Recent Submissions

  • Synthesis and stereoselective reduction of α-fluoro-β-ketoesters by ketoreductases

    Vanagel, Matthew G.; Green, Tom; Rasley, Brian; Kuhn, Thomas (2024-05)
    Using commercially available ketoreductase (KRED) enzymes, α-fluoro-β-hydroxy esters were stereoselectively synthesized from racemic α-fluoro-β-keto esters through dynamic reductive kinetic resolution (DYRKR). The α-fluoro-β-keto esters were synthesized via Reformatsky reactions between an aromatic aldehyde and ethyl bromofluoroacetate and subsequent oxidation with Dess Martin Periodinane (DMP). Two enzymes were selected for their ability to yield either syn or anti diastereomers. Three aromatic substrates were reduced in high diastereomeric and enantiomeric excess and good yields. The KRED products were derivatized with (R)- and (S)-α-methoxy-α-trifluoromethylphenylacetic acid (MTPA) and analyzed via ¹⁹F NMR spectroscopy to determine their absolute stereochemistry via Mosher ester analysis. For the three substrates, KRED 110 yielded the anti 2S,3S isomer. KRED 130 predominantly yielded the syn 2S,3R isomer but with less specificity. The use of these commercially available KRED enzymes provides access to enantio- and diastereomerically pure α-fluoro-β-hydroxy esters from readily accessible racemic substrates. Optically pure α-fluoro-β-hydroxy esters may serve as useful intermediates in the synthesis of medicinally relevant compounds such as fluorinated amino acids or fluorinated sphingolipid derivatives.
  • Synthesis, characterization and cytotoxicities of novel organoplatinum(IV) complexes

    Cogley, Marcus O.; Howard, William A.; Oliver, S. Ryan; Kuhn, Thomas (2024-05)
    Breast cancer is the most common form of cancer in the world. In 2023, nearly 300,000 new cases of breast cancer were projected in the U.S. alone. When treating breast cancer, several therapies are utilized, often including chemotherapy. Organoplatinum(IV) complexes are among the newer chemotherapy drugs being developed as an alternative to cisplatin, the first platinumbased anticancer drug. Two novel organoplatinum(IV) complexes: [Pt(CH₃)₂X₂{bipy-(CO₂H)₂}] (X = Br, I) have been isolated and structurally characterized by single-crystal X-ray diffraction. Nuclear magnetic resonance and infrared spectroscopic data were also collected to confirm these new compounds and provide useful reference values. The anticancer potential of each compound was assessed via in vitro 3-4,5-dimethylthiazol-2,5-diphenyltetrazolium bromide (MTT) assays using human breast cancer cells (cell line ZR-75-1). EC₅₀ values were determined as 3020 μM, for Pt(CH₃)₂Br₂{bipy-(CO₂H)₂} and 86.0 μM, for Pt(CH₃)₂I₂{bipy-(CO₂H)₂}; for comparison, the EC₅₀ value for cisplatin against the ZR 75-1 cells was 16.4 μM. While these compounds were not as effective as cisplatin, the single-crystal X-ray diffraction data showed evidence of intermolecular π-π interactions within the unit cell which suggest that the bipyridyl ligands can potentially interact with tumor DNA nucleobases in the DNA double helix.
  • 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.
  • Pollution trapping by strong temperature inversions in Fairbanks, Alaska

    Cesler-Maloney, Meeta V.; Simpson, William R.; Mao, Jingqiu; Guerard, Jennifer; Stuefer, Martin (2023-12)
    In cold climates during winter, surface-based temperature inversions reduce vertical dispersion within the atmospheric boundary layer. Reduced vertical dispersion coupled with stagnant horizontal winds causes pollution emitted near the ground level to accumulate to unhealthy amounts. To study pollution trapping, we measured vertical differences in fine particulate matter and ozone across a shallow 20-meter vertical scale during surface-based inversions in Fairbanks, Alaska and showed that pollution trapping occurs on this extremely shallow scale. In winter 2022, trace gases were measured by long-path differential absorption spectroscopy to probe vertical dispersion on a taller scale, up to ~200 m above the surface. We added horizontal dispersion to a one-dimensional Eulerian chemical transport model and used the model with both vertical and horizontal dispersion, but without chemistry, to simulate the vertically resolved measurements of SO₂. The model achieved excellent results with correlation to the observations having a coefficient of R = 0.88. Steady-state transport residence times calculated from the model were on the order of hours, indicating limited time for chemical processing during winter in Fairbanks. Within the model, only ground-based emissions sources were included and there was no interaction between air above and below the boundary layer height, suggesting that ground-based sources dominate pollution measured at ground level. With the knowledge that ground level sources have a large impact on pollution, we carried out an analysis of trace gases and fine particulate matter measured near ground level that was used to better understand the response to pollution control strategies in Fairbanks. This analysis shows that the total amount of pollution in Fairbanks has been trending down over the past nine years. Following a September 2022 legal change that mandated lower sulfur content in heating oil, the amount of sulfur dioxide gas dropped significantly during winter 2022-2023 as compared to the prior three-year average.
  • Effects of calcium magnesium acetate on small ponds in interior Alaska

