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- All Subjects: Environmental engineering
- Creators: Arizona State University
- Creators: Yan, Hao
Description
The elaborate signals of animals are often costly to produce and maintain, thus communicating reliable information about the quality of an individual to potential mates or competitors. The properties of the sensory systems that receive signals can drive the evolution of these signals and shape their form and function. However, relatively little is known about the ecological and physiological constraints that may influence the development and maintenance of sensory systems. In the house finch (Carpodacus mexicanus) and many other bird species, carotenoid pigments are used to create colorful sexually selected displays, and their expression is limited by health and dietary access to carotenoids. Carotenoids also accumulate in the avian retina, protecting it from photodamage and tuning color vision. Analogous to plumage carotenoid accumulation, I hypothesized that avian vision is subject to environmental and physiological constraints imposed by the acquisition and allocation of carotenoids. To test this hypothesis, I carried out a series of field and captive studies of the house finch to assess natural variation in and correlates of retinal carotenoid accumulation and to experimentally investigate the effects of dietary carotenoid availability, immune activation, and light exposure on retinal carotenoid accumulation. Moreover, through dietary manipulations of retinal carotenoid accumulation, I tested the impacts of carotenoid accumulation on visually mediated foraging and mate choice behaviors. My results indicate that avian retinal carotenoid accumulation is variable and significantly influenced by dietary carotenoid availability and immune system activity. Behavioral studies suggest that retinal carotenoid accumulation influences visual foraging performance and mediates a trade-off between color discrimination and photoreceptor sensitivity under dim-light conditions. Retinal accumulation did not influence female choice for male carotenoid-based coloration, indicating that a direct link between retinal accumulation and sexual selection for coloration is unlikely. However, retinal carotenoid accumulation in males was positively correlated with their plumage coloration. Thus, carotenoid-mediated visual health and performance or may be part of the information encoded in sexually selected coloration.
ContributorsToomey, Matthew (Author) / McGraw, Kevin J. (Thesis advisor) / Deviche, Pierre (Committee member) / Smith, Brian (Committee member) / Rutowski, Ronald (Committee member) / Verrelli, Brian (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molecular dynamics (MD) simulations provide a particularly useful approach to understanding conformational change in biomolecular systems. MD simulations provide an atomistic, physics-based description of the motions accessible to biomolecular systems on the pico- to micro-second timescale, yielding important insight into the free energy of the system, the dynamical stability of contacts and the role of correlated motions in directing the motions of the system. In this thesis, I use molecular dynamics simulations to provide molecular mechanisms that rationalize structural, thermodynamic, and mutation data on the interactions between the lac repressor headpiece and its O1 operator DNA as well as the ERK2 protein kinase. I performed molecular dynamics simulations of the lac repressor headpiece - O1 operator complex at the natural angle as well as at under- and overbent angles to assess the factors that determine the natural DNA bending angle. I find both energetic and entropic factors contribute to recognition of the natural angle. At the natural angle the energy of the system is minimized by optimization of protein-DNA contacts and the entropy of the system is maximized by release of water from the protein-DNA interface and decorrelation of protein motions. To identify the mechanism by which mutations lead to auto-activation of ERK2, I performed a series of molecular dynamics simulations of ERK1/2 in various stages of activation as well as the constitutively active Q103A, I84A, L73P and R65S ERK2 mutants. My simulations indicate the importance of domain closure for auto-activation and activity regulation. My results enable me to predict two loss-of-function mutants of ERK2, G83A and Q64C, that have been confirmed in experiments by collaborators. One of the powerful capabilities of MD simulations in biochemistry is the ability to find low free energy pathways that connect and explain disparate structural data on biomolecular systems. An extention of the targeted molecular dynamics technique using constraints on internal coordinates will be presented and evaluated. The method gives good results for the alanine dipeptide, but breaks down when applied to study conformational changes in GroEL and adenylate kinase.
