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- All Subjects: Biology
- Genre: Masters Thesis
- Creators: Arizona State University
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 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
Description
Globally, about two-thirds of the population is latently infected with herpes simplex virus type 1 (HSV-1). HSV-1 is a large double stranded DNA virus with a genome size of ~150kbp. Small defective genomes, which minimally contain an HSV-1 origin of replication and packaging signal, arise naturally via recombination during viral DNA replication. These small defective genomes can be mimicked by constructing a bacterial plasmid containing the HSV-1 origin of replication and packaging signal, transfecting these recombinant plasmids into mammalian cells, and infecting with a replicating helper virus. The absence of most viral genes in the amplicon vector allows large pieces of foreign DNA (up to 150kbp) to be incorporated. The HSV-1 amplicon is replicated and packaged by the helper virus to form HSV-1 particles containing the amplicon DNA. We constructed a novel HSV-1 amplicon vector system containing lambda phage-derived attR sites to facilitate insertion of transgenes by Invitrogen Gateway recombination. To demonstrate that the amplicon vectors work as expected, we packaged the vector constructs expressing Emerald GFP using the replication-competent helper viruses OK-14 or HSV-mScartlet-I-UL25 in Vero cells and demonstrate that the vector stock can subsequently transduce and express Emerald GFP. In further work, we will insert transgenes into the amplicon vector using Invitrogen Gateway recombination to study their functionality.
ContributorsVelarde, Kimberly (Author) / Hogue, Ian B (Thesis advisor) / Manfredsson, Fredric (Committee member) / Sandoval, Ivette (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2021
Description
As the planet is rapidly urbanizing, understanding the ecological effects of urbanization is a grand challenge for modern biology. For example, increased city temperatures known as the urban heat island effect, disproportionately impact nocturnal taxa and this consideration is widely overlooked. Slight shifts in the thermal microclimate have a cascade of ramifications that directly impact species density and distribution. Animal behavior is a trait that may explain why some species thrive after urbanization when others go locally extinct. In this study I followed 22 adult females of the western black widow, Latrodectus hesperus, from both urban and undisturbed Sonoran Desert habitats. First, I began looking for differences between urban and desert spiders under field conditions: boldness, voracity, web size and body condition. Both urban and desert spiders were then brought to the laboratory to see how their behavior changed. I found no behavioral differences between urban and desert spiders in the field or the laboratory. I did find that spider behavior differed between the field and the laboratory. Specifically, boldness in the laboratory was significantly lower compared to the field. Voracity was more repeatable in the laboratory versus the field, and boldness was strongly positively correlated with voracity in the laboratory, but not in the field. These behavioral shifts from the field to the laboratory favor the conclusion that black widow behavior is highly plastic and context dependent. Lastly, I monitored web temperature of black widow microhabitat continuously for an entire year using iButton data loggers. I found microhabitat temperatures differences between urban and desert sites were greatest at night and absent during the daytime. I uncovered a seasonal effect with the highest magnitude temperature difference occurring during the springtime. Additionally, behavior was significantly correlated with field temperatures; the boldest spiders come from the warmest webs. However, I found little evidence that temperature predicts spider body condition or voracity, and body condition does not predict its behavioral expression. My results highlight the importance of studying animal behavior to increase understanding of the factors that shape distribution and density in a lethal pest species.
