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- Creators: Barrett, The Honors College
- Creators: School of Politics and Global Studies
Description
ABSTRACT Whole genome sequencing (WGS) and whole exome sequencing (WES) are two comprehensive genomic tests which use next-generation sequencing technology to sequence most of the 3.2 billion base pairs in a human genome (WGS) or many of the estimated 22,000 protein-coding genes in the genome (WES). The promises offered from WGS/WES are: to identify suspected yet unidentified genetic diseases, to characterize the genomic mutations in a tumor to identify targeted therapeutic agents and, to predict future diseases with the hope of promoting disease prevention strategies and/or offering early treatment. Promises notwithstanding, sequencing a human genome presents several interrelated challenges: how to adequately analyze, interpret, store, reanalyze and apply an unprecedented amount of genomic data (with uncertain clinical utility) to patient care? In addition, genomic data has the potential to become integral for improving the medical care of an individual and their family, years after a genome is sequenced. Current informed consent protocols do not adequately address the unique challenges and complexities inherent to the process of WGS/WES. This dissertation constructs a novel informed consent process for individuals considering WGS/WES, capable of fulfilling both legal and ethical requirements of medical consent while addressing the intricacies of WGS/WES, ultimately resulting in a more effective consenting experience. To better understand components of an effective consenting experience, the first part of this dissertation traces the historical origin of the informed consent process to identify the motivations, rationales and institutional commitments that sustain our current consenting protocols for genetic testing. After understanding the underlying commitments that shape our current informed consent protocols, I discuss the effectiveness of the informed consent process from an ethical and legal standpoint. I illustrate how WGS/WES introduces new complexities to the informed consent process and assess whether informed consent protocols proposed for WGS/WES address these complexities. The last section of this dissertation describes a novel informed consent process for WGS/WES, constructed from the original ethical intent of informed consent, analysis of existing informed consent protocols, and my own observations as a genetic counselor for what constitutes an effective consenting experience.
ContributorsHunt, Katherine (Author) / Hurlbut, J. Benjamin (Thesis advisor) / Robert, Jason S. (Thesis advisor) / Maienschein, Jane (Committee member) / Northfelt, Donald W. (Committee member) / Marchant, Gary (Committee member) / Ellison, Karin (Committee member) / Arizona State University (Publisher)
Created2013
Description
The original mediums were not texts or technologies; they were ritual actors performing acts of mediumship. Mediating between determined norms (the status quo) and emergent trends (change), they invoked divine authority to conjure meanings that proved adaptive, nonadaptive and/or maladaptive. With the advent of the written word, ritual became formalized and codified. The medium became a communication device, something abstract and external to the human condition. It then became possible to speak of "media effects" imposing influence in a logical deterministic manner. Yet with the advent of new media, we are witnessing a return to modes of cultural discourse that are spontaneous, interactive, communal and unscripted, all hallmarks of ritual action. This "ritual return" centers on the emergence of the "prosumer" (producer/consumer), a figure actively engaged in mediating practices. While resembling the original archaic "medium" in some respects, the prosumer is a "literate ritualist" allied with a multiplicity of cultural tribes. Thus the "new media" has given rise to "the new medium." The pages that follow focus on acts of contemporary mediumship, examining related concepts such as "ecology," "niche," "role," "affordance," and "trope." Each section considers how specific mediating practices afford and constrain modes of ritualized behavior. I call this practice-oriented approach to media studies "praxism."
ContributorsGyori, Bradford (Author) / Goggin, Maureen (Thesis advisor) / Baker, Aaron (Committee member) / Hjorleifur Jonsson (Committee member) / Arizona State University (Publisher)
Created2011
Description
Aside from uplifting and tearing down the mood of a young LGBTQ+ kid, journalistic media has the potential to alter the way audiences understand and react to individuals of the LGBTQ+ community. Looking at the rhetorical approaches, frameworks, and expanded narratives of news sources, this project engages with the concepts of same-sex marriage, lifestyles, bans, and children in education in order to attain an understanding of what media messages are being shared, how they are being communicated, and what the implications of such rhetoric are. Summary of the findings:
• Same-sex marriage as the win that cannot be repeated.
Infamously known as the central legal battle for the LGBTQ+ community, same-sex marriage finds itself in many political speeches, campaigns, and social commentaries. Interestingly, after being legalized through a Supreme Court decision in the United States, Same-Sex Marriage finds itself framed as the social inevitability that should not be repeated in politics or any legal shift. In other words, “the gays have won this battle, but not the war.”
• There are risks around the “LGBTQ+ lifestyle” and its careful catering to an elite minority and the mediation through bans.
The risks of the LGBTQ+ “lifestyle” date back far, with many connotations being attached to being LGBTQ+ (AIDS epidemics, etc.). In modern journalism, many media outlets portray LGBTQ+ individuals to be a tiny minority (.001% according to some) that demands the whole society to adhere to their requests. This framework portrays the LGBTQ+ community as oppressors and obsessed advocates that can never “seem to get enough” (ex: more than just marriage). The bans are framed as the neutralizing factor to the catering.
