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A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai)

A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai) species proceeded by an analysis of if and how the ESA should apply to the Sonoran population. Analysis of current plans and interagency cooperations followed by a multi-step proposal on how best to conserve the Sonoran population of Desert tortoise.
ContributorsKulik, Elise Chikako (Author) / Kusumi, Kenro (Thesis director) / Tollis, Marc (Committee member) / Wilson Sayres, Melissa (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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The modern tetraploid species Gossypium barbadense L. (AD2) traces its origins to an allopolyploidy event between diploid progenitors G. raimondii (DT Genome, Americas) and G. herbaceum (AT Genome, Asia/Africa). In this study, nine fiber-related genes consisting of seven MYB transcription factors, a cellulose synthase homolog, and a tubulin homolog were

The modern tetraploid species Gossypium barbadense L. (AD2) traces its origins to an allopolyploidy event between diploid progenitors G. raimondii (DT Genome, Americas) and G. herbaceum (AT Genome, Asia/Africa). In this study, nine fiber-related genes consisting of seven MYB transcription factors, a cellulose synthase homolog, and a tubulin homolog were resequenced across 54 G. barbadense lines spanning the wild-to-domesticated spectrum. Tests for nucleotide diversity (π), linkage disequilibrium (LD), and Tajima’s D were performed to examine the extent to which evolutionary forces have acted on these nine loci in G. barbadense. Results indicated that the AT-genome loci had significantly higher levels of diversity and lower levels of LD relative to homoelogous loci from the DT-genome. Additionally, all loci showed signatures of a population size expansion after a bottleneck or selective sweep and/or purifying selection. As previously shown for a sister tetraploid taxa (G. hirsutum), gene conversion resulting from a DT-genome allele invasion into the AT-genome likely explains the higher levels of diversity and lower levels of intragenic LD in the AT-genome. Given the relatively very low level of genetic diversity in elite lines, introduction of novel alleles from wild, land race, or obsolete lines into modern Pima cotton breeding programs is needed to expand the narrow gene pool of G. barbadense for continual yield improvements.
ContributorsNadon, Brian Davis (Author) / Gaxiola, Roberto (Thesis director) / Kusumi, Kenro (Committee member) / Dyer, John (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
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The ringtail (Bassariscus astutus), a member of the Procyonidae, is capable of 180 degrees of hindlimb reversal during headfirst descent down a vertical substrate. The goal of this study was to determine the presence or absence of myological adaptations related to hindlimb reversal in the ringtail. Data for B. astutus

The ringtail (Bassariscus astutus), a member of the Procyonidae, is capable of 180 degrees of hindlimb reversal during headfirst descent down a vertical substrate. The goal of this study was to determine the presence or absence of myological adaptations related to hindlimb reversal in the ringtail. Data for B. astutus are presented, including muscle weights and muscle maps ascertained from the dissection of four hindlimbs. Data from the current study were compared to published accounts of other species capable of hindlimb reversal, including procyonids (raccoon, coati, kinkajou, olingo), a mustelid (marten), palm civet, mongoose, tree squirrel, common tree shrew, and slow loris. Muscle mass data from this study demonstrate that the hip adductors of scansorial mammals are significantly more robust than those of terrestrial mammals, indicating a myological adaptation for climbing, but not necessarily hindlimb reversal. Among hindlimb reversers, the majority exhibit one belly of m. sartorius, the presence of m. extensor digiti I longus, and a fibular origin for m. fibularis longus. These characteristics indicate an emphasis on hip extension, ankle plantarflexion, and pes inversion. However, these characteristics are more likely due to phylogeny than hindlimb reversal because of their presence in closely-related non-reversers. Additional data on families outside of Carnivora may help determine if these myological traits are indeed due to phylogeny. Other myological data, such as moment arms and cross sectional areas, may provide evidence of adaptations for hindlimb reversal.
ContributorsLiu, Margaret Chuan (Author) / Fisher, Rebecca (Thesis director) / Hinrichs, Richard (Committee member) / Kusumi, Kenro (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
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While a number of vertebrates, including fishes, salamanders, frogs, and lizards, display regenerative capacity, the process is not necessarily the same. It has been proposed that regeneration, while evolutionarily conserved, has diverged during evolution. However, the extent to which the mechanisms of regeneration have changed between taxa still remains elusive.

