Barrett, The Honors College Thesis/Creative Project Collection
Barrett, The Honors College at Arizona State University proudly showcases the work of undergraduate honors students by sharing this collection exclusively with the ASU community.
Barrett accepts high performing, academically engaged undergraduate students and works with them in collaboration with all of the other academic units at Arizona State University. All Barrett students complete a thesis or creative project which is an opportunity to explore an intellectual interest and produce an original piece of scholarly research. The thesis or creative project is supervised and defended in front of a faculty committee. Students are able to engage with professors who are nationally recognized in their fields and committed to working with honors students. Completing a Barrett thesis or creative project is an opportunity for undergraduate honors students to contribute to the ASU academic community in a meaningful way.
Displaying 1 - 10 of 43
Description
The focus of human decomposition studies has traditionally been on how external factors affect the decomposition of a body. There is much less literature on how the decomposition of a human cadaver affects its local ecosystem. This study attempts to address the knowledge gap in current literature regarding how the decomposition of human cadavers affects the bioavailability of essential plant nutrients (P, K, Ca, Fe, C and N) as well as toxins (As and Pb) in soil. By studying the bioavailability of plant nutrients, especially nitrogen, and toxins, this research hopes to inform new technologies and techniques for locating clandestine gravesites. The objectives of this study were twofold: 1) determine whether soils exposed to cadaveric decomposition can be visually distinguished from one another via macroscopic and microscopic observation and 2) observe general changes in nutrient and toxic element bioavailability and changes in carbon and nitrogen isotope ratios over time as well as spatially across a body. Visual analyses of soil samples, both macro- and microscopically did not show potential in distinguishing soil exposed to cadaver decomposition from unexposed soil. Relative bioavailability as well as overall bioavailable concentrations of both plant nutrients and toxins were highly elevated after 12 months. Toxins, such as As and Pb, tended to have greater bioavailable concentrations at the near-torso positions, though no consistent spatial trends between nutrient bioavailable concentrations were observed between the three individuals. Nitrogen concentrations and nitrogen isotope (δ15N) ratios show strong potential as markers of clandestine graves throughout the study period. While this research demonstrates further need to uncover what factors influence bioavailability of elements in gravesoil, it shows that the bioavailability of plant nutrients and toxins as well as δ15N ratios are greatly affected by cadaver decomposition, and emerging technologies in gravesite detection based on plant or soil changes have a solid foundation.
ContributorsAnderson, Sara Rae (Author) / Kobojek, Kimberly (Thesis director) / Gordon, Gwyneth (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
A lab protocol was created in order to introduce arson evidence analysis to students. The procedures dictate a thorough introduction from evidence handling procedures to analysis of common accelerant mass spectrum. The objectives of the lab protocol included classifying and describing various pieces of arson evidence and common accelerants as well as synthesizing information about accelerant composition to interpret GC-MS data output. This would allow the student to experience first-hand what the subsection of arson analysis has to offer in the field of forensic science which could help the student decide on more specialties to study later on. I was unable to run the lab protocol in a laboratory setting, therefore in the future I want to use the lab protocol and receive feedback in order to improve the protocol so the student is receiving the best possible learning outcomes. The experience of creating a lab protocol in forensic science gave myself a greater understanding of what goes on behind an academic learning procedure and more insight on arson evidence analysis.
