Welcome to the UAF Graduate School's Thesis Repository! Here we will have the digital theses that are given to us by past graduate and doctoral students.

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  • Bioavailability and chemical characterization of soil organic matter in Arctic soils

    Dai, Xiaoyan; Ping, Chien-Lu; White, Dan; Hines, Mark; Chapin, Terry; Candler, Rudy; Valentine, David (2001-08)
    The purpose of this research was to evaluate bioavailability and chemical characteristics of soil organic matter (SOM) in Arctic tundra soils. Five soil horizons in three different sites located in the Arctic Slope of Alaska were used for this research. This thesis comprises five chapters, each of which described a method that can be used to study the bioavailability and chemical characteristics of SOM in these samples. Chapter One used laboratory incubation technique to determine CO2 evolution from the soils. The cumulative CO2 respired from the samples during the incubation period was used as index of bioavailability of SOM. Chapter Two utilized cross polarization magic angle spinning (CPMAS) 13C NMR and liquid-state 13C NMR techniques to evaluate the chemical composition of SOM. Chapter Three described how pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) was used to characterize SOM. Chapter Four summarized different approaches for characterizing SOM, and Chapter Five used amino sugar contents in soils to assess the microbial contribution to SOM. The laboratory incubation study indicated that temperature had a positive effect on the CO2 evolution from these samples, and the tundra soils would have higher potential to contribute to greenhouse gas emissions with elevated temperature. Among the extractable soil organic fractions, neutrals such as hydrophilic neutrals (HIN), hydrophobic neutrals (HON) and low-molecular-weight neutrals (LMN) are more bioavailable than these such as humic acid (HA) and fulvic acid (FA). Liquid-state and solid-state 13C NMR and Py-GC/MS techniques exhibited more potential for evaluating the relative quality of SOM compared to the wet chemical analysis method. Together with the laboratory incubation method, these techniques can be used to identify the chemical composition of SOM, and to establish correlations between the chemical composition and bioavailability of SOM. Amino sugars in soil can provide insights into the microbial contribution to SOM and to the quality and bioavailability of SOM due to their microbial origin. Bacterial-derived muramic acid and fungal-derived glucosamine can be used to differentiate between bacterial and fungal contributions to SOM. Coupled with chemical composition changes resulted from incubation at different temperatures, these results can be used to interpret the dynamics of microbial population.
  • Smoke without fire: wildfire smoke affects phenolic composition of wild blueberry fruits (Vaccinium uliginosum)

    Weingartner, Laura G.; Mulder, Christa; Tomco, Patrick; Bret-Harte, Syndonia (2023-12)
    Wildfire smoke can induce changes in plant growth, phenology, and chemical composition. The frequency and intensity of wildfires have increased over the last thirty years in Alaska, and smoke has the potential to affect important wild fruit plants, such as bog blueberry (Vaccinium uliginosum L.), a food source for many Alaskans and wild animals. We exposed bog blueberry plants to wood smoke at different stages in fruit development: early-season when the plants were flowering ("early-smoked"), mid-season when fruits were unripe ("mid-smoked"), and late-season when fruits were fully ripe ("late-smoked"). We measured anthocyanins, proanthocyanidins, and total phenolics in the ripe fruits, as well as branch growth, leaf anthocyanin levels, fruit set, and flower, fruit, and leaf phenology. Impact of smoke exposure on anthocyanins depended on fruit developmental state: fruits exposed late in the season had no changes in anthocyanin concentration, while early- and mid-smoked fruits showed increases in anthocyanins. Changes in proanthocyanidins followed a similar pattern to anthocyanins, but differences between treatments were not statistically significant. Total phenolic compounds were not different across treatments. Leaf anthocyanins from mid-smoked and late-smoked plants were higher than the control, while early-smoked leaves were unaffected. Early-smoked plants had lower fruit set than the control, but there was no effect of smoke exposure on mid- and late-smoked fruit abundance. Smoke caused treated plants to lose leaves at a faster rate than control plants, but did not change the timing of leaf color change. Smoke did not affect branch growth or flower and fruit phenology. Our study shows that smoke has immediate effects on bog blueberry in the increase of anthocyanins in leaves and fruits, and seasonal effects in lower leaf longevity and limited fruit set in plants exposed while flowering. These results indicate higher stress levels in smoke-exposed plants that might result in higher fruit quality due to the health benefits of anthocyanins, but at the expense of fruit abundance.
  • Effects of desformylflustrabromine on compulsive-like and social behaviors in mouse models of OCD and autism

    Van Flein, Isaac; Bult-Ito, Abel; Drew, Kelly; Kitaysky, Alexander (2023-12)
    Obsessive-Compulsive Disorder (OCD) and autism spectrum disorders (ASD) share a number of similar deficits, including altered cholinergic activity in the central nervous system (CNS), manifestation of repetitive, restricted, and compulsive-like patterns of behavior, and frequent co-morbid presentation. Desformylflustrabromine is a novel positive allosteric modulator of α4β2 nicotinic acetylcholine receptors, which has recently been shown to be able to reduce compulsive-like behavior in a non-induced mouse model of OCD. In this study, I attempted to replicate the compulsive-like behavior-reducing effects of desformylflustrabromine in the mouse model of OCD, as well as expose the model to a novel assessment; social behavior, as measured by the 3-Chamber Social test. Furthermore, I altered the model with prenatal exposure to valproic acid to induce an ASD-like construct. This ASD animal model has been used extensively to study the social deficits and neurochemistry of ASD, although limited data exists on co-morbid models. By exposing the OCD model to valproic acid, I attempted to establish two additional models; a comorbid OCD / ASD model in the compulsive-like high-activity (HA) strain and an ASD model in the non-compulsive-like low-activity (LA) strain. All mouse models and controls participated in a battery of behavioral tests quantifying compulsive-, anxiety-, and depression-like behaviors, as well as the 3-chamber social test to quantify social preference behaviors. The ASD model was not strongly established, and the desformylflustrabromine appeared to be inactive in all strains and models. I assessed potential reasons for the failure to establish a robust ASD construct in the OCD mouse model, and the failure of desformylflustrabromine to have any significant effect, in contrast with previous research using the drug in the OCD mouse model.
  • Exploring competing gold system models in the Valdez Creek region, Clearwater Mountains, Alaska

