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Item Comparing juvenile physiology and morphology of two high-elevation pines, Pinus albicaulis and Pinus balfouriana(Montana State University - Bozeman, College of Letters & Science, 2023) Sparks, Katherine Elizabeth; Chairperson, Graduate Committee: Danielle UlrichWhitebark pine (Pinus albicaulis, PIAL) and foxtail pine (P. balfouriana, PIBA) are slow-growing, high-elevation, five needled ("high five") white pines and are foundation and keystone species in alpine and subalpine environments, providing essential resources and habitat for many species including the Clark's nutcracker and grizzly bears. In recent years, PIAL has experienced significant decline due to an amalgamation of climate change, white pine blister rust, and mountain pine beetle. As a result, PIAL is listed as endangered under the Canadian Species at Risk Act and threatened under the United States Endangered Species Act. Conversely, PIBA has experienced minimal decline. PIBA also exists in two disjunct populations, one in southern California (PIBAS) and one in northern California (PIBA N), resulting in the species being split into two sub-species (P. balfouriana subsp. austrina and balfouriana). Our study compared the physiology and morphology of the two species (PIAL and PIBA) and the two foxtail populations (PIBA N and PIBAS) to better understand how they interact with and respond to abiotic and biotic stressors in their high-elevation environments. We grew four-year-old PIAL and PIBA juveniles in a common greenhouse environment. In total, we measured 159 traits describing their morphology, biomass, stomata, xylem, budburst phenology, physiology, whole plant Volatile Organic Compounds (wpVOCs), phloem volatile resin (PVR) compounds, and Non-Structural Carbohydrates (NSCs). We found that PIAL and PIBA displayed different suites of traits that enable them to persist in their high elevation habitats, characterized by similar abiotic stressors (cold temperatures, high winds, summer drought) and biotic stressors (white pine blister rust, bark beetle). The two foxtail populations were similar for most traits except for wpVOC concentration and composition where PIBAS had significantly higher wpVOC concentration than PIBA N. For most traits, PIAL was most similar to PIBA N and differed the most with PIBAS while PIBA N was the intermediate being more similar to both groups, especially in wpVOC composition and concentration.Item Comparing network models of gap gene interaction during Drosophila melanogaster development(Montana State University - Bozeman, College of Letters & Science, 2021) Andreas, Elizabeth Anne; Chairperson, Graduate Committee: Tomas GedeonEarly development of Drosophila melanogaster (fruit fly) facilitated by the gap gene network has been shown to be incredibly robust, and the same patterns emerge even when the process is seriously disrupted. In this thesis we plan to investigate this robustness using a previously developed computational framework called Dynamic Signatures Generated by Regulatory Networks (DSGRN). The principal result of this research has been in extending DSGRN to study how tissue-scale behavior arises from network behavior in individual cells, such as gap gene expression along the anterior-posterior (A-P) axis of the Drosophila embryo. Essentially, we extend DSGRN to study cellular systems where each cell contains the same network structure but operates under a parameter regime that changes continuously from cell to cell. We then use this extension to study the robustness of two different models of the gap gene network by looking at the number of paths in each network that can produce the observed gap gene expression. While we found that both networks are capable or replicating the data, we hypothesize that one network is a better fit than the other. This is significant in two ways; finding paths shows us that the spatial data can be replicated using a single network with different parameters along the A-P axis, and that we may be able to use this extension of DSGRN to rank network models.Item Structure and function of a prokaryotic argonaute from Pseudomonas aeruginosa(Montana State University - Bozeman, College of Agriculture, 2020) Erickson, Reece Sheridan; Chairperson, Graduate Committee: Blake WiedenheftArgonautes (Ago) are structurally and functionally diverse proteins present in all domains of life. A common feature of these ancient proteins is their ability to bind nucleic acid guides that target the protein to complementary sequences. Although eukaryotic argonautes (eAgo) have been well-studied, we still know very little about the function of prokaryotic argonautes (pAgo) in bacterial and archaeal species. To address this gap in our knowledge, my thesis focused on determining the biochemical properties as well as the cellular