• LGBTQ+ children and topics in academic and social spaces are the extreme degree.
When it comes to LGBTQ+ issues and conversations as they revolve around children, media outlets have some of the most passionate opinions about them. Often portrayed as “the line that shouldn’t be crossed,” LGBTQ+ issues, as they find themselves in schools and other spaces, are thus portrayed as bearable to a certain degree, never completely. Claims of indoctrination are also presented prominently even when institutional efforts are to protect LGBTQ+ kids.
• Same-sex marriage as the win that cannot be repeated.
Infamously known as the central legal battle for the LGBTQ+ community, same-sex marriage finds itself in many political speeches, campaigns, and social commentaries. Interestingly, after being legalized through a Supreme Court decision in the United States, Same-Sex Marriage finds itself framed as the social inevitability that should not be repeated in politics or any legal shift. In other words, “the gays have won this battle, but not the war.”
• There are risks around the “LGBTQ+ lifestyle” and its careful catering to an elite minority and the mediation through bans.
The risks of the LGBTQ+ “lifestyle” date back far, with many connotations being attached to being LGBTQ+ (AIDS epidemics, etc.). In modern journalism, many media outlets portray LGBTQ+ individuals to be a tiny minority (.001% according to some) that demands the whole society to adhere to their requests. This framework portrays the LGBTQ+ community as oppressors and obsessed advocates that can never “seem to get enough” (ex: more than just marriage). The bans are framed as the neutralizing factor to the catering.
• LGBTQ+ children and topics in academic and social spaces are the extreme degree.
When it comes to LGBTQ+ issues and conversations as they revolve around children, media outlets have some of the most passionate opinions about them. Often portrayed as “the line that shouldn’t be crossed,” LGBTQ+ issues, as they find themselves in schools and other spaces, are thus portrayed as bearable to a certain degree, never completely. Claims of indoctrination are also presented prominently even when institutional efforts are to protect LGBTQ+ kids.
ContributorsNieto Calderon, Ramon Antonio (Author) / Himberg, Julia (Thesis director) / Sturges, Robert (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
22q11.2 Deletion Syndrome (22q11.2DS) is one of the most frequent chromosomal microdeletion syndromes in humans. This case study focuses on the language and reading profile of a female adult with 22q11.2 Deletion Syndrome who was undiagnosed until the age of 27 years old. To comprehensively describe the participant's profile, a series of assessment measures was administered in the speech, language, cognition, reading, and motor domains. Understanding how 22q11.2DS has impacted the life of a recently diagnosed adult will provide insight into how to best facilitate long-term language and educational support for this population and inform future research.
ContributorsPhilp, Jennifer Lynn (Author) / Scherer, Nancy (Thesis director) / Peter, Beate (Committee member) / Department of Speech and Hearing Science (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
President Donald Trump announced his candidacy in June 2015, and the America immediately knew that he was an unorthodox candidate. Early on in his campaign, Trump isolated groups of people and treated them as enemies, but none so consistently as the news media. What began as criticism of "fake news," turned into calling the news media "the opposition party." However, media professionals agree that when the Trump administration called the news media the "enemy of the American people" \u2014 a line had been crossed. In the last two years Trump has denied simple fact and credible journalism countless times. His avid use of social media allows his messages to reach millions of people in moments - which had the potential to be a positive thing. However, Twitter is often where Trump turns to dispute the media, science, fact or anything else that "opposes" him. If Americans cannot believe the news media, cannot believe science, and cannot believe established fact, what can they believe? Allowing one man, in this case, Trump, to become the beacon of truth is dangerous and destructive to democracy. The news media must do their best to recapture the trust and faith of the American people by producing good, honest journalism. Seasoned journalism professionals say that his attacks on the media are likely a facade, just another way to appeal to his base, but that those attacks have the potential to wreak havoc in American society. Regardless of Trump's intentions, the toxicity between him and news media could have consequences that reach far beyond his presidency.
ContributorsPenningroth, Kendra Rene (Author) / Crane, Steve (Thesis director) / Downie, Leonard (Committee member) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / School of Criminology and Criminal Justice (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
There are problems in the breeding practices of miniature horses. This study seeks to determine the source of these detrimental outcomes based on an evaluation of primary attributes selected for by breeders and the lack of genetic information and understanding of these attributes. In order to do this a program model was created to test the effects of selection criteria on breeder behavior and the resultant foals of these crosses. Moving forwards this program will evolve into a database of the equine genome for different horses. This will allow breeders to input their horses and do faux crosses in order to decrease the incidence of negative and detrimental outcomes.
