Signature Areas of Research

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Areas of research and scholarship that bring the University of Saskatchewan distinct recognition and help to position USask among the most distinguished universities in Canada and among the very best in the world.

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SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies
(Methods, 0001) Todd, Clarence; Jin, Lingling; McQuillan, Ian
This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake [20] workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at https://github.com/USask-BINFO/SV-JIM
Caffeine and Nicotine with N-Substituted Diazirine Photoaffinity Labels Form Adducts at Tyrosine-39 of α-Synuclein
(ACS Publications, 0002-04) Mejia-Gutierrez, Melissa; Moser, Brigitte; Pirlot, Marissa; Zhang, Haixia; Chumala, Paulos; Katselis, George S.; Palmer, David R.; Krol, Ed S.
Aggregates of the protein α-synuclein are found in Lewy bodies in the brains of Parkinson’s disease (PD) patients. Small molecules that can attenuate or halt α-synuclein aggregation have been studied as potential therapeutics for PD. However, we have a limited understanding of how these molecules bind to α-synuclein. We previously identified that caffeine, nicotine, and 1-aminoindan all bind to both the N- and C-terminus of α-synuclein, although the binding location remains unknown. In an effort to identify these binding regions on α-synuclein, we synthesized diazirine photoaffinity probes attached to caffeine (C-Dz), nicotine (N-Dz), and 1-aminoindan (I-Dz) and allowed each to react with α-synuclein in vitro. We then treated the incubation mixture with trypsin and employed time-of-flight mass spectrometry to analyze the resulting peptides. Our findings reveal a distinctive binding pattern among the probes: C–Dz forms covalent bonds with Tyr-39 and Glu-20, while N-Dz selectively forms a covalent bond with Tyr-39. Intriguingly, we could not detect the labeling of I-Dz to any specific amino acids. All of the diazirine-bound peptides were found near the N-terminus. Our results suggest that the N-terminal region near Tyr-39 bears further study to elucidate the binding interactions of small molecules with α-synuclein and may be a target for anti-PD agents.
Hydrological and economic assessment of the Upper Qu’Appelle Water Supply Project : report for Western Economic Diversification
(University of Saskatchewan Global Institute for Water Security, 1/31/2020) Lindenschmidt, Karl-Erich; Lloyd-Smith, Patrick; Razavi, Saman; Carlson, Hayley; Terry, Julie; Mustakim Ali Shah, Syed
This report describes some water resource management modeling, water quality modeling, and economic implications of the Upper Qu’Appelle Water Supply Project.
High-Resolution Large-Eddy Simulations of Flow in the Complex Terrain of the Canadian Rockies
(Earth and Space Science, 10/25/2023) Rohanizadegan, Mina; Petrone, Richard; Pomeroy, John W.; Kosovic, Branko; Muñoz-Esparza, Domingo; Helgason, Warren
Improving the calculation of land-atmosphere fluxes of heat and water vapor in mountain terrain requires better resolution of thermally driven diurnal winds (i.e., valley, slope winds) due to differential heating by terrain and radiative fluxes. In this study, the Weather Research and Forecasting model is used to simulate flow in large-eddy simulation (LES) mode over the complex terrain of the Fortress Mountain and Marmot Creek research basins, Kananaskis Valley, Canadian Rockies, Alberta in mid-summer. The model was used to examine the temporal and spatial evolution of local winds and near-surface boundary layer processes with variability in topography and elevation. Numerically resolving complex terrain wind flow effects require smaller grid cell size. However, the use of terrain-following coordinates in most numerical weather prediction models results in large numerical errors when flow over steep terrain is simulated. These errors propagate through the domain and can result in numerical instability. To avoid this issue when simulating flow over steep terrain a local smoothing approach was used, where smoothing is applied only where slope exceeds some predetermined threshold. LES results from local smoothing were compared with a mesoscale model and LES with global smoothing. Simulations are evaluated using sounding data and meteorological stations. The differences in flow patterns and reversals in two mountain basins suggest that valley geometry and volume is relevant to the break up of inversion layers, removal of cold-air pools, and strength of thermally driven winds.
