• Description, phylogenetic analysis and taphonomy of a new Thalattosaur from the Brisbois member of the Vester Formation (Carnian/Norian) of central Oregon

      Metz, Eric T.; Druckenmiller, Patrick; Fowell, Sarah; Whalen, Michael (2019-05)
      Thalattosaurs are a poorly understood group of exclusively Triassic, secondarily aquatic tetrapods. Despite being first described over a century ago, their morphology and evolutionary history has been clouded by a spotty fossil record and poor specimen preservation. Here, a new thalattosaur genus is established on the basis of newly-discovered three dimensional cranial and postcranial elements from multiple individuals of different ontogenetic stages. The specimens were found within a single calcareous conglomerate nodule from the Brisbois Member of the Vester Formation in central Oregon, USA. The Brisbois Member thalattosaur is a relatively large taxon with an estimated total length of 4 - 5 m. Numerous cranial autapomorphies help diagnose the new taxon, including a ventrally deflected rostrum bearing a rugose ornamentation. The first three dimensionally preserved thalattosaur braincase anatomy is also described along with elements from nearly every region of the postcranium. Using high resolution surface laser scans, the first three-dimensional digital reconstruction of any thalattosaur skull is presented. Phylogenetic analysis indicates the Brisbois Member thalattosaur is a basal member of Thalattosauroidea, a clade that includes other taxa with highly modified rostra from Europe and China.
    • Detachment folds of the northeastern Brooks Range, Alaska: A basis for geometric and kinematic models of detachment folds

      Homza, Thomas Xavier; Wallace, Wesley K.; Hanks, C. L.; Layer, P. W.; Shapiro, L. (1995)
      Detachment anticlines are defined by mechanically competent rock layers and form both by internal deformation of an adjacent weak layer and detachment above a lower competent unit. This study is important for: (1) Other fold-and-thrust belts. Detachment folds are probably very common in fold-and-thrust belts worldwide, but they are rarely recognized as such and are commonly mistaken for other fold-types. This is partly because a rigorous general model for detachment folds that allows for changes in detachment depth and for fixed-arc length kinematics is lacking in the geologic literature. A general detachment fold model is presented here that: (a) is based on observations of natural folds in the northeastern Brooks Range of Alaska; (b) does not assume constant detachment depth or hinge-migration kinematics and; (c) allows quantification of non-plane strain. The folds observed can be modeled kinematically as fixed-hinge buckle folds, whereas the fold geometry and distribution of strain indicators in each fold precludes the migrating-hinge kinematic interpretation that is common in published models. Layer-parallel shortening, initial fold asymmetry, initial stratigraphic thickness of the incompetent unit, and the nature of rheological gradations each predictably influence fold evolution. This study suggests a general scenario for the evolution of a typical detachment fold. The area defined by a detachment anticline increases rapidly during early stages of folding and this is accompanied by a decrease in depth to detachment beneath synclines and the formation of fixed-hinge parasitic and disharmonic folds. This trend continues until the interlimb angle of the primary fold reaches 90$\sp\circ$. Increased shortening requires volume-loss in the core and/or an increase in detachment depth beneath the fold. Finally, depending on the rheology of the system, the fold may lock and/or be truncated by a thrust fault. (2) Regional tectonics. The western part of the northeastern Brooks Range is mostly a passive-roof duplex, but this study shows that forward-propagating deformation occurred at various structural positions. (3) Economics. Detachment folds may form petroleum traps that require a treatment different than that for fault-bend or fault-propagation folds. Detachment fold traps may exist beneath the coastal plain of the Arctic National Wildlife Refuge.
    • Detecting the effects of environmental change on Alaska's small mammal fauna using machine-learning-based geographic and isotopic niche modeling

