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ASU Electronic Theses and Dissertations


This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.

In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.

Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.


Subject
Date Range
2010 2019


Advocacy groups work across many aspects of “death with dignity” practice and treatment, and provide insight across multiple aspects of “death with dignity”. This study argues that key advocacy groups in the American death with dignity movement influenced the broader conceptualization of death with dignity in a way that makes patients more able to achieve it. This influence has been a dynamic process across different periods of practice starting the discussion of “death with dignity” in 1985 through today, although this thesis extends only to 2011. The question in this study is how do the three main historical advocacy groups …

Contributors
Cohan, Hailey E, Ellison, Karin, O'Neil, Erica, et al.
Created Date
2019

In most diploid cells, autosomal genes are equally expressed from the paternal and maternal alleles resulting in biallelic expression. However, as an exception, there exists a small number of genes that show a pattern of monoallelic or biased-allele expression based on the allele’s parent-of-origin. This phenomenon is termed genomic imprinting and is an evolutionary paradox. The best explanation for imprinting is David Haig's kinship theory, which hypothesizes that monoallelic gene expression is largely the result of evolutionary conflict between males and females over maternal involvement in their offspring. One previous RNAseq study has investigated the presence of parent-of-origin effects, or …

Contributors
Underwood, Avery, Wilson, Melissa, Buetow, Kenneth, et al.
Created Date
2019

Access to testing for the human immunodeficiency virus (HIV), as well as other care services related to HIV/AIDS, have greatly improved in Tanzania over the last decade. Despite the country’s efforts to increase the number of individuals who get tested for HIV annually, it is estimated that only 52.2-70.0% of people living with HIV (PLWH) knew their HIV positive status at the end of 2017. In addition, research in Tanzania has shown that HIV-related stigma and discrimination are widespread and contribute to low uptake of HIV testing and non-adherence to antiretroviral treatment (ART). In order to achieve the goals set …

Contributors
Allen, Megan, Jacobs, Bertram, Neuberg, Steven, et al.
Created Date
2019

The Basilisk lizard is known for its agile locomotion capabilities on granular and aquatic media making it an impressive model organism for studying multi-terrain locomotion mechanics. The work presented here is aimed at understanding locomotion characteristics of Basilisk lizards through a systematic series of robotic and animal experiments. In this work, a Basilisk lizard inspired legged robot with bipedal and quadrupedal locomotion capabilities is presented. A series of robot experiments are conducted on dry and wet (saturated) granular media to determine the effects of gait parameters and substrate saturation, on robot velocity and energetics. Gait parameters studied here are stride …

Contributors
Jayanetti, Vidu, Marvi, Hamid, Emady, Heather, et al.
Created Date
2019

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 …

Contributors
Hurtado, Jonathan, Chen, Qiang, Arntzen, Charles, et al.
Created Date
2019

Greater than 11% of the total population of Americans age 12 and older were illicit drug users with close to 1 million suffering from cocaine use disorder in 2017 alone (SAMHSA, 2017), yet there are no effective pharmacological treatments for this disorder. Previous research from the Neisewander Laboratory in male rats found that administration of a 5-HT1BR agonist facilitates cocaine intake when given prior to a daily self-administration session, while inhibiting cocaine intake and attenuating drug-seeking behavior following 21 days of protracted abstinence, yet it is not known whether such effects are observed in female rats. Women face unique challenges …

Contributors
Scott, Samantha Nicola, Neisewander, Janet L, Olive, Michael F, et al.
Created Date
2019

The study was to analyze the extent of bacterial transport in a two-dimensional tank under saturated conditions. The experiments were done in a 2-D tank packed with 3,700 in3 of fine grained, homogenous, chemically inert sand under saturated conditions. The tank used for transport was decontaminated by backwashing with 0.6% chlorine solution with subsequent backwashing with chlorine-neutral water (tap water and Na2S2O3) thus ensuring no residual chlorine in the tank. The transport of bacteria was measured using samples collected from ports at vertical distances of 5, 15 and 25 inches (12.7, 38.1 and 63.5 cm) from the surface of the …

Contributors
Mondal, Indrayudh, Abbaszadegan, Morteza, Dahlen, Paul, et al.
Created Date
2019

