, multi-basin wetland complex in southern Alberta, Canada, that is used to treat effluent from municipal and beef slaughterhouse sources. Using a combination of approaches, I show that there was limited SO42- processing throughout the wetland. Mass balances constructed for two distinct hydrologic periods showed that Frank Lake shifted from a SO42- source during wet years (2013 - 2015) to a sink during drought years (2021 - 2022). Yet I found little evidence of active SO42- processing in surveys conducted during drought years. SO42- remained the dominant form of sulfur (S) among all three basins (>95% of total S), implying little net change in the S pool. Similarly, dual stable isotope (34S and 18O) analysis showed limited isotopic enrichment among wetland basins, implying limited transformation of SO42- via microbial reduction. Sediment incubations confirmed the patterns observed with stable isotopes, showing little net removal of SO42- throughout the wetland. The preferential reduction of nitrate (NO3-) and other more energetically favourable constituents of the effluent may restrict the extent of microbial SO42- reduction throughout Frank Lake. The limited extent of emergent and submerged vegetation may also limit SO42- uptake by plants. Given the limited SO42- processing in Frank Lake, and the headwater position of this wetland complex in the broader aquatic network, my work provides context for previous reports of increasing salt concentrations documented in rivers of the South Saskatchewan River watershed.
Investigating the structure-function relationship of anti-mitotic natural products in Canadian prairie plants
(Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, 2024) Healy Knibb, Shannon M.; University of Lethbridge. Faculty of Arts and Science; Golsteyn, Roy
This thesis investigates Canadian prairie plants as sources of natural product compounds capable of inhibiting human cell division. Natural products present an opportunity to identify novel anti-mitotic compounds to address the lack of known inhibitors for many mitotic regulatory proteins. By biology-guided fractionation, we purified the natural products anemonin from Pulsatilla nuttalliana and (+)-6-tuliposide A from Erythronium grandiflorum, and this is the first report of their anti-mitotic activities. We then conducted a comparative study between pulchelloid A (from Gaillardia aristata), anemonin and (+)-6-tuliposide A, and identified unique mitotic arrest profiles, suggesting distinct protein targets and mechanisms of action consistent with the widespread relationship between structure and function in biology. The discovery of natural product inhibitors from Canadian prairie plant species holds tremendous potential for advancing our understanding of mitotic regulation and contributes to the development of targeted treatments for precision medicine.
tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut
(Oxford University Press, 2024) Krahn, Natalie; Zhang, Jingji; Melnikov, Sergey V.; Tharp, Jeffery M.; Villa, Alessandra; Patel, Armaan; Howard, Rebecca J.; Gabir, Haben; Patel, Trushar R.; Stetefeld, Jörg; Puglisi, Joseph; Söll, Dieter
Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).
Factor-dependent internal ribosome entry site and -1 programmed frameshifting signal in the Bemisia-associated dicistrovirus 2
(MDPI, 2024) Chen, Yihang; Chapagain, Subash; Chien, Jodi; Pereira, Higor S.; Patel, Trushar R.; Inoue-Nagata, Alice K.; Jan, Eric
The dicistrovirus intergenic (IGR) IRES uses the most streamlined translation initiation mechanism: the IRES recruits ribosomes directly without using protein factors and initiates translation from a non-AUG codon. Several subtypes of dicistroviruses IRES have been identified; typically, the IRESs adopt two -to three overlapping pseudoknots with key stem-loop and unpaired regions that interact with specific domains of the ribosomal 40S and 60S subunits to direct translation. We previously predicted an atypical IGR IRES structure and a potential -1 programmed frameshift (-1 FS) signal within the genome of the whitefly Bemisia-associated dicistrovirus 2 (BaDV-2). Here, using bicistronic reporters, we demonstrate that the predicted BaDV-2 -1 FS signal can drive -1 frameshifting in vitro via a slippery sequence and a downstream stem-loop structure that would direct the translation of the viral RNA-dependent RNA polymerase. Moreover, the predicted BaDV-2 IGR can support IRES translation in vitro but does so through a mechanism that is not typical of known factorless dicistrovirus IGR IRES mechanisms. Using deletion and mutational analyses, the BaDV-2 IGR IRES is mapped within a 140-nucleotide element and initiates translation from an AUG codon. Moreover, the IRES does not bind directly to purified ribosomes and is sensitive to eIF2 and eIF4A inhibitors NSC1198983 and hippuristanol, respectively, indicating an IRES-mediated factor-dependent mechanism. Biophysical characterization suggests the BaDV-2 IGR IRES contains several stem-loops; however, mutational analysis suggests a model whereby the IRES is unstructured or adopts distinct conformations for translation initiation. In summary, we have provided evidence of the first -1 FS frameshifting signal and a novel factor-dependent IRES mechanism in this dicistrovirus family, thus highlighting the diversity of viral RNA-structure strategies to direct viral protein synthes