      Baltensperger, Andrew P.; Huettmann, Falk; Welker, Jeffrey; Verbyla, David; Olson, Link; Ickert-Bond, Stefanie (2015-05)
      As anthropogenic climate change continues to alter biomes, ecosystems, and wildlife communities, determining how the niche spaces of species will respond is vital for determining appropriate conservation policy that promotes biodiversity and species persistence. In Alaska, quantifications of dietary patterns and geographic distributions of small mammals (rodents and shrews) are incomplete. As a result, wildlife managers are often ill-equipped to adequately account for these ecologically important taxa. I used stable isotopes, open-access occurrence records, and machine learning methods to model the dietary and geographic niche spaces of 17 species of small mammals in mainland Alaska. I also calculated the degree of niche overlap among species to estimate potential competition among conspecifics for both food and space. Using `bio-blitz' sampling along two statewide megatransects, I documented small mammal species richness and collected stable isotope samples at 20 locations across Alaska. Stable isotope (δ¹⁵N and δ¹³C) mixing models were used to define proportions of fungi, herbaceous plants, woody plants, lichens, and mosses in the diets of each species and to outline their fundamental and realized foraging niches. I created spatial distribution models for each species for the years 2010 and 2100 by applying machine learning methods to 4,408 unique occurrence records attributed with 27 and 33 environmental predictor variables, respectively. Spatial relationships between co-occurring species helped to determine the dominant structure of small mammal community assemblages for both time periods. Land change analyses identified regions of species loss, persistence, or gain over time. Stable isotopes (δ¹⁵N and δ¹³C) of shrews, rodents, fungi, and herbaceous plants were also modeled spatially to create continuous baseline isoscape predictions for Alaska. Dietary niche models showed a high degree of fundamental niche overlap among species at the statewide scale, whereas realized niches were more segregated at the study area scale. This suggests that species may be plastic in their use of shared resources in order to avoid competition. Isoscape models highlighted mid-elevations in the Yukon-Tanana Uplands, Brooks Range foothills, and the Yukon-Kuskokwim Delta as isotopic `hot-spots.' Isotope values were considerably higher than trophic baselines in these regions, indicating where small mammals may have been consuming more fungi than herbaceous plants. On average, 2010 distribution models accurately predicted the occurrence of species in the field 75% of the time, and a composite species richness model highlighted biodiversity hotspots (11-13 species) across the Yukon-Tanana Uplands and western Brooks Range. Community assemblage analysis for 2010 parsed species into 5 main community groups: northern, cold-climate, interior, continental, and southern, but membership to these communities was predicted to remain largely unchanged by 2100. Individual distributions, however, were predicted to change dramatically by 2100 as members of the northern, cold-climate, and interior communities shifted northward, inland, and upward in elevation following moving climate envelopes. Regions such as southwest Alaska and the Seward Peninsula experienced projected declines in species richness, while the number of species inhabiting the western Brooks Range and Alaska Range were predicted to increase. Results indicated that while species assemblages were robust in their organization over time, evidence of dietary niche plasticity suggests that communities may remain amenable to the addition of new species as shifting distributions overlap in new and unexpected patterns. Mid-elevations in topographically diverse regions such as the Brooks Range, Alaska Range, and the Yukon-Tanana Uplands will likely be centers for increased species richness and contact zones for novel species interactions in the future. These models, intended for public use, describe baseline conditions and future projections of small mammal niche ecology, with far-reaching implications for terrestrial trophic systems. I recommend that wildlife conservation and management decisions consider these models as we seek to describe and conserve biodiversity and the persistence of small mammal species across Alaska in a future altered by climate change.
    • Detection of volcanic SO₂ in the North Pacific Region using ASTER and MODIS

      Kearney, Courtney (2005-08)
      This study investigates the detection of volcanic SO₂ using TIR satellite-based and UV ground-based measurements at volcanoes in the North Pacific during eruptions and low level degassing. The ASTER and MODIS sensors with spatial resolutions of 0.09 and 1.0 km, respectively, are used to quantify SO₂ from the 8.6 um absorption feature of the gas species. Three volcanoes within this region were studied: Mt. Cleveland to test the implementation of the MAP ̲SO2 software, Bezymianny to determine the sensitivity of the algorithm to input parameters during eruption conditions, and Shishaldin to evaluate the detection of SO₂ during low level degassing. Total SO₂ estimates from the January 2004 Bezymianny eruption range from 15.5 kt to 87.2 kt at 0210 UTC depending on the input parameters. An emission rate of 0.295 kt·min⁻¹ and transport rate of 16.6 m·s⁻¹ were estimated from time sequential MODIS passes. SO₂ flux estimates at Shishaldin Volcano on 26 May 2004 were 164 t·day⁻¹ from ASTER and 58 t·day⁻¹ on 31 July 2004 from MUSe. The data show that SO₂ during low level degassing and eruptive conditions can be detected in the region and the sensors from this study provide a detection continuum from low to high SO₂ concentrations.
    • Detection, source location, and analysis of volcano infrasound

