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Description
Many factors are at play within the genome of an organism, contributing to much of the diversity and variation across the tree of life. While the genome is generally encoded by four nucleotides, A, C, T, and G, this code can be expanded. One particular mechanism that we examine in this thesis is modification of bases—more specifically, methylation of Adenine (m6A) within the GATC motif of Escherichia coli. These methylated adenines are especially important in a process called methyl-directed mismatch repair (MMR), a pathway responsible for repairing errors in the DNA sequence produced by replication. In this pathway, methylated adenines identify the parent strand and direct the repair proteins to correct the erroneous base in the daughter strand. While the primary role of methylated adenines at GATC sites is to direct the MMR pathway, this methylation has also been found to affect other processes, such as gene expression, the activity of transposable elements, and the timing of DNA replication. However, in the absence of MMR, the ability of these other processes to maintain adenine methylation and its targets is unknown.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
ContributorsBoyer, Gwyneth (Author) / Lynch, Michael (Thesis director) / Behringer, Megan (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
There has been a recent push for queer fiction, especially in the young adult genre, whose focus is gay and lesbian relationships. This growth is much needed in terms of visibility and the furthering of acceptance, but there are still subjects within the LGBTQ+ community that need to be addressed, including bisexual, asexual, and non-binary erasure. There are many people who claim that these identities do not exist, are labels used as a stepping stone on one's journey to discovering that they are homosexual, or are invented excuses for overtly promiscuous or prudish behavior. The existence of negative stereotypes, particularly those of non-binary individuals, is largely due to a lack of visibility and respectful representation within media and popular culture. However, there is still a dearth of non-binary content in popular literature outside of young adult fiction. Can You See Me? aims to fill the gap in bisexual, asexual, and non-binary representation in adult literature. Each of the four stories that make up this collection deals with an aspect of gender and/or sexuality that has been erased, ignored, or denied visibility in American popular culture. The first story, "We'll Grow Lemon Trees," examines bisexual erasure through the lens of sociolinguistics. A bisexual Romanian woman emigrates to Los Angeles in 1989 and must navigate a new culture, learn new languages, and try to move on from her past life under a dictatorship where speaking up could mean imprisonment or death. The second story "Up, Down, All Around," is about a young genderqueer child and their parents dealing with microaggressions, examining gender norms, and exploring personal identity through imaginary scenarios, each involving an encounter with an unknown entity and a colander. The third story, "Aces High," follows two asexual characters from the day they're born to when they are 28 years old, as they find themselves in pop culture. The two endure identity crises, gender discrimination, erasure, individual obsessions, and prejudice as they learn to accept themselves and embrace who they are. In the fourth and final story, "Mile Marker 72," a gay Mexican man must hide in plain sight as he deals with the death of his partner and coming out to his best friend, whose brother is his partner's murderer.
ContributorsOchser, Jordyn M. (Author) / Bell, Matt (Thesis director) / Free, Melissa (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The current study investigated whether intermittent restraint stress (IRS) would impair fear extinction learning and lead to increased anxiety and depressive- like behaviors and then be attenuated when IRS ends and a post- stress rest period ensues for 6 weeks. Young adult, male Sprague Dawley rats underwent restraint stress using wire mesh (6hr/daily) for five days with two days off before restraint resumed for three weeks for a total of 23 restraint days. The groups consisted of control (CON) with no restraint other than food and water restriction yoked to the restrained groups, stress immediate (STR-IMM), which were restrained then fear conditioned soon after the end of the IRS paradigm, and stress given a rest for 6 weeks before fear conditioning commenced (STR-R6). Rats were fear conditioned by pairing a 20 second tone with a footshock, then given extinction training for two days (15 tone only on each day). On the first day of extinction, all groups discriminated well on the first trial, but then as trials progressed, STR-R6 discriminated between tone and context less than did CON. On the second day of extinction, STR- IMM froze more to context in the earlier trials than compared to STR-R6 and CON. As trials progressed STR-IMM and STR-R6 froze more to context than compared to CON. Together, CON discriminated between tone and context better than did STR-IMM and STR-R6. Sucrose preference, novelty suppressed feeding, and elevated plus maze was performed after fear extinction was completed. No statistical differences were observed among groups for sucrose preference or novelty suppressed feeding. For the elevated plus maze, STR-IMM entered the open arms and the sum of both open and closed arms fewer than did STR- R6 and CON. We interpret the findings to suggest that the stress groups displayed increased hypervigilance and anxiety with STR-R6 exhibiting a unique phenotype than that of STR-IMM and CON.
