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 44
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
Cloud computing and web services enable the creation of applications that are faster and more interconnected than traditional applications. This project explores the possible ways in which cloud computing and web services can be used to extend already existing applications by developing a data storage web service for 3D modeling applications. The implementation of the service is described, and several example applications are shown that utilize the service. Additionally, related web based applications are discussed along with their influence on the project. The project shows the benefits that cloud-based web services can bring to 3D modeling applications, such as improved collaboration and more comprehensive history tracking.
ContributorsFerry, Mark Travis (Author) / Chen, Yinong (Thesis director) / Balasooriya, Janaka (Committee member) / Barrett, The Honors College (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
For my thesis project, I have developed a cash register web application for the Arizona State University Barrett Dining Hall. I previously worked at the Barrett Dining Hall, and I would occasionally step in as a cashier. This work is how I came to be familiar with the system and all its inefficiencies. The system requires multiple user inputs to implement even the most basic of tasks, is not user-friendly, and therefore very prone to error. In the event that multiple incorrect inputs are entered, the software will freeze, and the user will have to turn off the computer and turn it back on. In theory, this application is an improvement over the software system that is currently in place in that the user interface has been specifically designed to be user-friendly. This application reduces the number of required user inputs by automating certain tasks (such as pricing and determining the meal period), thereby reducing the chance of user error. It is also an improvement in that it allows students to log in to the system to view how many meals they have left, how much M&G is in their account, and how many guest passes they have left. This functionality is extremely important because this is a feature that is not currently in place, and is something that students have actively complained about. Currently, if students want to check on their meal plan, they have to either physically go to a dining hall and ask the cashier, or call a toll-free number. The two technologies used to develop this application are C# and XML. These technologies were chosen because I wanted to learn something new for this project to broaden my knowledge. I also happened to be taking a class at the start of this project that utilized C# and XML for Web Applications, and it seemed like the perfect opportunity to transfer over the skills I had been learning.
ContributorsLewis, Q. Mariha Paishance (Author) / Chen, Yinong (Thesis director) / Nakamura, Mutsumi (Committee member) / School of International Letters and Cultures (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Tenga is an e-commerce demo web application for students studying Distributed Software Development and Software Integration and Engineering at Arizona State University (ASU). The application, written in C#, aims to empower students to understand how complex systems are build. Complementing the two courses taught at ASU, it seeks to demonstrate how the concepts taught in the two classes can be applied to the real world. In addition to the practical software development process, Tenga also bring in the topics that students are inexperienced with such as recommendation systems and ranking algorithms. Tenga is going to be used in classrooms to help students to learn fundamental issues in Web software development and software integration and to understand tools and skill sets required to built a web application.
ContributorsKawanzaruwa, Allen Tom (Author) / Chen, Yinong (Thesis director) / Nakamura, Mutsumi (Committee member) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The areas of cloud computing and web services have grown rapidly in recent years, resulting in software that is more interconnected and and widely used than ever before. As a result of this proliferation, there needs to be a way to assess the quality of these web services in order to ensure their reliability and accuracy. This project explores different ways in which services can be tested and evaluated through the design of various testing techniques and their implementations in a web application, which can be used by students or developers to test their web services.
ContributorsHilliker, Mark Paul (Author) / Chen, Yinong (Thesis director) / Nakamura, Mutsumi (Committee member) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
In order to adequately introduce students to computer science and robotics in an exciting and engaging manner certain teaching techniques should be used. In recent years some of the most popular paradigms are Visual Programming Languages. Visual Programming Languages are meant to introduce problem solving skills and basic programming constructs inherent to all modern day languages by allowing users to write programs visually as opposed to textually. By bypassing the need to learn syntax students can focus on the thinking behind developing an algorithm and see immediate results that help generate excitement for the field and reduce disinterest due to startup complexity and burnout. The Introduction to Engineering course at Arizona State University supports this approach by teaching students the basics of autonomous maze traversing algorithms and using ASU VIPLE, a Visual Programming Language developed to connect with and direct real-world robots. However, some startup time is needed to learn how to interface with these robots using ASU VIPLE. That is why the HTML5 Autonomous Robot Web Simulator was created -- by encouraging students to use the simulator the problem solving behind autonomous maze traversing algorithms can be introduced more quickly and with immediate affirmation. Our goal was to improve this simulator and add features so that the simulator could be accessed and used for a more wide variety of introductory Computer Science lessons. Features scattered across past implementations of robotic simulators were aggregated in a cross platform solution. Upon initial development, a classroom test group revealed usability concerns and a demonstration of students' mental models. Mean time for task completion was 8.1min - compared to 2min for the authors. The simulator was updated in response to test group feedback and new instructor requirements. The new implementation reduces programming overhead while maintaining a learning environment with support for even the most complex applications.
ContributorsRodewald, Spencer (Co-author, Co-author) / Patel, Ankit (Co-author) / Chen, Yinong (Thesis director) / Chattin, Linda (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12