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Description
Human land use and land cover change alter key features of the landscape that may favor habitat selection by some species. Lizards are especially sensitive to these alterations because they rely on their external environment for regulating their body temperature. However, because of their diverse life-history traits and strategies, some

Human land use and land cover change alter key features of the landscape that may favor habitat selection by some species. Lizards are especially sensitive to these alterations because they rely on their external environment for regulating their body temperature. However, because of their diverse life-history traits and strategies, some are able to respond well to disturbance by using their habitat in various ways. To understand how they use their habitat and how human modifications may impact their ability to do this, biologists must identify where they occur and the habitat characteristics on which they depend. Therefore, I used species occupancy modeling to determine (1) whether disturbance predicts the presence of two sympatric congeneric (species of the same genus) lizard species Sceloporus grammicus and S. torquatus, and (2) which habitat characteristics are essential for predicting their occupancy and detection. I focused my study in central Mexico, a region of prevalent land use and land cover change. Here, I conducted visual encounter and habitat surveys at 100 1-hectare sites during the spring of 2019. I measured vegetation and ground cover, average tree diameter, and abundance of refuges. I recorded air temperature, relative humidity, and elevation. I summarized sites as either undisturbed or disturbed, based on the presence of human development. I also summarized sites by ecosystem type, desert or forest, based on vegetation composition (i.e., desert-adapted vs. non-desert-adapted plants), evidence of remnant forest, air temperature, and relative humidity. I found that S. torquatus was more likely to be present in disturbed habitat, whereas S. grammicus was more likely to be present in areas with leaf litter, tree cover, and woody debris. S. torquatus was twice as likely to be detected in forests than deserts, and S. grammicus was more likely to be detected at sites with high elevation and high relative humidity, low temperature, and herbaceous and grass cover. These results emphasize the utility of species occupancy modeling for estimating detection and occupancy in dynamic landscapes.
ContributorsFlores, Jennifer (Author) / Martins, Emília P. (Thesis advisor) / Bateman, Heather L (Thesis advisor) / Zuniga-Vega, J. Jaime (Committee member) / Arizona State University (Publisher)
Created2020
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Description
Adoptive transfer of T cells engineered to express synthetic antigen-specific T cell receptors (TCRs) has provocative therapeutic applications for treating cancer. However, expressing these synthetic TCRs in a CD4+ T cell line is a challenge. The CD4+ Jurkat T cell line expresses endogenous TCRs that compete for space, accessory proteins,

Adoptive transfer of T cells engineered to express synthetic antigen-specific T cell receptors (TCRs) has provocative therapeutic applications for treating cancer. However, expressing these synthetic TCRs in a CD4+ T cell line is a challenge. The CD4+ Jurkat T cell line expresses endogenous TCRs that compete for space, accessory proteins, and proliferative signaling, and there is the potential for mixed dimer formation between the α and β chains of the endogenous receptor and that of the synthetic cancer-specific TCRs. To prevent hybridization between the receptors and to ensure the binding affinity measured with flow cytometry analysis is between the tetramer and the TCR construct, a CRISPR-Cas9 gene editing pipeline was developed. The guide RNAs (gRNAs) within the complex were designed to target the constant region of the α and β chains, as they are conserved between TCR clonotypes. To minimize further interference and confer cytotoxic capabilities, gRNAs were designed to target the CD4 coreceptor, and the CD8 coreceptor was delivered in a mammalian expression vector. Further, Golden Gate cloning methods were validated in integrating the gRNAs into a CRISPR-compatible mammalian expression vector. These constructs were transfected via electroporation into CD4+ Jurkat T cells to create a CD8+ knockout TCR Jurkat cell line for broadly applicable uses in T cell immunotherapies.
ContributorsHirneise, Gabrielle Rachel (Author) / Anderson, Karen (Thesis advisor) / Mason, Hugh (Committee member) / Lake, Douglas (Committee member) / Arizona State University (Publisher)
Created2020
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Description
The intracellular motility seen in the cytoplasm of angiosperm plant pollen tubes is known as reverse fountain cytoplasmic streaming (i.e., cyclosis). This effect occurs when organelles move anterograde along the cortex of the cell and retrograde down the center of the cell. The result is a displacement of cytoplasmic volume