Humanity’s evolving story : sharing scientific research outcomes in a changing world
(United Nations University Institute for Water, Environment and Health and Global Water Futures, 10/6/2022) Sandford, Robert William
Never before has how science tells its stories been more important. The story humanity has been telling itself about itself over the past two hundred years has proven to be dangerous to our future. Science has the power to change the path of that narrative and alter the next chapter of humanity’s story so that it is not our final chapter.
Sharing Is Caring: Helping Institutions and Health Organizations Leverage Data for Educational Improvement
(Ubiquity Press, 10/7/2024) Sebok-Syer, Stefanie S.; Smirnova, Alina; Duwell, Ethan; George, Brian; Triola, Marc; Feddock, Christopher; Chahine, Saad; Rubright, Jonathan D.; Thoma, Brent
Competency-based medical education (CBME) has produced large collections of data, which can provide valuable information about trainees and medical education systems. Many organizations continue to struggle with accessing, collecting, governing, analyzing, and visualizing their clinical and/or educational data. This hinders data sharing efforts within and across organizations, which are foundational in supporting system-wide improvements. Challenges to data sharing within medical education include variability in legislation, existing data policies, heterogeneity of data, inadequate data infrastructure, and various intended purposes or uses. In this eye opener, the authors describe four case studies to illustrate some of the aforementioned challenges and characterize the complexity of data sharing within medical education along two dimensions: organizational (single vs. multiple) and data type (clinical and/or educational). With the goal of better supporting data sharing initiatives, the authors introduce an action-oriented blueprint that includes a three-stage process (i.e., preparation, execution, and iteration) to highlight crucial aspects of data sharing. This evidence-informed model incorporates current best practices and aims to support data sharing initiatives within their own organizations and across multiple organizations. Finally, organizations can use this model to conceptually guide and track their progression throughout the data sharing process.
Modelling the regional sensitivity of snowmelt, soil moisture, and streamflow generation to climate over the Canadian Prairies using a basin classification approach
(Hydrology and Earth System Sciences, 10/9/2023) He, Zhihua; Shook, Kevin; Spence, Christopher; Pomeroy, John W.; Whitfield, Colin
This study evaluated the effects of climate perturbations on snowmelt, soil moisture, and streamflow generation in small Canadian Prairies basins using a modelling approach based on classification of basin biophysical characteristics. Seven basin classes that encompass the entirety of the Prairies Ecozone in Canada were determined by cluster analysis of these characteristics. Individual semi-distributed virtual basin (VB) models representing these classes were parameterized in the Cold Regions Hydrological Model (CRHM) platform, which includes modules for snowmelt and sublimation, soil freezing and thawing, actual evapotranspiration (ET), soil moisture dynamics, groundwater recharge, and depressional storage dynamics including fill and spill runoff generation and variable connected areas. Precipitation (P) and temperature (T) perturbation scenarios covering the range of climate model predictions for the 21st century were used to evaluate climate sensitivity of hydrological processes in individual land cover and basin types across the Prairies Ecozone. Results indicated that snow accumulation in wetlands had a greater sensitivity to P and T than that in croplands and grasslands in all basin types. Wetland soil moisture was also more sensitive to T than the cropland and grassland soil moisture. Jointly influenced by land cover distribution and local climate, basin-average snow accumulation was more sensitive to T in the drier and grassland-characterized basins than in the wetter basins dominated by cropland, whilst basin-average soil moisture was most sensitive to T and P perturbations in basins typified by pothole depressions and broad river valleys. Annual streamflow had the greatest sensitivities to T and P in the dry and poorly connected Interior Grasslands (See Fig. 1) basins but the smallest in the wet and well-connected Southern Manitoba basins. The ability of P to compensate for warming-induced reductions in snow accumulation and streamflow was much higher in the wetter and cropland-dominated basins than in the drier and grassland-characterized basins, whilst decreases in cropland soil moisture induced by the maximum expected warming of 6 ∘C could be fully offset by a P increase of 11 % in all basins. These results can be used to (1) identify locations which had the largest hydrological sensitivities to changing climate and (2) diagnose underlying processes responsible for hydrological responses to expected climate change. Variations of hydrological sensitivity in land cover and basin types suggest that different water management and adaptation methods are needed to address enhanced water stress due to expected climate change in different regions of the Prairies Ecozone
Influencing water futures: summary of a roadmap for maximizing knowledge uptake in the final years of the Global Water Futures program
(Global Water Futures, 11/16/2022) Morrison, Monica; Goucher, Nancy
As we continue to encourage and document research relationships, moving into the GWF’s final stages, KM seeks to supply answers to the following questions: What have we done –what relationships have we built, and what new knowledge has resulted? What did we learn? And, how does this strengthen Canada’s water future? KM work will focus on inventory activities to answer the first, and synthesis activities to respond to the second and third of these questions. Knowledge mobilization should be the driving force for GWF’s Operations and Annual Science meetings over the next year, shifting the focus from research findings to meeting user needs through knowledge exchange and research application.
