Matching Items (3)
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- All Subjects: Genomics
- All Subjects: Evaporative water loss
- Genre: Academic theses
- Genre: Masters Thesis
- Creators: Denardo, Dale F.
- Resource Type: Text
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
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes can result in unequal gene expression between the sexes (e.g., between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression which prevents deleterious side effects from having too much or too little expression of genes on sex chromsomes. The green anole is part of a group of species that recently underwent an adaptive radiation. The green anole has XX/XY sex determination, but the content of the X chromosome and its evolution have not been described. Given its status as a model species, better understanding the green anole genome could reveal insights into other species. Genomic analyses are crucial for a comprehensive picture of sex chromosome differentiation and dosage compensation, in addition to understanding speciation.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
ContributorsRupp, Shawn Michael (Author) / Wilson Sayres, Melissa A (Thesis advisor) / Kusumi, Kenro (Committee member) / DeNardo, Dale (Committee member) / Arizona State University (Publisher)
Created2016
Description
The alarming decline of insect pollinators is due in part to agrochemical exposure and climate warming. This thesis focuses on understanding how exposure to a commonly used fungicide and high air temperature affect the flight behavior and physiology of the very important commercial pollinator, Apis mellifera. I found that honey bees reared on pollen contaminated with field-realistic levels of a fungicide (Pristine®) commonly applied to almond blossoms before pollination had smaller thoraxes, possibly due to inhibition of protein digestion, plausibly reducing flight capability. By flying unloaded bees in low density air to elicit maximal performance, I found that consumption of high doses of fungicide during development inhibited maximal flight performance, but consumption of field-realistic doses did not.
To understand climatic-warming effects on honey bees, I flew unloaded foragers at various air densities and temperatures to assess the effects of flight muscle temperature (29 to 44°C) on maximal aerobic metabolism. Flight metabolic rate peaked at a muscle temperature of 39°C and decreased by ~2% per degree below and ~5% per degree above this optimum. Carrying nectar loads increased flight muscle temperatures and flight metabolism of foragers flying at air temperatures of 20 or 30°C. Yet, remarkably, bees flying at 40°C were able to carry loads without heating up or increasing metabolic rate. Bees flying at 40°C increased evaporative cooling and decreased metabolic heat production to thermoregulate. High speed video revealed that bees flying at 40°C air temperature lowered their wing beat frequency while increasing stroke amplitude, increasing flight efficiency. My data also suggests that cooler bees use wing kinematic strategies that increase flight stability and maneuverability while generating excess heat that warms their flight muscle toward optimum. High water loss rates during flight likely limit foraging in dry air temperatures above 46°C, suggesting that CTmax measures of resting honey bees significantly overestimate when high air temperature will negatively impact flight and foraging.
ContributorsGlass, Jordan Robert (Author) / Harrison, Jon F. (Thesis advisor) / Denardo, Dale F. (Committee member) / Dudley, Robert (Committee member) / Fewell, Jennifer H. (Committee member) / Arizona State University (Publisher)
Created2023