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Description
Since Darwin popularized the evolution theory in 1895, it has been completed and studied through the years. Starting in 1990s, evolution at molecular level has been used to discover functional molecules while studying the origin of functional molecules in nature by mimicing the natural selection process in laboratory. Along this line, my Ph.D. dissertation focuses on the in vitro selection of two important biomolecules, deoxynucleotide acid (DNA) and protein with binding properties. Chapter two focuses on in vitro selection of DNA. Aptamers are single-stranded nucleic acids that generated from a random pool and fold into stable three-dimensional structures with ligand binding sites that are complementary in shape and charge to a desired target. While aptamers have been selected to bind a wide range of targets, it is generally thought that these molecules are incapable of discriminating strongly alkaline proteins due to the attractive forces that govern oppositely charged polymers. By employing negative selection step to eliminate aptamers that bind with off-target through charge unselectively, an aptamer that binds with histone H4 protein with high specificity (>100 fold)was generated. Chapter four focuses on another functional molecule: protein. It is long believed that complex molecules with different function originated from simple progenitor proteins, but very little is known about this process. By employing a previously selected protein that binds and catalyzes ATP, which is the first and only protein that was evolved completely from random pool and has a unique α/β-fold protein scaffold, I fused random library to the C-terminus of this protein and evolved a multi-domain protein with decent properties. Also, in chapter 3, a unique bivalent molecule was generated by conjugating peptides that bind different sites on the protein with nucleic acids. By using the ligand interactions by nucleotide conjugates technique, off-the shelf peptide was transferred into high affinity protein capture reagents that mimic the recognition properties of natural antibodies. The designer synthetic antibody amplifies the binding affinity of the individual peptides by ∼1000-fold to bind Grb2 with a Kd of 2 nM, and functions with high selectivity in conventional pull-down assays from HeLa cell lysates.
ContributorsJiang, Bing (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Scholars have written much about home and meaning, yet they have said little about the professionally furnished model home viewed as a cultural artifact. Nor is there literature addressing how the home building industry uses these spaces to promote images of family life to increase sales. This research notes that not only do the structure, design, and layout of the model home formulate cultural identity but also the furnishings and materials within. Together, the model home and carefully selected artifacts placed therein help to express specific chosen lifestyles as that the home builder determines. This thesis considers the model home as constructed as well as builder's publications, descriptions, and advertisements. The research recognizes the many facets of merchandising, consumerism, and commercialism influencing the design and architecture of the suburban home. Historians of visual and cultural studies often investigate these issues as separate components. By contrast, this thesis offers an integrated framework of inquiry, drawing upon such disciplines as cultural history, anthropology, and material culture. The research methodology employs two forms of content analysis - image and text. The study analyzes 36 model homes built in Phoenix, Arizona, during the period 1955-1956. The thesis explores how the builder sends a message, i.e. images, ideals, and aspirations, to the potential home buyer through the design and decoration of the model home. It then speculates how the home buyer responds to those messages. The symbiotic relationship between the sender and receiver, together, tells a story about the Phoenix lifestyle and the domestic ideals of the 1950s. Builders sent messages surrounding convenience, spaciousness, added luxury, and indoor-outdoor living to a growing and discriminating home buying market.
ContributorsGolab, Coreen R (Author) / Brandt, Beverly K. (Thesis advisor) / Bernardi, Jose (Committee member) / Schleif, Corine (Committee member) / Arizona State University (Publisher)
Created2013
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cyanovirin-N (CV-N) is a naturally occurring lectin originally isolated from the cyanobacteria Nostoc ellipsosporum. This 11 kDa lectin is 101 amino acids long with two binding sites, one at each end of the protein. CV-N specifically binds to terminal Manα1-2Manα motifs on the branched, high mannose Man9 and Man8 glycosylations found on enveloped viruses including Ebola, Influenza, and HIV. wt-CVN has micromolar binding to soluble Manα1-2Manα and also inhibits HIV entry at low nanomolar concentrations. CV-N's high affinity and specificity for Manα1-2Manα makes it an excellent lectin to study for its glycan-specific properties. The long-term aim of this project is to make a variety of mutant CV-Ns to specifically bind other glycan targets. Such a set of lectins may be used as screening reagents to identify biomarkers and other glycan motifs of interest. As proof of concept, a T7 phage display library was constructed using P51G-m4-CVN genes mutated at positions 41, 44, 52, 53, 56, 74, and 76 in binding Domain B. Five CV-N mutants were selected from the library and expressed in BL21(DE3) E. coli. Two of the mutants, SSDGLQQ-P51Gm4-CVN and AAGRLSK-P51Gm4-CVN, were sufficiently stable for characterization and were examined by CD, Tm, ELISA, and glycan array. Both proteins have CD minima at approximately 213 nm, indicating largely β-sheet structure, and have Tm values greater than 40°C. ELISA against gp120 and RNase B demonstrate both proteins' ability to bind high mannose glycans. To more specifically determine the binding specificity of each protein, AAGRLSK-P51Gm4-CVN, SSDGLQQ-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN were sent to the Consortium for Functional Glycomics (CFG) for glycan array analysis. AAGRLSK-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN, have identical specificities for high mannose glycans containing terminal Manα1-2Manα. SSDGLQQ-P51Gm4-CVN binds to terminal GlcNAcα1-4Gal motifs and a subgroup of high mannose glycans bound by P51G-m4-CVN. SSDGLQQ-wt-CVN was produced to restore anti-HIV activity and has a high nanomolar EC50 value compared to wt-CVN's low nanomolar activity. Overall, these experiments show that CV-N Domain B can be mutated and retain specificity identical to wt-CVN or acquire new glycan specificities. This first generation information can be used to produce glycan-specific lectins for a variety of applications.