    Suhey, Jane Marguerite; Regan, Sean; Nadin, Elisabeth; Kreiner, Douglas (2023-12)
    Gold deposits located within the accretionary and subduction-related tectonic environment of south-central Alaska are interpreted to have formed via devolatilization of hydrous assemblages through regional metamorphism (orogenic model) or by intrusion-related hydrothermal processes (intrusion-related gold system model). The Valdez Creek mining district is located in the southern Clearwater Mountains of south-central Alaska along the intermontane-insular belt suture of the North American Cordillera. The 67-56 Ma south-vergent Valdez Creek shear zone resulted in the thrusting of North American-derived Maclaren schist (intermontane) structurally above lower greenschist-facies rocks of the Clearwater metasediments (Insular). The ~ 5km thick ductile shear zone preserves a complete inverted Barrovian metamorphic gradient ranging from lower greenschist-facies conditions in the south to upper-amphibolite-facies in the north. This event records the terminal suturing of the Wrangellia composite terrane with the North American margin. Placer gold mining and lode gold exploration is currently focused within the footwall of the Valdez Creek shear zone. The region also contains previously undated Cretaceous intrusive rocks associated with gold-in-soil geochemical anomalies. Here, competing gold system models were investigated to identify the predominant mineralization process. This information is used to improve exploration strategies in the area and further develop our understanding of gold formation in the Clearwater Mountains, Alaska. Constraining mechanisms of gold mineralization through integrating structural analysis, geochemistry, and a multiphase geochronologic framework provides a robust tool to determine dominant ore-forming mechanisms. ⁴⁰Ar/³⁹Ar and ²⁰⁶Pb/²³⁸U geochronological methods were used to determine the timing of gold mineralization and constrain ages of igneous rocks associated with known lode sources. Detrital gold geochemistry methods were used to compare placer gold and lode gold compositions. Bulk rock major and trace element geochemical methods were also used to evaluate a primary gold-model by investigating compositional differences of gold-like elements across the Valdez Creek shear zone. Detailed mapping and structural analysis were completed to test if gold mineralization is compatible with shear zone activity (supporting an orogenic model) or if mineralization was unrelated to regional metamorphism and overprinted by the shear zone from 67-56 Ma (supporting an intrusion-related gold system model). The ²⁰⁶Pb/²³⁸U zircon data collected from the alkali pluton suite and the placer system indicates gold-hosting veins were localized within and adjacent to alkaline plutons in the region. These data also indicate that detritus in the placer system was locally derived. White mica ⁴⁰Ar/³⁹Ar geochronology integration ages from undeformed gold-bearing quartz veins proximal to intrusions supports a young mineralization age for gold between 62.11 Ma to 66.58 Ma. Similarities in gold chemistry were also identified within placer gold samples collected from current mining operations and a lode gold location within the catchment. Structural observations show gold-bearing mineralization in quartz veins is likely synchronous with the penetrative deformation associated with the Valdez Creek shear zone. Discrete and network vein orientations throughout the shear zone have geometries compatible with top-to-the-south shear sense of the Valdez Creek shear zone. These results are compatible with a local gold lode source for the Valdez Creek placer deposit that formed coeval with the Valdez Creek shear zone. Bulk rock major and trace element geochemistry results from across the Valdez Creek shear zone metamorphic gradient show a systematic decrease in As, Cu, Ni, Zn, Pb, and Au across the greenschist-amphibolite facies transition indicating that auriferous fluids may have been derived from the shear zone. We hypothesize that metamorphic fluids generated from the dehydroxylation of chlorite occurred simultaneously with shearing along the Valdez Creek shear zone. In this system, auriferous fluids were likely concentrated within or proximal to rigid intrusion(s) in the footwall of the shear zone, coinciding with vein development and fluid channelization, similar in process to the Juneau Gold Belt.
  • Relative abundance and movement ecology of tiger sharks Galeocerdo cuvier in the waters surrounding Bimini, the Bahamas

    Smukall, Matthew J.; Seitz, Andrew; Grubbs, Ralph Dean; Guttridge, Tristan; Kruse, Gordon (2023-12)
    Shark populations are under increased anthropogenic pressures around the world. Large-bodied shark species are upper trophic level predators, and therefore there is concern that declining numbers of sharks may have significant implications for ecosystems. In response to these conservation concerns there has been increased focus on the implementation of regulations, fishery management plans, national plans of action, and marine management zones in some nations. However, large sharks are often highly mobile and can move readily across jurisdictional boundaries. Therefore, there is a need to monitor long-term relative abundances within regions and simultaneously examine the duration to which species remain in these areas. The Bahamas was established as a 'Shark Sanctuary' in 2011, but long-term abundance and movement data are lacking for many species. The goal of this study is to determine the relative abundance and movement ecology for tiger sharks Galeocerdo cuvier in the waters around Bimini, The Bahamas. Fishery independent ongline surveys from 1984 to 2019 suggest that the local relative abundance remained stable during this time. Gear selectively prevented direct comparisons of catch rates to other surveys, but for context abundance trend were analyzed from the directed shark fishery in the nearby southeastern USA, which interacts with the same population of tiger sharks. This analysis showed an increasing abundance trend in USA waters during the late 1990s and early 2000s, after which abundances stabilized. Conventional tagging and passive acoustic and satellite telemetry were used to determine residency, regional movements, and long-term philopatry of young-of-the-year to mature tiger sharks. Overall data for juveniles were sparse, likely due to constraints of energetic condition and high natural mortality. Large juvenile and mature tiger sharks displayed seasonal local residency that was negatively correlated with water temperature, but also dispersed widely throughout the region, and spent significant time outside of Bahamas territorial waters. Taken together, these results highlight that localized conservation measures offer some level of protection for tiger sharks, however they do spend time in multiple jurisdictions and regional cooperation on management plans is important.
  • Microplastics in spotted seal stomachs from the Bering and Chukchi Seas in 2012 and 2020

