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- Creators: Arizona State University
Description
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 concentrations by engineering a proteoliposome transporter composed of an uptake protein reconstituted into a liposome vesicle. To achieve this, the uptake protein, Kup, from E. coli, was isolated through protein extraction and purification procedures. The new and simple extraction methodology developed in this study was highly efficient and resulted in purified Kup at ~1 mg/mL. A new method was also developed to insert purified Kup protein into the bilayers of liposome vesicles. Finally, removal of CsCl (10 and 100 ppb) was demonstrated by spiking the constructed proteoliposome in lab-fortified water, followed by incubation and ultracentrifugation, and measuring Cs+ with inductively coupled plasma mass spectrometry (ICP-MS).
The ICP-MS results from testing water contaminated with 100 ppb CsCl, revealed that adding 0.1 – 8 mL of Kup proteoliposome resulted in 0.29 – 12.7% Cs removal. Addition of 0.1 – 2 mL of proteoliposome to water contaminated with 10 ppb CsCl resulted in 0.65 – 3.43% Cs removal. These removal efficiencies were greater than the control, liposome with no protein.
A linear relationship was observed between the amount of proteoliposome added to the contaminated water and removal percentage. Consequently, by adding more volumes of proteoliposome, removal can be simply improved. This suggests that with ~ 60-70 mL of proteoliposome, removal of about 90% can be achieved. The novel technique developed herein is a contribution to emerging technologies in the water and wastewater treatment industry.
The objective of this study was to develop an innovative and simple method to remove Cs+ present at low concentrations by engineering a proteoliposome transporter composed of an uptake protein reconstituted into a liposome vesicle. To achieve this, the uptake protein, Kup, from E. coli, was isolated through protein extraction and purification procedures. The new and simple extraction methodology developed in this study was highly efficient and resulted in purified Kup at ~1 mg/mL. A new method was also developed to insert purified Kup protein into the bilayers of liposome vesicles. Finally, removal of CsCl (10 and 100 ppb) was demonstrated by spiking the constructed proteoliposome in lab-fortified water, followed by incubation and ultracentrifugation, and measuring Cs+ with inductively coupled plasma mass spectrometry (ICP-MS).
The ICP-MS results from testing water contaminated with 100 ppb CsCl, revealed that adding 0.1 – 8 mL of Kup proteoliposome resulted in 0.29 – 12.7% Cs removal. Addition of 0.1 – 2 mL of proteoliposome to water contaminated with 10 ppb CsCl resulted in 0.65 – 3.43% Cs removal. These removal efficiencies were greater than the control, liposome with no protein.
A linear relationship was observed between the amount of proteoliposome added to the contaminated water and removal percentage. Consequently, by adding more volumes of proteoliposome, removal can be simply improved. This suggests that with ~ 60-70 mL of proteoliposome, removal of about 90% can be achieved. The novel technique developed herein is a contribution to emerging technologies in the water and wastewater treatment industry.
ContributorsHakim Elahi, Sepideh (Author) / Conroy-Ben, Otakuye (Thesis advisor) / Abbaszadegan, Morteza (Committee member) / Fox, Peter (Committee member) / Arizona State University (Publisher)
Created2018
Description
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 and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
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 and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
ContributorsMondal, Manas (Author) / Guo, Jia (Thesis advisor) / Gould, Ian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2018
Description
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 forecast the potential winners and losers of riparian habitat xerification and invasion.
I measured habitat and monitored herpetofauna at 18 sites near the confluence of the San Pedro River and Gila River in Pinal County, Arizona in 2016 and 2017. Sites were divided into three categories based on dominant tree genus; Populus-Salix, Prosopis, and Tamarix, which represented native riparia, xeric riparia, and invaded riparia, respectively.
Habitat measurements indicated that sites varied significantly in structure, and that dominant tree species was a useful descriptor of habitat physiognomy. Results from herpetofauna trapping demonstrated that Scaphiopus couchii, a fossorial anuran, occupy Prosopis sites at a much higher rate than at Tamarix sites, which were almost completely avoided. S. couchii was also found to be closely tied to xero-riparian habitat components present at Prosopis sites and soil analyses indicate that aspects of soil moisture and texture play an important role in the partitioning of this species across altered riparian habitats. Lizard abundance was found to be significantly lower in Tamarix habitat, with the majority of captures attributed to the generalist whiptail Aspidoscelis tigris. Additionally, more than half of lizard species that were analyzed displayed a negative association to Tamarix habitat. Of the three habitat types considered, Populus-Salix supported the greatest abundance of lizards.