While a number of vertebrates, including fishes, salamanders, frogs, and lizards, display regenerative capacity, the process is not necessarily the same. It has been proposed that regeneration, while evolutionarily conserved, has diverged during evolution. However, the extent to which the mechanisms of regeneration have changed between taxa still remains elusive. In the salamander limb, cells dedifferentiate to a more plastic state and aggregate in the distal portion of the appendage to form a blastema, which is responsible for outgrowth and tissue development. In contrast, no such mechanism has been identified in lizards, and it is unclear to what extent evolutionary divergence between amniotes and anamniotes has altered this mechanism. Anolis carolinensis lizards are capable of regenerating their tails after stress-induced autotomy or self-amputation. In this investigation, the distribution of proliferating cells in early A. carolinensis tail regeneration was visualized by immunohistochemistry to examine the location and quantity of proliferating cells. An aggregate of proliferating cells at the distal region of the regenerate is considered indicative of blastema formation. Proliferating cell nuclear antigen (PCNA) and minichromosome maintenance complex component 2 (MCM2) were utilized as proliferation markers. Positive cells were counted for each tail (n=9, n=8 respectively). The percent of proliferating cells at the tip and base of the regenerating tail were compared with a one-way ANOVA statistical test. Both markers showed no significant difference (P=0.585, P=0.603 respectively) indicating absence of a blastema-like structure. These results suggest an alternative mechanism of regeneration in lizards and potentially other amniotes.
ContributorsTokuyama, Minami Adrianne (Author) / Kusumi, Kenro (Thesis director) / Wilson-Rawls, Jeanne (Committee member) / Menke, Douglas (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
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Description
Anole lizards that inhabit the islands and mainland of the Caribbean basin have evolved morphological traits adapted to the microhabitat that they occupy. The anoles on these islands have been characterized as "ecomorphs" or morphologically and behaviorally-adapted groups, including: crown-giant, trunk-crown, trunk, grass-bush, twig, and trunk-ground. Ecomorphs display morphological features

Anole lizards that inhabit the islands and mainland of the Caribbean basin have evolved morphological traits adapted to the microhabitat that they occupy. The anoles on these islands have been characterized as "ecomorphs" or morphologically and behaviorally-adapted groups, including: crown-giant, trunk-crown, trunk, grass-bush, twig, and trunk-ground. Ecomorphs display morphological features that are specifically adapted to the habitat that the anole occupies. One key morphological difference is tail length. While the anoles Anolis carolinensis and A. sagrei have similar ratios of tail length versus snout-to-vent length (SVL), they occupy different microhabitats. Specifically, A. carolinensis inhabits trunk-crown habitats while A. sagrei is found in trunk-ground regions. In this study, I focused on analysis of the caudal vertebrae of these two species, to determine if the structure of the osteological elements reflected differences in microhabitat adaptation. Skeletal preparations reveal that A. carolinensis have 40 \u2014 46 caudal vertebrae, and A. sagrei have 38 \u2014 49 caudal vertebrae. Transverse processes are present in Ca1-8 in A. carolinensis whereas transverse processes in A. sagrei span from Ca1-42 vertebrae. Ca6\u201440 have autotomy planes in A. sagrei, whereas only Ca8\u201417 have autotomy planes in A. carolinensis. These findings indicate that A. carolinensis are limited in the ability to autotomize their tail compared to A. sagrei. A. carolinensis, living higher in the trees than A. sagrei, might incur a greater impairment of locomotor function if autotomized. There appears to be no differences between males and females of both species in respect to vertebrae lengths. Differences between A. carolinensis and A. sagrei in terms of vertebral length are found in Ca12-15, 29-30, 34, and 37. The finding indicates that almost all caudal vertebrae between A. carolinensis and A. sagrei have similar relative lengths, but seven vertebrae have statistically significant differences. The biological significance of the findings is not clear, but functional and myological studies may help elucidate the reason of the observed differences.
ContributorsLasku, Eris (Author) / Kusumi, Kenro (Thesis director) / Fisher, Rebecca (Committee member) / Hsieh, Tonia (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2013-05
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While there is extensive information available about organizations that receive donated organs for transplant, much less is known about those that accept tissue and whole bodies for medical education and research. Throughout the United States, nontransplant anatomical donation organizations exist within an ambiguous sector of the donation industry, unencumbered by

