Matching Items (28)
Description
Sensitivity is a fundamental challenge for in vivo molecular magnetic resonance imaging (MRI). Here, I improve the sensitivity of metal nanoparticle contrast agents by strategically incorporating pure and doped metal oxides in the nanoparticle core, forming a soluble, monodisperse, contrast agent with adjustable T2 or T1 relaxivity (r2 or r1). I first developed a simplified technique to incorporate iron oxides in apoferritin to form "magnetoferritin" for nM-level detection with T2- and T2* weighting. I then explored whether the crystal could be chemically modified to form a particle with high r1. I first adsorbed Mn2+ ions to metal binding sites in the apoferritin pores. The strategic placement of metal ions near sites of water exchange and within the crystal oxide enhance r1, suggesting a mechanism for increasing relaxivity in porous nanoparticle agents. However, the Mn2+ addition was only possible when the particle was simultaneously filled with an iron oxide, resulting in a particle with a high r1 but also a high r2 and making them undetectable with conventional T1-weighting techniques. To solve this problem and decrease the particle r2 for more sensitive detection, I chemically doped the nanoparticles with tungsten to form a disordered W-Fe oxide composite in the apoferritin core. This configuration formed a particle with a r1 of 4,870mM-1s-1 and r2 of 9,076mM-1s-1. These relaxivities allowed the detection of concentrations ranging from 20nM - 400nM in vivo, both passively injected and targeted to the kidney glomerulus. I further developed an MRI acquisition technique to distinguish particles based on r2/r1, and show that three nanoparticles of similar size can be distinguished in vitro and in vivo with MRI. This work forms the basis for a new, highly flexible inorganic approach to design nanoparticle contrast agents for molecular MRI.
ContributorsClavijo Jordan, Maria Veronica (Author) / Bennett, Kevin M (Thesis advisor) / Kodibagkar, Vikram (Committee member) / Sherry, A Dean (Committee member) / Wang, Xiao (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2012
Description
Thiol functionalization is one potentially useful way to tailor physical and chemical properties of graphene oxides (GOs) and reduced graphene oxides (RGOs). Despite the ubiquitous presence of thiol functional groups in diverse chemical systems, efficient thiol functionalization has been challenging for GOs and RGOs, or for carbonaceous materials in general. In this work, thionation of GOs has been achieved in high yield through two new methods that also allow concomitant chemical reduction/thermal reduction of GOs; a solid-gas metathetical reaction method with boron sulfides (BxSy) gases and a solvothermal reaction method employing phosphorus decasulfide (P4S10). The thionation products, called "mercapto reduced graphene oxides (m-RGOs)", were characterized by employing X-ray photoelectron spectroscopy, powder X-ray diffraction, UV-Vis spectroscopy, FT-IR spectroscopy, Raman spectroscopy, electron probe analysis, scanning electron microscopy, (scanning) transmission electron microscopy, nano secondary ion mass spectrometry, Ellman assay and atomic force microscopy. The excellent dispersibility of m-RGOs in various solvents including alcohols has allowed fabrication of thin films of m-RGOs. Deposition of m-RGOs on gold substrates was achieved through solution deposition and the m-RGOs were homogeneously distributed on gold surface shown by atomic force microscopy. Langmuir-Blodgett (LB) films of m-RGOs were obtained by transferring their Langmuir films, formed by simple drop casting of m-RGOs dispersion on water surface, onto various substrates including gold, glass and indium tin oxide. The m-RGO LB films showed low sheet resistances down to about 500 kΩ/sq at 92% optical transparency. The successful results make m-RGOs promising for applications in transparent conductive coatings, biosensing, etc.
ContributorsJeon, Kiwan (Author) / Seo, Dong-Kyun (Thesis advisor) / Jones, Anne K (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2013
Description
Glycosaminoglycans (GAGs) are a class of complex biomolecules comprised of linear, sulfated polysaccharides whose presence on cell surfaces and in the extracellular matrix involve them in many physiological phenomena as well as in interactions with pathogenic microbes. Decorin binding protein A (DBPA), a Borrelia surface lipoprotein involved in the infectivity of Lyme disease, is responsible for binding GAGs found on decorin, a small proteoglycan present in the extracellular matrix. Different DBPA strains have notable sequence heterogeneity that results in varying levels of GAG-binding affinity. In this dissertation, the structures and GAG-binding mechanisms for three strains of DBPA (B31 and N40 DBPAs from B. burgdorferi and PBr DBPA from B. garinii) are studied to determine why each strain has a different affinity for GAGs. These three strains have similar topologies consisting of five α-helices held together by a hydrophobic core as well as two long flexible segments: a linker between helices one and two and a C-terminal tail. This structural arrangement facilitates the formation of a basic pocket below the flexible linker which is the primary GAG-binding epitope. However, this GAG-binding site can be occluded by the flexible linker, which makes the linker a negative regulator of GAG-binding. ITC and NMR titrations provide KD values that show PBr DBPA binds GAGs with higher affinity than B31 and N40 DBPAs, while N40 binds with the lowest affinity of the three. Work in this thesis demonstrates that much of the discrepancies seen in GAG affinities of the three DBPAs can be explained by the amino acid composition and conformation of the linker. Mutagenesis studies show that B31 DBPA overcomes the pocket obstruction with the BXBB motif in its linker while PBr DBPA has a retracted linker that exposes the basic pocket as well as a secondary GAG-binding site. N40 DBPA, however, does not have any evolutionary modifications to its structure to enhance GAG binding which explains its lower affinity for GAGs. GMSA and ELISA assays, along with NMR PRE experiments, confirm that structural changes in the linker do affect GAG-binding and, as a result, the linker is responsible for regulating GAG affinity.
