The Fast Regulation of Photosynthesis in Diatoms: an inquiry into the physiological and physical origins of non-photochemical chlorophyll fluorescence quenching.

Diatoms are renowned for their robust ability to perform NPQ (Non-Photochemical Quenching of chlorophyll fluorescence) as a dissipative response to heightened light stress on photosystem II, plausibly explaining their dominance over other algal groups in turbulent light environs. Their NPQ mechanism has been principally attributed to a xanthophyll cycle involving the lumenal pH regulated reversible de-epoxidation of diadinoxanthin. The principal goal of this dissertation is to reveal the physiological and physical origins and consequences of the NPQ response in diatoms during short-term transitions to excessive irradiation. The investigation involves diatom species from different originating light environs to highlight the diversity of diatom NPQ and to facilitate the detection of core mechanisms common among the diatoms as a group. A chiefly spectroscopic approach was used to investigate NPQ in diatom cells. Prime methodologies include: the real time monitoring of PSII excitation and de-excitation pathways via PAM fluorometry and pigment interconversion via transient absorbance measurements, the collection of cryogenic absorbance spectra to measure pigment energy levels, and the collection of cryogenic fluorescence spectra and room temperature picosecond time resolved fluorescence decay spectra to study excitation energy transfer and dissipation. Chemical inhibitors that target the trans-thylakoid pH gradient, the enzyme responsible for diadinoxanthin de-epoxidation, and photosynthetic electron flow were additionally used to experimentally manipulate the NPQ response. Multifaceted analyses of the NPQ responses from two previously un-photosynthetically characterised species, Nitzschia curvilineata and Navicula sp., were used to identify an excitation pressure relief ‘strategy’ for each species. Three key areas of NPQ were examined: (i) the NPQ activation/deactivation processes, (ii) how NPQ affects the collection, dissipation, and usage of absorbed light energy, and (iii) the interdependence of NPQ and photosynthetic electron flow. It was found that Nitzschia cells regulate excitation pressure via performing a high amplitude, reversible antenna based quenching which is dependent on the de-epoxidation of diadinoxanthin. In Navicula cells excitation pressure could be effectively regulated solely within the PSII reaction centre, whilst antenna based, diadinoxanthin de-epoxidation dependent quenching was implicated to be used as a supplemental, long-lasting source of excitation energy dissipation. These strategies for excitation balance were discussed in the context of resource partitioning under these species’ originating light climates. A more detailed investigation of the NPQ response in Nitzschia was used to develop a comprehensive model describing the mechanism for antenna centred non-photochemical quenching in this species. The experimental evidence was strongly supportive of a mechanism whereby: an acidic lumen triggers the diadinoxanthin de-epoxidation and protonation mediated aggregation of light harvesting complexes leading to the formation of quencher chlorophyll a-chlorophyll a dimers with short-lived excited states; quenching relaxes when a rise in lumen pH triggers the dispersal of light harvesting complex aggregates via deprotonation events and the input of diadinoxanthin. This model may also be applicable for describing antenna based NPQ in other diatom species.

An investigation into the functional role of the D1:1 and D1:2 polypeptides in photosystem II in cyanobacteria : the effect of changing PSI/PSII ratio on photoinhibition in Synechococcus sp. PCC7942 /

The cyanobacterium Synechococcus sp. PCC 7942 (Anacystis nidulans R2) adjusts its photosynthetic function by changing one of the polypeptides of photosystem II. This polypeptide, called Dl, is found in two forms in Synechococcus sp. PCC 7942. Changing the growth light conditions by increasing the light intensity to higher levels results in replacement of the original form of D 1 polypeptide, D 1: 1, with another form, D 1 :2. We investigated the role of these two polypeptides in two mutant strains, R2S2C3 (only Dl:l present) and R2Kl (only Dl:2 present) In cells with either high or low PSI/PSII. R2S2C3 cells had a lower amplitude for 77 K fluorescence emission at 695 nm than R2Kl cells. Picosecond fluorescence decay kinetics showed that R2S2C3 cells had shorter lifetimes than R2Kl cells. The lower yields and shorter lifetimes observed in the D 1 and Dl:2 containing cells. containing cells suggest that the presence of D 1: 1 results in more photochemical or non-photochemical quenching of excitation energy In PSII. One of the most likely mechanisms for the increased quenching in R2S2C3 cells could be an increased efficiency in the transfer of excitation energy from PSII to PSI. However, photophysical studies including 77 K fluorescence measurements and picosecond time resolved decay kinetics comparing low and high PSI/PSII cells did not support the hypothesis that D 1: 1 facilitates the dissipation of excess energy by energy transfer from PSII to PSI. In addition physiological studies of oxygen evolution measurements after photoinhibition treatments showed that the two mutant cells had no difference in their susceptibility to photoinhibition with either high PSI/PSII ratio or low PSI/PSII ratio. Again suggesting that, the energy transfer efficiency from PSII to PSI is likely not a factor in the differences between Dl:l and Dl:2 containing cells.

