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- Member of: ASU Electronic Theses and Dissertations
Description
Well-established model systems exist in four out of the seven major classes of vertebrates. These include the mouse, chicken, frog and zebrafish. Noticeably missing from this list is a reptilian model organism for comparative studies between the vertebrates and for studies of biological processes unique to reptiles. To help fill in this gap the green anole lizard, Anolis carolinensis, is being adapted as a model organism. Despite the recent release of the complete genomic sequence of the A. carolinensis, the lizard lacks some resources to aid researchers in their studies. Particularly, the lack of transcriptomic resources for lizard has made it difficult to identify genes complete with alternative splice forms and untranslated regions (UTRs). As part of this work the genome annotation for A. carolinensis was improved through next generation sequencing and assembly of the transcriptomes from 14 different adult and embryonic tissues. This revised annotation of the lizard will improve comparative studies between vertebrates, as well as studies within A. carolinensis itself, by providing more accurate gene models, which provide the bases for molecular studies. To demonstrate the utility of the improved annotations and reptilian model organism, the developmental process of somitogenesis in the lizard was analyzed and compared with other vertebrates. This study identified several key features both divergent and convergent between the vertebrates, which was not previously known before analysis of a reptilian model organism. The improved genome annotations have also allowed for molecular studies of tail regeneration in the lizard. With the annotation of 3' UTR sequences and next generation sequencing, it is now possible to do expressional studies of miRNA and predict their mRNA target transcripts at genomic scale. Through next generation small RNA sequencing and subsequent analysis, several differentially expressed miRNAs were identified in the regenerating tail, suggesting miRNA may play a key role in regulating this process in lizards. Through miRNA target prediction several key biological pathways were identified as potentially under the regulation of miRNAs during tail regeneration. In total, this work has both helped advance A. carolinensis as model system and displayed the utility of a reptilian model system.
ContributorsEckalbar, Walter L (Author) / Kusumi, Kenro (Thesis advisor) / Huentelman, Matthew (Committee member) / Rawls, Jeffery (Committee member) / Wilson-Rawls, Norma (Committee member) / Arizona State University (Publisher)
Created2012
Description
Skeletal muscle injury may occur from repetitive short bursts of biomechanical strain that impair muscle function. Alternatively, variations of biomechanical strain such as those held for long-duration are used by clinicians to repair muscle and restore its function. Fibroblasts embedded within the unifying connective tissue of skeletal muscle experience these multiple and diverse mechanical stimuli and respond by secreting cytokines. Cytokines direct all stages of muscle regeneration including myoblasts differentiation, fusion to form myotubes, and myotube functionality. To examine how fibroblasts respond to variations in mechanical strain that may affect juxtapose muscle, a myofascial junction was bioengineered that examined the interaction between the two cell types. Fibroblasts were experimentally shown to increase myoblast differentiation, and fibroblast biomechanical strain mediated the extent to which differentiation occurred. Intereleukin-6 is a strain-regulated cytokine secreted by fibroblasts was determined to be necessary for fibroblast-mediated myoblast differentiation. Myotubes differentiated in the presence of strained fibroblasts express greater number of acetylcholine receptors, greater acetylcholine receptor sizes, and modified to be more or less sensitive to acetylcholine-induced contraction. This study provides direct evidence that strained and non-strained fibroblasts can serve as a vehicle to modify myoblast differentiation and myotube functionality. Further understanding the mechanisms regulating these processes may lead to clinical interventions that include strain-activated cellular therapies and bioengineered cell engraftment for mediating the regeneration and function of muscle in vivo.
ContributorsHicks, Michael (Author) / Standley, Paul R (Thesis advisor) / Rawls, Jeffrey (Committee member) / Lake, Douglas (Committee member) / Hinrichs, Richard (Committee member) / Arizona State University (Publisher)
Created2014
Description
When air is supplied to a conditioned space, the temperature and humidity of the air often contribute to the comfort and health of the occupants within the space. However, the vapor compression system, which is the standard air conditioning configuration, requires air to reach the dew point for dehumidification to occur, which can decrease system efficiency and longevity in low temperature applications.
