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Valley Fever, also known as coccidioidomycosis, is a respiratory disease that affects 10,000 people annually, primarily in Arizona and California. Due to a lack of gene annotation, diagnosis and treatment of Valley Fever is severely limited. In turn, gene annotation efforts are also hampered by incomplete genome sequencing. We intend

Valley Fever, also known as coccidioidomycosis, is a respiratory disease that affects 10,000 people annually, primarily in Arizona and California. Due to a lack of gene annotation, diagnosis and treatment of Valley Fever is severely limited. In turn, gene annotation efforts are also hampered by incomplete genome sequencing. We intend to use proteogenomic analysis to reannotate the Coccidioides posadasii str. Silveira genome from protein-level data. Protein samples extracted from both phases of Silveira were fragmented into peptides, sequenced, and compared against databases of known and predicted proteins sequences, as well as a de novo six-frame translation of the genome. 288 unique peptides were located that did not match a known Silveira annotation, and of those 169 were associated with another Coccidioides strain. Additionally, 17 peptides were found at the boundary of, or outside of, the current gene annotation comprising four distinct clusters. For one of these clusters, we were able to calculate a lower bound and an estimate for the size of the gap between two Silveira contigs using the Coccidioides immitis RS transcript associated with that cluster's peptides \u2014 these predictions were consistent with the current annotation's scaffold structure. Three peptides were associated with an actively translated transposon, and a putative active site was located within an intact LTR retrotransposon. We note that gene annotation is necessarily hindered by the quality and level of detail in prior genome sequencing efforts, and recommend that future studies involving reannotation include additional sequencing as well as gene annotation via proteogenomics or other methods.
ContributorsSherrard, Andrew (Author) / Lake, Douglas (Thesis director) / Grys, Thomas (Committee member) / Mitchell, Natalie (Committee member) / Computing and Informatics Program (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has captured human attention because it is a pathogen that has contributed to global amphibian declines. Despite increased research, much is still unknown about how it develops. For example, the fact that Bd exhibits phenotypic plasticity during development was only recently identified. In

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has captured human attention because it is a pathogen that has contributed to global amphibian declines. Despite increased research, much is still unknown about how it develops. For example, the fact that Bd exhibits phenotypic plasticity during development was only recently identified. In this thesis, the causes of phenotypic plasticity in Bd are tested by exposing the fungus to different substrates, including powdered frog skin and keratin, which seems to play an important role in the fungus's colonization of amphibian epidermis. A novel swelling structure emerging from Bd germlings developed when exposed to keratin and frog skin. This swelling has not been observed in Bd grown in laboratory cultures before, and it is possible that it is analogous to the germ tube Bd develops in vivo. Growth of the swelling suggests that keratin plays a role in the phenotypic plasticity expressed by Bd.
ContributorsBabb-Biernacki, Spenser Jordan (Author) / Collins, James P. (Thesis director) / Roberson, Robert (Committee member) / Brus, Evan (Committee member) / School of Film, Dance and Theatre (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Nutritional balance is a requirement for the survival of all species. This balance is important for complex eusocial organisms as it influences the growth and development of the colony. Leafcutter ants function as tri-trophic systems, harvesting mixed vegetation to cultivate a fungus garden that in return supplies the colony with

Nutritional balance is a requirement for the survival of all species. This balance is important for complex eusocial organisms as it influences the growth and development of the colony. Leafcutter ants function as tri-trophic systems, harvesting mixed vegetation to cultivate a fungus garden that in return supplies the colony with food. Examining how the colony deals with nutrient balance is of particular interest because this species forages to provide nutrients for the fungus. There seems to be a feedback system between the fungus and the workers that influences how much of a particular macronutrient should be collected. The objective of this thesis study was to examine the foraging behavior of the desert leaf cutter ant, Acromyrmex versicolor. This study asked how nutrition, in particular the ratio of carbohydrates to proteins, influences the foraging behavior of the colony. It was hypothesized that given a choice of high protein and high carbohydrate diets the leafcutters would forage towards a balance ratio. The results from this experiment showed that A. versicolor forage towards a target ratio of protein to carbohydrate to based diets. This p:c ratio was calculated to be 1:6.2; 1 gram of protein to 6.2 grams of carbohydrate. When colonies were restricted to the high carbohydrate diet, they increased food consumption, consistent with the expectation that they would forage to reach their protein nutrient requirement, however, they reduced foraging on that diet. This suggests that ants avoid overconsuming protein, even when doing so provided more optimal carbohydrate intake. From this study I concluded that nutritional balance is a foraging goal for ant societies, similar to organisms. These results also open the question of how nutrient regulation by leafcutter ants is regulated around their mutualist relationship with another organism, the fungus.
ContributorsFarris, Megan Alexandra (Author) / Fewell, Jennifer (Thesis director) / Harrison, Jon (Committee member) / Smith, Nate (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
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Description
Chemical fertilizers are commonly used for controlled environment agriculture because they provide essential plant nutrient efficiently. However, rising fertilizer costs, global phosphorous shortage, and the negative impacts of producing and using chemical fertilizer are concerns for sustainable crop production. As sustainable alternatives to chemical fertilizers, there is a growing interest

Chemical fertilizers are commonly used for controlled environment agriculture because they provide essential plant nutrient efficiently. However, rising fertilizer costs, global phosphorous shortage, and the negative impacts of producing and using chemical fertilizer are concerns for sustainable crop production. As sustainable alternatives to chemical fertilizers, there is a growing interest in using organic fertilizers with beneficial plant growth promoting microorganisms. The objectives of this research were to investigate how the application of plant growth promoting bacteria and arbuscular mycorrhizal fungi influences plant growth of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum) seedlings in soilless media under organic fertilization. In the first study, the effects of Azosprillium brasilense and Rhizophagus intraradices inoculation on lettuce and tomato seedling growth were quantified under two different organic fertilizer types compared to under chemical fertilizer. The results showed that A. brasilense and R. intraradices had little to no effect on any growth parameter measured in either species regardless of fertilizer type. In the second study, an investigation of the co-inoculation of A. brasilense and R. intraradices or increasing the application frequency of A. brasilense or/and R. intraradices increased plant growth promoting effects in lettuce ‘Cherokee’ and ‘Rex’ grown under organic fertilization. An application frequency of every 2-days of the R. intraradices without or with A. brasilense increased shoot fresh weight in both lettuce cultivars by 51-58%, compared to un-inoculated control. In contrast, lettuce seedling growth were similar without or with applying R. intraradices weekly or A. brasilense regardless of frequency. Together, the results suggest that applying R. intraradices with a proper application frequency can enhance plant growth of lettuce under organic fertilization.
ContributorsMcClintic, Nicklas Charles (Author) / Park, Yujin (Thesis advisor) / Penton, Christopher R (Committee member) / Chen, Changbin (Committee member) / Arizona State University (Publisher)
Created2022
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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