Browsing by Author "Montgomery, Tai, committee member"

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Open Access
Assessment of mosquito and animal model factors in Aedes-borne arbovirus transmission and disease
(Colorado State University. Libraries, 2021) Miller, Megan Rae, author; Foy, Brian, advisor; Wilusz, Jeffrey, committee member; Kading, Rebekah, committee member; Montgomery, Tai, committee member; Magunda, Forgivemore, committee member
To view the abstract, please see the full text of the document.
Open Access
Error correcting optical mapping data
(Colorado State University. Libraries, 2016) Washimkar, Darshan, author; Boucher, Christina, advisor; Pallickara, Sangmi Lee, committee member; Montgomery, Tai, committee member
Optical Mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome (Schwartz et al., Science 1993). Recently it has been used for scaffolding contigs and assembly validation for large-scale sequencing projects — for example, the maize (Zhou et al., PLoS Genetics, 2009), goat (Dong et al., Nature Biotech. 2013), and amborella (Chamala et al., Science 2013) genomes. However, a major impediment in the use of this data is the variety and quantity of the errors in the raw optical mapping data, which are referred to as Rmaps. The challenges associated with using Rmap data—and thus, optical mapping data—is analogous to dealing with insertion and deletions in the alignment of long reads. Moreover, they are arguably harder since the data is integral and susceptible to inaccuracy. We develop cOMet to tackle error correct Rmap data, which to the best of our knowledge is the is the only non-proprietary error correction method. Our results demonstrate that cOMet has high accuracy on simulated E. coli (str. K-12 substr. MG1655) genome.
Open Access
Exploring user-defined gestures for alternate interaction space for smartphones and smartwatches
(Colorado State University. Libraries, 2016) Arefin Shimon, Shaikh Shawon, author; Ruiz, Jaime, advisor; Draper, Bruce, committee member; Montgomery, Tai, committee member
In smartphones and smartwatches, the input space is limited due to their small form factor. Although many studies have highlighted the possibility of expanding the interaction space for these devices, limited work has been conducted on exploring end-user preferences for gestures in the proposed interaction spaces. In this dissertation, I present the results of two elicitation studies that explore end-user preferences for creating gestures in the proposed alternate interaction spaces for smartphones and smartwatches. Using the data collected from the two elicitation studies, I present gestures preferred by end-users for common tasks that can be performed using smartphones and smartwatches. I also present the end-user mental models for interaction in proposed interaction spaces for these devices, and highlight common user motivations and preferences for suggested gestures. Based on the findings, I present design implications for incorporating the proposed alternate interaction spaces for smartphones and smartwatches.
Open Access
Factor dependent archaeal transcription termination
(Colorado State University. Libraries, 2017) Walker, Julie, author; Santangelo, Thomas J., advisor; Montgomery, Tai, committee member; Stargell, Laurie, committee member; Yao, Tingting, committee member
RNA polymerase activity is regulated by nascent RNA sequences, DNA template sequences and conserved transcription factors. Transcription factors regulate the activities of RNA polymerase (RNAP) at each stage of the transcription cycle: initiation, elongation, and termination. Many basal transcription factors with common ancestry are employed in eukaryotic and archaeal systems that directly bind to RNAP and influence intramolecular movements of RNAP and modulate DNA or RNA interactions. We describe and employ a flexible methodology to directly probe and quantify the binding of transcription factors to the archaeal RNAP in vivo. We demonstrate that binding of the conserved and essential archaeal transcription factor TFE to the archaeal RNAP is directed, in part, by interactions with the RpoE subunit of RNAP. As the surfaces involved are conserved in many eukaryotic and archaeal systems, the identified TFE-RNAP interactions are likely conserved in archaeal-eukaryal systems and represent an important point of contact that can influence the efficiency of transcription initiation. While many studies in archaea have focused on elucidating the mechanism of transcription initiation and elongation, studies on termination were slower to emerge. Transcription factors promoting initiation and elongation have been characterized in each Domain but transcription termination factors have only been identified in bacteria and eukarya. Here we characterize the first archaeal termination factor (termed Eta) capable of disrupting the transcription elongation complex, detail the rate of and requirements for Eta-mediated transcription termination and describe a role for Eta in transcription termination in vivo. Eta-mediated transcription termination is energy-dependent, requires upstream DNA sequences and disrupts transcription elongation complexes to release the nascent RNA to solution. Deletion of TK0566 (encoding Eta) is possible, but results in slow growth and renders cells sensitive to DNA damaging agents. Structure-function studies reveal that the N-terminal domain of Eta is not necessary for Eta-mediated termination in vitro, but Thermococcus kodakarensis cells lacking the N-terminal domain exhibit slow growth compared to parental strains. We report the first crystal structure of Eta that will undoubtedly lead to further structure-function analyses. The results obtained argue that the mechanisms employed by termination factors in archaea, eukarya, and bacteria to disrupt the transcription elongation complex may be conserved and that Eta stimulates release of stalled or arrested transcription elongation complexes.
