Repository logo

Browsing by Author "Osborne Nishimura, Erin, committee member"

Now showing 1 - 3 of 3
  • Thumbnail Image
    ItemOpen Access
    Floristic inventory of private and public lands in southwestern Gunnison County, Colorado, A; and a software tool to assist in the generation of herbarium specimen labels
    (Colorado State University. Libraries, 2018) Maher, Madeline A., author; Simmons, Mark, advisor; Maurer, Ruth, committee member; Sloan, Daniel, committee member; Osborne Nishimura, Erin, committee member
    I conducted an inventory of vascular flora on public and private property in southwestern Gunnison County, Colorado. The study area consisted of 3,004 acres of private land and 1,850 acres of adjacent public land managed by the Bureau of Land Management (BLM). While a small part of the BLM area was surveyed in the late 1990s, the majority of the study area represented a gap in the existing floristic research to date in the Rocky Mountains. Fieldwork was conducted in the growing seasons of 2016 and 2017. Six hundred five herbarium specimens were generated, representing 315 species and infraspecific taxa. Combining my findings with reliable observations and existing collections from the area, a checklist of 330 species and infraspecific taxa was compiled, representing ten percent of the known Colorado flora. The variable landscape of the area includes submontane to subalpine forests, wetlands, grasslands, sagebrush shrublands, xeric mesa tops, and rocky cliffs. Taken together these areas provide habitat for two species previously unknown in the county (Trifolium kingii, Pyrola picta), two further species that are considered vulnerable or imperiled in Colorado (Iliamna rivularis, Draba rectifructa), and 30 vulnerable or imperiled plant community types. The presence of species and communities of conservation concern not previously documented in the region emphasizes the need for continued floristic study of private lands and other undersampled areas. In order to efficiently make labels for the aforementioned herbarium specimens, I developed a Python program to generate formatted, print-ready labels from a comma-separated value (CSV) file. Efficiently generating specimen labels can be challenging for newcomers to the field, or for those unable to use existing tools. Several software tools exist for automatic specimen label generation, but these either require a significant learning curve to use, are not consistently maintained, are not compatible with multiple operating systems, or rely on proprietary software. My program generates labels in HTML, and these are formatted for print using Cascading Style Sheets (CSS) and the Mustache template system. The program does not rely on any proprietary software, is compatible with any operating system on which Python 3.0 or later can be installed, and is easily customizable to suit the user's needs. The minimal nature of the tool makes it easy and efficient to use. The tool will be especially useful to students learning to manage their collection data and produce their own specimen labels. As such, it could be a convenient resource for plant-taxonomy and related courses in which students make collections.
  • Thumbnail Image
    ItemOpen Access
    Influence and regulation of PCBP2 and YTHDF2 RNA-binding proteins during self-renewal and differentiation of human induced pluripotent stem cells
    (Colorado State University. Libraries, 2019) Heck, Adam M., author; Wilusz, Carol J., advisor; Wilusz, Jeffrey, advisor; Osborne Nishimura, Erin, committee member; Montgomery, Tai, committee member; Zhou, Wen, committee member
    Embryonic stem cells (ESCs) are able to self-renew or differentiate into any cell type in the body, a property known as pluripotency that enables them to initiate early growth and development. However, the ethical implications of harvesting and manipulating ESCs hinders their use in basic research and the clinical applications. Thus, the discovery that somatic cells can be exogenously reprogrammed into induced pluripotent stem cells (iPSCs) offers new and exciting possibilities for gene therapy, personalized medicine and basic research. However, more research is needed into the mechanisms involved in regulating pluripotency in order for iPSCs to reach their full potential in the research lab and clinic. To maintain a state of self-renewal, yet also be able to rapidly differentiate in response to external signals, pluripotent stem cells need to exert tight control over gene expression through transcriptional and post-transcriptional mechanisms. There are several notable transcriptional networks that regulate pluripotency, but the post-transcriptional mechanisms remain poorly characterized. mRNA decay is one form of post-transcriptional regulation that can help to both maintain the steady-state of a transcriptome or facilitate its rapid remodeling. To this end, degradation rates are influenced by the elements contained in an mRNA and the RNA-binding proteins (RBPs) they associate with. Previous reports have indicated the RNA modification N6-methyladenosine (m6A) and C-rich sequence elements (CREs) can affect mRNA decay in pluripotent stem cells. Therefore, we sought to further understand the roles of m6A and CREs in mRNA decay in stem cells by characterizing the expression and mRNA targets of two RBPs that recognize these elements, YTHDF2 and PCBP2, respectively. In this thesis, I report YTHDF2 is differentially regulated in pluripotent and differentiated cells and that YTHDF2 contributes to pluripotency by targeting a group of mRNAs encoding factors important for neural development. The down-regulation of YTHDF2 during neural differentiation is consistent with increased expression of neural factors during this time. Moreover, YTHDF2 expression is regulated at the level of translation via elements located in the first 300 nucleotides of the 3' untranslated region of YTHDF2 mRNA. Based on these results, I propose that stem cells are primed for rapid differentiation by transcribing low levels of mRNAs encoding neural factors that are subsequently targeted for degradation, in part by YTHDF2, until differentiation is induced. On the other hand, PCBP2 is up-regulated upon differentiation of pluripotent stem cells and regulates several mRNAs associated with pluripotency and development, including LIN28B. Notably, expression of long non-coding RNAs (lncRNAs) that contain human endogenous retrovirus element H (HERV-H) is influenced by PCBP2. HERV-H lncRNAs are almost exclusively expressed in stem cells and play a role in maintaining a pluripotent state, although their functions are not fully understood. Intriguingly, some HERV-lncRNAs can also regulate PCBP2 expression, as altering the expression of LINC01356 or LINC00458 effects PCBP2 protein levels. Based on these results, I propose the reciprocal regulation of PCBP2 and HERV-H lncRNAs influences whether stem cells maintain a state of self-renewal or differentiate. Taken together, these findings demonstrate that YTHDF2 and PCBP2 post-transcriptionally regulate gene expression in stem cells and influence pluripotency.
  • Thumbnail Image
    ItemOpen Access
    Post-initiation regulatory mechanisms of transcription in the Archaea
    (Colorado State University. Libraries, 2023) Wenck, Breanna Renée, author; Santangelo, Thomas, advisor; Hansen, Jeffrey C., committee member; Osborne Nishimura, Erin, committee member; Wilusz, Carol, committee member
    Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. Archaeal systems contain simplified, basal regulatory transcription components and mechanisms homologous to their eukaryotic counterparts, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. Many archaeal genomes are organized with histone proteins that resemble the core eukaryotic histone fold, which permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that impacts transcription regulation and gene expression. Despite such semblance between the eukaryotic and archaeal core histone folds, archaeal genomes lack the canonical N and C terminal extensions that are abundantly modified to regulate transcription in eukaryotic genomes. Much of what is known regarding factor-mediated transcription regulation in the Archaea is limited; however combined and continued efforts across the field provide tidbits of information, but many pieces are still missing. This thesis aims to i) delineate the role key residues within the histone-DNA complex and archaeal histone-based architecture and key residues within the histone-DNA complex have on the progression of the transcription apparatus, characterize factor-mediated transcription termination, and explore chromatin- and TFS-mediated regulatory effects on transcription via global RNA polymerase (RNAP) positions.