Matching Items (120)
Description
In eukaryotes, most messenger RNA precursors (pre-mRNA) undergo extensive processing, leading to the cleavage of the transcript followed by the addition of a poly(A) tail. This process is executed by a large complex known as the Cleavage and Polyadenylation Complex (CPC). Its central subcomplex, the Cleavage and Polyadenylation Specificity Factor (CPSF) complex is responsible for recognizing a short hexameric element AAUAAA located at the 3’end in the nascent mRNA molecule and catalyzing the pre-mRNA cleavage. In the round nematode C. elegans, the cleavage reaction is executed by a subunit of this complex named CPSF3, a highly conserved RNA endonuclease. While the crystal structure of its human ortholog CPSF73 has been recently identified, we still do not understand the molecular mechanisms and sequence specificity used by this protein to induce cleavage, which in turn would help to understand how this process is executed in detail. Additionally, we do not understand in additional factors are needed for this process. In order to address these issues, we performed a comparative analysis of the CPSF3 protein in higher eukaryotes to identify conserved functional domains. The overall percent identities for members of the CPSF complex range from 33.68% to 56.49%, suggesting that the human and C. elegans orthologs retain a high level of conservation. CPSF73 is the protein with the overall highest percent identity of the CPSF complex, with its active site-containing domain possessing 74.60% identity with CPSF3. Additionally, we gathered and expressed using a bacterial expression system CPSF3 and a mutant, which is unable to perform the cleavage reaction, and developed an in vitro cleavage assay to test whether CPSF3 activity is necessary and sufficient to induce nascent mRNA cleavage. This project establishes tools to better understand how CPSF3 functions within the CPC and sheds light on the biology surrounding the transcription process as a whole.
ContributorsGallante, Christina (Author) / Mangone, Marco (Thesis director) / Sharma, Shalini (Committee member) / Hrach, Heather (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The successful reduction of CO2 and protons by a light-induced cobalt porphyrin/cytb562 hybrid metalloenzyme in water is reported. Incorporation of the porphyrin into a protein scaffold results in increases in CO and H2 production over naked porphyrin. Rational point mutations to the CoPPIX binding site of cytb562 modulate production, indicating possible further improvements in catalytic activity.
ContributorsGwerder, Noah D (Author) / Ghirlanda, Giovanna (Thesis director) / Williams, Peter (Committee member) / Mangone, Marco (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Duchenne muscular dystrophy (DMD) is a lethal, X-linked disease which occurs in approximately 1 in 3,500 male births. This disease is characterized by progressive muscle wasting and causes premature death. One of the earliest symptoms of this disease is mitochondrial dysfunction. Dystrophin is a protein found under the sarcolemma. The N terminus binds to actin and the C terminus binds to dystrophin glycoprotein complex (DGC). DMD is caused by mutations in the dystrophin gene. C. elegans possess an ortholog of dystrophin, DYS-1. Though there is evidence that C. elegans can be used as a model organism to model DMD, nematode DGC has not been well characterized. Additionally, while we know that mitochondrial dysfunction has been found in humans and other model organisms, this has not been well defined in C. elegans. In order to address these issues, we crossed the SJ4103 worm strain (myo-3p::GFP(mit)) with dys-1(cx18) in order to visualize and quantify changes in mitochondria in a dys-1 background. SJ4103;cx18 nematodes were found to have less mitochondrial than SJ4103 which suggests mitochondrial dysfunction does occur in dys-1 worms. Furthermore, mitochondrial dysfunction was studied by knocking down members of the DGC, dys-1, dyb-1, sgn-1, sgca-1, and sgcb-1 in SJ4103 strain. Knock down of each gene resulted in decrease in abundance of mitochondria which suggests that each member of the DGC contributes to the overall health of nematode muscle. The ORF of dyb-1 was successfully cloned and tagged with GFP in order to visualize this DGC member C. elegans. Imaging of the transgenic dyb-1::GFP worm shows green fluoresce expressed in which suggests that dyb-1 is a functional component of the muscle fibers. This project will enable us to better understand the effects of dystrophin deficiency on mitochondrial function as well as visualize the expression of certain members of the DGC in order to establish C. elegans as a good model organism to study this disease.
