The biological significance of photosynthesis is indisputable as it is necessary for nearly all life on earth. Photosynthesis provides chemical energy for plants, algae, and bacteria, while heterotrophic organisms rely on these species as their ultimate food source. The initial step in photosynthesis requires the absorption of sunlight to create electronic excitations. Light-harvesting proteins play the functional role of capturing solar radiation and transferring the resulting excitation to the reaction centers where it is used to carry out the chemical reactions of photosynthesis. Despite the wide variety of light-harvesting protein structures and arrangements, most light-harvesting proteins are able to utilize the captured solar energy for charge separation with near perfect quantum efficiency. This thesis will focus on understanding the energy transfer dynamics and photophysics of a specific subset of light-harvesting antennae known as phycobiliproteins. These proteins are extracted from cryptophyte algae and are investigated using steady-state and ultrafast spectroscopic techniques.

Photosynthetic electron transport produces ATP and NADPH which support carbon fixation by the Calvin Cycle. To avoid over-reduction of the electron transport chain, plants must balance absorption and consumption of light energy. Mitochondrial alternative oxidase (AOX) is a non-energy-conserving electron sink, making it an ideal candidate to oxidize excess reductant and regulate chloroplastic redox state. Wild-type (WT) and transgenic Nicotiana tabacum lines with enhanced or suppressed AOX protein levels were grown under low light (LL) and moderate light (ML). LL-grown plants were also shifted to ML. AOX transcript and protein levels were enhanced in WT plants under ML. Chlorophyll fluorescence, gas exchange, and contents of chlorophyll, carbohydrate, and malondialdehyde were measured. Lack of AOX protein decreased Photosystem II (PSII) quantum efficiency and CO2 assimilation rates while enhancing PSII excitation pressure compared to WT. These findings suggest a role for AOX in mediating the chloroplast-mitochondrion relationship during acclimation to higher irradiance.

The biological significance of photosynthesis is indisputable as it is necessary for nearly all life on earth. Photosynthesis provides chemical energy for plants, algae, and bacteria, while heterotrophic organisms rely on these species as their ultimate food source. The initial step in photosynthesis requires the absorption of sunlight to create electronic excitations. Light-harvesting proteins play the functional role of capturing solar radiation and transferring the resulting excitation to the reaction centers where it is used to carry out the chemical reactions of photosynthesis. Despite the wide variety of light-harvesting protein structures and arrangements, most light-harvesting proteins are able to utilize the captured solar energy for charge separation with near perfect quantum efficiency. This thesis will focus on understanding the energy transfer dynamics and photophysics of a specific subset of light-harvesting antennae known as phycobiliproteins. These proteins are extracted from cryptophyte algae and are investigated using steady-state and ultrafast spectroscopic techniques.

Many ecological systems follow a seasonal cycle affecting primary production, carbon flux, and vegetative gas emissions. The seasonal variation of ecological systems are both affected by and have effects upon climatic factors. A quantitative estimate of the seasonal variation of vegetation is required to characterize ecological systems and their interaction with climate. Monitoring the spaliotemporal variation of foliar biomass density (FBD) over one year will provide a quantitative estimate of the annual cycle and regional variation of photosynthetic activity. FBD is a quantitative measure of leafy material per unit of area produ\:ed by photosynthetically active vegetation. This seasonal variation in FBD is an important parameter for global and other large scale investigations of ecological, hydrological, and biogeochemical systems which require data and expertise from a variety of sources and disciplines. Therefore, FBD is potentially of great utility for ecologists, hydrologists, climatologists, and atmospheric scientists. Recent regional scale investigations of ecological systems concluded that the repetitive coverage and synoptic view of remotely sensed measurements provide data to monitor the seasonal variation of biomass. A method to estimate the seasonal variation of FBD at global scales has not been developed. The objective of this research is to develop a methodology that could be used to estimate the seasonal variation of FBD for the entire terrestrial biosphere. By coupling global satellite data, measured field data, and a vegetation classification, a model was developed to estimate the global spatiotemporal variation of FBD. Comparisons between literature estimates of FBD and estimated FBD from this model were made as a means of validation. A more specific comparison was conducted between grasslands based on work conducted in the Senegalese Sahel region in Africa. Finally, a sensitivity analysis was performed to characterize the potential propagation of error associated with the literature FBD estimates used to drive this model. / Graduation date: 1992

C4 photosynthesis is an advanced complement to the more ancestral and more commonpathway refereed to as C3. C4 metabolism has evolved in several taxa, and it is theorized thatit worked as an adaptation to the low CO 2 levels characteristic of late geological time. Theadaptation also carries with it some resistance to the negative effects brought on by hightemperatures and drought. C4 metabolism is, however, not free, meaning that underconditions of lower temperature and higher CO2-levels, C3 photosynthesis is still moreviable. This makes it interesting to study how C4-species might shift their ranges in responseto climate change, as it implies both elevated CO 2 levels and higher mean temperatures inmost parts of the world. In this report, I develop a model based on the CO 2/O2 specificity of Rubisco from Spinach(Spinacia oleracea) at different temperatures, using data found in literature on the subject.The resulting model has some success in describing the current distribution of C4 species,using temperature and CO2 concentration as explanatory variables.