    Rea, Caryn L. (1986-09)
    Deicing winter roads with chlorides has been common practice in northern areas. Corrosion of vehicles, structures, and pavements has resulted in damage, and roadside vegetation and public water supplies have been severely impacted by heavy salt usage. Calcium magnesium acetate (CMA) was identified as a promising alternative to chloride salts. This research focused on the effects on planktonic algae and bacteria in small ponds, to help assess the environmental acceptability of CMA in Alaska. The most serious consequence resulting from CMA was a dissolved oxygen concentration decrease, partly attributable to increased bacteria populations utilizing oxygen during degradation of acetate. Algal biomass recovered toward the end of the summer indicating that the algae may be utilizing some of the carbon dioxide being released by the bacteria. Rapid turnover times of acetate by bacteria in the fall and continued low dissolved oxygen indicated that some of the acetate was being recycled.
  • Clearance of beta-amyloid 42 (Aβ-42) and tau proteins in Alzheimers Disease (AD)

    Tackett, Alex; Duffy, Lawrence K.; Drew, Kelly L.; Rasley, Brian T. (2023-05)
    Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the main cause of dementia among the elderly worldwide. Despite intense efforts to develop drugs for preventing and treating AD, no effective therapies are available yet, posing a growing burden at the personal, medical, and socioeconomic levels. AD is characterized by the production and aggregation of amyloid 0 (A0) peptides derived from amyloid precursor protein (APP), the presence of hyperphosphorylated microtubule-associated protein Tau (MAPT), and chronic inflammation leading to neuronal loss. A0 accumulation and hyperphosphorylated Tau are responsible for the main histopathological features of AD, A0 plaques, and neurofibrillary tangles (NFTs), respectively. However, the full spectrum of molecular factors that contribute to AD pathogenesis is not known. Non-coding (nc)RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) regulate gene expression at the transcriptional and posttranscriptional levels in various diseases, serving as biomarkers and potential therapeutic targets. There is rising recognition that ncRNAs have been implicated in both the onset and pathogenesis of AD. Here, the ncRNAs implicated post-transcriptionally in the main AD pathways and discuss the growing interest in targeting regulatory ncRNAs therapeutically to combat AD by using a series of multifunctional molecules that contained APP, and Tau-recognition moieties and E3 ligase-binding moieties to enhance APP, and Tau degradation. The goals involve the exploration into non-invasive biomarker screening for cognitive dementia related to Alzheimer’s Disease (AD) and in canine blood samples. The specific aims are towards the identification and development of non-invasive AD-related biomarkers for detection screening before the onset of pathophysiological symptoms related to cognitive deterioration seen in AD. The purpose of the project is concentration on the clearance of A0 and Tau through the liver.
  • Impacts of sex, biometals homeostasis, and dietary fructose on non-alcoholic fatty liver disease pathogenesis

    Morrell, Emilie A.; Burkhead, Jason; Duffy, Larry; Knall, Cindy; Weber, Jesse (2023-05)
    Non-alcoholic fatty liver disease (NAFLD) is a broad-spectrum liver disorder that ranges from simple hepatic steatosis to its more severe form, non-alcoholic steatohepatitis, which is marked by hepatic inflammation and cirrhosis. Estimates indicated NAFLD prevalence is currently between 25-30% of adults worldwide. Currently, there are no treatment options for NAFLD other than weight loss, as the etiology of this disease remains elusive. Prior studies have indicated that NAFLD is likely a multifactorial disease arising from interactions between factors like: genetics, nutrition, age, sex, hormone levels, lipid regulation, and biometals homeostasis. While prior studies have largely done an excellent job at defining the NAFLD landscape there are many factors known to impact NAFLD pathogenesis that remain understudied. This study aimed to examine the impacts of some of these factors; namely, biometals homeostasis, dietary fructose intake, and sex. This study first reviewed prior findings to outline the current understanding of the impacts of biological Cu on lipid metabolism and regulation. Next, we used dietary treatments in an animal model (Wistar rat) to examine the interplay between sex, dietary fructose and biometals homeostasis in NAFLD pathogenesis. Finally, an integrated network analysis of human RNA-Seq data was conducted to identify key genes involved in NALFD pathogenesis that were correlated with our factors of interest. In our review we identified some of the potential mechanisms by which copper (Cu) deficiency may promote NAFLD. These included increased immune cell activation, increased lipid biosynthesis, increased oxidative stress, and alterations to mitochondrial metabolism regulation. 1H nuclear magnetic resonance metabolomics results from the animal model identified distinct metabolic phenotypes that were highly correlated with diet and sex. Additionally, ICP-MS and western blot analysis identified previously unknown sex-specific responses to both fructose supplementation and restricted copper intake. Finally, our RNA-Seq integrated network analysis of human samples identified 66 total and 10 novel hub genes that are likely key regulators of NAFLD-related pathways. Enrichment analysis of the hub genes identified overrepresentation of genes related to the CAMKK2 pathway, oxidative phosphorylation, and regulation of mitochondrial transcription. All of the hub genes correlated with both disease status and sex were found to escape X-inactivation, suggesting XIST escapee genes may disproportionately impact sex-specific mechanisms of NAFLD pathogenesis. These results suggest sex, biometals homeostasis, and dietary fructose all impact NAFLD pathogenesis and further investigation into their roles should be pursued.
  • Effects of diet and hibernation in skeletal muscle performance