      McKee, Kathleen F.; Fee, David; Haney, Matthew; Szuberla, Curt; Tape, Carl; West, Michael (2017-12)
      The study of volcano infrasound focuses on low frequency sound from volcanoes, how volcanic processes produce it, and the path it travels from the source to our receivers. In this dissertation we focus on detecting, locating, and analyzing infrasound from a number of different volcanoes using a variety of analysis techniques. These works will help inform future volcano monitoring using infrasound with respect to infrasonic source location, signal characterization, volatile flux estimation, and back-azimuth to source determination. Source location is an important component of the study of volcano infrasound and in its application to volcano monitoring. Semblance is a forward grid search technique and common source location method in infrasound studies as well as seismology. We evaluated the effectiveness of semblance in the presence of significant topographic features for explosions of Sakurajima Volcano, Japan, while taking into account temperature and wind variations. We show that topographic obstacles at Sakurajima cause a semblance source location offset of ~360-420 m to the northeast of the actual source location. In addition, we found despite the consistent offset in source location semblance can still be a useful tool for determining periods of volcanic activity. Infrasonic signal characterization follows signal detection and source location in volcano monitoring in that it informs us of the type of volcanic activity detected. In large volcanic eruptions the lowermost portion of the eruption column is momentum-driven and termed the volcanic jet or gas-thrust zone. This turbulent fluid-flow perturbs the atmosphere and produces a sound similar to that of jet and rocket engines, known as jet noise. We deployed an array of infrasound sensors near an accessible, less hazardous, fumarolic jet at Aso Volcano, Japan as an analogue to large, violent volcanic eruption jets. We recorded volcanic jet noise at 57.6° from vertical, a recording angle not normally feasible in volcanic environments. The fumarolic jet noise was found to have a sustained, low amplitude signal with a spectral peak between 7-10 Hz. From thermal imagery we measure the jet temperature (~260 °C) and estimate the jet diameter (~2.5 m). From the estimated jet diameter, an assumed Strouhal number of 0.19, and the jet noise peak frequency, we estimated the jet velocity to be ~79 - 132 m/s. We used published gas data to then estimate the volatile flux at ~160 - 270 kg/s (14,000 - 23,000 t/d). These estimates are typically difficult to obtain in volcanic environments, but provide valuable information on the eruption. At regional and global length scales we use infrasound arrays to detect signals and determine their source back-azimuths. A ground-coupled airwave (GCA) occurs when an incident acoustic pressure wave encounters the Earth's surface and part of the energy of the wave is transferred to the ground. GCAs are commonly observed from sources such as volcanic eruptions, bolides, meteors, and explosions. They have been observed to have retrograde particle motion. When recorded on collocated seismo-acoustic sensors, the phase between the infrasound and seismic signals is 90°. If the sensors are separated wind noise is usually incoherent and an additional phase is added due to the sensor separation. We utilized the additional phase and the characteristic particle motion to determine a unique back-azimuth solution to an acoustic source. The additional phase will be different depending on the direction from which a wave arrives. Our technique was tested using synthetic seismo-acoustic data from a coupled Earth-atmosphere 3D finite difference code and then applied to two well-constrained datasets: Mount St. Helens, USA, and Mount Pagan, Commonwealth of the Northern Mariana Islands Volcanoes. The results from our method are within ~<1° - 5° of the actual and traditional infrasound array processing determined back-azimuths. Ours is a new method to detect and determine the back-azimuth to infrasonic signals, which will be useful when financial and spatial resources are limited.
    • DETERMINATION OF VALUABLE AREAS FOR MIGRATORY SONGBIRDS ALONG THE EAST-ASIAN AUSTRALASIAN FLYWAY (EEAF), AND AN APPROACH FOR STRATEGIC CONSERVATION PLANNING