Open Access
Functionalization of pyridines and other azines via phosphorus ligand-coupling reactions
(Colorado State University. Libraries, 2019) Hilton, Michael C., author; McNally, Andrew, advisor; Reynolds, Melissa, committee member; Crans, Debbie, committee member; Montgomery, Tai, committee member
Nitrogen heterocycles are ubiquitous in pharmaceutical compounds with pyridine being one of the most frequently occurring examples. The discovery and development of new drugs rely heavily on our ability to modify these commonly occurring structures. The functionalization of pyridine has a long history but despite this, there remain some deficiencies in this area of synthesis. Reactions which expand upon the known methodologies are of tremendous value to medicinal chemists who frequently work with pyridines and similar azines. Chapter one will cover the relevance of pyridines in pharmaceuticals and will explain how structural features contribute to their presence in drugs. Conventional and newer methods to functionalize pyridine are also addressed. Chapter two will describe the work of the McNally lab in the development of heterocyclic phosphonium salts as reagents to selectively functionalize pyridines. An application of these salts is as precursors to form C−O bonds from alkoxide nucleophiles. Chapter three presents the development of a strategy to construct bis-heterobiaryls using phosphorus ligand-coupling. This method offers an alternative to the widely used metal-catalyzed approaches which often struggle in the synthesis of bis-heterobiaryls. Lastly, chapter four will expand upon this work showing a new approach to prepare bis-heterobiaryls using heteroaryl halides. This route enables easy access to 2,2'-bipyridines which are difficult to synthesize using conventional methods.
Open Access
In vitro and in vivo studies on pre-mRNA splicing in plants
(Colorado State University. Libraries, 2017) Albaqami, Mohammed M., author; Reddy, A. S. N., advisor; Wilusz, Jeffrey, committee member; Ben-Hur, Asa, committee member; Montgomery, Tai, committee member
To view the abstract, please see the full text of the document.
Open 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.
Open Access
mRNA localization in Caenorhabditis elegans embryogenesis
(Colorado State University. Libraries, 2021) Parker, Dylan M., author; Osborne Nishimura, Erin, advisor; Ben Hur, Asa, committee member; Montgomery, Tai, committee member; Stasevich, Tim, committee member; Santangelo, Tom, committee member
From guiding cell specification to regulating protein output, post-transcriptional regulation of mRNA is essential for life. As a result, many mechanisms underlying post-transcriptional regulation are highly conserved across the kingdoms of life. As the spatial resolution of microscopy and sequencing assays has increased, mRNA localization has emerged as a prevalent form of post-transcriptional regulation directing various cellular processes. Perhaps most notably, our understanding of post-transcriptional mRNA regulation and cellular function as a whole has been revolutionized by the discovery that many well-studied mRNA foci, such as germ granules, P-bodies, and stress granules, do not follow the lock-and-key principle of stoichiometric complex formation, but are actually phase-separated, biomolecular condensates. Due to their liquid-like nature, biomolecular condensates can aggregate or disperse component transcripts and proteins with exquisite environmental and temporal sensitivity. As a result, biomolecular condensates can regulate myriad processes as varied as co-translationally organizing protein components for complex assembly (Budding yeast translation factor mRNA granules), reinforcing translation inhibition (Germ granules) or activation (Neuronal granules), and facilitating the organization of other organelles (Axonemal dynein foci/kl-bodies). While an influx of studies have provided insights into the function of well-studied and novel biomolecular condensates alike, much remains unknown. What factors govern assembly and disassembly of condensates? How do they interact with one another? Is condensation the cause or consequence of the functional regulation of any particular mRNA? To begin to answer these questions, this thesis defines Caenorhabditis elegans as a model organism for exploring mRNA localization, its mechanisms, and its functions with a focus on condensate transcripts. Thus, the discoveries made have contributed to the fields of post-transcriptional gene regulation, mRNA localization, and condensate biology by elucidating mechanisms of localization, improving on methods of observing localization patterns, and establishing C. elegans as a tractable model for exploration of mRNA localization.