An investigation of geological and geochemical characteristics of late-Quaternay sediments in the Georgian Bay Region, Southern Ontario

Core samples of postglacial sediments and sediment surface samples from Shepherd Lake on the Bruce Peninsula, Harts Lake on the Canadian Shield, and two cores from Georgian Bay (core P-l in the western deep part and core P-7 in the eastern shallow part) have been analyzed for pH, grain size distribution, water content, bulk density, loss on ignition at 4500C and 11000 C, major oxides (Si02 ,A1203,!FeO,MgO,CaO, Na20,K20,Ti02 ,MnO and P205) and trace elements (Ba,Zr,Sr,y,S, Zn,Cu,Ni,Ce and Rb). The sediment in Georgian Bay are generally fine grained (fine silt to very fine silty clay) and the grain size decreases from the Canadian Shield (core p-7) towards the Bruce Peninsula (core P-l) along the assumed direction of sediment transport. This trend coincides with a decrease in sorting coefficient and an increase in roundness. Other physical characteristics, such as water content, bulk density and loss on ignition are positively correlated with the composition of sediments and their compaction, as well as with the energy of the depositional environment. Analyses of sediment surface samples from Shepherd Lake and Harts Lake indicate the influence of bedrock and surficial deposits in the watershed on pH condition that is also influenced by the organic matter content and probably I ! I man's activities. Organic matter content increases significantly in the surface sediment in these small lakes as a result of either natural eutrophication or anthropogenic organic loading. The extremely high organic matter content in Shepherd Lake sediment indicates rapid natural eutrophication in this closed basin and high biological productivity during postglacial time, probably due to high nutrient levels and shallow depth. The chemical composition of the Canadian Shield bedrock is positively correlated with the chemical characteristics of predominantly inorganic lake sediments that were derived from the Shield rocks by glacial abrasion and by postglacial weathering and erosion of both bedrock and surficial deposits. High correlation coefficients were found between organic matter in lake sediments and major oxides (Si02,AI203,.~FeO, MgO,CaO,K20 and MnO) , as well as some trace elements (Ba,Y, S,Zn,Cu,Ni and Rb). The chemical composition of sediments in Harts Lake and core P-7 in Georgian Bay on the Canadian Shield differs from the chemistry of sediments in Shepherd Lake and core P-l in Georgian Bay on the Bruce Peninsula. The difference between cores P-l and P-7 is indicated by values of Si02 , AI203 ,:LFeo,Mgo,CaO,Ba,Zr,Sr,y and S, and also by the organic matter content. This study indicates that the processes of sediment transport, depositional environment, weathering of the rocks and surficial deposits in the watershed, as well as chemical composition of source rocks all affect the chemical characteristics of lake sediments. The stratigraphic changes and variations in lake sediment chemistry with regard to major oxides, trace elements, and organic matter content are probably related to the history of glacial and postglacial lake stages of the Georgian Bay Region and, therefore, the geochemical data can make a useful contribution to a better understanding of the Late-Quaternary history of the Great Lakes.

Localization of the mechanism of pH-dependent non- photochemical fluorescence quenching in thylakoid membranes

