Department of Physical Sciences

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https://hdl.handle.net/20.500.14078/11

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Computational analysis of upscaled fibrotic liver multi-lobule flows and metabolism
(2024) Coombe, Dennis; Wallace, Cooper; Rezania, Vahid; Tuszynski, Jack A.
The modeling of fibrotic effects on fluid flow and metabolism in the liver can be computationally challenging. This paper combines innovative concepts based on fundamental physics to address such issues at the level of the liver functional unit, the lobule, and upscales and extends this to a multi-lobule tissue scale analysis. Fibrosis effects on fluid flow and metabolism are introduced using percolation theory and its consequences are explored for single lobule and multi-lobule patterns, without and with distortion.
Evaluating continental channel-hosted Lockeia orientation as a paleoflow indicator: insights from the Jurassic Brushy Basin Member, Western United States
(2025) King, M. Ryan; Timmer, Eric R.; Furlong, Carolyn M.; Gingras, Murray K.; Hayes, Derek A.; Nadon, Gregory C.; Tweet, Justin S.; Santucci, Vincent L.
Although bivalves can orient infaunal body position to current direction, trace fossils of bivalves have rarely been corroborated against paleocurrent directions determined from physical sedimentary structures. This study compares Lockeia (bivalve-generated trace fossil) orientation and length to the three-dimensional bedform cross-strata dip direction from fluvial deposits at two localities in the Late Jurassic Brushy Basin Member (Morrison Formation) of the western United States. Lockeia mean orientation at each site are comparable, but tangential, to physical sedimentary structure mean orientations. Comparing accuracy (within one standard deviation) and precision (within two standard deviations) in-context of five macroform surfaces, the Lockeia measurements are more accurate indicators of current direction than the physical sedimentary structures. Conversely, the physical sedimentary structures are more precise than the Lockeia measurements. This dissimilarity is partly a function of the variability of cross-stratum dip orientation produced by three-dimensional bedforms resultant from the tangential nature of the bedform, its preservation, and the method by which these are measured. Lockeia has greater paleocurrent representation accuracy than physical sedimentary structures since it is a linear measurement rather than a collection of measurements that can be tangential to paleoflow. Lockeia measurements show shifts vertically and laterally with macroform changes indicating potential use for identifying local changes in paleocurrent direction.
Locomotion traces emplaced by modern stalkless comatulid crinoids (featherstars)
(2023) Myers, Reed A.; Furlong, Carolyn M.; Gingras, Murray K.; Zonneveld, John-Paul
Modern crinoids have the ability to use their arms to crawl along the sea floor and some are capable of swimming short distances. The first and only evidence of crinoid locomotion reported from the rock record was described from the Middle Jurassic of the Cabeço da Ladeira Lagerstätte (Portugal) resulting in description of the ichnotaxon Krinodromos bentou. Although the mechanics of crinoid movement are well documented the morphological ranges of crinoid motility tracks are unknown. This study uses observations of crinoid movement and their effects on sediment using modern comatulid crinoids to propose possible trace fossil morphologies. Using 20 experimental trials supported by photography, video analyses, 3D orthogrammetry and resin casting, the morphological ranges of crinoid motility tracks are included in five distinct morphologies attributed to ambling, crawling, walking, running, and landing/taking-off traces, the latter of which are emplaced before and after swimming. Traces produced by ambling occur as epigenic hook-shaped grooves. Crawling traces comprise closely spaced hook-shaped grooves and ridges preserved in concave and convex epirelief. Walking traces consist of semi-bilaterally symmetrical collections of three or more grooves, and associated ridges, preserved in convex and concave epirelief. Running traces consist of semi-bilaterally symmetrical collections of one to three straight to semi-sinusoidal grooves and associated ridges preserved in concave and convex epirelief. Landing/taking-off traces are mounded features preserved in convex epirelief, with grooves radiating from the center. The five trace types described in this paper provide insight into morphological features that can be associated with modern crinoid activities and used to identify crinoid trace fossils, which are rarely reported, in the rock record.
Induced or natural? Toward rapid expert assessment, with application to the Mw 5.2 Peace River earthquake sequence
(2023) Salvage, Rebecca O.; Eaton, David W.; Furlong, Carolyn M.; Dettmer, Jan; Pedersen, Per K.