ContributorsDavis, Marissa Lynn (Author) / Oberle, Eric (Thesis director) / Martin, Thomas (Committee member) / College of Letters and Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
This study focused on the connection between the EnvZ/OmpR two-component regulatory system and the iron homeostasis system in Escherichia coli, specifically how a mutant form of EnvZ11/OmpR is able to reduce the expression of fepA::lacZ, a reporter gene fusion in E. coli. FepA is one of several outer membrane siderophore receptors that allow extracellular siderophores bound to iron to enter the cells to power various biological processes. Previous studies have shown that in E. coli cells that expressed a mutant allele of envZ, called envZ11, which led to altered expression of various iron genes including down regulation of fepA::lacZ. The wild type EnvZ/OmpR system is not considered to regulate iron genes, but because these envz11 strains had downregulated fepA::lacZ, this study was undertaken to understand the connection and mechanisms of this downregulation. A large number of Lac+ revertants were obtained from the B32-2483 strain (envz11 and fepA::lacZ) and 7 Lac+ revertants that had reversion mutations not directly correcting the envZ11 allele were further characterized. With P1 phage transduction genetic mapping that involved moving a kanamycin resistance marker linked to fepA::lacZ, two Lac+ revertants were found to have their reversion mutations in the fepA promoter region, while the other five revertants had their mutations mapping outside the fepA region. These two revertants underwent DNA sequencing and found to carry two different single base pair mutations in two different locations of the fepA promoter region. Each one is in the Fur repressor binding region, but one also may have affected the Shine-Dalgarno region involved in translation initiation. All 7 reveratants underwent beta-galactosidase assays to measure fepA::lacZ expression. The two revertants that had mutations in the fepA promoter region had significantly increased fepA activity, with the revertant with the Shine-Dalgarno mutation having the most elevated fepA expression. The other 5 revertants that did not map in the fepA region had fepA expression elevated to the same level as that found in the wild type EnvZ/OmpR background. The data suggest that the negative effect of envZ11 can be overcome by multiple mechanisms, including directly correcting the envZ11 allele or changing the fepA promoter region.
ContributorsKalinkin, Victor Arkady (Co-author) / Misra, Rajeev (Co-author, Thesis director) / Mason, Hugh (Committee member) / Foy, Joseph (Committee member) / Biomedical Informatics Program (Contributor) / School of Life Sciences (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Mammary gland development in humans during puberty involves the enlargement of breast tissue, but this is not true in non-human primates. To identify potential causes of this difference, I examined variation in substitution rates across genes related to mammary development. Genes undergoing purifying selection show slower-than-average substitution rates, while genes undergoing positive selection show faster rates. These may be related to the difference between humans and other primates. Three genes were found to be accelerated were FOXF1, IGFBP5, and ATP2B2, but only the latter one was found in humans and it seems unlikely that it would be related to the differences between mammary gland development at puberty between humans and non-human primates.
ContributorsArroyo, Diana (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Schwartz, Rachel (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Alternative polyadenylation (APA) is the biological mechanism in which the same gene can have multiple 3'untranslated region (3'UTR) isoforms due to the presence of multiple polyadenylation signal (PAS) elements within the pre mRNAs. Because APA produces mRNA transcripts that have different 3'UTR isoforms, certain transcripts may be subject to post-transcriptional regulation by regulatory non-coding RNAs, such as microRNAs or RNA binding proteins defects of which have been implicated in diseases such as cancer. Despite the increasing level of information, functional understanding of the molecular mechanisms involved in transcription is still poorly understood, nor is it clear why APA is necessary at a cell or tissue-specific level. To address these questions I wanted to develop a set of sensor strain plasmids capable of detecting cleavage and polyadenylation in vivo, inject the complete sensor strain plasmid into C. elegans and prepare stable transgenic lines, and perform proof-of-principle RNAi feeding experiments targeting genes associated with the cleavage and polyadenylation complex machinery. I demonstrated that it was possible to create a plasmid capable of detecting cleavage and polyadenylation in C. elegans; however, issues arose during the RNAi assays indicating the sensor strain plasmid was not sensitive enough to the RNAi to effectively detect in the worms. Once the problems involved with sensitivity and variability in the RNAi effects are resolved, the plasmid would be able to better address questions regarding the functional understanding of molecular mechanisms involved in transcription termination.
ContributorsWilky, Henry Patrick (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Blazie, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Script supervising is a job on a film set that is often overlooked; however, without the script supervisor there could be countless errors in a movie. Script supervisors keep track of the continuity of the script, including matching actions, eye-lines, and all of the details in the set. The other main task of the script supervisor is to record information; he or she keeps track of the director's favorite takes, general camera information, and what each shot covers. My thesis covers an in-depth look at the practice of script supervising as well as my experiences script supervising two feature films.
ContributorsGeske, Victoria Manette (Author) / LaMont, Christopher (Thesis director) / Bernstein, Gregory (Committee member) / Barrett, The Honors College (Contributor) / School of Film, Dance and Theatre (Contributor)
Created2014-12