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Several debilitating neurological disorders, such as Alzheimer's disease, stroke, and spinal cord injury, are characterized by the damage or loss of neuronal cell types in the central nervous system (CNS). Human neural progenitor cells (hNPCs) derived from human pluripotent stem cells (hPSCs) can proliferate extensively and differentiate into the various neuronal subtypes and supporting cells that comprise the CNS. As such, hNPCs have tremendous potential for disease modeling, drug screening, and regenerative medicine applications. However, the use hNPCs for the study and treatment of neurological diseases requires the development of defined, robust, and scalable methods for their expansion and neuronal differentiation. To that end a rational design process was used to develop a vitronectin-derived peptide (VDP)-based substrate to support the growth and neuronal differentiation of hNPCs in conventional two-dimensional (2-D) culture and large-scale microcarrier (MC)-based suspension culture. Compared to hNPCs cultured on ECMP-based substrates, hNPCs grown on VDP-coated surfaces displayed similar morphologies, growth rates, and high expression levels of hNPC multipotency markers. Furthermore, VDP surfaces supported the directed differentiation of hNPCs to neurons at similar levels to cells differentiated on ECMP substrates. Here it has been demonstrated that VDP is a robust growth and differentiation matrix, as demonstrated by its ability to support the expansions and neuronal differentiation of hNPCs derived from three hESC (H9, HUES9, and HSF4) and one hiPSC (RiPSC) cell lines. Finally, it has been shown that VDP allows for the expansion or neuronal differentiation of hNPCs to quantities (>1010) necessary for drug screening or regenerative medicine purposes. In the future, the use of VDP as a defined culture substrate will significantly advance the clinical application of hNPCs and their derivatives as it will enable the large-scale expansion and neuronal differentiation of hNPCs in quantities necessary for disease modeling, drug screening, and regenerative medicine applications.
ContributorsVarun, Divya (Author) / Brafman, David (Thesis advisor) / Nikkhah, Mehdi (Committee member) / Stabenfeldt, Sarah (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation describes fundamental studies of hollow carbon nanostructures, which may be used as electrodes for practical energy storage applications such as batteries or supercapacitors. Electron microscopy is heavily utilized for the nanoscale characterization. To control the morphology of hollow carbon nanostructures, ZnO nanowires serve as sacrificial templates. The first part of this dissertation focuses on the optimization of synthesis parameters and the scale-up production of ZnO nanowires by vapor transport method. Uniform ZnO nanowires with 40 nm width can be produced by using 1100 °C reaction temperature and 20 sccm oxygen flow rate, which are the two most important parameters.
The use of ethanol as carbon source with or without water steam provides uniform carbonaceous deposition on ZnO nanowire templates. The amount of as-deposited carbonaceous material can be controlled by reaction temperature and reaction time. Due to the catalytic property of ZnO surface, the thicknesses of carbonaceous layers are typically in nanometers. Different methods to remove the ZnO templates are explored, of which hydrogen reduction at temperatures higher than 700 °C is most efficient. The ZnO templates can also be removed under ethanol environment, but the temperatures need to be higher than 850 °C for practical use.
Characterizations of hollow carbon nanofibers show that the hollow carbon nanostructures have a high specific surface area (>1100 m2/g) with the presence of mesopores (~3.5 nm). The initial data on energy storage as electrodes of electrochemical double layer capacitors show that high specific capacitance (> 220 F/g) can be obtained, which is related to the high surface area and unique porous hollow structure with a thin wall.
The use of ethanol as carbon source with or without water steam provides uniform carbonaceous deposition on ZnO nanowire templates. The amount of as-deposited carbonaceous material can be controlled by reaction temperature and reaction time. Due to the catalytic property of ZnO surface, the thicknesses of carbonaceous layers are typically in nanometers. Different methods to remove the ZnO templates are explored, of which hydrogen reduction at temperatures higher than 700 °C is most efficient. The ZnO templates can also be removed under ethanol environment, but the temperatures need to be higher than 850 °C for practical use.