    Sletten, Alexandria; Horstmann, Lara; Iken, Katrin; Bryan, Anna (2023-12)
    Microplastics pose a significant threat to marine ecosystems across multiple trophic levels. Spotted seals (Phoca largha) are piscivorous and occupy one of the higher trophic positions in the Bering and Chukchi seas, putting them at risk of ingesting microplastics through prey. This project aimed to determine if microplastics are present in the stomachs of spotted seals harvested for subsistence purposes and compare their presence spatially between two harvest locations, Gambell and Shishmaref, AK. Microplastics are predicted to increase in the Arctic over time due to climate warming and subsequent deposition of microplastics from melting sea ice. Therefore, we examined stomachs from 2012 and 2020 to explore temporal changes. Furthermore, as spotted seal pups (<1 yr of age) and non-pups forage differently, we expected a difference in microplastic ingestion between age classes. We processed stomachs using enzymatic digestion and vacuum filtration. Use of the enzyme digestion method enabled microplastic detection while preserving the hard parts of prey items (e.g., fish otoliths and shrimp carapaces) for diet analysis. We then examined filters with a stereomicroscope, and calculated microplastic frequency of occurrence (FO). A total of 34 (16 from 2012 and 18 from 2020) stomachs from Gambell and Shishmaref have been examined, and a total of 211 microplastic particles were isolated from 33 stomachs (97.1% FO), containing 1 to 23 particles per stomach. Our analysis showed no significant difference in FO between pups and non-pups, between the two harvesting locations, or between harvest years. Additionally, there was no significant difference in the microplastic concentration among the spotted seal stomachs examined in this study. Our data indicate that microplastic ingestion has not changed in frequency between age class, harvest location, or year. This baseline study was successful in isolating microplastics in the stomachs of spotted seals and showed that microplastics have been ingested consistently by spotted seals for at least the past decade. Furthermore, we found increased microplastic abundance in spotted seal stomachs when seals consumed prey at higher trophic levels and prey from benthic zones. Continued study of microplastic ingestion, including absorption and accumulations of the contaminants, is needed to assess potential impacts on the health of spotted seals and other ice-associated pinnipeds, who serve as indicators of ecosystem health in the Bering and Chukchi seas.
  • Avian divergence and speciation across Beringia examined using comparative mitogenomics

    Collier, K. A.; Winker, Kevin; Wolf, Diana; Sikes, Derek (2023-12)
    Accurate knowledge of divergence and speciation processes is critical for understanding key aspects of biodiversity. As a well-known, speciose group of vertebrates, an increased understanding of how birds diverge and speciate allows us to better manage extant avian diversity and understand how it develops over time. Additionally, birds often exhibit complex and variable patterns of divergence, resulting in complexes of taxonomic uncertainty. Filling gaps in our knowledge of divergence across time and space increases our ability to correctly identify and understand not just avian diversity but clade-level patterns in speciation processes. These higher-order findings give us tools to compare and understand biodiversity more broadly across a wide range of taxa. In this thesis, I investigated both temporal and spatial elements of avian divergence, with an emphasis on the high-latitude system of Beringia, which is of particular interest for speciation due to its position at the meeting point of the Eurasian and American continental avifaunas. Chapter 1 describes my investigation of the temporal dynamics of Beringian divergence. The cyclic opening and closing of the Bering Strait due to glacial cycles intermittently isolated and reunited Asia and North America during the Pleistocene (2.6 Mya to 10 Kya). This was hypothesized to produce an uncertain number of associated 'pulses' of avian divergence events spanning that time period. I used a pairwise sampling approach among 39 taxa and a mitogenomic dataset under Bayesian modeling and found no statistical evidence for multiple vicariance events. Instead, divergence times were spread fairly evenly across a large period of time, appearing as a single vicariance event. This is biologically unusual given the system and the cyclic nature of the most likely abiotic driver (glacial cycles) and may be the result of multiple overlaid periods of divergence and gene flow in taxa with older divergence dates. In Chapter 2, I examine the relative contributions of phenotypic and genetic divergence in pairwise comparisons of diverging bird lineages in high- versus low-latitude systems in Beringia and the Philippines. Phenotypic divergence in birds is assumed to be largely due to selection (Price 2008), with genetic divergence assumed to be more driven by time in isolation. I hypothesize that the Beringian system should have less divergence overall than the Philippines, but that a greater proportion of the divergence should be phenotypic, due in part to increased population connectivity in high-latitude systems as a result of larger long- term range fluctuations as a result of Pleistocene glacial cycles. Increased connectivity should be particularly effective in removing neutral, rather than phenotypic, divergence, where selection may be in operation, in part due to a nonlinear, inverse relationship between gene flow and neutral divergence. To test this, I used standardized measures of phenetic and genetic divergence and used linear regressions to quantify the relationship between divergence metrics and the rates of divergence in each system. Beringia showed lower levels of genetic and phenotypic divergence than the Philippines, but the relationship between data types was stronger and the rate of divergence higher than in the Philippine system. I suggest that this is a result of decreased time spent in allopatry in high-latitude systems, but recognize that an increased rate of phenotypic divergence, possibly due to increased selection pressure at high latitudes, also might play a role.
  • Estimating relative indices of groundfish abundance from multiple fishery-independent data sources: a comparison of intercalibrating model-based abundance estimators

