Matching Items (70)
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Description
There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water

There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water and sunlight. As a part of the photosynthetic electron transport chain (PETC) of the green algae Chlamydomonas reinhardtii, water is split via Photosystem II (PSII) and the electrons flow through a series of electron transfer cofactors in cytochrome b6f, plastocyanin and Photosystem I (PSI). The terminal electron acceptor of PSI is ferredoxin, from which electrons may be used to reduce NADP+ for metabolic purposes. Concomitant production of a H+ gradient allows production of energy for the cell. Under certain conditions and using the endogenous hydrogenase, excess protons and electrons from ferredoxin may be converted to molecular hydrogen. In this work it is demonstrated both that certain mutations near the quinone electron transfer cofactor in PSI can speed up electron transfer through the PETC, and also that a native [FeFe]-hydrogenase can be expressed in the C. reinhardtii chloroplast. Taken together, these research findings form the foundation for the design of a PSI-hydrogenase fusion for the direct and continuous photo-production of hydrogen in vivo.
ContributorsReifschneider, Kiera (Author) / Redding, Kevin (Thesis advisor) / Fromme, Petra (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Telomerase is a unique reverse transcriptase that has evolved specifically to extend the single stranded DNA at the 3' ends of chromosomes. To achieve this, telomerase uses a small section of its integral RNA subunit (TR) to reiteratively copy a short, canonically 6-nt, sequence repeatedly in a processive manner using

Telomerase is a unique reverse transcriptase that has evolved specifically to extend the single stranded DNA at the 3' ends of chromosomes. To achieve this, telomerase uses a small section of its integral RNA subunit (TR) to reiteratively copy a short, canonically 6-nt, sequence repeatedly in a processive manner using a complex and currently poorly understood mechanism of template translocation to stop nucleotide addition, regenerate its template, and then synthesize a new repeat. In this study, several novel interactions between the telomerase protein and RNA components along with the DNA substrate are identified and characterized which come together to allow active telomerase repeat addition. First, this study shows that the sequence of the RNA/DNA duplex holds a unique, single nucleotide signal which pauses DNA synthesis at the end of the canonical template sequence. Further characterization of this sequence dependent pause signal reveals that the template sequence alone can produce telomerase products with the characteristic 6-nt pattern, but also works cooperatively with another RNA structural element for proper template boundary definition. Finally, mutational analysis is used on several regions of the protein and RNA components of telomerase to identify crucial determinates of telomerase assembly and processive repeat synthesis. Together, these results shed new light on how telomerase coordinates its complex catalytic cycle.
ContributorsBrown, Andrew F (Author) / Chen, Julian J. L. (Thesis advisor) / Jones, Anne (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
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Description
The communication of genetic material with biomolecules has been a major interest in cancer biology research for decades. Among its different levels of involvement, DNA is known to be a target of several antitumor agents. Additionally, tissue specific interaction between macromolecules such as proteins and structurally important regions of DNA

The communication of genetic material with biomolecules has been a major interest in cancer biology research for decades. Among its different levels of involvement, DNA is known to be a target of several antitumor agents. Additionally, tissue specific interaction between macromolecules such as proteins and structurally important regions of DNA has been reported to define the onset of certain types of cancers.

Illustrated in Chapter 1 is the general history of research on the interaction of DNA and anticancer drugs, most importantly different congener of bleomycin (BLM). Additionally, several synthetic analogues of bleomycin, including the structural components and functionalities, are discussed.

Chapter 2 describes a new approach to study the double-strand DNA lesion caused by antitumor drug bleomycin. The hairpin DNA library used in this study displays numerous cleavage sites demonstrating the versatility of bleomycin interaction with DNA. Interestingly, some of those cleavage sites suggest a novel mechanism of bleomycin interaction, which has not been reported before.

Cytidine methylation has generally been found to decrease site-specific cleavage of DNA by BLM, possibly due to structural change and subsequent reduced bleomycin-mediated recognition of DNA. As illustrated in Chapter 3, three hairpin DNAs known to be strongly bound by bleomycin, and their methylated counterparts, were used to study the dynamics of bleomycin-induced degradation of DNAs in cancer cells. Interestingly, cytidine methylation on one of the DNAs has also shown a major shift in the intensity of bleomycin induced double-strand DNA cleavage pattern, which is known to be a more potent form of bleomycin induced cleavages.