Fusion proteins that specifically interact with biochemical marks on chromosomes represent a new class of synthetic transcriptional regulators that decode cell state information rather than deoxyribose nucleic acid (DNA) sequences. In multicellular organisms, information relevant to cell state, tissue identity, and oncogenesis is often encoded as biochemical modifications of histones, which are bound to DNA in eukaryotic nuclei and regulate gene expression states. In 2011, Haynes et al. showed that a synthetic regulator called the Polycomb chromatin Transcription Factor (PcTF), a fusion protein that binds methylated histones, reactivated an artificially-silenced luciferase reporter gene. These synthetic transcription activators are derived from …

Contributors
Vargas, Daniel A., Haynes, Karmella, Wang, Xiao, et al.
Created Date
2019

An insect society needs to share information about important resources in order to collectively exploit them. This task poses a dilemma if the colony must consider multiple resource types, such as food and nest sites. How does it allocate workers appropriately to each resource, and how does it adapt its recruitment communication to the specific needs of each resource type? In this dissertation, I investigate these questions in the ant Temnothorax rugatulus. In Chapter 1, I summarize relevant past work on food and nest recruitment. Then I describe T. rugatulus and its recruitment behavior, tandem running, and I explain its …

Contributors
Cho, John Yohan, Pratt, Stephen C, Hölldobler, Bert, et al.
Created Date
2019

There is a growing consensus that photodegradation accelerates litter decomposition in drylands, but the mechanisms are not well understood. In a previous field study examining how exposure to solar radiation affects decomposition of 12 leaf litter types over 34 months in the Sonoran Desert, litter exposed to UV/blue wavebands of solar radiation decayed faster. The concentration of water-soluble compounds was higher in decayed litter than in new (recently senesced) litter, and higher in decayed litter exposed to solar radiation than other decayed litter. Microbial respiration of litter incubated in high relative humidity for 1 day was greater in decayed litter …

Contributors
Bliss, Michael Scott, Day, Thomas A., Garcia-Pichel, Ferran, et al.
Created Date
2019

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 …

Contributors
Zhang, Jian, Johnston, Stephen Albert, Chang, Yung, et al.
Created Date
2018

Guided by Tinto’s Theory of College Student Departure, I conducted a set of five studies to identify factors that influence students’ social integration in college science active learning classes. These studies were conducted in large-enrollment college science courses and some were specifically conducted in undergraduate active learning biology courses. Using qualitative and quantitative methodologies, I identified how students’ identities, such as their gender and LGBTQIA identity, and students’ perceptions of their own intelligence influence their experience in active learning science classes and consequently their social integration in college. I also determined factors of active learning classrooms and instructor behaviors that …

Contributors
Cooper, Katelyn, Brownell, Sara E, Stout, Valerie, et al.
Created Date
2018

Aboveground net primary production (ANPP) and belowground net primary production (BNPP) may not be influenced equally by the same factors in arid grasslands. Precipitation is known to affect ANPP and BNPP, while soil fauna such as nematodes affect the BNPP through herbivory and predation. This study on black grama grass (Bouteloua eriopoda) in the Chihuahuan Desert investigates the effects of precipitation and nematode presence or absence on net primary production (NPP) as well as the partitioning between the aboveground and belowground components, in this case, the fraction of total net primary production occurring belowground (fBNPP). I used a factorial experiment …

Contributors
Wiedenfeld, Amy, Sala, Osvaldo, Gerber, Leah, et al.
Created Date
2018

The Multiple Antibiotic Resistance Regulator Family (MarR) are transcriptional regulators, many of which forms a dimer. Transcriptional regulation provides bacteria a stabilized responding system to ensure the bacteria is able to efficiently adapt to different environmental conditions. The main function of the MarR family is to create multiple antibiotic resistance from a mutated protein; this process occurs when the MarR regulates an operon. We hypothesized that different transcriptional regulator genes have interactions with each other. It is known that Salmonella pagC transcription is activated by three regulators, i.e., SlyA, MprA, and PhoP. Bacterial Adenylate Cyclase-based Two-Hybrid (BACTH) system was used …