    Sebens, Tristan Noble Glendenning; Cunningham, Curry J.; Mueter, Franz; Bryan, Meaghan; Adkison, Milo (2023-12)
    Stock assessments are critical tools for sustainable fisheries management, and abundance indices estimated from fishery-independent data represent a crucial data source for these assessments. However, financial constraints on these surveys limit the number of samples taken per year, and/or the frequency with which regions are sampled. Additionally, it remains challenging for any individual survey to sample the entire domain of a stock due to contact-selectivity of the sampling gear and the accessibility of specific habitats to specific gear types. Further, the cost of operating fishery-independent surveys can result in surveys conducted on biennial or triennial schedules, resulting in temporal gaps in survey timeseries that may limit their ability to adequately index short lived species. One method by which these challenges might be addressed is through the use of model-based estimators, which estimate relative and/or absolute indices of abundance by intercalibrating data collected by multiple surveys with different spatial, temporal, or habitat footprints. While recent research has explored a number of potential applications of these methods, little to no prior research has assessed the relative performance of these methods in terms of the accuracy or uncertainty of their estimates. In the first chapter of this thesis, I fit Random Walk Timeseries (RWTS) models, Generalized Additive Models (GAM), and Vector Autoregressive Spatiotemporal Models to data collected by three fishery-independent surveys across four species/region case studies, and compare the model-estimated indices to design-based indices estimated by the Alaska Fisheries Science Center (AFSC) Bottom Trawl Survey (BTS) as a reference abundance timeseries. In the second chapter, I then simulate an age-structured and spatially heterogenous population dynamics for the Pacific Cod (Gadus macrocephalus)) stock in the Gulf of Alaska, to explore the reliability of intercalibrated indices of abundance. To do so I generate artificial survey catch data for three fishery-independent surveys, fit GAM and VAST survey intercalibration models, and then assess the accuracy and precision of the model-based indices. Results from the real species-region case studies in Chapter 1 suggest that RWTS, GAM, and VAST models all exhibit comparable performance, but the model structures used in this analysis struggled to estimate indices of abundance consistent with established abundance estimates in the presence of conflicting survey catch-rate signals. Results from the simulation experiment in Chapter 2 also suggest that the accuracy of the model-estimated indices is strongly influenced by the level of contrast in the size-selectivity profiles of the constituent surveys, and the rate at which the size-composition of the surveyed stock changes. I recommend that future work explores forms of these model-based estimators which estimate size-specific changes in abundance, and whether or not the inclusion of those elements improved the accuracy and precision of the estimated indices of abundance.
  • When beavers get burned, do fish get fried? The role of beavers to mediate wildfire effects on arctic grayling in boreal Alaska

    Samuel, William T.; Falke, Jeffrey; Tape, Kenneth; Seitz, Andrew; Panda, Santosh (2023-12)
    Wildfire is a dominant natural disturbance process throughout boreal North America and fires are increasing in size, frequency, and severity. However, little is known about how wildfire affects boreal fish populations and aquatic habitat despite the substantial impacts of fire on ecosystem processes, and even less is known about how fire effects are mediated by species interactions. For example, North American Beavers (Castor canadensis) are affected by and can influence wildfire dynamics, and their engineering has complex effects on aquatic habitats. North American Beavers therefore have the potential to mediate wildfire effects on aquatic ecosystems and fish populations. Here I investigated relationships between wildfire and the distribution of beavers and a common fish species across a fire-dominated riverscape in Interior Alaska. First, I used satellite imagery to locate and enumerate beaver ponds throughout five large watersheds (total area: 20,711 km²) and modeled the relationship of beaver pond density (ponds per km²) as a function of wildfire history, stream geomorphology, hydrology, and vegetation composition. I then used a simulation to conceptualize the impacts of wildfire and beaver dams on Arctic Grayling (Thymallus arcticus) habitat availability under variable hydrologic conditions. Next, I sampled 62 streams for Arctic Grayling environmental DNA (eDNA) and sampled 10 of those streams for Arctic Grayling abundance. I used a generalized linear model (GLM) and N-mixture model to understand the relationship between eDNA concentration and Arctic Grayling abundance and distribution throughout the study area. I found that wildfire metrics explained most variation in beaver pond density (pseudo R² = 0.75) across the landscape and were positively associated with beaver pond density, although geomorphological and hydrological parameters were also important. My simulations indicated that beaver dams can create substantial barriers to fish dispersal during low water conditions (up to 20% reduced habitat availability in some river basins) and can severely reduce (up to 65%) habitat availability in some tributary streams. I found that eDNA concentration was moderately correlated with Arctic Grayling abundance (GLM: pseudo R² = 0.45) and unexplained variation was likely due to the spatial mismatch between fish sampling and scale of eDNA representation. However, I estimated eDNA residence time of about 6.7 hours in one stream, and eDNA appeared to accumulate longitudinally throughout the tributary, indicating that an eDNA sample near the downstream end was likely a good relative representation of Arctic Grayling abundance in a tributary. Results from the N-mixture model indicated that stream geomorphology and hydrology were the most important predictors for Arctic Grayling abundance (eDNA concentration), wildfires had a negative effect, and beaver dam density had a mixed effect on Arctic Grayling abundance. Overall, this study illustrated that beaver densities can increase after wildfires in Interior Alaska stream networks, which could result in negative impacts on Arctic Grayling habitat availability if beavers impair fish passage; however, these effects are dependent on the environmental context and suggest beaver-fish interactions may be best managed on a case-by-case basis.
  • Indigenous self-determination in co-production of knowledge

    Rudolf, Margaret Hope Cysewski; Trainor, Sarah; Hirsch, Alexander; Hum, Richard; Topkok, Sean Asikłuk (2023-12)
    Analyzing and comprehending co-production of knowledge (CPK) in the context of working with Arctic Indigenous communities on climate change research is the main goal for this interdisciplinary doctoral dissertation. CPK is shared decision-making on every step of the research process with research partners from communities, agencies, or organizations. CPK with Arctic Indigenous communities requires dedicated consideration of equity, ethics, cultural worldviews, and colonization. Key concepts from Indigenous critical methodologies are used to analyze both the CPK theory and implementation. CPK has the potential to be an ethical space to question the status quo of research processes and support Indigenous self-determination. Critiquing NSF's Navigating the New Arctic as a case study, there were many missteps in not following CPK in the development of the program and projects, along with not following United Nations Declaration on the Rights of Indigenous Peoples' Free, Prior, and Informed Consent (Ch. 2). There are significant lessons to be learned from the literature on collaborative methodology, including Indigenous methodologies. Through synthesis work, a model was developed compiling factors of success to achieving CPK along with a discussion of perspectives on those factors and success metrics. The objective of the synthesis work is the development of tools to support transparent communication and co-design of research projects (Ch. 3). CPK happens in-between the boundaries of disciplines, cultures, and science-policy-community. Thirteen experts in boundary spanning co-produced lessons-learned and recommendations based on their expertise and experiences. The project co-produced strategies to overcome funding barriers and the cultural divide to Alaska Native communities utilizing a boundary analysis framework (Ch. 4). Applying the CPK and boundary spanning concepts, themes of success in improving Arctic observing were developed from homogenous focus groups. With thirty-four participants representing scientists, science coordination experts, policy experts, and Indigenous community leaders and scholars, co-analysis was impractical. Following the Rapid Assessment Process utilizing focus groups, themes of success and corresponding science and Indigenous perspectives were developed (Ch. 5).
  • Controlling dust concentration in a fan housing using settling chambers and water sprays