DNA secondary structures are known to play important roles in gene regulation. Chapter 4 demonstrates a structural change of the BCL2 promoter element as a result of its dynamic interaction with the individual domains of hnRNP LL, which is essential to facilitate the transcription of BCL2. Furthermore, an in vitro protein synthesis technique has been employed to study the dynamic interaction between protein domains and the i-motif DNA within the promoter element. Several constructs were made involving replacement of a single amino acid with a fluorescent analogue, and these were used to study FRET between domain 1 and the i-motif, the later of which harbored a fluorescent acceptor nucleotide analogue.
ContributorsRoy, Basab (Author) / Hecht, Sidney M. (Thesis advisor) / Jones, Anne (Committee member) / Levitus, Marcia (Committee member) / Chaput, John (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified

Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified across all gold:silver ratios by a linear shift in the plasmon band maxima against alloy composition. The molar absorptivities of the NPs decreased non-linearly with increasing gold content from 2.0 x 108 M-1 cm-1 (fÉmax = 404 nm) for pure silver to 4.1 x 107 M-1 cm-1 (fÉmax = 511 nm) for pure gold. The NPs were immobilized onto transparent indium-tin oxide composite electrodes using layer-by-layer (LbL) deposition with poly(diallyldimethylammonium) acting as a cationic binder. The UV-Vis absorbance of the LbL film was used to calculate the surface coverage of alloy NPs on the electrode. Typical preparations had average NP surface coverages of 2.8 x 10-13 mol NPs/cm2 (~5% of cubic closest packing) with saturated films reaching ~20% of ccp for single-layer preparations (1.0 ~ 10-12 mol NPs/cm2). X-ray photoelectron spectroscopy confirmed the presence of alloy NPs in the LbL film and showed silver enrichment of the NP surfaces by ~9%. Irreversible oxidative dissolution (dealloying) of the less noble silver atoms from the NPs on LbL electrodes was performed by cyclic voltammetry (CV) in sulfuric acid. Alloy NPs with higher gold content required larger overpotentials for silver dealloying. Dealloying of the more-noble gold atoms from the alloy NPs was also achieved by CV in sodium chloride. The silver was oxidized first to cohesive silver chloride, and then gold dealloyed to soluble HAuCl4- at higher potentials. Silver oxidation was inhibited during the first oxidative scan, but subsequent cycles showed typical, reversible silver-to-silver chloride voltammetry. The potentials for both silver oxidation and gold dealloying also shifted to more oxidizing potentials with increasing gold content, and both processes converged for alloy NPs with >60% gold content. Charge-mediated electrochemistry of silver NPs immobilized in LbL films, using Fc(meOH) as the charge carrier, showed that 67% of the NPs were electrochemically inactive.
ContributorsStarr, Christopher A (Author) / Buttry, Daniel A (Thesis advisor) / Petuskey, William (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Hydrogenases catalyze the interconversion of protons, electrons, and hydrogen according to the reaction: 2H+ + 2e- <-> H2 while using only earth abundant metals, namely nickel and iron for catalysis. The enzymatic turnover of Clostridium acetobutylicum [FeFe]-hydrogenase has been investigated through the use of electrochemical and scanning probe techniques. Scanning