Contributors
Tao, Zenan, Shi, Yixin, Wang, Xuan, et al.
Created Date
2018

Patients who attend genetic counseling appointments report high anxiety and varied satisfaction levels following their appointments. It has been suggested in previous literature that some of the increase in anxiety and reduction in satisfaction is caused by lack of prior information. Here, I investigated whether providing patients with a glossary of genetic terms prior to their counseling appointment improves patient satisfaction and reduces anxiety in an oncology genetic counseling appointment. I surveyed 96 patients attending their first genetic counseling appointment at Banner MD Anderson Cancer Center and analyzed 92 patients for which I had complete data. Patients were randomly selected …

Contributors
Peon, Lidia Maria, Wilson Sayres, Melissa A, Buetow, Kenneth H, et al.
Created Date
2018

The introduction of livestock to the vast majority of public lands may be used to simulate the conditions provided by herbivorous grazers in the past, however little data has been collected on the effects of livestock grazing in Sonoran desert habitats. Vegetative species that are characteristic of the Arizona Upland subdivision of the Sonoran desert did not evolve with extensive grazing by large ungulate populations, and therefore the response to livestock grazing is of particular interest. Four historic Parker 3-step clusters in south-central Arizona were sampled in three cohorts between 1953 and 2016 to interpret changes in rangeland health using …

Contributors
Dunn, Kellie Ann, Alford, Eddie, Cunningham, Stanley, et al.
Created Date
2018

Evolution is the foundation of biology, yet it remains controversial even among college biology students. Acceptance of evolution is important for students if we want them to incorporate evolution into their scientific thinking. However, students’ religious beliefs are a consistent barrier to their acceptance of evolution due to a perceived conflict between religion and evolution. Using pre-post instructional surveys of students in introductory college biology, Study 1 establishes instructional strategies that can be effective for reducing students' perceived conflict between religion and evolution. Through interviews and qualitative analyses, Study 2 documents how instructors teaching evolution at public universities may be …

Contributors
Barnes, Maryann, Brownell, Sara, Nesse, Randolph, et al.
Created Date
2018

For interspecific mutualisms, the behavior of one partner can influence the fitness of the other, especially in the case of symbiotic mutualisms where partners live in close physical association for much of their lives. Behavioral effects on fitness may be particularly important if either species in these long-term relationships displays personality. Animal personality is defined as repeatable individual differences in behavior, and how correlations among these consistent traits are structured is termed behavioral syndromes. Animal personality has been broadly documented across the animal kingdom but is poorly understood in the context of mutualisms. My dissertation focuses on the structure, causes, …

Contributors
Marting, Peter Reilly, Pratt, Stephen C, Wcislo, William T, et al.
Created Date
2018

Endocrine disruptors are chemicals that interact with the hormone system to negative effect. They ‘disrupt’ normal processes to cause diseases like vaginal cancer and obesity, reproductive issues like t-shaped uteri and infertility, and developmental abnormalities like spina bifida and cleft palate. These chemicals are ubiquitous in our daily lives, components in everything from toothpaste to microwave popcorn to plastic water bottles. My dissertation looks at the history, science, and regulation of these impactful substances in order to answer the question of how endocrine disruptors appeared, got interpreted by different groups, and what role science played in the process. My analysis …

Contributors
Abboud, Alexis, Maienschein, Jane A, Crow, Michael M, et al.
Created Date
2018

The ability to tolerate bouts of oxygen deprivation varies tremendously across the animal kingdom. Adult humans from different regions show large variation in tolerance to hypoxia; additionally, it is widely known that neonatal mammals are much more tolerant to anoxia than their adult counterparts, including in humans. Drosophila melanogaster are very anoxia-tolerant relative to mammals, with adults able to survive 12 h of anoxia, and represent a well-suited model for studying anoxia tolerance. Drosophila live in rotting, fermenting media and a result are more likely to experience environmental hypoxia; therefore, they could be expected to be more tolerant of anoxia …

Contributors
Campbell, Jacob B, Harrison, Jon F, Gadau, Juergen, et al.
Created Date
2018

The most advanced social insects, the eusocial insects, form often large societies in which there is reproductive division of labor, queens and workers, have overlapping generations, and cooperative brood care where daughter workers remain in the nest with their queen mother and care for their siblings. The eusocial insects are composed of representative species of bees and wasps, and all species of ants and termites. Much is known about their organizational structure, but remains to be discovered. The success of social insects is dependent upon cooperative behavior and adaptive strategies shaped by natural selection that respond to internal or external …