    Krishnan, Jishnu K.S.; Oliver, S. Ryan; Drew, Kelly L.; Weltzin, Maegan D.; Kuhn, Thomas B. (2022-12)
    Hibernating animals, such as the arctic ground squirrel (AGS), are subjected to a wide range of temperature variations. During hibernation, when they are predominantly physically inactive, body temperature can drop as low as -3°C, while in summer, body temperature can climb as high as 40°C. Torpor is a state of inactivity in an animal induced by a lack of food, which is followed by a fall in body temperature and metabolic rate. Torpor lasts around 21 days in AGS, and the progression of torpor begins with early torpor, followed by mid and late torpor, and culminates with interbout arousal lasting less than 24 hours. AGS exhibit reduced muscular atrophy and protein loss despite lengthy periods of immobility, hypometabolism, and severe hypothermic conditions during hibernation. Skeletal muscle plasticity, unique to mammalian hibernators, may explain why cardiac and respiratory skeletal muscle can function at hypothermic temperatures during and after hibernation. As a result, understanding the effects of ambient temperature on muscle physiology and contractile function is critical. The focus of this research was to investigate skeletal muscle contractile performance and fatigue resistance in ex vivo muscle tissues during hypothermic temperature stress. Ex vivo tissue organ bath functional assays were performed in hibernator and/or non-hibernator rodent models to determine changes in performance and fatigue resistance in the AGS diaphragm induced by polyunsaturated fatty acid dietary modification or ambient hypothermic stress. This study lends support to the idea that diet and hypothermic stress might modify certain functional aspects of skeletal muscle, most likely via membrane lipid composition, ambient temperature, and torpor interaction. Furthermore, summer active AGS has a higher fatigue resistance than mid torpor AGS during the hibernating season. Furthermore, skeletal muscle fatigue resistance was significantly lower in Sprague Dawley rats than in both summer active and hibernating AGS. Preliminary data also suggested that hypothermic stress, to some extent, enhanced fatigue resistance regardless of torpor status or species difference.
  • Development of a MUC1 cancer immunotherapy using complement targeted liposomes and organoplatinum (IV) complex as an effective anticancer drug

    Arabi, Ameneh; Kullberg, Max; Howard, Bill; Martinson, Holly; Duffy, Lawrence; Kuhn, Thomas (2022-12)
    The development of therapeutic and preventive cancer vaccines has been on the rise in the past decade. Extensive tumor antigen libraries supply researchers with a wide variety of targets for developing cancer vaccines. Cancer vaccines aim to induce tumor regression, eradicate tumors and establish lasting antitumor memory, while avoiding adverse reactions. However, achieving this goal is hampered by the challenges of finding tumor antigens to incite an effective immune response and creating an efficient delivery system to deliver the antigen to target cells. In this thesis, we discuss how to integrate Toll Like Receptor (TLR) agonists with a MUC1 cancer vaccine to improve its effectiveness. The goal of our research was to increase drug delivery targeting efficiency by encapsulating a MUC1 immunogenic peptide within C3 liposomes. The work described herein shows that C3 liposomes were effective at targeting delivery of MUC1 antigen to Antigen Presenting Cells (APCs), which resulted in a T and B cell immune response against MUC1. Furthermore, the addition of TLR agonists to vaccine formulations boosted vaccine effectiveness, creating a more potent treatment against MUC1 expressing cancer. Another goal of this thesis research was to synthesize organoplatinum compounds. Currently, platinum-based chemotherapy drugs are a popular option for treating cancer, however, treatment is still limited by bystander toxicity. Four octahedral organoplatinum (IV) compounds, namely [Pt(CH₃)₂X₂{bipy-R₂}] (X = Br, I; bipy-R₂ = 2,2'-bipyridine, 2,2'-bipyridine-4,4'-dicarboxylic acid), have been isolated and structurally characterized by single-crystal X-ray diffraction. The anticancer potential of each compound was assessed via an in vitro MTT assay.
  • An examination of a sleep-related hypermotor epilepsy associated mutation in complex α4β2* nicotinic acetylcholine receptors