Hydrogenases catalyze the interconversion of protons, electrons, and hydrogen according to the reaction: 2H+ + 2e- <-> H2 while using only earth abundant metals, namely nickel and iron for catalysis. The enzymatic turnover of Clostridium acetobutylicum [FeFe]-hydrogenase has been investigated through the use of electrochemical and scanning probe techniques. Scanning tunneling microscopy (STM) imaging revealed sub-monolayer surface coverage. Cyclic voltammetry yielded a catalytic, cathodic hydrogen production signal similar to that observed for a platinum electrode. From the direct observation of single enzymes and the macroscopic electrochemical measurements obtained from the same electrode, the apparent turnover frequency (TOF) per single enzyme molecule as a function of potential was determined. The TOF at 0.7 V vs. Ag/AgCl for the four SAMs yielded a decay constant for electronic coupling (β) through the SAM of ~ 0.82 Å -1, in excellent agreement with published values for similar SAMs. One mechanism used by plants to protect against damage is called nonphotochemical quenching (NPQ). Triggered by low pH in the thylakoid lumen, NPQ leads to conversion of excess excitation energy in the antenna system to heat before it can initiate production of harmful chemical species by photosynthetic reaction centers. Here a synthetic hexad molecule that functionally mimics the role of the antenna in NPQ is described. When the hexad is dissolved in an organic solvent, five zinc porphyrin antenna moieties absorb light, exchange excitation energy, and ultimately decay by normal photophysical processes. However, when acid is added, a pH-sensitive dye moiety is converted to a form that rapidly quenches the first excited singlet states of all five porphyrins, converting the excitation energy to heat and rendering the porphyrins kinetically incompetent to perform useful photochemistry. Charge transport was also studied in single-molecule junctions formed with a 1,7-pyrrolidine-substituted 3,4,9,10-Perylenetetracarboxylic diimide (PTCDI) molecule. A reduction in the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals energy gap due to the electronic properties of the substituents is seen when compared to an unsubstituted-PTCDI. The small HOMO-LUMO energy gap allows for switching between electron- and hole-dominated charge transport with a gate voltage, thus demonstrating a single-molecule ambipolar field effect transistor.
ContributorsMadden, Christopher (Author) / Moore, Thomas A. (Thesis advisor) / Jones, Anne (Committee member) / Tao, Nongjian (Committee member) / Arizona State University (Publisher)
Created2012
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Description
The heliobacterial reaction center (HbRC) is widely considered the simplest and most primitive photosynthetic reaction center (RC) still in existence. Despite the simplicity of the HbRC, many aspects of the electron transfer mechanism remain unknown or under debate. Improving our understanding of the structure and function of the HbRC is

The heliobacterial reaction center (HbRC) is widely considered the simplest and most primitive photosynthetic reaction center (RC) still in existence. Despite the simplicity of the HbRC, many aspects of the electron transfer mechanism remain unknown or under debate. Improving our understanding of the structure and function of the HbRC is important in determining its role in the evolution of photosynthetic RCs. In this work, the function and properties of the iron-sulfur cluster FX and quinones of the HbRC were investigated, as these are the characteristic terminal electron acceptors used by Type-I and Type-II RCs, respectively. In Chapter 3, I develop a system to directly detect quinone double reduction activity using reverse-phase high pressure liquid chromatography (RP-HPLC), showing that Photosystem I (PSI) can reduce PQ to PQH2. In Chapter 4, I use RP-HPLC to characterize the HbRC, showing a surprisingly small antenna size and confirming the presence of menaquinone (MQ) in the isolated HbRC. The terminal electron acceptor FX was characterized spectroscopically and electrochemically in Chapter 5. I used three new systems to reduce FX in the HbRC, using EPR to confirm a S=3/2 ground-state for the reduced cluster. The midpoint potential of FX determined through thin film voltammetry was -372 mV, showing the cluster is much less reducing than previously expected. In Chapter 7, I show light-driven reduction of menaquinone in heliobacterial membrane samples using only mild chemical reductants. Finally, I discuss the evolutionary implications of these findings in Chapter 7.
ContributorsCowgill, John (Author) / Redding, Kevin (Thesis advisor) / Jones, Anne (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Graphene oxide membranes have shown promising gas separation characteristics specially for hydrogen that make them of interest for industrial applications. However, the gas transport mechanism for these membranes is unclear due to inconsistent permeation and separation results reported in literature. Graphene oxide membranes made by filtration, the most common synthesis

Graphene oxide membranes have shown promising gas separation characteristics specially for hydrogen that make them of interest for industrial applications. However, the gas transport mechanism for these membranes is unclear due to inconsistent permeation and separation results reported in literature. Graphene oxide membranes made by filtration, the most common synthesis method, contain wrinkles affecting their gas separation characteristics and the method itself is difficult to scale up. Moreover, the production of graphene oxide membranes with fine-tuned interlayer spacing for improved molecular separation is still a challenge. These unsolved issues will affect their potential impact on industrial gas separation applications.

