Phytoplankton chlorophyll-a fluorescence, measured in situ, can be applied as a tool to estimate primary production in the ocean over a large range of temporal and spatial scales. This non-invasive technique allows for fast assessments of photo-physiological parameters in contrast to the traditional methodologies (14C uptake and O2 evolution). The main photo-physiological parameters derived by the available instruments are yields, and as such, require careful interpretation. The comprehension of the main sources of variability of the photochemical and the light absorption efficiencies in marine phytoplankton has increased in the past years, largely by studies using monospecific cultures. In natural communities, however, the development of primary production models based on chlorophyll-a fluorescence remain limited as they are simultaneously subjected to a wide range of environmental and biological factors. This study will test the hypothesis that photo-physiological models for primary production estimates can be improved when key phytoplankton features, such as the pigments composition and dominant cell size, are taking into account. The approach was to contrast the photo-physiological parameters derived from measurements in distinct oceanographic regions, as well as those derived in a specific environment with presented different nutrient concentration according to the time of sampling. In addition, we showed for monospecific cultures, how the photo-physiological parameters are quantitatively related to the production of carbon under the interactive effects of taxonomic composition and cell size. The proportions of photosynthetic and photoprotective pigments present in the community were related to the bulk photochemical efficiency and the cross-section of light absorption, but varied among oceanographic regions and the depth of the water column. A parameterization of fluorescence-derived primary production rates, using four dominant size classes, was derived for natural phytoplankton communities under different nutrients conditions in a coastal environment, showing that the parameters differed among size classes above a threshold of nutrient concentration. The direct conversion rates between fluorescence-derived primary production and carbon assimilation rates, computed for two distinct phytoplankton cell sizes grown in controlled laboratorial conditions, showed that cell size strongly influences the efficiency of light absorption and photochemistry, however species-specific responses in photosynthetic energy allocation dominated the differences observed in how absorbed light is utilized to carbon assimilation, i.e., in the electron requirements for carbon assimilation. The results highlighted the importance of the tight coupling of nutrients availability and phytoplankton communities, as well as for measurements of chlorophyll-a fluorescence in the ocean and primary production models. This work presents a novel contribution to the increasing efforts to apply fluorescence-based techniques to understand and parameterize primary production estimates in marine systems, especially at highly dynamic environments. / A fluorescência da clorofila-a do fitoplâncton, medida in situ, pode ser uma ferramenta para estimar produção primária no oceano em grande escala temporal e espacial. Esta técnica não-invasiva permite análises rápidas de parâmetros foto-fisiológicos ao contrário de metodologias tradicionais (assimilação de 14C e produção de O2). Os principais parâmetros foto-fisiológicos de instrumentos disponíveis hoje tratam-se de eficiências, e como tal, requerem cuidados em serem interpretados. A compreensão das principais fontes de variabilidade da eficiência fotoquímica e de absorção de luz no fitoplâncton marinho tem aumentado nos últimos anos, em sua maioria em cultivos monoespecíficos. Em comunidades naturais, entretanto, o desenvolvimento de modelos de produção primária baseados na fluorescência da clorofila-a ainda é limitado uma vez que estão sujeitos à uma ampla gama de fatores ambientais e biológicos. Esse estudo testa a hipótese de que modelos foto-fisiológicos para estimar produção primária podem ser aprimorados considerando-se características fundamentais do fitoplâncton, como a composição de pigmentos e tamanho celular dominante. A estratégia foi contrastar parâmetros foto-fisiológicos derivados de medidas em regiões oceanográficas distintas, assim como medidas em um ambiente específico com diferentes concentrações de nutrientes ao longo do período amostrado. Adicionalmente, apresentamos através de cultivos monoespecíficos, como parâmetros foto-fisiológicos são quantitativamente relacionados à produção de carbono e os efeitos interativos da composição taxonômica e tamanho celular nessa relação. A proporção de pigmentos fotossintéticos e fotoprotetores da comunidade foram relacionados à eficiência fotoquímica e seção transversal de absorção de luz, porém variaram de acordo com a região oceanográfica e profundidade na coluna d\'água. Uma parameterização de taxas de produção primária derivadas da fluorescência, usando quatro classes de tamanho dominantes, foi proposta para comunidades naturais de fitoplâncton sob condições de nutrientes diferentes em um ambiente costeiro, mostrando que os parâmetros diferiram entre as classes de tamanho acima de um limiar de concentração de nutrientes. As taxas de conversão diretas entre produção primária derivada da fluorescência e taxas de assimilação de carbono, computadas para dois tamanhos de fitoplâncton crescidos em condições controladas em laboratório, mostraram que tamanho celular influencia as eficiências de absorção de luz e fotoquímica, porém respostas espécie-específicas na alocação de energia fotossintética dominaram as diferenças observadas em como a luz absorvida é utilizada para assimilação de carbono, ou seja, na razão de elétrons exigidos para assimilação de carbono. Os resultados destacam a importância do acoplamento da disponibilidade de nutrientes com a comunidade fitoplanctônica, assim como das medidas de fluorescência da clorofila-a no oceano e nos modelos de produção primária. Este trabalho apresenta uma contribuição inédita nos esforços crescentes em aplicar técnicas baseadas na fluorescência para entender e parameterizar estimativas de produção primária nos sistemas marinhos, especialmente em ambientes altamente dinâmicos.