Contributors
Rodriguez Messan, Marisabel, Kang, Yun, Castillo-Chavez, Carlos, et al.
Created Date
2018

Persistent cooperation between unrelated conspecifics rarely occurs in mature eusocial insect societies. In this dissertation, I present evidence of non-kin cooperation in the Nearctic honey ant Myrmecocystus mendax. Using microsatellite markers, I show that mature colonies in the Sierra Ancha Mountain of central Arizona contain multiple unrelated matrilines, an observation that is consistent with primary polygyny. In contrast, similar analyses suggest that colonies in the Chiricahua Mountains of southeastern Arizona are primarily monogynous. These interpretations are consistent with field and laboratory observations. Whereas cooperative colony founding was observed frequently among groups of Sierra Ancha foundresses, founding in the Chiricahua population …

Contributors
Eriksson, Ti, Gadau, Jürgen, Taylor, Jay, et al.
Created Date
2018

The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, …

Contributors
Mathis, Nicholas, Walker, Sara I, Davies, Paul CW, et al.
Created Date
2018

Lignocellulosic biomass represents a renewable domestic feedstock that can support large-scale biochemical production processes for fuels and specialty chemicals. However, cost-effective conversion of lignocellulosic sugars into valuable chemicals by microorganisms still remains a challenge. Biomass recalcitrance to saccharification, microbial substrate utilization, bioproduct titer toxicity, and toxic chemicals associated with chemical pretreatments are at the center of the bottlenecks limiting further commercialization of lignocellulose conversion. Genetic and metabolic engineering has allowed researchers to manipulate microorganisms to overcome some of these challenges, but new innovative approaches are needed to make the process more commercially viable. Transport proteins represent an underexplored target in …

Contributors
Kurgan, Gavin, Wang, Xuan, Nielsen, David, et al.
Created Date
2018

The properties of adjuvants to stimulate an immune response to treat cancer has sparked a major area of research in the field of immunotherapy. Given the presence of multiple RNA sensors in mammalian host cells for eliciting innate immunity, synthetic RNA nanostructures present a unique opportunity for adjuvant exploration. While RNA nanostructures are organic and biocompatible in nature than other adjuvants, they could be tailored to have desired structural stability and functional diversity for in vivo application. In this study, a rectangular RNA origami nanostructure was designed to contain double-stranded RNA motifs and possess high structural stability. Using in vitro …

Contributors
Rodriguez del Villar, Ryan Luis, Chang, Yung, Liu, Xiaowei, et al.
Created Date
2018

Understanding the diversity, evolutionary relationships, and geographic distribution of species is foundational knowledge in biology. However, this knowledge is lacking for many diverse lineages of the tree of life. This is the case for the desert stink beetles in the tribe Amphidorini LeConte, 1862 (Coleoptera: Tenebrionidae) – a lineage of arid-adapted flightless beetles found throughout western North America. Four interconnected studies that jointly increase our knowledge of this group are presented. First, the darkling beetle fauna of the Algodones sand dunes in southern California is examined as a case study to explore the scientific practice of checklist creation. An updated …

Contributors
Johnston, Murray Andrew, Franz, Nico M, Cartwright, Reed, et al.
Created Date
2018

Human-inhabited or -disturbed areas pose many unique challenges for wildlife, including increased human exposure, novel challenges, such as finding food or nesting sites in novel structures, anthropogenic noises, and novel predators. Animals inhabiting these environments must adapt to such changes by learning to exploit new resources and avoid danger. To my knowledge no study has comprehensively assessed behavioral reactions of urban and rural populations to numerous novel environmental stimuli. I tested behavioral responses of urban, suburban, and rural house finches (Haemorhous mexicanus) to novel stimuli (e.g. objects, noises, food), to presentation of a native predator model (Accipiter striatus) and a …

Contributors
Weaver, Melinda, McGraw, Kevin J, Rutowski, Ronald, et al.
Created Date
2018