ContributorsRuben, Melissa (Author) / Ghirlanda, Giovanna (Thesis advisor) / Allen, James (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2013
Description
Objectives: Although childhood obesity has received growing attention, parents still fail to recognize overweight and obesity in their children. Accurate identification of overweight or obesity in their child is associated with the parent's responsiveness to interventions aimed at preventing weight-related health issues. Recent research shows that a child's age and gender are associated with parental misperception of their child's weight status, but little is known about the interaction of these factors across various age groups. This study examined the association between a wide range of parent, child, and household factors and the accuracy of parental perception of their child's body weight status compared to parent-measured body weight status. Methods: Data were collected from a random-digit-dial telephone survey of 1708 households located in five low-income New Jersey cities with large minority populations. A subset of 548 children whose parents completed the survey and returned a worksheet of parent-measured heights and weights were the focus of the analysis. Bivariate and multivariate analyses were performed to determine the factors significantly associated with parental perception of their child's body weight status. Results: Based on parent-measure heights and weights, 36% of the children were overweight or obese (OWOB). Only 21% of OWOB children were perceived by their parents as OWOB. Child gender, child body mass index (BMI) and parent BMI were significant independent predictors of parents' accuracy at perceiving their child's body weight status. Conclusion: Boys, OWOB children, and children of OWOB parents had significantly greater odds of parental underestimation of their body weight status. Parents had better recognition of OWOB in their daughters, especially older daughters, than in their sons, suggesting parental gender bias in identifying OWOB in children. Further research is needed regarding parental gender bias and its implications in OWOB identification in children.
ContributorsBader, Wendy (Author) / Ohri-Vachaspati, Punam (Thesis advisor) / Lloyd, Kristen (Committee member) / Crespo, Noe (Committee member) / Arizona State University (Publisher)
Created2013
Description
Objectives Through a cross-sectional observational study, this thesis evaluates the relationship between food insecurity and weight status, eating behaviors, the home food environment, meal planning and preparation, and perceived stress as it relates to predominantly Hispanic/Latino parents in Phoenix, Arizona. The purpose of this study was to address gaps in the literature by examining differences in "healthy" and "unhealthy" eating behaviors, foods available in the home, how time and low energy impact meal preparation, and the level of stress between food security groups. Methods Parents, 18 years or older, were recruited during two pre-scheduled health fairs, from English as a second language classes, or from the Women, Infants, and Children's clinic at a local community center, Golden Gate Community Center, in Phoenix, Arizona. An interview, electronic, or paper survey were offered in either Spanish or English to collect data on the variables described above. In addition to the survey, height and weight were collected for all participants to determine BMI and weight status. One hundred and sixty participants were recruited. Multivariate linear and logistic regression models, adjusting for weight status, education, race/ethnicity, income level, and years residing in the U.S., were used to assess the relationship between food security status and weight status, eating behaviors, the home food environment, meal planning and preparation, and perceived stress. Results Results concluded that food insecurity was more prevalent among parents reporting lower income levels compared to higher income levels (p=0.017). In adjusted models, higher perceived cost of fruits (p=0.004) and higher perceived level of stress (p=0.001) were associated with food insecurity. Given that the sample population was predominately women, a post-hoc analysis was completed on women only. In addition to the two significant results noted in the adjusted analyses, the women-only analysis revealed that food insecure mothers reported lower amounts of vegetables served with meals (p=0.019) and higher use of fast-food when tired or running late (p=0.043), compared to food secure mothers. Conclusion Additional studies are needed to further assess differences in stress levels between food insecure parents and food insecure parents, with special consideration for directionality and its relationship to weight status.
