Matching Items (297)
Description
DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.
ContributorsLiu, Minghui (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2013
Description
Since Darwin popularized the evolution theory in 1895, it has been completed and studied through the years. Starting in 1990s, evolution at molecular level has been used to discover functional molecules while studying the origin of functional molecules in nature by mimicing the natural selection process in laboratory. Along this line, my Ph.D. dissertation focuses on the in vitro selection of two important biomolecules, deoxynucleotide acid (DNA) and protein with binding properties. Chapter two focuses on in vitro selection of DNA. Aptamers are single-stranded nucleic acids that generated from a random pool and fold into stable three-dimensional structures with ligand binding sites that are complementary in shape and charge to a desired target. While aptamers have been selected to bind a wide range of targets, it is generally thought that these molecules are incapable of discriminating strongly alkaline proteins due to the attractive forces that govern oppositely charged polymers. By employing negative selection step to eliminate aptamers that bind with off-target through charge unselectively, an aptamer that binds with histone H4 protein with high specificity (>100 fold)was generated. Chapter four focuses on another functional molecule: protein. It is long believed that complex molecules with different function originated from simple progenitor proteins, but very little is known about this process. By employing a previously selected protein that binds and catalyzes ATP, which is the first and only protein that was evolved completely from random pool and has a unique α/β-fold protein scaffold, I fused random library to the C-terminus of this protein and evolved a multi-domain protein with decent properties. Also, in chapter 3, a unique bivalent molecule was generated by conjugating peptides that bind different sites on the protein with nucleic acids. By using the ligand interactions by nucleotide conjugates technique, off-the shelf peptide was transferred into high affinity protein capture reagents that mimic the recognition properties of natural antibodies. The designer synthetic antibody amplifies the binding affinity of the individual peptides by ∼1000-fold to bind Grb2 with a Kd of 2 nM, and functions with high selectivity in conventional pull-down assays from HeLa cell lysates.
ContributorsJiang, Bing (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Stable isotopes were measured in the groundwaters of the Salt River Valley basin in central Arizona to explore the utility of stable isotopes for sourcing recharge waters and engineering better well designs. Delta values for the sampled groundwaters range from -7.6‰ to -10‰ in 18O and -60‰ to -91‰ in D and display displacements off the global meteoric water line indicative of surficial evaporation during river transport into the area. Groundwater in the basin is all derived from top-down river recharge; there is no evidence of ancient playa waters even in the playa deposits. The Salt and Verde Rivers are the dominant source of groundwater for the East Salt River valley- the Agua Fria River also contributes significantly to the West Salt River Valley. Groundwater isotopic compositions are generally more depleted in 18O and D with depth, indicating past recharge in cooler climates, and vary within subsurface aquifer layers as sampled during well drilling. When isotopic data were evaluated together with geologic and chemical analyses and compared with data from the final well production water it was often possible to identify: 1) which horizons are the primary producers of groundwater flow and how that might change with time, 2) the chemical exchange of cations and anions via water-rock interaction during top-down mixing of recharge water with older waters, 3) how much well production might be lost if arsenic-contributing horizons were sealed off, and 4) the extent to which replacement wells tap different subsurface water sources. In addition to identifying sources of recharge, stable isotopes offer a new and powerful approach for engineering better and more productive water wells.
ContributorsBond, Angela Nicole (Author) / Knauth, Paul (Thesis advisor) / Hartnett, Hilairy (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2010
Description
Microbially induced calcium carbonate precipitation (MICP) is attracting increasing attention as a sustainable means of soil improvement. While there are several possible MICP mechanisms, microbial denitrification has the potential to become one of the preferred methods for MICP because complete denitrification does not produce toxic byproducts, readily occurs under anoxic conditions, and potentially has a greater carbonate yield per mole of organic electron donor than other MICP processes. Denitrification may be preferable to ureolytic hydrolysis, the MICP process explored most extensively to date, as the byproduct of denitrification is benign nitrogen gas, while the chemical pathways involved in hydrolytic ureolysis processes produce undesirable and potentially toxic byproducts such as ammonium (NH4+). This thesis focuses on bacterial denitrification and presents preliminary results of bench-scale laboratory experiments on denitrification as a candidate calcium carbonate precipitation mechanism. The bench-scale bioreactor and column tests, conducted using the facultative anaerobic bacterium Pseudomonas denitrificans, show that calcite can be precipitated from calcium-rich pore water using denitrification. Experiments also explore the potential for reducing environmental impacts and lowering costs associated with denitrification by reducing the total dissolved solids in the reactors and columns, optimizing the chemical matrix, and addressing the loss of free calcium in the form of calcium phosphate precipitate from the pore fluid. The potential for using MICP to sequester radionuclides and metal contaminants that are migrating in groundwater is also investigated. In the sequestration process, divalent cations and radionuclides are incorporated into the calcite structure via substitution, forming low-strontium calcium carbonate minerals that resist dissolution at a level similar to that of calcite. Work by others using the bacterium Sporosarcina pasteurii has suggested that in-situ sequestration of radionuclides and metal contaminants can be achieved through MICP via hydrolytic ureolysis. MICP through bacterial denitrification seems particularly promising as a means for sequestering radionuclides and metal contaminants in anoxic environments due to the anaerobic nature of the process and the ubiquity of denitrifying bacteria in the subsurface.