Based on information available at the time, several questionnaire‐based schemes have been developed to provide a qualitative assessment of whether a specific earthquake (or earthquake sequence) was likely induced by anthropogenic activities or is inferred to be natural. From a pragmatic perspective, the value of this assessment is arguably the greatest in the immediate aftermath of an event (hours to days), because it could then better serve to guide regulatory response. However, necessary information is often incomplete or uncertain, and there remains a lack of scientific consensus on the most distinctive attributes of induced (vs. natural) earthquake sequences. We present a case study of the 5.2 Peace River earthquake sequence (Alberta, Canada), evaluated using two published frameworks for origin interpretation. The Alberta Energy Regulator initially considered the sequence to be natural, but a study published ~4 mo later came to the opposite interpretation. Prior to this publication, we convened a panel of experts who completed questionnaires as set out by the frameworks; results using both schemes indicate that experts believe the sequence was likely induced. Based on these expert responses, we critically evaluate information that was available publicly in the weeks to months following the mainshock on 30 November 2022; reassess the relative importance of various components of the questionnaires from a parsimonious, rapid‐response perspective; and consider other types of information that could be critical for near‐real‐time assessment of whether an event was induced or natural.
Biodegradation in oil sands process-affected water: a comprehensive laboratory analysis of the in situ biodegradation of dissolved organic acids
(2024) Asiedu, Evelyn; Zhao, Kankan; Anwar, Mian Nabeel; Ross, Matthew S.; Balaberda, Amy-lynne; Ulrich, Ania C.
Oil sands process-affected water (OSPW) is a by-product of the extraction of bitumen, and volumes of OSPW have accumulated across the Alberta oil sands region due to the governments zero-discharge policy. Some dissolved organics in OSPW, including toxic naphthenic acids (NAs), can be biodegraded in oxic conditions, thereby reducing the toxicity of OSPW. While there has been much focus on degradation of NAs, the biodegradation of other dissolved organic chemicals by endogenous organisms remains understudied. Here, using the HPLC–ultrahigh resolution Orbitrap mass spectrometry, we examined the microbial biodegradation of dissolved organic acids in OSPW. Non-targeted analysis enabled the estimation of biodegradation rates for unique heteroatomic chemical classes detected in negative ion mode. The microcosm experiments were conducted with and without nutrient supplementation, and the changes in the microbial community over time were investigated. Without added nutrients, internal standard–adjusted intensities of all organics, including NAs, were largely unchanged. The addition of nutrients increased the biodegradation rate of O2− and SO2− chemical classes. While anoxic biodegradation can occur in tailings ponds and end pit lakes, microbial community analyses confirmed that the presence of oxygen stimulated biodegradation of the OSPW samples studied. We detected several aerobic hydrocarbon-degrading microbes (e.g., Pseudomonas and Brevundimonas), and microbes capable of degrading sulfur-containing hydrocarbons (e.g., Microbacterium). Microbial community diversity decreased over time with nutrient addition. Overall, the results from this study indicate that toxic dissolved organics beyond NAs can be biodegraded by endogenous organisms in OSPW, but reaffirms that biological treatment strategies require careful consideration of how nutrients and dissolved oxygen may impact efficacy.
Research recast(ed): S3E15 - Creative chemists on creating a cleaner, greener future for everyone
(2024) Leschyshyn, Brooklyn; Smadis, Natalie; Lee, Roland; Mundle, Trevor
On today’s episode we had the pleasure of being joined by Dr. Roland Lee and Trevor Mundle. The two test our preconceived notion of the truth behind environmentally friendly products. Dr. Roland Lee and Trevor Mundle collaborate between the MacEwan lab and Green Tech, bringing together experts in chemistry, finance, investment, and sustainable practices. They use cutting-edge pyrolysis technology to convert various feedstocks into valuable products, which reduces emissions, fossil fuel dependencies, water usage, and landfill needs. Their objective is to transform waste streams into valuable resources.