The intracellular motility seen in the cytoplasm of angiosperm plant pollen tubes is known as reverse fountain cytoplasmic streaming (i.e., cyclosis). This effect occurs when organelles move anterograde along the cortex of the cell and retrograde down the center of the cell. The result is a displacement of cytoplasmic volume causing a cyclic motion of organelles and bulk liquid. Visually, the organelles appear to be traveling in a backwards fountain hence the name. The use of light microscopy bioimaging in this study has documented reverse fountain cytoplasmic streaming for the first time in fungal hyphae of Rhizopus oryzae and other members in the order Mucorales (Mucoromycota). This is a unique characteristic of the mucoralean fungi, with other fungal phyla (e.g., Ascomycota, Basidiomycota) exhibiting unidirectional cytoplasmic behavior that lacks rhythmic streaming (i.e., sleeve-like streaming). The mechanism of reverse fountain cytoplasmic streaming in filamentous fungi is currently unknown. However, in angiosperm plant pollen tubes it’s correlated with the arrangement and activity of the actin cytoskeleton. Thus, the current work assumes that filamentous actin and associated proteins are directly involved with the cytoplasmic behavior in Mucorales hyphae. From an evolutionary perspective, fungi in the Mucorales may have developed reverse fountain cytoplasmic streaming as a method to transport various organelles over long and short distances. In addition, the mechanism is likely to facilitate driving of polarized hyphal growth.
ContributorsShange, Phakade Mdima (Author) / Roberson, Robert W. (Thesis advisor) / Gile, Gillian (Committee member) / Baluch, Debra (Committee member) / Arizona State University (Publisher)
Created2020
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Description
The analysis focuses on a two-population, three-dimensional model that attempts to accurately model the growth and diffusion of glioblastoma multiforme (GBM), a highly invasive brain cancer, throughout the brain. Analysis into the sensitivity of the model to

changes in the diffusion, growth, and death parameters was performed, in order to find

The analysis focuses on a two-population, three-dimensional model that attempts to accurately model the growth and diffusion of glioblastoma multiforme (GBM), a highly invasive brain cancer, throughout the brain. Analysis into the sensitivity of the model to

changes in the diffusion, growth, and death parameters was performed, in order to find a set of parameter values that accurately model observed tumor growth for a given patient. Additional changes were made to the diffusion parameters to account for the arrangement of nerve tracts in the brain, resulting in varying rates of diffusion. In general, small changes in the growth rates had a large impact on the outcome of the simulations, and for each patient there exists a set of parameters that allow the model to simulate a tumor that matches observed tumor growth in the patient over a period of two or three months. Furthermore, these results are more accurate with anisotropic diffusion, rather than isotropic diffusion. However, these parameters lead to inaccurate results for patients with tumors that undergo no observable growth over the given time interval. While it is possible to simulate long-term tumor growth, the simulation requires multiple comparisons to available MRI scans in order to find a set of parameters that provide an accurate prognosis.
ContributorsTrent, Austin Lee (Author) / Kostelich, Eric (Thesis advisor) / Gumel, Abba (Committee member) / Kuang, Yang (Committee member) / Arizona State University (Publisher)
Created2020
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Description
Honeycomb sandwich panels have been used in structural applications for several decades in various industries. While these panels are lightweight and rigid, their design has not evolved much due to constraints imposed by available manufacturing processes and remain primarily two-dimensional extrusions sandwiched between facings. With the growth in Additive Manufacturing,

Honeycomb sandwich panels have been used in structural applications for several decades in various industries. While these panels are lightweight and rigid, their design has not evolved much due to constraints imposed by available manufacturing processes and remain primarily two-dimensional extrusions sandwiched between facings. With the growth in Additive Manufacturing, more complex geometries can now be produced, and advanced design techniques can be implemented into end use parts to obtain further reductions in weight, as well as enable greater multi-functionality. The question therefore is: how best to revisit the design of these honeycomb panels to obtain these benefits?