      Beiring, Maria (2013-07)
      Having valuable high-quality stopover sites available for migratory birds is one of the key factors for the success of migration. However, beside the conservation of breeding and wintering grounds, the actual protection of valuable stopover sites has often been somewhat neglected. Overall 93 of 315 passerine species along the East-Asian Australasian Flyway (EEAF) are declining. That’s the highest overall number of threatened passerines on any known flyway. Additionally, the high human density in South-East Asia and the ongoing degradation of natural resources further poses a serious problem and threat to migratory songbirds and necessitates urgent action. This study aims to identify valuable areas for migratory songbirds along the vast EAAF (China, Japan, Korea, Far Eastern Russia and Alaska) and to develop a first approach for Strategic Conservation Planning. The main methodological framework encompasses predictive modeling (TreeNet, stochastic gradient boosting) and the Strategic Conservation Planning Tool ‘Marxan’. Overall, six models were created by using mistnet data (fall migration) of five selected index species (Arctic Warbler, Yellow Wagtail, Bluethroat, Siberian Rubythroat & Black- faced Bunting) as well as a by developing a ‘Species Richness Index’ (songbirds) and choosing widely used predictive environmental layers. In northern Russia and Alaska, most contiguous areas with a high index of occurrence are concentrated on the coastline of the Pacific Rim with smaller patterns in the interior and differences between their extents. In central-east Asia contiguous areas were found along the coastline stretching deeper inland than for the other regions. For the ‘Species Richness Index’, valuable areas were mostly predicted for the areas along the border of China and Russia, and comprise large parts of the Manchurian forest (deciduous). In general, it’s notable that the characteristics of the predicted hotspots seem to be linked to the habitat preferences of the selected songbirds during the breeding season. At the same time the generally extensive contiguous areas with a high index of occurrence indicate a higher variability in habitat use during fall migration than during the breeding season, too. Moreover the results indicate broad-front migration and putting the concept of a few and narrow migration hotspots in doubt. Nevertheless, the areas with a high index of occurrence have to be seen in view of the actual availability of high-quality staging sites as well. In the framework of Strategic Conservation Planning, five reserve solution scenarios with different focuses (Species Richness, boreal index Species, subboreal index species & all species with consideration of vulnerable areas) were created by using a simulated annealing algorithm implemented in Marxan. In general, only a low percentage (10 - 31 %) of the current protection network covers the reserves for the selected index species generated by Marxan. All reserve solutions should be seen as a first approach and public baseline for future conservation planning processes whereby there is a need of further refinement and assessment throughout a stakeholder’s involvement. Nevertheless, because this is the first Top-down approach for the given study area, the results are important to conservation planners for incorporating areas of high conservation value for migratory songbirds.
    • Determining face, predictive, construct validity and novel receptor targets in a spontaneous compulsive-like mouse model

      Mitra, Swarup; Bult-Ito, Abel; Drew, Kelly; Duffy, Lawrence K.; Dunlap, Kriya (2017-08)
      Obsessive-compulsive disorder (OCD) is one of the most prevalent neuropsychiatric disorders with no known etiology. Genetic variation, sex differences and physiological stages, such as pregnancy, postpartum and menopause in females, are important factors that are thought to modulate the pathophysiology of the disorder. Deeper understanding of these factors and their role in modulating behaviors is essential to unraveling the complex clinical heterogeneity of OCD. Using a novel mouse model that exhibits a spontaneous compulsive-like phenotype, I investigated the role of strain differences, sex differences, ovarian sex hormones and postpartum lactation in influencing compulsive-like and affective behaviors. Due to the lack of definite neural substrates and first line therapeutic options for treatment resistant patients, I also probed into the role of positive allosteric modulation of nicotinic acetylcholine receptor subtype as a therapeutic target for translational prospects. The thesis showed several significant and novel findings. Strain and sex comparisons of the compulsive-like mouse strains (BIG1 and BIG2) showed that the behavioral outcomes and HPA axis response can be influenced by sex, genotype and sex by genotype interactions. Acute ovariectomy and behavioral assessments after one week, which mimics surgical menopause in humans, increased the compulsive-like behaviors in the BIG strains only. Acute ovariectomy also exacerbated anxiety-like behaviors in the compulsive-like BIG strains. This exacerbation of compulsive-like behaviors was restored only by estrogen and not progesterone, while estrogen and progesterone both restored anxietylike behaviors based on the strain and the type of behavioral assessments. Lactating postpartum compulsive-like female mice were protected against compulsive-like behaviors and showed enhanced responsiveness to selective serotonin reuptake inhibitors (SSRIs) compared to the non-lactating and the nulliparous females. Finally, acute and chronic administration of desformylflustrabromine (dFBr), a positive allosteric modulator of α4β2 nicotinic acetylcholine receptors, resulted in the attenuation of compulsive-like behaviors in the mouse model, while not affecting anxiety-like behaviors. The current thesis work therefore provides a foundation for further exploration of factors like strain, sex, physiological status and cholinergic receptor subtypes in mouse models to understand the neurobiology and behavioral correlates of OCD in humans.
    • Determining the immune status of Steller sea lions (Eumetopias jubatus): an environmental agents of disease perspective