Snowcover : accumulation, relocation, and management
(National Hydrology Research Institute, 1995) Pomeroy, John; Gray, Donald M.
Much of Canada's water supply is derived from snow. In most parts of the country, the annual spring freshet plays a key role in sustaining our aquatic ecosystems, while for semi-arid, boreal, alpine and arctic regions, snow is an important source of fresh water. In the context of sustainable development, i.e., the balanced management of natural resources to achieve a long-term, reasonable level of economic well-being while maintaining environmental values, snow plays a vital part. On the Canadian Prairies, for instance, snow management practices now often go hand-in-hand with no-tillage practices in the ongoing effort to sustain agricultural production over the long term. As another example, research conducted under the Canadian Model Forest Programme has highlighted the important role of snow in sustainable forestry management practices. Snow can be considered as a physical resource, a raw material possessing properties that contribute to the production of food, fibre and other beneficial products for human use and enjoyment. As with the sun, the soil, the air and the rain, the natural behaviour of snow can be studied, understood and ultimately managed. In a country such as Canada, a better understanding of snow processes will make a significant contribution to hydrological science. This scientific report on snowcover accumulation, relocation and management is a necessary step on the road to sustainable development. The dedication of the authors in preparing this comprehensive report that will be widely used by engineers, agriculture and forestry practitioners, scientists and university students is gratefully acknowledged.
Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife
(National Institute of Environmental Health Sciences (NIEHS), 1998) Berg, Martin Van den; Birnbaum, Linda; Bosveld, Albertus T.C.; Brunstrom, Björn; Cook, Philip; Feely, Mark; Giesy, John; Hanberg, Annika; Hasegawa, Ryuichi; Kennedy, Sean W.; Kubiak, Timothy; Larsen, John Christian; Leeuwen, F.X. Rolaf van; Liem, A.K. Djien; Nolt, Cynthia; Peterson, Richard E.; Poellinger, Lorenz; Safe, Stephen; Schrenk, Dieter; Tillitt, Donald; Tysklind, Mats; Younes, Maged; Waern, Fredrik; Zacharewski, Tim
An expert meeting was organized by the World Health Organization (WHO) and held in Stockholm on 15-18 June 1997. The objective of this meeting was to derive consensus toxic equivalency factors (TEFs) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and dioxinlike polychlorinated biphenyls (PCBs) for both human, fish, and wildlife risk assessment. Based on existing literature data, TEFs were (re)evaluated and either revised (mammals) or established (fish and birds). A few mammalian WHO-TEFs were revised, including 1,2,3,7,8-pentachlorinated DD, octachlorinated DD, octachlorinated DF, and PCB 77. These mammalian TEFs are also considered applicable for humans and wild mammalian species. Furthermore, it was concluded that there was insufficient in vivo evidence to continue the use of TEFs for some di-ortho PCBs, as suggested earlier by Ahlborg et al. [Chemosphere 28:1049-1067 (1994)]. In addition, TEFs for fish and birds were determined. The WHO working group attempted to harmonize TEFs across different taxa to the extent possible. However, total synchronization of TEFs was not feasible, as there were orders of a magnitude difference in TEFs between taxa for some compounds. In this respect, the absent or very low response of fish to mono-ortho PCBs is most noticeable compared to mammals and birds. Uncertainties that could compromise the TEF concept were also reviewed, including nonadditive interactions, differences in shape of the dose-response curve, and species responsiveness. In spite of these uncertainties, it was concluded that the TEF concept is still the most plausible and feasible approach for risk assessment of halogenated aromatic hydrocarbons with dioxinlike properties.
