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 46
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
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
This project is a Game Engine for 2D Fighting Games which uses Simple DirectMedia Layer and C++. The Game Engine's goal is to model the conventions the genre has for dynamically handling combat between two characters. The characters can be in a variety of different states that animate certain features while also responding to the environment based on key statuses. There is a playable test game that is the subject of a user study. The Game Engine's capabilities are shown by the test game and the limitations / missing features are discussed.
ContributorsStanton, Nicholas Scott (Author) / Kobayashi, Yoshihiro (Thesis director) / Hansford, Dianne (Committee member) / Computer Science and Engineering Program (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This paper details the process for designing both a simulation of the board game Jaipur, and an artificial intelligence (AI) agent that can play the game against a human player. When designing an AI for a card game, there are two major problems that can arise. The first is the difficulty of using a search space to analyze every possible set of future moves. Due to the randomized nature of the deck of cards, the search space rapidly leads to an exponentially growing set of potential game states to analyze when one tries to look more than one turn ahead. The second aspect that poses difficulty is the element of uncertainty that exists from opponent feedback. Certain moves are weak to specific opponent reactions, and these are difficult to predict due to hidden information. To circumvent these problems, the AI uses a greedy approach to decision making, attempting to maximize the value of its plays immediately, and not play for future turns. The agent utilizes conditional statements to evaluate the game state and choose a game action that it deems optimal, a heuristic to place an expected value (EV) of the goods it can choose from, and selects the best one based on this evaluation. Initial implementation of the simulation was done using C++ through a terminal application, and then was translated to a graphical interface using Unity and C#.
ContributorsOrr, James Christopher (Author) / Kobayashi, Yoshihiro (Thesis director) / Selgrad, Justin (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Speech recognition in games is rarely seen. This work presents a project, a 2D computer game named "The Emblems" which utilizes speech recognition as input. The game itself is a two person strategy game whose goal is to defeat the opposing player's army. This report focuses on the speech-recognition aspect of the project. The players interact on a turn-by-turn basis by speaking commands into the computer's microphone. When the computer recognizes a command, it will respond accordingly by having the player's unit perform an action on screen.
ContributorsNguyen, Jordan Ngoc (Author) / Kobayashi, Yoshihiro (Thesis director) / Maciejewski, Ross (Committee member) / Barrett, The Honors College (Contributor) / Computing and Informatics Program (Contributor) / Computer Science and Engineering Program (Contributor)
Created2014-05
Description
The project, "The Emblems: OpenGL" is a 2D strategy game that incorporates Speech Recognition for control and OpenGL for computer graphics. Players control their own army by voice commands and try to eliminate the opponent's army. This report focuses on the 2D art and visual aspects of the project. There are different sprites for the player's army units and icons within the game. The game also has a grid for easy unit placement.
ContributorsHsia, Allen (Author) / Kobayashi, Yoshihiro (Thesis director) / Maciejewski, Ross (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2014-05
Description
The objective of this creative project was to gain experience in digital modeling, animation, coding, shader development and implementation, model integration techniques, and application of gaming principles and design through developing a professional educational game. The team collaborated with Glendale Community College (GCC) to produce an interactive product intended to supplement educational instructions regarding nutrition. The educational game developed, "Nutribots" features the player acting as a nutrition based nanobot sent to the small intestine to help the body. Throughout the game the player will be asked nutrition based questions to test their knowledge of proteins, carbohydrates, and lipids. If the player is unable to answer the question, they must use game mechanics to progress and receive the information as a reward. The level is completed as soon as the question is answered correctly. If the player answers the questions incorrectly twenty times within the entirety of the game, the team loses faith in the player, and the player must reset from title screen. This is to limit guessing and to make sure the player retains the information through repetition once it is demonstrated that they do not know the answers. The team was split into two different groups for the development of this game. The first part of the team developed models, animations, and textures using Autodesk Maya 2016 and Marvelous Designer. The second part of the team developed code and shaders, and implemented products from the first team using Unity and Visual Studio. Once a prototype of the game was developed, it was show-cased amongst peers to gain feedback. Upon receiving feedback, the team implemented the desired changes accordingly. Development for this project began on November 2015 and ended on April 2017. Special thanks to Laura Avila Department Chair and Jennifer Nolz from Glendale Community College Technology and Consumer Sciences, Food and Nutrition Department.
ContributorsNolz, Daisy (Co-author) / Martin, Austin (Co-author) / Quinio, Santiago (Co-author) / Armstrong, Jessica (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Valderrama, Jamie (Committee member) / School of Arts, Media and Engineering (Contributor) / School of Film, Dance and Theatre (Contributor) / Department of English (Contributor) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Herberger Institute for Design and the Arts (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05