    Quevedo Delgado, Cristian Alonso; Arya, Sampurna N.; Ghosh, Tathagata; Fan, Long (2023-12)
    Dust generation is a consequence of various activities in the mining industry. The industry generates dust in quantities that can present occupational health hazard and equipment damage. A notable instance of equipment deterioration is the corrosion and erosion experienced by fan blades in underground mines. This thesis introduces settling chambers and water spray as feasible techniques commonly used for controlling dust in underground mine operations. The research aims to provide a low capital cost and maintenance-free system to capture the dust particles upwind of the main fan. The research focuses on an underground polymetallic mine in Peru, serving as a case study. It was conducted in two distinct phases. In the first phase, airflow data in the upcast shaft and the fan housing was collected from the collaborating mine in Peru. Subsequently, a 3D model of the shaft and the fan housing system was developed, and a Computational Fluid Dynamics (CFD) simulation of the airflow in the system was performed. The results of the CFD simulation were compared against the airflow data from the mine, and the CFD model was validated. The 3D model of the upcast shaft-fan housing system was adapted to incorporate the settling chamber, which underwent variations in shape, length, and hydraulic diameter, resulting in the creation of 18 modified models. For each model, CFD simulation was conducted in steady-state condition to establish flow in the computational domain, followed by transient-state simulations to replicate the behavior of dust and assess the settling chamber's efficiency in capturing dust particles with aerodynamic diameter ranging from 1 μm to 400 μm. Furthermore, Sensitivity analysis was performed to examine the effect of shape, length, hydraulic diameter, and airflow velocity on the capture efficiency of the settling chamber. Analysis of the simulation results indicated a significant dust reduction of up to 60%. The second phase of the research involved simulated the capture of dust using water spray system within a return entry. Different water spray nozzles, characterized by varying spray angles, velocities, and droplet sizes, were simulated to evaluate their impact on dust capture efficiency. The analysis of the results revealed that the system could achieve a dust capture efficiency of up to 60%.
  • Eavesdropping on killer whales: distribution, calling rates, and acoustic abundance of fish-eating and mammal-eating killer whales in the Gulf of Alaska

    Myers, Hannah J.; Konar, Brenda; Horstmann, Lara; Matkin, Craig; Mueter, Franz; Guazzo, Regina; Ford, John (2023-12)
    The widespread loss of apex consumers in marine, terrestrial, and freshwater ecosystems throughout the world has precipitated profound trophic cascades and switches to different ecological states. However, conserving top predators can deliver broad biodiversity benefits and improve ecosystem resiliency. Effective conservation and management policy is predicated on a species' distribution and abundance in a given area and time. In this dissertation, I provide new insight into killer whale (Orcinus orca) distribution, vocal behavior, and abundance in the Gulf of Alaska using passive acoustic monitoring and advance long-term monitoring capacity for this species. First, I describe the year-round spatiotemporal distribution and daily acoustic residency patterns of southern Alaska resident (fish-eating) and two populations of transient (mammal-eating) killer whales. I found distinct seasonal patterns across locations for each genetically distinct population and discovered that both resident and transient killer whales used the coastal monitoring areas more extensively than previously known--including in winter. Second, I estimated resident and transient killer whale calling rates, a prerequisite to acoustic abundance estimation. I found that the mean calling rate for southern Alaska resident (fish-eating) killer whales was consistent across space, time, ambient noise level, which pod was calling, and the presence of other pods. Gulf of Alaska transient (mammal-eating) killer whale calling rates were higher than resident's and differed across locations. AT1 transients (mammal-eating) produced fewer calls more rapidly than Gulf of Alaska transients, and their mean rate was stable across spatiotemporal factors. Although transients call less often than residents, I found that once vocalizing, they do so at a higher rate. Finally, I estimated and modeled the year-round daily acoustic abundance of resident and transient killer whales across distinct areas in the Gulf of Alaska and developed Bayesian time series models to describe seasonal patterns and predict future abundance. Acoustic abundance estimates for the southern Alaska resident and Gulf of Alaska transient killer whales matched expectations from visual studies. I established distinct seasonal abundance patterns across areas, and acoustic monitoring enabled killer whale abundance estimation across a greater spatiotemporal extent than other methods. This work is critical for an accurate understanding of killer whales' top-down forcing effects in the marine ecosystem, as well as to inform conservation and management policy for this federally protected species.
  • Environmental and biotic habitat attributes affect rocky intertidal community variability in glacially influenced estuaries

    McArthur, Madeleine G.; Konar, Brenda; Schram, Julie; Umanzor, Schery (2023-12)
    Climate change is increasing the rate of glacial recession in high latitude coastal environments. The associated increase in cold, sediment-laden freshwater into the nearshore may alter a wide array of water attributes, which will likely have ecosystem-wide impacts. One of these potential impacts is a change in typical levels of ecological community variability, which can be an indicator of stress in response to an environmental impact. Fluctuation in community composition over time is natural and can be affected by environmental conditions, as well as by the presence of habitat forming, spatially dominant organisms. The goal of this study was to determine how variation in environmental attributes and spatially dominant species contributes to the variability of rocky intertidal community assemblages in glacially influenced estuaries. The environmental attributes of interest were both dynamic in nature (water temperature, salinity, dissolved oxygen, turbidity, and pCO₂), and static (substrate type, wave exposure, beach slope, and distance to freshwater). Variation in the proportions of three spatially dominant organisms, Mytilus trossulus (mussels), Balanus spp. (barnacles), and Fucus spp. (rockweed) were examined as biotic habitat attributes. The average attachment strength of mussels was also surveyed. It was hypothesized that 1) dynamic environmental attributes would be more strongly correlated to community variability patterns than static attributes, 2) higher proportions of spatially dominant species would correspond to lower levels of community variability, and 3) community variability would be lower when mussels had higher attachment strength. To document community variability, as well as proportions of spatially dominant species, percent cover and biomass data were collected along with environmental data from 2019 to 2022. Barnacle cover, rockweed cover, and substrate characteristics (cover of gravel and total cover of bare rock) were significantly correlated to community variability levels based on percent cover data. Community variability levels based on biomass data were significantly correlated to mussel cover, rockweed biomass, substrate aspects (cover of gravel and mud), distance to a freshwater source, and variation in dissolved oxygen levels. All relationships between community variability and each of these attributes were negative, except distance to freshwater and dissolved oxygen variation. These results highlight significant drivers of community variability in glacially influenced estuaries, providing insights into how these communities may be affected by the progression of climate change.
  • Marine methane: sources and potential adverse effects