ContributorsShah, Vrishti Bimal (Author) / Conrad, Cheryl (Thesis director) / Newbern, Jason (Committee member) / Judd, Jessica (Committee member) / School of Life Sciences (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Due to artificial selection, dogs have high levels of phenotypic diversity, yet, there appears to be low genetic diversity within individual breeds. Through their domestication from wolves, dogs have gone through a series of population bottlenecks, which has resulted in a reduction in genetic diversity, with a large amount of linkage disequilibrium and the persistence of deleterious mutations. This has led to an increased susceptibility to a multitude of diseases, including cancer. To study the effects of artificial selection and life history characteristics on the risk of cancer mortality, we collected cancer mortality data from four studies as well as the percent of heterozygosity, body size, lifespan and breed group for 201 dog breeds. We also collected specific types of cancer breeds were susceptible to and compared the dog cancer mortality patterns to the patterns observed in other mammals. We found a relationship between cancer mortality rate and heterozygosity, body size, lifespan as well as breed group. Higher levels of heterozygosity were also associated with longer lifespan. These results indicate larger breeds, such as Irish Water Spaniels, Flat-coated Retrievers and Bernese Mountain Dogs, are more susceptible to cancer, with lower heterozygosity and lifespan. These breeds are also more susceptible to sarcomas, as opposed to carcinomas in smaller breeds, such as Miniature Pinschers, Chihuahuas, and Pekingese. Other mammals show that larger and long-lived animals have decreased cancer mortality, however, within dog breeds, the opposite relationship is observed. These relationships could be due to the trade-off between cellular maintenance and growing fast and large, with higher expression of growth factors, such as IGF-1. This study further demonstrates the relationships between cancer mortality, heterozygosity, and life history traits and exhibits dogs as an important model organism for understanding the relationship between genetics and health.
ContributorsBalsley, Cassandra Sierra (Author) / Maley, Carlo (Thesis director) / Wynne, Clive (Committee member) / Tollis, Marc (Committee member) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Vitellogenin (vg) is a precursor protein of egg yolk in honeybees, but it is also known to have immunological functions. The purpose of this experiment was to determine the effect of vg on the viral load of deformed wing virus (DWV) in worker honey bees (Apis mellifera). I hypothesized that a reduction in vg expression would lead to an increase in the viral load. I collected 180 worker bees and split them into four groups: half the bees were subjected to a vg gene knockdown by injections of double stranded vg RNA, and the rest were injected with green fluorescent protein (gfp) double stranded RNA. Half of each group was thereafter injected with DWV, and half given a sham injection. The rate of mortality in all four groups was higher than expected, leaving only 17 bees total. I dissected these bees' fat bodies and extracted their RNA to test for vg and DWV. PCR results showed that, out of the small group of remaining bees, the levels of vg were not statistically different. Furthermore, both groups of virus-injected bees showed similar viral loads. Because of the high mortality rate bees and the lack of differing levels of vg transcript between experimental and control groups, I could not draw conclusions from these results. The high mortality could be caused by several factors: temperature-induced stress, repeated stress from the two injections, and stress from viral infection. In addition, it is possible that the vg dsRNA batch I used was faulty. This thesis exemplifies that information cannot safely be extracted when loss of sampling units result in a small datasets that do not represent the original sampling population.
ContributorsCrable, Emma Lewis (Author) / Amdam, Gro (Thesis director) / Wang, Ying (Committee member) / Dahan, Romain (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Researchers suggests that college students' involvement and use of resources on campus are important for success, in the form of satisfaction and GPA, in the first year. College officials invest substantial resources in activities to encourage freshmen students to become involved in campus activities and utilize resources that promote successful outcomes, yet we do not know which activities best relate to success. Using a self-report survey, we sought to corroborate previous research that has shown that overall levels of involvement and use of resources relate to satisfaction/GPA. Furthermore, we disentangled which individual types of involvement and use of resources are most highly correlated with satisfaction and GPA. And finally, we identified the barriers and benefits to involvement and resource use, according to the students themselves. We found evidence that higher levels of involvement were related to satisfaction and attending faculty office hours appears to be particularly important, given a significant relation to both satisfaction and GPA. Implications for program promotion and resource allocation are discussed.
ContributorsPaley, Madeleine (Author) / Foster, Stacie (Thesis director) / Spinrad, Tracy (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
The purpose of this essay is to explain how celebrities manage their brand, as an image and commodity, using social media. Merriam-Webster defines "celebrity" as the "state of being celebrated." This essay will continue to explain how this state of celebration is a manufactured idea by the individual and the media's portrayal. Celebrities are "well-known for their well-knowness" (Boorstin, 1961, p. 58). Boorstin (1961) explains celebrities achieve fame not for their achievements, but by creating a unique personality (as cited in Turner, 2004). Crowd culture, networks, and audience knowledge are tools celebrities must use to navigate digital nuances. They must manage performance of self, adhere to internet social norms, and the obsessive fame culture. Celebrities are often referred to have "star power" and have a certain "charisma." This cultural identity is "negotiated and formed" contrived by a team through promotion, publicity, and advertising (Turner, 2004). Celebrities market themselves through branded content, media used to promote a product, on their social media pages while targeting crowd cultures. Networks truly define how celebrities must brand themselves on social media. This person-to-person contact establishes fan and consumer connections that build the celebrity's base and following. Despite campaigning in a digital world, it goes back to people connecting with people, not accounts linking to accounts. Celebrities manufacture all of these strategies and tactics as they market themselves as a commodity to target crowd culture audiences. This is why targeting crowd cultures is vitally important for celebrities. This essay explores the techniques of select celebrities as they succeed and fail navigating digital nuances.