Building on a Legacy : Working with users to revitalize the CRHM hydrological model
(Global Water Futures Core Computer Science, 2/1/2023) Roy, Banani
A computer scientist's personal account of the challenges involved in collaboratively migrating the CRHM hydrological modelling tool.
Giftwrapped Data : Working together on a model-agnostic platform for speeding up predictions for water management
(Global Water Futures Core Modelling Team, 2/1/2023) Keshavarz, Kasra
A young engineer's personal account of collaborating with hydrological modelers to develop a new model-agnostic workflow to expedite data preparation.
Both Eyes on the Ice : Investigating a hazard on the Slave River
(Global Water Futures Integrated Modeling Program for Canada, 2/1/2023) Lindenschmidt, Karl-Erich
Personal account from a scientist about learning from his local guide while conducting river ice research in the Canadian Northwest Territories.
More than Cold Dirt : Discovering the human face of climate change research in northern Canada
(Global Water Futures Geogenic Contamination of Groundwater Resources in Subarctic Regions, 2/1/2023) Skierszkan, Elliott K.
Personal account of a researcher's experience learning from local people while investigating groundwater contamination related to thawing permafrost in Canada's Yukon Territory.
Come Hail or High Water : Exchanging insurance and drought knowledge to advance research and its application
(Global Water Futures, 2/1/2023) Wheaton, Elaine
Personal account of a climate scientist's interactions with knowledge users looking at extreme weather in the Canadian West.
The Search for the Perfect Flood : Working together to build a deeper relationship with the river
(Global Water Futures We Need More than Just Water, 2/1/2023) Jardine, Timothy D
Personal account of a scientist's working relationship with a local guide in northern Saskatchewan.
Long period return level estimates of extreme precipitation
(University of Victoria Pacific Climate Impacts Consortium, 2/27/2020) Zwiers, Francis; Ben Alaya, Mohamed Ali; Zhang, Xuebin
To better use climate information available in the historical record, a recommended approach is composing precipitation as the product of precipitable water and precipitation efficiency.
Morphologically complex plant macrofossils from the Late Silurian of Arctic Canada
(Botanical Society of America, 2002-06) Kotyk, Michele E.; Basinger, James F.; Gensel, Patricia G.; de Freitas, Tim A.
In addition to vegetative remains, fertile remains from ten plants, representing seven distinct taxa whose size and complexity are much greater than most contemporaneous fossils, are reported from late Ludlow (Ludfordian) sediments of Bathurst Island in Nunavut, Canada. Evidence for the age of these beds is gathered from stratigraphic relationships and index fossils including conodonts, graptolites, and brachiopods. Zosterophylls dominate the collection, some of which constitute the earliest record of fertile structures arranged in dense clusters and longitudinal rows along axes. Representatives include a plant that resembles Bathurstia, one species of Zosterophyllum, and two specimens that bear affinity to this genus. Distichophytum is also represented, as is a new zosterophyll named Macivera gracilis. The prevalence of sporangial clustering and reduced sporangial stalks in this flora leads to a discussion of the origins and significance of these morphological features. Following a review of some of the other Silurian floras, particularly the Baragwanathia-bearing Lower Plant Assemblage of Victoria, Australia, which also shows morphological advancement over the rhyniophytoid-dominated floras common to Laurussia, it is concluded that the Bathurst Island flora presents the best evidence to date of substantial morphological diversity, complexity, and stature of vascular land plants in this period.
Hydrology and Water Resources of Saskatchewan
(Centre for Hydrology, University Saskatchewan, Saskatoon, Saskatchewan, 2005) Pomeroy, John; de Boer, Dirk; Martz, Lawrence W.