ContributorsVillanova, Christina (Author) / Bruening, Meg (Thesis advisor) / Ohri-Vachaspati, Punam (Committee member) / Vega-Lopez, Sonia (Committee member) / Arizona State University (Publisher)
Created2014
Description
Fruit and vegetable (FV) consumption continues to lag far behind US Department of Agriculture (USDA) recommendations. Interventions targeting individuals' dietary behaviors address only a small fraction of dietary influences. Changing the food environment by increasing availability of and excitement for FV through local food production has shown promise as a method for enhancing intake. However, the extent to which local production is sufficient to meet recommended FV intakes, or actual intakes, of specific populations remains largely unconsidered. This study was the first of its kind to evaluate the capacity to support FV intake of Arizona's population with statewide production of FV. We created a model to evaluate what percentage of Dietary Guidelines for Americans (DGA) recommendations, as well as actual consumption, state-level FV production could meet in a given year. Intake and production figures were amended to include estimates of only fresh, non-tropical FV. Production was then estimated by month and season to illustrate fluctuations in availability of FV. Based on our algorithm, Arizona production met 184.5% of aggregate fresh vegetable recommendations, as well as 351.9% of estimated intakes of Arizonans, but met only 29.7% of recommended and 47.8% of estimated intake of fresh, non-tropical fruit. Much of the excess vegetable production can be attributed to the dark-green vegetable sub-group category, which could meet 3204.6% and 3160% of Arizonans' aggregated recommendations and estimated intakes, respectively. Only minimal seasonal variations in the total fruit and total vegetable categories were found, but production of the five vegetable sub-groups varied between the warm and cool seasons by 19-98%. For example, in the starchy vegetable group, cool season (October to March) production met only 3.6% of recommendations, but warm season (April to November) production supplied 196.5% of recommendations. Results indicate that Arizona agricultural production has the capacity to meet a large proportion of the population's FV needs throughout much of the year, while at the same time remaining a major producer of dark-green vegetables for out-of-state markets.
ContributorsVaudrin, Nicole (Author) / Wharton, Christopher (Christopher Mack), 1977- (Thesis advisor) / Bruening, Meg (Thesis advisor) / Ohri-Vachaspati, Punam (Committee member) / Villalobos, J. Rene (Committee member) / Arizona State University (Publisher)
Created2013
Description
There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water and sunlight. As a part of the photosynthetic electron transport chain (PETC) of the green algae Chlamydomonas reinhardtii, water is split via Photosystem II (PSII) and the electrons flow through a series of electron transfer cofactors in cytochrome b6f, plastocyanin and Photosystem I (PSI). The terminal electron acceptor of PSI is ferredoxin, from which electrons may be used to reduce NADP+ for metabolic purposes. Concomitant production of a H+ gradient allows production of energy for the cell. Under certain conditions and using the endogenous hydrogenase, excess protons and electrons from ferredoxin may be converted to molecular hydrogen. In this work it is demonstrated both that certain mutations near the quinone electron transfer cofactor in PSI can speed up electron transfer through the PETC, and also that a native [FeFe]-hydrogenase can be expressed in the C. reinhardtii chloroplast. Taken together, these research findings form the foundation for the design of a PSI-hydrogenase fusion for the direct and continuous photo-production of hydrogen in vivo.
ContributorsReifschneider, Kiera (Author) / Redding, Kevin (Thesis advisor) / Fromme, Petra (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Consumers search before making virtually any purchase. The notion that consumers engage in costly search is well-understood to have deep implications for market performance. However to date, no theoretical model allows for the observation that consumers often purchase more than a single product in an individual shopping occasion. Clothing, food, books, and music are but four important examples of goods that are purchased many items at a time. I develop a modeling approach that accounts for multi-purchase occasions in a structural way. My model shows that as preference for variety increases, so does the size of the consideration set. Search models that ignore preference for variety are, therefore, likely to under-predict the number of products searched. It is generally thought that lower search costs increase retail competition which pushes prices and assortments down. However, I show that there is an optimal number of products to offer depending on the intensity of consumer search costs. Consumers with high search costs prefer to shop at a store with a large assortment of goods and purchase multiple products, even if the prices that firm charges is higher than competing firms' prices. On the other hand, consumers with low search costs tend to purchase fewer goods and shop at the stores that have lower prices, as long as the store has a reasonable assortment offering. The implications for market performance are dramatic and pervasive. In particular, the misspecification of demand model in which search is important and/or multiple discreteness is observed will produce biased parameter estimates leading to erroneous managerial conclusions.
ContributorsAllender, William Jacob (Author) / Richards, Timothy J. (Thesis advisor) / Park, Sungho (Committee member) / Hamilton, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
I compare the effect of anonymous social network ratings (Yelp.com) and peer group recommendations on restaurant demand. I conduct a two-stage choice experiment in which restaurant visits in the first stage are informed by online social network reviews from Yelp.com, and visits in the second stage by peer network reviews. I find that anonymous reviewers have a stronger effect on restaurant preference than peers. I also compare the power of negative reviews with that of positive reviews. I found that negative reviews are more powerful compared to the positive reviews on restaurant preference. More generally, I find that in an environment of high attribute uncertainty, information gained from anonymous experts through social media is likely to be more influential than information obtained from peers.
ContributorsTiwari, Ashutosh (Author) / Richards, Timothy J. (Thesis advisor) / Qiu, Yueming (Committee member) / Grebitus, Carola (Committee member) / Arizona State University (Publisher)
Created2013