    Mahmuda, Sadia; Aggarwal, Srijan; Rea, Lorrie; Dev, Subhabrata (2023-12)
    Recently, there has been an increase in the occurrence of incidents involving spills of oil and natural gas, such as methane. The world experiences at least one major spill in each decade. An illustrative case is the Deepwater Horizon oil disaster in 2010 in the Gulf of Mexico. This catastrophe resulted in the discharge of about 205.8 million gallons of oil and 225,000 metric tons of methane gas into the Gulf of Mexico. More recently, in 2022, the Nord Stream pipeline leak occurred, which was the largest single methane release ever recorded. It released up to 500K tons of methane underwater, a greenhouse gas with a significantly higher potency than carbon dioxide. Due to the Deepwater Horizon incident, mammals, sea turtles, birds, fish, and invertebrates were adversely affected and caused damage to the corals. More than 90 bird species died, and 1300 miles of shoreline became polluted. The fishing industry suffered a significant reduction. This study systematically reviewed the source and impact of methane in the marine environment, utilizing 271 peer-reviewed academic publications, eight non-peer-reviewed sources, and 44 online resources. In the marine environment, methane can come from various sources such as methane hydrate, methane seeps, pockmarks, mud volcanoes, microbial activities, and anthropogenic sources or human-induced activities. Sediment typically contains methane from methane seeps, methane hydrates, mud volcanoes, and microbial activity. In the water column, methane is produced from diffusion from hydrates, seeps, hydrothermal vents, and thermogenic and anthropogenic sources. On the other hand, air-water interface methane comes from the atmospheric exchange or diffusion from the water column or sediment. In marine water, methane undergoes various reactions. Methane reacts with oxygen, producing carbon dioxide in aerobic conditions. Conversely, in anaerobic conditions, methane is anaerobically oxidized, coupling with sulfate reduction mediating by sulfate-reducing bacteria and methanotrophic archaea. These microorganisms, bacteria, and archaea derive the majority of their carbon and energy from methane, and they can proliferate their number where they find excess methane. However, excess methane can create anoxic conditions by reducing oxygen concentration. Invertebrates utilize methane through a symbiotic relationship with methane-consuming microorganisms. Moreover, the marine ecosystem exhibits complex interdependencies among the organisms and methane.
  • Preserving reflections of ourselves: the past, present, and future of Alaska's museums

    Linn, Angela J.; Ehrlander, Mary; Koskey, Michael; Jonaitis, Aldona (2023-12)
    While museums are very good at collecting, preserving, documenting, and interpreting the histories of our communities, we have not done a very good job with our own histories. No comprehensive publication holistically examines the development of museums in Alaska, let alone looks critically at the "big three" (Alaska State Museums, University of Alaska Museum of the North, and the Anchorage Museum) with a goal of establishing a connection between the historical context, the individuals who shaped those museums, and the institutions' current states of being. This dissertation uses the academic fields of history, museology, and ethnography to discover and analyze how we find ourselves in the current state, while offering suggestions for moving ahead in a positive way. In this dissertation I examine the past, present, and future of Alaska's museums. I do this by first assembling a more complete history of the "big three" using archival primary sources, published literature, and interviews. Second, I examine the current state of museums with their strengths and challenges through a combination of literature review, interviews, surveys, and participant observation. Finally, I consider the way Alaska's museums might respond to the changes facing museums around the world by reflecting on current museological literature, current events, and examining two case studies based on my work at the University of Alaska Museum of the North located on the campus of the University of Alaska Fairbanks.
  • Volcanic gas quantification under suboptimal conditions