ContributorsBarr, Daniel Alan (Author) / van der Vaart, Arjan (Thesis advisor) / Matyushov, Dmitry (Committee member) / Wolf, George (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
Intimate coupling of Ti2 photocatalysis and biodegradation (ICPB) offers potential for degrading biorecalcitrant and toxic organic compounds much better than possible with conventional wastewater treatments. This study reports on using a novel sponge-type, Ti2-coated biofilm carrier that shows significant adherence of Ti2 to its exterior and the ability to accumulate biomass in its interior (protected from UV light and free radicals). First, this carrier was tested for ICPB in a continuous-flow photocatalytic circulating-bed biofilm reactor (PCBBR) to mineralize biorecalcitrant organic: 2,4,5-trichlorophenol (TCP). Four mechanisms possibly acting of ICPB were tested separately: TCP adsorption, UV photolysis/photocatalysis, and biodegradation. The carrier exhibited strong TCP adsorption, while photolysis was negligible. Photocatalysis produced TCP-degradation products that could be mineralized and the strong adsorption of TCP to the carrier enhanced biodegradation by relieving toxicity. Validating the ICPB concept, biofilm was protected inside the carriers from UV light and free radicals. ICPB significantly lowered the diversity of the bacterial community, but five genera known to biodegrade chlorinated phenols were markedly enriched. Secondly, decolorization and mineralization of reactive dyes by ICPB were investigated on a refined Ti2-coated biofilm carrier in a PCBBR. Two typical reactive dyes: Reactive Black 5 (RB5) and Reactive Yellow 86 (RY86), showed similar first-order kinetics when being photocatalytically decolorized at low pH (~4-5), which was inhibited at neutral pH in the presence of phosphate or carbonate buffer, presumably due to electrostatic repulsion from negatively charged surface sites on Ti2, radical scavenging by phosphate or carbonate, or both. In the PCBBR, photocatalysis alone with Ti2-coated carriers could remove RB5 and COD by 97% and 47%, respectively. Addition of biofilm inside macroporous carriers maintained a similar RB5 removal efficiency, but COD removal increased to 65%, which is evidence of ICPB despite the low pH. A proposed ICPB pathway for RB5 suggests that a major intermediate, a naphthol derivative, was responsible for most of the residual COD. Finally, three low-temperature sintering methods, called O, D and DN, were compared based on photocatalytic efficiency and Ti2 adherence. The DN method had the best Ti2-coating properties and was a successful carrier for ICPB of RB5 in a PCBBR.
ContributorsLi, Guozheng (Author) / Rittmann, Bruce E. (Thesis advisor) / Halden, Rolf (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2011
Description
A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.
ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the 1970s James Watson recognized the inability of conventional DNA replication machinery to replicate the extreme termini of chromosomes known as telomeres. This inability is due to the requirement of a building block primer and was termed the end replication problem. Telomerase is nature's answer to the end replication problem. Telomerase is a ribonucleoprotein which extends telomeres through reverse transcriptase activity by reiteratively copying a short intrinsic RNA sequence to generate 3' telomeric extensions. Telomeres protect chromosomes from erosion of coding genes during replication, as well as differentiate native chromosome ends from double stranded breaks. However, controlled erosion of telomeres functions as a naturally occurring molecular clock limiting the replicative capacity of cells. Telomerase is over activated in many cancers, while inactivation leads to multiple lifespan limiting human diseases. In order to further study the interaction between telomerase RNA (TR) and telomerase reverse transcriptase protein (TERT), vertebrate TERT fragments were screened for solubility and purity following bacterial expression. Soluble fragments of medaka TERT including the RNA binding domain (TRBD) were identified. Recombinant medaka TRBD binds specifically to telomerase RNA CR4/CR5 region. Ribonucleotide and amino acid pairs in close proximity within the medaka telomerase RNA-protein complex were identified using photo-activated cross-linking in conjunction with mass spectrometry. The identified cross-linking amino acids were mapped on known crystal structures of TERTs to reveal the RNA interaction interface of TRBD. The identification of this RNA TERT interaction interface furthers the understanding of the telomerase complex at a molecular level and could be used for the targeted interruption of the telomerase complex as a potential cancer treatment.
