The success of unmanned aerial vehicles (UAV) in the Iraq and Afghanistan conflicts has led to increased interest in further digitalization of the United States armed forces. Although unmanned systems have been a tool of the military for several decades, only recently have advances in the field of Micro-Electro-Mechanical Systems (MEMS) technology made it possible to develop systems capable of being transported by an individual soldier. These miniature unmanned systems, more commonly referred to as micro air vehicles (MAV), are envisioned by the Department of Defense as being an integral part of maintaining America?s military superiority. As researchers continue to make advances in the miniaturization of flight hardware, a new problem with regard to MAV field operations is beginning to present itself. To date, little work has been done to determine an effective means of collecting, analyzing, and handling information that can satisfy the goal of using MAVs as tools for persistent surveillance. Current systems, which focus on the transmission of analog video streams, have been very successful on larger UAVs such as the RQ-11 Raven but have proven to be very demanding of the operator. By implementing a new and innovative data processing methodology, currently existing hardware can be adapted to effectively present critical information with minimal user input. Research currently being performed at Texas A&M University in the areas of attitude determination and image processing has yielded a new application of photographic projection. By replacing analog video with spatially aware high-resolution images, the present MAV handheld ground control stations (GCS) can be enhanced to reduce the number of functional manpower positions required during operation. Photographs captured by an MAV can be displayed above pre-existing satellite imagery to give an operator a lasting reference to the location of objects in his vicinity. This newly generated model also increases the functionality of micro air vehicles by allowing for target tracking and energy efficient perch and stare capabilities, both essential elements of persistent surveillance.

<p>The dynamics of impacting components is of particular interest to engineers due to concerns about noise and wear, but is particularly difficult to study due to impact's non-linear nature. To begin transferring concepts studied purely analytically to the world of physical mechanisms, four experiments are outlined, and important non-linear concepts highlighted with these systems. A linear oscillator with a kicked impact, an impacting forced pendulum, two impacting forced pendulums, and a cam follower pair are studied experimentally, with complementary numerical results.</p><p>Some important ideas highlighted are limit cycles, basins of attraction with many wells, grazing, various forms of coexistence, super-persistent chaotic transients, and liftoff. These concepts are explored using a variety of non-linear tools such as time lag embedding and stochastic interrogation, and discussions of their intricacies when used in non-smooth systems yield important observations for the experimentalist studying impacting systems. </p><p>The focus is on experimental results with numerical validation, and spends much time discussing identification of these concepts from an experiment-first mindset, rather than the more traditional analytical-first approach. As such a large volume of experimentally important information on topics such as transducers and forcing mechanism construction are included in the appendices.</p> / Dissertation

Chemical species carry information in two dimensions, in their concentrations and their isotopic signatures. The concentrations of metabolites or synthetic compounds describe the composition of a chemical or biological system, while isotopic signatures describe processes in the system by their reaction pathways, regulation, and responses to external stimuli. Stable isotopes are unique tracers of these processes because their natural abundances are modulated by isotope effects occurring in physical processes as well as in chemical reactions. Nuclear magnetic resonance (NMR) spectroscopy is a prime technique not only for identification and quantification of small molecules in complex systems but also for measuring intramolecular distribution of stable isotopes in metabolites and other small molecules. In this thesis, we use quantitative NMR in three fields: in food science, environmental pollutant tracing, and plant-climate science. The phospholipid (PL) composition of food samples is of high interest because of their nutritional value and technological properties. However, the analysis of PLs is difficult as they constitute only a small fraction of the total lipid contents in foods. Here, we developed a method to identify PLs and determine their composition in food samples, by combining a liquid-liquid extraction approach for enriching PLs, with specialized 31P,1H-COSY NMR experiments to identify and quantify PLs. Wide-spread pollution with synthetic compounds threatens the environment and human health. However, the fate of pollutants in the environment is often poorly understood. Using quantitative deuterium NMR spectroscopy, we showed for the nitrosamine NDMA and the pesticide DDT how intramolecular distributions (isotopomer patterns) of the heavy hydrogen isotope deuterium reveal mechanistic insight into transformation pathways of pollutants and organic compounds in general. Intramolecular isotope distributions can be used to trace a pollutant’s origin, to understand its environmental transformation pathways and to evaluate remediation approaches. The atmospheric CO2 concentration ([CO2]) is currently rising at an unprecedented rate and plant responses to this increase in [CO2] influence the global carbon cycle and will determine future plant productivity. To investigate long-term plant responses, we developed a method to elucidate metabolic fluxes from intramolecular deuterium distributions of metabolites that can be extracted from historic plant material. We show that the intramolecular deuterium distribution of plant glucose depends on growth [CO2] and reflects the magnitude of photorespiration, an important side reaction of photosynthesis. In historic plant samples, we observe that photorespiration decreased in annual crop plants and natural vegetation over the past century, with no observable acclimation, implying that photosynthesis increased. In tree-ring samples from all continents covering the past 60 – 700 years, we detected a significantly smaller decrease in photorespiration than expected. We conclude that the expected “CO2 fertilization” has occurred but was significantly less pronounced in trees, due to opposing effects. The presented applications show that intramolecular isotope distributions not only provide information about the origin and turnover of compounds but also about metabolic regulation. By extracting isotope distributions from archives of plant material, metabolic information can be obtained retrospectively, which allows studies over decades to millennia, timescales that are inaccessible with manipulation experiments.