In this work, a Bio-Inspired Design approach was taken to answer this question, primarily since the hexagonal lattice is so commonly found in wasp and bee nests, including the well-known bee’s honeycomb that inspired these panel designs to begin with. Whereas prior honeycomb panel design has primarily focused on the hexagonal shape of the unit cell, in this work we examine the relationship between the various parameters constituting the hexagonal cell itself, specifically the wall thickness and the corner radius, and also examine out-of-plane features that have not been previously translated into panel design. This work reports findings from a study of insect nests across 70 species using 2D and 3D measurements with optical microscopy and X-ray tomography, respectively. Data from these biological nests were used to identify design parameters of interest, which were then translated into design principles. These design principles were implemented in the design of honeycomb panels manufactured with the Selective Laser Sintering process and subjected to experimental testing to study their effects on the mechanical behavior of these panels.
ContributorsGoss, Derek Lee (Author) / Bhate, Dhruv (Thesis advisor) / Lewis, Sharon (Committee member) / Nam, Changho (Committee member) / Arizona State University (Publisher)
Created2020
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Description
Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide and exhibits a male-bias in occurrence and mortality. Previous studies have provided insight into the role of inherited genetic regulation of transcription in modulating sex-differences in HCC etiology and mortality. This study uses pathway analysis to add insight

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide and exhibits a male-bias in occurrence and mortality. Previous studies have provided insight into the role of inherited genetic regulation of transcription in modulating sex-differences in HCC etiology and mortality. This study uses pathway analysis to add insight into the biological processes that drive sex-differences in HCC etiology as well as a provide additional framework for future studies on sex-biased cancers. Gene expression data from normal, tumor adjacent, and HCC liver tissue were used to calculate pathway scores using a tool called PathOlogist that not only takes into consideration the molecules in a biological pathway, but also the interaction type and directionality of the signaling pathways. Analysis of the pathway scores uncovered etiologically relevant pathways differentiating male and female HCC. In normal and tumor adjacent liver tissue, males showed higher activity of pathways related to translation factors and signaling. Females did not show higher activity of any pathways compared to males in normal and tumor adjacent liver tissue. Work suggest biologic processes that underlie sex-biases in HCC occurrence and mortality. Both males and females differed in the activation of pathways related apoptosis, cell cycle, signaling, and metabolism in HCC. These results identify clinically relevant pathways for future research and therapeutic targeting.
ContributorsRehling, Thomas E (Author) / Buetow, Kenneth (Thesis advisor) / Wilson, Melissa (Committee member) / Maley, Carlo (Committee member) / Arizona State University (Publisher)
Created2021
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Description
In the US, menstrual education, which provides key information about menstrual hygiene and health to both young girls and boys, historically lacks biologically accurate information about the menstrual cycle and perpetuates harmful perceptions about female reproductive health. When people are unable to differentiate between normal and abnormal menstrual bleeding, based