    Smith, Tyler; Weltzin, Maegan; Kuhn, Thomas; Drew, Kelly; Dunlap, Kriya (2022-08)
    Epilepsy is a disease that involves large networks of neurons. As such, studying the pathology of epilepsy has been complicated. Investigating epilepsy through the lens of Sleep-related Hypermotor Epilepsy (SHE) presents itself as a good strategy as SHE is linked to a variety of single point mutations. These mutations affect receptors, the most prominent being mutations in nicotinic acetylcholine receptors (nAChRs). nAChRs are pentameric ligand-gated ion channels. Five individual subunits combine to form a functional receptor. These nAChRs can either be homomeric, where all 5 subunits are the same, or heteromeric where there are different subunits combining. The most common CNS nAChRs are the homomeric [alpha] 7 nAChR and the heteromeric [alpha]4[beta]2 nAChR. Within these heteromeric nAChRs other subunits, such as the [alpha] 3 and [alpha] 5 subunits, can be incorporated into the accessory position. Many of the mutations in nAChRs linked to SHE are present in the transmembrane (TM) regions of the [alpha]4 and [beta]2 subunits of these [alpha]4[beta]2 nAChRs. However, less is known about the SHE mutations present in the intracellular loop regions. The [alpha]4[beta]2 subtype is widely distributed throughout the CNS. Our study looks at both [alpha]4[beta]2 isoforms as well as the more complex [alpha]4[beta]2)₂[alpha]3 and [alpha]4[beta]2)₂[alpha]5. The [alpha]3 and [alpha]5 accessory subunits are more highly expressed within the thalamocortical loop, the network implicated in SHE. Some prior research has been conducted on the [alpha]4[beta]2)₂[alpha]5 subtype and has shown that incorporation of the [alpha] 5 subunit increases the resulting receptor's Ca²⁺ permeability. Minimal work has been done on [alpha]4[beta]2)₂[alpha]3 subtype but research has shown that incorporating the [alpha]3 subunit into the [alpha]4[beta]2 nAChR results in low sensitivity to ACh and can be potentiated by compounds like NS-9283. We investigated the incorporation of the [alpha]4R³³⁶H SHE mutation into the [alpha]4[beta]2 isoforms as well as the ([alpha]4[beta]2)₂[alpha]3 and ([alpha]4[beta]2)₂[alpha]5 subtypes. Our results revealed that the [alpha]4R³³⁶H SHE mutation altered ACh pharmacology and overall receptor function. We also demonstrated that incorporation of the [alpha]3 or [alpha]5 subunits into the [alpha]4[beta]2 subtype caused changes in response to physiologically-relevant ligands. Our study adds to the knowledge of how the [alpha]4R³³⁶H SHE mutation contributes to changes in nAChR pharmacology and function. We also add to the growing knowledge of residues within the intracellular cytoplasmic loop region and their importance. Results from this study may be applicable to future studies involving generalized epilepsy, in which nAChRs are implicated. Study results could also be applicable to other neurological disorders such as Alzheimer's disease, Parkinson's disease, autism, and schizophrenia. These diseases, in many instances, involve alterations to various nAChR subtypes such as [alpha]7, [alpha]4[beta]2, [alpha]5 containing and [alpha]3-containing nAChRs.
  • Impairment of DNA repair by oncogenic virus HHV8

