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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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    Surface-based temperature inversions and permafrost dynamics in the mountains of northcentral Yukon: linking observations and downscaled climate models
    (Lethbridge, Alta. : University of Lethbridge, Dept. of Geography and Environment, 2026) Noad, Nicholas Craig; University of Lethbridge. Faculty of Arts and Science; Bonnaventure, Philip
    Surface-based temperature inversions (SBIs) exert a dominant control on surface air temperature patterns in high-latitude mountain environments. Long-term climate observations are sparse in these regions, so gridded climate datasets are commonly utilized. However, SBIs are poorly represented in these datasets, introducing systematic bias into permafrost models that rely on gridded or downscaled air temperature fields. In this thesis, I investigate the role of SBIs in shaping surface air temperature variability in subarctic Yukon valleys and evaluate how improved representation of these patterns influence permafrost modelling outcomes. Using a dense network of in-situ air temperature sensors along elevational transects, we quantify the spatial and temporal variability of SBIs in dissimilar valley environments. Results demonstrate that strong SBIs in subarctic valleys with strong gradients of warming with elevation near the valley bottom and much weaker gradients above. These inversion-driven patterns are poorly resolved in coarse-resolution reanalysis datasets, leading to systematic biases in air temperature estimates. To address this limitation, inversion-aware bias reduction approaches for downscaling reanalysis air temperatures are evaluated and developed. A physically informed model (DReaMIT) is introduced to improve transferability. Results show that incorporating SBI processes substantially improves representation of air temperature patterns and reduces model error. Finally, the influence of SBI-aware climate forcing on permafrost and ground thermal regimes is assessed using the Northern Ecosystem Soil (NEST) model. Results demonstrate that SBI-driven temperature adjustments can significantly alter predicted ground temperatures and active layer thickness. While snow redistribution remains the dominant control on local variability, SBI-related air temperature adjustments can exceed its influence at some sites. Overall, this thesis highlights the critical importance of representing SBIs in permafrost modelling and provides new methods for reducing SBI-related bias in climate forcing data in high-latitude complex terrain, improving confidence in predictions of permafrost change in high-latitude mountain environments.
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    New In vitro dna polymerase activity and fidelity assay reveals age-dependent changes in Arabidopsis thaliana
    (PAGEPress, 2011) Golubov, Andrey; Maheshwari, Priti; Bilichak, Andriy; Kovalchuk, Igor
    DNA polymerase is an enzyme that adds nucleotides to the growing DNA chain during replication and DNA repair. DNA polymerase activity and fidelity are important characteristics that reflect the ability of DNA polymerase to add nucleotides and then proofread newly synthesized DNA. We have developed a protocol allowing analysis of polymerase activity and fidelity using crude Arabidopsis thaliana plant extracts. It is based on the ability of DNA polymerases in the extract to elongate the fluorescently labelled primer annealed to a short complementary template. For analysis, fluorescently labelled products were separated on a denaturing polyacrylamide gel and visualized using a high performance blot imager. Analysis of tissue prepared from 5-, 12- and 21-day-old Arabidopsis plants showed an age-dependent decrease in polymerase activity, an increase in polymerase fidelity and a tendency to an increase in exo- (endo) nucleolytic activity.
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    Epigenetic memory in mammals
    (Frontiers Media, 2011) Migicovsky, Zoe; Kovalchuk, Igor
    Epigenetic information can be passed on from one generation to another via DNA methylation, histone modifications, and changes in small RNAs, a process called epigenetic memory. During a mammal’s lifecycle epigenetic reprogramming, or the resetting of most epigenetic marks, occurs twice. The first instance of reprogramming occurs in primordial germ cells and the second occurs following fertilization. These processes may be both passive and active. In order for epigenetic inheritance to occur the epigenetic modifications must be able to escape reprogramming. There are several examples supporting this non-Mendelian mechanism of inheritance including the prepacking of early developmental genes in histones instead of protamines in sperm, genomic imprinting via methylation marks, the retention of CenH3 in mammalian sperm and the inheritance of piwi-associated interfering RNAs. The ability of mammals to pass on epigenetic information to their progeny provides clear evidence that inheritance is not restricted to DNA sequence and epigenetics plays a key role in producing viable offspring.
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    A novel method of transgene delivery into triticale plants using the Agrobacterium transferred DNA-derived nano-complex
    (Oxford University Press, 2012) Ziemienowicz, Alicja; Shim, Youn-Seb; Matsuoka, Aki; Eudes, Francois; Kovalchuk, Igor
    Genetic transformation of monocotyledonous plants still presents a challenge for plant biologists and biotechnologists because monocots are difficult to transform with Agrobacterium tumefaciens, whereas other transgenesis methods, such as gold particle mediated transformation, result in poor transgene expression because of integration of truncated DNA molecules. We developed a method of transgene delivery into monocots. This method relies on the use of an in vitro-prepared nano-complex consisting of transferred DNA, virulence protein D2, and recombination protein A delivered to triticale microspores with the help of a Tat2 cell-penetrating peptide. We showed that this approach allowed for single transgene copy integration events and prevented degradation of delivered DNA, thus leading to the integration of intact copies of the transgene into the genome of triticale plants. This resulted in transgene expression in all transgenic plants regenerated from microspores transfected with the full transferred DNA/protein complex. This approach can easily substitute the bombardment technique currently used for monocots and will be highly valuable for plant biology and biotechnology
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    Microsatellite instability in Arabidopsis increases with plant development
    (Oxford University Press, 2010) Golubov, Andrey; Yao, Youli; Maheshwari, Priti; Bilichak, Andriy; Boyko, Alex; Belzile, Francois; Kovalchuk, Igor
    Plant development consists of the initial phase of intensive cell division followed by continuous genome endoreduplication, cell growth, and elongation. The maintenance of genome stability under these conditions is the main task performed by DNA repair and genome surveillance mechanisms. Our previous work showed that the rate of homologous recombination repair in older plants decreases. We hypothesized that this age-dependent decrease in the recombination rate is paralleled with other changes in DNA repair capacity. Here, we analyzed microsatellite stability using transgenic Arabidopsis (Arabidopsis thaliana) plants that carry the nonfunctional β-glucuronidase gene disrupted by microsatellite repeats. We found that microsatellite instability increased dramatically with plant age. We analyzed the contribution of various mechanisms to microsatellite instability, including replication errors and mistakes of DNA repair mechanisms such as mismatch repair, excision repair, and strand break repair. Analysis of total DNA polymerase activity using partially purified protein extracts showed an age-dependent decrease in activity and an increase in fidelity. Analysis of the steady-state RNA level of DNA replicative polymerases α, δ, Pol I-like A, and Pol I-like B and the expression of mutS homolog 2 (Msh2) and Msh6 showed an age-dependent decrease. An in vitro repair assay showed lower efficiency of nonhomologous end joining in older plants, paralleled by an increase in Ku70 gene expression. Thus, we assume that the more frequent involvement of nonhomologous end joining in strand break repair and the less efficient end-joining repair together with lower levels of mismatch repair activities may be the main contributors to the observed age-dependent increase in microsatellite instability.