ContributorsMorgan, Ashli M (Author) / Wang, Xu (Thesis advisor) / Allen, James (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2015
Description
Two-dimensional transition metal dichalcogenides (TMDCs) such as
molybdenum disulfide (MoS2), tungsten disulfide (WS2), molybdenum diselenide (MoSe2) and tungsten diselenide (WSe2) are attractive for use in biotechnology, optical and electronics devices due to their promising and tunable electrical, optical and chemical properties. To fulfill the variety of requirements for different applications, chemical treatment methods are developed to tune their properties. In this dissertation, plasma treatment, chemical doping and functionalization methods have been applied to tune the properties of TMDCs. First, plasma treatment of TMDCs results in doping and generation of defects, as well as the synthesis of transition metal oxides (TMOs) with rolled layers that have increased surface-to-volume ratio and are promising for electrochemical applications. Second, chemical functionalization is another powerful approach for tuning the properties of TMDCs for use in many applications. To covalently functionalize the basal planes of TMDCs, previous reports begin with harsh treatments like lithium intercalation that disrupt the structure and lead to a phase transformation from semiconducting to metallic. Instead, this work demonstrates the direct covalent functionalization of semiconducting MoS2 using aryl diazonium salts without lithium treatments. It preserves the structure and semiconducting nature of MoS2, results in covalent C-S bonds on basal planes and enables different functional groups to be tethered to the MoS2 surface via the diazonium salts. The attachment of fluorescent proteins has been used as a demonstration and it suggests future applications in biology and biosensing. The effects of the covalent functionalization on the electronic transport properties of MoS2 were then studied using field effect transistor (FET) devices.
molybdenum disulfide (MoS2), tungsten disulfide (WS2), molybdenum diselenide (MoSe2) and tungsten diselenide (WSe2) are attractive for use in biotechnology, optical and electronics devices due to their promising and tunable electrical, optical and chemical properties. To fulfill the variety of requirements for different applications, chemical treatment methods are developed to tune their properties. In this dissertation, plasma treatment, chemical doping and functionalization methods have been applied to tune the properties of TMDCs. First, plasma treatment of TMDCs results in doping and generation of defects, as well as the synthesis of transition metal oxides (TMOs) with rolled layers that have increased surface-to-volume ratio and are promising for electrochemical applications. Second, chemical functionalization is another powerful approach for tuning the properties of TMDCs for use in many applications. To covalently functionalize the basal planes of TMDCs, previous reports begin with harsh treatments like lithium intercalation that disrupt the structure and lead to a phase transformation from semiconducting to metallic. Instead, this work demonstrates the direct covalent functionalization of semiconducting MoS2 using aryl diazonium salts without lithium treatments. It preserves the structure and semiconducting nature of MoS2, results in covalent C-S bonds on basal planes and enables different functional groups to be tethered to the MoS2 surface via the diazonium salts. The attachment of fluorescent proteins has been used as a demonstration and it suggests future applications in biology and biosensing. The effects of the covalent functionalization on the electronic transport properties of MoS2 were then studied using field effect transistor (FET) devices.
ContributorsChu, Ximo (Author) / Wang, Qing Hua (Thesis advisor) / Sieradzki, Karl (Committee member) / Green, Alexander (Committee member) / Chan, Candace (Committee member) / Arizona State University (Publisher)
Created2018
Description
The highly predictable structural and thermodynamic behavior of deoxynucleic acid (DNA) and ribonucleic acid (RNA) have made them versatile tools for creating artificial nanostructures over broad range. Moreover, DNA and RNA are able to interact with biological ligand as either synthetic aptamers or natural components, conferring direct biological functions to the nucleic acid devices. The applications of nucleic acids greatly relies on the bio-reactivity and specificity when applied to highly complexed biological systems.
This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
ContributorsZhou, Yu (Ph.D.) (Author) / Yan, Hao (Thesis advisor) / Green, Alexander (Thesis advisor) / Woodbury, Neal (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2019
Description
Synthetic biology is an emerging engineering disciple, which designs and controls biological systems for creation of materials, biosensors, biocomputing, and much more. To better control and engineer these systems, modular genetic components which allow for highly specific and high dynamic range genetic regulation are necessary. Currently the field struggles to demonstrate reliable regulators which are programmable and specific, yet also allow for a high dynamic range of control. Inspired by the characteristics of the RNA toehold switch in E. coli, this project attempts utilize artificial introns and complementary trans-acting RNAs for gene regulation in a eukaryote host, S. cerevisiae. Following modification to an artificial intron, splicing control with RNA hairpins was demonstrated. Temperature shifts led to increased protein production likely due to increased splicing due to hairpin loosening. Progress is underway to demonstrate trans-acting RNA interaction to control splicing. With continued development, we hope to provide a programmable, specific, and effective means for translational gene regulation in S. cerevisae.