    Podlutskaya, Viktorija; Weltzin, Maegan; Kuhn, Thomas; Drew, Kelly; Oliver, Ryan (2022-08)
    Cancer is a growing disease burden worldwide. Lifestyle and environmental factors are the largest contributors to cancer development (90-95%) in contrast to genetics (5-10% of cases,); of the environmental factors, infections contribute 15-20% of the "external" risk in developing cancer. In the US, breast cancer is the most common type of cancer with 284,000 new cases expected in 2021, with the next most common being prostate and lung cancer. Viruses have long been suspected to promote cancerous transformations. Kaposi Sarcoma Associated Herpesvirus (KSHV) is implicated in Kaposi Sarcoma (KS) cancer transformation and in vitro is found in BCBL1 cells. KSHV is a herpesvirus, also named Human Herpesvirus 8 (HHV8). The connection between viral infection and increase in cancer has been documented, but the details of cellular mechanisms involved therein are lacking. We hypothesize that during active viral infection, cellular DNA is not repaired properly, leading to the accumulation of DNA damage and mutations; these in turn, could lead to the transformation of normal, albeit virus-infected cells, into cancer-predisposed cells, and later tumor formation. The goal of this thesis was to investigate DNA repair during an active viral infection of HHV8. BCBL1 is a clonal lymphoma cell line isolated in 1995 from an HIV seronegative patient with a body cavity-based lymphoma. Chapter 1 is a mini review on what is known about this oncogenic virus, DNA repair pathways, and cancer and how these three relate to each other is discussed. Chapter 2 compares DNA repair dynamics of two distinct repair pathways in virally active cells versus virally dormant cells. Our research suggests that host processes controlling DNA repair mechanisms are manipulated to favor virus production. Chapter 3 is a general conclusion summarizing our significant findings from Chapter 2.
  • 3T3-L1 adipocytes as a model of Glut4 translocation

    Collin, Aline; Duffy, Lawrence; Coker, Robert; Coker, Melynda Sheri; Drew, Kelly (2021-12)
    Type 2 diabetes (T2D), a lethal disease, reveals an alarming increase of epidemic proportions and, by 2050, an estimated 1 in 3 adults in the US will suffer from it. Persistent and systemic inflammatory and oxidative stress in adipose tissue and skeletal muscle are recognized as key players in the progression of T2D. T2D is characterized by insulin resistance, the inability of cells to respond to standard circulating levels of insulin, resulting in hyperglycemia. In adipocytes and skeletal muscle, glucose uptake, a vital step in blood glucose regulation, predominantly occurs via the glucose transporter 4 (Glut4) in an insulindependent recruitment from a cytosolic vesicle. Under inflammatory stress, these cells have demonstrated a lack of Glut4 presence in the plasma membrane, leading to a lack of glucose transport within these cells. 3T3-L1 murine adipocytes are a key model to study insulin signaling in vitro. Mature adipocytes are converted from fibroblasts in a lengthy process requiring chemical induction. Several inducers have been tested in hopes to shorten the time span required for differentiation. However, the use of different inducers and changes in the differentiation programming could have consequences on the phenotype of the mature adipocytes. For this reason, we sought to evaluate the differences in 3T3-L1 fibroblasts induced with either 3-isobutyl-1-methylxanthine (IBMX), or troglitazone. In addition to pharmaceutical recourse to restore insulin signaling and glucose uptake in cells under inflammatory duress, a dietary approach has been considered. Natural products such as blueberries have been of particular interest due to their health benefit including antioxidant benefits and their ability to modulate biochemical pathways. Wild Alaskan blueberries are of particular interest due to their link to a reduced prevalence of T2D in Alaskan Native populations. Here, we report differences in the phenotype of 3T3-L1 adipocytes based on the inducer of adipogenesis and a lack of increase in plasma membrane Glut4. Our studies demonstrate a higher expression of adipocyte biomarkers in cells treated with troglitazone compared to IBMX, but a higher expression of total Glut4 in cells treated with IBMX compared to troglitazone. In both phenotypes, we note a lack of insulin-induced increase of plasma membrane levels of Glut4 in 3T3-L1 mature adipocytes. Finally, we demonstrate an insulin-like benefit of Alaskan blueberry extracts on plasma membrane Glut4.
  • Age related dementias

    Soltani, Shahab; Duffy, Lawrence K.; Cruz, Bradley K.; Dunlap, Kriya L. (2021-12)
    During the last few decades, the average life expectancy has dramatically increased in the U.S.A. and globally. As a result, the diseases associated with age, such as dementia, significantly impact families, society, and government. Dementia is a broad term describing memory loss, cognitive dysfunctions, and limited social skills caused by many factors such as aging, stroke, and genetic background. Although the primary etiology remains unclear but inflammatory reactions, neurodegeneration, vascular abnormalities play an important role in the progression of these disorders. Therefore, treatment is mainly supportive to relieve the symptoms of dementia and not to cure dementia or slow down its progression. This review discusses the most common disorders that cause dementia, including Alzheimer's disease, vascular dementia, and Parkinson's disease, as well as their symptoms, diagnosis, and treatments. Also covered are the studies that were performed on these disorders and animal models for each disease.
  • Assessment of an Alaskan willow with potential for polychlorinated biphenyl rhizoremediation