Higher plants have evolved a well-conserved set of photoprotective mechanisms, collectively designated Non-Photochemical Quenching of chlorophyll fluorescence (qN), to deal with the inhibitory absorption of excess light energy by the photosystems. Their main contribution originates from safe thermal deactivation of excited states promoted by a highly-energized thylakoid membrane, detected via lumen acidification. The precise origins of this energy- or LlpH-dependent quenching (qE), arising from either decreased energy transfer efficiency in PSII antennae (~ Young & Frank, 1996; Gilmore & Yamamoto, 1992; Ruban et aI., 1992), from alternative electron transfer pathways in PSII reaction centres (~ Schreiber & Neubauer, 1990; Thompson &Brudvig, 1988; Klimov et aI., 1977), or from both (Wagner et aI., 1996; Walters & Horton, 1993), are a source of considerable controversy. In this study, the origins of qE were investigated in spinach thylakoids using a combination of fluorescence spectroscopic techniques: Pulse Amplitude Modulated (PAM) fluorimetry, pump-probe fluorimetry for the measurement of PSII absorption crosssections, and picosecond fluorescence decay curves fit to a kinetic model for PSII. Quenching by qE (,..,600/0 of maximal fluorescence, Fm) was light-induced in circulating samples and the resulting pH gradient maintained during a dark delay by the lumenacidifying capabilities of thylakoid membrane H+ ATPases. Results for qE were compared to those for the addition of a known antenna quencher, 5-hydroxy-1,4naphthoquinone (5-0H-NQ), titrated to achieve the same degree of Fm quenching as for qE. Quenching of the minimal fluorescence yield, F0' was clear (8 to 130/0) during formation of qE, indicative of classical antenna quenching (Butler, 1984), although the degree was significantly less than that achieved by addition of 5-0H-NQ. Although qE induction resulted in an overall increase in absorption cross-section, unlike the decrease expected for antenna quenchers like the quinone, a larger increase in crosssection was observed when qE induction was attempted in thylakoids with collapsed pH gradients (uncoupled by nigericin), in the absence of xanthophyll cycle operation (inhibited by DTT), or in the absence of quenching (LlpH not maintained in the dark due to omission of ATP). Fluorescence decay curves exhibited a similar disparity between qE-quenched and 5-0H-NQ-quenched thylakoids, although both sets showed accelerated kinetics in the fastest decay components at both F0 and Fm. In addition, the kinetics of dark-adapted thylakoids were nearly identical to those in qEquenched samples at F0' both accelerated in comparison with thylakoids in which the redox poise of the Oxygen-Evolving Complex was randomized by exposure to low levels of background light (which allowed appropriate comparison with F0 yields from quenched samples). When modelled with the Reversible Radical Pair model for PSII (Schatz et aI., 1988), quinone quenching could be sufficiently described by increasing only the rate constant for decay in the antenna (as in Vasil'ev et aI., 1998), whereas modelling of data from qE-quenched thylakoids required changes in both the antenna rate constant and in rate constants for the reaction centre. The clear differences between qE and 5-0H-NQ quenching demonstrated that qE could not have its origins in the antenna alone, but is rather accompanied by reaction centre quenching. Defined mechanisms of reaction centre quenching are discussed, also in relation to the observed post-quenching depression in Fm associated with photoinhibition.

Palaeopigment accumulation and implcations for paleolimnology over the lost century for two Ontario lakes

Crawford Lake is a meromictic lake, which is 24 m deep and has an area of 2.5 ha, and has never been reported to have mixed below 16 m. Lady Evelyn Lake, which became a reservoir when a dam was built in 1916, is dimictic with a maximum depth of about 35 m. 1 My research proved that both native chlorophylls and the ratio of chlorophyll derivatives to total carotenoids were better preserved in the shallower lake (Crawford Lake) because it was meromictic. Thus the anaerobic conditions in Crawford Lake below 16 m (monimolimnion) provide excellent conditions for pigment preservation. Under such conditions, the preservation of both chlorophylls and carotenoids, including oscillaxanthin and myxoxanthophyll, are extremely good compared with those of Lady Evelyn Reservoir, in which anaerobic conditions are rarely encountered at the mud-water interface. During the period from 1500 to 1900 A. D. in Crawford Lake, the accumulation rates of oscillaxanthin and myxoxanthophyll were extremely high, but those of chlorophyll derivatives and total carotenoids were relatively low. This was correlated with the presence of a dense benthic mat of cyanobacteria near the lake's chemocline. Competition for light between the deep dwelling cyanobacteria and overlying phytoplankton in this meromictic lake would have been intensified as the lake became more and more eutrophic (1955-1991 A. D.). During the period from 1955 to 1991 A. D., the accumulation rates of chlorophyll derivatives and total carotenoids in the sediment core from Crawford Lake (0-7.5 cm, 1955-present) increased. During this same period, the accumulation rates of cyanobacterial pigments (Le. oscillaxanthin and myxoxanthophyll) declined as the lake became more eutrophic. Because the major cyanobacteria in Crawford Lake are benthic mat forming Lyngbya and Oscillatoria and not phytoplankton, eutrophication resulted in a decline of the mat forming algal pigments. This is important because in previous palaeolimnological studies the concentrations of oscillaxanthin and myxoxanthophyll have been used as correlates with lake trophic levels. The results of organic carbon a13c analysis on the Crawford Lake sediment core supported the conclusions from the pigment study as noted above. High values of a13c at the depth of 34-48 cm (1500-1760 A. D.) were related to a dense population of benthic Oscillatoria and Lyngbya living on the bottom of the lake during that period. The Oscillatoria and Lyngbya utilized the bicarbonate, which had a high a 13C value. Very low values were found at 0-7 cm in the Crawford sediment core. At this time phytoplankton was the main primary producer, which enriched 12C by photosynthetic assimilation.