ContributorsHamdan, Nasser (Author) / Kavazanjian, Edward (Thesis advisor) / Rittmann, Bruce E. (Thesis advisor) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2013
Description
The need for a renewable and sustainable light-driven energy source is the motivation for this work, which utilizes a challenging, yet practical and attainable bio-inspired approach to develop an artificial oxygen evolving complex, which builds upon the principles of the natural water splitting mechanism in oxygenic photosynthesis. In this work, a stable framework consisting of a three-dimensional DNA tetrahedron has been used for the design of a bio-mimic of the Oxygen-Evolving Complex (OEC) found in natural Photosystem II (PSII). PSII is a large protein complex that evolves all the oxygen in the atmosphere, but it cannot be used directly in artificial systems, as the light reactions lead to damage of one of Photosystem II's core proteins, D1, which has to be replaced every half hour in the presence of sunlight. The final goal of the project aims to build the catalytic center of the OEC, including the Mn4CaCl metal cluster and its protein environment in the stable DNA framework of a tetrahedron, which can subsequently be connected to a photo-stable artificial reaction center that performs light-induced charge separation. Regions of the peptide sequences containing Mn4CaCl ligation sites are implemented in the design of the aOEC (artificial oxygen-evolving complex) and are attached to sites within the tetrahedron to facilitate assembly. Crystals of the tetrahedron have been obtained, and X-ray crystallography has been used for characterization. As a proof of concept, metal-binding peptides have been coupled to the DNA tetrahedron which allowed metal-containing porphyrins, specifically Fe(III) meso-Tetra(4-sulfonatophenyl) porphyrin chloride, to be encapsulated inside the DNA-tetrahedron. The porphyrins were successfully assembled inside the tetrahedron through coordination of two terminal histidines from the orthogonally oriented peptides covalently attached to the DNA. The assembly has been characterized using Electron Paramagnetic Resonance (EPR), optical spectroscopy, Dynamic Light Scattering (DLS), and x-ray crystallography. The results reveal that the spin state of the metal, iron (III), switches during assembly from the high-spin state to low-spin state.
ContributorsRendek, Kimberly Nicole (Author) / Fromme, Petra (Thesis advisor) / Chen, Julian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological soil crusts (BSCs) are critical components of arid and semiarid environments and provide the primary sources of bioavailable macronutrients and increase micronutrient availability to their surrounding ecosystems. BSCs are composed of a variety of microorganisms that perform a wide range of physiological processes requiring a multitude of bioessential micronutrients, such as iron, copper, and molybdenum. This work investigated the effects of BSC activity on soil solution concentrations of bioessential elements and examined the microbial production of organic chelators, called siderophores. I found that aluminum, vanadium, copper, zinc, and molybdenum were solubilized in the action of crusts, while nickel, zinc, arsenic, and zirconium were immobilized by crust activity. Potassium and manganese displayed behavior consistent with biological removal and mobilization, whereas phosphorus and iron solubility were dominated by abiotic processes. The addition of bioavailable nitrogen altered the effects of BSCs on soil element mobilization. In addition, I found that the biogeochemical activites of BSCs were limited by molybdenum, a fact that likely contributes to co-limitation by nitrogen. I confirmed the presence of siderophore producing microbes in BSCs. Siderophores are low-molecular weight organic compounds that are released by bacteria to increase element solubility and facilitate element uptake; siderophore production is likely the mechanism by which BSCs affect the patterns I observed in soil solution element concentrations. Siderophore producers were distributed across a range of bacterial groups and ecological niches within crusts, suggesting that siderophore production influences the availability of a variety of elements for use in many physiological processes. Four putative siderophore compounds were identified using electrospray ionization mass spectrometry; further attempts to characterize the compounds confirmed two true siderophores. Taken together, the results of my work provide information about micronutrient cycling within crusts that can be applied to BSC conservation and management. Fertilization with certain elements, particularly molybdenum, may prove to be a useful technique to promote BSC growth and development which would help prevent arid land degradation. Furthermore, understanding the effects of BSCs on soil element mobility could be used to develop useful biomarkers for the study of the existence and distribution of crust-like communities on ancient Earth, and perhaps other places, like Mars.