The photosynthetic water oxidation reaction is catalyzed by an inorganic Mn4OxCaClyHCO3-z cluster at the heart of the oxygen evolving complex (OEC) in photosystem II. In the absence of an atomic resolution crystal structure, the precise molecular organization of the OEC remains unresolved. Accordingly, the role of the protein and inorganic cofactors of PSII (Ca2+, HCO3- and Cl-) in the mechanism of O2-evolution await clarification. In this study, rapid 18O-isotope exchange measurements were applied to monitor the substrate-water binding kinetics as a function of the intermediate S-states of the catalytic site (i.e. S3, S2 and S1) in Triton X-100 solubilized membrane preparations that are enriched in photosystem II activity and are routinely used to evaluate cofactor requirements. Consistent with the previous determinations of the 18O exchange behavior in thylakoids, the initial 18O exchange measurements of native PSII membranes at m/e = 34 (which is sensitive to the 16O18O product) show that the ‘fast’ and ‘slowly’ exchanging substrate-waters are bound to the catalytic site in the S3 state, immediately prior to O2 release. Although the slowly exchanging water is bound throughout the entire S-state cycle, the kinetics of the fast exchanging water remains too fast in the S2, S1 [and S0] states to be resolved using the current instrumentation, and left open the possibility that the second substrate-water only binds to the active site after the formation of the S3 state. Presented is the first direct evidence to show that fast exchanging water is already bound to the OEC in the S2 state. Rapid 18O-isotope exchange measurements for Ex-depleted PSII (depleted of the 17- and 23-kDa extrinsic proteins) in the S2 state reveals a resolvable fast kinetic component of 34k2 = 120 ± 14 s-1. The slowing down of the fast phase kinetics is discussed in terms of increased water permeation and the effect on the local dielectric following removal of the extrinsic subunits. In addition, the first direct evidence to show the involvement of calcium in substrate-water binding is also presented. Strontium replacement of the OEC Ca2+-site reveals a factor of ~3-4 increase in the 18O exchange of the slowly exchanging water across the S3, S2 and S1 states while the kinetics of the fast exchanging water remain unchanged. Finally, a re-investigation of the proposed role for bicarbonate as an oxidizable electron donor to photosystem II was unable to discern any 18O enrichment of the photosynthetically evolved O2 in the presence of 18O-bicarbonate. A working model for O2-evolution in terms of these results is presented.

The Small Cab-like Proteins (SCPs) in the cyanobacterium Synechocystis sp. PCC 6803 accumulate in cells grown under different stress conditions. Genes coding for SCPs have been found in all sequenced organisms performing oxygenic photosynthesis and even in the genomes of cyanophages. Deletion of multiple scp genes in Synechocystis resulted in mutants with severely impaired growth and altered pigment content. These findings indicate the importance of SCPs in photosynthesis; however, their specific function is not well understood. SCPs share a chlorophyll-binding motif with the plant light harvesting complex, suggesting that they bind chlorophyll. Here I describe my findings, which unambiguously show that SCPs are able to bind chlorophyll in vitro. Although they affect both the stoichiometric ratio of Photosystem I to II and chlorophyll stability, they do not seem to be directly involved in non-photochemical quenching. I was able to reveal the location of the SCPs within the cyanobacterial cell: in stressed cells they attach to Photosystem II in the thylakoid membrane. Furthermore, I revealed the presence of another light-harvesting like (Lil)/SCP protein in Synechocystis sp. PCC 6803. The gene, slr1544, codifying for this newly characterised LilA protein, co-transcribes together with scpD and also appears to bind to Photosystem II during stress.