Research recast(ed): S3E3 - Bringing young minds to MacEwan through experiences, experiments, and fun with Dr. Emily Milne, Dr. Kaitlyn Towle, and Steven Campbell
(2023) Leschyshyn, Brooklyn; Smadis, Natalie; Milne, Emily; Towle, Kaitlyn; Campbell, Steven
On today’s episode, we talk to Dr. Emily Milne, Kaitlyn Towle, and Steven Cambell about MacEwanCYU. With the help of MacEwan, students from Ben Calf Robe can learn about what the university has to offer. Their project helps to inspire young minds and invite them to aspire to a secondary education.
Research recast(ed): MacEwan Celebrates Month of Scholarship - Dr. Erin Walton
(2022) Ekelund, Brittany; Cave, Dylan; Walton, Erin
Today’s episode is literally out of this world as we talk about meteorites, asteroids and moon rocks with geologist Dr. Erin Walton, an associate professor in the Department of Physical Sciences at MacEwan University, whose primary research focuses on shock metamorphism recorded in martian meteorites. Along the way, we’ll discuss mentorship, space colonization and the economic benefit of finding impact craters. We will also get a glimpse into Dr. Walton’s new exciting avenue of research into her all-time favorite asteroid, 4-Vesta.
Research recast(ed): MacEwan celebrates month of scholarship - Dr. Samuel Mugo
(2022) Ekelund, Brittany; Cave, Dylan; Mugo, Samuel
Today we learn about smart technology and the democratization of health through point-of-need sensors with Dr. Samuel Mugo, a professor of analytical chemistry at MacEwan University, whose research program involves the use of smart sensor technology for human and animal health and wellness, as well as agri-food chemical analysis. Along the way, we will learn about the United Nations Sustainable Development goals, and find out how chemistry and technology can come together to address food security and help people take control of their physical and mental wellness.
Using GIS and remote sensing to monitor industrial impacts to archaeological sites in the Athabasca Oil Sands of Alberta
(2021) Wadsworth, William T. D.; Dersch, Ave; Woywitka, Robin; Supernant, Kisha
The Athabasca Oil Sands (AOS) region of Alberta has one of the densest accumulations of known archaeological sites, and possibly the most archaeological sites at risk, in the country. Expanding industrial development has been a characteristic of this region for decades, and as a result, abundant archaeological work has been done and regulatory requirements put in place to mitigate site disturbance. Until recently, there has been little quantitative evidence to assess human impact on archaeological resources in the region. The goal of this paper is to raise awareness of the critical need to incorporate new archaeological remote sensing strategies to improve site monitoring approaches. We present methods and results from our GIS-based analysis that seeks to locate and partially characterize impacted sites. We argue that combining publicly accessible remote sensing products with geospatial archaeological site information allows for better documenting and monitoring of industry impacts in the AOS. We show that 43% of all sites sampled (n=1943) are disturbed. Of these sites, 160 were potentially affected by Historical Resources Act non-compliant impacts (including five HRV 1 sites). We contextualize our results within current systemic challenges and we recommend the incorporation of community monitoring programs to ground-truth similar GIS analyses and increase our ability to effectively monitor industrial impacts to archaeological sites.
Topographic setting of archaeological survey in the Boreal Forest of Alberta
(2021) Woywitka, Robin; Michalchuk, Benjamin
The archaeological record of the Canadian Boreal Forest is dominated by shallowly buried sites with little to no datable artifacts or stratigraphy. This has led to characterizations of the region as an area of low scientific interpretive value. However, the factors that underlie this skew to shallow sites are rarely formally examined. Here we use a geomorphon-based terrain classification to assess the role of topographic setting in the placement of archaeological survey points. Our results show that there is considerable bias in current archaeological survey methods towards landforms that disperse sediment. This reduces the likelihood of finding deeply buried or stratified sites and calls into question the assertion that datable sites are largely absent from the region. We recommend that increased sampling of low-lying terrain should be a regular component of Boreal Forest survey methodology.
Late Pleistocene and Early Holocene obsidian in Alberta and human dispersal into North America’s ice-free corridor
(2023) Kristensen, Todd; Allan, Timothy E.; Ives, John W.; Woywitka, Robin; Yanicki, Gabriel; Rasic, Jeffrey T.
