Matching Items (146)
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 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
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 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
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 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
Description
Although social learning and attachment theories suggest that parent-adolescent relationships influence adult romantic relationships, research on this topic is limited. Most research examining relations between mother-adolescent and father-adolescent relationship quality and young adult romantic relationship quality has found significant effects of mother-adolescent relationship quality. Findings on fathers have been less consistent. These relations have not been examined among youth who experienced parental divorce, which often negatively impacts parent-child relationships and romantic outcomes. Further, no prior studies examined interactive effects of mother-adolescent and father-adolescent relationship quality on romantic attachment. The current study used longitudinal data from the control group of a randomized controlled trial of a preventative intervention for divorced families to examine unique and interactive effects of mother-adolescent and father-adolescent relationship quality on young adult romantic attachment. The 72 participants completed measures of mother-adolescent relationship quality and father-adolescent relationship quality during adolescence (ages 15-19), and completed a measure of romantic attachment (anxiety and avoidance) during young adulthood (ages 24-28). Findings revealed significant interactive effects of mother-adolescent and father-adolescent relationship quality on young adult romantic anxiety. The pattern of results suggests that having a high quality relationship with one's father can protect children from negative effects of having a low quality relationship with one's mother on romantic anxiety. These results suggest the importance of examining effects of one parent-adolescent relationship on YA romantic attachment in the context of the other parent-adolescent relationship. Exploratory analyses of gender revealed that father-adolescent relationship quality significantly interacted with gender to predict romantic avoidance; this relation was stronger for males. These results suggest that nonresidential fathers play an important role in adolescents' working models of relationships and their subsequent romantic attachment.
ContributorsCarr, Colleen (Author) / Wolchik, Sharlene A (Thesis advisor) / Doane, Leah (Committee member) / Tein, Jenn-Yun (Committee member) / Arizona State University (Publisher)
Created2013
Description
Accumulating evidence implicates exposure to adverse childhood experiences in the development of hypocortisolism in the long-term, and researchers are increasingly examining individual-level mechanisms that may underlie, exacerbate or attenuate this relation among at-risk populations. The current study takes a developmentally and theoretically informed approach to examining episodic childhood stressors, inherent and voluntary self-regulation, and physiological reactivity among a longitudinal sample of youth who experienced parental divorce. Participants were drawn from a larger randomized controlled trial of a preventive intervention for children of divorce between the ages of 9 and 12. The current sample included 159 young adults (mean age = 25.5 years; 53% male; 94% Caucasian) who participated in six waves of data collection, including a 15-year follow-up study. Participants reported on exposure to negative life events (four times over a 9-month period) during childhood, and mothers rated child temperament. Six years later, youth reported on the use of active and avoidant coping strategies, and 15 years later, they participated in a standardized psychosocial stress task and provided salivary cortisol samples prior to and following the task. Path analyses within a structural equation framework revealed that a multiple mediation model best fit the data. It was found that children with better mother-rated self-regulation (i.e. low impulsivity, low negative emotionality, and high attentional focus) exhibited lower total cortisol output 15 years later. In addition, greater self-regulation in childhood predicted greater use of active coping in adolescence, whereas a greater number of negative life events predicted increased use of avoidant coping in adolescence. Finally, a greater number of negative events in childhood predicted marginally lower total cortisol output, and higher levels of active coping in adolescence were associated with greater total cortisol output in young adulthood. Findings suggest that children of divorce who exhibit better self-regulation evidence lower cortisol output during a standardized psychosocial stress task relative to those who have higher impulsivity, lower attentional focus, and/or higher negative emotionality. The conceptual significance of the current findings, including the lack of evidence for hypothesized relations, methodological issues that arose, and issues in need of future research are discussed.
ContributorsHagan, Melissa (Author) / Luecken, Linda (Thesis advisor) / MacKinnon, David (Committee member) / Wolchik, Sharlene (Committee member) / Doane, Leah (Committee member) / Arizona State University (Publisher)
Created2013
Description
Although anxiety may be developmentally appropriate, it can become problematic in some youth. From an ecological perspective, social systems, like family and friendships, are theorized to influence developmental trajectories toward (mal)adjustment, but empirical evidence is scant with regard to the relative impact of subjective satisfaction with family and friendship on anxiety problem development. This thesis study used a subsample of approximately 50% Hispanic/Latino clinic-referred youth (n = 71, ages 6-16 years). Overall, results suggest that the effect of friendship satisfaction on anxiety varied as a function of age but not ethnicity, such that there was a significant negative relationship between child-reported friendship satisfaction and anxiety levels for older children (approx. 9 years and older) but not for younger children. The effect of family satisfaction on anxiety also varied as a function of age, such that older children showed a positive relation between child reported family satisfaction and parent reported anxiety. Furthermore, a positive relation between family satisfaction and anxiety was found only for the H/L children. Post hoc analyses regarding cultural underpinnings of this finding and implications for future research are discussed, as are the results regarding differences between parent and child reports of anxiety.
