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Description
Human breath is a concoction of thousands of compounds having in it a breath-print of physiological processes in the body. Though breath provides a non-invasive and easy to handle biological fluid, its analysis for clinical diagnosis is not very common. Partly the reason for this absence is unavailability of cost

Human breath is a concoction of thousands of compounds having in it a breath-print of physiological processes in the body. Though breath provides a non-invasive and easy to handle biological fluid, its analysis for clinical diagnosis is not very common. Partly the reason for this absence is unavailability of cost effective and convenient tools for such analysis. Scientific literature is full of novel sensor ideas but it is challenging to develop a working device, which are few. These challenges include trace level detection, presence of hundreds of interfering compounds, excessive humidity, different sampling regulations and personal variability. To meet these challenges as well as deliver a low cost solution, optical sensors based on specific colorimetric chemical reactions on mesoporous membranes have been developed. Sensor hardware utilizing cost effective and ubiquitously available light source (LED) and detector (webcam/photo diodes) has been developed and optimized for sensitive detection. Sample conditioning mouthpiece suitable for portable sensors is developed and integrated. The sensors are capable of communication with mobile phones realizing the idea of m-health for easy personal health monitoring in free living conditions. Nitric oxide and Acetone are chosen as analytes of interest. Nitric oxide levels in the breath correlate with lung inflammation which makes it useful for asthma management. Acetone levels increase during ketosis resulting from fat metabolism in the body. Monitoring breath acetone thus provides useful information to people with type1 diabetes, epileptic children on ketogenic diets and people following fitness plans for weight loss.
ContributorsPrabhakar, Amlendu (Author) / Tao, Nongjian (Thesis advisor) / Forzani, Erica (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Black carbon (BC) is the product of incomplete combustion of biomass and fossil fuels. It is found ubiquitously in nature and is relevant to studies in atmospheric science, soil science, oceanography, and anthropology. Black carbon is best described using a combustion continuum that sub-classifies BC into slightly charred biomass, char,

Black carbon (BC) is the product of incomplete combustion of biomass and fossil fuels. It is found ubiquitously in nature and is relevant to studies in atmospheric science, soil science, oceanography, and anthropology. Black carbon is best described using a combustion continuum that sub-classifies BC into slightly charred biomass, char, charcoal and soot. These sub-classifications range in particle size, formation temperature, and relative reactivity. Interest in BC has increased because of its role in the long-term storage of organic matter and the biogeochemistry of urban areas. The global BC budget is unbalanced. Production of BC greatly outweighs decomposition of BC. This suggests that there are unknown or underestimated BC removal processes, and it is likely that some of these processes are occurring in soils. However, little is known about BC reactivity in soil and especially in desert soil. This work focuses on soot BC, which is formed at higher temperatures and has a lower relative reactivity than other forms of BC. Here, I assess the contribution of soot BC to central AZ soils and use the isotopic composition of soot BC to identify sources of soot BC. Soot BC is a significant (31%) fraction of the soil organic matter in central AZ and this work suggests that desert and urban soils may be a storage reservoir for soot BC. I further identify previously unknown removal processes of soot BC found naturally in soil and demonstrate that soil soot BC undergoes abiotic (photo-oxidation) and biotic reactions. Not only is soot BC degraded by these processes, but its chemical composition is altered, suggesting that soot BC contains some chemical moieties that are more reactive than others. Because soot BC demonstrates both refractory and reactive character, it is likely that the structure of soot BC; therefore, its interactions in the environment are complex and it is not simply a recalcitrant material.
ContributorsHamilton, George (Author) / Hartnett, Hilairy E (Thesis advisor) / Herckes, Pierre (Committee member) / Hall, Sharon (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal

Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal of the tightly bound sugar phosphates from the active sites of RuBisCO. In this work, we investigated the ATP/ADP dependent oligomerization equilibrium of fluorescently tagged Rca for a wide range of concentrations using fluorescence correlation spectroscopy. Results show that in the presence of ADP-Mg2+, the oligomerization state of Rca gradually changes in steps of two subunits. The most probable association model supports the dissociation constants (K_d) of ∼4, 1, 1 μM for the monomer-dimer, dimer-tetramer, and tetramer-hexamer equlibria, respectively. Rca continues to assemble at higher concentrations which are indicative of the formation of aggregates. In the presence of ATP-Mg2+, a similar stepwise assembly is observed. However, at higher concentrations (30-75 µM), the average oligomeric size remains relatively unchanged around six subunits per oligomer. This is in sharp contrast with observations in ADP-Mg2+, where a marked decrease in the diffusion coefficient of Rca was observed, consistent with the formation of aggregates. The estimated K_d values obtained from the analysis of the FCS decays were similar for the first steps of the assembly process in both ADP-Mg2+ and ATP-Mg2+. However, the formation of the hexamer from the tetramer is much more favored in ATP-Mg2+, as evidenced from 20 fold lower K_d associated with this assembly step. This suggests that the formation of a hexameric ring in the presence of ATP-Mg2+. In addition to that, Rca aggregation is largely suppressed in the presence of ATP-Mg2+, as evidenced from the 1000 fold larger K_d value for the hexamer-24 mer association step. In essence, a fluorescence-based method was developed to monitor in vitro protein oligomerization and was successfully applied with Rca. The results provide a strong hint at the active oligomeric structure of Rca, and this information will hopefully help the ongoing research on the mechanistic enzymology of Rca.
ContributorsChakraborty, Manas (Author) / Levitus, Marcia (Thesis advisor) / Angell, Charles (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Americans spend upwards of 90% of their time indoors, hence indoor air quality (IAQ) and the impact of IAQ on human health is a major public health concern. IAQ can be negatively impacted by outdoor pollution infiltrating indoors, the emission of indoor pollutants, indoor atmospheric chemistry and poor ventilation. Energy

Americans spend upwards of 90% of their time indoors, hence indoor air quality (IAQ) and the impact of IAQ on human health is a major public health concern. IAQ can be negatively impacted by outdoor pollution infiltrating indoors, the emission of indoor pollutants, indoor atmospheric chemistry and poor ventilation. Energy saving measures like retrofits to seal the building envelope to prevent the leakage of heated or cooled air will impact IAQ. However, existing studies have been inconclusive as to whether increased energy efficiency is leading to detrimental IAQ. In this work, field campaigns were conducted in apartment homes in Phoenix, Arizona to evaluate IAQ as it relates to particulate matter (PM), carbonyls, and tobacco specific nitrosamines (TSNA).

To investigate the impacts of an energy efficiency retrofit on IAQ, indoor and outdoor air quality sampling was carried out at Sunnyslope Manor, a city-subsidized senior living apartment complex. Measured indoor formaldehyde levels before the building retrofit exceeded reference exposure limits, but in the long term follow-up sampling, indoor formaldehyde decreased for the entire study population by a statistically significant margin. Indoor PM levels were dominated by fine particles and showed a statistically significant decrease in the long term follow-up sampling within certain resident subpopulations (i.e. residents who reported smoking and residents who had lived longer at the apartment complex). Additionally, indoor glyoxal and methylglyoxal exceeded outdoor concentrations, with methylglyoxal being more prevalent pre-retrofit than glyoxal, suggesting different chemical pathways are involved. Indoor concentrations reported are larger than previous studies. TSNAs, specifically N'-nitrosonornicotine (NNN), 4-(methyl-nitrosamino)-4-(3-pyridyl)-butanal (NNA) and 4-(methylnitrosoamino)-1-(3-pyridyl)-1-butanone (NNK) were evaluated post-retrofit at Sunnyslope Manor. Of the units tested, 86% of the smoking units and 46% of the non-smoking units had traces of at least one of the nitrosamines.
ContributorsFrey, Sarah E (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew P (Thesis advisor) / Destaillats, Hugo (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Atomic force microscopy (AFM) has become an important tool to characterize and image surfaces with nanoscale resolution. AFM imaging technique has been utilized to study a wide range of substances such as DNA, proteins, cells, silicon surfaces, nanowires etc. Hence AFM has become extremely important in the field of biochemistry,

Atomic force microscopy (AFM) has become an important tool to characterize and image surfaces with nanoscale resolution. AFM imaging technique has been utilized to study a wide range of substances such as DNA, proteins, cells, silicon surfaces, nanowires etc. Hence AFM has become extremely important in the field of biochemistry, cell biology and material science. Functionalizing the AFM tip made it possible to detect molecules and their interaction using recognition imaging at single molecule level. Also the unbinding force of two molecules can be investigated based on AFM based single molecule force spectroscopy.

In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.

In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
ContributorsSenapati, Subhadip (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Geopolymers, a class of X-ray amorphous, ceramic-like aluminosilicate materials are produced at ambient temperatures through a process called geopolymerization. Due to both low energy requirement during synthesis and interesting mechanical and chemical properties, geopolymers are grabbing enormous attention. Although geopolymers have a broad range of applications including thermal/acoustic

Geopolymers, a class of X-ray amorphous, ceramic-like aluminosilicate materials are produced at ambient temperatures through a process called geopolymerization. Due to both low energy requirement during synthesis and interesting mechanical and chemical properties, geopolymers are grabbing enormous attention. Although geopolymers have a broad range of applications including thermal/acoustic insulation and waste immobilization, they are always prepared in monolithic form. The primary aim of this study is to produce new nanostructured materials from the geopolymerization process, including porous monoliths and powders.