ContributorsPierce, Ellen (Author) / Jacoby, Jim (Thesis director) / Himberg, Julia (Committee member) / Department of English (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
In an effort to combat the lack of diversity in Children's Literature, this project displays a piece of literature titled Stories & Stages: A Tale of Two Sisters, in the form of a children's chapter book for a middle grade audience. Focusing on characters of a Hispanic background without relying on stereotypes or false characterizations, the novel works to inspire young minds and reflect a true representation of the world children are living in. This is done using research on different aspects of Children's Literature, including: the definition of children's literature, diversity, girlhood, and sibling relationships. This research provides the basis for the project, as does personal experience and background. Following the novel is a recording of the background research involved and a documentations of the creative process. Keywords: Children's Literature, Diversity
ContributorsFlores, Abriana Lorraine (Author) / Elliott, Lisa (Thesis director) / Haddy, Lana (Committee member) / Division of Teacher Preparation (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
The Way Home is a full-length young adult novel. The story is split between the perspectives of Theo and Ella, best friends from high school who are starting their freshman year in college. Neither is extremely excited about the start of the new phase of their lives; Theo struggles with severe anxiety and is just hoping to survive the four years; and dark memories in Ella's past don't seem to want to let her start over. A series of murders happening in town don't help their nerves at all, making it hard to focus on the "college experience." They were supposed to be there for each other... But then Ella goes missing, and Theo is left without a clue of where she went. While he searches for her desperately, she wakes up miles away from home, surrounded by strangers. In their efforts to find one another again, they instead find themselves presented with opportunities to study the impossible: magic. Things become stranger and stranger as murders, magic, police investigations, and ever-looming final exams begin to challenge Theo and Ella in ways they never expected. In writing this novel, I hoped to depict the transition from high school to college and the worries and wonders that come with it. The story is almost split directly in half, beginning with normal school life and shifting into the world of magic. The conflicts presented to the characters during the first half, such as grades, majors, and socializing, persist throughout the second half, but are also metaphorized once the characters begin studying magic. I chose to include a protagonist with an anxiety disorder because I believe mental disabilities are not represented enough in YA literature, though it is something that many high school and college students deal with. I wanted to create a character that could inform others and that students with similar mental disorders could relate to. Additional themes I deal with include newfound independence, individuality, growth, and friendship.
ContributorsWoner, Catherine Flynn (Author) / Blasingame, James (Thesis director) / Irish, Jennifer (Committee member) / Department of English (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Over the past three decades, medical anthropology research, published within both public health and anthropological journals, demonstrates both the prevalence of traditional folk medicine in Latino populations in the United States and the potential difficulty of negotiating these beliefs and practices with clinical, western biomedicine. I bring attention to what might be a narrative of divergent values that occurs in Latino communities in the United States. A well-documented source (Pachter, 1994) of this clash is the culturally pervasive use of folk medicine in Latino layperson populations seeking biomedical care in the Unites States (U.S.). Numerous studies (Padilla, 2001; Koss 1972) suggest that a significant portion of Latinos in the continental United States call upon folk knowledge to diagnose, reinterpret, and treat illness. The Puerto Rican population seems to be no exception, though few studies are specific to native-born Puerto Ricans living in Puerto Rico, where the issue of access to quality public health care becomes increasingly problematic. In this honors undergraduate thesis project, I conduct a review of the literature that bridges anthropology and public health research and proceed to describe a study I conducted on Culebra Island, Puerto Rico in May of 2015. The study aims to determine whether patient satisfaction can be linked to being treated by a physician hailing from a similar cultural background, or if an irredeemable disparity between patient and provider present a roadblock to health outcomes. I found that the Puerto Rican physicians are receptive to folk illness (symptoms) and consider folk therapy as part of the treatment regimen. The physicians make patients feel understood, which might improve treatment adherence and thus health outcomes. Still, respondents demonstrated that there is high patient trust in the biomedical model by emphasizing the use of conventional medications in tandem with the folk therapy. Nevertheless, the health care provider's disposition in regards to folk knowledge and modalities are important but does not present a roadblock to optimal care and health outcomes as much as access, available services or clinic resources.
ContributorsVanasse-Torres, Elena Georgina (Author) / Maupin, Jonathan (Thesis director) / Maienschein, Jane (Thesis director) / MartÃÂnez, AirÃÂn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05