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- Creators: Brahms, Johannes, 1833-1897
Description
Identifying associations between genotypes and gene expression levels using next-generation technology has enabled systematic interrogation of regulatory variation underlying complex phenotypes. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation (Main, 2009). Interest in the existence of allele-specific expression in autosomal genes evolved with the increased awareness of the important role that variation in non-coding DNA sequences can play in determining phenotypic diversity, and the essential role parent-of-origin expression has in early development (Knight, 2004). As new implications of high-throughput sequencing are conceived, it is becoming increasingly important to develop statistical methods tailored to large and formidably complex data sets in order to maximize the biological insights derived from next-generation sequencing experiments. Here, a Bayesian hierarchical probability model based on the beta-binomial distribution is proposed as a possible approach for quantifying allele-specific expression from whole genome (WGS) and whole transcriptome (RNA-seq) data. Pipeline for the analysis of WGS and RNA-seq data sets from ten samples was developed and implemented, while allele-specific expression (ASE) was quantified from both haplotypes using individuals heterozygous at the tested variants utilizing the described methodology. Both computational and statistical framework applied accurately quantified ASE, achieving high reproducibility of already described allele-specific genes in the literature. In conclusion, described methodology provides a solid starting point for quantifying allele specific expression across whole genomes.
ContributorsMalenica, Ivana (Author) / Craig, David (Thesis director) / Rosenberg, Michael (Committee member) / Szelinger, Szabolcs (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
It has been 30 years since research has tried to determine how adults decide if an infant is male or female (Seavey et al., 1975; Sidorowicz & Lunney, 1980), with research at that time indicating that participants tended to label infants as male. The purpose of this study is to investigate whether adults today can identify infant gender above chance, and what tools adults use to assign gender labels to babies. I hypothesize that females, social science majors, students who frequently interact with children, and students who are very confident will all assign gender labels more accurately than their counterparts. I showed a video to University students featuring five sets of parents playing with their infants. The video featuring three male and two female babies was edited to remove any gender identifying information. Students were asked to guess whether each of the infants was male or female, and to explain how they came to that conclusion. One sample t-tests revealed that students overall were able to correctly identify infant gender significantly more than what would be expected due to chance for 4 out of 5 infants. The results did not support my hypothesis that social science majors or people who frequently interact with children are better at assigning gender labels. This study did find a significant correlation between confidence and accuracy. When asked to explain how participants assigned infant gender labels, I found a significant correlation between infant physical movement and correct students labeling the infant as male. There was also a significant relationship between parental voice being and participants labeling infants as female whether the infant was actually female or not. Unlike research from the late 1970's and early 1980's, college students today can accurately assign gender labels to infants. This suggests that either the conceptualization of gender in the U.S. culture has changed enough since previous research over 3 decades ago, that there is something about parent-baby play that helps people correctly identify infant gender, or both.
ContributorsLove, Echo (Author) / Shapiro, Alyson (Thesis director) / Mikulski, Ariana (Committee member) / Martin, Carol (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
Capstone project, I began developing an animated series called Legends of Gaia. The show follows a small group of people of mixed ages and backgrounds, as they travel across the world trying to stop the Galliean Empire, a technologically booming western power that has begun fighting a war for world domination. The purpose of this paper is to better explain the origins and inspirations of the mythology of my series, as well as the major two supernatural characters of my series, and the general geography (both physical and metaphysical) of the series. When first developing this series, I looked into the works of Joseph Campbell, as he wrote the book(s) on mythology in many ways. His most famous writings are probably the Hero's Journey and the Monomyth, the basic outline of the journey that most heroes go through, from the call ordinary world, to the call of the adventure, all the way to the hero returning (Campbell 211). Many classic examples of story telling follow the pattern Campbell outlined, and my work is no exception. However, I did not want my series to be a beat for beat retread of the Hero's Journey, and so some parts, such as the Refusal of the Call, when the hero rejects the adventure and befalls a tragedy, were skipped, while others, such as the resurrection, were realized in different ways. Using the Resurrection as an example, in my series the main female character, Diana is reborn twice throughout the series. Once in the final battle with the main villain into her true, goddess form, and the other when her battles are over, and she is reborn in her mortal form permanently.
