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- Creators: School of Life Sciences
- Creators: Bernstein, Gregory
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
Fringe: Abstract Fringe is a feature length screenplay and a work of original science fiction. The story takes place in the future, on a planet far from Earth but it is told from the human perspective and is meant to draw into question many issues present in society today: prejudice, hatred, multiculturalism, war, and social division. The screenplay seeks to pose an allegorical relationship between the humanity living on the planet, and the enemies they face, and the present day conflict between America and the Middle East or ISIS. The story follows Miles as he is forced to ally with his sworn enemy, the Lue, and learn to fight together to save his world from destruction. Miles begins the film bitter, resentful, and filled with prejudice towards his foes, much like a majority of Americans today. Instead of focussing on that conflict though, my story unites these two bitter enemies and asks them to put aside their violent and hateful pasts to fight a new, more powerful foe together. As the events unfold my characters learn that their enemies can be just like them and that they have something valuable to offer their world. My screenplay is about finding commonality with the enemy, on both sides of a conflict. By the end of my tale, Miles learns that there is good to be found in the world, even in his sworn enemies, if he looks close enough. It may seem like an archetypal plot on the surface but I worked hard to create a world that has not been seen in film before, an original science fiction universe that can bring these issues into the light and entertain an audience while doing so. I feel that my screenplay does just that, offering entertainment with and edge of social commentary, and stays true to the science fiction form.
ContributorsTrcic, Colton Walker (Author) / Maday, Gregory (Thesis director) / Bernstein, Gregory (Committee member) / WPC Graduate Programs (Contributor) / W. P. Carey School of Business (Contributor) / School of Film, Dance and Theatre (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Students Organize for Syria (SOS) is the student led initiative for Syria. With 18 registered chapters across the United States, this student organization is targeting a multidimensional cause by different means. Though it is now a national movement, it started off with one group at Arizona State University, with one student. Zana Alattar, founder and student director of SOS, tells the story of how she took an ASU organization, Save Our Syrian Freedom (SOS Freedom), to the national level as SOS. As a pre-medical student, she also combines her work in human rights with her future in healthcare. After all, health and human rights have long maintained a synergistic relationship.
ContributorsAlattar, Zana (Author) / Graff, Sarah (Thesis director) / McClurg, Sharolyn (Committee member) / School of Molecular Sciences (Contributor) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Many bacteria actively import environmental DNA and incorporate it into their genomes. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is expected to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function alleles at transformation loci and an increased mutational load from recombining with DNA from dead cells create additional costs to transformation. These costs have been shown to outweigh many of the benefits of recombination under a variety of likely parameters. We investigate an additional proposed benefit of sexual recombination, the Red Queen hypothesis, as it relates to bacterial transformation. Here we describe a computational model showing that host-pathogen coevolution may provide a large selective benefit to transformation and allow transforming cells to invade an environment dominated by otherwise equal non-transformers. Furthermore, we observe that host-pathogen dynamics cause the selection pressure on transformation to vary extensively in time, explaining the tight regulation and wide variety of rates observed in naturally competent bacteria. Host-pathogen dynamics may explain the evolution and maintenance of natural competence despite its associated costs.
ContributorsPalmer, Nathan David (Author) / Cartwright, Reed (Thesis director) / Wang, Xuan (Committee member) / Sievert, Chris (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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
Description
Although the number of women earning college degrees and entering the workforce is increasing, a gender gap persists at top leadership positions. Women are faced with numerous challenges throughout the talent pipeline, challenges that often drive women out of the workforce. This paper looks at the power of mentoring and how women, particularly young women, have the potential to overcome these challenges through a successful mentoring relationship. We use examples of successful mentoring programs at the corporate and university level to support the development of a mentoring program at the high school level. Our paper presents the research and development process behind the Young Women in Leadership (YWiL) Workshop, a half-day event that focused on bringing awareness to the importance of mentoring and leadership at the high school level while providing young women with the confidence and knowledge to begin to establish their own mentoring relationships.
ContributorsRust, Brenna (Co-author) / Myers, Sheridan (Co-author) / Desch, Tim (Thesis director) / Kalika, Dale (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Accountancy (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor) / WPC Graduate Programs (Contributor) / W. P. Carey School of Business (Contributor)
Created2015-05
Description
‘why we bend' a Bachelor of Fine Arts honors thesis exhibition by Ximenna Hofsetz and Tiernan Warner brings together installation, digital, sculptural, and printed artwork. The main focus concerns memory; and its vague, formless, and hazy nature. The work also examines what would happen if cognitive space could be physically mapped? What would it look like in sculptural form? Memory erodes and distorts with time. We influence our memories as much as they affect us. Thus, just as relationships are ever-changing, and our memories of those we interact with constantly shifting, our relationships with our own memories are malleable and evolve through time. This transient nature of memory is depicted in the various stylistic means of this exhibition by referencing time and space as well as personal memories and ephemera in both concrete and abstract ways. ‘why we bend’ implements a variety of multimedia techniques to examine recollection and its hold on us.