We utilize pXRF to source the oldest obsidian artifacts in Alberta, Canada. The province lacks obsidian outcrops and hosts much of the late Pleistocene Ice-Free Corridor, the northern and southern ends of which are in proximity to obsidian outcrops in Yukon, Alaska, Idaho, and Wyoming. The early presence of these obsidians in Alberta informs models of human dispersion. Results point to an early establishment of relationships in the central Ice-Free Corridor that reached into Oregon, Idaho, and Alaska. Alberta appears to have been entered by people from the south who had ties to the Pacific Northwest and Intermountain West. After biotic viability of a full Corridor, limited evidence suggests that northern people from Beringia may have trickled south and admixed with southern populations in the central Corridor region. Upon deglaciation of access routes through the Rocky Mountains, obsidian from western sources in British Columbia arrived relatively quickly in northern Alberta.
Lead (Pb) sorption to hydrophobic and hydrophilic zeolites in the presence and absence of MTBE
(2021) Zhang, Yunhui; Alessi, Daniel S.; Chen, Ning; Luo, Mina; Hao, Weiduo; Alam, Md. Samrat; Flynn, Shannon L.; Kenney, Janice; Konhauser, Kurt O.; Ok, Yong Sik; Al-Tabbaa, Abir
The co-contamination of the environment by metals and organic pollutants is a significant concern, and one such example is lead (Pb) and methyl tert-butyl ether (MTBE) due to their historic use as fuel additives. Clinoptilolite is an abundant and efficient zeolite for metal removal, but the potential interference of co-existing organic pollutants on metal removal, such as MTBE, have rarely been discussed. In this study, a combination of batch sorption tests and synchrotron-based X-ray absorption spectroscopic analyses were employed to investigate Pb sorption mechanism(s) onto clinoptilolite in the presence and absence of MTBE. A comparison was made to synthetic ZSM-5 zeolite to gain insights into differences in Pb binding mechanisms between hydrophilic (clinoptilolite) and hydrophobic (ZSM-5) zeolites. Site occupancy and surface precipitation contributed equally to Pb removal by clinoptilolite, while surface precipitation was the main Pb removal mechanism for ZSM-5 followed by site occupancy. Despite the negligible effect of 100 mg/L MTBE on observed Pb removal from solution by both zeolites, a surface-embedded Pb removal mechanism, through the Mg site on clinoptilolite surface, arises when MTBE is present. This study provides an understanding of atomic-level Pb uptake mechanisms on zeolites, with and without co-contaminating MTBE, which aids in their application in water treatment at co-contaminated sites.
Settling behaviors of microplastic disks in water
(2023) Yang, Ge; Yu, Zijian; Baki, Abul B. M.; Yao, Weiwei; Ross, Matthew S.; Chi, Wanqing; Zhang, Wenming
Microplastic (MP) disks have not been studied for settling behaviors in aquatic environments, which affects the transport and fate of MPs. Therefore, settling experiments were conducted on MP disks of three shapes and four common-seen materials. Lighter MP disks (with density ρs = 1.038 g/cm3 and length l ≤ 5 mm) followed rectilinear vertical trajectories, while heavier MP disks (ρs = 1.161–1.343 g/cm3 and l = 5 mm) followed zigzag trajectories with oscillations and rotations. The mean terminal settling velocities of MP disks were 19.6–48.8 mm/s. Instantaneous settling velocities of heavier MP disks fluctuated. Existing formulas could not accurately predict the settling velocity of MP disks; thus, a new model was proposed with an error of 15.5 %. Finally, the Red - I* diagram (Red is the disk Reynolds number and I* is the dimensionless moment of inertia) was extended for MP disks to predict settling trajectories.
Ice, mountains, and people: applying a multi-proxy approach to reveal changes in Alberta’s alpine ecosystems through ice patch research
(2023) Tirlea, Diana; Kristensen, Todd; Osicki, Aaron; Jensen, Britta; Williams, Krista; Caners, Richard; Lumley, Lisa; Woywitka, Robin
Glacial archaeology has grown and progressed rapidly in recent decades with technological innovations and shifting socio-political issues. However, research on ice patches in the Canadian Rocky Mountains is in its infancy. While Holocene glacial ice retreat, advance, and morphology are well studied in Canada, ice patches in general tend to be understudied because of their limited geomorphological impact on landscapes. This oversight is concerning as their isolated nature, lower elevation, and small mass make ice patches even more susceptible to climate change than glaciers. The importance of documenting these features is heightened by a persisting but tenuous biological importance to a range of modern species. The lack of flow in ice patches also makes them excellent archives of palaeoenvironmental and organic-based cultural materials, as layers of ice and preserved contents are not as distorted as they may be by flow in glaciers.