    Slater, Heather Ann; Leigh, Mary Beth; O'Hara, Todd; Trainor, Tom; Rasley, Brian (2010-05)
    "Polychlorinated Biphenyls (PCBs) are priority pollutants targeted for remediation efforts in many areas of the world. Rhizoremediation, the use of plants and their associated root microorganisms for the degradation of a pollutant, may be an inexpensive and effective approach to biodegrading PCBs and detoxifying contaminated soils in situ. Two Alaskan native tree species, Salix alaxensis (willow) or Picea glauca (white spruce), were assessed for the ability to stimulate microbial PCB degradation by measuring PCB loss, toxicity and microbial community shifts in soil microcosms following the addition of crushed roots. Incubation of polluted soils with root crushates of S. alaxensis led to significant losses (up to 30% in 180 days) of several PCB congeners, including many of the most toxic congeners, PCB 77, 105 and 169. Soil toxicity, measured using the Microtox assay, also decreased as a result of treatment with willow-roots. Treatment of soils with salicylate, a willow secondary compound hypothesized to promote aromatic pollutant biodegradation, inhibited PCB degradation, suggesting that other willow biodegradation are responsible for biostimulation. The disappearance of PCB congeners, detoxification of soil, and detection of microbes with PCB degrading abilities suggests that S. alaxensis is a promising plant candidate for rhizoremediation of PCBs"--Leaf iii
  • Design, function, and applicability of a new multiple axis-differential optical absorption spectrometer for observing halogen chemistry in the Arctic

    Carlson, Daniel A. (2010-05)
    "Every springtime reactive halogen species (e.g. bromine atoms and bromine monoxide radicals, BrO) are photochemically released into the Arctic atmosphere by heterogeneous reactions on snow/ice surfaces. These halogens subsequently alter the chemical pathways of the atmosphere by depleting ozone levels to near zero, taking over as the primary oxidizer. An autocatalytic chemical mechanism for the release of reactive halogens from ice surfaces has been described; however, the environmental conditions that lead to halogen production are still unclear, limiting our ability to understand and predict these halogen chemical events. This thesis describes the design and operation of a new autonomous multiple axis-differential optical absorption spectrometer (MAX-DOAS) instrument, which is capable of long term data collection at remote unmanned locations. Novel design features include frost detection and removal, instrumental tilt correction, an enclosed optical scan head, robust data acquisition software, satellite communications compatibility, and low power consumption (~3 Watts). Laboratory and field tests demonstrate that this new instrument is capable of producing high quality BrO measurements. This instrument holds great promise for furthering our understanding of reactive halogens in the polar regions, in particular through investigations of environmental conditions leading to halogen release as well as by validating and improving satellite methods"--Leaf iii
  • Dissolution and sorption of hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine and 2, 4, 6-trinitrotoluene residues from detonated phyllosilicate mineral surfaces

    Jaramillo, Ashley Marie (2010-08)
    "Military training and testing exercises using explosive ordnances has resulted in training range surface soil becoming contaminated with high explosive (HE) residues. Composition B (Comp B) is a commonly used military formulation composed of 2, 4, 6-trinitrotoluene (TNT) and hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), two toxic HE materials. The potential risk of human exposure to these compounds and the efficacy of remediation efforts depend on the fate and transport of each compound in the environment. Numerous investigations of the temporal fate of HE compounds in soil materials have been conducted, however, most of these studies relied on the application of HEs to soils through aqueous addition. The purpose of this study is to investigate the dissolution and sorption of TNT and RDX originating from Comp B residues loaded to pure mineral phase surfaces through detonation. Detonation caused the heterogeneous loading of TNT and RDX onto each mineral substrate surface. Composition B residues dissolved rapidly (within 9 hours) for all samples, but maximum concentrations for either compound were not sustained due to precipitation from solution and/or sorption onto each mineral substrate surface"--Leaf iii
  • Assessment of fungal and bacterial bioaerosols in ambient air in Fairbanks, Alaska

    Patil, Mitali S.; Cahill, Catherine; Leigh, Mary Beth; Kuhn, Thomas (2011-12)
    Bioaerosols are solid or liquid particles of biological origin that are suspended in the surrounding air or other gaseous environments. Bioaerosols can cause diseases, allergenic or toxicological reactions, respiratory distress, and can be potential bioterrorism threats. Studies concerning ambient bioaerosols have never focused upon central Alaska, and only one experiment has utilized the DRUM (Davis Rotating Unit for Monitoring) impactor as the collection apparatus. This study focuses on the assessment and identification of fungi and bacteria present in the ambient air collected by the DRUM impactor from March 2008 to January 2009. The samples were collected on MylarTM and aluminum substrates (with or without apiezon coating) and subjected to DNA extraction and nested PCR using universal primers for the 16S rRNA gene in bacteria and ITS (internal transcribed spacer) region in fungi. The PCR products were used to generate a clone library, and selected clones from each sample clone library were sequenced. Sequences were taxonomically classified using BLAST for fungal identification and RDP Pipeline for bacterial identification to the genus level. Numerous species of bacteria (i.e., Ralstonia sp., Bradyrhizobium sp., Sphingomonas sp.) and fungi (i.e. Fusarium sp., Cladosporium sp., Penicillium sp.) were identified from the clone libraries, thus indicating that the DRUM impactor has potential for monitoring biological content in the air. The resulting patterns in bacteria and fungi during the course of the year indicate that the DRUM sampler may also have the potential to detect fluctuations in populations that result from meteorological conditions, seasonal cycles, and climatic conditions.
  • Tropospheric reactive bromine and meteorology over the Arctic Ocean