In view of the current interest in porous geopolymers for non-traditional applications, it is becoming increasingly important to develop synthetic techniques to introduce interconnected pores into the geopolymers. This study presents a simple synthetic route to produce hierarchically porous geopolymers via a reactive emulsion templating process utilizing triglyceride oil. In this new method, highly alkaline geopolymer resin is mixed with canola oil to form a homogeneous viscous emulsion which, when cured at 60 °C, gives a hard monolithic material. During the process, the oil in the alkaline emulsion undergoes a saponification reaction to decompose into water-soluble soap and glycerol molecules which are extracted to yield porous geopolymers. Nitrogen sorption studies indicates the presence of mesopores, whereas the SEM studies reveals that the mesoporous geopolymer matrix is dotted with spherical macropores. The method exhibits flexibility in that the pore structure of the final porous geopolymers products can be adjusted by varying the precursor composition.

In a second method, the geopolymerization process is modified to produce highly dispersible geopolymer particles, by activating metakaolin with sodium silicate solutions containing excess alkali, and curing for short duration under moist conditions. The produced geopolymer particles exhibit morphology similar to carbon blacks and structured silicas, while also being stable over a wide pH range.

Finally, highly crystalline hierarchical faujasite zeolites are prepared by yet another modification of the geopolymerization process. In this technique, the second method is combined with a saponification reaction of triglyceride oil. The resulting hierarchical zeolites exhibit superior CO2-sorption properties compared to equivalent commercially available and currently reported materials. Additionally, the simplicity of all three of these techniques means they are readily scalable.
ContributorsMedpelli, Dinesh (Author) / Seo, Dong-Kyun (Thesis advisor) / Herckes, Pierre (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Chloroform (CHCl3) is an important atmospheric pollutant by its direct health effects as well as by its contribution to photochemical smog formation. Chloroform outgassing from swimming pools is not typically considered a source of atmospheric CHCl3 because swimming pools are scarce compared to other sources. However, large urban areas in

Chloroform (CHCl3) is an important atmospheric pollutant by its direct health effects as well as by its contribution to photochemical smog formation. Chloroform outgassing from swimming pools is not typically considered a source of atmospheric CHCl3 because swimming pools are scarce compared to other sources. However, large urban areas in hot climates such as Phoenix, AZ contain a substantial amount of swimming pools, potentially resulting in significant atmospheric fluxes. In this study, CHCl3 formation potential (FP) from disinfection of swimming pools in Phoenix was investigated through laboratory experiments and annual CHCl3 emission fluxes from swimming pools were estimated based on the experimental data.

Swimming pool water (collected in June 2014 in Phoenix) and model contaminants (Pharmaceuticals and Personal Care Products (PPCPs), Endocrine Disrupting Compounds (EDCs), artificial sweeteners, and artificial human waste products) were chlorinated in controlled laboratory experiments. The CHCl3 production during chlorination was determined using Gas Chromatography-Mass Spectrometry (GC-MS) following solid-phase microextraction (SPME). Upon chlorination, all swimming pool water samples and contaminants produced measureable amounts of chloroform. Chlorination of swimming pool water produced 0.005-0.134 mol CHCl3/mol C and 0.004-0.062 mol CHCl3/mol Cl2 consumed. Chlorination of model contaminants produced 0.004-0.323 mol CHCl3/mol C and 0.001-0.247 mol CHCl3/mol Cl2 consumed. These numbers are comparable and indicate that the model contaminants react similarly to swimming pool water during chlorination. The CHCl3 flux from swimming pools in Phoenix was estimated at approximately 3.9-4.3 Gg/yr and was found to be largely dependent on water temperature and wind speed while air temperature had little effect. This preliminary estimate is orders of magnitude larger than previous estimates of anthropogenic emissions in Phoenix suggesting that swimming pools might be a significant source of atmospheric CHCl3 locally.
ContributorsRose, Christy J (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew (Committee member) / Hayes, Mark (Committee member) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Atmospheric particulate matter has a substantial impact on global climate due to its ability to absorb/scatter solar radiation and act as cloud condensation nuclei (CCN). Yet, little is known about marine aerosol, in particular, the carbonaceous fraction. In the present work, particulate matter was collected, using High Volume (HiVol) samplers,

