Theses and Dissertations at Montana State University (MSU)
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Item Intercontinental distributions of species of Cortinarius, subgenus Phlegmacium, associated with Populus in western North America(2014-10) Cripps, Cathy L.; Liimatainen, Kare; Niskanen, Tuula; Dima, Balint; Bishop, Richard F.; Ammarati, Joseph F.Three species of Cortinarius subg. Phlegmacium, Cortinarius argutus Fr. and Cortinarius hedyaromaticus C. Cripps & O.K. Mill. (section Arguti stat. nov.) and Cortinarius talus Fr. (section Multiformes), are compared from western North America and Europe. Phylogenetic analysis of the ITS region shows that C. argutus and C. hedyaromaticus are separate, closely related species with rooting stipes. Cortinarius talus is a pale species with a bulbous stipe and a sweet odor similar to that of C. hedyaromaticus; C. argutus lacks this sweet odor. All three species have intercontinental distributions and are associated with deciduous trees, primarily Populus tremuloides Michx., Populus tremula L., but also Salix spp. This study highlights the importance of the study of type specimens and molecular analysis to stabilize the application of established names.Item Designing virus-like nanoparticles as T 1-enhanced MRI contrast agents(Montana State University - Bozeman, College of Letters & Science, 2014) Qazi, Shefah Alma; Chairperson, Graduate Committee: Trevor Douglas; Lars O. Liepold, Md Joynal Abedin, Ben Johnson, Peter Prevelige, Joseph A. Frank and Trevor Douglas were co-authors of the article, 'P22 viral capsids as nanocomposite high-relaxivity MRI contrast agents' in the journal 'Molecular pharmaceutics' which is contained within this thesis.; Masaki Uchida, Robert Usselman, Riley Shearer, Ethan Edwards and Trevor Douglas were co-authors of the article, 'Manganese (III) porphyrins complexed with P22 virus-like particles as T1-enhanced contrast agents for magnetic resonance imaging (MRI)' in the journal 'Journal of bioinorganic chemistry' which is contained within this thesis.; Masaki Uchida, Hisanori Kosuge, Michael V. McConnell, and Trevor Douglas were co-authors of the article, 'Expression and biophysical characterization of RGD targeting peptide on surface of P22 via C-terminus extension of DEC and P22 coat protein' which is contained within this thesis.The field of nanotechnology is a rapidly growing field. In the past few decades, nanoparticles have been utilized for use in biomedical applications with a huge impact in enhancing diagnostic techniques. Protein cages and virus-like particles are biological examples of nanoparticles. They are highly symmetric, well-defined architectures made from multiple protein subunits and can be genetically or chemically engineered to impart desired new functionalities and have been used for design of nanomaterials for improving current diagnostic techniques, as discussed in this thesis. One of the main techniques for diagnosis used today is magnetic resonance imaging (MRI) as it provides good spatial resolution of soft tissues without using harmful ionizing radiation. However, due to poor sensitivity of this technique, contrast agents are often utilized by clinicians to aid in diagnosis of diseased tissues. The main MRI contrast agents used in T1-enhanced imaging are small Gd-containing molecules. Due to the toxicity of free Gd ions, these agents are administered in a tightly chelated form. Even in this form, high doses increase the risk of toxicity. Thus, it is important to reduce overall dosage of these contrast agents. In this thesis, we discuss design principles for virus-like particle based MRI contrast agents as next generation diagnostics which can overcome the above mentioned barriers. Conjugating clinically approved contrast agents to nano-sized virus-like particles changes the intrinsic properties of the contrast agent, directly impacting and increasing MRI contrast. Modifying the interior surface of these cage-like containers to grow functionalizable polymers provides multiple sites for conjugation of small molecule contrast agents, resulting in high payload of these agents. Modifying the exterior surface of these cage-like containers to present targeting ligands and enable them to localize at desired tissues of interest. All three of these design considerations contribute to higher contrast, significantly lower clinical dose requirements, and allow for safe administration of Gd (III) ions for enhanced imaging. As gadolinium-based contrast agents are directly linked with nephrogenic systemic fibrosis, a rare but deadly disease that causes hardening of tissues and organs, an alternate low-risk metal-complex, Mn (III) porphyrins, has also been explored for bioconjugation to virus-like particles.Item A fiber optic array for the detection of sub-surface carbon dioxide at carbon sequestration sites(Montana State University - Bozeman, College of Engineering, 2014) Soukup, Benjamin John; Chairperson, Graduate Committee: Kevin S. RepaskyA fiber sensor array for sub-surface CO 2 concentrations measurements was developed for monitoring geologic carbon sequestration sites. The fiber sensor array uses a temperature-tunable distributed feedback (DFB) laser outputting a nominal wavelength of 2.004 microns. Light from this DFB laser is directed to one of the four probes via an in-line 1x4 fiber optic switch. Each of the probes is placed underground and utilizes filters that allow only soil gas to enter the probe. Light from the