ContributorsWhitten, Jamison Mckall (Author) / Kobojek, Kimberly (Thesis director) / Armendariz Guajardo, Jose (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Breast cancer is the leading cause of cancer-related deaths of women in the united states. Traditionally, Breast cancer is predominantly treated by a combination of surgery, chemotherapy, and radiation therapy. However, due to the significant negative side effects associated with these traditional treatments, there has been substantial efforts to develop alternative therapies to treat cancer. One such alternative therapy is a peptide-based therapeutic cancer vaccine. Therapeutic cancer vaccines enhance an individual's immune response to a specific tumor. They are capable of doing this through artificial activation of tumor specific CTLs (Cytotoxic T Lymphocytes). However, in order to artificially activate tumor specific CTLs, a patient must be treated with immunogenic epitopes derived from their specific cancer type. We have identified that the tumor associated antigen, TPD52, is an ideal target for a therapeutic cancer vaccine. This designation was due to the overexpression of TPD52 in a variety of different cancer types. In order to start the development of a therapeutic cancer vaccine for TPD52-related cancers, we have devised a two-step strategy. First, we plan to create a list of potential TPD52 epitopes by using epitope binding and processing prediction tools. Second, we plan to attempt to experimentally identify MHC class I TPD52 epitopes in vitro. We identified 942 potential 9 and 10 amino acid epitopes for the HLAs A1, A2, A3, A11, A24, B07, B27, B35, B44. These epitopes were predicted by using a combination of 3 binding prediction tools and 2 processing prediction tools. From these 942 potential epitopes, we selected the top 50 epitopes ranked by a combination of binding and processing scores. Due to the promiscuity of some predicted epitopes for multiple HLAs, we ordered 38 synthetic epitopes from the list of the top 50 epitope. We also performed a frequency analysis of the TPD52 protein sequence and identified 3 high volume regions of high epitope production. After the epitope predictions were completed, we proceeded to attempt to experimentally detected presented TPD52 epitopes. First, we successful transduced parental K562 cells with TPD52. After transduction, we started the optimization process for the immunoprecipitation protocol. The optimization of the immunoprecipitation protocol proved to be more difficult than originally believed and was the main reason that we were unable to progress past the transduction of the parental cells. However, we believe that we have identified the issues and will be able to complete the experiment in the coming months.
ContributorsWilson, Eric Andrew (Author) / Anderson, Karen (Thesis director) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Bloodstain pattern analysis can provide telling evidence from a crime scene based on the clues left in the blood, but the field itself is highly problematic since the evidence extracted is dependent upon the interpretation of the analyst. Although some aspects of this type of analysis have been scientifically supported, most are not seen as positively accurate. Since certainty is the basis for acceptance of courtroom testimony, it is important that these unsettled aspects become more understood. This experiment examines the diameter of a weapon and how it affects its cast-off pattern. Weapons with four different diameters were used to generate 5 sample patterns under controlled conditions from each weapon diameter for a total of 20 patterns consisting of 3,367 droplets. The length and width of the pattern, the total number of droplets in the pattern, and the percentage of each droplet type (classified into low-velocity, medium-velocity, and high-velocity droplets) were recorded, averaged, and compared to each other individually using a t-test difference of two means assuming unequal variances. The results reveal that a higher percentage of droplets greater than 4 mm may indicate the use of a weapon with a wider diameter. The data also shows differences between the weapons that may be related to other factors besides the diameter of the weapon such as surface area or the curvature of the weapon. Still, more testing must be conducted to support these theories.
ContributorsBetz, Alexandra Marie (Author) / Kobojek, Kimberly (Thesis director) / Jacobson, David (Committee member) / School of Humanities, Arts, and Cultural Studies (Contributor) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Introduction: Human papillomavirus (HPV) infection is seen in up to 90% of cases of cervical cancer, the third leading cancer cause of death in women. Current HPV screening focuses on only two HPV types and covers roughly 75% of HPV-associated cervical cancers. A protein based assay to test for antibody biomarkers against 98 HPV antigens from both high and low risk types could provide an inexpensive and reliable method to screen for patients at risk of developing invasive cervical cancer. Methods: 98 codon optimized, commercially produced HPV genes were cloned into the pANT7_cGST vector, amplified in a bacterial host, and purified for mammalian expression using in vitro transcription/translation (IVTT) in a luminescence-based RAPID ELISA (RELISA) assay. Monoclonal antibodies were used to determine immune cross-reactivity between phylogenetically similar antigens. Lastly, several protein characteristics were examined to determine if they correlated with protein expression. Results: All genes were successfully moved into the destination vector and 86 of the 98 genes (88%) expressed protein at an adequate level. A difference was noted in expression by gene across HPV types but no correlation was found between protein size, pI, or aliphatic index and expression. Discussion: Further testing is needed to express the remaining 12 HPV genes. Once all genes have been successfully expressed and purified at high concentrations, DNA will be printed on microscope slides to create a protein microarray. This microarray will be used to screen HPV-positive patient sera for antibody biomarkers that may be indicative of cervical cancer and precancerous cervical neoplasias.