Characterizations of hollow carbon nanofibers show that the hollow carbon nanostructures have a high specific surface area (>1100 m2/g) with the presence of mesopores (~3.5 nm). The initial data on energy storage as electrodes of electrochemical double layer capacitors show that high specific capacitance (> 220 F/g) can be obtained, which is related to the high surface area and unique porous hollow structure with a thin wall.
ContributorsSong, Yian (Author) / Liu, Jingyue (Committee member) / Smith, David (Committee member) / McCartney, Martha (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation presents research findings regarding the exploitation of localized surface plasmon (LSP) of epitaxial Ag islands as a means to enhance the photoluminescence (PL) of Germanium (Ge) quantum dots (QDs). The first step of this project was to investigate the growth of Ag islands on Si(100). Two distinct families of Ag islands have been observed. “Big islands” are clearly faceted and have basal dimensions in the few hundred nm to μm range with a variety of basal shapes. “Small islands” are not clearly faceted and have basal diameters in the 10s of nm range. Big islands form via a nucleation and growth mechanism, and small islands form via precipitation of Ag contained in a planar layer between the big islands that is thicker than the Stranski-Krastanov layer existing at room-temperature.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
ContributorsKong, Dexin (Author) / Drucker, Jeffery (Thesis advisor) / Chen, Tingyong (Committee member) / Ros, Robert (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
Photocatalytic water splitting is a promising technique to produce H2 fuels from water using sustainable solar energy. To better design photocatalysts, the understanding of charge transfer at surfaces/interfaces and the corresponding structure change during the reaction is very important. Local structural and chemical information on nanoparticle surfaces or interfaces can be achieved through characterizations on transmission electron microscopy (TEM). Emphasis should be put on materials structure changes during the reactions in their “working conditions”. Environmental TEM with in situ light illumination system allows the photocatalysts to be studied under light irradiation when exposed to H2O vapor. A set of ex situ and in situ TEM characterizations are carried out on typical types of TiO2 based photocatalysts. The observed structure changes during the reaction are correlated with the H2 production rate for structure-property relationships.
A surface disordering was observed in situ when well-defined anatase TiO2 rhombohedral nanoparticles were exposed to 1 Torr H2O vapor and 10suns light inside the environmental TEM. The disordering is believed to be related to high density of hydroxyl groups formed on surface oxygen vacancies during water splitting reactions.
Pt co-catalyst on TiO2 is able to split pure water producing H2 and O2. The H2 production rate drops during the reaction. Particle size growth during reaction was discovered with Z-contrast images. The particle size growth is believed to be a photo-electro-chemical Ostwald ripening.
Characterizations were also carried out on a more complicated photocatalyst system: Ni/NiO core/shell co-catalyst on TiO2. A decrease of the H2 production rate resulting from photo-corrosion was observed. The Ni is believed to be oxidized to Ni2+ by OH• radicals which are intermediate products of H2O oxidation. The mechanism that the OH• radicals leak into the cores through cracks on NiO shells is more supported by experiments.
Overall this research has done a comprehensive ex situ and in situ TEM characterizations following some typical TiO2 based photocatalysts during reactions. This research has shown the technique availability to study photocatalyst inside TEM in photocatalytic conditions. It also demonstrates the importance to follow structure changes of materials during reactions in understanding deactivation mechanisms.
A surface disordering was observed in situ when well-defined anatase TiO2 rhombohedral nanoparticles were exposed to 1 Torr H2O vapor and 10suns light inside the environmental TEM. The disordering is believed to be related to high density of hydroxyl groups formed on surface oxygen vacancies during water splitting reactions.
Pt co-catalyst on TiO2 is able to split pure water producing H2 and O2. The H2 production rate drops during the reaction. Particle size growth during reaction was discovered with Z-contrast images. The particle size growth is believed to be a photo-electro-chemical Ostwald ripening.