      Kennedy, Stephanie Nichole; O'Hara, Todd; Ferrante, Andrea; Kuhn, Thomas; Trainor, Thomas; Rea, Lorrie (2019-05)
      The integrity of the immune system is paramount for preserving overall health for many organisms. Investigating environmental and physiological factors that may be associated with alterations of the immune status in non-traditional sentinel species, like the Steller sea lion (SSL), is a prominent undertaking in eco-immunology research. Changes to immune homeostasis likely impacts the health and survival of SSLs. Recent studies have reported that mercury concentrations in hair in 24 to 36% of newborn SSLs of the Western Aleutian Islands (WAI) exceed thresholds (>30 ppm) for potential adverse effects. Many of these individuals were from WAI rookeries that have historically experienced significant population declines with some slow to recover. Retrospective, and ongoing, analyses of mercury in lanugo coats (natal hair) from young pups of the WAI demonstrate in utero exposure to relatively high levels of mercury during late gestation. Therefore, this dissertation focuses on the notion that dietary acquired mercury could potentially alter immune response in SSLs, especially young pups, and may contribute to the lack of recovery from population declines. In order to gain an understanding of the potential for mercury to adversely affect the immune response of SSLs, selected aspects of immunity were measured (blood cell counts, haptoglobin, immunoglobulins, and cytokines) and investigated within the context of body condition, age, mercury exposure and regional population dynamics. In Chapter Two, the acute phase response protein, haptoglobin, was found to vary significantly with age and region. Individual SSL pups with greater concentrations of mercury had lower predicted concentrations of haptoglobin. In Chapter Three, a colorimetric protein A enzyme-linked immunosorbent assay was modified for enhancing accurate measurement of immunoglobulin concentrations in SSL serum. This improved methodology was then used in Chapter Four for comparing immunoglobulins in young developing SSL pups and dams as a measure of maternal investment of immunity among different rookeries. Lastly, Luminex multiplex technologies were employed for quantifying cell-signaling proteins (cytokines) in SSL serum to compare associations among rookery pups in Chapter Five. Although mercury concentrations in some individuals exceed adverse effects thresholds that are defined for other mammals, no statistically significant associations were found between immunoglobulins and cytokines relative to mercury concentrations in young developing pups. These thesis chapters provide a powerful baseline and improved methods for ongoing and future assessments of haptoglobin, immunoglobulins, and cytokines (combined with traditional hematologic measures) observed in young developing SSL pups in regions experiencing population decline when compared with rookeries with stable or increasing pup production. Some of these findings, especially for haptoglobin, are indicative of alterations in immune status in young SSL pups born to dams from different natal rookeries with higher mercury exposure. Understanding the cause of the differences in the immune status of young SSLs will require additional assessments of the maternal-fetal interface of immunity and other factors like nutrition, metabolic status, and infectious disease that may shape neonatal immunity leading to the regional differences observed.
    • Developing a decision support system for emergency management services in the Fairbanks North Star Borough, Alaska

      Schaefer, Katherine E. (2012-12)
      Every year the Fairbanks North Star Borough (FNSB), in interior Alaska, responds to common emergencies, as well as disasters of varying types. This research first tested several geographic information systems (GIS) based network analysis models to demonstrate how these models could serve as 'decision support' tools for emergency planning and response. Six network analysis models based on FNSB data were evaluated to determine the response times of local fire stations. Each model was tested against real call times and simulated summertime fire emergency response call times to verify model accuracy. The simulated times matched the modeled predictions with remarkably high R2 values of 0.946, 0.941, and 0.940 for conditions that represented no adjustment to road data, a time penalty for slopes, and a small time penalty for all turns, respectively. The corresponding results with culled real-time call data had a much lower accuracy of 0.403, 0.429, and 0.415, respectively. The lower accuracy for real-time data was primarily due to discrepancies in response time recording protocols. This study also divided FNSB into evacuation zones and created a map book with critical infrastructure and key resources necessary for improved emergency management.
    • Developing Stable Isotope Biomarkers Of Yup'ik Traditional And Market Foods To Detect Associations With Chronic Disease Risk