functions of a pAgo from the organism Pseudomonas aeruginosa PACS2 (PaAgo). Here, we show that PaAgo plays a role in regulating the expression of transposons within PACS2. I also present results indicating that deletion of the PaAgo gene and its neighboring genes causes toxicity to P. aeruginosa. Finally, I provide evidence that PaAgo and a neighboring protein are binding partners and form a multi-protein complex. Future work will focus on copurifying and sequencing PaAgo nucleic acid guides as well as clarifying the mechanisms guide acquisition and biological function.Item Morphological adaptations facilitating attachment for archaeal viruses(Montana State University - Bozeman, College of Letters & Science, 2019) Hartman, Ross Alan; Chairperson, Graduate Committee: Mark J. YoungLittle is known regarding the attachment and entry process for any archaeal virus. The virus capsid serves multiple biological functions including: to protect the viral genome during transit between host cells, and to facilitate attachment and entry of the viral genome to a new host cell. Virus attachment is conducted without expenditure of stored chemical energy i.e. ATP hydrolysis. Instead, virus particles depend on diffusion for transportation and attachment from one host cell to another. This thesis examines the attachment process for two archaeal viruses. Sulfolobus turreted icosahedral virus (STIV) is well characterized for an archaeal virus. Still, no information is available concerning STIV attachment or entry. The research presented here shows that STIV attaches to a host cell pilus. Furthermore, combining the previously determined atomic model for the virus, with cryo-electron tomography, a pseudo-atomic model of the interaction between the host pilus and virus was determined. Based on this data, a model is proposed for the maturation of the virus capsid from a noninfectious to an infectious form, by dissociation of accessory proteins. Finally, a locus of genes is identified in the host cell, encoding proteins essential for viral infection, that are likely components of the pili structure recognized by STIV. The isolation of a new archaeal virus, Thermoproteus Piliferous Virus 1 (TSPV1), is also presented here. The TSPV1 virion has numerous fibrous extensions from the capsid, of varying length, that are the first observed for any virus. The capsid 2-3nm fibers likely serve to extend the effective surface area of the virus, facilitating attachment to host cells. Characterization of this new virus was conducted, including genome sequencing and determination of the protein identity for the capsid fibers. The research presented here provides a substantial advancement in our knowledge of the attachment process for archaeal viruses. Attachment to host pili is now emerging as a common theme for archaeal viruses. Furthermore, the isolation of the new archaeal virus TSPV1 demonstrates a novel strategy to increase the probability of interaction between a virus and host cell.Item Taxonomic studies on click-beetles (Coleoptera: Elateridae)(Montana State University - Bozeman, College of Letters & Science, 2019) Etzler, Frank Eric; Chairperson, Graduate Committee: Michael A. Ivie; Paul J. Johnson was a co-author of the article, 'Athoplastus johnson and etzler (Coleoptera: Elateridae: Dendrometrinae), a new genus of click beetle from the northwestern continental USA' in the journal 'Coleopterists bulletin' which is contained within this dissertation.Click-beetles (Coleoptera: Elateridae) have historic difficulties at the subfamilial, tribal, and generic level, with many genera poorly defined at the global scale. This dissertation makes the definitions of four groups work world-wide to enable easier communication between regions. These clearer definitions also serve as foundations for future studies at higher levels, such as the tribal and subfamilial level. In this work, two new genera are described, seven species are described as new, 109 new combinations are proposed, and 5 new names are proposed to correct new homonyms. Keys to species are provided for the North American species in Athoplastus and Hemicrepidius and the species north of Mexico for Paradonus. A key to genera in the Limonius genus-group is provided, with a key to species provided for the newly described genus in that group. Important morphological characters are illustrated for each genus or genus group, and habitus photos are provided for all species in the examined regions for the genera Athoplastus, Hemicrepidius, and Paradonus.Item Systematic analysis of Russula in the North American Rocky Mountain alpine zone(Montana State University - Bozeman, College of Agriculture, 2020) Noffsinger, Chance Ray; Chairperson, Graduate Committee: Cathy L. CrippsRussula Pers. (Russulales) is an important ectomycorrhizal fungal genus in alpine and Arctic regions where