To improve performance, some systems dehumidify the air before cooling. One common dehumidifier is the desiccant wheel, in which solid desiccant absorbs moisture out of the air while rotating through circular housing. This system improves performance, especially when the desiccant is regenerated with waste or solar heat; however, the heat of regeneration is very large, as the water absorbed during dehumidification must be evaporated. N-isopropylacrylamide (NIPAAm), a sorbent that oozes water when raised above a certain temperature, could potentially replace traditional desiccants in dehumidifiers. The heat of regeneration for NIPAAm consists of some sensible heat to bring the sorbent to the regeneration temperature, plus some latent heat to offset any liquid water that is evaporated as it is exuded from the NIPAAm. This means the NIPAAm regeneration heat has the potential to be much lower than that of a traditional desiccant.
Models were created for a standard vapor compression air conditioning system, two desiccant systems, and two theoretical NIPAAm systems. All components were modeled for simplified steady state operation. For a moderate percent of water evaporated during regeneration, it was found that the NIPAAm systems perform better than standard vapor compression. When compared to the desiccant systems, the NIPAAm systems performed better at almost all percent evaporation values. The regeneration heat was modeled as if supplied by an electric heater. If a cheaper heat source were utilized, the case for NIPAAm would be even stronger.
Future work on NIPAAm dehumidification should focus on lowering the percent evaporation from the 67% value found in literature. Additionally, the NIPAAm cannot exceed the lower critical solution temperature during dehumidification, indicating that a NIPAAm dehumidification system should be carefully designed such that the sorbent temperature is kept sufficiently low during dehumidification.
To improve performance, some systems dehumidify the air before cooling. One common dehumidifier is the desiccant wheel, in which solid desiccant absorbs moisture out of the air while rotating through circular housing. This system improves performance, especially when the desiccant is regenerated with waste or solar heat; however, the heat of regeneration is very large, as the water absorbed during dehumidification must be evaporated. N-isopropylacrylamide (NIPAAm), a sorbent that oozes water when raised above a certain temperature, could potentially replace traditional desiccants in dehumidifiers. The heat of regeneration for NIPAAm consists of some sensible heat to bring the sorbent to the regeneration temperature, plus some latent heat to offset any liquid water that is evaporated as it is exuded from the NIPAAm. This means the NIPAAm regeneration heat has the potential to be much lower than that of a traditional desiccant.
Models were created for a standard vapor compression air conditioning system, two desiccant systems, and two theoretical NIPAAm systems. All components were modeled for simplified steady state operation. For a moderate percent of water evaporated during regeneration, it was found that the NIPAAm systems perform better than standard vapor compression. When compared to the desiccant systems, the NIPAAm systems performed better at almost all percent evaporation values. The regeneration heat was modeled as if supplied by an electric heater. If a cheaper heat source were utilized, the case for NIPAAm would be even stronger.
Future work on NIPAAm dehumidification should focus on lowering the percent evaporation from the 67% value found in literature. Additionally, the NIPAAm cannot exceed the lower critical solution temperature during dehumidification, indicating that a NIPAAm dehumidification system should be carefully designed such that the sorbent temperature is kept sufficiently low during dehumidification.
ContributorsKocher, Jordan Daniel (Author) / Wang, Robert (Thesis advisor) / Phelan, Patrick (Committee member) / Parrish, Kristen (Committee member) / Arizona State University (Publisher)
Created2019
Description
Damage to the central nervous system due to spinal cord or traumatic brain injury, as well as degenerative musculoskeletal disorders such as arthritis, drastically impact the quality of life. Regeneration of complex structures is quite limited in mammals, though other vertebrates possess this ability. Lizards are the most closely related organism to humans that can regenerate de novo skeletal muscle, hyaline cartilage, spinal cord, vasculature, and skin. Progress in studying the cellular and molecular mechanisms of lizard regeneration has previously been limited by a lack of genomic resources. Building on the release of the genome of the green anole, Anolis carolinensis, we developed a second generation, robust RNA-Seq-based genome annotation, and performed the first transcriptomic analysis of tail regeneration in this species. In order to investigate gene expression in regenerating tissue, we performed whole transcriptome and microRNA transcriptome analysis of regenerating tail tip and base and associated tissues, identifying key genetic targets in the regenerative process. These studies have identified components of a genetic program for regeneration in the lizard that includes both developmental and adult repair mechanisms shared with mammals, indicating value in the translation of these findings to future regenerative therapies.