ContributorsNoonan, Kathryn Alexander (Author) / Hartnett, Hilairy (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Shock, Everett (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
Ponderosa pine forests are a dominant land cover type in semiarid montane areas. Water supplies in major rivers of the southwestern United States depend on ponderosa pine forests since these ecosystems: (1) receive a significant amount of rainfall and snowfall, (2) intercept precipitation and transpire water, and (3) indirectly influence runoff by impacting the infiltration rate. However, the hydrologic patterns in these ecosystems with strong seasonality are poorly understood. In this study, we used a distributed hydrologic model evaluated against field observations to improve our understandings on spatial controls of hydrologic patterns, appropriate model resolution to simulate ponderosa pine ecosystems and hydrologic responses in the context of contrasting winter to summer transitions. Our modeling effort is focused on the hydrologic responses during the North American Monsoon (NAM), winter and spring periods. In Chapter 2, we utilized a distributed model explore the spatial controls on simulated soil moisture and temporal evolution of these spatial controls as a function of seasonal wetness. Our findings indicate that vegetation and topographic curvature are spatial controls. Vegetation controlled patterns during dry summer period switch to fine-scale terrain curvature controlled patterns during persistently wet NAM period. Thus, a climatic threshold involving rainfall and weather conditions during the NAM is identified when high rainfall amount (such as 146 mm rain in August, 1997) activates lateral flux of soil moisture and frequent cloudy cover (such as 42% cloud cover during daytime of August, 1997) lowers evapotranspiration. In Chapter 3, we investigate the impacts of model coarsening on simulated soil moisture patterns during the NAM. Results indicate that model aggregation quickly eradicates curvature features and its spatial control on hydrologic patterns. A threshold resolution of ~10% of the original terrain is identified through analyses of homogeneity indices, correlation coefficients and spatial errors beyond which the fidelity of simulated soil moisture is no longer reliable. Based on spatial error analyses, we detected that the concave areas (~28% of hillslope) are very sensitive to model coarsening and root mean square error (RMSE) is higher than residual soil moisture content (~0.07 m3/m3 soil moisture) for concave areas. Thus, concave areas need to be sampled for capturing appropriate hillslope response for this hillslope. In Chapter 4, we investigate the impacts of contrasting winter to summer transitions on hillslope hydrologic responses. We use a distributed hydrologic model to generate a consistent set of high-resolution hydrologic estimates. Our model is evaluated against the snow depth, soil moisture and runoff observations over two water years yielding reliable spatial distributions during the winter to summer transitions. We find that a wet winter followed by a dry summer promotes evapotranspiration losses (spatial averaged ~193 mm spring ET and ~ 600 mm summer ET) that dry the soil and disconnect lateral fluxes in the forested hillslope, leading to soil moisture patterns resembling vegetation patches. Conversely, a dry winter prior to a wet summer results in soil moisture increases due to high rainfall and low ET during the spring (spatially averaged 78 mm ET and 232 mm rainfall) and summer period (spatially averaged 147 mm ET and 247 mm rainfall) which promote lateral connectivity and soil moisture patterns with the signature of terrain curvature. An opposing temporal switch between infiltration and saturation excess runoff is also identified. These contrasting responses indicate that the inverse relation has significant consequences on hillslope water availability and its spatial distribution with implications on other ecohydrological processes including vegetation phenology, groundwater recharge and geomorphic development. Results from this work have implications on the design of hillslope experiments, the resolution of hillslope scale models, and the prediction of hydrologic conditions in ponderosa pine ecosystems. In addition, our findings can be used to select future hillslope sites for detailed ecohydrological investigations. Further, the proposed methodology can be useful for predicting responses to climate and land cover changes that are anticipated for the southwestern United States.
ContributorsMahmood, Taufique Hasan (Author) / Vivoni, Enrique R. (Thesis advisor) / Whipple, Kelin X. (Committee member) / Shock, Everett (Committee member) / Heimsath, Arjun M. (Committee member) / Ruddell, Benjamin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Membrane protein structure is continuing to be a topic of interest across the scientific community. However, high resolution structural data of these proteins is difficult to obtain. The amino acid transport protein, Outer Envelope Protein, 16kDa (OEP16) is a transmembrane protein channel that allows the passive diffusion of amino acids across the outer chloroplast membrane, and is used as a model protein in order to establish methods that ultimately reveal structural details about membrane proteins using nuclear magnetic resonance (NMR) spectroscopy. Methods include recombinant expression of isotope enriched inclusion bodies, purification and reconstitution in detergent micelles, and pre-characterization techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and high pressure liquid chromatography (HPLC). High resolution NMR spectroscopy was able to assign 99% of the amide backbone and the chemical shifts provided detailed secondary structure of OEP16 on a per residue basis using the software TALOS+. Relaxation studies explored the intramolecular dynamics of OEP16 and results strongly support the resonance assignments. Successful titration studies were able to locate residues important for amino acid binding for import into the chloroplast as well as provide information on how the transmembrane helices of OEP16 are packed together. For the first time there is experimental evidence that can assign the location of secondary structure in OEP16 and creates a foundation for a future three dimensional structure.