      Nash, Sarah H.; O'Brien, Diane; Bersamin, Andrea; Boher, Bert; Kristal, Alan (2013)
      This dissertation addresses the need for valid measures of dietary intake for use in studies of chronic disease risk in the Yup'ik population of Southwest Alaska. The Yup'ik people have experienced dietary changes over the past century, as consumption of traditional foods has been increasingly supplemented or replaced by market-purchased foods. Determining whether this dietary change is associated with increases in chronic disease risk is important for making nutritional recommendations for disease prevention. However, monitoring dietary change is challenging, in part due to the limitations of self-reported methods of dietary assessment. Dietary biomarkers are promising alternatives to self-reported methods, because they can provide unbiased, reliable estimates of intake. In this dissertation, I present evidence towards the validation of stable isotope dietary biomarkers. Stable isotope ratios vary among foods that are important in Yup'ik diets, and are incorporated into tissues, including several commonly collected biological sample types. They are simple, inexpensive and reliable measures that would be powerful tools for dietary assessment if they could be validated as biomarkers of certain foods. This work was conducted with two Yup'ik study populations that participated in studies conducted by the Center for Alaska Native Health Research. I begin by showing that the nitrogen isotope ratio is a marker of the marine component of traditional food intake, and the carbon isotope ratio is a marker of market food intake. I then calibrate a model of sugar intake based on both the carbon and nitrogen isotope ratios. I focus specifically on sugars because intake of sugary foods and beverages has been linked to obesity-related disease risk in other US populations. Finally, I use this dual isotope model to assess associations of sugar intake with chronic disease risk factors. I find that sugar intake is associated with blood pressure, blood lipids, leptin and adiponectin, suggesting a potential adverse effect of sugar intake on Yup'ik health. The findings of this dissertation provide substantial evidence to support carbon and nitrogen isotope ratios as markers of Yup'ik dietary intake, and demonstrate their potential to be informative in studies of associations between dietary intake and the health of Yup'ik people.
    • Development and characterization of a capillary electrophoresis instrument with laser-induced fluorescence detection for on-line monitoring of glutamate in vivo via microdialysis

      Swearingen, Kristian Edward (2005-12)
      To elucidate the roles of key neurochemicals in the metabolic suppression of Arctic ground squirrels, a technique is required that is capable of on-line, in vivo, high temporal resolution, quantitative detection of neurotransmitters. A capillary electrophoresis instrument has been built that is coupled to microdialysis by flow-gated injection. Primary amines recovered in vivo via microdialysis are derivatized on-column by cyanide-catalyzed formation of fluorescent isoindoles with naphthalene-2,3-dialdehyde for laser-induced fluorescence detection. The system is capable of detecting base-line glutamate in vivo in 15-second intervals.
    • Development of a Fe Boltzmann temperature lidar

      Breese, Justin (2001-08)
      An iron Boltzmann temperature lidar allows the measurement of temperatures and iron densities in the mesopause region (8̃0-100 km). This thesis describes the initial development of a new Boltzmann temperature lidar at Poker Flat Research Range. An excimer-pumped dye laser system was installed in April 1999. During 1999 and 2000 this system was calibrated against the resident sodium system. Observations of iron were made in the winter of 2000 and spring 2001. Temperature measurements were made in December of 2000. The thesis presents an operational analysis of the lidar system performance and a scientific analysis of the data obtained. the midwinter temperature measurements indicate the mesopause is above the mesospheric iron layer at this high-latitude site. The new lidar is an important development as it can be combined with Rayleigh lidar measurements to provide direct temperature profile soundings over the 30 to 90 km altitude range.
    • Development of a parameterization for mesoscale hydrological modeling and application to landscape and climate change in the Interior Alaska boreal forest ecosystem