ContributorsClark, Ryan Carter (Author) / Johnson, James C (Thesis advisor) / Bang, Christofer (Thesis advisor) / Sullivan, Brian (Committee member) / Arizona State University (Publisher)
Created2021
Description
Dryland ecosystems are integral to the global agricultural system and play an important role in soil carbon (C) storage. Despite their importance, drylands are currently facing many challenges including climate-change induced rainfall variability and soil degradation. These challenges are predicted to have effects on the soil microbial communities in drylands. Compost, an organic soil amendment, is a land management strategy that has been proposed to increase soil C storage as well as improve soil conditions in drylands, specifically in restoration and agricultural sites where degradation has affected soil properties like microbial biomass and respiration. Compost additions and rainfall variability may interact to affect soil moisture, an important catalyst for microbial activity. Assessing microbial activity responses under compost applications and variable moisture will aid in understanding how land management strategies will be affected by climate change in the future. This study investigates how soil microbial activity from a degraded dryland restoration site is affected by different compost applications amounts and variable soil moistures. A laboratory incubation study was conducted in a controlled environmental chamber for 60 days. Soils were amended with different treatments of compost (0, 0.35, and 0.70 g cm -2) and water pulses (5, 10, and 15 mm) in a full factorial design. Each treatment received the same cumulative amount of water throughout the incubation, but pulses were administered in different frequencies (every 5, 10, and 15 days). Soil respiration and soil water content were measured daily, and microbial biomass was measured at the end of the incubation to assess treatment effects on microbial activity. Microbial respiration and soil water content increased with increasing compost additions and water pulse sizes. Microbial biomass did not have consistent increases with compost additions or water pulse size. Cumulative microbial respiration was highest with the large-infrequent pulse size and smallest with the small-frequent pulse size. These results suggest that microbial activity and carbon dynamics in soils where compost amendments are used will respond to future changes in precipitation variability. The results of this study can aid in understanding how microbial activity is influenced by compost applications, which will be critical in making informed management decisions in the context of climate change.
ContributorsAmari, Katherine Nicole (Author) / Throop, Heather L (Thesis advisor) / Ball, Becky A (Committee member) / Blankinship, Joseph C (Committee member) / Gherardi, Laureano A (Committee member) / Cueva Rodriguez, Alejandro H (Committee member) / Arizona State University (Publisher)
Created2021
Description
Adaptive therapy utilizes competitive interactions between resistant and sensitive cells by keeping some sensitive cells to control tumor burden with the aim of increasing overall survival and time to progression. The use of adaptive therapy to treat breast cancer, ovarian cancer, and pancreatic cancer in preclinical models has shown significant results in controlling tumor growth. The adaptive therapy model comes from the integrated pest management agricultural strategy, predator prey model, and the unique intra- and inter-tumor heterogeneity of tumors. The purpose of this thesis is to analyze and compare gemcitabine dose response on hormone refractory breast cancer cells retrieved from mice using an adaptive therapy strategy with standard therapy treatment. In this study, we compared intermittent (drug holiday) adaptive therapy with maximum tolerated dose therapy. The MCF7 resistant cell lines to both fulvestrant and palbociclib were injected into the mammary fat pads of 8 weeks old NOD/SCID gamma (NSG) mice which were then treated with gemcitabine. Tumor burden graphs were made to track tumor growth/decline during different treatments while Drug Dose Response (DDR) curves were made to test the sensitivity of the cell lines to the drug gemcitabine. The tumor burden graphs showed success in controlling the tumor burden with intermittent treatment. The DDR curves showed a positive result in using the adaptive therapy treatment method to treat mice with gemcitabine. Due to some fluctuating DDR results, the sensitivity of the cell lines to gemcitabine needs to be further studied by repeating the DDR experiment on the other mice cell lines for stronger results.
ContributorsConti, Aviona Christina (Author) / Maley, Carlo (Thesis advisor) / Blattman, Joseph (Committee member) / Anderson, Karen (Committee member) / Arizona State University (Publisher)
Created2022
Description
Alzheimer’s disease (AD) is one of the most prevalent neurodegenerative diseases worldwide, with no effective treatments or preventions. Evidence suggests that environmental factors, including dietary nutrients, contribute to the etiology of AD. Choline is an essential nutrient found in many common foods. Choline is produced endogenously, but not at levels sufficient for healthy metabolic function and thus requires dietary supplementation. Literature shows that ~90% of Americans do not meet the adequate intake threshold for dietary choline consumption and therefore are dietary choline-deficient. While dietary choline supplementation throughout life has been shown to have significant health benefits, such as reducing AD pathology and improving cognition in a mouse model of AD, the impacts of dietary choline deficiency are unknown. Experiments were designed to understand the effects of dietary choline deficiency in healthy, non-transgenic mice (NonTg) and in the 3xTg-AD mouse model of AD. From 3 to 12 months of age, mice received either adequate choline (ChN) in the diet or were put on a choline-deficient (Ch-) diet. A Ch- diet leads to significant weight gain throughout life in both the NonTg and 3xTg-AD mice, with AD mice showing a greater increase. Additionally, impaired glucose metabolism, which is a risk factor for AD, was induced in both NonTg Ch- and 3xTg-AD Ch- mice. Interestingly, Ch- induced cardiomegaly in 3xTg-AD mice and elevated markers of cardiac dysfunction in NonTg mice to similar levels in 3xTg-AD mice. Finally, Ch- exacerbated amyloid-β plaque pathology and tau hyperphosphorylation in the hippocampus and cortex of 3xTg-AD mice. Proteomic analyses revealed Ch- induced changes in hippocampal proteins associated with postsynaptic receptor regulation, microtubule stabilization, and neuronal development, as well as well-known AD-associated proteins (MAPT, BACE1, MECP2, CREBBP). Proteomic analyses also revealed Ch- induced changes of plasma proteins associated with secondary pathologies of AD including inflammation, immune response insulin metabolism, and mitochondrial dysfunction (SAA1, SAA2, IDE, HSPD1, VDAC-1, VDACE-2). Taken together, these data suggest that dietary choline deficiency induces system-wide cellular and molecular dysfunction associated with AD across several pathogenic axes, through proteomic changes not only in the hippocampus but also in the plasma.
