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Mass spectrometry: reverse process for synbody discovery & validation of peptide microarray data : a story of landing lights

Description

A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are…

A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.

ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)

Created2011

Meditation and Sleep Applications: Testing Piano Music Modality to Reduce Anxiety and Stress in College Students

Description

My research aims to determine the effectiveness of meditation and sleep applications (apps) on the reduction of anxiety and stress in college students, with a focus on sedative piano music. Results showed a significant reduction of stress and anxiety levels in college students when listening to sedative piano music versus…

My research aims to determine the effectiveness of meditation and sleep applications (apps) on the reduction of anxiety and stress in college students, with a focus on sedative piano music. Results showed a significant reduction of stress and anxiety levels in college students when listening to sedative piano music versus non-sedative piano music. Music along with other therapy modalities in meditation and sleep apps show promise in reducing students’ anxiety and stress and promoting their successes.

ContributorsPantha, Bidur (Author) / Brian, Jennifer (Thesis director) / Patten, Kristopher (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

Assessing Social Sustainability in US Cities: A Systems Approach

Description

Brundtland’s definition of sustainability is the ability to “meet the needs of the present without compromising the ability of future generations to meet their needs” (IISD, 2021). But what if there are no future generations? Social sustainability, the sector of sustainability that foregrounds the well-being and livelihoods of people (and thereby continuation of…

Brundtland’s definition of sustainability is the ability to “meet the needs of the present without compromising the ability of future generations to meet their needs” (IISD, 2021). But what if there are no future generations? Social sustainability, the sector of sustainability that foregrounds the well-being and livelihoods of people (and thereby continuation of humanity), is included in definitions within the sustainability field, but less developed in sustainability practice. In an effort to bridge this gap of knowledge, 14 U.S. cities and over 100 sustainability policies were analyzed for their social sustainability performance. An eight-item analytical framework that deals with differing areas of social equity guided the analysis. Results found that most cities’ sustainability departments fell short of truly addressing social sustainability concerns. Out of the eight items, the most frequently addressed were housing security and racial and gender equality whereas few, if any, cities addressed the more specific social concerns of immigration, technology and media, or arts/cultural preservation. Future research is recommended to gain a better understanding of the ways existing cities can improve in this area.

ContributorsWeekes, Daniel Buckner (Co-author) / Tam, Joey (Co-author) / Brian, Jennifer (Thesis director) / Keeler, Lauren Withycombe (Thesis director) / N/A, N/A (Committee member) / Dean, W.P. Carey School of Business (Contributor) / Department of Economics (Contributor) / Department of Supply Chain Management (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

The Exploration of Ethical Complexities of Selective Abortion in the United States

Description

Abortion is one of the most polarizing moral issues in our society today. This issue divides the country into two separate groups: Pro-choice or Pro-life. Our thesis analyzes published reviewed articles, media articles, policy papers, and perspective, opinion, and commentary pieces to discuss the ethical implications of selective abortion, specifically…

Abortion is one of the most polarizing moral issues in our society today. This issue divides the country into two separate groups: Pro-choice or Pro-life. Our thesis analyzes published reviewed articles, media articles, policy papers, and perspective, opinion, and commentary pieces to discuss the ethical implications of selective abortion, specifically sex-selective abortion and genetic-selective abortion. Our thesis provides an overview of selective abortion, explores women’s bodily autonomy in the U.S., addresses the complexities of both sex-selective and genetic-selective abortion, and finally evaluates the U.S.’s regulation of selective abortion. Through these topics, we were able to determine the implications selective abortion has on the disabled community and how selective abortion is being used to ban abortion overall in the U.S.

ContributorsMcNeill, Ashley Rianne (Co-author) / Nguyen, Nhu (Co-author) / Brian, Jennifer (Thesis director) / Manninen, Bertha (Committee member) / Edson College of Nursing and Health Innovation (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

The Explorations of Ethical Complexities of Selective Abortion in the United States

Description

Abortion is one of the most polarizing moral issues in our society today. This issue divides the country into two separate groups: Pro-choice or Pro-life. Our thesis analyzes published reviewed articles, media articles, policy papers, and perspective, opinion, and commentary pieces to discuss the ethical implications of selective abortion, specifically…

Abortion is one of the most polarizing moral issues in our society today. This issue divides the country into two separate groups: Pro-choice or Pro-life. Our thesis analyzes published reviewed articles, media articles, policy papers, and perspective, opinion, and commentary pieces to discuss the ethical implications of selective abortion, specifically sex-selective abortion and genetic-selective abortion. Our thesis provides an overview of selective abortion, explores women’s bodily autonomy in the U.S., addresses the complexities of both sex-selective and genetic-selective abortion, and finally evaluates the U.S.’s regulation of selective abortion. Through these topics, we were able to determine the implications selective abortion has on the disabled community and how selective abortion is being used to ban abortion overall in the U.S.