Based on this study, the deleterious effects of xerfication on a riparian herpetofauna community may be lesser than those of Tamarix invasion. These two forms of riparian habitat shift often co-occur, with the ultimate cause being changes in hydrologic regime. This may imply that a bottom-up approach, wherein historic hydrology is restored to restore or maintain native habitats, to riverine management is appropriate for riparian herpetofauna conservation.
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 forecast the potential winners and losers of riparian habitat xerification and invasion.
I measured habitat and monitored herpetofauna at 18 sites near the confluence of the San Pedro River and Gila River in Pinal County, Arizona in 2016 and 2017. Sites were divided into three categories based on dominant tree genus; Populus-Salix, Prosopis, and Tamarix, which represented native riparia, xeric riparia, and invaded riparia, respectively.
Habitat measurements indicated that sites varied significantly in structure, and that dominant tree species was a useful descriptor of habitat physiognomy. Results from herpetofauna trapping demonstrated that Scaphiopus couchii, a fossorial anuran, occupy Prosopis sites at a much higher rate than at Tamarix sites, which were almost completely avoided. S. couchii was also found to be closely tied to xero-riparian habitat components present at Prosopis sites and soil analyses indicate that aspects of soil moisture and texture play an important role in the partitioning of this species across altered riparian habitats. Lizard abundance was found to be significantly lower in Tamarix habitat, with the majority of captures attributed to the generalist whiptail Aspidoscelis tigris. Additionally, more than half of lizard species that were analyzed displayed a negative association to Tamarix habitat. Of the three habitat types considered, Populus-Salix supported the greatest abundance of lizards.
Based on this study, the deleterious effects of xerfication on a riparian herpetofauna community may be lesser than those of Tamarix invasion. These two forms of riparian habitat shift often co-occur, with the ultimate cause being changes in hydrologic regime. This may imply that a bottom-up approach, wherein historic hydrology is restored to restore or maintain native habitats, to riverine management is appropriate for riparian herpetofauna conservation.
ContributorsRiddle, Sidney Bishop (Author) / Bateman, Heather L. (Thesis advisor) / Albuquerque, Fabio (Committee member) / Saul, Steven E (Committee member) / Arizona State University (Publisher)
Created2018
Description
The geotechnical community typically relies on recommendations made from numerical simulations. Commercial software exhibits (local) numerical instabilities in layered soils across soil interfaces. This research work investigates unsaturated moisture flow in layered soils and identifies a possible source of numerical instabilities across soil interfaces and potential improvement in numerical schemes for solving the Richards' equation. The numerical issue at soil interfaces is addressed by a (nonlinear) interface problem. A full analysis of the simplest soil hydraulic model, the Gardner model, identifies the conditions of ill-posedness of the interface problem. Numerical experiments on various (more advanced and practical) soil hydraulic models show that the interface problem can also be ill-posed under certain circumstances. Spurious numerical ponding and/or oscillations around soil interfaces are observed consequently. This work also investigates the impact of different averaging schemes for cell-centered conductivities on the propensity of ill-posedness of the interface problem and concludes that smaller averaging conductivities are more likely to trigger numerical instabilities. In addition, an agent-based stochastic soil model, with hydraulic properties defined at the finite difference cell level, results in a large number of interface problems. This research compares sequences of stochastic realizations in heterogeneous unsaturated soils with the numerical solution using homogenized soil parameters. The mean of stochastic realizations is not identical to the solution obtained from homogenized soil parameters.
ContributorsLiu, Ruowen (Author) / Welfert, Bruno D (Thesis advisor) / Houston, Sandra L. (Committee member) / Jackiewicz, Zdzislaw (Committee member) / Ringhofer, Christian (Committee member) / Zapata, Claudia E (Committee member) / Arizona State University (Publisher)
Created2017
Description
A key factor in the success of social animals is their organization of work. Mathematical models have been instrumental in unraveling how simple, individual-based rules can generate collective patterns via self-organization. However, existing models offer limited insights into how these patterns are shaped by behavioral differences within groups, in part because they focus on analyzing specific rules rather than general mechanisms that can explain behavior at the individual-level. My work argues for a more principled approach that focuses on the question of how individuals make decisions in costly environments.
In Chapters 2 and 3, I demonstrate how this approach provides novel insights into factors that shape the flexibility and robustness of task organization in harvester ant colonies (Pogonomyrmex barbatus). My results show that the degree to which colonies can respond to work in fluctuating environments depends on how individuals weigh the costs of activity and update their behavior in response to social information. In Chapter 4, I introduce a mathematical framework to study the emergence of collective organization in heterogenous groups. My approach, which is based on the theory of multi-agent systems, focuses on myopic agents whose behavior emerges out of an independent valuation of alternative choices in a given work environment. The product of this dynamic is an equilibrium organization in which agents perform different tasks (or abstain from work) with an analytically defined set of threshold probabilities. The framework is minimally developed, but can be extended to include other factors known to affect task decisions including individual experience and social facilitation. This research contributes a novel approach to developing (and analyzing) models of task organization that can be applied in a broader range of contexts where animals cooperate.