ContributorsHumphrey, Julia (Author) / Pina, Armando A (Thesis advisor) / Doane, Leah (Committee member) / Bradley, Robert (Committee member) / Arizona State University (Publisher)
Created2013
Description
Type 1 Diabetes Mellitus (T1DM) is a chronic disease that requires maintaining tight metabolic control through complex behavioral and pharmaceutical regimens. Subtle cognitive impairments and stress response dysregulation may partially account for problems negotiating life changes and maintaining treatment adherence among emerging adults. The current study examined whether young adults with T1DM physiologically respond to psychological stress in a dysregulated manner compared to non-diabetic peers, and if such individuals also demonstrated greater cognitive declines following psychological stress. Participants included 23 young adults with T1DM and 52 non-diabetic controls yoked to T1DM participants based on age, gender, ethnicity, participant education, and maternal education. Participants completed a laboratory-based social stressor, pre- and post-stressor neurocognitive testing, provided fingerstick blood spots (for glucose levels) and salivary samples (for cortisol levels) at five points across the protocol, and completed psychosocial questionnaires. Related measures ANOVAs were conducted to assess differences between T1DM participants and the average of yoked controls on cortisol and cognitive outcomes. Results demonstrated that differences in cortisol reactivity were dependent on T1DM participants' use of insulin pump therapy (IPT). T1DM participants not using IPT demonstrated elevated cortisol reactivity compared to matched controls. There was no difference in cortisol reactivity between the T1DM participants on IPT and matched controls. On the Stroop task, performance patterns did not differ between participants with T1DM not on IPT and matched controls. The performance of participants with T1DM on IPT slightly improved following the stressor and matched controls slightly worsened. On the Trail Making Test, the performance of participants with T1DM was not different following the stressor whereas participants without T1DM demonstrated a decline following the stressor. Participants with and without T1DM did not differ in patterns of performance on the Rey Verbal Learning Task, Sustained Attention Allocation Task, Controlled Oral Word Association Task, or overall cortisol output across participation. The results of this study are suggestive of an exaggerated cortisol response to psychological stress in T1DM and indicate potential direct and indirect protective influences of IPT.
ContributorsMarreiro, Catherine (Author) / Luecken, Linda (Thesis advisor) / Doane, Leah (Thesis advisor) / Barrera, Manuel (Committee member) / Aiken, Leona (Committee member) / Arizona State University (Publisher)
Created2013
Description
In order to analyze data from an instrument administered at multiple time points it is a common practice to form composites of the items at each wave and to fit a longitudinal model to the composites. The advantage of using composites of items is that smaller sample sizes are required in contrast to second order models that include the measurement and the structural relationships among the variables. However, the use of composites assumes that longitudinal measurement invariance holds; that is, it is assumed that that the relationships among the items and the latent variables remain constant over time. Previous studies conducted on latent growth models (LGM) have shown that when longitudinal metric invariance is violated, the parameter estimates are biased and that mistaken conclusions about growth can be made. The purpose of the current study was to examine the impact of non-invariant loadings and non-invariant intercepts on two longitudinal models: the LGM and the autoregressive quasi-simplex model (AR quasi-simplex). A second purpose was to determine if there are conditions in which researchers can reach adequate conclusions about stability and growth even in the presence of violations of invariance. A Monte Carlo simulation study was conducted to achieve the purposes. The method consisted of generating items under a linear curve of factors model (COFM) or under the AR quasi-simplex. Composites of the items were formed at each time point and analyzed with a linear LGM or an AR quasi-simplex model. The results showed that AR quasi-simplex model yielded biased path coefficients only in the conditions with large violations of invariance. The fit of the AR quasi-simplex was not affected by violations of invariance. In general, the growth parameter estimates of the LGM were biased under violations of invariance. Further, in the presence of non-invariant loadings the rejection rates of the hypothesis of linear growth increased as the proportion of non-invariant items and as the magnitude of violations of invariance increased. A discussion of the results and limitations of the study are provided as well as general recommendations.
ContributorsOlivera-Aguilar, Margarita (Author) / Millsap, Roger E. (Thesis advisor) / Levy, Roy (Committee member) / MacKinnon, David (Committee member) / West, Stephen G. (Committee member) / Arizona State University (Publisher)
Created2013
Description
The beginning of college is a period in which increased alcohol use often coincides with greater involvement in romantic relationships. Existing literature yields inconsistent findings regarding the influence of different relationship statuses on drinking behavior, perhaps because these studies have not accounted for recent changes in the way college students engage in dating/sexual relationships. In the current college environment, many students who define themselves as non-daters are nonetheless sexually active, a phenomenon referred to as the 'hook up' culture. The present study sought to address this issue by examining the effects of both relationship status and sexual activity on heavy episodic drinking (HED) among 1,467 college students over the course of their first three semesters. Results indicated that the effects of relationship status depended on whether or not an individual was sexually active. Non-dating but sexually active students reported rates of heavy drinking comparable to students who defined themselves as casual daters, but non-dating students who were not sexually active reported drinking behavior similar to those involved in committed relationships. Further, transitions between low and high risk relationship/sexual activity statuses were associated with corresponding changes in HED. Transitioning into a high risk status was associated with greater levels of heavy episodic drinking, whereas transitioning into a low risk status was associated with decreases in this behavior. Together, results indicate that engaging in nonexclusive dating or sexual relationships may play an important role in the development of problematic patterns of alcohol use during the early college years. These findings have potentially important implications both for future research and for prevention and intervention efforts targeting high risk college drinkers.
ContributorsZalewski, Suzanne (Author) / Corbin, Willaim (Thesis advisor) / Doane, Leah (Committee member) / Chassin, Laurie (Committee member) / Arizona State University (Publisher)
Created2012
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 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