In the US, menstrual education, which provides key information about menstrual hygiene and health to both young girls and boys, historically lacks biologically accurate information about the menstrual cycle and perpetuates harmful perceptions about female reproductive health. When people are unable to differentiate between normal and abnormal menstrual bleeding, based on a lack of quality menstrual education, common gynecological conditions often remain underreported. This raises a question as to how girls’ menstrual education experiences influence the ways in which they perceive normal menstrual bleeding and seek treatment for common abnormalities, such as heavy, painful, or irregular menstrual bleeding. A mixed methods approach allowed evaluation of girls’ abilities to recognize abnormal menstrual bleeding. A literature review established relevant historical and social context on the prevalence and quality of menstrual education in the US. Then, five focus groups, each including five to eight college-aged women, totaling thirty-three participants, allowed for macro-level analysis of current challenges and gaps in knowledge related to menstruation. To better examine the relationship between menstrual education and reproductive health outcomes, twelve semi-structured, one-on-one interviews allowed micro-level analysis. Those interviews consisted of women diagnosed with endometriosis and polycystic ovary syndrome, common gynecological conditions that include abnormal menstrual bleeding. Developing a codebook of definitions and exemplars of significant text segments and applying it to the collected data revealed several themes. For example, mothers, friends, teachers, the Internet, and social media are among the most common sources of information about menstrual hygiene and health. Yet, women reported that those sources of information often echoed stigmatized ideas about menstruation, eliciting feelings of shame and fear. That poor quality of information was instrumental to women’s abilities to detect and report abnormal menstrual bleeding. Women desire and need biologically accurate information about reproductive health, including menstruation and ovulation, fertility, and methods of birth control as treatments for abnormal menstrual bleeding. Unfortunately, menstrual education often leaves girls ill-equipped to identify and seek treatment for common gynecological conditions. Those findings may influence current menstrual education, incorporating biological information and actively dismissing common misconceptions about menstruation that influence stigma.
ContributorsSantora, Emily Katherine (Author) / Maienschein, Jane (Thesis advisor) / Ellison, Karin (Committee member) / Hurlbut, Ben (Committee member) / Arizona State University (Publisher)
Created2021
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Description
When exposed to abiotic stresses, Escherichia coli responds by activating various stress-mitigating pathways. Initiation of stress responses partially relies on the RNA polymerase (RNAP) to transcribe genes necessary to tolerate various stresses, including nutritional deprivation and heat exposure. Consequently, RNAP mutations impacting transcription can have pleiotropic effects on the cell

When exposed to abiotic stresses, Escherichia coli responds by activating various stress-mitigating pathways. Initiation of stress responses partially relies on the RNA polymerase (RNAP) to transcribe genes necessary to tolerate various stresses, including nutritional deprivation and heat exposure. Consequently, RNAP mutations impacting transcription can have pleiotropic effects on the cell physiology and the ability to tolerate stress. Previously, while investigating antibiotic-resistant mutations arising in the absence of major antibiotic efflux pumps, four mutants containing alterations in the RNA polymerase beta subunit gene (rpoB) were isolated (Cho & Misra, 2021). Of the four mutants, one (RpoB58) was found to be thermotolerant, permitting homogenous, stable growth at temperatures up to 47°C, whereas the parental rpoB wildtype (RpoB-WT) was only able to do so up to 45°C. Additionally, RNA-Seq analysis indicated that the RpoB58 mutant had a ‘stringent’ profile that is normally seen under nutritionally deprived conditions. To better understand the regulatory pathways used to confer stress tolerance, this thesis sought to further characterize and investigate the intracellular mechanisms contributing to the thermotolerance conferred by the rpoB58 mutation. The RpoB58 mutant was found to be significantly more tolerant to both continuous heat stress (up to 47°C) and short-term heat (55°C) and ethanol (25%) exposure. Additionally, the RpoB58 mutant tolerated the absence or depletion of major heat shock chaperones DnaJ and DnaK that normally play key roles during temperature stresses by reducing protein misfolding. RNA-Seq data and reporter gene assays showed reduced expression of genes involved in protein synthesis. A similar reduction in the expression of protein synthesis genes was observed when cells were grown in growth-limiting minimal media. Interestingly, growth in minimal medium rescued the ΔdnaJ defect like the rpoB58 mutation. Based on these data, it was proposed that a decrease in protein synthesis, whether caused by rpoB58 or the growth medium, would result in less growth-inhibiting protein misfolding and aggregation, especially at higher growth temperatures where proteins are susceptible to denaturation and aggregation. As a result of these investigations, a possible mechanistic insight was provided as to how the rpoB58 mutation confers thermotolerance.
ContributorsYeh, Melody (Author) / Misra, Rajeev RM (Thesis advisor) / Wang, Xuan XW (Committee member) / Muralinath, Maneesha MM (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Parabasalia is a phylum of flagellated protists with a large range of cell sizes, spanning from as little as 7 µm in length (e.g. Pentatrichomonas hominis) to well over 300 µm (e.g. Pseudotrichonympha grassii). Many Parabasalia are associated with animals in mutualistic, parasitic, or commensal relationships. The largest