    Kushner, D. Skye; Lopez, Taryn; Kern, Christoph; Larsen, Jessica; Simpson, William (2023-12)
    Volcanic gas emissions are challenging to quantify. Achieving high confidence in gas composition, column concentrations, and emission rates acquired using remote sensing techniques is thought to require optimal atmospheric conditions. These conditions are often not met, creating a reluctance to preform measurements under non-ideal atmospheric conditions with inherent uncertainty about how useful those measurements may be. In the case of volcanic eruptions, the hazardous nature of the volcanic plume creates an environment where it is often not safe to collect measurements. This dissertation presents three projects which aim to constrain the quantity of two specific volcanic gases, mercury (Hg) and sulfur dioxide (SO₂), released under non-ideal measurement conditions. Specifically, chapter 2 aims to constrain Hg emission during volcanic eruptions, chapter 3 aims to characterize the uncertainty in SO₂ emission rates acquired under specific non-ideal atmospheric conditions, and chapter 4 aims to improve constraints on plume altitude for scanning remote sensing measurements of SO₂ emission rates acquired from a single instrument. Ash is a potential sink of volcanically-sourced atmospheric mercury, and the concentration of particle-bound Hg may provide constraints on Hg emissions during eruptions. In Chapter 2, the Hg concentrations in 227 bulk ash samples from the Mt. Spurr (1992), Redoubt (2009), and Augustine (2006) volcanic eruptions are examined to investigate large-scale spatial, temporal, and volcanic-source trends. No significant difference in Hg concentrations is found in bulk ash by distance from the eruption source or for discrete eruptive events at each volcano, suggesting that in-plume reactions converting gaseous Hg⁰ to adsorbed Hg²⁺ are happening on timescales shorter or longer than considered in this study (minutes to hours) and any additional in-plume controls may be masked by intra-volcanic sample variability. A significant difference is found in Hg concentration in ash among volcanic sources, which indicates that specific volcanoes may emit comparatively high or low quantities of Hg. These findings allow for the calculation of minimum, first-order estimates of volcanic Hg emissions during eruption in combination with total mass estimates of ashfall deposits. Mt. Spurr is found to be a high Hg emitting volcano such that its 1992 particulate Hg emissions likely contributed substantially to the global eruptive volcanic Hg budget for that year. Based on this study, previous approaches that used long-term Hg/SO₂ mass ratios to estimate eruptive total Hg under-account for Hg emitted in explosive events, and global volcanogenic Total Hg estimates need revisiting. A large source of error in SO₂ emission rates derived from mobile differential optical absorption spectroscopy (DOAS) is the uncertainty in atmospheric light paths between the scattered sunlight and the instrument, particularly under non-ideal atmospheric conditions such as the presence of clouds beneath the volcanic plume. In Chapter 3, numerical simulations using the McArtim model are used to examine the radiative transfer associated with zenith-facing mobile DOAS traverses for scenarios where there is a cloud layer between the instrument and the volcanic plume. In total, 217 permutations of atmospheric optical conditions are considered, allowing for the determination of errors associated with atmospheric scattering. Objective criteria are also developed for selecting SO₂ baselines and plume limits for each simulated traverse. This study then applies models to a real-world dataset from the 2021 Cumbre Vieja eruption to explore the effects of ground-level haze on a measured SO₂ column densities for the volcanic plume. All modeling results find large modifications in the shape of the analyzed plume SO₂ column density versus distance curve, even under scenarios with translucent clouds. Despite modification of the plume shape, the presence of a low cloud or haze layer is typically not a large source of error in determination of the total SO₂ quantity measured over the entirety of the traverse, which suggests that fairly accurate SO₂ emission rate measurements can be obtained even under non-ideal atmospheric measurement conditions. The real-world dataset from Cumbre Vieja is found to be best explained by a layer of ground-level laze containing SO₂ and a volcanic plume located between 2 - 4 km altitude. A large source of uncertainty in SO₂ emission rates derived from scanning DOAS instruments is the cross-sectional area of the detection, which is determined from the vertical and horizontal distance of the plume from the instrument. In Chapter 4, a novel method is employed to estimate plume altitude based on modeled wind speed data and validated against available webcam imagery at Cleveland Volcano in the Aleutian Islands, Alaska. This estimated plume altitude is used to calculate SO2 emission rates from single-station campaign scanning DOAS measurements at Cleveland Volcano, Gareloi Volcano, and Korovin Volcano (Alaska) in 2019, where the instrument was deployed for several days at each site. This method is also applied to a long-term dataset of scanning SO2 measurements acquired from a permanent scanning DOAS instrument installed at Cleveland Volcano September 2022 - June 2023. It is found that the method of estimating plume altitude in the long-term dataset produces a lower emission rate and a smaller sample variance than assuming a fixed summit plume altitude. The remaining variance in the data is then interpreted to represent variability in SO₂ emissions during times of relative quiescence at each studied volcano.
  • Biorecovery of rare earth elements from hard rock, extraction and analysis

    Kebe, Moustapha; Ghosh, Tathagata; Briggs, Brandon R.; Aggarwal, Srijan (2023-12)
    The advancement toward green energy, the development of precise weaponry, and the conquest of space have made the consumption of rare earth elements and critical elements supersede their production. Rare earth elements are vital and critical for modern technology. Rare earth elements consist of Scandium, Yttrium, and the fifteen elements in the Lanthanide group. These elements are mainly categorized into two types based on their atomic number: Light Rare Earth Elements (LREE) and Heavy Rare Earth Elements (HREE). The conventional methods of extracting economic rare earth elements are widely known, and these methods are found in abundance. However, considering the critical nature of rare earth elements, and the challenge to avoid environmental degradation, finding an alternate method of extracting rare earth elements that is both economically and eco-friendly is needed to overcome the disruption in demand and supply of these elements. One of the many potential methods of rare earth elements extraction is bioleaching or bio-recovery using bacteria, fungi, and archaea. This method has drawn the attention of several researchers in the quest for sustainable and feasible extraction techniques of rare earth elements and other critical elements (CEs). Bio-recovery or bioleaching as compared to physicochemical methods is considered one of the most promising techniques for recovering critical elements. A specific type of bacterial strain the Shewanella oneidensis MR-1 was incubated with rock samples from two distinct locations (North Pole Hills and the Prince of Wales Island) to recover rare earth elements. The experiment was performed under standardized conditions to ensure the reliability of the results. Three major parameters such as the process duration, particle size, and incubation period were tested to evaluate their impact on the recovery process. A total recovery of 30.85 ppb and 7.6 ppb at North Pole Hills and Prince of Wales Island, respectively. The process duration parameter was found to be irrelevant throughout the experiment and the effect of particle sizes ranging below 150 Mesh shows a positive response to the bio-recovery processes compared to particle sizes ranging between +-0.5mm. Maximum recovery was recorded with the samples from North Pole Hills compared to the samples from the Prince of Wales Island. The Bioleaching process was compared with the traditional acid leaching process, and a total of 291.73 ppb was recovered from the North Pole Hills and 107.75 ppb at the Prince of Wales Island. This experiment sets a road map to understand the microbial interaction on hard rock with varying sample sizes and process time.
  • The effect of cold exposure and activity on skeletal muscle physiology: a study of human and animal models

    Johannsen, Michelle M.; O'Brien, Kristin; Fedorov, Vadim; Oliver, Scott Ryan; O'Brien, Diane; Barnes, Brian (2023-12)
    Environmental factors and physical activity have the potential to modulate skeletal muscle physiology in beneficial ways. Cold exposure and endurance exercise, specifically, may improve aerobic capacity and atrophy resistance. I utilized three models to examine the effect of cold exposure and activity level on skeletal muscle physiology: quantitation of body composition and energy expenditure estimates in humans participating in a transmountain race, comparative proteomic analysis of skeletal muscle in hibernating and summer active American black bears (Ursus americanus), and an experimental study of the combined effects of cold exposure and endurance training on white adipose tissue, and gastrocnemius and soleus muscles in Sprague-Dawley rats. Body composition analysis of participants of the transmountain race revealed significant fat but not lean body mass loss despite significant caloric deficit. Proteomic analysis of American black bear skeletal muscle revealed an upregulation of glycolytic, inflammatory, immune response, and lipid transport proteins, and a decrease of lipid, and amino acid catabolism proteins during hibernation. Modulation of metabolism and the immune system during hibernation appears to mitigate skeletal muscle atrophy, despite prolonged inactivity and fasting. In Sprague-Dawley rats, cold or exercise alone have similar effects on body composition but exert unique effects on oxidative and glycolytic skeletal muscles that overall supports enhanced aerobic capacity. When combined, cold and exercise appear to improve oxygen diffusion via reduced cross-sectional area of some fiber types in oxidative skeletal muscle but have opposing effects in glycolytic muscles. In summary, skeletal muscle is highly plastic and perturbations such as cold, fasting, and endurance training result in cellular remodeling and changes in protein expression that improves aerobic capacity and conserves skeletal muscle mass across species.
  • Dynamics of the Earth's thermosphere across a range of spatial and temporal scales