DFB laser interacts with CO 2 within the probe before being directed back through the switch. The DFB laser is tuned across two CO 2 absorption features where a transmission measurement is made, allowing the CO 2 concentration to be retrieved. This process is repeated for each probe, allowing CO 2 concentration measurements to be made as a function of time for each probe. The fiber sensor array was deployed for fifty-eight days at the Zero Emission Research Technology (ZERT) field site and for a twenty-eight day period at the Kevin Dome geologic carbon sequestration site. Background measurements indicate the instrument can monitor background levels as low as 1,000 parts per million (ppm). During a thirty-four day sub-surface CO 2 release, elevated CO 2 concentrations were readily detected by each of the four probes with values ranging to over 60,000 ppm.Item Characterization of the [FeFe]-hydrogenase : toward understanding and implementing biohydrogen production(Montana State University - Bozeman, College of Letters & Science, 2014) Swanson, Kevin Daniel; Chairperson, Graduate Committee: John W. PetersHydrogen may provide an avenue for a clean renewable fuel source, yet the methods to produce hydrogen are either extremely energy intensive, rely on fossil fuels, or require expensive noble metal catalysts. Biology may hold the keys necessary to unlocking new technologies that could change how hydrogen is produced. Microbial processes also produce hydrogen and harbor enzymes that carryout the reversible reduction of protons to hydrogen gas. These enzymes are capable of producing hydrogen at high rates comparable to platinum catalysts, but biological hydrogen catalysts can produce hydrogen using abundant elements carbon, oxygen, nitrogen, sulfur, iron, nickel and selenium. Biological hydrogen catalysts are termed hydrogenases, and though hydrogenases use abundant elements they are extraordinarily complex. This has made it difficult to construct model complexes using inorganic synthesis that can replicate the activities of their biological counterparts. One way to circumvent this problem is to use microbial hydrogen production and let microbes produce and maintain these enzymes inside a cell. Microbial hydrogen production also has the added benefit that hydrogen production could be engineered to connect with other metabolic processes such as photosynthesis and fermentation. Engineering microbes for hydrogen production could eventually allow for the production of hydrogen using inexpensive energy inputs such as solar energy or waste materials. Yet, there are many barriers that need to be overcome in order to engineer a robust microbial organism. One of the primary difficulties of developing this technology has been the oxygen sensitivity of hydrogenases. Hydrogenases when exposed to atmospheric concentrations of oxygen either completely inactivate or their rates are significantly slowed. To engineer a hydrogenase that is more amenable for microbial hydrogen production, the optimization of expressing and purifying hydrogenase enzymes has been developed. Methodologies have been developed to characterize how oxygen inactivates hydrogenase enzymes, and a new methodology has been explored to help find novel hydrogenase gene sequences that may help in engineering oxygen tolerant enzymes.Item Electronic structure determination of model complexes of [Mo-3Fe-4S] clusters and method development of in situ reductive amination using amine-boranes(Montana State University - Bozeman, College of Letters & Science, 2014) Towey, Bradley David; Chairperson, Graduate Committee: Thomas S. LivinghouseIn nature, bacteria are able to convert inert nitrogen gas to ammonia using the iron molybdenum-cofactor of the nitrogenase enzyme. Even though the crystal structure and the magnetic coupling of the iron molybdenum-cofactor cluster have been elucidated, the bonding site(s) and the mechanism of the reduction are not understood. The reactivity towards nitrogenase substrates of the iron molybdenum-cofactor from synthetic [Mo-3Fe-4S] biomimetic models has previously been examined, but these models are limited to reducing N,N single and double bonds, protons, acetylene, and acetonitrile. The reactivity of these clusters is dictated by their electronic structure, which is tuned by the chelating ligands. To study the ligand donations, a simpler cluster with a homoleptic ligand environment, the MoFe 3S 4(S 2CNEt 2) 5 complex, was synthesized and analyzed with S K-edge X-ray absorption spectroscopy. The S K-edge is convoluted due to the different sulfur environments and only plausible assignments could be inferred based on Slater's rules for effective oxidation states. Iron sulfide bonds have been characterized using S K-edge X-ray absorption spectroscopy, however, little is known regarding molybdenum sulfide bonding. The tetrahedral MoS 4 2- compound was utilized to understand the Mo-S bonding with X-ray absorption spectroscopy in conjunction with computational methods. The terminal sulfides of MoS 4 2- donate approximately five electrons to the formally +6 charge on the Mo center. Since the charge delocalization of transition metal dithiocarbamate complexes have not been studied extensively, the experimental electronic structure of Zn(II), Cu(II), Fe(II), Fe(III), and Mo(IV) dithiocarbamate complexes were examined. The dithiocarbamate ligands exhibit classical bonding in which the ionic character increases with increasing positive charge on the