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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

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
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Description
Immunotherapy has been revitalized with the advent of immune checkpoint blockade

treatments, and neo-antigens are the targets of immune system in cancer patients who

respond to the treatments. The cancer vaccine field is focused on using neo-antigens from

unique point mutations of genomic sequence in the cancer patient for making

personalized cancer vaccines. However,

Immunotherapy has been revitalized with the advent of immune checkpoint blockade

treatments, and neo-antigens are the targets of immune system in cancer patients who

respond to the treatments. The cancer vaccine field is focused on using neo-antigens from

unique point mutations of genomic sequence in the cancer patient for making

personalized cancer vaccines. However, we choose a different path to find frameshift

neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on

frameshift antigens.

In this dissertation, I have summarized and characterized all the potential frameshift

antigens from microsatellite regions in human, dog and mouse. A list of frameshift

antigens was validated by PCR in tumor samples and the mutation rate was calculated for

one candidate – SEC62. I develop a method to screen the antibody response against

frameshift antigens in human and dog cancer patients by using frameshift peptide arrays.

Frameshift antigens selected by positive antibody response in cancer patients or by MHC

predictions show protection in different mouse tumor models. A dog version of the

cancer vaccine based on frameshift antigens was developed and tested in a small safety

trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell

immune responses. Further, I built the human exon junction frameshift database which

includes all possible frameshift antigens from mis-splicing events in exon junctions, and I

develop a method to find potential frameshift antigens from large cancer

immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer

diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that

ii

early treatment gives significantly better protection than late treatment and the correct

time point for treatment is crucial to give the best clinical benefit. A model for early

treatment is developed with these results.

Frameshift neo-antigens from microsatellite regions and mis-splicing events are

abundant at mRNA level and they are better antigens than neo-antigens from point

mutations in the genomic sequences of cancer patients in terms of high immunogenicity,

low probability to cause autoimmune diseases and low cost to develop a broadly effective

vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for

cancer vaccine development.
ContributorsZhang, Jian (Author) / Johnston, Stephen Albert (Thesis advisor) / Chang, Yung (Committee member) / Stafford, Phillip (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Antibodies are naturally occurring proteins that protect a host during infection through direct neutralization and/or recruitment of the innate immune system. Unfortunately, in some infections, antibodies present unique hurdles that must be overcome for a safer and more efficacious antibody-based therapeutic (e.g., antibody dependent viral enhancement (ADE) and inflammatory pathology).

Antibodies are naturally occurring proteins that protect a host during infection through direct neutralization and/or recruitment of the innate immune system. Unfortunately, in some infections, antibodies present unique hurdles that must be overcome for a safer and more efficacious antibody-based therapeutic (e.g., antibody dependent viral enhancement (ADE) and inflammatory pathology). This dissertation describes the utilization of plant expression systems to produce N-glycan specific antibody-based therapeutics for Dengue Virus (DENV) and Chikungunya Virus (CHIKV). The Fc region of an antibody interacts with Fcγ Receptors (FcγRs) on immune cells and components of the innate immune system. Each class of immune cells has a distinct action of neutralization (e.g., antibody dependent cell-mediated cytotoxicity (ADCC) and antibody dependent cell-mediated phagocytosis (ADCP)). Therefore, structural alteration of the Fc region results in novel immune pathways of protection. One approach is to modulate the N-glycosylation in the Fc region of the antibody. Of scientific significance, is the plant’s capacity to express human antibodies with homogenous plant and humanized N-glycosylation (WT and GnGn, respectively). This allows to study how specific glycovariants interact with other components of the immune system to clear an infection, producing a tailor-made antibody for distinct diseases. In the first section, plant-produced glycovariants were explored for reduced interactions with specific FcγRs for the overall reduction in ADE for DENV infections. The results demonstrate a reduction in ADE of our plant-produced monoclonal antibodies in in vitro experiments, which led to a greater survival in vivo of immunodeficient mice challenged with lethal doses of DENV and a sub-lethal dose of DENV in ADE conditions. In the second section, plant-produced glycovariants were explored for increased interaction with specific FcγRs to improve ADCC in the treatment of the highly inflammatory CHIKV. The results demonstrate an increase ADCC activity in in vitro experiments and a reduction in CHIKV-associated inflammation in in vivo mouse models. Overall, the significance of this dissertation is that it can provide a treatment for DENV and CHIKV; but equally importantly, give insight to the role of N-glycosylation in antibody effector functions, which has a broader implication for therapeutic development for other viral infections.
ContributorsHurtado, Jonathan (Author) / Chen, Qiang (Thesis advisor) / Arntzen, Charles (Committee member) / Borges, Chad (Committee member) / Lake, Douglas (Committee member) / Arizona State University (Publisher)
Created2019
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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,