The oxygen that we breathe and food that we eat are products of the natural photosynthesis. Molecular oxygen is crucial for life on Earth owing to its role in the glycolysis and citric acid pathways that yield in aerobic organisms the energy-rich ATP molecules. Photosynthetic water oxidation, which produces molecular oxygen from water and sunlight, is performed by higher plants, algae and cyanobacteria. Within the molecular structure of a plant cell, photosynthesis is performed by a specific intracellular organelle – the chloroplast. Chloroplasts contain a membrane system, the thylakoid membrane, which comprises lipids, quinones and a very high content of protein complexes. The unique photosynthetic oxidation of water into molecular oxygen, protons and electrons is performed by the Mn4CaO5 cluster in photosystem II (PSII) complex. Understanding the mechanism of water oxidation by Mn4CaO5 cluster is one of the great challenges in science nowadays. When the mechanism of this process is fully understood, artificial photosynthetic systems can be designed that have high efficiencies of solar energy conversion by imitating the fundamental principle of natural system. These systems can be used in future for generation of fuels from sunlight.   In this thesis, the efficiency of water-splitting process in natural photosynthetic preparations was studied by measuring the flash-induced oxygen evolution pattern (FIOP). The overall aim is to achieve a deeper understanding of oxygen evolving mechanism of the Mn4O5Ca cluster via developing a complete kinetic and energetic model of the light-induced redox reactions within PSII complex. On the way to reach this goal, the hydrogen peroxide that is electrochemically generated on surface of Pt-cathode was discovered. The chemical effect of electrochemically produced H2O2 that can interfere in the oxygen evolution pathway or change the observed FIOP data was demonstrated. Therefore, in order to record the clean FIOP data that are further characterized by global fitting program (GFP), H2O2 has to be abolished by catalase addition and by purging the flow buffer of the Joliot-type electrode with nitrogen gas.      After FIOPs free of H2O2-induced effects were achieved, these clean data were then applied to a global fitting approach (GFP) in order to (i) result a comprehensive figure of all S-state decays whose kinetic rates were simultaneously analyzed in a high reliability and consistency, (ii) the dependence of miss parameter on S-state transitions and the oxidation state of tyrosine D (YD) can be tested, (iii) how dependent of all S-state re-combinations (to S1 state) on the various pH/pD values can be also determined in case of using Cyanidioschyzon merolae (C. merolae) thylakoids. Our data support previous suggestions that the S0 → S1 and S1 → S2 transitions involve low or no misses, while high misses occur in the S2 → S3 transition or the S3 → S0 transition. Moreover, the appearance of very slow S2 decay was clearly observed by using the GFP analysis, while there are no evidences of very slow S3 decay were recorded under all circumstances. The unknown electron donor for the very slow S2 decay which can be one of the substances of PSII-protective branch (i.e. cytochrome b559, carotenoid or ChlZ) will be determined in further researches.

Photosystem II (PSII) is the membrane-bound oxidoreductase peptide complex responsible for the oxidation of water to molecular oxygen and reduction of plastoquinone to plastoquinol. Primary electron transfer is initiated upon absorption of a photon by the primary donor chl resulting in electron transfer and production of a P680+QA charge separated state. P680+ is reduced by YZ (Y161 of the D1 polypeptide subunit), one of two redox-active tyrosine residues found in PSII. This produces a neutral tyrosyl radical (YZ ) which is subsequently reduced by electrons derived from water at the oxygen-evolving complex (OEC). The OEC is composed of four manganese, one calcium ion, and one chloride ion. Four photons are required to convert water to O2, each photon advancing the OEC through successive oxidation states or S states. The exact chemical mechanism of water oxidation in PSII is not known. However, proton-coupled electron transfer (PCET) is thought to be one of the fundamental steps in driving the extraction of electrons and protons from water. Here, the mechanism of water oxidation is investigated with focus on PCET events using vibrational spectroscopy. Vibrational spectroscopy is sensitive to changes in protein structure, charge, and hydrogen bonding, and is ideal for the study of fast events coupled with light-induced electron transfer. The results presented here demonstrate the utility of time-resolved infrared spectroscopy in the detection of intermediates of photosynthetic water oxidation. We suggest that proton transfer may precede manganese oxidation during water oxidation based on time-resolved infrared and difference FT-IR spectroscopic results. The mechanism of PCET associated with YZ reduction is investigated. Using reaction-induced difference FT-IR spectroscopy, the identity of the chloride binding site is speculated through the use of bromide exchange at the OEC. Also, proton transfer reactions at the OEC are investigated using azide as a vibrational probe. The advances in the understanding of photosynthetic water oxidation gained in this work will aid in the elucidation of the chemical mechanism of this important reaction. Understanding the details of photosynthetic water oxidation will assist in the development of technology aimed at harnessing the energy of the sun for the benefit of humankind.

