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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,

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
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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

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
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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

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
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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

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

Soiled: An Environmental Podcast is a six episode series that addresses common environmental topics and debunks myths that surround those topics.

ContributorsTurner, Natalie Ann (Co-author) / Kuta, Tiffany (Co-author) / Jones, Cassity (Co-author) / Boyer, Mackenzie (Thesis director) / Ward, Kristen (Committee member) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

For this Creative Project, I decided to explore the elements that set novellas apart from other genres and then experiment writing in the form. In doing so, I took into account three main categories: Plot Structure, Character Development, Style/Format, and then used my findings to write 45 pages of a

For this Creative Project, I decided to explore the elements that set novellas apart from other genres and then experiment writing in the form. In doing so, I took into account three main categories: Plot Structure, Character Development, Style/Format, and then used my findings to write 45 pages of a novella titled Emmy and Me.

ContributorsBingham, Roxanne Marie (Author) / Irish, Jennifer (Thesis director) / Danielson, Jonathan (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Filmmakers seek to create story pieces that are visually beautiful and engage the full attention of their audience. They typically abide by a 3-step process moving through pre-production, production, and post-production. Within each step, there are a series of tasks that need to be accomplished in order to reach the

Filmmakers seek to create story pieces that are visually beautiful and engage the full attention of their audience. They typically abide by a 3-step process moving through pre-production, production, and post-production. Within each step, there are a series of tasks that need to be accomplished in order to reach the completed film. A successful film requires careful planning and strategy in pre-production, timely and decisive execution in production, and minimal unforeseen retouching in post-production.<br/><br/>Even though filmmakers have continued to follow the same formula throughout the decades, the filmmaking process has remained largely inefficient. It is extremely common for pre-production planning to be undercut, for production filming to run far too long, and for post-production VFX and editing to send the project over budget. These instances can cause major issues as the project is being finalized. In many scenarios portions of the project need to be reshot, the box office revenue isn’t enough to make up for extensive VFX retouching, or the project may never even come to fruition. <br/><br/>The reason for this recurring theme of films being over budget and out of time is quite simply that technology has made filmmakers lazy. “Fix it in post” is a disgustingly common phrase used in the film industry. It describes the utter abuse of computer retouching in the post-production phase of filmmaking. Despite working in an industry that seeks to entertain the human eye, filmmakers have become blind to all of the small mistakes that could cost them hundreds of hours and millions of dollars in the long run.

ContributorsKlewicki, Tallee Jo (Author) / Shin, Dosun (Thesis director) / Eliciana, Nascimento (Committee member) / The Design School (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

My project is designed to provide art education to incarcerated youth in Arizona. This project will address two current issues in Arizona; the underfunding of art programs and high rates of incarceration. As of 2021, there are no state-funded art programs in Arizona. Arizona is tied with Texas for the

My project is designed to provide art education to incarcerated youth in Arizona. This project will address two current issues in Arizona; the underfunding of art programs and high rates of incarceration. As of 2021, there are no state-funded art programs in Arizona. Arizona is tied with Texas for the eighth highest rate of incarceration in the country. In Arizona, 750 out of every 100,000 people are incarcerated. This project is an art course for incarcerated youth. The project includes a packet detailing the course content and assignment details, a class syllabus, a course flyer, and a certificate of completion. The course is intended to be taught at the Adobe Mountain School facility. The course is designed so that it can be implemented in other facilities in the future. The class will be taught by volunteers with a background in studio art, design, or art education. Each student will receive a course packet that they can use to keep track of information and assignments. Instructors will use the course packet to teach the class. The course focuses on drawing with charcoal and oil pastel, which will build a foundation in drawing skills. The course covers a twelve-week semester. The course content packet includes a week-by-week breakdown of the teaching material and project descriptions. The course consists of two main projects and preparatory work. The preparatory work includes vocabulary terms, art concepts, drawing guides, brainstorming activities, and drawing activities. The two main prompts are designed for students to explore the materials and to encourage self-reflection. The class is curated so that students can create art in a low-risk, non-judgemental environment. The course will also focus on establishing problem-solving and critical thinking skills through engaging activities.

ContributorsSheppard, Eve (Author) / Cornelia, Wells (Thesis director) / Jennifer, Nelson (Committee member) / School of Art (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This paper explores the well-known Atkins Diet, as it also places a strong regulation on macromolecule consumption, specifically carbohydrates, in order to assist with the weight loss process. A review of available literature will be used to investigate: the history of the diet, necessity of macromolecule consumption, the impact this

This paper explores the well-known Atkins Diet, as it also places a strong regulation on macromolecule consumption, specifically carbohydrates, in order to assist with the weight loss process. A review of available literature will be used to investigate: the history of the diet, necessity of macromolecule consumption, the impact this has on the individual biochemical pathways (glycolysis/gluconeogenesis) and the microbiome as a whole, as well as overall success rates and long-term health complications/benefits. Additionally personal statements from various individuals who have experience with the diet, myself included, will be incorporated into a holistic analysis of the effectiveness and longevity of the Atkins weight-loss strategy.

ContributorsButler, Jessica Carol (Author) / Sellner, Erin (Thesis director) / Gray, Tiffany (Committee member) / College of Health Solutions (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Soiled: An Environmental Podcast is a six episode series where common environmental topics are discussed and misconceptions surrounding these topics are debunked.

ContributorsKuta, Tiffany T (Co-author) / Jones, Cassity (Co-author) / Turner, Natalie (Co-author) / Boyer, Mackenzie (Thesis director) / Ward, Kristen (Committee member) / Civil, Environmental and Sustainable Eng Program (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05