Open Access
Opioid bioavailability in the retina modulates sleep/wake behavior
(Colorado State University. Libraries, 2023) Berezin, Casey-Tyler, author; Vigh, Jozsef, advisor; Hentges, Shane, committee member; Bailey, Susan, committee member; Montgomery, Tai, committee member
Opioids, such as the prototypical opioid morphine, primarily exert their analgesic and rewarding effects through μ-opioid receptors (MORs), and it has been shown that acute morphine treatment negatively impacts sleep/wake behavior through MORs. Continued opioid administration exacerbates sleep/wake disturbances, such that approximately 80% of chronic users report persistent sleep disturbances, including insomnia and daytime sleepiness. These opioid-induced sleep disturbances (OISD) are associated with negative outcomes such as increased drug craving, relapse and negative affect (i.e. anxiety/depression), as well as hyperalgesia in chronic pain patients. Therefore, therapeutic interventions for OISD are expected to improve the outcomes of long-term opioid use in general. However, the neuronal population(s) and cellular mechanism(s) mediating sleep/wake changes in response to chronic opioid treatment are not currently known. Although many neuronal populations in the brain contribute to sleep/wake behavior, the photoentrainment of sleep/wake cycles to environmental light/dark cycles is uniquely regulated by intrinsically photosensitive retinal ganglion cells (ipRGCs). Importantly, light-evoked firing by ipRGCs is modulated by activation of their MORs, and endogenous MOR activation has been shown to modulate an ipRGC-driven behavior, the pupillary light reflex. Additionally, opioids (e.g. morphine) are routinely detected in the human eye to diagnose overdose-related deaths, and morphine accumulates in the mouse retina upon chronic systemic administration. Therefore, the central hypothesis addressed in the current work is that the bioavailability of opioids (i.e. endogenous opioid peptides and/or opioid drugs) in the retina contributes to the modulation of sleep/wake behavior. In Chapter 2, we show that endogenous opioid peptides in the retina contribute to healthy sleep/wake behavior. Using a mouse model with a cell-specific knockout of MORs expressed by ipRGCs (McKO), we show that endogenous activation of these MORs is important for maintaining activity and suppressing slow-wave sleep during the mouse's active period. Concurrent work showed that the MORs expressed by ipRGCs also contribute to morphine-driven changes in sleep/wake behavior during a chronic treatment paradigm. Thus, both endogenous opioid peptides and opioid drugs modulate sleep/wake behavior via the activation of the MORs expressed by ipRGCs. Systemically applied opioid drugs penetrate the blood-retina barrier and accumulate in the retina. Thus, ipRGCs may be liable to opioid modulation throughout chronic opioid treatment, contributing to the development and persistence of OISD. In Chapter 3, we investigate the relationship between opioid transporter expression at the blood-retina barrier and morphine deposition in the retina. We show that low expression of the opioid extruder permeability glycoprotein (P-gp) may allow morphine to persist in the retina, compared to the brain where P-gp expression is high and morphine is more quickly cleared from the tissue. In Chapter 4, we discuss how upregulation of P-gp at the blood-retina barrier via the non-steroidal anti-inflammatory drug diclofenac may reduce opioid bioavailability in the retina, thereby alleviating OISD. This work demonstrates a previously unknown contribution of ipRGC signaling to opioid-modulated sleep/wake changes, and identifies a potential therapeutic target for OISD.
Open Access
PersoSys: a user-defined gestural interface for personalized interaction
(Colorado State University. Libraries, 2015) Fahimi, Ghazal, author; Ruiz, Jaime, advisor; Boucher, Christina, committee member; Montgomery, Tai, committee member
Recently, there has been an emergence of research projects pertaining to gesture-based interactions which have focused on procedures to design intuitive gestures. However, little work has been conducted in regard to discovering best-practices in the field of gesture customization by end-users--research which has the potential to vastly improve user experience beyond the potential of the predefined gestures. Gesture customization goes deeper into the gestural interface logic and makes it possible for users to map flexible tasks to their own defined gestures. In this thesis, we describe the PersoSys system, a touchless, 3-dimensional gesture-based interaction framework, that makes use of an Intel Perceptual SDK camera to control the operations of a PC through hand gesture commands. The system allows users to define a personalized input gesture for a set of tasks, thereby enabling them to trigger those tasks by performing the mapped gestures. Furthermore, the user interface of the system is designed in an arrangement that offers customizations in a simple and convenient way, concealing much of the complexity from the user. In this thesis, we describe the hardware and software implementation of PersoSys, and several use cases designed to bring more convenient interaction to users. We also examined the effectiveness of our system by conducting an experiment that obtains qualitative and quantitative feedback from users. The results imply that users are pleased with the configuration process and automatically executing the long sequences of tasks by performing their desired gestures.
Open Access
Regioselective functionalization of pyridines and other azines
(Colorado State University. Libraries, 2021) Boyle, Benjamin T., author; McNally, Andrew, advisor; Chen, Eugene, committee member; Ackerson, Chris, committee member; Montgomery, Tai, committee member
Pyridines and diazines serve as cores in pharmaceuticals and are common motifs in organomaterials and ligands. Selective functionalization of these motifs is of importance for discovery and optimization of new bioactive molecules. Pyridine functionalization is of interest for synthetic chemists, and despite modern advances in derivatization challenges and limitations remain. Chapter one focuses on the impact of pyridines and diazines in the pharmaceutical industry. Classical and modern methods for C-H functionalization are discussed. Chapter two describes work on phosphorus ligand-coupling for bisazine synthesis using a three-stage protocol. This method provides an alternative to traditional metal-catalysis for bisazine synthesis and can be applied to drug-like fragments. This work is expanded on in chapter three by using a tandem SNAr-ligand-coupling strategy for bisazine synthesis, in particular 2,2'-bipyridines. Chapter four describes a facile SNAr reaction by phosphines on iodopyridines. A bis-salt N-phopsphonium pyridinium is the key intermediate and provides a broad scope of reactivity. Chapter five shifts towards functionalization of the 3-position of pyridine through a Zincke-type intermediate. By exploiting a ring-opening-functionlization-rearomatization strategy a selective halogenation of pyridines was achieved. The Zincke imine intermediate is also viable for other functionalizations and provides products directly from the C-H bond on the initial pyridine.