ContributorsDorr, Brandon Arthur (Author) / Wang, Xiao (Thesis director) / Green, Alexander (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Amino acid analysis (AAA) of egg white lysozyme and bovine Achilles tendon collagen was performed using 1H solution-state nuclear magnetic resonance (NMR) spectroscopy. The proteins were hydrolyzed in 6M HCL with and without 0.02% phenol at 110\u00B0C for 24, 48, and 72 hours. For both proteins, 18 of 20 amino acids were characterized including hydroxyproline and hydroxylysine in collagen, using 1-dimensional (1D) and 2-dimensional (2D) NMR spectroscopy experiments. Errors ranging from <1% to 8% were seen in treatments with and without phenol. Both proteins could be correctly identified within their own species using the online database search AACompIdent. The proposed approach is a simple analytical technique that does not require the use of column separation or amino acid derivatization prior to compositional analysis.
ContributorsBaranowski, Michael Edward (Author) / Yarger, Jeffery (Thesis director) / Holland, Gregory (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Herberger Institute for Design and the Arts (Contributor)
Created2014-05
Characterization of a Lipid Coating on the Surface of Silk Produced by the Embiid Antipaluria urichi
Description
Insects of the order Embiidina spin sheets of very thin silk fibers from their forelimbs to build silken shelters on bark and in leaf litter in tropical climates. Their shelters are very stiff and hydrophobic to keep out predators and rain. In this study, the existence of an outer lipid coating on silk produced by the embiid Antipaluria urichi is shown using scanning and transmission electron microscopy, FT-IR, and water drop contact angle analysis. Subsequently, the composition of the lipid layer is then characterized by 1H NMR and GC-MS.
ContributorsOsborn Popp, Thomas Michael (Author) / Yarger, Jeffery (Thesis director) / Holland, Gregory (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-05
Description
The parameters of microwave-assisted acid hydrolysis (MAAH) and 1H NMR highly affect the quantitative analysis of protein hydrolysates. Microwave-induction source, NMR spectral resolution, and data analysis are key parameters in the nuclear magnetic resonance – amino acid analysis (NMR-AAA) workflow where errors accrue due to lack of an optimized protocol. Hen egg white lysozyme was hydrolyzed using an 800W domestic microwave oven for varying time points between 10-25 minutes, showing minimal protein hydrolysis after extended time periods. Studies on paramagnetic doping with varying amounts of gadolinium chloride for increased NMR resolution resulted in little T1 reduction in a majority of amino acids and resulted in significant line broadening in concentrations above 1µM. The use of the BAYESIL analysis tool with HOD suppressed 1H-NMR spectra resulted in misplaced template peaks and errors greater than 1% for 10 of 13 profiled amino acids with the highest error being 7.6% (Thr). Comparatively, Chenomx NMR Suite (v7.1) analysis resulted in errors of less than 1% for 9 of 13 profiled amino acids with a highest error value of 3.6% (Lys). Using the optimized protocol, hen egg white lysozyme C was identified at rank 1 with a score of 64 in a Gallus gallus species wide AACompIdent search. This technique reduces error associated with sample handling relative to previously used amino acid analysis (AAA) protocols and requires no derivatization or additional processing of the sample prior to analysis.
ContributorsJordan, Jacob Smith (Author) / Yarger, Jeffery (Thesis director) / Van Horn, Wade (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Plastics make up a large proportion of solid waste that ends up in landfills and pollute ecosystems, and do not readily decompose. Composites from fungus mycelium are a recent and promising alternative to replace plastics. Mycelium is the root-like fibers from fungi that grow underground. When fed with woody biomass, the mycelium becomes a dense mass. From there, the mycelium is placed in mold to take its shape and grow. Once the growth process is done, the mycelium is baked to end the growth, thus making a mycelium brick. The woody biomass fed into the mycelium can include materials such as sawdust and pistachio shells, which are all cheap feedstock. In comparison to plastics, mycelium bricks are mostly biodegradable and eco-friendly. Mycelium bricks are resistant to water, fire, and mold and are also lightweight, sustainable, and affordable. Mycelium based materials are a viable option to replace less eco-friendly materials. This project aims to explore growth factors of mycelium and incorporate nanomaterials into mycelium bricks to achieve strong and sustainable materials, specifically for packaging materials. The purpose of integrating nanomaterials into mycelium bricks is to add further functionality such as conductivity, and to enhance properties such as mechanical strength.
ContributorsWong, Cindy (Author) / Wang, Qing Hua (Thesis director) / Green, Alexander (Committee member) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05