      Endalamaw, Abraham Melesse; Bolton, William R.; Young-Robertson, Jessica M.; Hinzman, Larry; Morton, Donald; Mölders, Nicole; Fochesatto, G. Javier (2017-08)
      The Interior Alaska boreal forest ecosystem is one of the largest ecosystems on Earth and lies between the warmer southerly temperate and colder Arctic regions. The ecosystem is underlain by discontinuous permafrost. The presence or absence of permafrost primarily controls water pathways and ecosystem composition. As a result, the region hosts two distinct ecotypes that transition over a very short spatial scale - often on the order of meters. Accurate mesoscale hydrological modeling of the region is critical as the region is experiencing unprecedented ecological and hydrological changes that have regional and global implications. However, accurate representation of the landscape heterogeneity and mesoscale hydrological processes has remained a big challenge. This study addressed this challenge by developing a simple landscape model from the hill-slope studies and in situ measurements over the past several decades. The new approach improves the mesoscale prediction of several hydrological processes including streamflow and evapotranspiration (ET). The impact of climate induced landscape change under a changing climate is also investigated. In the projected climate scenario, Interior Alaska is projected to undergo a major landscape shift including transitioning from a coniferous-dominated to deciduous-dominated ecosystem and from discontinuous permafrost to either a sporadic or isolated permafrost region. This major landscape shift is predicted to have a larger and complex impact in the predicted runoff, evapotranspiration, and moisture deficit (precipitation minus evapotranspiration). Overall, a large increase in runoff, evapotranspiration, and moisture deficit is predicted under future climate. Most hydrological climate change impact studies do not usually include the projected change in landscape into the model. In this study, we found that ignoring the projected ecosystem change could lead to an inaccurate conclusion. Hence, climate-induced vegetation and permafrost changes must be considered in order to fully account for the changes in hydrology.
    • Development of a reservoir stimulation model at Pilgrim Hot Springs, Alaska using TOUGH2

      Chittambakkam, Arvind A.; Daadan, Ronald; Prakash, Anupma; Haselwimmer, Christian (2013-08)
      This study has developed numerical simulations of the Pilgrim Hot Springs geothermal system, Alaska using the TOUGH2 software package for the purposes of assessing the resource potential for both direct use applications and electrical generation. This work has included the development of two simulation models, describing fluid and heat flow in the geothermal system, that were built using geological and geophysical constraints with model simulation parameters optimized via a history matching of subsurface temperature profiles. The reservoir simulation models were used to predict the heat loss from the system for both conductive and convective heat fluxes. These reservoir simulation models served as the basis for the development of reservoir stimulation models encompassing three production scenarios with various configurations of production and injection wells. These reservoir stimulation models were used to estimate the thermal energy from the production wells. The major significance of these stimulation models is that they help to determine the feasibility of development of the reservoir for production. The reservoir simulation models estimate about 26-28 MW thermal energy and the stimulation models estimate about 46-50 MW thermal energy for the Pilgrim Hot Springs geothermal system. These estimated values indicate a favorable resource when compared to other low temperature systems such as, Chena Hot Springs, Alaska; Wabuska, Nevada; Amedee, California; and Wineagle, California.
    • Development of acetylcholine-binding protein (AChBP) as a biosensor for serotonin ligands

      Ataian, Yeganeh; Schulte, Marvin; Duffy, Lawrence; Kuhn, Thomas; Bult-Ito, Abel (2018-05)
      Acetylcholine-binding protein (AChBP) is a water-soluble novel protein with a high sequence similarity (15-30% identity) to ligand-gated ion channel (LGIC) receptors. The crystal structure of AChBP is used to study the extracellular domain of the pentameric LGICs such as nicotinic acetylcholine receptors (nAChRs) and 5-hydroxytryptamine type 3 receptors (5-HT₃Rs); and homology models have been developed to study receptor-ligand interactions. The 5-HT₃ serotonin receptors are potential therapeutic targets for multiple nervous system disorders such as alcohol and drug dependence, anxiety, depression, schizophrenia, sleep, cognition, memory, and chemotherapy-induced and post-operative nausea and vomiting. Therefore, the ligands that target the 5-HT₃Rs are considered powerful therapeutic agents. As such, 5-HT₃ serotonin receptors have been the targets of drug discovery efforts. The main objective of the current protein engineering project was to develop a soluble serotonin-binding protein using AChBP, which would mimic the specificity of the native 5-HT₃ serotonin receptor. Once developed, this soluble protein would be used as a model to design an array of receptors, which could be placed on biosensors for high-throughput drug screening (HTDS). The results of site-directed mutagenesis of AChBP demonstrated that mutation of certain AChBP residues to its equivalent in serotonin resulted in an increased affinity of AChBP for serotonin ligands, and that each individual mutation increased the affinity of AChBP to a certain degree. It indicates that this approach is going in the right direction but multiple mutations will probably be needed to get to an AChBP whose affinity is equivalent to wild-type serotonin. In addition, the most significant changes appeared to be in the C-loop as it produced the largest increase in affinity of AChBP for serotonin agonists. The results also support the proposed C-loop closure model for the receptor, and based on data presented here, a new alignment of the C-loop is suggested.
    • Development of postsynaptic function in muscle membrane