    Swanson, William; Simpson, William; Guerard, Jennifer; Trainor, Thomas; Mao, Jingqiu (2021-08)
    During late winter and spring in the Arctic, unique chemistry produces high levels of reactive bromine radicals (e.g., bromine atomic radicals and bromine monoxide, BrO) in the lower troposphere. These high levels of bromine radicals react with and reduce ambient ozone and oxidize gaseous elemental mercury. These reactive bromine species are chemically released from frozen saline surfaces and are affected by meteorological processes such as transport and mixing. Prior work has proposed that heterogenous reactions on snowpack surfaces as well as on atmospheric particle surfaces contribute to the reactive bromine production. We investigate these hypotheses using an extensive dataset of lower-tropospheric BrO observations from the Arctic Ocean and Utqiaġvik (formerly Barrow). First, we combine BrO observations with meteorological data and use principal component analysis to determine what environmental processes are correlated with BrO. We find that increased levels of reactive bromine under two sets of meteorological conditions: 1) stable, poorly vertically mixed conditions with temperature inversions, and 2) low-atmospheric-pressure conditions with increased vertical mixing. A principal component regression model based on these correlations predicted both the vertical column density of BrO in the lowest 2 km of the troposphere (R = 0.45) and the vertical column density of BrO in the lowest 200 m (R = 0.54). Next, we compare BrO observations to a global chemicaltransport model, GEOS-Chem, which was recently modified to add a blowing snow sea salt aerosol particle source. The GEOS-Chem model including the blowing snow process predicts monthly averaged BrO within experimental error for 9 of 13 total months of observations in Spring 2015 but cannot replicate hourly peaks in observed BrO. The model also predicts BrO during the Fall, which is not supported by the observations, potentially indicating a problem with the blowing snow model. We improve GEOS-Chem by adding a snowpack source of molecular bromine arising from deposition of precursor species such as ozone. Adding this snowpack molecular bromine source improves the agreement between the model and the observed monthly BrO at Utqiaġvik. However, a prior literature form of this model that had assumed an increased daytime yield of molecular bromine due to photochemistry leads to overprediction of radical bromine and is not supported. We find that using both the blowing snow aerosol particle source and the snowpack molecular bromine source together in GEOS-Chem increases model skill in simulating Arctic reactive bromine events. Our global chemical model improvements should improve prediction of the effect of climate change on Arctic reactive bromine levels and help assess their implications for ozone depletion and mercury deposition.
  • Vetting model and satellite-based estimates of regional scale carbon exchange at northern high latitudes using solar-viewing infrared spectroscopy