ContributorsZook, James Duncan (Author) / Fromme, Petra (Thesis advisor) / Chen, Julian (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2012
Description
Early spacecraft missions to Mars, including the Marnier and Viking orbiters and landers revealed a morphologically and compositionally diverse landscape that reshaped widely held views of Mars. More recent spacecraft including Mars Global Surveyor, Mars Odyssey, Mars Express, Mars Reconnaissance Orbiter, and the Mars Exploration Rovers have further refined, enhanced, and diversified our understanding of Mars. In this dissertation, I take a multiple-path approach to planetary and Mars science including data analysis and instrument development. First, I present several tools necessary to effectively use new, complex datasets by highlighting unique and innovative data processing techniques that allow for the regional to global scale comparison of multiple datasets. Second, I present three studies that characterize several processes on early Mars, where I identify a regional, compositionally distinct, in situ, stratigraphically significant layer in Ganges and Eos Chasmata that formed early in martian history. This layer represents a unique period in martian history where primitive mantle materials were emplaced over large sections of the martian surface. While I originally characterized this layer as an effusive lava flow, based on the newly identified regional or global extent of this layer, I find the only likely scenario for its emplacement is the ejecta deposit of the Borealis Basin forming impact event. I also re-examine high thermal inertia, flat-floored craters identified in Viking data and conclude they are typically more mafic than the surrounding plains and were likely infilled by primitive volcanic materials during, or shortly after the Late Heavy Bombardment. Furthermore, the only plausible source for these magmas is directly related to the impact process, where mantle decompression melting occurs as result of the removal of overlying material by the impactor. Finally, I developed a new laboratory microscopic emission and reflectance spectrometer designed to help improve the interpretation of current remote sensing or in situ data from planetary bodies. I present the design, implementation, calibration, system performance, and preliminary results of this instrument. This instrument is a strong candidate for the next generation in situ rover instruments designed to definitively assess sample mineralogy and petrology while preserving geologic context.
ContributorsEdwards, Christopher (Author) / Christensen, Philip R. (Thesis advisor) / Bell, James (Committee member) / Sharp, Thomas (Committee member) / Clarke, Amanda B (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2012
Description
Molybdenum and uranium isotope variations are potentially powerful tools for reconstructing the paleoredox history of seawater. Reliable application and interpretation of these proxies requires not only detailed knowledge about the fractionation factors that control the distribution of molybdenum and uranium isotopes in the marine system, but also a thorough understanding of the diagenetic processes that may affect molybdenum and uranium isotopes entering the rock record. Using samples from the Black Sea water column, the first water column profile of 238U/235U variations from a modern euxinic basin has been measured. This profile allows the direct determination of the 238U/235U fractionation factor in a euxinic marine setting. More importantly however, these data demonstrate the extent of Rayleigh fractionation of U isotopes that can occur in euxinic restricted basins. Because of this effect, the offset of 238U/235U between global average seawater and coeval black shales deposited in restricted basins is expected to depend on the degree of local uranium drawdown from the water column, potentially complicating the interpretation 238U/235U paleorecords. As an alternative to the black shales typically used for paleoredox reconstructions, molybdenum and uranium isotope variations in bulk carbonate sediments from the Bahamas are examined. The focus of this work was to determine what processes, if any, fractionate molybdenum and uranium isotopes during incorporation into bulk carbonate sediments and their subsequent diagenesis. The results demonstrate that authigenic accumulation of molybdenum and uranium from anoxic and sulfidic pore waters is a dominant process controlling the concentration and isotopic composition of these sediments during early diagenesis. Examination of ODP drill core samples from the Bahamas reveals similar behavior for sediments during the first ~780ka of burial, but provides important examples where isolated cores and samples occasionally demonstrate additional fractionation, the cause of which remains poorly understood.
ContributorsRomaniello, Stephen J. (Author) / Anbar, Ariel (Thesis advisor) / Hartnett, Hilairy (Committee member) / Herrmann, Achim (Committee member) / Shock, Everett (Committee member) / Wadhwa, Meenakshi (Committee member) / Arizona State University (Publisher)
Created2012