Persistent organic pollutants and heavy metals are released into the environment through different anthropogenic processes. They are of concern because they tend to bioaccumulate in the food chain and show adverse health effects ranging from acute to chronic toxicity. These pollutants need therefore to be monitored to conserve the environment. Conventionally, samples are sent to a laboratory for analysis by standard techniques such as chromatography and spectroscopy. Although these conventional techniques display high accuracy and low detection limits, they are expensive, require the use of highly trained personnel and tedious sample preparation. In comparison, electrochemical methods such as biosensors are sensitive, low cost and simple to operate. In this thesis, the determination of selected persistent organic pollutants (polybrominated diphenyl ethers, polybrominated biphenyls and polychlorinated biphenyls) and heavy metals (Cd, Pb and Cu) was achieved by the use of amperometric inhibition biosensor based on horseradish peroxidase (HRP) immobilized on the surface of platinum-polyaniline modified electrode. Polyaniline (PANI) film was electrochemically deposited on the platinum electrode surface. The film was characterized by cyclic voltammetry and spectrometric techniques. The CV results proved that the PANI was electroactive and exhibited a fast reversible electrochemistry. Characteristic Ultraviolet–Visible and Fourier Transform Infrared features of the polymer film were identified. They revealed that PANI film synthesized in this study is the conductive emeraldine salt. Horseradish peroxidase based biosensor was constructed by electrostatic attachment of the enzyme onto Pt-PANI electrode surface. Spectrometric and cyclic voltammetric results indicated that the immobilized HRP retained its bioelectrocatalytic activity towards the reduction of hydrogen peroxide. The Pt/PANI/HRP biosensor showed a linear response over a concentration range of 0.05 to 3.17 mM with a detection limit of 36.8 nM. Apparent Michaelis- Menten constant ( app M K ) was calculated as 1.04 mM. This implied that the HRP biosensor had a high affinity for H2O2. Furthermore, the fabricated biosensor showed high sensitivity, good reproducibility, repeatability and long-term stability. The Pt/PANI/HRP biosensor was applied to the determination of selected persistent organic pollutants and heavy metals. The latter was found to inhibit the HRP enzyme’s activity. The percentage inhibition of the investigated persistent organic pollutants decreases in the following order: 2,2´4,4´,6-pentabrominated diphenyl ether> 2-brominated biphenyl> 2-chlorinated biphenyl> 2,2´,4,5,5´-pentachlorinated biphenyl> 2,4,4´-trichlorinated biphenyl. In the case of heavy metals, the degree of inhibition of heavy metals was highest for Cd2+, followed by Cu2+ and then Pb2+. Kinetic study for the amperometric response to H2O2, recorded in the absence and presence of persistent organic pollutants and heavy metals revealed that for polybrominated diphenyl ethers, the inhibition process corresponded to a competitive type whereas for polybrominated biphenyls, polychlorinated biphenyls and heavy metals, it corresponded to the on-competitive type. The biosensor exhibited high sensitivity towards the determination of the metals and persistent organic pollutants as pollutants in real water samples, namely tap water and landfill leachate samples. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2010.