    Jacobs, Nicole; Simpson, William R.; Euskirchen, Eugénie S.; Guerard, Jennifer; Maxwell, David A. (2021-08)
    Carbon exchange in the Boreal Forest and its response to a warming climate is a critical process that needs to be understood for more accurate predictions of climate change. Therefore, we established a ground-based long-term monitoring site at the University of Alaska Fairbanks in Fairbanks, Alaska, USA (64.859°N, 147.850°W) operating a solar-viewing Bruker EM27/SUN Fourier transform infrared spectrometer (FTS). This instrument measures vertically integrated column abundances of carbon dioxide (CO₂), methane (CH₄), and carbon monoxide (CO), termed Xgas, i.e., XCO₂. These measurements are directly comparable to satellite-based measurements, for which these ground-based observations provide validation data. Measurements of XCO₂ and XCH₄ have to be extremely precise because variability in atmospheric columns of CO₂ and CH₄ is often less than 1% of the background levels of these long-lived gases. Therefore, the observations in Fairbanks were carefully vetted through comparisons of results from two retrieval algorithms applied to the same observed spectra, comparisons of observations from two EM27/SUN FTS operating side-byside, and comparisons between an EM27/SUN FTS and measurements from a Bruker IFS125HR in the Total Carbon Column Observing Network (TCCON) at Caltech, Pasadena, California. These data are all collected over a period of about 4.5 years. Comparisons of retrieval methods indicate that the results are tightly correlated, but there are offsets that could be corrected with an appropriate scaling factor. Observed biases between two colocated EM27/SUN FTS were in agreement within instrument precision. Biases between the EM27/SUN and TCCON retrievals at Caltech are larger and more variable than biases between the two EM27/SUN FTS in Fairbanks, which may be partially explained by differences in spectral resolution. These biases are also similar to those reported in previous studies. Vetted Fairbanks observations are used in combination with those from two TCCON sites in the Boreal Forest, East Trout Lake, Saskatchewan, Canada (54.354°N, 104.987°W) and Sodankylä, Finland (67.367°N, 26.631°E), to evaluate quality control methods and bias in XCO₂ from the NASA Orbiting Carbon Observatory 2 (OCO-2). This study yielded alternative quality control thresholds and bias correction, tailored to Boreal Forest regions that allow for increased data throughput and reduced seasonality in bias over northern high latitude regions. In particular, increased data throughput in spring and autumn months made it possible to measure XCO₂ seasonal cycles using satellite-based measurements. In this analysis, we found that the Asian Boreal Forest region stood out as having the largest seasonal amplitude and earliest seasonal drawdown of any region. There is also a pronounced west-to-east gradient of increasing seasonal amplitude and earlier seasonal drawdown across the Eurasian continent. Comparisons with two independent global CO₂ models are good, showing high correlation and spatial agreement. Analysis of modeled (GEOS-Chem) surface contact tracer contributions reveals that the largest seasonal amplitudes occur in regions that have the largest contributions from land-based surface contact tracers with 15 or 30 day atmospheric lifetimes, suggesting that accumulations of CO₂ exchanges during atmospheric transport on approximately monthly timescales play an important role in shaping observed XCO₂ seasonal cycles in northern high latitude regions. Furthermore, surface contact tracer contributions from land were more correlated with XCO₂ seasonal amplitude than estimates of total annual fluxes or seasonal amplitudes of flux estimates within a region, emphasizing the importance of understanding the effects of atmospheric transport when interpreting observations of XCO₂.
  • Enhancing tumor antigen presentation with complement targeted liposomes

    Francian, Alexandra; Kullberg, Max; Kuhn, Thomas; Burkhead, Jason; Knall, Cindy (2021-08)
    Tumor-mediated immune evasion and suppression can be prohibitive to successful cancer treatment and recovery. A defining trait of cancer progression is when tumor cells develop the ability to evade detection by the immune system. Advanced tumors can suppress the presentation of antigens to effector immune cells by secreting regulatory cytokines and by downregulating the expression of major histocompatibility complex I (MHC I) receptors on the surface of tumor cells. Effective anti-tumor immunity requires the processing and persistent presentation of tumor antigens to effector cells. The cells responsible for this are antigen presenting cells (APCs), which initiate the immune response against cancer by engulfing and presenting tumor antigens to effector immune cells. APCs present tumor antigens, which provide specific targets for helper T cells and cytotoxic T lymphocytes, allowing the immune system to distinguish cancer cells from noncancerous cells. There are many different types of tumor antigens, and the increased effort to sequence reactive epitopes and establish a database makes tumor antigen immunotherapy a promising avenue for treatments and vaccines. Immunotherapies have been developed to restore the immune response against tumors without the toxic side effects of chemotherapeutic drugs. This research describes a promising cancer immunotherapy utilizing a liposome nanoparticle that binds to endogenous complement C3 proteins in serum and is internalized by APCs through the complement C3 receptor, resulting in direct delivery of encapsulated compounds. APCs were shown to internalize C3-bound liposomes containing ovalbumin (OVA), a model antigen, resulting in a significant increase in activated T cells that recognize OVA, reduced tumor growth in all mice (n=5), and complete elimination of both treated and distal tumors in two out of five mice (40%). Blood from treated mice had lower percentages of immunosuppressive cells, higher percentages of B cells, and increased anti-OVA IgG1. Collectively, treatment with OVA C3-liposomes is able to induce the activation of both cell-mediated and humoral immune responses. C3-liposomes encapsulating a melanoma tumor antigen, TRP-2, were able to reduce and eliminate established tumors in a melanoma tumor model in 6 out 7 mice (86%), with the addition of checkpoint blockade, anti-CTLA-4, improving the results (tumor reduction in all mice; n=3). C3-liposomes were also able to induce expression of costimulatory molecules and the production of proinflammatory cytokines and factors in targeted APCs. These results indicate that C3-liposome delivery of tumor antigens to APCs initiates a potent and systemic antitumor immune response.

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