ContributorsBley, Christopher James (Author) / Chen, Julian (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
The goal of the study was twofold: (i) to investigate the synthesis of hematite-impregnated granular activated carbon (Fe-GAC) by hydrolysis of Fe (III) and (ii) to assess the effectiveness of the fabricated media in removal of arsenic from water. Fe-GAC was synthesized by hydrolysis of Fe(III) salts under two Fe (III) initial dosages (0.5M and 2M) and two hydrolysis periods (24 hrs and 72 hrs). The iron content of the fabricated Fe-GAC media ranged from 0.9% to 4.4% Fe/g of the dry media. Pseudo-equilibrium batch test data at pH = 7.7±0.2 in 1mM NaHCO3 buffered ultrapure water and challenge groundwater representative of the Arizona Mexico border region were fitted to a Freundlich isotherm model. The findings suggested that the arsenic adsorption capacity of the metal (hydr)oxide modified GAC media is primarily controlled by the surface area of the media, while the metal content exhibited lesser effect. The adsorption capacity of the media in the model Mexican groundwater matrix was significantly lower for all adsorbent media. Continuous flow short bed adsorber tests (SBA) demonstrated that the adsorption capacity for arsenic in the challenge groundwater was reduced by a factor of 3 to 4 as a result of the mass transport effects. When compared on metal basis, the iron (hydr)oxide modified media performed comparably well as existing commercial media for treatment of arsenic. On dry mass basis, the fabricated media in this study removed less arsenic than their commercial counterparts because the metal content of the commercial media was significantly higher.
ContributorsJain, Arti (Author) / Hristovski, Kiril (Thesis advisor) / Olson, Larry (Committee member) / Madar, David (Committee member) / Edwards, David (Committee member) / Arizona State University (Publisher)
Created2011
Description
Filtration for microfluidic sample-collection devices is desirable for sample selection, concentration, preprocessing, and downstream manipulation, but microfabricating the required sub-micrometer filtration structure is an elaborate process. This thesis presents a simple method to fabricate polydimethylsiloxane (PDMS) devices with an integrated membrane filter that will sample, lyse, and extract the DNA from microorganisms in aqueous environments. An off-the-shelf membrane filter disc was embedded in a PDMS layer and sequentially bound with other PDMS channel layers. No leakage was observed during filtration. This device was validated by concentrating a large amount of cyanobacterium Synechocystis in simulated sample water with consistent performance across devices. After accumulating sufficient biomass on the filter, a sequential electrochemical lysing process was performed by applying 5VDC across the filter. This device was further evaluated by delivering several samples of differing concentrations of cyanobacterium Synechocystis then quantifying the DNA using real-time PCR. Lastly, an environmental sample was run through the device and the amount of photosynthetic microorganisms present in the water was determined. The major breakthroughs in this design are low energy demand, cheap materials, simple design, straightforward fabrication, and robust performance, together enabling wide-utility of similar chip-based devices for field-deployable operations in environmental micro-biotechnology.
ContributorsLecluse, Aurelie (Author) / Meldrum, Deirdre (Thesis advisor) / Chao, Joseph (Thesis advisor) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2011
Description
As the use of engineered nanomaterials (ENMs) in consumer products becomes more common, the amount of ENMs entering wastewater treatment plants (WWTPs) increases. Investigating the fate of ENMs in WWTPs is critical for risk assessment and pollution control. The objectives of this dissertation were to (1) quantify and characterize titanium (Ti) in full-scale wastewater treatment plants, (2) quantify sorption of different ENMs to wastewater biomass in laboratory-scale batch reactors, (3) evaluate the use of a standard, soluble-pollutant sorption test method for quantifying ENM interaction with wastewater biomass, and (4) develop a mechanistic model of a biological wastewater treatment reactor to serve as the basis for modeling nanomaterial fate in WWTPs. Using titanium (Ti) as a model material for the fate of ENMs in WWTPs, Ti concentrations were measured in 10 municipal WWTPs. Ti concentrations in pant influent ranged from 181 to 3000 µg/L, and more than 96% of Ti was removed, with effluent Ti concentrations being less than 25 µg/L. Ti removed from wastewater accumulated in solids at concentrations ranging from 1 to 6 µg Ti/mg solids. Using transmission electron microscopy, spherical titanium oxide nanoparticles with diameters ranging from 4 to 30 nm were found in WWTP effluents, evidence that some nanoscale particles will pass through WWTPs and enter aquatic systems. Batch experiments were conducted to quantify sorption of different ENM types to activated sludge. Percentages of sorption to 400 mg TSS/L biomass ranged from about 10 to 90%, depending on the ENM material and functionalization. Natural organic matter, surfactants, and proteins had a stabilizing effect on most of the ENMs tested. The United States Environmental Protection Agency's standard sorption testing method (OPPTS 835.1110) used for soluble compounds was found to be inapplicable to ENMs, as freeze-dried activated sludge transforms ENMs into stable particles in suspension. In conjunction with experiments, we created a mechanistic model of the microbiological processes in membrane bioreactors to predict MBR, extended and modified this model to predict the fate of soluble micropollutants, and then discussed how the micropollutant fate model could be used to predict the fate of nanomaterials in wastewater treatment plants.