Atmospheric particulate matter has a substantial impact on global climate due to its ability to absorb/scatter solar radiation and act as cloud condensation nuclei (CCN). Yet, little is known about marine aerosol, in particular, the carbonaceous fraction. In the present work, particulate matter was collected, using High Volume (HiVol) samplers, onto quartz fiber substrates during a series of research cruises on the Atlantic Ocean. Samples were collected on board the R/V Endeavor on West–East (March–April, 2006) and East–West (June–July, 2006) transects in the North Atlantic, as well as on the R/V Polarstern during a North–South (October–November, 2005) transect along the western coast of Europe and Africa. The aerosol total carbon (TC) concentrations for the West–East (Narragansett, RI, USA to Nice, France) and East–West (Heraklion, Crete, Greece to Narragansett, RI, USA) transects were generally low over the open ocean (0.36±0.14 μg C/m3) and increased as the ship approached coastal areas (2.18±1.37 μg C/m3), due to increased terrestrial/anthropogenic aerosol inputs. The TC for the North–South transect samples decreased in the southern hemisphere with the exception of samples collected near the 15th parallel where calculations indicate the air mass back trajectories originated from the continent. Seasonal variation in organic carbon (OC) was seen in the northern hemisphere open ocean samples with average values of 0.45 μg/m3 and 0.26 μg/m3 for spring and summer, respectively. These low summer time values are consistent with SeaWiFS satellite images that show decreasing chlorophyll a concentration (a proxy for phytoplankton biomass) in the summer. There is also a statistically significant (p<0.05) decline in surface water fluorescence in the summer. Moreover, examination of water–soluble organic carbon (WSOC) shows that the summer aerosol samples appear to have a higher fraction of the lower molecular weight material, indicating that the samples may be more oxidized (aged). The seasonal variation in aerosol content seen during the two 2006 cruises is evidence that a primary biological marine source is a significant contributor to the carbonaceous particulate in the marine atmosphere and is consistent with previous studies of clean marine air masses.
ContributorsHill, Hansina Rae (Author) / Herckes, Pierre (Thesis advisor) / Westerhoff, Paul (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped

Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.
ContributorsGurunathan, Kaushik (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Woodbury, Neal (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Bioparticles comprise a diverse amount of materials ubiquitously present in nature. From proteins to aerosolized biological debris, bioparticles have important roles spanning from regulating cellular functions to possibly influencing global climate. Understanding their structures, functions, and properties provides the necessary tools to expand our fundamental knowledge of biological

Bioparticles comprise a diverse amount of materials ubiquitously present in nature. From proteins to aerosolized biological debris, bioparticles have important roles spanning from regulating cellular functions to possibly influencing global climate. Understanding their structures, functions, and properties provides the necessary tools to expand our fundamental knowledge of biological systems and exploit them for useful applications. In order to contribute to this efforts, the work presented in this dissertation focuses on the study of electrokinetic properties of liposomes and novel applications of bioaerosol analysis. Using immobilized lipid vesicles under the influence of modest (less than 100 V/cm) electric fields, a novel strategy for bionanotubule fabrication with superior throughput and simplicity was developed. Fluorescence and bright field microscopy was used to describe the formation of these bilayer-bound cylindrical structures, which have been previously identified in nature (playing crucial roles in intercellular communication) and made synthetically by direct mechanical manipulation of membranes. In the biological context, the results of this work suggest that mechanical electrostatic interaction may play a role in the shape and function of individual biological membranes and networks of membrane-bound structures. A second project involving liposomes focused on membrane potential measurements in vesicles containing trans-membrane pH gradients. These types of gradients consist of differential charge states in the lipid bilayer leaflets, which have been shown to greatly influence the efficacy of drug targeting and the treatment of diseases such as cancer. Here, these systems are qualitatively and quantitatively assessed by using voltage-sensitive membrane dyes and fluorescence spectroscopy. Bioaerosol studies involved exploring the feasibility of a fingerprinting technology based on current understanding of cellular debris in aerosols and arguments regarding sampling, sensitivity, separations and detection schemes of these debris. Aerosolized particles of cellular material and proteins emitted by humans, animals and plants can be considered information-rich packets that carry biochemical information specific to the living organisms present in the collection settings. These materials could potentially be exploited for identification purposes. Preliminary studies evaluated protein concentration trends in both indoor and outdoor locations. Results indicated that concentrations correlate to certain conditions of the collection environment (e.g. extent of human presence), supporting the idea that bioaerosol fingerprinting is possible.
ContributorsCastillo Gutiérrez, Josemar Andreina (Author) / Hayes, Mark A. (Thesis advisor) / Herckes, Pierre (Committee member) / Ghrilanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011