it occurs in association with Salix, Betula, Dryas, and Polygonum. Despite Russula’s importance and abundance in Arctic and alpine systems there has been no in-depth systematic analysis of the genus in these habitats. This is also true for alpine areas of the Rocky Mountains where only four species of Russula have been casually reported above treeline. The genus Russula is large, diverse, and intraspecific morphological variation makes taxonomic classification difficult, which means verification using molecular techniques is necessary. This research compared Rocky Mountain alpine Russula collections to Arctic and alpine collections from Europe using an in-depth morphological study and a systematic molecular analysis of the nuc rDNA ITS1-5.8S-ITS2 region (ITS barcode) and the second largest subunit of the RNA polymerase II gene (RPB2). Over 130 Russula collections were sequenced including type material. This research confirmed eight species with intercontinental distributions in Arctic and alpine habitats, including R. nana, R. laccata, R. subrubens, R. cf. pascua, R. heterochroa, R. saliceticola, R. purpureofusca, and R. laevis. Two species are reported from subalpine habitats at treeline; R. montana with conifers and R. altaica with Betula. The Russula present in the Rocky Mountain alpine represent a subset of those known from other Arctic-alpine habitats and data show that multiple Russula species independently colonized alpine habitats. This is the first formal report of R. altaica, R. saliceticola, and R. subrubens in the Rocky Mountains and of R. heterochroa and R. purpureofusca in North America. Previous work matched sequences extracted from ectomycorrhiza in Canada to R. laevis, but this is the first work to collect this species and report it in North America. A key for the identification of alpine Russula in North America is provided. A history of Arctic and alpine mycology in North America is included and provides background material for the study. This work contributes to our knowledge of biodiversity in Arctic and alpine systems and will promote future ecological and taxonomic research on alpine Russula because little is known about these species or how to identify them.Item Genetic exploration of spike and seed morphology in a two-rowed barley nested association mapping panel(Montana State University - Bozeman, College of Agriculture, 2018) Getz, Megan Marie; Chairperson, Graduate Committee: Jamie ShermanBarley (Hordeum vulgare) is unique as it has six-rowed cultivars and two-rowed cultivars. The six-rowed has three fertile florets on each spikelet, while two-rowed has only a single fertile center floret per spikelet. This by itself affects seed uniformity as seed produced in the lateral florets tend to be less symmetrical and smaller in size than the center floret. Yield and plumpness are also affected by spike morphology. While the genes and alleles affecting six-rowed vs. two-rowed spikes are known, there are a number of other genes that affect additional spike morphological traits such as number of seeds per head, length of head, and compaction of spikelets. Here, a two-rowed Nested Association Mapping (NAM) population was used to genetically dissect barley spike and seed morphology. To create the population, 13 diverse founder lines of barley were crossed with Conlon, a high yielding, plump, spring variety. Approximately 80 progenies were selected from each of the Conlon by founder crosses, and then backcrossed to Conlon in hopes of exposing the advantageous traits while adapting lines to the Great Plains of the Northwest. The population varying for spike and seed morphology was grown out in a field trial in Bozeman, MT and Logan, UT where phenotypic data was collected throughout the stages of growth and harvest. At maturity (Zadok's 50) stage five heads from each of the lines were collected. Digital Image Analysis was used to measure spike length, kernel count, density, and seed size. Genetic maps were created for each family as well as a consensus map for the whole population. Associations between the phenotypic data and the genotypic data observed in the individual families and consensus map allowed us to identify QTLs conserved across multiple families as well as unique to individual families. Evidence of pleiotropic effects between traits was observed. Some of the QTLs previously were identified, and some are novel. One of the families was of particular interest due to unique QTLs impacting seeds per spike and seed weight. Additionally, several novel QTLs were identified on chromosome 7H that highly impact seed traits.Item Biophysical characterization of P22 bacteriophage and adenoassociated viruses(Montana State University - Bozeman, College of Letters & Science, 2016) Kant, Ravi; Chairperson, Graduate Committee: Brian Bothner; Aida Llauro, Vamseedhar Rayaprolu, Shefah