Characterizations were also carried out on a more complicated photocatalyst system: Ni/NiO core/shell co-catalyst on TiO2. A decrease of the H2 production rate resulting from photo-corrosion was observed. The Ni is believed to be oxidized to Ni2+ by OH• radicals which are intermediate products of H2O oxidation. The mechanism that the OH• radicals leak into the cores through cracks on NiO shells is more supported by experiments.
Overall this research has done a comprehensive ex situ and in situ TEM characterizations following some typical TiO2 based photocatalysts during reactions. This research has shown the technique availability to study photocatalyst inside TEM in photocatalytic conditions. It also demonstrates the importance to follow structure changes of materials during reactions in understanding deactivation mechanisms.
ContributorsZhang, Liuxian (Author) / Crozier, Peter (Thesis advisor) / Smith, David (Committee member) / Chan, Candace (Committee member) / Liu, Jingyue (Committee member) / Arizona State University (Publisher)
Created2015
Description
In this dissertation, the interface chemistry and electronic structure of plasma-enhanced atomic layer deposited (PEALD) dielectrics on GaN are investigated with x-ray and ultraviolet photoemission spectroscopy (XPS and UPS). Three interrelated issues are discussed in this study: (1) PEALD dielectric growth process optimization, (2) interface electronic structure of comparative PEALD dielectrics on GaN, and (3) interface electronic structure of PEALD dielectrics on Ga- and N-face GaN. The first study involved an in-depth case study of PEALD Al2O3 growth using dimethylaluminum isopropoxide, with a special focus on oxygen plasma effects. Saturated and self-limiting growth of Al2O3 films were obtained with an enhanced growth rate within the PEALD temperature window (25-220 ºC). The properties of Al2O3 deposited at various temperatures were characterized to better understand the relation between the growth parameters and film properties. In the second study, the interface electronic structures of PEALD dielectrics on Ga-face GaN films were measured. Five promising dielectrics (Al2O3, HfO2, SiO2, La2O3, and ZnO) with a range of band gap energies were chosen. Prior to dielectric growth, a combined wet chemical and in-situ H2/N2 plasma clean process was employed to remove the carbon contamination and prepare the surface for dielectric deposition. The surface band bending and band offsets were measured by XPS and UPS for dielectrics on GaN. The trends of the experimental band offsets on GaN were related to the dielectric band gap energies. In addition, the experimental band offsets were near the calculated values based on the charge neutrality level model. The third study focused on the effect of the polarization bound charge of the Ga- and N-face GaN on interface electronic structures. A surface pretreatment process consisting of a NH4OH wet chemical and an in-situ NH3 plasma treatment was applied to remove carbon contamination, retain monolayer oxygen coverage, and potentially passivate N-vacancy related defects. The surface band bending and polarization charge compensation of Ga- and N-face GaN were investigated. The surface band bending and band offsets were determined for Al2O3, HfO2, and SiO2 on Ga- and N-face GaN. Different dielectric thicknesses and post deposition processing were investigated to understand process related defect formation and/or reduction.