ContributorsHutchins, Elizabeth (Author) / Kusumi, Kenro (Thesis advisor) / Rawls, Jeffrey A. (Committee member) / Denardo, Dale F. (Committee member) / Huentelman, Matthew J. (Committee member) / Arizona State University (Publisher)
Created2015
Description
Hydrophobic ionizable organic compounds (HIOCs) like per- and polyfluoroalkyl substances (PFAS), certain pharmaceuticals, and surfactants have been detected in groundwater, wastewater, and drinking water. Anion exchange resin treatment is an effective process for removal of anionic contaminants from water. Spent anion exchange resins are conventionally regenerated with high alcohol by volume (ABV) methanol in solution with brine. While effective for regeneration of resins saturated with inorganic anions such as sulfate, nitrate, and perchlorate, HIOCs prove more resistant to regeneration. This research investigated the efficacy of using novel cosolvent solutions with brine to regenerate resins saturated with organic carboxylate and sulfonate anions to understand the effects cosolvent properties have on regenerative ability. Experiments were conducted on six PFAS compounds to evaluate trends in regeneration for three alcohols. For all PFAS species, equivalent ABV and brine solutions showed greatest regeneration with 1-propanol over ethanol and methanol. Experiments with the pharmaceutical sodium diclofenac were conducted showing similar regeneration of 75% methanol and 25% 1-propanol for equivalent salt concentrations and higher regeneration with 1-propanol than ethanol and methanol for equivalent ABV. A series of experiments with surfactant dodecylbenzene sulfonate determined that the key parameters to determine regeneration of the resin for an alcohol cosolvent solution were cosolvent volume fraction, molar mass, Kow value, solution ionic strength, and dielectric constant. Individual assessments on the cost-effectiveness, flammability, and sustainability of cosolvent solutions point to possible future experiments and opportunities for recycled distillery waste streams as regenerative solutions for anion exchange resin.
ContributorsGraham, Cole David (Author) / Boyer, Treavor H (Thesis advisor) / Conroy-Ben, Otakuye (Committee member) / Garcia Segura, Sergio (Committee member) / Arizona State University (Publisher)
Created2022
Description
Traumatic injury to the central nervous or musculoskeletal system in traditional amniote models, such as mouse and chicken, is permanent with long-term physiological and functional effects. However, among amniotes, the ability to regrow complex, multi-tissue structures is unique to non-avian reptiles. Structural regeneration is extensively studied in lizards, with most species able to regrow a functional tail. The lizard regenerated tail includes the spinal cord, cartilage, de novo muscle, vasculature, and skin, and unlike mammals, these tissues can be replaced in lizards as adults. These studies focus on the events that occur before and after the tail regrowth phase, identifying conserved mechanisms that enable functional tail regeneration in the green anole lizard, Anolis carolinensis. An examination of coordinated interactions between peripheral nerves, Schwann cells, and skeletal muscle reveal that reformation of the lizard neuromuscular system is dependent upon developmental programs as well as those unique to the adult during late stages of regeneration. On the other hand, transcriptomic analysis of the early injury response identified many immunoregulatory genes that may be essential for inhibiting fibrosis and initiating regenerative programs. Lastly, an anatomical and histological study of regrown alligator tails reveal that regenerative capacity varies between different reptile groups, providing comparative opportunities within amniotes and across vertebrates. In order to identify mechanisms that limit regeneration, these cross-species analyses will be critical. Taken together, these studies serve as a foundation for future experimental work that will reveal the interplay between reparative and regenerative mechanisms in adult amniotes with translational implications for medical therapies.