ContributorsLopez, Richard (Author) / Collis, Adam (Thesis director) / Valenti, F. Miguel (Committee member) / Barzso, Tain (Committee member) / Barrett, The Honors College (Contributor) / Herberger Institute for Design and the Arts (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
The front cover of Uncle What-Is-It is Coming to Visit, a 1993 children’s book by Michael-Willhoite, features two white children frightened by the hairy arm and upturned wrist of an unseen adult. The arm is clad in a frilly pink and orange sleeve, and gaudy bracelets hang from the wrist. The plot hinges on the children’s uncertainty about an uncle they have yet to meet; they know he is gay but are unsure of what it means. Before their mother can explain, she is distracted by a kitchen mishap and the siblings turn to other neighborhood children for answers. They encounter a host of descriptions that terrify them: one neighbor describes gay people as “fags [and] queers [who] really want to be women.” He shows the children a newspaper clipping photo of “a large man dressed in a frilly dress [with] a turban piled high with fruit on his head,” an implicitly racialized caricature reminiscent of Latina style icon Carmen Miranda. Another neighbor describes gay people as “dressed up in black leather. Zippers and chains all over...Dark glasses [and] chaps” (Willhoite, 1993). After having nightmares of men with sinister expressions in tropical-themed drag and leather, the children are overjoyed to discover that their uncle seems “normal.” Relative to depictions of other gay people in the book, Uncle Brett is normal because he is nonthreatening—he is white with short, straight, brown hair; he wears a plain, blue, collared shirt and brown dress pants; he carries a brown briefcase; and he enjoys and excels at activities appropriate for his gender, like catch. Although the book seems to have an affirming message about accepting queer people, it sends a clear message about which queer people are to be feared by children and which are nonthreatening. Nonthreatening queers are those who seem most like people mainstream western society considers normal: people who conform to expected gender roles, who have a vested interest parenting, and who are white and middle-upper class. These nonthreatening queers are by far the most represented in queer-themed literature for children. Based on a survey of 68 children’s books with queer characters, this paper argues that the representation of queer identities in children’s literature upholds more than challenges heteronormativity. I will first address ways many of the books perpetuate gender normativity by problematizing young male characters’ gender-transgressing behavior, portraying queer adults with less threatening gender presentations, and upholding gender binarism; next, I will address how the majority of the books promote repro-narrativity by focusing on monogamous couples’ strong desires and concerted efforts to have/raise children; I will then address race and class and the way white and upper-middle class queer characters are overrepresented while non-white and lower-class queer characters are underrepresented or not represented at all.
ContributorsLester, Jasmine (Author) / Danielson, Marivel (Thesis director) / Blasingame, James (Committee member) / Kuo, Karen (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
Visual aides, such as PowerPoint slides, hand-outs, and lecture notes on whiteboards, are often used in classrooms to convey important content to learners, especially in high school and college. When using these visual learning aides, it is important to consider which qualities of these presentations can affect learning— positively or negatively—and how those qualities interact with individual student characteristics. In the present study, we examine the overlap between audio and text and how the effects of overlap potentially interact with reading comprehension abilities. The examination of these potential influences on learning in this study is inspired by Cognitive Load Theory, the Dual-Channel Assumption, and prior research.
ContributorsHarry, Danielle (Author) / McNamara, Danielle (Thesis director) / Presson, Clark (Committee member) / Jackson, Tanner (Committee member) / Roscoe, Rod (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
Glioblastoma multiforme is associated with a very low survival rate and is recognized as the most vicious form of intracranial cancer. The Akt gene pathway has three different isoforms, each of which has a different role in the tumors of GBM. Preliminary data suggests that Akt3 may work to decrease tumorigenicity. A produced image that visualizes the subcellular localization of Akt3 led the author to believe that Akt3 may reduce tumorigenicity by decreasing genomic instability caused by the cancer. To explore this, flow cytometry was performed on GBM cell lines with Akt3v1 over-expression, Akt3v2 over-expression, and a control glioma cell line.
