Matching Items (4)

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Improving the Valley Fever Gene Annotation Through Proteogenomic Analysis

Description

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

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.

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Date Created
  • 2016-12

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The Explutrientoration of Macronutrient Regulation in the Desert Leafcutter

Description

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

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.

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Date Created
  • 2015-12

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Phenotypic Plasticity and Early Life Cycle Development of the Chytrid Fungus Batrachochytrium dendrobatidis

Description

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

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.

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Date Created
  • 2016-05

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Reverse Fountain Cytoplasmic Streaming in Rhizopus Oryzae

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

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.

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Date Created
  • 2020