The air-water interface is abundant in the environment, thus it is an important proxy for atmospheric processes such as the uptake and transfer of molecules, heterogeneous reactions, photochemistry, and cloud condensation. This thesis aims to elucidate the role of semi-soluble and insoluble organic coatings on atmospheric processes at the air-water interface. Using glancing-angle LIF it was found that monolayer coatings of 1-octanol and of octanoic acid have opposing effects on the ozonation rate of pyrene at the air-water interface. LIF was also coupled with a Profile Analysis Tensiometer (PAT-1) to measure the effect of stearic acid coating compression on the uptake of HCl to a water droplet. Due to preliminary issues with this novel technique, no significant uptake suppression was observed. The oxidation of benzene by OH radical was also explored briefly, as were the photophysics of photosensitizers and the angle dependence of Raman signal from a D2O pendent droplet.

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Perfluoroalkyl carboxylates (PFCAs) and perfluoroalkane sulfonates (PFSAs)are anthropogenic fluorinated surfactants that have been detected in almost every environmental compartment studied, yet their production and applications are far outweighed by those of other higher molecular weight fluorinated surfactants used in commerce. These fluorinated surfactants are widely incorporated in commercial products, yet their post-application fate has not been extensively studied. This thesis examines various biological and environmental processes involved in the fate of these surfactants upon consumer disposal. Specific focus was directed towards the environmental chemistry of polyfluoroalkyl phosphate esters (PAPs), perfluoroalkyl phosphonates (PFPAs), and perfluoroalkyl phosphinates (PFPiAs), and their potential roles as sources of perfluoroalkyl acids (PFAAs) in the environment. PAPs are established biological precursors of PFCAs, while PFPAs and PFPiAs are newly discovered PFAAs in the environment. Incubation with wastewater treatment plant (WWTP) microbes demonstrated the ability of PAPs to yield both fluorotelomer alcohols (FTOHs), which are established precursors of PFCAs, and the corresponding PFCAs themselves. WWTP biosolids-applied soil-plant microcosms revealed that PAPs can significantly accumulate in plants along with their degradation metabolites. This has implications for potential wildlife and human exposure through the consumption of plants grown and/or livestock raised on farmlands that have been amended with contaminated biosolids. A number of compound-and environmental-specific factors were observed to significantly influence the partitioning of PFPAs and PFPiAs between aqueous media and soil, as well as, aquatic biota during sorption and bioaccumulation experiments respectively. In both processes, PFPAs were primarily observed in the aqueous phase, while PFPiAs predominated in soil and biological tissues, consistent with the few environmental observations of these chemicals made to date. Detection of the PAP diesters (diPAPs), PFPiAs, and fluorotelomer sulfonates (FTSAs),all of which are used commercially, in human sera is evidence of human exposure to commercial fluorinated products, but the pathways by which this exposure occurs remain widely debated. Overall, this work presents novel findings on the environmental fate of commercial fluorinated surfactants and each of the process studied shows a clear link between the use of commercial products and the fluorochemical burden currently observed in the environment.

Tyrosyl phosphorylation plays an important role in many fundamental cellular processes, including cell growth, differentiation and proliferation. The levels of phosphotyrosine (pY) are regulated by the opposing actions of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs). A limitation to understanding the roles of PTPs in physiological and pathological cell signaling has been the absence of global proteomic approaches that enable the systematic and comprehensive analysis of PTP expression, regulation and function. This dissertation describes the development and application of novel proteomic methodologies that permit the global analysis of PTP expression (qPTPome), regulation (by oxidation and nitrosylation; q-oxPTPome) and substrates/binding proteins. These methods provide a workflow to begin assessing PTP function at a systems level, rather than its current targeted format. Application of these techniques will provide invaluable information to begin bridging the gap in our understanding of PTP and PTK function in normal and malignant cell signaling.

Perfluoroalkyl carboxylates (PFCAs) and perfluoroalkane sulfonates (PFSAs)are anthropogenic fluorinated surfactants that have been detected in almost every environmental compartment studied, yet their production and applications are far outweighed by those of other higher molecular weight fluorinated surfactants used in commerce. These fluorinated surfactants are widely incorporated in commercial products, yet their post-application fate has not been extensively studied. This thesis examines various biological and environmental processes involved in the fate of these surfactants upon consumer disposal. Specific focus was directed towards the environmental chemistry of polyfluoroalkyl phosphate esters (PAPs), perfluoroalkyl phosphonates (PFPAs), and perfluoroalkyl phosphinates (PFPiAs), and their potential roles as sources of perfluoroalkyl acids (PFAAs) in the environment. PAPs are established biological precursors of PFCAs, while PFPAs and PFPiAs are newly discovered PFAAs in the environment. Incubation with wastewater treatment plant (WWTP) microbes demonstrated the ability of PAPs to yield both fluorotelomer alcohols (FTOHs), which are established precursors of PFCAs, and the corresponding PFCAs themselves. WWTP biosolids-applied soil-plant microcosms revealed that PAPs can significantly accumulate in plants along with their degradation metabolites. This has implications for potential wildlife and human exposure through the consumption of plants grown and/or livestock raised on farmlands that have been amended with contaminated biosolids. A number of compound-and environmental-specific factors were observed to significantly influence the partitioning of PFPAs and PFPiAs between aqueous media and soil, as well as, aquatic biota during sorption and bioaccumulation experiments respectively. In both processes, PFPAs were primarily observed in the aqueous phase, while PFPiAs predominated in soil and biological tissues, consistent with the few environmental observations of these chemicals made to date. Detection of the PAP diesters (diPAPs), PFPiAs, and fluorotelomer sulfonates (FTSAs),all of which are used commercially, in human sera is evidence of human exposure to commercial fluorinated products, but the pathways by which this exposure occurs remain widely debated. Overall, this work presents novel findings on the environmental fate of commercial fluorinated surfactants and each of the process studied shows a clear link between the use of commercial products and the fluorochemical burden currently observed in the environment.