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
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Description
We examined the evolutionary morphological responses of Drosophila melanogaster that had evolved at constant cold (16°), constant hot (25°C), and fluctuating (16° and 25°C). Flies that were exposed to the constant low mean temperature developed larger thorax, wing, and cell sizes than those exposed to constant high mean temperatures. Males

We examined the evolutionary morphological responses of Drosophila melanogaster that had evolved at constant cold (16°), constant hot (25°C), and fluctuating (16° and 25°C). Flies that were exposed to the constant low mean temperature developed larger thorax, wing, and cell sizes than those exposed to constant high mean temperatures. Males and females both responded similarly to thermal treatments in average wing and cell size. The resulting cell area for a given wing size in thermal fluctuating populations remains unclear and remains a subject for future research.
ContributorsAdrian, Gregory John (Author) / Angilletta, Michael (Thesis director) / Harrison, Jon (Committee member) / Rusch, Travis (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Description
Three populations of experimentally evolved Drosophila melanogaster populations made up of high temperature (H, constant 25 ᵒC), low temperature (C, constant 16 ᵒC) and temporal homogeneity (T, environment changes between 16 ᵒC and 25 ᵒC) were prepared and assayed to determine difference in citrate synthase activity. Between the three groups,

Three populations of experimentally evolved Drosophila melanogaster populations made up of high temperature (H, constant 25 ᵒC), low temperature (C, constant 16 ᵒC) and temporal homogeneity (T, environment changes between 16 ᵒC and 25 ᵒC) were prepared and assayed to determine difference in citrate synthase activity. Between the three groups, the results were inconclusive: the resulting reaction rates in units of nmol min-1mgfly-1 were 81.8 + 20.6, 101 + 15.6, and 96.9 + 25.2 for the hot (H), cold (C), and temporally homogeneous (T) groups, respectively. We conclude that the high associated variability was due to a lack of control regarding the collection time of the experimentally evolved Drosophila.
ContributorsBelohlavek, David (Author) / Angilletta, Michael (Thesis director) / Francisco, Wilson (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
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Description
There is considerable recent interest in the dynamic nature of immune function in the context of an animal’s internal and external environment. An important focus within this field of ecoimmunology is on how availability of resources such as energy can alter immune function. Water is an additional resource that drives

There is considerable recent interest in the dynamic nature of immune function in the context of an animal’s internal and external environment. An important focus within this field of ecoimmunology is on how availability of resources such as energy can alter immune function. Water is an additional resource that drives animal development, physiology, and behavior, yet the influence hydration has on immunity has received limited attention. In particular, hydration state may have the greatest potential to drive fluctuations in immunity and other physiological functions in species that live in water-limited environments where they may experience periods of dehydration. To shed light on the sensitivity of immune function to hydration state, I first tested the effect of hydration states (hydrated, dehydrated, and rehydrated) and digestive states on innate immunity in the Gila monster, a desert-dwelling lizard. Though dehydration is often thought to be stressful and, if experienced chronically, likely to decrease immune function, dehydration elicited an increase in immune response in this species, while digestive state had no effect. Next, I tested whether dehydration was indeed stressful, and tested a broader range of immune measures. My findings validated the enhanced innate immunity across additional measures and revealed that Gila monsters lacked a significant stress hormone response during dehydration (though results were suggestive). I next sought to test if life history (in terms of environmental stability) drives these differences in dehydration responses using a comparative approach. I compared four confamilial pairs of squamate species that varied in habitat type within each pair—four species that are adapted to xeric environments and four that are adapted to more mesic environments. No effect of life history was detected between groups, but hydration was a driver of some measures of innate immunity and of stress hormone concentrations in multiple species. Additionally, species that exhibited a stress response to dehydration did not have decreased innate immunity, suggesting these physiological responses may often be decoupled. My dissertation work provides new insight into the relationship between hydration, stress, and immunity, and it may inform future work exploring disease transmission or organismal responses to climate change.
ContributorsMoeller, Karla T (Author) / DeNardo, Dale (Thesis advisor) / Angilletta, Michael (Committee member) / French, Susannah (Committee member) / Rutowski, Ronald (Committee member) / Sabo, John (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Desert environments provide considerable challenges to organisms because of high temperatures and limited food and water resources. Accordingly, desert species have behavioral and physiological traits that enable them to cope with these constraints. However, continuing human activity as well as anticipated further changes to the climate and the

Desert environments provide considerable challenges to organisms because of high temperatures and limited food and water resources. Accordingly, desert species have behavioral and physiological traits that enable them to cope with these constraints. However, continuing human activity as well as anticipated further changes to the climate and the vegetative community pose a great challenge to such balance between an organism and its environment. This is especially true in the Arabian Desert, where climate conditions are extreme and environmental disturbances substantial. This study combined laboratory and field components to enhance our understanding of dhub (Uromastyx aegyptius) ecophysiology and determine whether habitat protection influences dhub behavior and physiology.

