Theses and Dissertations at Montana State University (MSU)

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    An analysis of fossil identification guides to improve data reporting in citizen science programs
    (Montana State University - Bozeman, College of Letters & Science, 2018) Butler, Dava; Chairperson, Graduate Committee: Greg Francis
    An increasing number of organizations use untrained volunteers to gather scientific data. This citizen science movement builds enthusiasm for science by engaging the public, as well as providing a way to gather large amounts of information at little or no expense. The challenge of citizen science is obtaining accurate information from participants. Identifying an image style that increases correct identifications helps not only the citizen science movement but also scientific instruction in general. This study tests three visual guides for identifying late Hemphillian (5-4.5 m.y.a.) fossils from Polk County, Florida. Each guide has identical layout and text, differing only in image style: color photos, grayscale photos, or illustrations. Teams of untrained participants each use one guide to identify fossils. Geology and paleontology professionals also identify fossils for comparison. Comparing results reveals that photographic images, either color or grayscale, produce results most similar to data from professionals.
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    The discovery and characterization of two archaeal viruses using culture-independent methods
    (Montana State University - Bozeman, College of Letters & Science, 2015) Hochstein, Rebecca Ann; Chairperson, Graduate Committee: Mark J. Young; Daniel Bollschweiller, Harald Engelhardt, C. Martin Lawrence, and Mark Young were co-authors of the article, 'Large tailed spindle viruses of archaea: a new way of doing viral business' in the journal 'Journal of virology' which is contained within this thesis.
    The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content, but rarely provide knowledge about virion morphology and or cellular host identity. This thesis describes research to utilize culture-independent methods to identify and to characterize two new archaeal viruses starting with viral metagenomic sequences. The first virus, Acidianus tailed spindle virus (ATSV), was initially identified by bioinformatic analysis of viral metagenomic datasets from a high temperature (80° C) acidic (pH 2) hot spring located in Yellowstone National Park, USA. ATSV was purified and characterized directly from environmental samples without dependency on culturing. Characterization included identification of the large tailed spindle shape virion morphology, determination of the complete 70.8 kbp circular ds DNA viral genome content, and identification of its cellular host. The host of ATSV, Acidianus hospitalis, was determined using CRISPR/Cas identification and CARD-FISH, and was confirmed by culturing. Additional characterization of ATSV included solving the structure of the major coat protein (MCP) by X-ray crystallography. The ATSV MCP reveals a decorated right-handed four helix bundle. The MCP is packed into the crystal as a four-start superhelix, for which the interfaces show biologically relevant interactions, indicating that ATSV might assemble using a multi-start helix. CryoEM images of ATSV show striations extending across the virion, supporting an assembly model in which long protein strands form the spindle virion structure. This is the first known model of spindle virus assembly. Culture-independent methods developed for ATSV purification and characterization were applied to a second virus, a pleomorphic particle found in high abundance in the CHAS viral fraction. Using mass spectrometry identification, viral metagenomics, deep sequencing, and host identification, a full virus genome and a host were linked to the virus particle, named Stygiolobus pleomorphic virus (SPV). SPV most likely represents a new virus family, with a unique particle morphology and gene content. Taken together, the results reported in this thesis provide an expanded pathway for the discovery, isolation and characterization of new viruses using culture-independent approaches.
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    Identification of economic wireworms using traditional and molecular methods
    (Montana State University - Bozeman, College of Agriculture, 2013) Etzler, Frank Eric; Chairperson, Graduate Committee: Michael A. Ivie; Kevin W. Wanner, Anuar Morales-Rodriquez and Michael A. Ivie were co-authors of the article, 'DNA barcoding to improve the species level management of wireworms' submitted to the journal 'Journal of economic entomology' which is contained within this thesis.; Michael A. Ivie was a co-author of the article, 'Review of the Limonius canus LeConte, 1853 (Coleoptera: Elateridae)' submitted to the journal 'The coleopterists bulletin' which is contained within this thesis.
    Interest in wireworms has grown in the past decade due to their increasing pest status, largely due to the removal of effective seed treatments from the market. Currently, there is no effective Integrated Pest Management (IPM) strategy to control for wireworms, due to the diverse number of species that make up complexes in cropland. The purpose of this study was to determine what wireworm species are present in Montana's croplands and develop tools to make species concepts accessible to non-specialists. This was done using DNA barcoding to associate wireworms with adults. DNA barcoding was done by amplifying the Cytochrome-Oxidase I (COI) region of the mitochondrial genome. Twenty-nine (29) species were successfully sequenced and 13 species had adult and larval associations made, including three new associations. In addition, a LUCID pictorial key was also created to help identify species occurring in Montana. A LUCID key is a computer-based key where a user identifies a specimen with the help of pictures of each character. During the wireworm study, one species-group in the genus Limonius was found to include many economic species, including two that are important in Montana. This group needed to be reevaluated due to controversies raised in a recent revision, many of which dealt with economic species. With the combined use of morphological characters and DNA data, eight species are now recognized as belonging to the group. All of these subprojects show the combined use of DNA and morphology as essential to fully understanding wireworm species. With a more precise knowledge of the species that make up the complexes in Montana's croplands, we can focus on developing IPM stratetgies for efficient control.