Parabasalia is a phylum of flagellated protists with a large range of cell sizes, spanning from as little as 7 µm in length (e.g. Pentatrichomonas hominis) to well over 300 µm (e.g. Pseudotrichonympha grassii). Many Parabasalia are associated with animals in mutualistic, parasitic, or commensal relationships. The largest Parabasalia species are obligate mutualists of termites, which help to digest lignocellulose. While the specific digestive roles of different protist species are mostly unknown, Parabasalia with different cell sizes are known to inhabit different regions of the termite hindgut. It is currently unclear whether these size differences are driven by selection or drift, but it is well known that cell size correlates with genome size in eukaryotes. Therefore, in order to gain insight into possible selection pressures or mechanisms for cell size increase, genome sizes were estimated for the five Parabasalia species that inhabit the hindgut of Coptotermes formosanus Shiraki. The cell volumes and C-values for the five protist species are 89,190 µm3 and 147 pg in Pseudotrichonympha grassii, 26,679 µm3 and 56 pg in Holomastigotoides hartmanni, 8,985 µm3 and 29 pg in Holomastigotoides minor, 1,996 µm3 and 12 pg in Cononympha leidyi , and 386 µm3 and 6 pg in Cononympha koidzumii. The positive correlation between genome size and cell size was maintained in this group (R2 = 0.76). These genome sizes are much larger than the previously estimated genome sizes of non-termite associated Parabasalia, which spanned 2-fold ranging from 0.088 pg (in Tetratrichomonas gallinarum) to 0.181 pg (in Trichomonas foetus). With these new estimates, the range now spans over 1,500-fold from 0.088 pg to 147 pg in P. grassii, implying potential differences in the level of selective pressures for genome size in termite-associated Parabasalia compared to other protists.
ContributorsMontoya, Samantha (Author) / Gile, Gillian (Thesis advisor) / Wideman, Jeremy (Committee member) / Chouvenc, Thomas (Committee member) / Arizona State University (Publisher)
Created2021
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Description
One of the most pronounced issues affecting the management of fisheries today is bycatch, or the unintentional capture of non-target species of marine life. Bycatch has proven to be detrimental for many species, including marine megafauna and pelagic fishes. One method of reducing bycatch is illuminated gillnets, which involves utilizing

One of the most pronounced issues affecting the management of fisheries today is bycatch, or the unintentional capture of non-target species of marine life. Bycatch has proven to be detrimental for many species, including marine megafauna and pelagic fishes. One method of reducing bycatch is illuminated gillnets, which involves utilizing the differences in biological visual capabilities and behaviors between species of bycatch and target fish catch. To date, all studies conducted on the effects of net illumination on bycatch and target fish catch have been conducted at night. In this study, the effects of net illumination on bycatch, target fish catch, and market value during both night and day periods at Baja California Sur, Mexico were compared. It was found that i) net illumination is effective (p < 0.05) at reducing bycatch of finfish during the day and at night, ii) net illumination at night is more effective (p < 0.05) at reducing bycatch for elasmobranchs, Humboldt squid, and aggregate bycatch than during the day, iii) time of day did not have an effect (p > 0.05) on sea turtle bycatch, and iv) net illumination did not significantly (p > 0.05)affect target catch or market value at night or during the day. These results suggest that net illumination may be an effective strategy for reducing finfish bycatch in fisheries that operate during the day or across 24 h periods, and is especially effective for reducing elasmobranch, Humboldt squid, and total bycatch biomass at night.
ContributorsDenton, Kyli Elise (Author) / Senko, Jesse (Thesis advisor) / Neuer, Susanne (Thesis advisor) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2021