While there is extensive information available about organizations that receive donated organs for transplant, much less is known about those that accept tissue and whole bodies for medical education and research. Throughout the United States, nontransplant anatomical donation organizations exist within an ambiguous sector of the donation industry, unencumbered by federal regulations. Although these companies adhere to the Uniform Anatomical Gift Act, the lack of a single entity responsible for overseeing their operations has led to public skepticism and animosity among competing businesses. Legislation has the potential to legitimize the industry. For it to be successful, however, the intricacies of a complex market that deals directly with the movement of human remains and intangible issues of human integrity and morality, must be thoroughly understood.
ContributorsGlynn, Emily Sanders (Author) / Brian, Jennifer (Thesis director) / Fisher, Rebecca (Committee member) / Barrett, The Honors College (Contributor) / School of Nutrition and Health Promotion (Contributor) / Department of English (Contributor)
Created2015-05
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Description

Chapter 1: Functional Specialization and Arm Length in Octopus bimaculoides<br/>Although studies are limited, there is some evidence that octopuses use their arms for specialized functions. For example, in Octopus maya and O. vulgaris, the anterior arms are utilized more frequently for grasping and exploring (Lee, 1992; Byrne et al., 2006a),

Chapter 1: Functional Specialization and Arm Length in Octopus bimaculoides<br/>Although studies are limited, there is some evidence that octopuses use their arms for specialized functions. For example, in Octopus maya and O. vulgaris, the anterior arms are utilized more frequently for grasping and exploring (Lee, 1992; Byrne et al., 2006a), while posterior arms are more frequently utilized for crawling in O. vulgaris (Levy et al., 2015). In addition, O. vulgaris uses favored arms when retrieving food and making contact with a T-maze as dictated by their lateralized vision (Byrne, 2006b). O. vulgaris also demonstrates a preference for anterior arms when retrieving food from a Y-maze (Gutnick et. al. 2020). In Octopus bimaculoides bending and elongation were more frequent in anterior arms than posterior arms during reaching and grasping tasks, and right arms displayed deformation more frequently than left arms, with the exception of the hectocotylus (R3) in males (Kennedy et. al. 2020). Given these observed functional differences, the goal of this study was to determine if morphological differences exist between different octopus arm identities, coded as L1-L4 and R1-R4. In particular, the relationship between arm length and arm identity was analyzed statistically. The dataset included 111 intact arms from 22 wild-caught specimens of O. bimaculoides (11 male and 11 female). Simple linear regressions and an analysis of covariance were performed to test the relationship between arm length and a number of factors, including body mass, sex, anterior versus posterior location, and left versus the right side. Mass had a significant linear relationship with arm length and a one-way ANOVA demonstrated that arm identity is significantly correlated with arm length. Moreover, an analysis of covariance demonstrated that independent of mass, arm identity has a significant linear relationship with arm length. Despite an overall appearance of bilateral symmetry, arms of different identities do not have statistically equivalent lengths in O. bimaculoides. Furthermore, differences in arm length do not appear to be related to sex, anterior versus posterior location, or left or right side. These results call into question the existing practice of treating all arms as equivalent by either using a single-arm measurement as representative of all eight or calculating an average length and suggest that morphological analyses of specific arm identities may be more informative.<br/><br/>Chapter 2: Predicting and Analyzing Octopus bimaculoides Sensitivity to Global Anesthetic<br/>Although global anesthetic is widely used in human and veterinary medicine the mechanism and impact of global anesthetic is relatively poorly comprehended, even in well-studied mammalian models. Invertebrate anesthetic is even less understood. In order to evaluate factors that impact anesthetic effectiveness analyses were conducted on 22 wild-caught specimens of Octopus bimaculoides during 72 anesthetic events.Three machine learning models: regression tree, random forest, and generalized additive model were utilized to make predictions of the concentration of anesthetic (percent ethanol by volume) from 11 features and to determine feature importance in making those predictions. The fit of each model was analyzed on three criteria: correlation coefficient, mean squared error, and relative error. Feature importance was determined in a model-specific manner. Predictions from the best performing model, random forest, have a .82 correlation coefficient with experimental values. Feature importance suggests that temperature on arrival and cohabitation factors strongly influence predictions for anesthesia concentration. This likely indicates the transportation process was incurring stress on the animals and that cohabitation was also stressful for the typically solitary O. bimaculoides. This long-term stress could lead to a decline in the animal’s well-being and a lower necessary ethanol concentration (Horvath et al., 2013). This analysis provides information to improve the care of octopus in laboratory settings and furthers the understanding of the effects of global anesthetic in invertebrates, particularly one with a distributed nervous system.