ContributorsMeshay, Ian Matthew (Author) / Anderson, Karen (Thesis director) / Magee, Mitch (Committee member) / Katchman, Benjamin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Background: Measles virus (MV) infections are the main cause of vaccine-preventable death in children younger than 5 years. The World Health Organization (WHO) has estimated there are over 20 million cases of measles every year. Currently, diagnostic methods rely on enzyme immunoassays (EIA) to detect IgM or IgG Abs in serum. These commercial assays measure reactivity against the immunodominant N antigen and can have a false negative rates of 20-30%. Centralized testing by clinical labs can delay rapid screening in an outbreak setting. This study aims to develop a rapid molecular diagnostic assay to detect IgG reactive to five individual MV proteins representing 85% of the measles proteome. Methods: MV genes were subcloned into pANT_cGST vector to generate C-terminal GST fusion proteins. Single MV cistrons were expressed using in vitro transcription/translation (IVTT) with human cell lysate. Expression of GST-tagged proteins was measured using a sandwich ELISA for GST expression using relative light units (RLUs) as readouts. Single MV antigens were used as bait to determine the IgG-dependent reactivity in 12 serum samples obtained from immunized animals with previously determined neutralization titer (NT) and the correlation between NT and ELISA reactivity was determined. Results: Protein expression of five measles genes of interest, M, N, F, H, and L, was measured. L exhibited the strongest protein expression with an average RLU value of 4.34 x 10^9. All proteins were expressed at least 50% greater than control (2.33 x 10^7 RLU). As expected, reactivity against the N was the highest, followed by reactivity against M, F, H and L. The best correlation with NT titer was reactivity against F (R^2 = 0.62). Conclusion: These data indicate that the expression of single MV genes M, N, F, H, and L are suitable antigens for serologic capture analysis of measles immunity.
ContributorsMushtaq, Zuena (Author) / Anderson, Karen (Thesis director) / Reyes del Valle, Jorge (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
Background: Human papillomavirus (HPV) is the cause of 99.7% of cervical cancers. Research of cervical cancer has made this disease mostly curable in the developing world. Head and neck cancer, which is increasingly caused by HPV, still is associated with a mortality rate of 50,000 in the US annually. This study proposed to evaluate the biology of HPV-16 in head and neck tumors by using RT-qPCR to measure the RNA expression and its relation to physical status of the virus. Methods: This study was to develop an assay that uses RT-qPCR to determine the quantitative expression of HPV-16 RNA coding for proteins E1, E2, E4, E5, E6, and E7 in tumor samples. The assay development started with creation of primers. It went on to test the primers on template DNA through traditional PCR and then on DNA from HPV-16 positive cell lines, SiHa and CaSki, using RT-qPCR. This paper also describes the troubleshooting methods taken for the PCR reaction. Once the primers are verified, the RT-qPCR process can be carried out on RNA purified from tumor samples. Results: No primer sets have been confirmed to produce a product through PCR or RT-qPCR. The primer sequences match up correctly with known sequences for HPV-16 E1, E2, E4, E5, E6, and E7. RT-qPCR showed results consistent with the hypothesis. Conclusion: The RT-qPCR protocol must be optimized to confirm the primer sequences work as desired. Then primers will be used to study physical status and RNA expression in HPV-positive and HPV-negative head and neck tumor samples. This assay can help shed light on which proteins are expressed most in tumors of the head and neck and will aid in the development of future screening and treatment options.
ContributorsKhazanovich, Jakob (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Sundaresan, Sri Krishna (Committee member) / Barrett, The Honors College (Contributor)
Created2015-05
Description
Cancer poses a significant burden on the global health system and represents a leading cause of death worldwide. For late-stage cancers, the traditional treatments of chemotherapy, radiation, and surgery are not always viable, and they can pose unnecessary health risks to the patients. New immunotherapies, such as adoptive cell transfer, are being developed and refined to treat such cancers. T cell immunotherapies in particular, where a patient’s T cell lymphocytes are isolated and amplified to be re-infused into the patient or where human cell lines are engineered to express T cell receptors for the recognition of common cancer antigens, are being expanded on because for some cancers, they could be the only option. Constructing an optimal pipeline for cloning and expression of antigen-specific TCRs has significant bearing on the efficacy of engineered cell lines for ACT. Adoptive T cell transfer, while making great strides, has to overcome a diverse T cell repertoire – cloning and expressing antigen-specific TCRs can mediate this understanding. Having identified the high frequency FluM1-specific TCR sequences in stimulated donor PBMCs, it was hypothesized that the antigen-specific TCR could be reconstructed via Gateway cloning methods and tested for expression and functionality. Establishing this pipeline would confirm an ability to properly pair and express the heterodimeric chains. In the context of downstream applications, neoantigens would be used to stimulate T cells, the α and β chains would be paired via single-cell or bulk methods, and instead of Gateway cloning, the CDR3 hypervariable regions α and β chains alone would be co-expressed using Golden Gate assembly methods.