In this study, high quality graphene oxide membranes are synthesized on polyester track etch substrates by different deposition methods and characterized by XRD, SEM, AFM as well as single gas permeation and binary (H2/CO2) separation experiments. Membranes are made from large graphene oxide sheets of different sizes (33 and 17 micron) using vacuum filtration to shed more light on their transport mechanism. Membranes are made from dilute graphene oxide suspension by easily scalable spray coating technique to minimize extrinsic wrinkle formation. Finally, Brodie’s derived graphene oxide sheets were used to prepare membranes with narrow interlayer spacing to improve their (H2/CO2) separation performance.

An inter-sheet and inner-sheet two-pathway model is proposed to explain the permeation and separation results of graphene oxide membranes obtained in this study. At room temperature, large gas molecules (CH4, N2, and CO2) permeate through inter-sheet pathway of the membranes, exhibiting Knudsen like diffusion characteristics, with the permeance for the small sheet membrane about twice that for the large sheet membrane. The small gases (H2 and He) exhibit much higher permeance, showing significant flow through an inner-sheet pathway, in addition to the flow through the inter-sheet pathway. Membranes prepared by spray coating offer gas characteristics similar to those made by filtration, however using dilute graphene oxide suspension in spray coating will help reduce the formation of extrinsic wrinkles which result in reduction in the porosity of the inter-sheet pathway where the transport of large gas molecules dominates. Brodie’s derived graphene oxide membranes showed overall low permeability and significant improvement in in H2/CO2 selectivity compared to membranes made using Hummers’ derived sheets due to smaller interlayer space height of Brodie’s sheets (~3 Å).
ContributorsIbrahim, Amr Fatehy Muhammad (Author) / Lin, Jerry Y.S. (Thesis advisor) / Mu, Bin (Committee member) / Lind, Mary (Committee member) / Green, Matthew (Committee member) / Wang, Qing (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Alloying in semiconductors has enabled many civilian technologies in optoelectronic, photonic fields and more. While the phenomenon of alloying is well established in traditional bulk semiconductors, owing to vastly available ternary phase diagrams, the ability to alloy in 2D systems are less clear. Recently anisotropic materials such as ReS2 and

Alloying in semiconductors has enabled many civilian technologies in optoelectronic, photonic fields and more. While the phenomenon of alloying is well established in traditional bulk semiconductors, owing to vastly available ternary phase diagrams, the ability to alloy in 2D systems are less clear. Recently anisotropic materials such as ReS2 and TiS3 have been extensively studied due to their direct-gap semiconductor and high mobility behaviors. This work is a report on alloys of ReS2 & ReSe2 and TiS3 &TiSe3.

Alloying selenium into ReS2 in the creation of ReS2xSe2-x, tunes the band gap and changes its vibrational spectrum. Depositing this alloy using bottom up approach has resulted in the loss of crystallinity. This loss of crystallinity was evidenced by grain boundaries and point defect shown by TEM images.

Also, in the creation of TiS3xSe3-x, by alloying Se into TiS3, a fixed ratio of 8% selenium deposit into TiS3 host matrix is observed. This is despite the vastly differing precursor amounts and growth temperatures, as evinced by detailed TEM, EDAX, TEM diffraction, and Raman spectroscopy measurements. This unusual behavior contrasts with other well-known layered material systems such as MoSSe, WMoS2 where continuous alloying can be attained. Cluster expansion theory calculations suggest that only limited composition (x) can be achieved. Considering the fact that TiSe3 vdW crystals have not been synthesized in the past, these alloying rejections can be attributed to energetic instability in the ternary phase diagrams estimated by calculations performed. Overall findings highlight potential means and challenges in achieving stable alloying in promising direct gap and high carrier mobility TiS3 materials.
ContributorsAgarwal, Ashutosh (Author) / Tongay, Sefaattin (Thesis advisor) / Green, Matthew (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2018
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Description
In this study, the differences in delivery of methylated and unmethylated prokaryotic

DNA in mammalian cells was investigated. 3 plasmids, DH5-α, ER2925 and

GM272 were extracted and transformed from E. coli bacteria. DH5-α is the regular

methylated plasmid, however,ER2925 and GM272 lack Dam and Dcm enzymes which

methylate adenine and internal cytosine in prokaryotes

In this study, the differences in delivery of methylated and unmethylated prokaryotic

DNA in mammalian cells was investigated. 3 plasmids, DH5-α, ER2925 and

GM272 were extracted and transformed from E. coli bacteria. DH5-α is the regular

methylated plasmid, however,ER2925 and GM272 lack Dam and Dcm enzymes which

methylate adenine and internal cytosine in prokaryotes respectively, hence they are

unmethylated. The 3 plasmids were delivered via different delivery vectors in two

cell lines, UMUC3 and MDA-MB-231 which are human bladder cancer cell line and

human triple negative breast cancer cell line, respectively.