In Chapters 2 and 3, I demonstrate how this approach provides novel insights into factors that shape the flexibility and robustness of task organization in harvester ant colonies (Pogonomyrmex barbatus). My results show that the degree to which colonies can respond to work in fluctuating environments depends on how individuals weigh the costs of activity and update their behavior in response to social information. In Chapter 4, I introduce a mathematical framework to study the emergence of collective organization in heterogenous groups. My approach, which is based on the theory of multi-agent systems, focuses on myopic agents whose behavior emerges out of an independent valuation of alternative choices in a given work environment. The product of this dynamic is an equilibrium organization in which agents perform different tasks (or abstain from work) with an analytically defined set of threshold probabilities. The framework is minimally developed, but can be extended to include other factors known to affect task decisions including individual experience and social facilitation. This research contributes a novel approach to developing (and analyzing) models of task organization that can be applied in a broader range of contexts where animals cooperate.
ContributorsUdiani, Oyita (Author) / Kang, Yun (Thesis advisor) / Fewell, Jennifer H (Thesis advisor) / Janssen, Marcus A (Committee member) / Castillo-Chavez, Carlos (Committee member) / Arizona State University (Publisher)
Created2016
Description
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 [i.e. dopamine], hormones [i.e. estrogen], peptides [i.e. oxytocin] and amines. This study focuses on the biogenic monoamine tyramine, which is produced in the tyrosine catecholamine biosynthesis pathway. Tyramine is known to be associated with peripheral vasoconstriction, increased cardiac output, increased respiration, elevated blood glucose and the release of norepinephrine. This research has found tyramine, and its specific receptor TAAR1, to be localized within mouse uterus and that this monoamine can induce uterine contractions at levels similar to oxytocin.
ContributorsObayomi, SM Bukola (Author) / Baluch, Debra P (Thesis advisor) / Deviche, Pierre (Thesis advisor) / Smith, Brian H. (Committee member) / Arizona State University (Publisher)
Created2017
Description
Throughout the Southwest, complex geology and physiography concomitant with climatic variability contribute to diverse stream hydrogeomorphologies. Many riparian plant species store their seeds in soil seed banks, and germinate in response to moisture pulses, but the climatic controls of this response are poorly understood. To better understand the ecological implications of a changing climate on riparian plant communities, I investigated seed bank responses to seasonal temperature patterns and to stream hydrogeomorphic type. I asked the following questions: Are there distinct suites of warm and cool temperature germinating species associated with Southwestern streams; how do they differ between riparian and terrestrial zones, and between ephemeral and perennial streams? How does alpha diversity of the soil seed bank differ between streams with ephemeral, intermittent, and perennial flow, and between montane and basin streams? Do streams with greater elevational change have higher riparian zone seed bank beta-diversity? Does nestedness or turnover contribute more to within stream beta-diversity?
I collected soil samples from the riparian and terrestrial zones of 21 sites, placing them in growth chambers at one of two temperature regimes, and monitoring emergence of seedlings for 12 weeks. Results showed an approximately equal number of warm and cool specialists in both riparian and terrestrials zones; generalists also were abundant, particularly in the riparian zone. The number of temperature specialists and generalists in the riparian zones did not differ significantly between perennial headwater and ephemeral stream types. In montane streams, alpha diversity of the soil seed bank was highest for ephemeral reaches; in basin streams the intermittent and perennial reaches had higher diversity. Spatial turnover was primarily responsible for within stream beta-diversity—reaches had different species assemblages. The large portion of temperature specialists found in riparian seed banks indicates that even with available moisture riparian zone plant community composition will likely be impacted by changing temperatures. However, the presence of so many temperature generalists in the riparian zones suggests that some component of the seed bank is adapted to variable conditions and might offer resilience in a changing climate. Study results confirm the importance of conserving multiple hydrogeomorphic reach types because they support unique species assemblages.
