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- Creators: School of Life Sciences
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
In recent years, companies have been expanding their business efforts on a global scale. This project explores this expansion of American-based multinational corporations (MNCs) in Ireland, and the comparison of how their culture motivation in the workplace. We did a cultural study using Hofstede and Trompenaars' cultural dimensions of the two countries then used McClelland's Needs Theory, Equity Theory, and Herzberg's Motivation-Hygiene Theory in order to create three research questions. (1) How does the manager define success for the firm as a whole and for their employees, (2) How is the definition of success reflected in the company's corporate culture (i.e. values, norms and practices), along with how cultural values, norms and practices affect the company, and (3) How do external forces (i.e. governmental factors, workplace technology, etc.) affect the workplace environment and motivation for employees? With these we hypothesized that for research question 1, we hypothesized that from our study of Hofstede's and Trompenaars' cultural frameworks, Irish employees will show a greater tendency to favor affiliation, nAff, as opposed to a need for achievement, nAch, in American employees, according to McClelland's Needs Theory. For research question 2, we predicted that motivation would be administered through style of feedback to employees and office norms, such as autonomy, flexible hours, and work-life balance. For research question 3, we hypothesized that Ireland would have an impact from external factors such as government and technology, whereas the U.S. employees would face no clear impact. We conducted eight, qualitative interviews using a questionnaire, either in person or via video conference. The interviewees were all managers in some facet and have all had some international experience. Through the analysis of the interviews, we found that the Irish employees focused on how employees are able to help or contribute to a group (nAff), instead of looking at how the contribution of a group can be used to meet individual goals (nAch). The American companies reflected Trompenaars' definition of individualism in which employees focus on collaborating in teams, as long as individual goals are met, and benchmarked collaboration as a performance measure, tying in the need for achievement, for research question one. For the second research question, we found that employees in Ireland had a focus on teamwork in the workplace and much higher respect for work-life balance. American firms, in contrast, had a greater focus on making sure employees were contributing, meeting their goals, and getting their work done. While American firms did acknowledge work-life balance and its importance, there was a priority for coming in early and/or staying late to make sure a job got done. Findings for our third question showed that government factors did impact Ireland more, due to labor laws such as required vacation days in Ireland, and that technology had less of an impact than expected, for both countries. More importantly was our finding that the companies in Ireland were greatly impacted by the decisions made by the business executives in the United States.
ContributorsSong, Jenny Jungwon (Co-author) / Brown, William (Co-author) / Arrfelt, Mathias (Thesis director) / Moore, James (Committee member) / Department of Marketing (Contributor) / Department of Management and Entrepreneurship (Contributor) / W.P. Carey School of Business (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
Same Bed is a twelve-piece book of poetry that explores the theme of sexual violence. The speaker of the poems is processing the trauma surrounding her rape which leads her to explore her own family's dynamics regarding gender, power, and acknowledgment of sexuality. The speaker also observes the broader issue of how society reacts to rape and the effects that can have on a survivor of sexual violence. In the peak of the manuscript, the speaker pieces together part of her own police report, pinning her own voice and perspective against her rapists.
ContributorsPetersen, Gabrielle Nicole (Author) / Ball, Sally (Thesis director) / Kelsey, Meghan (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / Department of Management and Entrepreneurship (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
DescriptionI made a full business plan and pitch to investors for a company I plan on starting next semester.
ContributorsOramas, Michael (Author) / Trujillo, Rhett (Thesis director) / Naumann, Gary (Committee member) / Department of Finance (Contributor) / Department of Management and Entrepreneurship (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
Although there are some key qualities that all good leaders employ, variations in effective leadership approaches are evident across different cultures. This project sought to compare and analyze the differences and similarities in leadership principles between Chinese and American business cultures, with emphasis on the divergence caused by the influences of history, culture and politics.
ContributorsLe Tourneur, Maxine Archondakis (Author) / McKinnon, David (Thesis director) / LePine, Marcie (Committee member) / Department of Supply Chain Management (Contributor) / Department of Management and Entrepreneurship (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Through the research of: accredited business articles, wedding sites such as The Knot, personal interviews with brides, research novels, television shows, and movies; this project will depict why and how traditional, American "White Weddings" have become so commercialized by advertisements and businesses as a result of various media channels' reinforcements of cultural ideals and norms about brides and weddings since the 1920s. The purpose of this paper is to identify the largest cultural and commercial forces that contributed to the growth and expansion of the wedding industry.
ContributorsHovendon, Allison Michelle (Author) / Suk, Mina (Thesis director) / Ostrom, Amy (Committee member) / Department of Management and Entrepreneurship (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12