Editorial: multiscale modeling for the liver
(2023) Ho, Harvey; Rezania, Vahid; Schwen, Lars Ole
The liver is the central metabolic organ in the mammalian body. Hepatic functions need to be understood from a multiscale perspective, i.e., at the organism, organ, lobular, cellular, and molecular levels that can span vastly different timeframes, e.g., from milliseconds of molecular events to months or years of chronic disease formation (cf. Figure 1). Computational models coupled with experimental measurements and clinical observations provide a viable and cost-effective means to investigate hepatic function. The Research Topic collected some recent results, clinical observations, and updated reviews or perspectives; the seven contributions are briefed below.
Dual continuum upscaling of liver lobule flow and metabolism to the full organ scale
(2022) Coombe, Dennis; Rezania, Vahid; Tuszynski, Jack A.
The liver is the body’s primary metabolic organ and its functions operate at multiple time and spatial scales. Here we employ multiscale modelling techniques to describe these functions consistently, based on methods originally developed to describe reactive fluid flow processes in naturally-fractured geological sediments. Using a fully discretized idealized lobule model for flow and metabolism, a dual continuum approach is developed in two steps: 1) Two interacting continua models for tissue and sinusoids properties, followed by 2) further upscaled dual continua models leading to an averaged lobule representation. Results (flows, pressures, concentrations, and reactions) from these two approaches are compared with our original model, indicating the equivalences and approximations obtained from this upscaling for flow, diffusion, and reaction parameters. Next, we have generated a gridded dual continuum model of the full liver utilizing an innovative technique, based on published liver outline and vasculature employing a vasculature generation algorithm. The inlet and outlet vasculature systems were grouped into five generations each based on radius size. With a chosen grid size of 1 mm3, our resulting discretized model contains 3,291,430 active grid cells. Of these cells, a fraction is occupied vasculature, while the dominant remaining fraction of grid cells approximates liver lobules. Here the largest generations of vasculature occupy multiple grid cells in cross section and length. The lobule grid cells are represented as a dual continuum of sinusoid vasculature and tissue. This represents the simplest gridded dual continuum representation of the full liver organ. With this basic model, numerous full liver drug metabolism simulations were run. A non-reactive PAC (paclitaxel) injection case including only convective transfer between vasculature and tissue was compared with including an additional diffusive transfer mechanism. These two cases were then rerun with tissue reaction, converting injected PAC to PAC-OH (6-hydroxypaclitaxel). There was little transfer of PAC from vasculature to tissue without the addition of diffusive transfer, and this had a significant observable effect on internal PAC distribution in the absence of reaction, and also on the distribution of PAC-OH for the reactive cases.
Uranium surface processes with sandstone and volcanic rocks in acidic and alkaline solutions
(2023) Kenney, Janice; Lezama-Pacheco, Juan; Fendorf, Scott; Alessi, Daniel S.; Weiss, Dominik J.
Understanding the behaviour of uranium waste, for disposal purposes, is crucial due to the correlation between pH values and the disposal of distinct types of waste, with low level waste typically associated with acidic pH values, and higher and intermediate level waste commonly related to alkaline pH values. We studied the adsorption of U(VI) on sandstone and volcanic rock surfaces at pH 5.5 and 11.5 in aqueous solutions with and without bicarbonate (2 mM HCO3–) using XAS and FTIR. In the sandstone system, U(VI) adsorbs as a bidentate complex to Si at pH 5.5 without bicarbonate and as uranyl carbonate species with bicarbonate. At pH 11.5 without bicarbonate, U(VI) adsorbs as monodentate complexes to Si and precipitates as uranophane. With bicarbonate at pH 11.5, U(VI) precipitated as a Na-clarkeite mineral or remained as a uranyl carbonate surface species. In the volcanic rock system, U(VI) adsorbed to Si as an outer sphere complex at pH 5.5, regardless of the presence of bicarbonate. At pH 11.5 without bicarbonate, U(VI) adsorbed as a monodentate complex to one Si atom and precipitated as a Na-clarkeite mineral. With bicarbonate at pH 11.5, U(VI) sorbed as a bidentate carbonate complex to one Si atom. These results provide insight into the behaviour of U(VI) in heterogeneous, real-world systems related to the disposal of radioactive waste.