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    Selective cloning of 16S rRNA molecules to describe naturally occurring microorganisms
    (Montana State University - Bozeman, College of Agriculture, 1990) Weller, Roland
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    Selection and characterization of genomic DNA clones of Pyrenophora teres and their application for disease diagnosis via the polymerase chain reaction (PCR)
    (Montana State University - Bozeman, College of Agriculture, 1990) Baltazar, Baltazar Montes
    Polymerase Chain Reaction (PCR) protocols were developed for the diagnosis of net and spot forms of Pvrenophora teres. Low copy number sequences selected from a P. teres f. sp. maculata random genomic library were used as a source of probes. Emphasis was placed on those sequences identifying DNA polymorphisms between net and spot isolates and with little or no sequence similarity with barley, wheat, or triticale genomes. Sequences identifying a large deletion in genomic DNAs of net and spot isolates were preferred over sequences detecting small DNA changes. Sequence data of two informative clones, pPtm-290, and pPtm-60, were used to construct primer sets to amplify the corresponding sequence in genomic DNAs of net and spot isolates present in barley plants infected with these pathogens. PCR results demonstrated the potential of the PCR as a diagnostic tool for P. teres. All the PCR experiments conducted with primers designated as Pt-1 and Pt-2 constructed using the sequence data from pPtm-290, showed a strict correlation between the presence of a 430 bp band and the presence of the pathogen in genomic DNAs of barley infected with the net form, spot form or both pathogens. PCR experiments with primers Pt-3 and Pt-4 constructed using sequence data from pPtm-60, indicated that it is possible to detect polymorphic bands between net and spot isolates as evidenced by the PCR products analyzed in an ethidium bromide agarose gel. PCR analysis offers a sensitive, rapid, inexpensive, and non-radioactive technique for the diagnosis of P. teres infection in field-grown barley plants. Future experiments should focus on the ability of the PCR to detect P. teres and P. graminea in infected barley seeds. Additionally, PCR-based protocols for P. teres diagnosis could possibly be incorporated in seed certification programs to avoid the distribution of infected seed in farmer fields.
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    Teaching weed seedling identification and crop staging and a survey of weeds in peppermint fields
    (Montana State University - Bozeman, College of Agriculture, 1992) Carda, Kristi Marie
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    Extraction of data from digital images of microorganisms
    (Montana State University - Bozeman, College of Engineering, 1993) Shope, Paul Andrew
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    A review of the ironclad beetles of the world : (Coleoptera Zopheridae: Phellopsini and Zopherini)
    (Montana State University - Bozeman, College of Agriculture, 2006) Foley, Ian Andrew; Chairperson, Graduate Committee: Michael A. Ivie; Matt Lavin (co-chair)
    Phellopsis LeConte is revised. Phellopsis porcata (LeConte) is returned to valid status and P. yulongensis NEW SPECIES is described. Phellopsis montana Casey NEW SYNONYMY (NS) and P. robustula Casey NS = P. porcata (LeConte). Phellopsis imurai Masumoto = P. amurensis (Heyden) NS. Species redescriptions, a key to species and notes on the history, biology and biogeography of the group are provided. Phylogenetic analyses support several changes to sustain monophyletic genera of Zopherini because the genera Meralius Casey, Nosoderma Solier, and Phloeodes LeConte were found to be polyphyletic. The genus Sesaspis Casey NEW STATUS is re-recognized, and redescribed to include the following species: Sesaspis denticulata (Solier), S. emarginatus (Horn) NEW COMBIATION (NC), S. lutosus (Champion) NC, S. doyeni (García-París et al.) NC, S. adami NEW SPECIES, S. ashei NEW SPECIES, and S. triplehorni NEW SPECIES. Phloeodes LeConte is clarified with 10 new synonymies [P. diabolicus (LeConte) = P. pustulosus (LeConte) NS, P. latipennis Casey NS, P. ovipennis Casey NS, P. elongatus Casey NS, P. scaber Casey NS, P. angustus Casey NS, and P. remotus Casey NS).
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