ContributorsNguyen, Nhu Quynh (Co-author) / McNeill, Ashley (Co-author) / Brian, Jennifer (Thesis director) / Manninen, Bertha (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Watts College of Public Service & Community Solut (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

Characterization and analysis of a novel platform for profiling the antibody response

Description

Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze…

Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze the factors affecting the binding patterns using monoclonal antibodies and determine how much information may be extracted from the sequences. Specifically, I examined the effects of antibody concentration, competition, peptide density, and antibody valence. Peptide binding could be detected at the low concentrations relevant to immunosignaturing, and a monoclonal's signature could even be detected in the presences of 100 fold excess naive IgG. I also found that peptide density was important, but this effect was not due to bivalent binding. Next, I examined in more detail how a polyreactive antibody binds to the random sequence peptides compared to protein sequence derived peptides, and found that it bound to many peptides from both sets, but with low apparent affinity. An in depth look at how the peptide physicochemical properties and sequence complexity revealed that there were some correlations with properties, but they were generally small and varied greatly between antibodies. However, on a limited diversity but larger peptide library, I found that sequence complexity was important for antibody binding. The redundancy on that library did enable the identification of specific sub-sequences recognized by an antibody. The current immunosignaturing platform has little repetition of sub-sequences, so I evaluated several methods to infer antibody epitopes. I found two methods that had modest prediction accuracy, and I developed a software application called GuiTope to facilitate the epitope prediction analysis. None of the methods had sufficient accuracy to identify an unknown antigen from a database. In conclusion, the characteristics of the immunosignaturing platform observed through monoclonal antibody experiments demonstrate its promise as a new diagnostic technology. However, a major limitation is the difficulty in connecting the signature back to the original antigen, though larger peptide libraries could facilitate these predictions.

ContributorsHalperin, Rebecca (Author) / Johnston, Stephen A. (Thesis advisor) / Bordner, Andrew (Committee member) / Taylor, Thomas (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)

Created2011

Use of random peptide reactivities to analyze host immune responses of African swine fever virus infection and immunization

Description

African Swine Fever (ASF), endemic in many African countries, is now spreading to other continents. Though ASF is capable of incurring serious economic losses in affected countries, no vaccine exists to provide immunity to animals. Disease control relies largely on rapid diagnosis and the implementation of movement restrictions and strict…

African Swine Fever (ASF), endemic in many African countries, is now spreading to other continents. Though ASF is capable of incurring serious economic losses in affected countries, no vaccine exists to provide immunity to animals. Disease control relies largely on rapid diagnosis and the implementation of movement restrictions and strict eradication programs. Developing a scalable, accurate and low cost diagnostic for ASF will be of great help for the current situation. CIM's 10K random peptide microarray is a new high-throughput platform that allows systematic investigations of immune responses associated with disease and shows promise as a diagnostic tool. In this study, this new technology was applied to characterize the immune responses of ASF virus (ASFV) infections and immunizations. Six sets of sera from ASFV antigen immunized pigs, 6 sera from infected pigs and 20 sera samples from unexposed pigs were tested and analyzed statistically. Results show that both ASFV antigen immunized pigs and ASFV viral infected pigs can be distinguished from unexposed pigs. Since it appears that immune responses to other viral infections are also distinguishable on this platform, it holds the potential of being useful in developing a new ASF diagnostic. The ability of this platform to identify specific ASFV antibody epitopes was also explored. A subtle motif was found to be shared among a set of peptides displaying the highest reactivity for an antigen specific antibody. However, this motif does not seem to match with any antibody epitopes predicted by a linear antibody epitope prediction.

ContributorsXiao, Liang (Author) / Sykes, Kathryn (Thesis advisor) / Zhao, Zhan-Gong (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)

Created2011

An Environmental and Economic Analysis of The Near Future of Lithium Ion Batteries

Description

Lithium ion batteries are quintessential components of modern life. They are used to power smart devices — phones, tablets, laptops, and are rapidly becoming major elements in the automotive industry. Demand projections for lithium are skyrocketing with production struggling to keep up pace. This drive is due mostly to the…

Lithium ion batteries are quintessential components of modern life. They are used to power smart devices — phones, tablets, laptops, and are rapidly becoming major elements in the automotive industry. Demand projections for lithium are skyrocketing with production struggling to keep up pace. This drive is due mostly to the rapid adoption of electric vehicles; sales of electric vehicles in 2020 are more than double what they were only a year prior. With such staggering growth it is important to understand how lithium is sourced and what that means for the environment. Will production even be capable of meeting the demand as more industries make use of this valuable element? How will the environmental impact of lithium affect growth? This thesis attempts to answer these questions as the world looks to a decade of rapid growth for lithium ion batteries.