I collected soil samples from the riparian and terrestrial zones of 21 sites, placing them in growth chambers at one of two temperature regimes, and monitoring emergence of seedlings for 12 weeks. Results showed an approximately equal number of warm and cool specialists in both riparian and terrestrials zones; generalists also were abundant, particularly in the riparian zone. The number of temperature specialists and generalists in the riparian zones did not differ significantly between perennial headwater and ephemeral stream types. In montane streams, alpha diversity of the soil seed bank was highest for ephemeral reaches; in basin streams the intermittent and perennial reaches had higher diversity. Spatial turnover was primarily responsible for within stream beta-diversity—reaches had different species assemblages. The large portion of temperature specialists found in riparian seed banks indicates that even with available moisture riparian zone plant community composition will likely be impacted by changing temperatures. However, the presence of so many temperature generalists in the riparian zones suggests that some component of the seed bank is adapted to variable conditions and might offer resilience in a changing climate. Study results confirm the importance of conserving multiple hydrogeomorphic reach types because they support unique species assemblages.
ContributorsSetaro, Danika (Author) / Stromberg, Juliet (Thesis advisor) / Franklin, Janet (Committee member) / Makings, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2016
Description
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 body mass index, percent body fat, blood glucose and HbA1c levels, insulin sensitivity and muscle protein fractional synthesis rate. The concentrations of specific plasma fatty acids, such as the saturated fatty acid (palmitate) and monounsaturated fatty acid (oleate) are known to be altered in obese/insulin resistant humans, and also to influence the protein synthesis in muscle. Therefore, it was evaluated that the effects of palmitate and oleate on syncytin-1 expression, as well as 4E-BP1 phosphorylation, a key mechanism regulating muscle protein synthesis in insulin stimulated C2C12 myotubes. The results showed that treatment with 20 nM insulin, 300 µM oleate, 300 µM oleate +20 nM insulin and 300 µM palmitate + 300 µM oleate elevated 4E-BP1 phosphorylation. At the same time, 20 nM insulin, 300 µM palmitate, 300 µM oleate + 20 nM insulin and 300 µM palmitate + 300 µM oleate elevated syncytin-1 expression. Insulin stimulated muscle syncytin-1 expression and 4E-BP1 phosphorylation, and this effect was comparable to that observed in the presence of oleate alone. However, the presence of palmitate + oleate diminished the stimulatory effect of insulin on muscle syncytin-1 expression and 4E-BP1 phosphorylation. These findings indicate oleate but not palmitate increased total 4E-BP1 phosphorylation regardless of insulin and the presence of palmitate in insulin mediated C2C12 cells. The presence of palmitate inhibited the upregulation of total 4EB-P1 phosphorylation. Palmitate but not oleate increased syncytin-1 expression in insulin mediated C2C12 myotubes. It is possible that chronic hyperinsulinemia in obesity and/or elevated levels of fatty acids such as palmitate in plasma could have contributed to syncytin-1 overexpression and decreased muscle protein fractional synthesis rate in obese/insulin resistant human muscle.
ContributorsRavichandran, Jayachandran (Author) / Katsanos, Christos (Thesis advisor) / Coletta, Dawn (Committee member) / Dickinson, Jared (Committee member) / Arizona State University (Publisher)
Created2017
Description
In a 2004 paper, John Nagy raised the possibility of the existence of a hypertumor \emph{i.e.}, a focus of aggressively reproducing parenchyma cells that invade part or all of a tumor. His model used a system of nonlinear ordinary differential equations to find a suitable set of conditions for which these hypertumors exist. Here that model is expanded by transforming it into a system of nonlinear partial differential equations with diffusion, advection, and a free boundary condition to represent a radially symmetric tumor growth. Two strains of parenchymal cells are incorporated; one forming almost the entirety of the tumor while the much more aggressive strain
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
ContributorsAlvarez, Roberto L (Author) / Milner, Fabio A (Thesis advisor) / Nagy, John D. (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Mahalov, Alex (Committee member) / Smith, Hal (Committee member) / Arizona State University (Publisher)
Created2014
Description
To ensure system integrity, robots need to proactively avoid any unwanted physical perturbation that may cause damage to the underlying hardware. In this thesis work, we investigate a machine learning approach that allows robots to anticipate impending physical perturbations from perceptual cues. In contrast to other approaches that require knowledge about sources of perturbation to be encoded before deployment, our method is based on experiential learning. Robots learn to associate visual cues with subsequent physical perturbations and contacts. In turn, these extracted visual cues are then used to predict potential future perturbations acting on the robot. To this end, we introduce a novel deep network architecture which combines multiple sub- networks for dealing with robot dynamics and perceptual input from the environment. We present a self-supervised approach for training the system that does not require any labeling of training data. Extensive experiments in a human-robot interaction task show that a robot can learn to predict physical contact by a human interaction partner without any prior information or labeling. Furthermore, the network is able to successfully predict physical contact from either depth stream input or traditional video input or using both modalities as input.
ContributorsSur, Indranil (Author) / Amor, Heni B (Thesis advisor) / Fainekos, Georgios (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2017