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Description
The elaborate signals of animals are often costly to produce and maintain, thus communicating reliable information about the quality of an individual to potential mates or competitors. The properties of the sensory systems that receive signals can drive the evolution of these signals and shape their form and function. However, relatively little is known about the ecological and physiological constraints that may influence the development and maintenance of sensory systems. In the house finch (Carpodacus mexicanus) and many other bird species, carotenoid pigments are used to create colorful sexually selected displays, and their expression is limited by health and dietary access to carotenoids. Carotenoids also accumulate in the avian retina, protecting it from photodamage and tuning color vision. Analogous to plumage carotenoid accumulation, I hypothesized that avian vision is subject to environmental and physiological constraints imposed by the acquisition and allocation of carotenoids. To test this hypothesis, I carried out a series of field and captive studies of the house finch to assess natural variation in and correlates of retinal carotenoid accumulation and to experimentally investigate the effects of dietary carotenoid availability, immune activation, and light exposure on retinal carotenoid accumulation. Moreover, through dietary manipulations of retinal carotenoid accumulation, I tested the impacts of carotenoid accumulation on visually mediated foraging and mate choice behaviors. My results indicate that avian retinal carotenoid accumulation is variable and significantly influenced by dietary carotenoid availability and immune system activity. Behavioral studies suggest that retinal carotenoid accumulation influences visual foraging performance and mediates a trade-off between color discrimination and photoreceptor sensitivity under dim-light conditions. Retinal accumulation did not influence female choice for male carotenoid-based coloration, indicating that a direct link between retinal accumulation and sexual selection for coloration is unlikely. However, retinal carotenoid accumulation in males was positively correlated with their plumage coloration. Thus, carotenoid-mediated visual health and performance or may be part of the information encoded in sexually selected coloration.
ContributorsToomey, Matthew (Author) / McGraw, Kevin J. (Thesis advisor) / Deviche, Pierre (Committee member) / Smith, Brian (Committee member) / Rutowski, Ronald (Committee member) / Verrelli, Brian (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.
ContributorsBarr, Daniel Alan (Author) / van der Vaart, Arjan (Thesis advisor) / Matyushov, Dmitry (Committee member) / Wolf, George (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
The most horrific, darkest, and powerful forms of the sublime take place inside the enclosure of the human psyche; the interior of the mind is the playground for the sublime--not the crag and canyon filled natural world. For Immanuel Kant and Edmund Burke, the driving force of the power of the sublime stems from the feelings of pain and fear: where is that more manifested than in the mind? Unlike the common, traditional, and overwhelmed discussion of Percy Shelley and his contemporaries and the power of the sublime in nature, I will argue that in The Cenci, Shelley, through well-chosen diction and precise composition of terrifying images, fashions characters and scenes in an emotion-driven play that elevates the mind of the reader to a transcendent sublime experience. Through a discussion of the theories of the aesthetic of the sublime laid out by Longinus, Burke, and Kant, I will provide a foundation for the later discussion of the rhetorical sublime evoked by Shelley in the ardent and horrifying play that is The Cenci. Looking at the conventional application of the theories of the sublime to romantic writing will make evident the holes in the discussion of the sublime and romantic writings that have almost forgotten the powerful and psychological rhetorical aspect of the sublime that is emphasized in the theoretical writings of both Burke and Kant. To clarify what is traditionally associated with Shelley and the sublime, a brief analysis of the Shelleyean sublime and Shelley's 1816 poem "Mont Blanc" will prepare the reader for an unconventional, but every bit important and powerful, function of the sublime in the 1819 play The Cenci based on the horrific happenings of a historical 16th century Italian noble family.
ContributorsGowan, Kaitlin (Author) / Lussier, Mark (Thesis advisor) / Corse, Douglas Taylor (Committee member) / Broglio, Ronald (Committee member) / Arizona State University (Publisher)
Created2011
Description
A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.
ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the 1970s James Watson recognized the inability of conventional DNA replication machinery to replicate the extreme termini of chromosomes known as telomeres. This inability is due to the requirement of a building block primer and was termed the end replication problem. Telomerase is nature's answer to the end replication problem. Telomerase is a ribonucleoprotein which extends telomeres through reverse transcriptase activity by reiteratively copying a short intrinsic RNA sequence to generate 3' telomeric extensions. Telomeres protect chromosomes from erosion of coding genes during replication, as well as differentiate native chromosome ends from double stranded breaks. However, controlled erosion of telomeres functions as a naturally occurring molecular clock limiting the replicative capacity of cells. Telomerase is over activated in many cancers, while inactivation leads to multiple lifespan limiting human diseases. In order to further study the interaction between telomerase RNA (TR) and telomerase reverse transcriptase protein (TERT), vertebrate TERT fragments were screened for solubility and purity following bacterial expression. Soluble fragments of medaka TERT including the RNA binding domain (TRBD) were identified. Recombinant medaka TRBD binds specifically to telomerase RNA CR4/CR5 region. Ribonucleotide and amino acid pairs in close proximity within the medaka telomerase RNA-protein complex were identified using photo-activated cross-linking in conjunction with mass spectrometry. The identified cross-linking amino acids were mapped on known crystal structures of TERTs to reveal the RNA interaction interface of TRBD. The identification of this RNA TERT interaction interface furthers the understanding of the telomerase complex at a molecular level and could be used for the targeted interruption of the telomerase complex as a potential cancer treatment.
ContributorsBley, Christopher James (Author) / Chen, Julian (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the first thirty years of the XX century, an old literary visual tradition was reborn in a series of new striking visual texts better known as calligrams. They were produced by some avant-garde poets such as Vicente Huidobro, José Juan Tablada, Alberto Hidalgo and Carlos Oquendo de Amat in Latin America, and Juan Larrea, Guillermo de Torre, Francisco Vighi, Luis Mosquera, and others in Spain. However, with few exceptions, the interpretation of those written drawings has caught little attention from literary critics. This research, contrasted to that of Willard Bohn's, is a contribution to the deciphering of such literary art form, designated here as the figurative visual poem. It is a proposal for its visual reading which draws from the fact that this type of text is concretely a drawing formed by written verses. As such, it can be regarded as a plastic writing, combining pictorial and verbal signs in one perceptible configuration on the page. The result of this semiotic operation is a hybrid product in which the iconic forms become symbolic and vice versa. It is in fact, an art object which should be approached as a text that can be seen as well as read. The study leads to the conclusion that Willard Bohn misreads the order in which language and image are articulated in the visual poem identified with the second order semiological system proposed by Roland Barthes, placing preeminence on language over image. This results in reading the avant-garde visual figurative poem in an ekphrastic fashion. Consequently, the role of the image in the system is left in an ambiguous realm at the time of deciphering this hybrid text. Our contribution to re-conducting this undertaking has been equally drawn from a semiotic stance taken from Louis Hjemslev that balances language and image as correlates of a semiotic function. Due to the signaling nature of both, language and figure, a visual poem becomes an iconic metaphor as well as a metaphoric icon, and moreover a self-referential sign, thus justifying its status of an autonomous art.
ContributorsSuarez, Nelson M (Author) / Acereda, Alberto (Thesis advisor) / Volek, Emil (Committee member) / Garcia-Fernandez, Carlos J (Committee member) / Arizona State University (Publisher)
Created2011
Description
The hagiographic comedy written by Tirso de Molina Los lagos de San Vicente (1607) presents the journey of Santa Casilda in search of the cure of an illness in her blood that affects her. Casilda rejects the medical assistance offered to her by Muslim doctors and miraculously she finds the cure in the Christian world. In this quest, the intellectual and theological evolution of the future saint in defense of the Christian faith is presented. This dissertation will study the resources that Tirso de Molina employs to show the rejection and displacement against the Islamic world represented by a series of erotic behaviors that, in the effort of dramatizing these impertinences they are characterized within a second discourse. Tirso de Molina takes advantage of the hagiographic comedy's discourse nature and the baroque's obscure literary characteristics to express his messages. This dissertation will study in detail how the combination of hagiographic theatrical elements with linguistic expressions are used to convey a subversive discourse that therefore suggests the application of queer theory as a frame of reference. As a result of this investigation it is concluded that Tirso de Molina promotes the hagiographic model and in order to contrast the triumph of the moral Catholic world over the immoral Muslim world the play writer makes references to the nefarious sin.