Results of this study showed that while body mass and body condition consistently diminished as the active season progressed, they were both greater in protected habitats compared to non-protected habitats, regardless of season. Dhubs surface activity and total body water decreased while evaporative water loss and body temperature increased as the active season progressed and ambient temperature got hotter. Total body water was also significantly affected by habitat protection.

Overall, this study revealed that, while habitat protection provided more vegetation, it had little effect on seasonal changes in surface activity. While resource availability in protected areas might allow for larger dhub populations, unprotected areas showed similar body morphometrics, activity, and body temperatures. By developing an understanding of how different coping strategies are linked to particular ecological, morphological, and phylogenetic traits, we will be able to make more accurate predictions regarding the vulnerability of species. By combining previous studies pertaining to conservation of protected species with the results of my study, a number of steps in ecosystem management are recommended to help in the preservation of dhubs in the Kuwaiti desert.
ContributorsAl-Sayegh, Mohammed (Author) / DeNardo, Dale (Thesis advisor) / Angilletta, Michael (Committee member) / Smith, Andrew (Committee member) / Sabo, John (Committee member) / Majeed, Qais (Committee member) / Arizona State University (Publisher)
Created2017
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Description

Studies of animal contests often focus solely on a single static measurement of fighting ability, such as the size or the strength of the individual. However, recent studies have highlighted the importance of individual variation in the dynamic behaviors used during a fight, such as, assessment strategies, decision making, and

Studies of animal contests often focus solely on a single static measurement of fighting ability, such as the size or the strength of the individual. However, recent studies have highlighted the importance of individual variation in the dynamic behaviors used during a fight, such as, assessment strategies, decision making, and fine motor control, as being strong predictors of the outcome of aggression. Here, I combined morphological and behavioral data to discover how these features interact during aggressing interactions in male virile crayfish, Faxonius virilis. I predicted that individual variation in behavioral skill for decision making (i.e., number of strikes thrown), would determine the outcome of contest success in addition to morphological measurements (e.g. body size, relative claw size). To evaluate this prediction, I filmed staged territorial interactions between male F. virilis and later analyzed trial behaviors (e.g. strike, pinches, and bout time) and aggressive outcomes. I found very little support for skill to predict win/loss outcome in trials. Instead, I found that larger crayfish engaged in aggression for longer compared to smaller crayfish, but that larger crayfish did not engage in a greater number of claw strikes or pinches when controlling for encounter duration. Future studies should continue to investigate the role of skill, by using finer-scale techniques such as 3D tracking software, which could track advanced measurements (e.g. speed, angle, and movement efficiency). Such studies would provide a more comprehensive understanding of the relative influence of fighting skill technique on territorial contests.

ContributorsNguyen, Phillip Huy (Author) / Angilletta, Michael (Thesis director) / McGraw, Kevin (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Due to what is known as the “biologically desert fallacy” and the pervasive westernized ideal of wilderness that has influenced widespread American Conservation culture for millennia, urban areas have long been deemed as areas devoid of biodiversity. However, cities can contribute significantly to regional biodiversity and provide vital niches for

Due to what is known as the “biologically desert fallacy” and the pervasive westernized ideal of wilderness that has influenced widespread American Conservation culture for millennia, urban areas have long been deemed as areas devoid of biodiversity. However, cities can contribute significantly to regional biodiversity and provide vital niches for wildlife, illuminating the growing awareness that cities are crucial to the future of conservation and combating the global biodiversity crisis. In terms of the biodiversity crisis, bats are a relevant species of concern. In many studies, different bat species have been broadly classified according to their ability to adapt to urban environments. There is evidence that urban areas can filter bat species based on traits and behavior, with many bats possessing traits that do not allow them to live in cities. The three broad categories are urban avoiders, urban adapters, or urban exploiters based upon where their abundance is highest along a gradient of urban intensity. A common example of an urban exploiter bat is a Mexican Free-tailed bat, which can thrive and rely on urban environments and it is found in the Phoenix Metropolitan area. Bats are important as even in urban environments they play vital ecological roles such as cactus pollination, insect management, and seed dispersal. Bat Crazy is a thesis project focused on urban enhancement and the field of urban biodiversity. The goals of this thesis are to observe how bio-conscious urban cities that work to promote species conservation can serve as a positive tool to promote biodiversity and foster community education and engagement for their urban environment.

ContributorsKaiser, Nicole (Author) / Senko, Jesse (Thesis director) / Angilletta, Michael (Committee member) / Lynch, John (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor)
Created2023-05