ContributorsHirneise, Gabrielle Rachel (Author) / Anderson, Karen (Thesis director) / Mason, Hugh (Committee member) / Hariadi, Hugh (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Marine conservation faces the unique challenge of trying to assess and protect species, like sharks, that have long migration tracks and are often targeted by fishing vessels in open and international waters. Over the last two decades, several large predatory shark populations have been greatly depleted despite local and international organizations designed to help regulate and prevent predator removal to avoid disturbing the food web those sharks balance (Myers, Baum, Shepherd, Powers, & Peterson, 2007). Forensic science is a powerful tool that could give shark conservation efforts an edge on identifying shark species currently being targeted by unsustainable fisheries in international waters. Allowing offenders who break international conservation laws to be prosecuted for their crimes. Unfortunately, this unique and powerful tool has not been given the opportunity to be utilized as it should be. An overview of national and international agencies, organizations, and laws disclosed a strong foundation for wildlife conservation. However, current international organizations and laws that govern international waters leave much to be desired in regards to protecting shark species that are threatened due to being popular targets for fishing vessels. This paper examines the level of forensic science involvement in shark conservation efforts through a literature review, revealing a severe lack of real-life application of forensic science to marine conservation cases. Current issues that marine wildlife forensic science encounters while attempting to increase forensic capability. And finally, presenting proposals for the future, and new challenges, which aim to strengthen the relationship between forensic science and marine conservation.
ContributorsParker, Jamie Caitlin (Author) / Kobojek, Kimberly (Thesis director) / Polidoro, Beth (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
As human beings we go through the world interpreting – seeing a situation, gathering context, and making a decision on the meaning of the thing we just experienced. The philosopher Martin Heidegger calls this way of being hermeneutics – a practice of interpretation. This method of approach does not ignore a person’s bias, instead bias is highlighted, understood, and possibly even overcome. In the following pages the basic definition and process of hermeneutics will be discussed. Leading into the difference between calculative and meditative thought – scientific and philosophical – in order to later discuss the possibility and need to merge the two in the field of Forensic Science. Forensic Scientist uses hermeneutic thought by way of merging calculative and meditative thinking. In order to support this claim artistic renderings of ‘the pieces of an unknowable whole’ were created to literally illustrate this truth.
Forensic science is tasked with using calculative thinking with scientifically accepted methods of measurement and detection as well as the meditative task of applying their data to messy, real-world events. In order to support my supposition of forensic scientists being hermeneutical workers, three paintings were created. The three paintings can be considered a tryptic of sorts due to the context in which they are presented: forensic science. They each tell a story that is weaved within each other – spatter indicating violence long past, the empty void of a body gone, and the cold decomposition of a victim found. It is the forensic scientist that must interpret each piece separately and is tasked with finding how and why they are put together. The hermeneutical work of the forensic scientist interpreting a crime scene uses the same methods as one who interprets text. A forensic scientist opens possibilities of meaning in the same way that Martin Heidegger’s hermeneutic circle does. There is interplay between the interpreter (the forensic scientist) and the text (the crime scene), questions are formed (what happened here?) and responses are made (evidence found at the scene). This question and response outlook is what make the forensic scientist a hermeneutic thinker.
Forensic science is tasked with using calculative thinking with scientifically accepted methods of measurement and detection as well as the meditative task of applying their data to messy, real-world events. In order to support my supposition of forensic scientists being hermeneutical workers, three paintings were created. The three paintings can be considered a tryptic of sorts due to the context in which they are presented: forensic science. They each tell a story that is weaved within each other – spatter indicating violence long past, the empty void of a body gone, and the cold decomposition of a victim found. It is the forensic scientist that must interpret each piece separately and is tasked with finding how and why they are put together. The hermeneutical work of the forensic scientist interpreting a crime scene uses the same methods as one who interprets text. A forensic scientist opens possibilities of meaning in the same way that Martin Heidegger’s hermeneutic circle does. There is interplay between the interpreter (the forensic scientist) and the text (the crime scene), questions are formed (what happened here?) and responses are made (evidence found at the scene). This question and response outlook is what make the forensic scientist a hermeneutic thinker.
ContributorsCraig, Catherine Anne (Author) / Kobojek, Kimberly (Thesis director) / Watrous, Lisa (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05