ContributorsMurphy, Anayanci (Author) / Foster, David William (Thesis advisor) / Sanchez, Angel (Committee member) / Acereda, Alberto (Committee member) / Urioste-Azcorra, Carmen (Committee member) / Volek, Emil (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT As referenced in Navajo ceremonial prayers and songs, "Saad bee hahoozhood jini," it began harmoniously with language. This dissertation examines and celebrates in new ways the meaning of language in Navajo literature. The first chapter is an introduction of this dissertation. I share my personal experiences with language, both English and Navajo, and how it has shaped me to be the person I am today as a Navajo speaker, student, educator, and professional. The second chapter contains an analysis and review of Western ideology of feminism and its place in Navajo society and a comparative study of several works written by Navajo authors, including Laura Tohe, Luci Tapahonso, and Nia Francisco, and how their creative works reflect the foundation of Navajo culture, Asdzaa Nadleehe, Changing Woman. The third chapter presents my own short fiction of Navajo characters living in today's society, a society that entails both positive and negative issues of Navajo life. These stories present realistic twenty-first century environments on the Navajo reservation. The fourth chapter consists of a short fiction written originally in the Navajo language. The story also represents the celebration of Navajo language as it thrives in today's time of tribal and cultural struggles. The sense of it being told in Navajo celebrates and preserves Navajo culture and language. The final chapter is the beginning of an oral narrative presented in written form, that of my grandmother's life story. This introduction of her story also is in itself a commemoration of language, oral Navajo language.
ContributorsWheeler, Jennifer L (Author) / Ortiz, Simon (Thesis advisor) / Tohe, Laura (Committee member) / Blasingame, James (Committee member) / Arizona State University (Publisher)
Created2011
Description
For my project, I delve into the relationships of Victor and the Monster as well as the relationships Victor shares with other characters that were underdeveloped within the original novel by Mary Shelley in the novel Franeknstein. I examine their relationships in two components. The first through my own interpretation of Victor and the Monster’s relationship within a creative writing piece that extends the novel as if Victor had lived rather than died in the arctic in order to explore the possibilities of a more complex set of relationships between Victor and the Monster than simply creator-creation. My writing focuses on the development of their relationship once all they have left is each other. The second part of my project focuses on an analytical component. I analyze and cite the reasoning for my creative take on Victor and the Monster as well as their relationship within the novel and Mary Shelley’s intentions.
ContributorsHodge Smith, Elizabeth Ann (Author) / Fette, Don (Thesis director) / Hoyt, Heather (Committee member) / Historical, Philosophical & Religious Studies (Contributor, Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
In this essay, I set out to explore and analyze how Shirley Jackson’s The Haunting of Hill House, and the character of Eleanor Vance in particular, disrupts and redefines the traditional conventions of the Female Gothic within the context of the 20th century. I utilize Tania Modleski's gendering of Freud's theory of psychoanalysis in her exploration of the ‘Female Uncanny,’ arguing that the source of the Uncanny in the Female Gothic can be found in the "fear of being lost in the mother." I argue that Jackson's complex personal life, including her fraught relationship with her mother and her difficult marriage with literary critic Edgar Hyman, color her fiction and the primary motivations of her protagonist, Eleanor Vance. I also outline the traditional structure of the Gothic novel and the heroine's journey. With the necessary context provided, I then explain how Eleanor Vance’s character rejects these Gothic traditions and ushers in a new era of Female Gothic fiction.
ContributorsAlcantar, Sarah (Author) / Fette, Donald (Thesis director) / Zarka, Emily (Committee member) / Department of Management and Entrepreneurship (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05