Qazi, Pedro J. de Pablo, Trevor Douglas and Brian Bothner were co-authors of the article, 'Stability, biomechanics and structural changes in P22 bacteriophage during maturation' which is contained within this thesis.; Vamseedhar Rayaprolu and Brian Bothner were co-authors of the article, 'Understanding of P22 bacteriophage maturation by QCM-D' which is contained within this thesis.; Navid Movahed, Dewey Brooke, Antonette Bennett, Mavis Agbandje-McKenna and Brian Bothner were co-authors of the article, 'Prolonged incubation with liposome leads to PLA2 activation in adeno-associated viruses' which is contained within this thesis.; Vamseedhar Rayaprolu and Brian Bothner were co-authors of the article, 'Comparison of the visco-elastic properties of viruses, virus based nanomaterials and active protein cages' which is contained within this thesis.The dsDNA tailed bacteriophages comprise the largest evolving life form in the biosphere. They are not only the most abundant organism on Earth, but also plausibly the most ancient. The ancient origin of phage suggests that they have had the ample opportunity to undergo the evolutionary changes necessary to perform intricate coordinated biological functions. Therefore, characterizing a tailed bacteriophage will help not only to understand biology, but also help us to establish a relationship between structure and function. Viruses display a dynamic equilibrium between structural conformations, stability, flexibility and rigidity which is essential for the perpetuation of life cycle. Understanding this complex biophysical relationship is a daunting task and requires a combination of multidimensional approaches. P22 is a tailed bacteriophage and displays a series of structural transitions during maturation. To understand the important biophysical changes in the P22 at different stages of maturation, we have introduced a suite of orthogonal techniques to address the distinct properties of intermediates. These include Differential Scanning Fluorimetry which probes the thermal stability of P22 capsids, Hydrogen-Deuterium Mass Spectrometry, which probes the conformational flexibility and Atomic Force Microscopy and Quartz Crystal Microbalance with dissipation, which probe the biomechanical transformation in the capsids. P22 investigation using these techniques reveals the large scale structural arrangements along with the expansion. Global rearrangement results in an increase in stability, rigidity and reduced dynamics. The sum results of these studies indicate that expansion is accompanied by large scale inter-subunit rearrangements which lead to the enhanced hydrophobic core at different quasi-equivalent axes. We have also studied Adeno-associated viruses, which is used as a gene delivery vehicle for the treatment of genetic disorders. AAVs lipase contains a lipase domain and its activation is important for the successful infection. Activation mechanism of lipase domain is not thoroughly understood. To understand the mechanism, we have developed a Liquid Chromatography-Mass Spectrometry assay sensitive enough to measure lipase products. This assay confirms that prolonged incubation of AAVs with liposome is able to activate the lipase domain without the involvement of receptors and co-receptors.Item Ontogenetic and stratigraphic cranial variation in the ceratopsid dinosaur 'Triceratops' from the Hell Creek Formation, Montana(Montana State University - Bozeman, College of Letters & Science, 2015) Scannella, John Benedetto; Chairperson, Graduate Committee: John R. Horner; John R. Horner was a co-author of the article, 'Torosaurus marsh, 1891 is Triceratops marsh, 1889 (Ceratopsidae: Chasmosaurinae): synonymy through ontoge' in the journal 'Journal of vertebrate paleontology' which is contained within this thesis.; John R. Horner was a co-author of the article, ''Nedoceratops: an example of a transitional morphology' in the journal 'Public library of science ONE' which is contained within this thesis.; Denver W. Fowler was a co-author of the article, 'A stratgraphic survey of Triceratops localities in the Hell Creek Formation, northeastern Montana (2006-2010)' in the 'Geological Society of America Special Paper 503' which is contained within this thesis.; Denver W. Fowler, Mark B. Goodwin and John R. Horner were co-authors of the article, 'Evolutionary trends in Triceratops from the Hell Creek Formation, Montana' submitted to the journal 'Proceedings of the National Academy of Sciences of the United States of America' which is contained within this thesis.; David W. Roberts and John R. Horner were co-authors of the article, 'A morphometric analysis of casque development and variation in the black-casqued hornbill (Ceratogymna atrata)' which is contained within this thesis.; Kristopher J. S. Purens and John R. Horner were co-authors of the article, 'A