ContributorsGhorayeb, Antoine (Author) / Neisewander, Janet (Thesis director) / Diehnelt, Chris (Committee member) / Moussallem, Suzan (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
The lonely, empty face panhandling on the street corner has a story to tell. At first glance, most people write the homeless off as less than worthy. However, there is a deeper connection and understanding of relationships and a sense of community unseen by the majority of passer-byers. Amidst the humdrum beat of every day life, there is toil to find basic necessities such as food, water, sanitation, and a place to rest. At the same time, there is laughter and friendship as they help one another through the hostilities of their circumstances. Combining the creative elements of photojournalism and qualitative interviewing, the basic daily needs and struggles of the homeless will be delved into to answer how friendship is pertinent to survival on the streets.
ContributorsFisher, Meghan (Author) / Hruschka, Daniel (Thesis director) / Hita, Liza (Committee member) / Newland, Judy (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
The purpose of my honors thesis project was to generate the tools needed for in vivo imaging by determining the optimal plasmid-fluorophore combination. To determine the optimal plasmid and fluorophore, asd plasmids were constructed with various promoters, origins of replications, and red fluorophores. The optimal asd plasmid for fluorescent in vivo imaging was determined by the plasmid stability, growth rate, and growth phase dependence on fluorescent intensity. The end goal is to be able to use the asd plasmid in vaccine strains for the purpose of in vivo imaging of the recombinant attenuated Salmonella vaccine (RASV).
ContributorsEudy, L. Adam (Author) / Curtiss, Roy (Thesis director) / Roland, Kenneth (Committee member) / Forbes, Stephen (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
Microfinance is a term that refers to providing basic financial services to the poor; it has become a powerful tool for poverty alleviation. The idea is a relatively new one - modern microfinance began through experiments in the 1970's - but it has grown quickly and currently serves over 155 million clients worldwide. There are many studies that provide evidence of the positive impact of microfinance and the movement has an array of enthusiastic proponents. It is certainly not the only solution in the battle against poverty, however, and there are also studies that question the true depth of its impact. In looking at microfinance around the globe, one thing becomes clear: although it is an international phenomenon, microfinance has definitely found more success in some regions over others.
ContributorsEdgell, Bailey (Author) / Mendez, Jose (Thesis director) / Schoellman, Todd (Committee member) / Forbes, Stephen (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12
Description
Prospective memory is defined as remembering to carry out specified actions in the future. Research has suggested that prospective memory retrieval is reliant on multiple cognitive processes to function, and the ways in which these different processes are used is dependent on a variety of variables relating to the prospective memory task at hand. The current study focuses on the strength of the association between the prospective
memory cue and the prospective memory intention. Based on literature suggesting that aspects of prospective memory are reliant on executive control functioning, the current study examined the possibility that executive control depletion would affect prospective memory ability on subsequent tasks. Results showed that depletion of executive control resources, measured objectively, did not impair prospective memory in either a low or
high cue-association condition. However, participants‟ subjective assessment of their own fatigue correlated significantly with their subsequent prospective memory performance, regardless of association condition. The results of the study indicate that depletion studies that fail to account for both objective and subjective measures suffer from an unclear interpretation of effects, and that recognition of perceived expectancies
of cognitive resource limitation can assist in improving prospective memory ability.
memory cue and the prospective memory intention. Based on literature suggesting that aspects of prospective memory are reliant on executive control functioning, the current study examined the possibility that executive control depletion would affect prospective memory ability on subsequent tasks. Results showed that depletion of executive control resources, measured objectively, did not impair prospective memory in either a low or
high cue-association condition. However, participants‟ subjective assessment of their own fatigue correlated significantly with their subsequent prospective memory performance, regardless of association condition. The results of the study indicate that depletion studies that fail to account for both objective and subjective measures suffer from an unclear interpretation of effects, and that recognition of perceived expectancies
of cognitive resource limitation can assist in improving prospective memory ability.
ContributorsCook, Carson (Author) / Brewer, Gene (Thesis director) / Presson, Clark (Committee member) / Homa, Donald (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12