Biochemical and biophysical methods in combination with electron microscopy were used to investigate structure and function of pigment-protein complexes in thylakoid membranes of various photosynthetic organisms.

This thesis explores localisations and roles of three auxiliary protein factors involved in the biogenesis of Photosystem II (PSII) in the cyanobacterium Synechocystis sp. PCC 6803 and contributes to subcellular localisation of the initial steps of PSII biogenesis and repair-related D1 synthesis. The main results consist in i) identification of a functional interaction of the protein factor Psb27 with a lumenal domain of the Photosystem II subunit CP43, ii) discovery of a novel pigment binding complex formed by the Ycf39 protein and high-light-inducible proteins implicated in photoprotection and delivery of recycled chlorophyll to newly synthesized D1 protein during the PSII reaction centre formation, iii) providing evidence that the early steps of PSII assembly and the repair-related D1 synthesis occur in the thylakoid membrane of Synechocystis, and iv) revealing that the cyanobacterial PsbP orthologue, CyanoP, assists in the early phase of PSII biogenesis as an assembly factor facilitating the association of D2 and D1 assembly modules.

Made available in DSpace on 2014-06-11T19:26:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-15Bitstream added on 2014-06-13T19:13:01Z : No. of bitstreams: 1 mendes_hsj_me_jabo.pdf: 731818 bytes, checksum: c05e33da45557d9dcf34ed4a5e86509b (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O trabalho objetivou avaliar o efeito do suprimento de potássio no desempenho de clones de eucalipto submetidos a duas condições de disponibilidade hídrica em casa de vegetação utilizando características biométricas e fisiológicas. Cinco genótipos de eucalipto foram submetidos a dois níveis de adubação potássica (K0 – sem complementação potássica e K1 – adição de 166 mg.dm-3 de K) e a dois regimes de irrigação (RI1 – irrigação diária, até o solo atingir 60% dos poros preenchidos com água (PPA), ou seja, plantas sem restrição hídrica, e RI2 - plantas irrigadas até o solo atingir 60% PPA, com posterior suspensão da irrigação, até o aparecimento de sintomas iniciais de deficiência hídrica). Foram conduzidos sete ciclos de suspensão de irrigação, sendo a quantidade de água reposta em cada vaso determinada pelo método gravimétrico. No início e ao final do experimento, foram avaliados o diâmetro do coleto, a altura, o número de folhas, a área foliar e a massa de matéria seca de folhas, caule, raízes, da parte aérea e total. Nos momentos de máximo estresse hídrico, foram avaliadas as seguintes características fisiológicas: teor relativo de clorofila total (ICC), medida da eficiência quântica do fotossistema II (Fv/Fm), taxa de assimilação líquida (A), condutância estomática (gs), taxa de transpiração (E), eficiência intrínseca do uso da água (EUAintr=A/E), eficiência instantânea do uso da água (EUAinst=A/gs), conteúdo relativo de água (CRA) e, ao final do experimento foi determinado o potencial hídrico foliar ( f). O experimento foi estabelecido no delineamento de blocos ao acaso, em esquema fatorial 5 x 2 x 2 (5 genótipos, 2 regimes de irrigação e 2 níveis de adubação potássica), com cinco repetições por tratamento. As médias de tratamentos foram comparadas pelo teste de Tukey a 5% de probabilidade... / The present study aimed to evaluate the supply potassium effect on the performance of the five eucalypt clones subjected to two water availability conditions in greenhouse from biometric and physiological traits. Five eucalypt genotypes were subjected to two levels of potassium supply (K0 – no potassium supplementation and K1 – addition of 166 mg dm-3 K) and two irrigation regimes (RI1- daily irrigation until the soil reaches 60% of pores filled with water (PFW), that is plants no water restriction, and RI2 – plants watered until the soil reaches 60% (PFW), with subsequent water suspension until the appearance of early water stress symptoms). Seven cycles of irrigation suspension were conducted, and the amount water replaced in each pot was determined by gravimetric method. At the beginning and the end of the experiment, were measured the collar diameter, height, leaf number, leaf area and dry weight mass of leaves, stems, roots, aerial parts and total. In the moment of maximum water stress were evaluated the following physiological traits: the chlorophyll content index (CCI), the quantum efficiency of photosystem II (Fv/Fm), net assimilation rate (A), stomatal conductance (gs), transpiration (E), intrinsic water use efficiency (WUEintr = A/E) and instantaneous water use efficiency (WUEinst = A/gs), relative water content (RWC) and at the end of the experiment was determined the leaf water potential ( f). The design experiment was established in the randomized blocks in factorial scheme 5 x 2 x 2 (5 genotypes, two irrigation regimes and two levels of potassium supplies), with five replicates. The treatment means were compared by Tukey test at 5% probability. Eucalypt clones present reduction in the biometric and physiological traits values under water limitations. For the physiological traits, the potassium supply caused effect reduction of the water stress. To the biometric... (Complete abstract click electronic access below)