ContributorsXu, Cindy (Author) / Kusumi, Kenro (Thesis advisor) / Newbern, Jason M (Thesis advisor) / Wilson-Rawls, Jeanne (Committee member) / Fisher, Rebecca E (Committee member) / Arizona State University (Publisher)
Created2020
Description
Satellite cells are adult muscle stem cells that activate, proliferate, and differentiate into myofibers upon muscle damage. Satellite cells can be cultured and manipulated in vitro, and thus represent an accessible model for studying skeletal muscle biology, and a potential source of autologous stem cells for regenerative medicine. This work summarizes efforts to further understanding of satellite cell biology, using novel model organisms, bioengineering, and molecular and cellular approaches. Lizards are evolutionarily the closest vertebrates to humans that regenerate entire appendages. An analysis of lizard myoprogenitor cell transcriptome determined they were most transcriptionally similar to mammalian satellite cells. Further examination showed that among genes with the highest level of expression in lizard satellite cells were an increased number of regulators of chondrogenesis. In micromass culture, lizard satellite cells formed nodules that expressed chondrogenic regulatory genes, thus demonstrating increased musculoskeletal plasticity. However, to exploit satellite cells for therapeutics, development of an ex vivo culture is necessary. This work investigates whether substrates composed of extracellular matrix (ECM) proteins, as either coatings or hydrogels, can support expansion of this population whilst maintaining their myogenic potency. Stiffer substrates are necessary for in vitro proliferation and differentiation of satellite cells, while the ECM composition was not significantly important. Additionally, satellite cells on hydrogels entered a quiescent state that could be reversed when the cells were subsequently cultured on Matrigel. Proliferation and gene expression data further indicated that C2C12 cells are not a good proxy for satellite cells. To further understand how different signaling pathways control satellite cell behavior, an investigation of the Notch inhibitor protein Numb was carried out. Numb deficient satellite cells fail to activate, proliferate and participate in muscle repair. Examination of Numb isoform expression in satellite cells and embryonic tissues revealed that while developing limb bud, neural tube, and heart express the long and short isoforms of NUMB, satellite cells predominantly express the short isoforms. A preliminary immunoprecipitation- proteomics experiment suggested that the roles of NUMB in satellite cells are related to cell cycle modulation, cytoskeleton dynamics, and regulation of transcription factors necessary for satellite cell function.
ContributorsPalade, Joanna (Author) / Wilson-Rawls, Norma (Thesis advisor) / Rawls, Jeffrey (Committee member) / Kusumi, Kenro (Committee member) / Newbern, Jason (Committee member) / Stabenfeldt, Sarah (Committee member) / Arizona State University (Publisher)
Created2020
Description
Although anion exchange resins (AERs) have been implemented for a wide range of aqueous contaminants including notorious perfluoroalkyl acids (PFAAs) that are of human health concern, the potential benefits and underlying chemistry of weak-base (WB) AERs are overlooked. To fill these key gaps in the literature, this research evaluated the removal and regeneration efficiency of WB-AER (IRA 67 and IRA 96) with strong-base (SB) AER as the baseline. Batch equilibrium tests were first conducted for the removal of nitrate, sulfate, 3-phenylpropionic acid, and six legacy PFAAs with contrasting properties at different solution pH using polyacrylic and polystyrene chloride-form AERs. In ambient (pH 7) and acidic (pH 4) solutions, the polymer composition was the controlling factor followed by the length of alkyl chain of the resin while AER basicity did not influence the selectivity for the selected contaminants. WB resin had higher capacity than SB analogs based on quantitative analysis using isotherm model parameters. Batch and column adsorption experiments showed significantly greater removal of PFAAs by polystyrene than polyacrylic AERs regardless of resin basicity, with the order of decreasing polyacrylic resin selectivity of PFOS >> PFHxS ≈ PFOA > PFBS > PFHxA ≈ PFBA. The removal performance of WB-AER was reversible, declining drastically at basic conditions and gradually regained once below the pKa of the resin due to the pH-dependent nature of amine groups. This was not the case for IRA 96 (i.e., polystyrene) which exhibited high removal of PFAAs irrelevant of pH because of the nonpolar character of polystyrene matrix. The non-hydrophobic IRA 67 (i.e., polyacrylic) had a satisfactory regeneration using non-toxic salt-only solutions comprising 1% NaOH and 0.5% NaOH + 0.5% NaCl, while IRA 96 was only amenable to brine/methanol regeneration. Important caveats on the validity of isotherm modeling in batch adsorption tests were discussed. Results for batch and column experiments using chloride-form and free-base form WB-AER, respectively, provide insights for industrial applications.
ContributorsKassar, Christian (Author) / Boyer, Treavor H. (Thesis advisor) / Westerhoff, Paul K. (Committee member) / Conroy-Ben, Otakuye (Committee member) / Arizona State University (Publisher)
Created2022