ContributorsYang, Jialing (Author) / Nemanich, Robert J (Thesis advisor) / Chen, Tingyong (Committee member) / Peng, Xihong (Committee member) / Ponce, Fernando (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2014
Description
Osteosarcoma is the most common bone cancer in children and adolescents. Patients with metastatic osteosarcoma are typically refractory to treatment. Numerous lines of evidence suggest that cytotoxic T-lymphocytes (CTL) limit the development of metastatic osteosarcoma. I have investigated the role of Programmed Death Receptor-1 (PD-1) in limiting the efficacy of immune mediated control of metastatic osteosarcoma. I show that human metastatic, but not primary, osteosarcoma tumors express the ligand for PD-1 (PD-L1) and that tumor infiltrating CTL express PD-1, suggesting this pathway may limit CTL control of metastatic osteosarcoma in patients. PD-L1 is also expressed on the K7M2 osteosarcoma tumor cell line that establishes metastases in mice, and PD-1 is expressed on tumor infiltrating CTL during disease progression. Blockade of PD-1/PD-L1 interactions dramatically improves the function of osteosarcoma-reactive CTL in vitro and in vivo, and results in decreased tumor burden and increased survival in the K7M2 mouse model of metastatic osteosarcoma. My results suggest that blockade of PD-1/PD-L1 interactions in patients with metastatic osteosarcoma should be pursued as a therapeutic strategy. However, PD-1/PD-L1 blockade treated mice still succumb to disease due to selection of PD-L1 mAb resistant tumor cells via up-regulation of other co-inhibitory T cell receptors. Combinational α-CTLA-4 and α-PD-L1 blockade treated mice were able to completely eradicate metastatic osteosarcoma, and generate immunity to disease. These results suggest that blockade of PD-1/PD-L1 interactions in patients with metastatic osteosarcoma, although improves survival, may lead to tumor resistance, requiring combinational immunotherapies to combat and eradicate disease.
ContributorsLussier, Danielle (Author) / Blattman, Joseph N. (Thesis advisor) / Anderson, Karen (Committee member) / Goldstein, Elliott (Committee member) / Lake, Douglas (Committee member) / Arizona State University (Publisher)
Created2015
Description
This dissertation presents research findings on the three materials systems: lateral Si nanowires (SiNW), In2Se3/Bi2Se3 heterostructures and graphene. The first part of the thesis was focused on the growth and characterization of lateral SiNW. Lateral here refers to wires growing along the plane of substrate; vertical NW on the other hand grow out of the plane of substrate. It was found, using the Au-seeded vapor – liquid – solid technique, that epitaxial single-crystal SiNW can be grown laterally along Si(111) substrates that have been miscut toward [11− 2]. The ratio of lateral-to-vertical NW was found to increase as the miscut angle increased and as disilane pressure and substrate temperature decreased. Based on this observation, growth parameters were identified whereby all of the deposited Au seeds formed lateral NW. Furthermore, the nanofaceted substrate guided the growth via a mechanism that involved pinning of the trijunction at the liquid/solid interface of the growing nanowire.
Next, the growth of selenide heterostructures was explored. Specifically, molecular beam epitaxy was utilized to grow In2Se3 and Bi2Se3 films on h-BN, highly oriented pyrolytic graphite and Si(111) substrates. Growth optimizations of In2Se3 and Bi2Se3 films were carried out by systematically varying the growth parameters. While the growth of these films was demonstrated on h-BN and HOPG surface, the majority of the effort was focused on growth on Si(111). Atomically flat terraces that extended laterally for several hundred nm, which were separated by single quintuple layer high steps characterized surface of the best In2Se3 films grown on Si(111). These In2Se3 films were suitable for subsequent high quality epitaxy of Bi2Se3 .
The last part of this dissertation was focused on a recently initiated and ongoing study of graphene growth on liquid metal surfaces. The initial part of the study comprised a successful modification of an existing growth system to accommodate graphene synthesis and process development for reproducible graphene growth. Graphene was grown on Cu, Au and AuCu alloys at varioua conditions. Preliminary results showed triangular features on the liquid part of the Cu metal surface. For Au, and AuCu alloys, hexagonal features were noticed both on the solid and liquid parts.
Next, the growth of selenide heterostructures was explored. Specifically, molecular beam epitaxy was utilized to grow In2Se3 and Bi2Se3 films on h-BN, highly oriented pyrolytic graphite and Si(111) substrates. Growth optimizations of In2Se3 and Bi2Se3 films were carried out by systematically varying the growth parameters. While the growth of these films was demonstrated on h-BN and HOPG surface, the majority of the effort was focused on growth on Si(111). Atomically flat terraces that extended laterally for several hundred nm, which were separated by single quintuple layer high steps characterized surface of the best In2Se3 films grown on Si(111). These In2Se3 films were suitable for subsequent high quality epitaxy of Bi2Se3 .