Body size plays a pervasive role in determining physiological and behavioral performance across animals. It is generally thought that smaller animals are limited in performance measures compared to larger animals; yet, the vast majority of animals on earth are small and evolutionary trends like miniaturization occur in every animal clade. Therefore, there must be some evolutionary advantages to being small and/or compensatory mechanisms that allow small animals to compete with larger species. In this dissertation I specifically explore the scaling of flight performance (flight metabolic rate, wing beat frequency, load-carrying capacity) and learning behaviors (visual differentiation visual Y-maze learning) across …

Contributors
Duell, Meghan, Harrison, Jon F., Smith, Brian H., et al.
Created Date
2018

Salivary cortisol is the least invasive way in measuring hormonal response during exercise without interruption. In nationally ranked fencers (n=21), changes in cortisol were monitored by measurement of salivary cortisol sampled throughout different rounds of three North American Cup tournaments during the 2017-2018 United States fencing season. The changes were also compared when looking at if a bout ended in a victory or defeat; the difference in rank between opponents; and the difference in score at the end of the bout. Immediately before the tournament cortisol levels were sampled, changes were in comparison to the initial sample as well as …

Contributors
Vie, Jerica Nicole, Baluch, D. Page, Sterner, Beckett, et al.
Created Date
2018

Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in …

Contributors
Aiello, Kenneth, Laubichler, Manfred D, Simeone, Michael, et al.
Created Date
2018

Radioactive cesium (137Cs), released from nuclear power plants and nuclear accidental releases, is a problem due to difficulties regarding its removal. Efforts have been focused on removing cesium and the remediation of the contaminated environment. Traditional treatment techniques include Prussian blue and nano zero-valent ion (nZVI) and nano-Fe/Cu particles to remove Cs from water; however, they are not efficient at removing Cs when present at low concentrations of about 10 parts-per-billion (ppb), typical of concentrations found in the radioactive contaminated sites. The objective of this study was to develop an innovative and simple method to remove Cs+ present at low …

Contributors
Hakim Elahi, Sepideh, Conroy-Ben, Otakuye, Abbaszadegan, Morteza, et al.
Created Date
2018

Single-cell proteomics and transcriptomics analysis are crucial to gain insights of healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment. As an urgent need to advance single-cell analysis, imaging-based technologies have been developed to detect and quantify multiple DNA, RNA …

Contributors
Mondal, Manas, Guo, Jia, Gould, Ian, et al.
Created Date
2018

Riparian systems in the arid southwest are heavily altered and, based on relative land-area, provision a disproportionately high number of native wildlife. Amphibians and reptiles are collectively the most threatened vertebrate taxa and, in the Sonoran Desert, are often reliant on riparian habitat. The link between amphibians and environmental water characteristics, as well as the association between lizards and habitat structure, make herpetofauna good organisms for which to examine the effects of environmental change. My objective was to relate capture rates of a fossorial anuran and lizard abundance to aspects of native, invaded, and shrub-encroached riparian habitats in order to …

Contributors
Riddle, Sidney Bishop, Bateman, Heather L., Albuquerque, Fabio, et al.
Created Date
2018

According to the World Health Organization, cancer is one of the leading causes of death around the world. Although early diagnostics using biomarkers and improved treatments with targeted therapy have reduced the rate of cancer related mortalities, there remain many unknowns regarding the contributions of the tumor microenvironment to cancer progression and therapeutic resistance. The tumor microenvironment plays a significant role by manipulating the progression of cancer cells through biochemical and biophysical signals from the surrounding stromal cells along with the extracellular matrix. As such, there is a critical need to understand how the tumor microenvironment influences the molecular mechanisms …

Contributors
Truong, Danh, Nikkhah, Mehdi, LaBaer, Joshua, et al.
Created Date
2018

Sexual violence, as defined by the Rape, Abuse, Incest National Network (RAINN), is used as an all-encompassing term to include crimes of sexual assault, rape, and sexual abuse (RAINN, 2016). There are numerous negative impacts of sexual violence on a victim. Victims of sexual violence experience negative health impacts, such as physical injuries from the result of sexual violence and unwanted reproductive consequences, such as the risk of sexually transmitted infections or unwanted pregnancy (Shahali et. al, 2016). They also suffer from long-term psychological impacts, such as long-term emotional trauma and post-traumatic stress disorder (PTSD) (Reddington & Kriesel, 2005). The …