Currently our understanding of both system and phytoplankton metabolism in large rivers is somewhat limited. Knowledge of the metabolic balance in such systems is necessary not only for proper management of the river itself, but also for the lakes into which they discharge. The River Continuum Concept proposes that the deep, turbid waters of large rivers have a poor light climate which leads to heterotrophic conditions (respiration > photosynthesis) yet this idea has been challenged. Similarly, it has been predicted that phytoplankton growth in large rivers is limited to areas of unusually favourable light climate and water retention (e.g. margins, backwaters), but the evidence is limited. Through longitudinal and diel measurements of Chl a, nutrient concentrations, dissolved oxygen and stable oxygen isotopes it was shown in this study that the lower Grand River was autotrophic during the two successive summers but either balanced or heterotrophic in other seasons. This implies that large rivers such as the Grand can be a transition zone for nutrients and a phytoplankton source, depending on season. Experimental incubations to measure oxygen production under varying irradiance demonstrated that phytoplankton could indeed grow (i.e., achieve positive net production) in the main river channel. Comparison of system and plankton metabolic rates further indicated that the phytoplankton were responsible for the major portion of the system production, but much less of the respiration. Sediment oxygen demand probably accounted for much of the additional respiration, but interactions with marginal and upstream habitats was probably an additional influence on both consumption and production of oxygen. The results further showed that stable oxygen isotope dynamics did not conform to the steady state model commonly used to infer metabolic patterns from environmental isotope data. A non-steady model was more successful and largely supported independent assessments of metabolism.

Nyanza Gulf is a large, shallow and long river-influenced embayment located in northeastern Lake Victoria. The gulf opens to the main lake through the narrow and deep Rusinga Channel, the exchange zone between the two ecosystems with different physical chemical and biogeochemical conditions. The main goals of this study are to characterize physicochemical and nutrient gradients along the gulf-main-lake transect, characterize and quantify the water and nutrient fluxes between the gulf and the main lake, and assess the response of phytoplankton community and photosynthesis to the spatially varying physical and nutrient conditions along the study transect. Between March 2005 and March 2006, measurements of physicochemical profiles as well as nutrient and the phytoplankton community analysis were conductued monthly along the study transect. Additionally, analysis of different surficial sediment phosphorus fractions was done in order to asses the potential role of bottom sediment in contributing to phosphorus enrichment in the lake water column. A box mass balance model was used to calculate the exchange of water and nutrient fluxes between different zones along the study transect and to estimate ecosystem metabolism in the gulf and the channel. Spatial variability in physicochemical and biogeochemical conditions was observed along the study transect, especially between the shallow and river-influenced inner-gulf, the deep and physically active Rusinga Channel, and the main lake, mainly in response to river inputs and varying morphometry along the study transect. The gulf had significantly higher electrical conductivity (EC), turbidity, total nitrogen (TN), and dissolved reactive silica (DRSi) but the levels declined monotonically along the channel in response to mixing with the main lake water. The channel and the main lake had, respectively, significantly higher dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) compared to the gulf. Spatial variability in morphometry and exposure to varying wind forcing lead to differential mixing and differential heating and cooling along the transect, resulting in density driven fronts and horizontal exchange of water and nutrients between the gulf and the main lake. Upwelling and downwelling maintained mixing conditions in the channel which consequently influenced nutrient recycling, the light environment and hence affecting phytoplankton community composition and productivity. The net residual water flow from the gulf to the main lake was 36 m3/s but the mixing flux was approximately 20 times higher and both fluxes accounted for a gulf exchange time of 1981 days. The advective and mixing fluxes between the gulf and the main lake resulted in net export of dissolved inorganic phosphorus (DIP; 400 kg P/d) from the main lake into the gulf and net export of DRSi (10 t Si/d) from the gulf into the main lake. In the deep, narrow and physically active Rusinga Channel there was net production of dissolved nutrients whereas in the gulf there was net consumption of dissolved nutrients, which helped to maintain high net ecosystem production (NEP; 566 mg C/m2/d) in the gulf in contrast the channel which showed net heterotrophy. The high NEP in the gulf and the associated high nutrient demand coupled with possibly low SRP to DIN supply ratio lead to P limitation of algal growth in the gulf as indicated by all indicators of nutrient status. This has important implications for management since increased P input into the gulf will translate into increased algal blooms in the gulf and therefore compromise water quality. Spatial variability in physical conditions and nutrient status along the study transect influenced phytoplankton community composition and photosynthesis. The shallow and turbid gulf was dominated by cyanobacteria but diatoms dominated in the channel in response to reduced turbidity and increased physical mixing and nutrient availability (DRSi, SRP). In the main lake seasonal stratification and deep mixing depth favoured both cyanobacteria and diatoms. The phytoplankton community in channel had a higher photosynthetic capacity (Fv/Fm, PBm) compared to both the gulf and the main lake.