Many of the factors that shape contaminant accumulation profiles in marine mammals also strongly influence fat soluble vitamin accumulation. Vitamin A and E are essential fat soluble nutrients for numerous biological processes, including reproduction, growth, endocrine and immune function. Contaminants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), can alter vitamin dynamics; as such these vitamins have been proposed as sensitive biomarkers of contaminant exposure in wildlife. In light of these considerations, the present thesis was aimed at better understanding the factors that influence the accumulation of lipophilic contaminants and vitamins in western Arctic beluga whales, and to determine if there was an interaction between the two. Maternal offloading to neonates during gestation reduced overall contaminant (PCBs and PBDEs) and vitamin (A and E) concentrations in reproductively active female whales. The PCB and PBDE congener pattern in mothers changed during gestation as a result of preferential transfer of light-low Log KOW congeners to the fetus. Overall, female beluga whales transferred approximately 11% of their PCB and PBDE blubber burden to their fetus. In terms of vitamins transfer, lower concentrations of tocopherols, retinol and retinyl esters were found in reproductively active females relative to males and reproductively inactive females. Metabolism was also found to be an important factor for contaminant and vitamin accumulation in beluga tissues. In a principal components analysis, PCBs clustered into metabolically-derived structure-activity groups, which separated along the first principal component according to its metabolic potential (metabolizable vs. recalcitrant). Contaminant-related up-regulation of metabolizing enzymes, including cytochrome P450, likely explained changes in the concentration and pattern of PCB and PBDE congeners, as well as hepatic, plasma, and blubber vitamin A and E. Since vitamins and lipophilic contaminants accumulated in beluga whales in the same way in relation to most biological processes, including sex, reproduction, size, condition, and feeding ecology, it was important to control and reduce the number of these confounding factors before claiming any tissue vitamin change was indeed the result of chemical exposure. In doing so, it was found that vitamin A and E homeostasis was influenced by PCBs in beluga whales, resulting in reduced hepatic storage and increased plasma and blubber concentrations. Overall, these results suggest that liver, plasma, and inner blubber vitamin A and E concentrations can be sensitive biomarkers of contaminant exposure only if major confounding effects are taken into consideration. The implications of altered vitamin dynamics on the health of beluga whales is unknown at this time; however, as Arctic marine mammals face continued stress related to climate change, increased human disturbance and emergence of infectious diseases, this study can serve as essential baseline data that can be used to monitor the health status of western Arctic beluga whales. / Graduate / 0383 / 0329 / 0768 / jpdesforges@gmail.com

Cities are sources of persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), to surrounding regions and beyond. A spatially resolved, (5×5 km2), dynamic contaminant fate model named Spatially Oriented or SO-MUM was developed by coupling the fugacity based Multimedia Urban Model (MUM) (Diamond et al., 2001; Diamond et al., 2010c) and the Boundary Layer Forecast Model and Air Pollution Prediction System (BLFMAPS) which was developed at Environment Canada (Daggupaty et al., 2006). MUM was updated to contain a revised surface film sub-model which takes into account the dynamic nature of surface films. SO-MUM was illustrated by application to the City of Toronto, Canada. Spatially resolved air emissions of Σ88PCB were estimated to be ~230 (40-480) kg y-1, 280 (50-580) g y-1 km-2, and 90 (16-190) mg y-1 capita-1 and Σ26PBDE were estimated to be 28 (6-63) kg y-1, 34 (7-77) g y-1 km-2 and 11 (2-25) mg y-1 capita-1. These emissions were back-calculated from measured air concentrations and spatial chemical mass inventories yielding emission rates per mass inventory of 0.4 (0.05-1.6) and 0.1 (0.01-0.7) g kg-1inventory y-1, for Σ88PCBs and Σ26PBDEs, respectively. Approximately 30% and 16% of PCB and PBDE emissions emanate from the city’s downtown. Air advection accounted for ~95% (PCB) and ~70% (PBDE) of total air emission losses with the remaining balance depositing to the city. The metric “Urban Travel Distance” or UTD was introduced for quantifying the extent of an urban plume resulting from spatially heterogeneous emissions. For PCBs and PBDEs the UTDs were ~25 and ~30 km. The updated surface film sub-model indicated that films “bounce” higher vapor pressure semi-volatile organic compounds (SVOCs) back into the air but they act as a transient sink from air for lower vapor pressure SVOCs, thereby facilitating transport to surface waters. Model calculations suggest that if the PCB inventory is reduced, volatilization from near-shore Lake Ontario will become a net source of PCBs to air, but that neither near-shore Lake Ontario nor soil would become a significant volatilization PBDE source to air.