      Owens, Jesse Lee; Kullberg, Richard W. (1987)
      The development of postsynaptic function in skeletal muscle of Xenopus laevis was studied in vivo in order to address the following questions: What changes take place in acetylcholine receptor (AChR) channel function during muscle development and when do they occur? Does muscle activity regulate the development of postsynaptic function? Do functionally different muscles have different programs of postsynaptic development? Single channel recordings from nonjunctional membrane revealed a class of low conductance (30 to 40 pS), long open time (2-3 ms) AChR channels which appeared on embryonic membrane within 21 h of fertilization. At 45 h of age, a second class of higher conductance (40 to 60 pS), brief open time ($<$1 ms) channels began to be expressed and over the course of 4 days became the most frequently observed channel type. Concurrently, the open time of the low conductance channel decreased by half during development. These data explain the developmental change in duration of synaptic currents previously observed in myotomal muscle, and they lay the foundation for further studies on the molecular mechanisms of AChR development. The effect of immobilization on the development of synaptic currents in myotomal muscle was investigated by allowing embryos to develop in a bath containing tetrodotoxin, which eliminated muscle activity during formation and maturation of the neuromuscular junction. In both control and tetrodotoxin-immobilized animals, synaptic current rise times and decays developed in an equivalent fashion, indicating that muscle activity is not required for normal development of AChR channel gating or acetylcholinesterase (AChE) deposition at the neuromuscular junction. The development of synaptic currents was compared in two functionally different muscles, the interhyoideus and the superior oblique. Each muscle has a characteristic program of synaptic current development during synaptogenesis and during metamorphosis. The contrasting development of synaptic currents from the two muscles can be explained by different programs of AChR and AChE development.
    • Development of respiratory centers in the bullfrog tadpole brainstem

      Reed, Mitchell D.; O'Brien, Kristin; Taylor, Barbara; Harris, Michael; Drew, Kelly; Iceman, Kimberly (2017-08)
      Among vertebrates, rhythmic motor behaviors such as breathing, swallowing, and sucking are controlled by rhythm generators or neural oscillators located at various sites in the medulla of the brainstem. That all vertebrates exhibit these behaviors, leads investigators to hypothesize common ancestry for the cellular networks responsible for homeostatic rhythm generation in the brainstem. While the locations and functions of rhythm generating sites controlling some of these behaviors have been well investigated, details regarding the development of these sites remain largely unknown. Recent work has suggested that neural oscillators in the rostral and caudal medulla, which contribute to ventilation in amphibians, may be homologous with those controlling breathing in mammals. I first investigated the developmental contributions of these regions to CO₂ sensitivity and rhythm generation in bullfrog tadpoles at different stages of metamorphosis. I then characterized the function and structure of a neural oscillator essential for lung rhythmogenesis in the tadpoles and compared it to similar oscillators in mammals. To investigate functional aspects of brainstem, I used a combination of single-unit and whole-nerve electrophysiology in the presence of pharmacological agents (neuronal receptor agonists and antagonists) or following removal of portions of the isolated brainstem of bullfrog tadpoles at different stages of metamorphosis. Structural studies were accomplished using immunohistochemistry, staining for phenotypic markers common to mammalian rhythmogenic sites, and assessing the difference between early and late metamorphic bullfrog tadpoles. Taken together, my results suggest that amphibians may indeed have a rhythmogenic site in the rostral medulla that is homologous to a mammalian rhythmogenic site; it is both structurally and functionally similar to the mammalian parafacial respiratory group/retrotrapezoid nucleus complex. This region undergoes structural and functional changes as tadpoles develop through metamorphosis. Understanding the development of respiration in amphibians may provide clues into the evolution and development of breathing in mammals.
    • Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA

      Spangler, Mark A.; Huettmann, Falk; Herriott, Ian C.; López, J. Andrés (Springer, 2017)
      We developed and describe a qPCR assay for the detection of wood frogs (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer set was designed to amplify a 115-bp region of the wood frog cytochrome B gene and assessed for target specificity. There was no evidence of amplification in eleven non-target species. We evaluated the utility of the primer set in qPCR assay by conducting geo-referenced eDNA field surveys in Interior Alaska. Results indicate that the assay consistently detects wood frog DNA in the environment to 1.83x10-3 pg/μL. The assay provides a complement to traditional survey methods and can be readily applied in a wider conservation and management context.