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Infections caused by the Hepatitis C Virus (HCV) are very common worldwide, affecting up to 3% of the population. Chronic infection of HCV may develop into liver cirrhosis and liver cancer which is among the top five of the most common cancers. Therefore, vaccines against HCV are under intense study in order to prevent HCV from harming people's health. The envelope protein 2 (E2) of HCV is thought to be a promising vaccine candidate because it can directly bind to a human cell receptor and plays a role in viral entry. However, the E2 protein production in cells is inefficient due to its complicated matured structure. Folding of E2 in the endoplasmic reticulum (ER) is often error-prone, resulting in production of aggregates and misfolded proteins. These incorrect forms of E2 are not functional because they are not able to bind to human cells and stimulate antibody response to inhibit this binding. This study is aimed to overcome the difficulties of HCV E2 production in plant system. Protein folding in the ER requires great assistance from molecular chaperones. Thus, in this study, two molecular chaperones in the ER, calreticulin and calnexin, were transiently overexpressed in plant leaves in order to facilitate E2 folding and production. Both of them showed benefits in increasing the yield of E2 and improving the quality of E2. In addition, poorly folded E2 accumulated in the ER may cause stress in the ER and trigger transcriptional activation of ER molecular chaperones. Therefore, a transcription factor involved in this pathway, named bZIP60, was also overexpressed in plant leaves, aiming at up-regulating a major family of molecular chaperones called BiP to assist protein folding. However, our results showed that BiP mRNA levels were not up-regulated by bZIP60, but they increased in response to E2 expression. The Western blot analysis also showed that overexpression of bZIP60 had a small effect on promoting E2 folding. Overall, this study suggested that increasing the level of specific ER molecular chaperones was an effective way to promote HCV E2 protein production and maturation.
ContributorsHong, Fan (Author) / Mason, Hugh (Thesis advisor) / Gaxiola, Roberto (Committee member) / Chang, Yung (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2011
Description
For over a century, researchers have been investigating collective cognition, in which a group of individuals together process information and act as a single cognitive unit. However, I still know little about circumstances under which groups achieve better (or worse) decisions than individuals. My dissertation research directly addressed this longstanding question, using the house-hunting ant Temnothorax rugatulus as a model system. Here I applied concepts and methods developed in psychology not only to individuals but also to colonies in order to investigate differences of their cognitive abilities. This approach is inspired by the superorganism concept, which sees a tightly integrated insect society as the analog of a single organism. I combined experimental manipulations and models to elucidate the emergent processes of collective cognition. My studies show that groups can achieve superior cognition by sharing the burden of option assessment among members and by integrating information from members using positive feedback. However, the same positive feedback can lock the group into a suboptimal choice in certain circumstances. Although ants are obligately social, my results show that they can be isolated and individually tested on cognitive tasks. In the future, this novel approach will help the field of animal behavior move towards better understanding of collective cognition.
ContributorsSasaki, Takao (Author) / Pratt, Stephen C (Thesis advisor) / Amazeen, Polemnia (Committee member) / Liebig, Jürgen (Committee member) / Janssen, Marco (Committee member) / Fewell, Jennifer (Committee member) / Hölldobler, Bert (Committee member) / Arizona State University (Publisher)
Created2013
Description
The spread of invasive species may be greatly affected by human responses to prior species spread, but models and estimation methods seldom explicitly consider human responses. I investigate the effects of management responses on estimates of invasive species spread rates. To do this, I create an agent-based simulation model of an insect invasion across a county-level citrus landscape. My model provides an approximation of a complex spatial environment while allowing the "truth" to be known. The modeled environment consists of citrus orchards with insect pests dispersing among them. Insects move across the simulation environment infesting orchards, while orchard managers respond by administering insecticide according to analyst-selected behavior profiles and management responses may depend on prior invasion states. Dispersal data is generated in each simulation and used to calculate spread rate via a set of estimators selected for their predominance in the empirical literature. Spread rate is a mechanistic, emergent phenomenon measured at the population level caused by a suite of latent biological, environmental, and anthropogenic. I test the effectiveness of orchard behavior profiles on invasion suppression and evaluate the robustness of the estimators given orchard responses. I find that allowing growers to use future expectations of spread in management decisions leads to reduced spread rates. Acting in a preventative manner by applying insecticide before insects are actually present, orchards are able to lower spread rates more than by reactive behavior alone. Spread rates are highly sensitive to spatial configuration. Spatial configuration is hardly a random process, consisting of many latent factors often not accounted for in spread rate estimation. Not considering these factors may lead to an omitted variables bias and skew estimation results. The ability of spread rate estimators to predict future spread varies considerably between estimators, and with spatial configuration, invader biological parameters, and orchard behavior profile. The model suggests that understanding the latent factors inherent to dispersal is important for selecting phenomenological models of spread and interpreting estimation results. This indicates a need for caution when evaluating spread. Although standard practice, current empirical estimators may both over- and underestimate spread rate in the simulation.
ContributorsShanafelt, David William (Author) / Fenichel, Eli P (Thesis advisor) / Richards, Timothy (Committee member) / Janssen, Marco (Committee member) / Arizona State University (Publisher)
Created2012
Description
Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.