    Itani, Rajan; Conde, Mark; Hampton, Donald; Bristow, William; Delamere, Peter (2023-12)
    This dissertation presents an investigation of aspects of the dynamics of Earth's thermosphere that do not harmonize with the current understanding. Three distinct thermospheric phenomena that correspond to different spatial and temporal scales were examined using Fabry-Perot interferometer measurements of wind and temperature to investigate aspects of thermospheric dynamics. Earth's thermosphere has very high kinematic viscosity and is highly convectively stable. Theory and physics-based models suggest that structures in the horizontal wind on small spatial scales (∼500 km or less) are unlikely to occur in the upper thermosphere. By contrast, a large-scale, persistent, strong wind flow that transports air parcels from the dayside of the polar cap to the nightside, known as cross-polar jet, was found to stall abruptly upon exiting the polar cap above Alaska. Stalling was observed most frequently around mid-winter during periods of low solar activity. The stalling of the crosspolar jet is considerably more abrupt than the first principle models would predict. This phenomenon was investigated as an example of dynamics occurring at intermediate spatial and temporal scales. Along with this meso-scale phenomena, oscillatory perturbations in observed winds and temperatures were examined to test whether these could be the signatures of gravity wave activity. These waves represent a local to synoptic scale behavior. Wave periods ranging from ∼30 min to ∼3 hr were observed. Our data show that gravity wave activity was a nearly ubiquitous feature of winds observed at ∼240 km altitude at auroral latitudes. The actual wave field appears to be complicated, presumably resembling ocean surface waves if they could be visualized. Oscillation amplitudes were typically found to increase with increasing geomagnetic activity and the wave response to geomagnetic activity was similar in both hemispheres. Periods and horizontal wavelengths of the observed oscillations fall within the previously reported range for thermospheric gravity waves. In addition, we examined the thermospheric neutral temperature data to see whether there is any temporal trend in measured temperatures on a time scale of decades. Studies suggest that the Earth's troposphere is warming globally because of anthropogenic emission of greenhouse gases. First principle models suggest that, unlike in the troposphere, greenhouse gases are expected to cool the thermosphere. Consistent with model expectations our data also show a thermospheric cooling trend and the rate of cooling is -27.4 ± 6.2 K/decade. The estimated rate of cooling is more than four times the corresponding uncertainty, indicating that the cooling is statistically significant. However, the observed cooling rate is up to an order of magnitude higher than suggested by simulation studies considering only the effect of CO₂. Nevertheless, the observed trend agrees well with observations of ionospheric temperature at these altitudes using incoherent scatter radar. This long-term temperature trend is an indicator of behavior at the largest spatial and temporal scales. Overall, these three studies together suggest significant shortcomings in our current paradigm for understanding the behavior of the thermosphere. Specifically, stalling of the cross-polar jet shows that spatial structures can arise on much more localized scales than currently appreciated. The ubiquitousness of gravity waves suggests that their role in thermospheric dynamics is probably much more significant than currently appreciated. The effect of anthropogenic changes in atmospheric chemistry appear to be much more substantial than expected. The lowest altitudes at which spacecraft can orbit for an operational useful length of time occur in the Earth's thermosphere. Conditions in the thermosphere impact spacecraft orbits. It is thus necessary to account for the thermospheric dynamics in order to predict the orbit with lowest possible uncertainty and for collision avoidance.
  • Model-based estimation of juvenile salmon spatial ecology in the eastern Bering Sea, Alaska

    Hart, Lilian; Cunningham, Curry; Yasumiishi, Ellen; Mueter, Franz (2023-12)
    Quantitative descriptions of juvenile salmon spatial ecology during the marine phase of their lifecycle are needed to help direct conservation efforts and uncover latent relationships between juvenile salmon and their environment. The NOAA Fisheries Essential Fish Habitat (EFH) program contributes to the conservation of species in the marine waters off of the coast of Alaska by identifying areas of particular importance to reproduction and growth. Salmon EFH definitions have not yet been updated using the species distribution modeling approach taken most recently in defining Alaska groundfish and crab EFH. Current EFH definitions for Alaskan salmon are geographically broad, do not quantitatively describe relationships between marine conditions and salmon, and lack estimates of uncertainty. This research estimated static (time-averaged) and dynamic (time-varying) juvenile salmon distributions in the eastern Bering Sea (EBS) by fitting species distribution models (SDMs) to fishery-independent survey data and environmental indices spanning the years 2002-2019. Following model selection, species distribution maps were generated using predictions based upon the best-performing static and dynamic models to inform EFH definitions for the juvenile life stage. In Chapter 1, roughly parallel nested model structures were fit within two SDM frameworks: generalized additive models (GAMs) and Vector Autoregressive Spatio-temporal (VAST) models. Results from Chapter 1 indicate that while there was evidence for spatial variation in juvenile salmon distributions through time, this variation was encompassed by the EFH boundaries predicted by static models. In terms of performance, GAM and VAST frameworks were largely comparable, although VAST models appeared to be more robust to issues associated with spatial imbalance in survey data. In Chapter 2, nested GAM model structures tested the influence of environmental covariates on variability in the abundance and/or distribution of five species of juvenile Pacific salmon in the EBS. Model selection results and mapping indicated that in-situ environmental covariates significantly influenced abundance of juvenile salmon, while annual covariates significantly influenced the distributions of juvenile salmon. Center of gravity estimates found some evidence for species distribution shifts inshore/offshore and to the north/south in response to specific hindcast environmental conditions. This work might be leveraged to update current salmon EFH definitions and inform future model-based conservation efforts.

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