The last part of this dissertation was focused on a recently initiated and ongoing study of graphene growth on liquid metal surfaces. The initial part of the study comprised a successful modification of an existing growth system to accommodate graphene synthesis and process development for reproducible graphene growth. Graphene was grown on Cu, Au and AuCu alloys at varioua conditions. Preliminary results showed triangular features on the liquid part of the Cu metal surface. For Au, and AuCu alloys, hexagonal features were noticed both on the solid and liquid parts.
ContributorsRathi, Somilkumar J (Author) / Drucker, Jeffery (Thesis advisor) / Smith, David (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2014
Description
GaN and AlGaN have shown great potential in next-generation power and RF electronics. However, these devices are limited by reliability issues such as leakage current and current collapse that result from surface and interface states on GaN and AlGaN. This dissertation, therefore, examined these electronic states, focusing on the following two points:
First, the surface electronic state configuration was examined with regards to the polarization bound 1013 charges/cm2 that increases with aluminum content. This large bound charge requires compensation either externally by surface states or internally by the space charge regions as relates to band bending. In this work, band bending was measured after different surface treatments of GaN and AlGaN to determine the effects of specific surface states on the electronic state configuration. Results showed oxygen-terminated N-face GaN, Ga-face GaN, and Ga-face Al0.25Ga0.75N surface were characterized by similar band bending regardless of the polarization bound charge, suggesting a Fermi level pinning state ~0.4-0.8 eV below the conduction band minimum. On oxygen-free Ga-face GaN, Al0.15Ga0.85N, Al0.25Ga0.75N, and Al0.35Ga0.65N, band bending increased slightly with aluminum content and thus did not exhibit the same pinning behavior; however, there was still significant compensating charge on these surfaces (~1013 charges/cm2). This charge is likely related to nitrogen vacancies and/or gallium dangling bonds.
In addition, this wozrk investigated the interface electronic state configuration of dielectric/GaN and AlGaN interfaces with regards to deposition conditions and aluminum content. Specifically, oxygen plasma-enhanced atomic layer deposited (PEALD) was used to deposit SiO2. Growth temperature was shown to influence the film quality, where room temperature deposition produced the highest quality films in terms of electrical breakdown. In addition, the valence band offsets (VBOs) appeared to decrease with the deposition temperature, which likely related to an electric field across the Ga2O3 interfacial layer. VBOs were also determined with respect to aluminum content at the PEALD-SiO2/AlxGa1-xN interface, giving 3.0, 2.9, 2.9, and 2.8 eV for 0%, 15%, 25%, and 35% aluminum content, respectively—with corresponding conduction band offsets of 2.5, 2.2, 1.9, and 1.8 eV. This suggests the largest difference manifests in the conduction band, which is in agreement with the charge neutrality level model.
First, the surface electronic state configuration was examined with regards to the polarization bound 1013 charges/cm2 that increases with aluminum content. This large bound charge requires compensation either externally by surface states or internally by the space charge regions as relates to band bending. In this work, band bending was measured after different surface treatments of GaN and AlGaN to determine the effects of specific surface states on the electronic state configuration. Results showed oxygen-terminated N-face GaN, Ga-face GaN, and Ga-face Al0.25Ga0.75N surface were characterized by similar band bending regardless of the polarization bound charge, suggesting a Fermi level pinning state ~0.4-0.8 eV below the conduction band minimum. On oxygen-free Ga-face GaN, Al0.15Ga0.85N, Al0.25Ga0.75N, and Al0.35Ga0.65N, band bending increased slightly with aluminum content and thus did not exhibit the same pinning behavior; however, there was still significant compensating charge on these surfaces (~1013 charges/cm2). This charge is likely related to nitrogen vacancies and/or gallium dangling bonds.