ContributorsHalcomb, Michael Jordan (Author) / Chen, Qiang (Thesis director) / Steele, Kelly (Committee member) / Barrett, The Honors College (Contributor) / College of Letters and Sciences (Contributor)
Created2015-05
Description
Division of labor among task specialists is a key feature of the organization of insect societies. Foraging and emigration are two distinct colony tasks that nonetheless depend on very similar behaviors, including searching outside the nest, evaluating discoveries, and recruiting nestmates. These subtasks are crucial to collective decisions about forager allocation and nest site selection. It remains unclear, however, whether the same ants are responsible for similar behavior in both contexts, and to what degree they show finer specializations among common subtasks. We are investigating these issues in the ant Temnothorax rugatulus, by making detailed behavioral descriptions of individually marked colonies as they forage and emigrate. There exists considerable heterogeneity among nest-movers, with a small proportion consistently responsible for a large share of recruitment. We found a similar pattern of heterogeneity amongst ants retrieving food during foraging, but had inconclusive results when examining recruitment to the food. It also appears that the ants that complete tasks during foraging are different from the ants that complete similar tasks during emigrations. These findings will shed light on the organization of division of labor and how it contributes to collective decision-making.
ContributorsSchaper, Gage (Contributor) / Pratt, Stephen (Thesis director) / Fewell, Jennifer (Committee member) / Shaffer, Zachary (Committee member) / Barrett, The Honors College (Contributor)
Created2013-05
Description
The objectives of this review include a discussion of the West Nile Virus phylogeny, transmission history, how the virus functions in the body and how it is a threat to public health, and then discusses these items related to vaccine technology surrounding West Nile Virus. This will include past developments, current research in the field and what it may take to develop such a vaccine safe and economical for human usage.
ContributorsSlinker, Haleigh Renee (Author) / Chen, Qiang (Thesis director) / Huffman, Holly (Committee member) / Oberstein, Bruce (Committee member) / Barrett, The Honors College (Contributor) / School of Letters and Sciences (Contributor)
Created2013-05
Description
In large part, the great success of eusocial insects is due to efficient division of labor (Duarte et al. 2011; Dornhaus 2008). Within ant colonies, the process of dividing labor is not clearly defined, but it may be key to understanding the productivity and success of these colonies. This study analyzed data from an experiment that was conducted with the goal of examining how finely division of labor is organized in ant colonies. The experiment considered the actions of all ants from three Temnothorax rugatulus colonies. The colonies were each carefully recorded during five distinct emigrations per colony. The experiment produced such a large quantity of data that it was challenging to analyze the results, a major obstacle for many studies of collective behavior. Therefore, I designed a computer program that successfully sorted all of the data and prepared it for an initial statistical analysis that was performed in R. The preliminary results suggest that while most of the ants perform little to no work, there is an overall pattern of elitism; it seems that division of labor in ants is not more finely divided than previously shown. Future studies should provide further analysis of the data and will be useful in forming a more complete understanding of the division of labor within the emigrations of Temnothorax rugatulus colonies.
ContributorsJones, Samantha (Author) / Pratt, Stephen (Thesis director) / Jones, Donald (Committee member) / Shaffer, Zachary (Committee member) / Barrett, The Honors College (Contributor) / W. P. Carey School of Business (Contributor)
Created2012-12
DescriptionThis paper provides an analysis of the differences in impacts made by companies that promote their sustainability efforts. A comparison of companies reveals that the ones with greater supply chain influence and larger consumer bases can make more concrete progress in terms of accomplishment for the sustainability realm.
ContributorsBeaubien, Courtney Lynn (Author) / Anderies, John (Thesis director) / Allenby, Brad (Committee member) / Janssen, Marco (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
Temnothorax ants are a model species for studying collective decision-making. When presented with multiple nest sites, they are able to collectively select the best one and move the colony there. When a scout encounters a nest site, she will spend some time exploring it. In theory she should explore the site for long enough to determine both its quality and an estimate of the number of ants there. This ensures that she selects a good nest site and that there are enough scouts who know about the new nest site to aid her in relocating the colony. It also helps to ensure that the colony reaches a consensus rather than dividing between nest sites. When a nest site reaches a certain threshold of ants, a quorum has been reached and the colony is committed to that nest site. If a scout visits a good nest site where a quorum has not been reached, she will lead a tandem run to bring another scout there so that they can learn the way and later aid in recruitment. At a site where a quorum has been reached, scouts will instead perform transports to carry ants and brood there from the old nest. One piece that is missing in all of this is the mechanism. How is a quorum sensed? One hypothesis is that the encounter rate (average number of encounters with nest mates per second) that an ant experiences at a nest site allows her to estimate the population at that site and determine whether a quorum has been reached. In this study, encounter rate and entrance time were both shown to play a role in whether an ant decided to lead a tandem run or perform a transport. Encounter rate was shown to have a significant impact on how much time an ant spent at a nest site before making her decision, and encounter rates significantly increased as migrations progressed. It was also shown to individual ants did not differ from each other in their encounter rates, visit lengths, or entrance times preceding their first transports or tandem runs, studied across four different migrations. Ants were found to spend longer on certain types of encounters, but excluding certain types of encounters from the encounter rate was not found to change the correlations that were observed. It was also found that as the colony performed more migrations, it became significantly faster at moving to the new nest.
ContributorsJohnson, Christal Marie (Author) / Pratt, Stephen (Thesis director) / Pavlic, Theodore (Committee member) / Shaffer, Zachary (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
Dental caries also known as tooth decay is a bacterial infection that causes demineralization and destruction of enamel dentin and cementum in the tooth. This bacterium, Streprococcus mutans, feeds on the carbohydrates in the mouth and produces lactic acids that result in dental caries. This thesis discusses the use of plants to produce antibodies, Guy 13 and anti-GTFB to treat this dental disease. We believe these plant-derived antibodies will be effective to treat dental caries and economical to produce.
ContributorsSayegh, Luvenia Crystal (Author) / Chen, Qiang (Thesis director) / Garg, Vikas (Committee member) / Barrett, The Honors College (Contributor) / School of Letters and Sciences (Contributor)
Created2014-12