Perfluorinated carboxylates (PFCAs) are persistent and ubiquitous in the environment. Humans are exposed to PFCAs through direct and indirect sources, although the relative importance of each is uncertain. Direct sources of PFCAs have been attributed to two primary fluorochemical manufacturing processes: electrochemical fluorination (ECF) and telomerization. A focus of this thesis was to elucidate an additional direct source of PFCAs resulting from the direct fluorination of polyolefin materials. High density polyethylene bottles with varying levels of fluorination were observed to contain significant amounts of PFCAs, particularly those with carbon chain-lengths ≤ C6, marking an unexplored source of PFCA exposure. PFCAs are also produced indirectly from the biotransformation of fluorotelomer-based compounds, such as polyfluoroalkyl phosphate esters (PAPs) and fluorotelomer alcohols (FTOHs). During this transformation process, two predominant classes of metabolic intermediates are formed: the fluorotelomer unsaturated aldehydes (FTUALs) and the fluorotelomer unsaturated carboxylic acids (FTUCAs). Another focus of this thesis was to examine the reactivity of FTUALs and FTUCAs with endogenous nucleophiles such as glutathione (GSH), select amino acids, and model proteins. FTUALs formed adducts with all nucleophiles examined, where those having shorter carbon chain lengths (i.e. 6:2 and 8:2 FTUAL) were more reactive than longer carbon chains (i.e. 10:2 FTUAL). By contrast, FTUCAs had comparably limited reactivity; although FTUCAs showed mild reactivity with GSH, they did not react with any other nucleophiles. In vitro and in vivo experiments were carried out to determine the extent of protein binding formed from the biotransformation of fluorotelomer-based compounds, including the 8:2 FTOH and the 6:2 PAP diester. A significant portion of these biotransformations yielded covalent protein binding at nmol/mg protein concentrations. Protein adducts were observed predominantly in rat liver and also in plasma and kidney. The formation of reactive intermediates may be toxicologically important through protein deactivation. Cellular toxicity of FTUALs was significantly higher compared to PFCAs and the acid metabolic intermediates (i.e. FTUCAs). The EC50 values calculated from dose-response incubations were dependant on chain length and functional group. The work in this thesis examined an unexplored consequence of indirect exposure to PFCAs, potentially impacting the relative importance of PFCA exposure sources.

Cities are sources of persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), to surrounding regions and beyond. A spatially resolved, (5×5 km2), dynamic contaminant fate model named Spatially Oriented or SO-MUM was developed by coupling the fugacity based Multimedia Urban Model (MUM) (Diamond et al., 2001; Diamond et al., 2010c) and the Boundary Layer Forecast Model and Air Pollution Prediction System (BLFMAPS) which was developed at Environment Canada (Daggupaty et al., 2006). MUM was updated to contain a revised surface film sub-model which takes into account the dynamic nature of surface films. SO-MUM was illustrated by application to the City of Toronto, Canada. Spatially resolved air emissions of Σ88PCB were estimated to be ~230 (40-480) kg y-1, 280 (50-580) g y-1 km-2, and 90 (16-190) mg y-1 capita-1 and Σ26PBDE were estimated to be 28 (6-63) kg y-1, 34 (7-77) g y-1 km-2 and 11 (2-25) mg y-1 capita-1. These emissions were back-calculated from measured air concentrations and spatial chemical mass inventories yielding emission rates per mass inventory of 0.4 (0.05-1.6) and 0.1 (0.01-0.7) g kg-1inventory y-1, for Σ88PCBs and Σ26PBDEs, respectively. Approximately 30% and 16% of PCB and PBDE emissions emanate from the city’s downtown. Air advection accounted for ~95% (PCB) and ~70% (PBDE) of total air emission losses with the remaining balance depositing to the city. The metric “Urban Travel Distance” or UTD was introduced for quantifying the extent of an urban plume resulting from spatially heterogeneous emissions. For PCBs and PBDEs the UTDs were ~25 and ~30 km. The updated surface film sub-model indicated that films “bounce” higher vapor pressure semi-volatile organic compounds (SVOCs) back into the air but they act as a transient sink from air for lower vapor pressure SVOCs, thereby facilitating transport to surface waters. Model calculations suggest that if the PCB inventory is reduced, volatilization from near-shore Lake Ontario will become a net source of PCBs to air, but that neither near-shore Lake Ontario nor soil would become a significant volatilization PBDE source to air.