ContributorsSorge, Marieke Alexandria (Author) / Fisher, Rebecca (Thesis director) / Zhao, Yunpeng (Committee member) / Marvi, Hamid (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Tremendous phenotypic variation exists across people with Turner syndrome (45,X). This variation likely stems from differential dosage of genes on the X chromosome. X-inactivation is the process whereby all X chromosomes in excess of one are silenced. However, about 15% of the genes on the silenced X chromosome escape this

Tremendous phenotypic variation exists across people with Turner syndrome (45,X). This variation likely stems from differential dosage of genes on the X chromosome. X-inactivation is the process whereby all X chromosomes in excess of one are silenced. However, about 15% of the genes on the silenced X chromosome escape this inactivation and are candidates for affecting phenotype in people with Turner syndrome. In this study we take an evolutionary approach to rank candidate genes that may contribute to phenotypic variation among people with Turner Syndrome. We incorporate analysis of patterns of DNA methylation from 46,XX and 45,X individuals, and estimates of variable X-inactivation status across 46,XX individuals, with patterns of gene expression conservation on the X chromosomes across five tissues and ten species. We find that genes that escape XCI are possible candidate genes for Turner syndrome phenotype, indicated by the constant levels of expression in escape genes and inactivated genes. Variation in these genes is expected to affect phenotype when dosage is altered from typical levels.
ContributorsSchaffer, Kara Nina (Author) / Wilson Sayres, Melissa (Thesis director) / Crook, Sharon (Committee member) / Narang, Pooja (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
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Electrical stimulation can be used to activate peripheral nerve fibers to restore sensation to individuals with amputation and the technique is also being investigated as a means of treating a wide range of diseases. Longitudinal intrafascicular electrodes (LIFEs) are one of several types of electrodes that have been used

Electrical stimulation can be used to activate peripheral nerve fibers to restore sensation to individuals with amputation and the technique is also being investigated as a means of treating a wide range of diseases. Longitudinal intrafascicular electrodes (LIFEs) are one of several types of electrodes that have been used to activate peripheral nerves. LIFEs can be used to activate small groups of fibers within a peripheral nerve fascicle, but the degree of their selectivity is uncertain. To investigate the effects of intrafascicular stimulation on nerve fiber activation, a mathematical, conductance-based model of an axon drawn from the literature was implemented and used to simulate the firing response of sensory nerve fibers in the presence of an applied monopolar electric field. Several axons were simulated to represent axons of different size, conductivity, spatial composition and location with respect to the electrode. Electric field profiles produced by pulses of different pulse widths and pulse amplitudes were created. Each fiber was placed within each resulting electric field and the firing threshold was determined. The effects of changes in pulse width, pulse amplitude, and distance on firing patterns were shown; all of these results were consistent with published experimental findings. The models showed lower firing threshold for smaller fibers than larger fibers and for fibers that were farther from the stimulating electrode than those that were closer. Firing threshold was also lower for stimuli of greater pulse width. Analysis of axon recruitment upon increases in pulse amplitude showed that the effects of fiber distance may be more pronounced than the effects of fiber size. This model can serve as a basis for further development to more accurately represent the effects of LIFEs and eventually may assist in the design of stimulation paradigms and waveforms to improve selectivity of axon activation when using LIFEs.
ContributorsSira, Alarmel (Author) / Abbas, James (Thesis director) / Crook, Sharon (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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New genomic resources allow for the investigation of gene family diversity in genome-enabled reptiles. The Toll-like Receptor (TLR) gene family recognizes pathogen-associated molecular patterns (PAMPs) and coevolves with environmental pathogens which makes it a strong candidate for looking at the interplay between gene family diversification and host-pathogen coevolution. Using a

New genomic resources allow for the investigation of gene family diversity in genome-enabled reptiles. The Toll-like Receptor (TLR) gene family recognizes pathogen-associated molecular patterns (PAMPs) and coevolves with environmental pathogens which makes it a strong candidate for looking at the interplay between gene family diversification and host-pathogen coevolution. Using a new orthology curation pipeline and phylogenetic reconstruction, a novel gene expansion event of TLR8 was identified to be exclusive to crocodilians and chelonians with species-specific pseudogenization events. A new gene, TLR21-like, was identified as a part of the TLR11 subfamily. These findings uncover reptile-specific gene family evolution and provide indications of the role of habitat in this process.
ContributorsMorales, Matheo (Author) / Kusumi, Kenro (Thesis director) / Dolby, Greer (Committee member) / Scott, Peter (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05