Estimated discharge of microplastics via urban stormwater during individual rain events
(2023) Ross, Matthew S.; Loutan, Alyssa; Groeneveld, Tianna M.; Molenaar, Danielle; Kroetch, Kimberly; Bujaczek, Taylor; Kolter, Sheldon; Moon, Sarah; Franczak, Brian C.
Urban stormwater runoff is an important pathway for the introduction of microplastics and other anthropogenic pollutants into aquatic environments. Highly variable concentrations of microplastics have been reported globally in runoff, but knowledge of key factors within urban environments contributing to this variability remains limited. Furthermore, few studies to date have quantitatively assessed the release of microplastics to receiving waters via runoff. The objectives of this study were to assess the influence of different catchment characteristics on the type and amount of microplastics in runoff and to provide an estimate of the quantity of microplastics discharged during rain events. Stormwater samples were collected during both dry periods (baseflow) and rain events from 15 locations throughout the city of Calgary, Canada’s fourth largest city. These catchments ranged in size and contained different types of predominant land use. Microplastics were found in all samples, with total concentrations ranging from 0.7 to 200.4 pcs/L (mean = 31.9 pcs/L). Fibers were the most prevalent morphology identified (47.7 ± 33.0%), and the greatest percentage of microplastics were found in the 125–250 µm size range (26.6 ± 22.9%) followed by the 37–125 µm size range (24.0 ± 22.3%). Particles were predominantly black (33.5 ± 33.8%), transparent (22.6 ± 31.3%), or blue (16.0 ± 21.6%). Total concentrations, dominant morphologies, and size distributions of microplastics differed between rain events and baseflow, with smaller particles and higher concentrations being found during rain events. Concentrations did not differ significantly amongst catchments with different land use types, but concentrations were positively correlated with maximum runoff flow rate, catchment size, and the percentage of impervious surface area within a catchment. Combining microplastic concentrations with hydrograph data collected during rain events, we estimated that individual outfalls discharged between 1.9 million to 9.6 billion microplastics to receiving waters per rain event. These results provide further evidence that urban stormwater runoff is a significant pathway for the introduction of microplastics into aquatic environments and suggests that mitigation strategies for microplastic pollution should focus on larger urbanized catchments.
A specific dispiropiperazine derivative that arrests cell cycle, induces apoptosis, necrosis and DNA damage
(2023) Liu, Victor P.; Li, Wai-Ming; Lofroth, Jack; Zeb, Mehreen; Patrick, Brian O.; Bott, Tina; Lee, Chow H.
Dispiropiperazine compounds are a class of molecules known to confer biological activity, but those that have been studied as cell cycle regulators are few in number. Here, we report the characterization and synthesis of two dispiropiperazine derivatives: the previously synthesized spiro[2′,3]- bis(acenaphthene-1′-one)perhydrodipyrrolo-[1,2-a:1,2-d]-pyrazine (SPOPP-3, 1), and its previously undescribed isomer, spiro[2′,5′] bis(acenaphthene-1′-one)perhydrodipyrrolo-[1,2-a:1,2-d]-pyrazine (SPOPP-5, 2). SPOPP-3 (1), but not SPOPP-5 (2), was shown to have anti proliferative activity against a panel of 18 human cancer cell lines with IC50 values ranging from 0.63 to 13 μM. Flow cytometry analysis revealed that SPOPP-3 (1) was able to arrest cell cycle at the G2/M phase in SW480 human cancer cells. Western blot analysis further confirmed the cell cycle arrest is in the M phase. In addition, SPOPP-3 (1) was shown to induce apoptosis, necrosis, and DNA damage as well as disrupt mitotic spindle positioning in SW480 cells. These results warrant further investigation of SPOPP-3 (1) as a novel anti-cancer agent, particularly for its potential ability to sensitize cancer cells for radiation induced cell death, enhance cancer immunotherapy, overcome apoptosis-related drug resistance and for possible use in synthetic lethality cancer treatments.

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