Matching Items (129)
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
Surveys have shown that several hundred billion weather forecasts are obtained by the United States public each year, and that weather news is one of the most consumed topics in the media. This indicates that the forecast provides information that is significant to the public, and that the public utilizes details associated with it to inform aspects of their life. Phoenix, Arizona is a dry, desert region that experiences a monsoon season and extreme heat. How then, does the weather forecast influence the way Phoenix residents make decisions? This paper aims to draw connections between the weather forecast, decision making, and people who live in a desert environment. To do this, a ten-minute survey was deployed through Amazon Mechanical Turk (MTurk) in which 379 respondents were targeted. The survey asks 45 multiple choice and ranking questions categorized into four sections: obtainment of the forecast, forecast variables of interest, informed decision making based on unique weather variables, and demographics. This research illuminates how residents in the Phoenix metropolitan area use the local weather forecast for decision-making on daily activities, and the main meteorological factors that drive those decisions.
ContributorsMarturano, Julia (Author) / Middel, Ariane (Thesis director) / Schneider, Florian (Committee member) / School of Geographical Sciences and Urban Planning (Contributor, Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Slum development and growth is quite popular in developing countries. Many studies have been done on what social and economic factors are the drivers in establishment of informal settlements at a single cross-section of time, however limited work has been done in studying their spatial growth patterns over time. This study attempts to study a sample of 30 informal settlements that exist in the National Capital Territory of India over a period of 40 years and identify relationships between the spatial growth rates and relevant factors identified in previous socio-economic studies of slums using advanced statistical methods. One of the key contributions of this paper is indicating the usefulness of satellite imagery or remote sensing data in spatial-longitudinal studies. This research utilizes readily available LANDSAT images to recognize the decadal spatial growth from 1970 to 2000, and also in extension, calculate the BI (transformed NDVI) as a proxy for the intensity of development for the settlements. A series of regression models were run after processing the data, and the levels of significance were then studied and compared to see which relationships indicated the highest levels of significance. It was observed that the change in BI had a higher strength of relationships with the change in independent variables than the settlement area growth. Also, logarithmic and cubic models showed the highest R-Square values than any other tested models.
ContributorsPrakash, Mihir (Author) / Guhathakurta, Subhrajit (Thesis advisor) / Myint, Soe W. (Committee member) / Aggarwal, Rimjhim (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
In recent years environmental life-cycle assessments (LCA) have been increasingly used to support planning and development of sustainable infrastructure. This study demonstrates the application of LCA to estimate embedded energy use and greenhouse gas (GHG) emissions related to materials manufacturing and construction processes for low and high density single-family neighborhoods typically found in the Southwest. The LCA analysis presented in this study includes the assessment of more than 8,500 single family detached units, and 130 miles of related roadway infrastructure. The study estimates embedded and GHG emissions as a function of building size (1,500 - 3000 square feet), number of stories (1 or 2), and exterior wall material composition (stucco, brick, block, wood), roof material composition (clay tile, cement tile, asphalt shingles, built up), and as a function of roadway typology per mile (asphalt local residential roads, collectors, arterials). While a hybrid economic input-out life-cycle assessment is applied to estimate the energy and GHG emissions impacts of the residential units, the PaLATE tool is applied to determine the environmental effects of pavements and roads. The results indicate that low density single family neighborhoods are 2 - 2.5 X more energy and GHG intensive, per residential dwelling (unit) built, than high density residential neighborhoods. This relationship holds regardless of whether the functional unit is per acre or per capita. The results also indicate that a typical low density neighborhood (less than 2 dwellings per acre) requires 78 percent more energy and resource in roadway infrastructure per residential unit than a traditional small lot high density (more than 6 dwelling per acre). Also, this study shows that new master planned communities tend to be more energy intensive than traditional non master planned residential developments.
ContributorsFrijia, Stephane (Author) / Guhathakurta, Subhrajit (Committee member) / Williams, Eric D. (Committee member) / Pijawka, David K (Committee member) / Arizona State University (Publisher)
Created2011
Description
This doctoral dissertation research aims to develop a comprehensive definition of urban open spaces and to determine the extent of environmental, social and economic impacts of open spaces on cities and the people living there. The approach I take to define urban open space is to apply fuzzy set theory to conceptualize the physical characteristics of open spaces. In addition, a 'W-green index' is developed to quantify the scope of greenness in urban open spaces. Finally, I characterize the environmental impact of open spaces' greenness on the surface temperature, explore the social benefits through observing recreation and relaxation, and identify the relationship between housing price and open space be creating a hedonic model on nearby housing to quantify the economic impact. Fuzzy open space mapping helps to investigate the landscape characteristics of existing-recognized open spaces as well as other areas that can serve as open spaces. Research findings indicated that two fuzzy open space values are effective to the variability in different land-use types and between arid and humid cities. W-Green index quantifies the greenness for various types of open spaces. Most parks in Tempe, Arizona are grass-dominant with higher W-Green index, while natural landscapes are shrub-dominant with lower index. W-Green index has the advantage to explain vegetation composition and structural characteristics in open spaces. The outputs of comprehensive analyses show that the different qualities and types of open spaces, including size, greenness, equipment (facility), and surrounding areas, have different patterns in the reduction of surface temperature and the number of physical activities. The variance in housing prices through the distance to park was, however, not clear in this research. This dissertation project provides better insight into how to describe, plan, and prioritize the functions and types of urban open spaces need for sustainable living. This project builds a comprehensive framework for analyzing urban open spaces in an arid city. This dissertation helps expand the view for urban environment and play a key role in establishing a strategy and finding decision-makings.