ESI-MS[n] of anticancer pt[iv] organoamido complexes and their interactions with DNA-model compounds /

The general solution behaviour and" the major fragmentation pathways of the anticanceractive PtIV coordination complexes, trans, trans, cis, cis-[PtCIOH{N(pFC6F4) CH2h(pY)2] (1), trans, cis, cis-[Pt(OH)2{N(p-FC6F4)CH2h(Py)2] (2), trans, cis, cis-[Pt(OH)2{N(p-HC6F4)CH2h(Py)2] (3), trans, trans, cis, cis-[PtCIOH{N(pHC6F4) CH2h(Py)2] (4), and trans, trans, cis, cis-[PtOH(OCH3){N(p-HC6F4)CH2h(PY)2] (5) (Py = pyridine) have been deduced by positive-ion tandem-in-time ESI-MS. Overall, the acquired full-scan, positive-ion ESI-MS spectra of 2, 3, and 5 were characterized by the presence of relatively low-intensity [M+Nar and [M+Kt mass spectral peaks, whereas those of 1 and 4 were dominated by extremely intense [M+Hr peaks. Complexes 2 and 3 were also noted to form [2M+Ht and [2M+Nat dilneric cations. The source of Na + and K+ ions is believed to be the sample, the solvent systems used or the transport line carrying the sample solutions into the ES ion source. Further, the fragmentation pathway of all complexes studied was found to be almost identical with concurrent loss of py and H20 molecules, loss of a {N(p-YC6F4)CH2} (Y = F, H) group and/or concomitant release of the latter group and a py ligand being the most conunon. The photochemical degradation behaviour of 1 and 2 was also investigated using either fluorescent or ultraviolet light and some products of that degradation were positively identified. Altogether, light irradiation of solutions of both complexes resulted in cation cationisation, reductive-elimination, ligand-release, ligand-exchange and ligand-addition reactions. Finally, positive- and negative-ion ESI-MSn spectra of 5' -GMP, guanosine, inosine and products of their reactions with 1, 2,3, and 4 were also recorded. On the whole, full-scan ESI-MS spectra of the pure nucleobases revealed the presence of cationic and anionic species that are highly reflective of both their solution ionic composition and their propensity t9 form polymeric clusters. Analyses of mass spectra acquired from their reaction solutions with the aforementioned platinum complexes indicated very slow kinetics. However, all complexes investigated formed, to various degrees, Pt-nucleobase adducts with guanosine and inosine, but not with 5'-GMP. The products included species having coordination numbers of III, IV, V, and VI, among which the first-time· observed, coordinatively saturated, jive-coordinate PtlI-nucleobase complexes were of most interest. The latter complexes are presumably stabilized by 7tback- donation involving the filled d orbitals of the PtII centre and the empty pz· orbital of MeCN. All products, whose peaks appeared inlull-scan ESI-MS spectra, are believed to represent solution species rather than artifacts of gas-phase processes. Finally, negativeion ESI-MSn spectra recorded in reaction solutions of 1 and 4 with guanosine and of the latter complex with inosine revealed the negative-ion-ESI-MS first-time observed, noncovalent, nucleoside-chloride adducts, with the source of chloride anion being complexes 1 and 4 theillselves. In contrast, no such adducts were observed to form with Na25'-GMP or its protonated fonn. Few suggestions are offered for the possible cause(s) behind the absence of such adduct ions.

Effect of pH on non-photochemical quenching in spinach photsystem 2 particles as measured by picosecond fluorescence decay kinetics

Single photon timing was used to study picosecond chlorophyll a fluorescence decay kinetics of pH induced non-photochemical quenching in spinach photosystem 2 particles. The characteristics of this quenching are a decrease in chlorophyll a fluorescence yield as well as a decrease in photochemistry at low pH. Picosecond kinetics of room temperature fluorescence temporally resolve the individual components of the steady state fluorescence yield into components that are related to primary energy conversion processes in photosystem 2. Four components were resolved for dark adapted (Fo), light saturated (Fm), and chemically reduced (Nadithionite) photosystem 2 reaction centres. The fastest and slowest components, indicative of energy transfer to and energy capture by the photosystem 2 reaction centre and uncoupled ("dead") chlorophyll, respectively, were not affected by changing pH from 6.5 to 4.0. The two intermediate components, indicative of electron transfer processes within the reaction centre of photosystem 2, were affected by the pH change. Results indicate that the decrease in the steady state fluorescence yield at low pH was primarily due to the decrease in lifetime and amplitude of the slower of the intermediate components. These results imply that the decrease in steady state fluorescence yield at low pH is not due to changes in energy transfer to and energy capture by the photosystem 2 reaction centre, but is related to changes in charge stabilization and charge recombination in the photosystem 2 reaction centre.