Contributors
Kim, Grace, Maienschein, Jane, Ellison, Karin, et al.
Created Date
2017

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 …

Contributors
Al-Sayegh, Mohammed Taher, DeNardo, Dale, Angilletta, Michael, et al.
Created Date
2017

In recent years, the use of biologically based (neurological, neuropsychological, genetic) evidence in criminal trials as support for claims of mental impairments among offenders has increased in popularity. However, research on how exposure to those arguments affects jury decision-making remains unclear. Specifically, arguments rooted in biology sometimes mitigate and sometimes aggravate judgments of criminal responsibility for mentally ill offenders, and this discrepancy seems to stem from the specific conditions by which that disorder was acquired. The following study’s aim was to uncover the precise mechanism(s) behind this elusive effect. Utilizing a 2x2 between subjects experimental design, participants were presented with …

Contributors
Hunter, Shelby, Schweitzer, Nick, Neal, Tess, et al.
Created Date
2017

In the past decades, single-cell metabolic analysis has been playing a key role in understanding cellular heterogeneity, disease initiation, progression, and drug resistance. Therefore, it is critical to develop technologies for individual cellular metabolic analysis using various configurations of microfluidic devices. Compared to bulk-cell analysis which is widely used by reporting an averaged measurement, single-cell analysis is able to present the individual cellular responses to the external stimuli. Particularly, oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) are two key parameters to monitor heterogeneous metabolic profiles of cancer cells. To achieve multi-parameter metabolic measurements on single cells, several technical …

Contributors
Song, Ganquan, Meldrum, Deirdre R., Goryll, Michael, et al.
Created Date
2017

The molt from pupae to adult stage, called eclosion, occurs at specific times of the day in many holometabolous insects. These events are not well studied within Lepidopteran species. It was hypothesized that the eclosion timing in a species may be shaped by strong selective pressures, such as sexual selection in the context of male-male competition. The daily timing of eclosion was measured for six species of nymphalid butterflies. This was done by rearing individuals to pupation, placing the pupa in a greenhouse, and video recording eclosion to obtain the time of day at which it occurred. Four species exhibited …

Contributors
Sencio, Kaylon, Rutowski, Ron, McGraw, Kevin, et al.
Created Date
2017

Principle-based ethical frameworks, which commonly make use of codes of ethics, have come to be the popular approach in guiding ethical behavior within scientific research. In this thesis project, I investigate the benefits and shortcomings of this approach, ultimately to argue that codes of ethics are valuable as an exercise in developing a reconciled value profile for a given research community, and also function well as an internal and external proclamation of values and norms. However, this approach results in technical adherence, at best, and given the extent to which scientific research now irreversibly shapes our experience as human beings, …

Contributors
Craer, Jennifer Ryan, Ellison, Karin, Sarewitz, Daniel, et al.
Created Date
2017

Functional traits research has improved our understanding of how plants respond to their environments, identifying key trade-offs among traits. These studies primarily rely on correlative methods to infer trade-offs and often overlook traits that are difficult to measure (e.g., root traits, tissue senescence rates), limiting their predictive ability under novel conditions. I aimed to address these limitations and develop a better understanding of the trait space occupied by trees by integrating data and process models, spanning leaves to whole-trees, via modern statistical and computational methods. My first research chapter (Chapter 2) simultaneously fits a photosynthesis model to measurements of fluorescence …

Contributors
Fell, Michael, Ogle, Kiona, Barber, Jarrett, et al.
Created Date
2017

Pregnancy and childbirth are both natural occurring events, but still little is known about the signaling mechanisms that induce contractions. Throughout the world, premature labor occurs in 12% of all pregnancies with 36% of infant deaths resulting from preterm related causes. Even though the cause of preterm labor can vary, understanding alternative signaling pathways, which affect muscle contraction, could provide additional treatment options in stopping premature labor. The uterus is composed of smooth muscle, which is innervated, with a plexus of nerves that cover the muscle fibers. Smooth muscle can be stimulated or modulated by many sources such as neurotransmitters …

Contributors
Obayomi, SM Bukola, Baluch, Debra P, Deviche, Pierre, et al.
Created Date
2017