ContributorsObrien, Shannon Nishino (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Hrach, Heather (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Cleavage and polyadenylation is a step in mRNA processing in which the 3’UTR is cleaved and a polyA tail is added to create a final mature transcript. This process relies on RNA sequence elements that guide a large multimeric protein complex named the Cleavage and Polyadenylation Complex to dock on the 3’UTR and execute the cleavage reaction. Interactions of the complex with the RNA and specific dynamics of complex recruitment and formation still remain largely uncharacterized. In our lab we have identified an Adenosine residue as the nucleotide most often present at the cleavage site, although it is unclear whether this specific element is a required instructor of cleavage and polyadenylation. To address whether the Adenosine residue is necessary and sufficient for the cleavage and polyadenylation reaction, we mutated this nucleotide at the cleavage site in three C. elegans protein coding genes, forcing the expression of these wt and mutant 3’UTRs, and studied how the cleavage and polyadenylation machinery process these genes in vivo. We found that interrupting the wt sequence elements found at the cleavage site interferes with the cleavage and polyadenylation reaction, suggesting that the sequence close to the end of the transcript plays a role in modulating the site of the RNA cleavage. This activity is also gene-specific. Genes such as ges-1 showed little disruption in the cleavage of the transcript, with similar location occurring in both the wt and mutant 3’UTRs. On the other hand, mutation of the cleavage site in genes such as Y106G6H.9 caused the activation of new cryptic cleavage sites within the transcript. Taken together, my experiments suggest that the sequence elements at the cleavage site somehow participate in the reaction to guide the cleavage reaction to occur at an exact site. This work will help to better understand the mechanisms of transcription termination in vivo and will push forward research aimed to study post-transcriptional gene regulation in eukaryotes.
ContributorsSteber, Hannah Suzanne (Author) / Mangone, Marco (Thesis director) / Harris, Robin (Committee member) / LaBaer, Joshua (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The issue of wild horse management in the American West has become prevalent in the media recently and management strategies are often criticized and opposed by the public. Horses have been a core feature of American history and culture nearly since the colonization of the western frontier, and popular media such as television and movies paint a romantic but often unrealistic picture of wild horses. Land management agencies must balance limited resources with an ever-growing wild horse population in order to properly manage public land so that it retains its ecological integrity and is still able to be used by multiple stakeholders, and they also must endure public criticism throughout the process. I used a photo elicitation survey to gather responses to photographic images of wild horses and determine how the public feels about wild horse management, given that horses are seen as a symbol of freedom and the American West. It was revealed that people who are unfamiliar with the issue still have opinions about how the horses should be managed, and these opinions often mirror what can be found in popular media.
ContributorsDuran, Kiana Alexis (Author) / Minteer, Ben (Thesis director) / Schoon, Michael (Thesis director) / Murphree, Julie (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Cultural Perceptions of Leisure and Well-being in Rock Climbing Communities of Peru and Arizona, USA
Description
In December of 2015, I made my way to rural Peru for a few weeks, my first visit to South America. While I was there, I observed a devotion to family and leisure activity, topics that were not heavily prioritized in my experience in Arizona. Upon my return, I became more involved in leisure activities, particularly running, hiking, yoga, and climbing. These involvements noticeably benefitted my health and well-being. The way the Peruvians I met prioritized these subjects fascinated me, and I wanted to study this difference between Arizona and Peru. In July of 2017, I returned to Peru for a semester abroad with my bags packed and the following research questions: 1) Are differences in motivation for rock climbing between Arizona and Peruvian climbers associated with cultural values? 2) Do leisure activities and the amount of time spent on them have an effect on quality of life? 3) Does the degree of climbing specialization impact perceptions of well-being? 4) What characteristics impact perceptions of quality of life among climbers? Are these characteristics affected by country of origin? My prediction was that Peruvians had higher quality of life due to their emphasis on leisure. Through this study, I learned that this conclusion was not as simple as I anticipated.
ContributorsMatta, Samantha Tania (Author) / Hultsman, Wendy (Thesis director) / Sampson, David (Committee member) / Lee, Rebecca (Committee member) / College of Integrative Sciences and Arts (Contributor) / School of Molecular Sciences (Contributor) / Division of Teacher Preparation (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
As human populations continue to expand, interactions with wildlife are expected to increase due to destruction of land and global climate change threatening native habitats. Established areas of protection are becoming essential to species survival and biodiversity protection. National Parks (NP) are a globally ubiquitous method employed to protect wildlife and habitats. Often NPs are mosaics of relatively small protected areas in a “sea” of human-dominated landscapes, and these remaining habitat “islands” are becoming essential to preventing species extinction. However, the establishment of a NP can lead to increased human-wildlife conflicts (HWC) and disenfranchisement of local communities, particularly along their borders. We conducted semi-structured interviews in six different countries to better understand the nature of HWCs at the borders of major NPs: (1) Khao Yai NP, Thailand; (2) Myall Lakes NP, Australia; (3) Chitwan NP, Nepal; (4) Kruger NP, South Africa; (5) Chingaza NP, Colombia, and (6) Yellowstone NP, United States. We evaluated affinity to wildlife, perception of conflicts, management success, and potential solutions at each park to better understand the global nature of HWCs.We also evaluated these data in relationship to the Human Development Index (HDI) to determine if there was a correlation between development and conflict issues. We found the intrinsic value of wildlife to not markedly differ between countries. Conflict was perceived as higher in the United States and Australia but was known to be of greater intensity in Nepal and South Africa. Management of NPs was well-regarded with a slight decrease from less-developed countries to more-developed countries, with solutions that were creative and unique to each region. Results appeared to be related to shifting baselines between countries and also to equivalency in a cross-cultural assessment. When these theories are taken into account, the complexity of HWCs globally is better understood. As our world continues to expand and NPs become some of the only contiguous native habitat and refuges for wildlife, it is important to understand the complex relationships occurring at the interface between natural and human communities and to explore effective solutions to these problems.