ContributorsKiser, Mehlika Ayla (Author) / Westerhoff, Paul K (Thesis advisor) / Rittmann, Bruce E. (Committee member) / Hristovski, Kiril D (Committee member) / Arizona State University (Publisher)
Created2011
Description
As the demand for power increases in populated areas, so will the demand for water. Current power plant technology relies heavily on the Rankine cycle in coal, nuclear and solar thermal power systems which ultimately use condensers to cool the steam in the system. In dry climates, the amount of water to cool off the condenser can be extremely large. Current wet cooling technologies such as cooling towers lose water from evaporation. One alternative to prevent this would be to implement a radiative cooling system. More specifically, a system that utilizes the volumetric radiation emission from water to the night sky could be implemented. This thesis analyzes the validity of a radiative cooling system that uses direct radiant emission to cool water. A brief study on potential infrared transparent cover materials such as polyethylene (PE) and polyvinyl carbonate (PVC) was performed. Also, two different experiments to determine the cooling power from radiation were developed and run. The results showed a minimum cooling power of 33.7 W/m2 for a vacuum insulated glass system and 37.57 W/m2 for a tray system with a maximum of 98.61 Wm-2 at a point when conduction and convection heat fluxes were considered to be zero. The results also showed that PE proved to be the best cover material. The minimum numerical results compared well with other studies performed in the field using similar techniques and materials. The results show that a radiative cooling system for a power plant could be feasible given that the cover material selection is narrowed down, an ample amount of land is available and an economic analysis is performed proving it to be cost competitive with conventional systems.
ContributorsOvermann, William (Author) / Phelan, Patrick (Thesis advisor) / Trimble, Steve (Committee member) / Taylor, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
A recent joint study by Arizona State University and the Arizona Department of Transportation (ADOT) was conducted to evaluate certain Warm Mix Asphalt (WMA) properties in the laboratory. WMA material was taken from an actual ADOT project that involved two WMA sections. The first section used a foamed-based WMA admixture, and the second section used a chemical-based WMA admixture. The rest of the project included control hot mix asphalt (HMA) mixture. The evaluation included testing of field-core specimens and laboratory compacted specimens. The laboratory specimens were compacted at two different temperatures; 270 °F (132 °C) and 310 °F (154 °C). The experimental plan included four laboratory tests: the dynamic modulus (E*), indirect tensile strength (IDT), moisture damage evaluation using AASHTO T-283 test, and the Hamburg Wheel-track Test. The dynamic modulus E* results of the field cores at 70 °F showed similar E* values for control HMA and foaming-based WMA mixtures; the E* values of the chemical-based WMA mixture were relatively higher. IDT test results of the field cores had comparable finding as the E* results. For the laboratory compacted specimens, both E* and IDT results indicated that decreasing the compaction temperatures from 310 °F to 270 °F did not have any negative effect on the material strength for both WMA mixtures; while the control HMA strength was affected to some extent. It was noticed that E* and IDT results of the chemical-based WMA field cores were high; however, the laboratory compacted specimens results didn't show the same tendency. The moisture sensitivity findings from TSR test disagreed with those of Hamburg test; while TSR results indicated relatively low values of about 60% for all three mixtures, Hamburg test results were quite excellent. In general, the results of this study indicated that both WMA mixes can be best evaluated through field compacted mixes/cores; the results of the laboratory compacted specimens were helpful to a certain extent. The dynamic moduli for the field-core specimens were higher than for those compacted in the laboratory. The moisture damage findings indicated that more investigations are needed to evaluate moisture damage susceptibility in field.
ContributorsAlossta, Abdulaziz (Author) / Kaloush, Kamil (Thesis advisor) / Witczak, Matthew W. (Committee member) / Mamlouk, Michael S. (Committee member) / Arizona State University (Publisher)
Created2011