ContributorsKim, Won Kyung (Author) / Wentz, Elizabeth (Thesis advisor) / Myint, Soe W (Thesis advisor) / Brazel, Anthony (Committee member) / Guhathakurta, Subhrajit (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
This study is an initial step in exploring how urban design typologies can help inform community asset research to broaden the definition of physical assets. Asset based community development research identifies specific types of physical assets such as streets, structures, housing or vacant lots. This research argues that a comprehensive look at physical assets is needed, taking into consideration urban typologies such as paths, landmarks, views and districts as well as the spatial relationships that influence their significance. Community asset literature and conditions specific to the Sunnyslope community in Phoenix, Arizona suggest that differences in ethnicity such as spatial segregation, and socio-economic status exist. However, the literature does not address how these differences in ethnicity might influence residents' perceptions of physical assets. This study explores the questions - How do perceptions of physical assets vary among women of different ethnicities? What, if any, are the reasons behind these ethnic differences in perception? The research applied a survey instrument with open-ended and close-ended questions, and a map to mark frequently used routes. Assets identified by recoding open-ended responses were statistically analyzed for frequencies. The most frequently mentioned assets were analyzed by GIS for spatial relationships. Women of White and Latino ethnicities frequently chose individual buildings and locations as physical assets over paths, views, districts and landmarks. White women identified urban typologies as physical assets. In contrast, Latino women identified no significant urban typologies as assets. The inclusion of urban typologies confirmed and expanded upon physical assets previously identified by other asset-based studies on the community of Sunnyslope. Notable differences in ethnicity were found in the perception of physical assets of economic significance, assets for use and assets of visual appeal. Besides ethnicity, age and proximity to assets also influenced asset perception of White and Latino women. Community organizations need to take into consideration the ethnic differences in perception of physical assets, in the context of culture, spatial segregation and differing family structures. The inclusion of urban typologies helped highlight the differences in ethnicities for physical assets of visual appeal, and the use of leisure and recreation facilities.
ContributorsThatte, Aparna (Author) / Ozel, Filiz (Thesis advisor) / Ahrentzen, Sherry (Thesis advisor) / Guhathakurta, Subhrajit (Committee member) / Arizona State University (Publisher)
Created2011
Description
The use of synthetic cathinones or "bath salts" has risen dramatically in recent years with one of the most popular being Methylendioxypyrovalerone (MDPV). Following the temporary legislative ban on the sale and distribution of this compound , a multitude of other cathinone derivatives have been synthesized. The current study seeks to compare the abuse potential of MDPV with one of the emergent synthetic cathinones 4-methylethcathinone (4-MEC), based on their respective ability to lower current thresholds in an intracranial self-stimulation (ICSS) paradigm. Following acute administration (0.1, 0.5, 1 and 2 mg/kg i.p.) MDPV was found to significantly lower ICSS thresholds at all doses tested (F4,35=11.549, p<0.001). However, following acute administration (0.3,1,3,10,30 mg/kg i.p) 4-MEC produced no significant ICSS threshold depression (F5,135= 0.622, p = 0.684). Together these findings suggest that while MDPV may possess significant abuse potential, other synthetic cathinones such as 4-MEC may have a drastically reduced potential for abuse.
ContributorsWegner, Scott Andrew (Author) / Olive, M. Foster (Thesis director) / Presson, Clark (Committee member) / Sanabria, Federico (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Department of Psychology (Contributor)
Created2013-05
Description
Chronic restraint stress impairs hippocampal-mediated spatial learning and memory, which improves following a post-stress recovery period. Here, we investigated whether brain derived neurotrophic factor (BDNF), a protein important for hippocampal function, would alter the recovery from chronic stress-induced spatial memory deficits. Adult male Sprague-Dawley rats were infused into the hippocampus with adeno- associated viral vectors containing the coding sequence for short interfering (si)RNA directed against BDNF or a scrambled sequence (Scr), with both containing the coding information for green fluorescent protein to aid in anatomical localization. Rats were then chronically restrained (wire mesh, 6h/d/21d) and assessed for spatial learning and memory using a radial arm water maze (RAWM) either immediately after stressor cessation (Str-Imm) or following a 21-day post-stress recovery period (Str-Rec). All groups learned the RAWM task similarly, but differed on the memory retention trial. Rats in the Str-Imm group, regardless of viral vector contents, committed more errors in the spatial reference memory domain than did non-stressed controls. Importantly, the typical improvement in spatial memory following recovery from chronic stress was blocked with the siRNA against BDNF, as Str-Rec-siRNA performed worse on the RAWM compared to the non-stressed controls or Str-Rec-Scr. These effects were specific for the reference memory domain as repeated entry errors that reflect spatial working memory were unaffected by stress condition or viral vector contents. These results demonstrate that hippocampal BDNF is necessary for the recovery from stress-induced hippocampal dependent spatial memory deficits in the reference memory domain.
ContributorsOrtiz, J. Bryce (Author) / Conrad, Cheryl D. (Thesis advisor) / Olive, M. Foster (Committee member) / Taylor, Sara (Committee member) / Bimonte-Nelson, Heather A. (Committee member) / Arizona State University (Publisher)
Created2013