Perfluorinated carboxylates (PFCAs) are persistent and ubiquitous in the environment. Humans are exposed to PFCAs through direct and indirect sources, although the relative importance of each is uncertain. Direct sources of PFCAs have been attributed to two primary fluorochemical manufacturing processes: electrochemical fluorination (ECF) and telomerization. A focus of this thesis was to elucidate an additional direct source of PFCAs resulting from the direct fluorination of polyolefin materials. High density polyethylene bottles with varying levels of fluorination were observed to contain significant amounts of PFCAs, particularly those with carbon chain-lengths ≤ C6, marking an unexplored source of PFCA exposure. PFCAs are also produced indirectly from the biotransformation of fluorotelomer-based compounds, such as polyfluoroalkyl phosphate esters (PAPs) and fluorotelomer alcohols (FTOHs). During this transformation process, two predominant classes of metabolic intermediates are formed: the fluorotelomer unsaturated aldehydes (FTUALs) and the fluorotelomer unsaturated carboxylic acids (FTUCAs). Another focus of this thesis was to examine the reactivity of FTUALs and FTUCAs with endogenous nucleophiles such as glutathione (GSH), select amino acids, and model proteins. FTUALs formed adducts with all nucleophiles examined, where those having shorter carbon chain lengths (i.e. 6:2 and 8:2 FTUAL) were more reactive than longer carbon chains (i.e. 10:2 FTUAL). By contrast, FTUCAs had comparably limited reactivity; although FTUCAs showed mild reactivity with GSH, they did not react with any other nucleophiles. In vitro and in vivo experiments were carried out to determine the extent of protein binding formed from the biotransformation of fluorotelomer-based compounds, including the 8:2 FTOH and the 6:2 PAP diester. A significant portion of these biotransformations yielded covalent protein binding at nmol/mg protein concentrations. Protein adducts were observed predominantly in rat liver and also in plasma and kidney. The formation of reactive intermediates may be toxicologically important through protein deactivation. Cellular toxicity of FTUALs was significantly higher compared to PFCAs and the acid metabolic intermediates (i.e. FTUCAs). The EC50 values calculated from dose-response incubations were dependant on chain length and functional group. The work in this thesis examined an unexplored consequence of indirect exposure to PFCAs, potentially impacting the relative importance of PFCA exposure sources.

DDT, an extremely widely used organochlorine pesticide, was banned in most developed countries more than 30 years ago. However, DDT residues, including 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE), still persist in the environment and have been identified as priority pollutants due to their toxicity and their ability to bioaccumulate and biomagnify in the food chain. In particular, DDE was long believed to be &quotenon-biodegradable&quote, however some microorganisms have now been isolated that are able to metabolise DDE in pure culture. Terrabacter sp. strain DDE-1 was enriched from a DDT-contaminated agricultural soil from the Canterbury plains and is able to metabolise DDE to 4-chlorobenzoic acid when induced with biphenyl. The primary objective of this study was to identify the gene(s) responsible for Terrabacter sp. strain DDE-1�s ability to metabolise DDE and, in particular, to investigate the hypothesis that DDE-1 degrades DDE cometabolically via a biphenyl degradation pathway. Catabolism of biphenyl by strain DDE-1 was demonstrated, and a biphenyl degradation (bph) gene cluster containing bphDA1A2A3A4BCST genes was identified. The bphDA1A2A3A4BC genes are predicted to encode a biphenyl degradation upper pathway for the degradation of biphenyl to benzoate and cis-2-hydroxypenta-2,4-dienoate and the bphST genes are predicted to encode a two-component signal transduction system involved in regulation of biphenyl catabolism. The bph gene cluster was found to be located on a linear plasmid, designated pBPH1. A plasmid-cured strain (MJ-2) was unable to catabolise both biphenyl and DDE, supporting the hypothesis that strain DDE-1 degrades DDE cometabolically via the biphenyl degradation pathway. Furthermore, preliminary evidence from DDE overlayer agar plate assays suggested that Pseudomonas aeruginosa carrying the strain DDE-1 bphA1A2A3A4BC genes is able to catabolise DDE when grown in the presence of biphenyl. A second objective of this study was to characterise pBPH1. The complete 84,054-bp sequence of the plasmid was determined. Annotation of the DNA sequence data revealed seventy-six ORFs predicted to encode proteins, four pseudogenes, and ten gene fragments. Putative functions were assigned to forty-two of the ORF and pseudogenes. Besides biphenyl catabolism, the major functional classes of the predicted proteins were transposition, regulation, heavy metal transport/resistance, and plasmid maintenance and replication. It was shown that pBPH1 has the terminal structural features of an actinomycete invertron, including terminal proteins and terminal inverted repeats (TIRs). This is the first report detailing the nucleotide sequence and characterisation of a (linear) plasmid from the genus Terrabacter.