morphometric analysis of trends in cranial morphology in Triceratops and 'Torosaurus' from the Hell Creek Formation, Montana' which is contained within this thesis.Hypotheses regarding the taxonomy and systematics of non-avian dinosaurs are based on analyses of morphology. As such, it is critical to assess the potential roles of intraspecific variation in systematic interpretations. Ontogenetic (developmental) change has been found to be a potential contributor to taxonomic confusion in the fossil record of dinosaurs. Similarly, variation between specimens found at different stratigraphic levels should be assessed in order to decipher variation within and between closely related taxa. The chasmosaurine ceratopsid Triceratops has had a complicated taxonomic history due to variation in cranial morphology between specimens. Recent work in the uppermost Cretaceous Hell Creek Formation (HCF) has produced a large (n>50) new sample of specimens. Using this data set its possible to reassess variation in Triceratops and further explore chasmosaurine paleobiology. Building on previous work on Triceratops ontogeny, examination of the parietal-squamosal frill finds that these bones underwent a dramatic transformation late in ontogeny. The short, solid frill of Triceratops expanded into a more elongate, thin, fenestrated condition, which had previously been found to characterize the coeval ceratopsid taxon Torosaurus latus. This suggests that these taxa are synonymous with Torosaurus representing the mature form of Triceratops rather than a distinct taxon. Further, Nedoceratops hatcheri, which is represented by a single specimen with a small fenestra in the parietal, is hypothesized to represent a transitional morphology between unfenestrated and fully fenestrated (Torosaurus) specimens. Detailed locality information for specimens collected over the course of the Hell Creek Project permits for the placement of specimens in stratigraphic context. The two currently recognized species, T. horridus and T. prorsus, are stratigraphically separated within the HCF and cladistic and stratocladistic analyses are consistent with the evolution of Triceratops incorporating anagenetic (transformational) change. Morphometric analyses of the extant archosaur Ceratogymna atrata (the Black-casqued hornbill) indicate that enlarged cranial structures function as objects of visual display. Morphometric studies of Triceratops further suggest that specimens found lower in the formation may have attained the Torosaurus frill morphology through ontogeny, whereas this basal condition became increasingly rare higher in the formation. Morphometric results are also consistent with early divergence between two distinct genera.Item A new multi-faceted framework for deciphering Diplodocid ontogeny(Montana State University - Bozeman, College of Letters & Science, 2015) Woodruff, David Cary; Chairperson, Graduate Committee: John R. Horner; Denver W. Fowler and John R. Horner were co-authors of the article, 'A new multi-faceted framework for deciphering Diplodocid ontogeny' which is contained within this thesis.Since sauropod dinosaurs lack the extravagant cranial features that are important to tracking ontogenetic trajectories (changes through growth), sauropods generally garner less focus on development than those dinosaurs with expressive cranial displays. The apparent lack of features that radically change through ontogeny has even led some to speculate that sauropods exhibited isometric growth. Yet within the past decade a small number of morphologic features have been demonstrated to undergo significant morphologic change; thus maturity can be tracked in ways other than histologic analysis (bone microstructure). The recognition of features that change dramatically through ontogeny hints at significant phylogenetic and biomechanical consequences in the immature sauropod condition. However the topic of morphologic ontogenetic change in sauropods is highly debated, with some question as to the validity of these apparent patterns. The current study will attempt to recognize additional morphologic and histologic features that can be used to infer maturity in diplodocid sauropods. By examining a broad range of features that span every aspect of the skeleton, the goal of this analysis is to substantiate previous ontogenetic inferences and conclusions. The findings of this analysis indicate that contrary to previous notions, diplodocid sauropods underwent radical ontogenetic changes in several skeletal elements. This analysis also establishes a suite of morphologic and histologic attributes that in combination can be used as a guide to identify maturational status in other diplodocid specimens. In addition this study also raises question to the validity of small bodied sauropod specimens that were previously recognized as distinct species.