Bioindication of ozone using milkweed plants in Southern Ontario

Ambient (03) ozone concentrations were compared to ozone damage on milkweed plants to determine if there was a correlation. Eight survey sites of at least 100 plants each were located within 5 kilometers of Air Quality Index (AQI) stations in southern Ontario. Sites were visited nine times from June-September (2007) and milkweed leaves from 75 plants were assessed using methods pioneered in the United States. Ambient 0 3 results were calculated into SUM65, seasonal cumulative 0 3, and total 03. The 0 3 exposure indices SUM65 and cumulative 0 3 were tested statistically to determine which index is biologically relevant to milkweed as an 0 3 damage indicator species. The milkweed damage indices were incidence of leaves damaged per plant, incidence of plants damaged per site, and total 0 3• The incidence of plants injured per site was the best damage parameter with an F(1,28)=17.37, p=0.0003 for SUM65 and F(1,28)=7.5, p=O.0106 for cumulative 03 .. Milkweed plants showed quantifiable ozone damage with minimal spatial differences in damage and thus have potential use as a biomonitor species in southern Ontario.

Freshwater dinoflagellates as proxies of cultural eutrophication: a case study from Crawford Lake, Ontario

Crawford Lake, Ontario, provides an ideal natural laboratory to study the response of freshwater dinoflagellates to cultural eutrophication. The anoxic bottom waters that result from meromixis in this small (2.4 ha) but deep (24 m) lake preserve varved sediments that host an exceptional fossil record. These annual layers provide dates for human activity (agriculture and land disturbance) around the lake over the last millennium by both Iroquoian village farmers (ca. A.D. 1268-1486) and Canadian farmers beginning ~A.D. 1883. The well established separate intervals of human activity around Crawford Lake, together with an abundance of available data from other fossil groups, allow us to further investigate the potential use of the cyst of freshwater dinoflagellates in studies of eutrophication. Cyst morphotypes observed have been assigned as Peridinium willei Huitfeldt-Kaas, Peridinium wisconsinense Eddy and Peridinium volzii Lemmermann and Parvodinium inconspicuum (Lemmermann) Carty. The latter two cyst-theca relationships were determined by culturing and by the exceptional preservation of thecae of P. inconspicuum in varves deposited at times of anthropogenic reductions in dissolved oxygen.

Non-pollen palynomorphs and thecamoebians as proxies of environmental and anthropogenic change: a case study from Lake Simcoe, Ontario, Canada

The distribution of aquatic microfossils and pollen in the long core from Lake Simcoe (LS07PC5) shows synchronous response since deglaciation, highlighting the potential of little-known non-pollen palynomorphs (NPP) as paleolimnological indicators. Upcore variations in NPP, thecamoebians and pollen reflect hydrological and climatic variations: onset of the Main Lake Algonquin, the draining of Lake Algonquin, the early Holocene drought, the midto late Holocene climate shifts including mid-Holocene drought and the Little Ice Age, and human settlement. The distribution of microfossils in the short cores (CB1 and SB1) shows the level of eutrophication decreasing gradually from Cook’s Bay to the Atherley Narrows outflow due to differences in the extent of anthropogenic impact and cumulative retention of phosphorous within sediments. Changes in assemblages and concentration of NPP within the cores reflect the history of settlement within Lake Simcoe basin, recording temporal differences in eutrophication.

Algal and protozoan response to Holocene climate change and anthropogenic impact: a case study from Sluice Pond, MA

Sluice Pond is a small (18 ha) and deep (Zmax 20.0 m) partially meromictic, pond in Lynn, Massachusetts that contains a diverse dinocyst record since the early Holocene. High dinocyst concentrations, including morphotypes not previously described, as well as the preservation of several specimens of cellulosic thecae are attributed to low dissolved oxygen (DO) in the basin. The fossil protozoan record supports the interpretation- thecamoebians were unable to colonize the basin until the middle Holocene and only became abundant when the drought-induced lowstand oxygenated the bottom waters. Protozoans tolerant of low DO became abundant through the late Holocene as water levels rose and cultural eutrophication produced a sharp increase in biochemical oxygen demand (BOD) beginning in the 17th century. Recent sediments contain a dominance of Peridinium willei, indicating cultural eutrophication and the planktonic ciliate Codonella cratera and the thecamoebian Cucurbitella tricuspis in the deep basin. Above the chemocline however, a diverse difflugiid thecamoebian assemblage is present.

Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.