ContributorsMelton, John (Author) / Brian, Jennifer (Thesis director) / Karwat, Darshawn (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)

Created2021-05

Assessing corporate bioethics: a qualitative exploration of how bioethics is enacted in biomedicine companies

Description

Corporations in biomedicine hold significant power and influence, in both political and personal spheres. The decisions these companies make about ethics are critically important, as they help determine what products are developed, how they are developed, how they are promoted, and potentially even how they are regulated. In the last…

Corporations in biomedicine hold significant power and influence, in both political and personal spheres. The decisions these companies make about ethics are critically important, as they help determine what products are developed, how they are developed, how they are promoted, and potentially even how they are regulated. In the last fifteen years, for-profit private companies have been assembling bioethics committees to help resolve dilemmas that require informed deliberation about ethical, legal, scientific, and economic considerations. Private sector bioethics committees represent an important innovation in the governance of emerging technologies, with corporations taking a lead role in deciding what is ethically appropriate or problematic. And yet, we know very little about these committees, including their structures, memberships, mandates, authority, and impact. Drawing on an extensive literature review and qualitative analysis of semi-structured interviews with executives, scientists and board members, this dissertation provides an in-depth analysis of the Ethics and Public Policy Board at SmithKline Beecham, the Ethics Advisory Board at Advanced Cell Technology, and the Bioethics Committee at Eli Lilly and offers insights about how ideas of bioethics and governance are currently imagined and enacted within corporations. The SmithKline Beecham board was the first private sector bioethics committee; its mandate was to explore, in a comprehensive and balanced analysis, the ethics of macro trends in science and technology. The Advanced Cell Technology board was created to be like a watchdog for the company, to prevent them from making major errors. The Eli Lilly board is different than the others in that it is made up mostly of internal employees and does research ethics consultations within the company. These private sector bioethics committees evaluate and construct new boundaries between their private interests and the public values they claim to promote. Findings from this dissertation show that criticisms of private sector bioethics that focus narrowly on financial conflicts of interest and a lack of transparency obscure analysis of the ideas about governance (about expertise, credibility and authority) that emerge from these structures and hamper serious debate about the possible impacts of moving ethical deliberation from the public to the private sector.

ContributorsBrian, Jennifer (Author) / Robert, Jason S (Thesis advisor) / Maienschein, Jane (Committee member) / Hurlbut, James B (Committee member) / Sarewitz, Daniel (Committee member) / Brown, Mark B. (Committee member) / Moreno, Jonathan D. (Committee member) / Arizona State University (Publisher)

Created2012

Identification of neo-antigens for a cancer vaccine by transcriptome analysis

Description

We propose a novel solution to prevent cancer by developing a prophylactic cancer. Several sources of antigens for cancer vaccines have been published. Among these, antigens that contain a frame-shift (FS) peptide or viral peptide are quite attractive for a variety of reasons. FS sequences, from either mistake in RNA…

We propose a novel solution to prevent cancer by developing a prophylactic cancer. Several sources of antigens for cancer vaccines have been published. Among these, antigens that contain a frame-shift (FS) peptide or viral peptide are quite attractive for a variety of reasons. FS sequences, from either mistake in RNA processing or in genomic DNA, may lead to generation of neo-peptides that are foreign to the immune system. Viral peptides presumably would originate from exogenous but integrated viral nucleic acid sequences. Both are non-self, therefore lessen concerns about development of autoimmunity. I have developed a bioinformatical approach to identify these aberrant transcripts in the cancer transcriptome. Their suitability for use in a vaccine is evaluated by establishing their frequencies and predicting possible epitopes along with their population coverage according to the prevalence of major histocompatibility complex (MHC) types. Viral transcripts and transcripts with FS mutations from gene fusion, insertion/deletion at coding microsatellite DNA, and alternative splicing were identified in NCBI Expressed Sequence Tag (EST) database. 48 FS chimeric transcripts were validated in 50 breast cell lines and 68 primary breast tumor samples with their frequencies from 4% to 98% by RT-PCR and sequencing confirmation. These 48 FS peptides, if translated and presented, could be used to protect more than 90% of the population in Northern America based on the prediction of epitopes derived from them. Furthermore, we synthesized 150 peptides that correspond to FS and viral peptides that we predicted would exist in tumor patients and we tested over 200 different cancer patient sera. We found a number of serological reactive peptide sequences in cancer patients that had little to no reactivity in healthy controls; strong support for the strength of our bioinformatic approach. This study describes a process used to identify aberrant transcripts that lead to a new source of antigens that can be tested and used in a prophylactic cancer vaccine. The vast amount of transcriptome data of various cancers from the Cancer Genome Atlas (TCGA) project will enhance our ability to further select better cancer antigen candidates.

ContributorsLee, HoJoon (Author) / Johnston, Stephen A. (Thesis advisor) / Kumar, Sudhir (Committee member) / Miller, Laurence (Committee member) / Stafford, Phillip (Committee member) / Sykes, Kathryn (Committee member) / Arizona State University (Publisher)

Created2012

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