abstract: Membrane proteins are a vital part of cellular structure. They are directly involved in many important cellular functions, such as uptake, signaling, respiration, and photosynthesis, among others. Despite their importance, however, less than 500 unique membrane protein structures have been determined to date. This is due to several difficulties with macromolecular crystallography, primarily the difficulty of growing large, well-ordered protein crystals. Since the first proof of concept for femtosecond nanocrystallography showing that diffraction patterns can be collected on extremely small crystals, thus negating the need to grow larger crystals, there have been many exciting advancements in the field. The technique has been proven to show high spatial resolution, thus making it a viable method for structural biology. However, due to the ultrafast nature of the technique, which allows for a lack of radiation damage in imaging, even more interesting experiments are possible, and the first temporal and spatial images of an undamaged structure could be acquired. This concept was denoted as time-resolved femtosecond nanocrystallography. This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2014

Diese Dissertation befasst sich mit der numerischen Behandlung dissipativer quantenmechanischer Prozesse im Rahmen der reduzierten Dichtematrix-Theorie. Zunächst werden Elektronen-Transferprozesse mit Hilfe einer hierarchischen Methode zur Lösung der Bewegungsgleichung der System-Dichtematrix untersucht. Hier liegt der Fokus auf der Untersuchung des Konvergenzverhaltens der Hierarchie mit der Anzahl der berücksichtigten Ebenen bei unterschiedlichen Abbruchverfahren. Es wird gezeigt, dass die Konvergenz stark von der Abbruchmethode und der Observablen abhängt. Weiterhin wird das lineare Absorptionsspektrum des B850 Pigment-Rings von Rhodispirillum molischianum mit verschiedenen Methoden zur Berücksichtigung der Effekte eines angekoppelten Bades berechnet. Diese Methoden basieren auf störungstheoretischen Ansätzen in der System-Bad-Kopplung. Es gelang unter Verwendung der modifizierten Redfield Theorie (MRT) einen Ausdruck für das Absorptionsspektrum herzuleiten. Bei der MRT werden Teile der System-Bad-Wechselwirkung exakt behandelt. Diese Methode wird in zwei Varianten diskutiert und anderen Methoden gegenübergestellt. Modellrechnungen werden für verschiedene Spektraldichten angefertigt, darunter eine, die aus einer Molekulardynamik(MD)- Simulation stammt. Ebenso wird der Einfluss statischer Unordnung der Pigment-Energien auf die Form des Absorptionsspektrums diskutiert. Dazu werden Spektren sowohl einer einzelnen Realisierung als auch des Ensembles dargestellt. Im Falle der Spektraldichte aus der MD-Simulation werden die Ensemble-Spektren zusätzlich mit experimentellen Daten verglichen. Weiterhin wird eine Rechnung mit der Hierarchie zum Spektrum des B850 Rings und weitere zur Populationsdynamik eines kleineren Systems diskutiert und mit Ergebnissen aus der MRT verglichen. Außerdem wird eine Methode zur stochastischen Propagation von mehrdimensionalen Wellenfunktionen entwickelt. Mit Hilfe von Sprung- Prozessen gelingt es die Freiheitsgrade des Systems zu entkoppeln, sodass mehrere eindimensionale Wellenfunktionen stochastisch propagiert werden können. Die exakte Wellenfunktion kann so als Ensemblemittel von Produkten eindimensionaler stochastischer Wellenfunktionen beschrieben werden.