In addition, this wozrk investigated the interface electronic state configuration of dielectric/GaN and AlGaN interfaces with regards to deposition conditions and aluminum content. Specifically, oxygen plasma-enhanced atomic layer deposited (PEALD) was used to deposit SiO2. Growth temperature was shown to influence the film quality, where room temperature deposition produced the highest quality films in terms of electrical breakdown. In addition, the valence band offsets (VBOs) appeared to decrease with the deposition temperature, which likely related to an electric field across the Ga2O3 interfacial layer. VBOs were also determined with respect to aluminum content at the PEALD-SiO2/AlxGa1-xN interface, giving 3.0, 2.9, 2.9, and 2.8 eV for 0%, 15%, 25%, and 35% aluminum content, respectively—with corresponding conduction band offsets of 2.5, 2.2, 1.9, and 1.8 eV. This suggests the largest difference manifests in the conduction band, which is in agreement with the charge neutrality level model.
ContributorsEller, Brianna (Author) / Nemanich, Robert J (Thesis advisor) / Chowdhury, Srabanti (Committee member) / McCartney, Martha (Committee member) / Ponce, Fernando (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
Description
Synthetic gene networks have evolved from simple proof-of-concept circuits to
complex therapy-oriented networks over the past fifteen years. This advancement has
greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a
mechanism that cells use to achieve a discrete number of mutually exclusive states in
response to environmental inputs. However, complex contextual connections of gene
regulatory networks in natural settings often impede the experimental establishment of
the function and dynamics of each specific gene network.
In this work, diverse synthetic gene networks are rationally designed and
constructed using well-characterized biological components to approach the cell fate
determination and state transition dynamics in multistable systems. Results show that
unimodality and bimodality and trimodality can be achieved through manipulation of the
signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to
communicate with each other.
Moreover, a synthetic quadrastable circuit is also built and experimentally
demonstrated to have four stable steady states. Experiments, guided by mathematical
modeling predictions, reveal that sequential inductions generate distinct cell fates by
changing the landscape in sequence and hence navigating cells to different final states.
Circuit function depends on the specific protein expression levels in the circuit.
We then establish a protein expression predictor taking into account adjacent
transcriptional regions’ features through construction of ~120 synthetic gene circuits
(operons) in Escherichia coli. The predictor’s utility is further demonstrated in evaluating genes’ relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks.
These combined results illustrate applications of synthetic gene networks to
understand the cell fate determination and state transition dynamics in multistable
systems. A protein-expression predictor is also developed to evaluate and tune circuit
dynamics.
complex therapy-oriented networks over the past fifteen years. This advancement has
greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a
mechanism that cells use to achieve a discrete number of mutually exclusive states in
response to environmental inputs. However, complex contextual connections of gene
regulatory networks in natural settings often impede the experimental establishment of
the function and dynamics of each specific gene network.
In this work, diverse synthetic gene networks are rationally designed and
constructed using well-characterized biological components to approach the cell fate
determination and state transition dynamics in multistable systems. Results show that
unimodality and bimodality and trimodality can be achieved through manipulation of the
signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to
communicate with each other.
Moreover, a synthetic quadrastable circuit is also built and experimentally
demonstrated to have four stable steady states. Experiments, guided by mathematical
modeling predictions, reveal that sequential inductions generate distinct cell fates by
changing the landscape in sequence and hence navigating cells to different final states.
Circuit function depends on the specific protein expression levels in the circuit.
We then establish a protein expression predictor taking into account adjacent
transcriptional regions’ features through construction of ~120 synthetic gene circuits
(operons) in Escherichia coli. The predictor’s utility is further demonstrated in evaluating genes’ relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks.
These combined results illustrate applications of synthetic gene networks to
understand the cell fate determination and state transition dynamics in multistable
systems. A protein-expression predictor is also developed to evaluate and tune circuit
dynamics.
ContributorsWu, Fuqing (Author) / Wang, Xiao (Thesis advisor) / Haynes, Karmella (Committee member) / Marshall, Pamela (Committee member) / Nielsen, David (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2017