metal. Piecing these models together, the MoFe 3S 4(S 2CNET 2) 5 cluster contains a covalent [Mo-3Fe-4S] core with ionic dithiocarbamate ligands surrounding and stabilizing the cluster. The last part of this thesis is the development of a new method for reductive amination of dimethylhydrazones to dimethylhydrazines using amine-boranes. Conventionally, the C=N bond is reduced with toxic or less selective reducing agents. A potent, and easy to handle tert-butylamine borane was used and prepared in situ towards the synthesis of dimethylhydrazines containing different functionalities in high yields.Item Mining spatiotemporal co-occurrence patterns from massive data sets with evolving regions(Montana State University - Bozeman, College of Engineering, 2014) Ganesan Pillai, Karthik; Chairperson, Graduate Committee: John Paxton; Rafal A. AngryK (co-chair)Due to the current rates of data acquisition, the growth of data volumes in nearly all domains of our lives is reaching historic proportions [5], [6], [7]. Spatiotemporal data mining has emerged in recent decades with the main goal focused on developing data-driven mechanisms for the understanding of the spatiotemporal characteristics and patterns occurring in the massive repositories of data. This work focuses on discovering spatiotemporal co-occurrence patterns (STCOPs) from large data sets with evolving regions. Spatiotemporal co-occurrence patterns represent the subset of event types that occur together in both space and time. Major limitations of existing spatiotemporal data mining models and techniques include the following. First, they do not take into account continuously evolving spatiotemporal events that have polygon-like representations. Second, they do not investigate and provide sufficient interest measures for the STCOPs discovery purposes. Third, computationally and storage efficient algorithms to discover STCOPs are missing. These limitations of existing approaches represent important hurdles while analyzing massive spatiotemporal data sets in several application domains that generate big data, including solar physics, which is an application of our interdisciplinary research. In this work, we address these limitations by i) introducing the problem of mining STCOPs from data sets with extended (region-based) spatial representations that evolve over time, ii) developing a set of novel interest measures, and iii) providing a novel framework to model STCOPs. We also present and investigate three novel approaches to STCOPs mining. We follow this investigation by applying our algorithm to perform a novel data-driven discovery of STCOPs from solar physics data.Item Microfossil paleontology and biostratigraphy of the early Mesoproterozoic Belt Supergroup, Montana(Montana State University - Bozeman, College of Letters & Science, 2014) Adam, Zachary Robert; Chairperson, Graduate Committee: David W. Mogk; Mark L. Skidmore (co-chair)The Belt Supergroup is one of few early Mesoproterozoic sites worldwide that record paleobiological evidence of enigmatic ancestral eukaryotes. Using low manipulation acid maceration techniques, two new assemblages of microfossils have been recovered from the Greyson and Chamberlain Formations of the early Mesoproterozoic Belt Supergroup of Montana. These microfossils provide a window into the paleobiology of early Mesoproterozoic Laurentia for the first time. By comparison with fossils from other deposits of comparable age, these assemblages may be used to infer key biochronological, paleoenvironmental and ontogenetic aspects about the original organisms. The Greyson Formation assemblage from outcrops along Newlan Creek includes populations of Tappania, Valeria, Satka, Dictyosphaera, Coneosphaera, Caudosphaera and longitudinally striated tubes. The assemblage also includes microbial mat networks of Siphonophycus and isolated occurrences of Oscillatoriopsis, Rugosoopsis and Obruchevella. The Newlan Creek microfossils are conspicuously similar to those from the broadly coeval Roper Group of Australia, pointing to the utility of recognizing an early Mesoproterozoic (~1550-1450 Ma) assemblage zone represented by Tappania plana, Valeria lophostriata, Satka favosa, and Dictyosphaera delicata. The Chamberlain Formation assemblage from drillcore near Black Butte includes Valeria, Leiosphaeridia, Synsphaeridium, Coniunctiophycus, Satka, Symplassosphaeridium and longitudinally-striated tubes. The Black Butte microfossils expand the assemblage diversity previously reported from Chamberlain Formation outcrops near Neihart, Montana. The Black Butte assemblage partially overlaps with, but is notably distinct from, the assemblage from Newlan Creek. The differences between the respective assemblages are most likely attributable to paleoecological zonation of the original organisms. The Black Butte microfossils are broadly consistent with assemblages reported from supratidal to intertidal shallow water deposits of the late Mesoproterozoic. By contrast, the Newlan Creek microfossils are comparable to the distal shelf environment assemblage of the Roper Group of Australia. Correlations between morphometric attributes of the fossils indicate the presence of modestly diverse, environmentally-partitioned ecosystems that included protistan-grade organisms capable of a variety of cell replication processes by the early Mesoproterozoic. Microfossils and macrofossils of the Belt Supergroup provide an unparalleled opportunity for resolving ecological and