In urban areas, emissions of nitrogen oxide radicals (NOx ≡ NO + NO2) to the atmosphere from anthropogenic activities such as fossil fuel combustion contribute to poor air quality through the production of ozone and particulate matter. Soils are also a significant global source of NOx, but at downind forest environments the deposition of transported reactive nitrogen can be much more important than local emissions. Data from a government monitoring network in the Toronto area from 2000-2007 was used to explore the impact of long-term trends in NO2 and other ozone precursors on local ozone levels. Non-linear chemistry and the influence of meteorology explained why reductions in precursor levels during this period did not lead to significant improvements in ozone. Data from this network was also used to investigate the ability of a satellite-borne spectrometer to represent spatial patterns of ground-level NO2 in the same region. Selection biases, resulting from the need to discard satellite data on cloudy days, were shown to affect locations differently and were most severe at a receptor site. The sum of all reactive nitrogen oxides including NOx is known as NOy. A custom-built instrument for high precision and time resolution measurements of reactive nitrogen oxides was tested under various lab and field conditions, and used in field work where direct biosphere-atmosphere exchange of NOy was measured by eddy covariance above two comparable North American mixed forests (Haliburton Forest Wildlife Reserve and the University of Michigan Biological Station). While these forests were found to be small net sources of NOx, they were subject to elevated rates of NOy deposition overall, driven by the transport of polluted air from upwind source regions. Wet deposition measurements were used to show that dry deposition contributed a significant fraction of total deposition during the observation periods.

Mechanistic aspects of carbonaceous aerosol toxicity were examined with respect to the ability of particles to catalyse reactive oxygen species-generating redox cycling reactions. To investigate the role of secondary organic material, we examined two systems. In the first, two-stroke engine exhaust particles were found to increase their ability to catalyse redox cycling in the presence of a reducing agent, dithiothreitol (DTT), when the exhaust was exposed to ozone. This occurred through deposition of redox-active secondary organic aerosol (SOA) onto the particle that was ten times more redox active per microgram than the primary engine particle. In the second system, naphthalene SOA formed highly redox active particles. Activity was strongly correlated to the amount of the 1,4- and 1,2-naphthoquinone measured in the particle phase. However, these species and the newly quantified naphthalene oxidation product 5-hydroxy-1,4-naphthoquinone accounted for only 30% of the observed DTT decay from the particles. Gas-particle partitioning coefficients suggest 1,4- and 1,2-naphthoquinone are not strong contributors to ambient particle redox activity at 25°C. However, a large number of redox active species are unidentified. Some of these may be highly oxidised products of sufficiently low vapour pressure to be atmospherically relevant. DTT activity of diesel particles was found to be high per unit mass. The activity was found to be associated with the insoluble fraction as filtration of the particles nearly eliminated DTT decay. Neither methanol nor dichloromethane extracts of diesel particles exhibited redox activity, indicating that the redox active species are associated with the black carbon portion of the particles. Examination of particle concentration techniques found that use of water condensation to grow and concentrate particles introduced a large organic artefact to the particles. Experiments with concentrated inorganic particles suggest that the source of this artefact is from irreversible uptake of water-soluble volatile organic compounds. Overall, carbonaceous redox active species can be thought of as a continuum from small, water-soluble species to redox active functionalities on elemental carbon backbones. In addition to clearly defined, quantifiable species, future research may need to consider examining broader chemical classes or redox-active chemical functionalities to overcome the inherent complexity of these constituents.

The aqueous phase photo-oxidation of water soluble organic compounds (WSOC) extracted from α-pinene ozonolysis secondary organic aerosol (SOA) was investigated using high resolution time-of-flight chemical ionization mass spectrometry (CI-ToFMS). The results have shown that WSOC get more functionalized and fragmented as the reaction proceeds. The capabilities of three reagent ions, were assessed; specifically, (H2O)nH+ ionizes organic compounds with carbon oxidation state (OSC) ≤ 1.3, whereas CH3C(O)O- and I(H2O)n- ionize highly oxygenated organics with OSC up to 4, with I(H2O)n- showing more selectivity. The aqueous phase OH oxidation of cis-pinonic acid and tricarballylic acid (a surrogate for 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA), recognized as a tracer of α-pinene SOA) were also studied. The respective rate constants at 301 K were measured to be 3.4(±0.5)×10^9 M^-1s^-1 at pH=2 and 3.1(±0.3)×10^8 M^-1s^-1 at pH=4.6. This work also illustrates possible aqueous phase mechanism for MBTCA formation from cis-pinonic oxidation.