This dissertation presents a detailed computational investigation into the vibrational properties of quinones involved in solar energy conversion processes in photosynthetic reaction centers. In particular, we focus on the vibrational properties of the ubiquinone molecule that occupies the QA binding site in purple bacterial photosynthetic reaction centers. To provide a foundation upon which to base computational studies of pigments in protein binding sites density functional theory based calculations of the vibrational properties of neutral ubiquinone in the gas phase and in solvent were undertaken. From single point energy calculations it was shown that at least eight ubiquinone conformers, each with slightly different FTIR spectra, could be present in solvent at room temperature. The calculated and experimental spectra for neutral ubiquinone in solution are very different from the spectra associated with ubiquinone in the QA binding in purple bacterial reaction centers. For this reason an ONIOM method was undertaken in which the pigment was treated using density functional theory based methods while the protein was treated using molecular mechanics. The ONIOM calculations not only modeled the experimental QA FTIR difference spectra but also resolved the long standing issue of whether a very strong hydrogen bond exists between the bound ubiquinone and the imidazole nitrogen of a histidine residue (HisM219). To further validate the usefulness of the ONIOM approach experimental isotope edited FTIR spectra obtained using purple bacterial reaction centers with a range of chainless symmetrical quinones incorporated were modeled. Again, the agreement between the calculated and experimental spectra is outstanding. We also modeled the vibrational properties of the ubisemiquinone anion radical both in solvent and in the QA binding site. Vibrational modes of ubisemiquinone display a greater degree of mixing of the various molecular groups of the molecule. Nonetheless the calculated FTIR spectra for ubisemiquinone in solution and in the QA site agree very well with that found experimentally. Vibrational frequencies of ubisemiquinone obtained from ONIOM calculated Raman spectra also agree very well with that found in experimental resonance Raman spectra associated with the ubisemiquinone anion radical in the QA binding site.

Transient absorption spectroscopy was used to study light induced electron transfer processes in Type 1 photosynthetic reaction centers. Flash induced absorption changes were probed at 800, 703 and 487 nm, and on multiple timescales from nanoseconds to tens of milliseconds. Both wild type and menB mutant photosystem I reaction centers from the cyanobacterium Synechocystis sp. PCC 6803 were studied. Photosystem I reaction centers from the green algae Chlamydomonas reinhardtii, and the newly discovered chlorophyll-d containing organism Acaryochloris marina, were also studied. The flash induced absorption changes obtained for menB mutant photosystem I reaction centers are distinguishable from wild type at 800 nm. MenB mutant photosystem I reaction centers displays a large amplitude decay phase with lifetime of ~50 ns which is absent in wild type photosystem I reaction centers. It is hypothesized that this ~50 ns phase is due to the formation of the triplet state of primary electron donor.

Currently our understanding of both system and phytoplankton metabolism in large rivers is somewhat limited. Knowledge of the metabolic balance in such systems is necessary not only for proper management of the river itself, but also for the lakes into which they discharge. The River Continuum Concept proposes that the deep, turbid waters of large rivers have a poor light climate which leads to heterotrophic conditions (respiration > photosynthesis) yet this idea has been challenged. Similarly, it has been predicted that phytoplankton growth in large rivers is limited to areas of unusually favourable light climate and water retention (e.g. margins, backwaters), but the evidence is limited. Through longitudinal and diel measurements of Chl a, nutrient concentrations, dissolved oxygen and stable oxygen isotopes it was shown in this study that the lower Grand River was autotrophic during the two successive summers but either balanced or heterotrophic in other seasons. This implies that large rivers such as the Grand can be a transition zone for nutrients and a phytoplankton source, depending on season. Experimental incubations to measure oxygen production under varying irradiance demonstrated that phytoplankton could indeed grow (i.e., achieve positive net production) in the main river channel. Comparison of system and plankton metabolic rates further indicated that the phytoplankton were responsible for the major portion of the system production, but much less of the respiration. Sediment oxygen demand probably accounted for much of the additional respiration, but interactions with marginal and upstream habitats was probably an additional influence on both consumption and production of oxygen. The results further showed that stable oxygen isotope dynamics did not conform to the steady state model commonly used to infer metabolic patterns from environmental isotope data. A non-steady model was more successful and largely supported independent assessments of metabolism.