macroevolutionary relationships among some of the Earth's oldest known eukaryotic organisms.Item Assessing credit riskiness around the world(Montana State University - Bozeman, College of Agriculture, 2014) Castiblanco Calderon, Jorge Luis; Chairperson, Graduate Committee: Myles WattsDuring the last few decades, the theoretical literature highlighting the importance of institutional frameworks on economic performance has exhibited much growth. Furthermore, given that modern advancements have allowed the collection of panel institutional data to become a more reliable procedure, a growing body of empirical research examining several of these theoretical claims has recently begun to flourish. This new empirical literature has given much attention to studying the connection between institutions and economic growth; however, the empirical connection between institutional development and several other important measures of economic performance remains largely unexplored. This thesis partially alleviates this insufficiency by presenting the first empirical study on the relationship between institutional development and private credit riskiness around the world. The analysis consists of applying a variety of model specifications to a select group of panel datasets on institutions. The results obtained suggest that, on average, a higher level of institutional development is associated with interest rate reductions that may, in turn, be due to lower levels of credit riskiness. Moreover, these results appear to be very robust to a wide array of sensitivity tests.Item Definition of alarm fatigue and its influence on staff performance(Montana State University - Bozeman, College of Engineering, 2014) Deb, Shuchisnigdha; Chairperson, Graduate Committee: David ClaudioAn alarm is a warning of an approaching situation which requires a response. This study considered the influences of alarms in the clinical health environment. The Emergency Care Research Institute considered alarm hazard as the number one health technology hazard for the years 2012 through 2014. The Joint Commission set a standard for all hospitals in the US to assess alarm fatigue in their monitoring process and to develop a systematic, coordinated approach to clinical alarm system management. In order to comply with this requirement, a working definition of alarm fatigue is necessary. To the very best of our knowledge, there have been no studies proposing a quantitative definition of alarm fatigue, a way to measure it, or exploring the influence of alarm fatigue on performance deterioration. This observational study undertook the objective of defining alarm fatigue and its role on performance deterioration in a quantitative way. A survey using a questionnaire proposed by the American College of Clinical Engineering Healthcare Technology Foundation was conducted before the observations to assess the attitude of nurses toward the existing alarm monitoring system at the hospital where the research took place. An extensive literature review and Hierarchical Task Analyses were conducted in order to reveal all the possible influencing factors behind alarm fatigue. From these, alarm fatigue was defined and measured in terms of mental workload and three types of affect: boredom, apathy, and distrust. A conceptual model was developed considering the significance of working conditions and staff individuality on alarm fatigue and, consequently, alarm fatigue on staff performance. Staff performance was measured in terms of response (yes/no), response time and number of ignored alarms. Several analytical approaches were performed to find association between alarm fatigue and staff performance. The results show that, in general, performance deterioration is actually influenced by a combination of alarm fatigue with working conditions and staff individuality. In the case of nurses and response time, alarm fatigue plays no role, only working conditions and staff individuality. These findings suggest that the role of alarm fatigue as a health hazard in the clinical environment should be reevaluated.Item The pursuit of hippo-ness : hippopotamus and human(Montana State University - Bozeman, College of Arts & Architecture, 2014) Franks, Alan Everett; Chairperson, Graduate Committee: Lucia RicciardelliThe relationship between human and animal is a complex and strange one, and many have written and theorized on the matter over the centuries. Animal theory has become ensconced in a debate that has evolved with public discourse and now exists in a realm that has become clouded with misperceptions. In this thesis, I explore ideas about human-animal relationships through the example of the hippopotamus and provide historical and cultural context for a reading of my accompanying film, "The Pursuit of Hippo-ness". Through both the film and the paper, I aim to raise questions about how we see and interact with the hippopotamus, drawing mainly from individual stories to reflect a multiplicity of an animal that is often seen in a negative light. By raising these questions about how we perceive animals, we should begin to recognize the impacts that it can have on conservation when some animals are seen as inferior in terms of their "value." Being cognizant of these prejudices or highly misconstrued understandings of animals, particularly those with negative connotations attached, we should begin to recognize the intrinsic value of the animals and the way in which our lives are intertwined with theirs.