Obesity and its underlying insulin resistance are caused by environmental and genetic factors. DNA methylation provides a mechanism by which environmental factors can regulate transcriptional activity. The overall goal of the work herein was to (1) identify alterations in DNA methylation in human skeletal muscle with obesity and its underlying insulin resistance, (2) to determine if these changes in methylation can be altered through weight-loss induced by bariatric surgery, and (3) to identify DNA methylation biomarkers in whole blood that can be used as a surrogate for skeletal muscle. Assessment of DNA methylation was performed on human skeletal muscle and …

Contributors
Day, Samantha Elaine, Coletta, Dawn K., Katsanos, Christos, et al.
Created Date
2017

Birds have shown promise as models of diabetes due to health and longevity despite naturally high plasma glucose concentrations, a condition which in diabetic humans leads to protein glycation and various complications. Research into mechanisms that protect birds from high plasma glucose have shown that some species of birds have naturally low levels of protein glycation. Some hypothesize a diet rich in carotenoids and other antioxidants protects birds from protein glycation and oxidative damage. There is little research, however, into the amount of protein glycation in birds of prey, which consume a high protein, high fat diet. No studies have …

Contributors
Ingram, Tana Dawn, Sweazea, Karen, Johnston, Carol, et al.
Created Date
2017

Synthetic gene networks have evolved from simple proof-of-concept circuits to complex therapy-oriented networks over the past fifteen years. This advancement has greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a mechanism that cells use to achieve a discrete number of mutually exclusive states in response to environmental inputs. However, complex contextual connections of gene regulatory networks in natural settings often impede the experimental establishment of the function and dynamics of each specific gene network. In this work, diverse synthetic gene networks are rationally designed and constructed using well-characterized biological components to approach the cell fate determination …

Contributors
Wu, Fuqing, Wang, Xiao, Haynes, Karmella, et al.
Created Date
2017

Leprosy and tuberculosis are age-old diseases that have tormented mankind and left behind a legacy of fear, mutilation, and social stigmatization. Today, leprosy is considered a Neglected Tropical Disease due to its high prevalence in developing countries, while tuberculosis is highly endemic in developing countries and rapidly re-emerging in several developed countries. In order to eradicate these diseases effectively, it is necessary to understand how they first originated in humans and whether they are prevalent in nonhuman hosts which can serve as a source of zoonotic transmission. This dissertation uses a phylogenomics approach to elucidate the evolutionary histories of the …

Contributors
Honap, Tanvi Prasad, Stone, Anne C, Rosenberg, Michael S, et al.
Created Date
2017

Obesity impairs skeletal muscle maintenance and regeneration, a condition that can progressively lead to muscle loss, but the mechanisms behind it are unknown. Muscle is primarily composed of multinucleated cells called myotubes which are derived by the fusion of mononucleated myocytes. A key mediator in this process is the cellular fusion protein syncytin-1. This led to the hypothesis that syncytin-1 could be decreased in the muscle of obese/insulin resistant individuals. In contrast, it was found that obese/insulin resistant subjects had higher syncytin-1 expression in the muscle compared to that of the lean subjects. Across the subjects, syncytin-1 correlated significantly with …

Contributors
Ravichandran, Jayachandran, Katsanos, Christos, Coletta, Dawn, et al.
Created Date
2017

The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed. My work characterizes how two …

Contributors
Daer, Rene, Haynes, Karmella, Brafman, David, et al.
Created Date
2017

What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory …

Contributors
Adams, Alyssa Michelle, Walker, Sara I, Davies, Paul CW, et al.
Created Date
2017

Predicting resistant prostate cancer is critical for lowering medical costs and improving the quality of life of advanced prostate cancer patients. I formulate, compare, and analyze two mathematical models that aim to forecast future levels of prostate-specific antigen (PSA). I accomplish these tasks by employing clinical data of locally advanced prostate cancer patients undergoing androgen deprivation therapy (ADT). I demonstrate that the inverse problem of parameter estimation might be too complicated and simply relying on data fitting can give incorrect conclusions, since there is a large error in parameter values estimated and parameters might be unidentifiable. I provide confidence intervals …

Contributors
Baez, Javier, Kuang, Yang, Kostelich, Eric, et al.
Created Date
2017