There is little in the natural environment, economy and society of Saskatchewan that is not intimately tied to and sustained by the flow and storage of water. Nowhere else in Canada does the lack or excess of water cause such widespread concern, nor are there many Canadian environments subject to greater seasonal change in precipitation and surface-water storage. Most major landforms of Saskatchewan were created by the deposition and erosion of sediments and rock by water and ice during the glacial and immediate postglacial periods. Saskatchewan’s contemporary hydrology determines the type and location of natural vegetation, soils, agriculture, communities and commerce. However, the scarcity, seasonality and unpredictability of the province’s water resources have proved critical impediments to the productivity of natural ecosystems and to sustainable settlement and economic activity. The hydrology of Saskatchewan is marked by several distinctive characteristics that govern the behaviour of water as a resource in the province (Gray, 1970): i) The extreme variability of precipitation and runoff results in frequent water shortages and excesses with respect to natural and human storage capacities and demand. ii) The seasonality of water supply is manifest in fall and winter by the storage of water as snow, and lake and ground ice, in early spring by rapid snowmelt resulting in most runoff, and in late spring and early summer by much of the annual rainfall. iii) The aridity and gentle topography result in poorly developed, disconnected and sparse drainage systems, and surface runoff that is both infrequent and spatially restricted. iv) The land cover and soils exert an inordinate control on hydrological processes because of small precipitation inputs and limited energy for evaporation and snowmelt. v) The flows in the major rivers of the southern half of the province are largely derived from the foothills and mountains in Alberta. In dry years, arable agriculture can fail over large parts of the province, whilst in wet years, flooding has caused widespread damage to rural and urban infrastructure. Climate change may increase the incidence of both drought and flooding, with earlier spring thaws and increased interannual and interseasonal variability of temperature and precipitation (Covich et al., 1997; Cutforth et al., 1999, Herrington et al., 1997). Changes to the seasonal timing of precipitation can have very severe effects on agriculture and ecosystems; runoff to water bodies and replenishment of groundwater are primarily supplied by spring snowmelt, growth of cereal grains is related to the quantity of rainfall falling between May and early July, maturing and timely harvesting of crops are dependent upon warm dry weather in mid to late summer, and spring runoff is governed by soil moisture reserves in the preceding fall and snowfall the preceding winter (de Jong and Kachanoski, 1987). Saskatchewan’s water resources are vulnerable, as there is little local runoff to the single greatest water resource of the southern prairies, the South Saskatchewan River, which derives overwhelmingly from the Rocky Mountains. Water supplies in the Alberta portion of the South Saskatchewan River system are approaching full apportionment in dry years and the uncertainty imposed by climate change impacts on runoff generation in the mountains makes managing the river increasing difficult. Local water bodies (streams, sloughs, dugouts) are fed by groundwater or small surface drainages, and little runoff is provided by most land surfaces within the ‘topographic catchment’. The effect of soils and vegetation on Saskatchewan hydrology is profound because of the interaction of snow, evaporation and vegetation. In the southern Prairies, water applied from rain or snowmelt to summer-fallowed fields contributes inordinately to runoff, whereas continuously cropped fields, grasses and trees undergo greater infiltration to soils and hence greater evaporation. In the North, evergreen forest canopy and root structures promote infiltration of rainfall or snowmelt to soils and subsequent evaporation. There is much greater runoff and streamflow in boreal forest drainage basins with large cleared areas. This chapter will discuss the key physical aspects of Saskatchewan’s hydrology and water resources, focussing on its drainage basins and the contribution of runoff to streams and lakes within them, its major rivers and their flows, water supply pipelines and river diversions, prairie hydrology, boreal forest hydrology, groundwater and an assessment of the future. Because of its sub-humid, cold region hydrology and low population, water quality concerns in Saskatchewan are primarily related to algal growth in dugouts, and a few cases of contaminated groundwater or immediate downstream effects from sewage outflows, rather than widespread diffuse-source pollution; this chapter will therefore focus on water quantity rather than quality.
Review of On Bullshit by Harry G. Frankfurt
(Princeton University Press, 2006-01-01) Pfeifer, Karl
According to Frankfurt’s analysis, bullshitting and lying necessarily differ in intention. I argue contra Frankfurt that (i) bullshitting can be lying, and that (ii) bullshitting need involve neither misrepresentation nor intention to deceive. My discussion suggests that bullshit is not capturable by a simple formula and that, although illuminating, Frankfurt’s analysis is limited to one paradigm.

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