ContributorsHofsetz, Ximenna Cedella (Author) / Gutierrez, Rogelio (Thesis director) / Hood, Mary (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Art (Contributor)
Created2014-12
Description
A Guiding Hand: Grief Response in Young Adults works to guide young adults thought the grieving process after the traumatic death of a loved one. It goes through the steps of grieving and what a person can expect when they suddenly lose someone dear. Written from the point of view of someone who had lost their best friend in a murder/suicide, A Guiding Hand, shares a personal view that is often missing in other books on grief. This piece works to prepare other young adults for the unexpected emotions that are associated with grief. It also works to provide coping strategies to help recover from a traumatic loss in a healthy manner and to put people in touch with resources they may not know exist in order to help with healing.
ContributorsSmith, Madison Ann (Author) / Foy, Joseph (Thesis director) / Shaeffer, John (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-12
Description
Beautiful Accidents is a debut drama-comedy feature screenplay written as a thesis project. For a screenwriter trying to bloom in the Film Industry, the big question is "where is your great feature script?" and "how many do you have?" The pressure is all about the quality of the work and how many feature screenplays are written. Thus, this draft has been in pre-production and conception for a year and a half now. The draft presented as the thesis project is the third draft of a total of three versions of the script. The first and second drafts are drastically different from this third draft in content and character development. After having the opportunity to attend the Cannes Film Festival, the inspiration for another new and improved third draft came to be. It runs 93 pages, and goes beyond presenting an example debut feature screenplay. Throughout the process of writing a feature screenplay, learning to write several drafts to reach a polished draft is a crucial part of the journey as a writer. This was not only a project that included writing a feature film screenplay, but it also contained valuable lessons about the growth of an inspiring writer in regards to being willing to go through several drafts. In addition to the third draft of the script, a teaser opening of the first scene was produced, directed, and starred in as another segment of the thesis project. Run Time: 2:51. The goal for this teaser opening is to serve as a visual sample along with the screenplay. When the time comes to search for investors and producers for the script, this teaser will accompany the material. The script is intentionally written to be a low budget film, so that production could take place independently and locally for a tight budget. The ultimate goal is to produce this film as either an independent film or a semi-independent as writer/director of the project. Synopsis: A quirky romantic comedy about two individuals, Meg and Dave, who believe they are narcissists explore their own perceived narcissism in one another. Meg is a budding music genius who is stuck at Law school, while Dave is a bartender and pool shark. At the ripe age of 22, Meg finds herself for the first time in her life, deeply fascinated in one other person other than herself: Dave, who happens to also be ten years older than her. Her first meeting with Dave is purely an accident, as their continued journey appears to have plenty of them. These accidents prove to be, however, beautiful.
ContributorsKheshtchin-Kamel, Amena (Author) / Montesano, Mark (Thesis director) / Bernstein, Gregory (Committee member) / Barrett, The Honors College (Contributor) / School of Film, Dance and Theatre (Contributor)
Created2015-05
Description
Body Integrity Identity Disorder Screenplay Abstract
The Body Integrity Identity Disorder Screenplay, tentatively entitled Detach, is a full-‐length feature film script. Based on a fascinating mental disorder (generally referred to as the acronym BIID) where an individual does not associate a limb with the rest of their body, the script follows a sufferer and a reporter attempting to write a story on his struggle.
As my creative sensibilities and skills have developed over the span of my undergraduate career, the most ambitious undertaking imaginable for myself at this moment is the completion of a feature script. This project was a significant test of my storytelling skills and ability to format an unusual tale into a conceivable film.
I am proud of the end result and believe that the final version of my screenplay is an accurate representation of my taste as a filmmaker. I hope to actualize this project one day and help facilitate a transformation of the script into a feature film.
The Body Integrity Identity Disorder Screenplay, tentatively entitled Detach, is a full-‐length feature film script. Based on a fascinating mental disorder (generally referred to as the acronym BIID) where an individual does not associate a limb with the rest of their body, the script follows a sufferer and a reporter attempting to write a story on his struggle.
As my creative sensibilities and skills have developed over the span of my undergraduate career, the most ambitious undertaking imaginable for myself at this moment is the completion of a feature script. This project was a significant test of my storytelling skills and ability to format an unusual tale into a conceivable film.
I am proud of the end result and believe that the final version of my screenplay is an accurate representation of my taste as a filmmaker. I hope to actualize this project one day and help facilitate a transformation of the script into a feature film.
ContributorsKitnick, Benjamin Allan (Author) / Bernstein, Gregory (Thesis director) / Miller, April (Committee member) / Barrett, The Honors College (Contributor) / School of Film, Dance and Theatre (Contributor)
Created2015-05