Luciferase and BCA assay were carried out to quantify transgene expression to

compare the efficacy of gene delivery in three aforementioned plasmids. In addition,

hydrodynamic diameter and zeta potential was measured for all delivery vectors, to

correlate with other transgene expression data. The results show that methylated

plasmid has significantly higher transgene expression in mammalian cell lines. This

can be either a result of smaller size and more positive zeta potential that the methylated

plasmid had, or a result of having Dam and Dcm enzymes which enhance binding

of DNA and transcription factors and enhance gene expression. Having smaller size

and more positive zeta potential was proven to be the case for the methylated plasmid

in this study. However the latter hypothesis should be investigated furthermore.
ContributorsMeraji, Seyedehmelika (Author) / Rege, Kaushal (Thesis advisor) / Nannegna, Brent (Committee member) / Green, Matthew (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Encapsulant is a key packaging component of photovoltaic (PV) modules, which protects the solar cell from physical, environmental and electrical damages. Ethylene-vinyl acetate (EVA) is one of the major encapsulant materials used in the PV industry. This work focuses on indoor accelerated ultraviolet (UV) stress testing and characterization to investigate

Encapsulant is a key packaging component of photovoltaic (PV) modules, which protects the solar cell from physical, environmental and electrical damages. Ethylene-vinyl acetate (EVA) is one of the major encapsulant materials used in the PV industry. This work focuses on indoor accelerated ultraviolet (UV) stress testing and characterization to investigate the EVA discoloration and delamination in PV modules by using various non-destructive characterization techniques, including current-voltage (IV) measurements, UV fluorescence (UVf) and colorimetry measurements. Mini-modules with glass/EVA/cell/EVA/backsheet construction were fabricated in the laboratory with two types of EVA, UV-cut EVA (UVC) and UV-pass EVA (UVP).

The accelerated UV testing was performed in a UV chamber equipped with UV lights at an ambient temperature of 50°C, little or no humidity and total UV dosage of 400 kWh/m2. The mini-modules were maintained at three different temperatures through UV light heating by placing different thickness of thermal insulation sheets over the backsheet. Also, prior to thermal insulation sheet placement, the backsheet and laminate edges were fully covered with aluminum tape to prevent oxygen diffusion into the module and hence the photobleaching reaction.

The characterization results showed that mini-modules with UV-cut EVA suffered from discoloration while the modules with UV-pass EVA suffered from delamination. UVf imaging technique has the capability to identify the discoloration region in the UVC modules in the very early stage when the discoloration is not visible to the naked eyes, whereas Isc measurement is unable to measure the performance loss until the color becomes visibly darker. YI also provides the direct evidence of yellowing in the encapsulant. As expected, the extent of degradation due to discoloration increases with the increase in module temperature. The Isc loss is dictated by both the regions – discolored area at the center and non-discolored area at the cell edges, whereas the YI is only determined at the discolored region due to low probe area. This led to the limited correlation between Isc and YI in UVC modules.

In case of UVP modules, UV radiation has caused an adverse impact on the interfacial adhesion between the EVA and solar cell, which was detected from UVf images and severe Isc loss. No change in YI confirms that the reason for Isc loss is not due to yellowing but the delamination.

Further, the activation energy of encapsulant discoloration was estimated by using Arrhenius model on two types of data, %Isc drop and ΔYI. The Ea determined from the change in YI data for the EVA encapsulant discoloration reaction without the influence of oxygen and humidity is 0.61 eV. Based on the activation energy determined in this work and hourly weather data of any site, the degradation rate for the encaspulant browning mode can be estimated.
ContributorsDolia, Kshitiz (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Green, Matthew (Thesis advisor) / Srinivasan, Devarajan (Committee member) / Arizona State University (Publisher)
Created2018