ContributorsDave, Nikhil (Author) / Velazquez, Ramon (Thesis advisor) / Piras, Ignazio (Committee member) / Mastroeni, Diego (Committee member) / Arizona State University (Publisher)
Created2022
Description
The TP53 tumor suppressor gene is the most frequently mutated gene in human cancers. In the highly aggressive triple negative breast cancer (TNBC), TP53 is mutated in 80% of cases. TNBC lacks viable drug targets, resulting in a low prognosis (12.2% 5 year survivability rate). As such, the discovery of druggable targets in TNBC would be beneficial. Mutated p53 protein typically occurs as a missense mutation and often endows cancer cells with gain of function (GOF) properties by dysregulating metabolic pathways. One of these frequently dysregulated pathways is the Hippo/Yes-associated protein-1 (YAP1)/WW Domain Containing Transcription Regulator 1 (TAZ) tumor suppressor pathway. This study therefore analyzed the involvement of the Hippo/YAP1/TAZ pathway in p53-mediated breast cancer cell invasion. From an RNA-seq screen in MCF10A cell lines harboring different TP53 missense mutations, each with a differing invasive phenotype, components of the Hippo pathway were found to correlate with cell invasion. To this end, the active and inactive forms of YAP1 and TAZ were studied. Phosphorylated (inactive) YAP1 and TAZ are retained in the cytoplasm and eventually degraded. Unphosphorylated (active) YAP1 and TAZ translocate to the nucleus to activate TEAD-family transcription factors, inducing cell survival and proliferation genes leading to increased cell invasion. Using quantitative western blot analysis, it was found that inactive TAZ expression was lower in the most invasive cell lines and higher in the least invasive cell lines (p = 0.003). Moreover, the ratio of inactive TAZ protein to total TAZ protein was also shown to be predominantly lower in the invasive cell lines compared to the non-invasive lines (p = 0.04). Finally, active TAZ expression was primarily higher in p53-mutant invasive cell lines and lower in non-invasive p53 mutant cells. Additionally, although YAP1 and TAZ are thought to be functionally redundant, the pattern seen in TAZ was not seen in the YAP1 protein. Taken together, the results demonstrated here suggest that TAZ holds a more dominant role in governing TNBC cell invasion compared to YAP1 and further highlights TAZ as a potential therapeutic target in TNBC.
ContributorsGrief, Dustin (Author) / LaBaer, Joshua (Thesis advisor) / Anderson, Karen (Committee member) / Nikkhah, Mehdi (Committee member) / Arizona State University (Publisher)
Created2022
Description
Alkanolamines are useful as building blocks for a variety of applications, ranging from medical applications such as drug and gene delivery. In this work, Escherichia coli was investigated as a viable candidate for the production of 5-amino-1-pentanol (5-AP). Taking advantage of the existing L-lysine degradation pathway, a novel route to 5-AP was constructed by co-expressing the genes cadA (encoding lysine decarboxylase, responsible for the conversion of L-lysine to cadaverine) and patA (encoding putrescine aminotransferase, responsible for the conversion of cadaverine to 5-amino-1-pentanal), followed by the endogenous reduction of 5-amino-pentanal (5-APL) to 5-AP. To avoid the competing conversion of 5-APL to 5-amino-1-pentanoate and avoid accumulation of byproduct 1-Δ-piperideine, further host engineering was performed to delete the gene patD also known as prr (encoding 5-amino-pentanal dehydrogenase). Flask scale fermentation experiments in minimal medium of the newly constructed pathway was conducted where 62.6 mg/L 5-AP was observed to be produced. It was hypothesized that 5-AP production could be boosted by optimizing production medium to M10 media. However, change in the culture medium resulted in the production of just 51 mg/L 5-AP. Shifts observed in HPLC chromatogram peaks made it difficult to conclude exact titers of 5-AP and can be further improved by exploring different analysis methods and optimization of the method currently in place.