ContributorsRagan, Kinley Ann (Author) / Schoon, Michael (Thesis director) / Schipper, Jan (Committee member) / Senko, Jesse (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Human activities around the world are threatening scores of wildlife species, pushing them closer to extinction. In order to address what many conservationists view as a global biodiversity crisis, it is vital that more people are inspired to care about wild animals and motivated to act in ways that help protect them. The up-close experiences and personal connections that people form with wild animals in zoos accredited by the Association of Zoos and Aquariums (AZA) or the World Association of Zoos and Aquariums (WAZA) can help achieve this. However, it is not very well understood how different types of encounters within these zoos may inspire conservation mindedness and pro-environmental behaviors. During this thesis project, surveys were conducted at the AZA-accredited Arizona Center for Nature Conservation/Phoenix Zoo to understand how interactive, hands-on animal experiences within zoos differ from passively viewing zoo animals when it comes to inspiring people to care about conservation. The Phoenix Zoo is home to two different species of giraffes, and guests can view them from the front of the Savanna Exhibit. Guests can also participate in the Giraffe Encounter, which is a much more interactive, hands-on experience. After surveying guests at both locations, the results showed that fewer people at the Giraffe Encounter responded that they often engage in pro-environmental behaviors. This may indicate that the people who participated in the Giraffe Encounter came to the zoo more for recreation and entertainment than to learn about wildlife. Despite this, more people learned something new about nature or conservation at the Giraffe Encounter than they did at the Savanna Exhibit. On average, guests also felt that the Giraffe Encounter motivated them to learn more about how to help animals in the wild than the Savanna Exhibit did. Overall, there is a strong correlation between having an interactive, hands-on experience with a zoo animal and caring more about wildlife conservation. However, more research still needs to be done in order to conclusively provide evidence for causation.
ContributorsBurgess, Christa Noell (Author) / Schoon, Michael (Thesis director) / Minteer, Ben (Committee member) / Allard, Ruth (Committee member) / School of Life Sciences (Contributor) / School of Sustainability (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
This paper covers the wild horse overpopulation case study at the Salt River in Arizona, exploring how Traditional Ecological Knowledge (TEK) might help foster solutions to a lengthy and heated controversy about how to manage wild horses and burros on the rangeland. Fikret Berke's Sacred Ecology defines traditional ecological knowledge as, "a cumulative body of knowledge, practice, and belief evolving by adaptive processes and handed down through generations by cultural transmission, about the relationship of living beings (including humans) with one another and with their environment," (Berkes, 3). In contrast to current management strategies, TEK utilizes knowledge that comes from direct experience and intuitive knowing, rather than science-based, techno-rational streams of knowledge. Drawing on three modern sustainability concepts that support and stem from TEK, including: everything is connected, complex solutions can further complicate problems and diversity as a key to resilience, this paper sets forth a number of specific solutions to be considered moving forward, guided by the wisdom of TEK.
ContributorsLyford, Rebecca (Author) / Schoon, Michael (Thesis director) / Murphey, Julia (Committee member) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Circles of Sustainability is a self-evaluation tool designed to build educator capacity in K-12 schools seeking sustainability solutions. Based on the Sustainable Schools Challenge Handbook from Memphis, Tennessee, Circles of Sustainability considers environmental impact and efficiency, a healthy and safe school environment, sustainability and environmental education, and engagement and empowerment as four key pillars of whole-school sustainability. Each pillar is composed of elements and rubric items, which are reviewed, totaled, and colored in on the front page of the tool to help educators visualize and evaluate the current state of sustainability at their school. Since its first iteration completed in May 2017, the tool has been used by 300 educators throughout the United States during ASU's Sustainability Teachers' Academy (STA) workshops. Circles of Sustainability is completed as part of an activity called "Evaluating Your Community," where educators complete the tool and then brainstorm sustainability projects and solutions for their school and community. This paper is a review and discussion of the research, informal feedback and formal feedback used to create the second iteration of the tool. A second iteration of the tool was created to make the tool more user-friendly and ensure each pillar, element, and rubric item are based in research. The informal feedback was conducted during STA workshops in Tempe, Arizona; Abingdon, Virginia; Princeton, New Jersey; Chicago, Illinois; Los Angeles, California; Tucson, Arizona; and Charlotte, North Carolina. The formal feedback was conducted using a survey distributed to teachers who participated in the Tucson and Charlotte workshops. Overall, educators have responded positively to the tool, and the second iteration will continue to be used in future STA workshops throughout the United States.
ContributorsColbert, Julia (Author) / Schoon, Michael (Thesis director) / Merritt, Eileen (Committee member) / School of Sustainability (Contributor) / Division of Teacher Preparation (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05