ContributorsBrookhouser, Brendan (Author) / Nielsen, David R (Thesis advisor) / Tonkovich, Anna L (Committee member) / Varman, Arul M (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bouteloua eriopoda (Torr.) Torr., also known as black grama, is a perennial bunchgrass native to arid and semiarid ecosystems in the southwestern region of North America. As a result of anthropogenic climate change, this region is predicted to increase in aridity and experience more frequent extreme drought and extreme wet years. This change in precipitation will no doubt affect black grama; however, few studies have investigated how the specific structural components of this grass will respond. The purpose of this study was to examine the effects of years since start of treatment and annual precipitation amount on tiller and stolon densities, and to test for interaction between the two predictor variables. Additionally, the effects of annual precipitation on ramets and axillary buds were investigated. By using 36 experimental plots that have been receiving drought, irrigated, or control treatments since 2007, tiller density was the most responsive component to both annual precipitation amount and years since start of treatment. Years since start of treatment and annual precipitation amount also had a statistically significant interaction, meaning the effect of precipitation amount on tiller density differs depending on how many years have passed since treatments began. Stolon density was the second-most responsive component; the predictor variables were found to have no statistically significant interaction, meaning their effects on stolon density are independent of one another. Ramet density, ramets per stolon, and axillary bud metabolic activity and density were found to be independent of annual precipitation amount for 2021. The results indicate that multiple-year extreme wet and multiple-year extreme dry conditions in the Southwest will both likely reduce tiller and stolon densities in black grama patches. Prolonged drought conditions reduced tiller and stolon production in black grama because of negative legacies from previous years. Reduced production during prolonged wet conditions could be due to increased competition between adjacent plants.
ContributorsSutter, Bryce Madison (Author) / Sala, Osvaldo E (Thesis advisor) / Makings, Elizabeth (Committee member) / Wojciechowski, Martin F (Committee member) / Arizona State University (Publisher)
Created2022
Description
Embryonic and juvenile development consist of a series of complex and rapid changes driven by a suite of crucially timed developmental cues within the cell. The developmental process begins at the moment of zygote activation, “jump-started” by maternal factors such as mRNA and proteins until transcription can be zygotically-driven. Regulation of transcription initiation plays a crucial role in this process, as minute changes in the timing, density, and characteristics of gene expression can have drastic effects on the zygote’s development. Specific promoter elements can be linked to different patterns of transcription, driving both ubiquitous and sharply regulated gene expression, thus forming the basis for the time-sensitive developmental processes. In order to better understand the genes expressed during different stages of development and the impact of promoter elements on transcription patterns and transcript concentrations within the cell, I created a Gene Expression and Promoter Atlas in two species within the cryptic species complex, Daphnia pulex. I surveyed five embryonic and two juvenile developmental stages in both a North American and mitochondrially European Daphnia pulex utilizing developmental landmarks to visually stages embryos. A total of 17,993 genes were identified in the European species and 15,295 were identified in the North American species, with 11,551 orthologs identified between the two. I utilized the transcription start site (TSS) profiling method STRIPE-seq to identify promoter motifs and RNA-seq to survey mRNA concentration at each stage, generating a wealth of genetic data. The methodology for library construction and the dataset generated therein provide an informative basis for further comparative developmental studies and the elucidation of full gene functionality in an emerging model organism.
ContributorsWalls, Sarah (Author) / Lynch, Michael (Thesis advisor) / Raborn, R. Taylor (Committee member) / Mangoni, Marco (Committee member) / Harris, Robin (Committee member) / Arizona State University (Publisher)
Created2022