Novel CO2 Regulated Proteins in Synechocystis PCC 6803

The large biodiversity of cyanobacteria together with the increasing genomics and proteomics metadata provide novel information for finding new commercially valuable metabolites. With the advent of global warming, there is growing interest in the processes that results in efficient CO2 capture through the use of photosynthetic microorganisms such as cyanobacteria. This requires a detailed knowledge of how cyanobacteria respond to the ambient CO2. My study was aimed at understanding the changes in the protein profile of the model organism, Synechocystis PCC 6803 towards the varying CO₂ level. In order to achieve this goal I have employed modern proteomics tools such as iTRAQ and DIGE, recombinant DNA techniques to construct different mutants in cyanobacteria and biophysical methods to study the photosynthetic properties. The proteomics study revealed several novel proteins, apart from the well characterized proteins involved in carbon concentrating mechanisms (CCMs), that were upregulated upon shift of the cells from high CO₂ concentration (3%) to that in air level (0.039%). The unknown proteins, Slr0006 and flavodiiron proteins (FDPs) Sll0217-Flv4 and Sll0219-Flv2, were selected for further characterization. Although slr0006 was substantially upregulated under C_i limiting conditions, inactivation of the gene did not result in any visual phenotype under various environmental conditions indicating that this protein is not essential for cell survival. However, quantitative proteomics showed the induction of novel plasmid and chromosome encoded proteins in deltaslr0006 under air level CO₂ conditions. The expression of the slr0006 gene was found to be strictly dependent on active photosynthetic electron transfer. Slr0006 contains conserved dsRNA binding domain that belongs to the Sua5/YrdC/YciO protein family. Structural modelling of Slr0006 showed an alpha/beta twisted open-sheet structure and a positively charged cavity, indicating a possible binding site for RNA. The 3D model and the co-localization of Slr0006 with ribosomal subunits suggest that it might play a role in translation or ribosome biogenesis. On the other hand, deletions in the sll0217-sll218- sll0219 operon resulted in enhanced photodamage of PSII and distorted energy transfer from phycobilisome (PBS) to PSII, suggesting a dynamic photoprotection role of the operon. Constructed homology models also suggest efficient electron transfer in heterodimeric Flv2/Flv4, apparently involved in PSII photoprotection. Both Slr0006 and FDPs exhibited several common features, including negative regulation by NdhR and ambiguous cellular localization when subjected to different concentrations of divalent ions. This strong association with the membranes remained undisturbed even in the presence of detergent or high salt. My finding brings ample information on three novel proteins and their functions towards carbon limitation. Nevertheless, many pathways and related proteins remain unexplored. The comprehensive understanding of the acclimation processes in cyanobacteria towards varying environmental CO₂ levels will help to uncover adaptive mechanisms in other organisms, including higher plants.

Andean indigenous food crops: nutritional value and bioactive compounds

The Andean area of South America is a very important center for the domestication of food crops. This area is the botanical origin of potato, peanut and tomato. Less well- known crops, such as quinoa (Chenopodium quinoa), kañiwa (Chenopodium pallidicaule) and kiwicha (Amaranthus caudatus), were also domesticated by ancient Andean farmers. These crops have a long history of safe use with the local populations and they have contributed to the nutrition and wellbeing of the people for centuries. Several studies have reported the nutritional value of Andean grains. They contain proteins with a balanced essential amino acid composition that are of high biological value, good quality oil and essential minerals, for example iron, calcium and zinc. They are potential sources of bioactive compounds such as polyphenols and dietary fiber. The main objective of the practical work was to assess the nutritional value of Andean native grains with a special emphasis on the bioactive components and the impact of processing. The compounds studied were phenolic acids, flavonoids, betalains and dietary fiber. The radical scavenging activity was measured as well. Iron, calcium and zinc content and their bioavailability were analyzed as well. The grains were processed by extrusion with the aim to study the effect of processing on the chemical composition. Quinoa, kañiwa and kiwicha are very good sources of dietary fiber, especially of insoluble dietary fiber. The phenolic acid content in Andean crops was low compared with common cereals like wheat and rye, but was similar to levels found in oat, barley, corn and rice. The flavonoid content of quinoa and kañiwa was exceptionally high. Kiwicha did not contain quantifiable amounts of these compounds. Only one variety of kiwicha contained low amounts of betalains. These compounds were not detected in kañiwa or quinoa. Quinoa, kañiwa and kiwicha are good sources of minerals. Their calcium, zinc and iron content are higher than the content of these minerals in common cereals. In general, roasting did not affect significantly mineral bioavailability. On the contrary, in cooked grains, there was an increase in bioavailability of zinc and, in the case of kañiwa, also in iron and calcium bioavailability. In all cases, the contents of total and insoluble dietary fiber decreased during the extrusion process. At the same time, the content of soluble dietary fiber increased. The content of total phenolics, phytic acid and the antioxidant activity decreased in kiwicha varieties during the extrusion process. In the case of quinoa, the content of total phenolic compounds and the radical scavenging activity increased during the extrusion process in all varieties. Taken together, the studies presented here demonstrate that the Andean indigenous crops have excellent potential as sources of minerals, flavonoids and dietary fiber. Further studies should be conducted to characterize the phenolic compound and antioxidant composition in processed grains and end products. Quinoa, kañiwa and kiwicha grains are consumed widely in Andean countries but they also have a significant, worldwide potential as a new cultivated crop species and as an imported commodity from South America. Their inclusion in the diet has the potential to improve the intake of minerals and health-promoting bioactive compounds. They may also be interesting raw materials for special dietary foods and functional foods offering natural sources of specific health-promoting components.

Warning system based on theoretical-experimental study of dispersion of soluble pollutants in rivers

Information about capacity of transport and dispersion of soluble pollutants in natural streams are important in the management of water resources, especially in planning preventive measures to minimize the problems caused by accidental or intentional waste, in public health and economic activities that depend on the use of water. Considering this importance, this study aimed to develop a warning system for rivers, based on experimental techniques using tracers and analytical equations of one-dimensional transport of soluble pollutants conservative, to subsidizing the decision-making in the management of water resources. The system was development in JAVA programming language and MySQL database can predict the travel time of pollutants clouds from a point of eviction and graphically displays the temporal distribution of concentrations of passage clouds, in a particular location, downstream from the point of its launch.

Development of an environmentally friendly method of starch oxidation by hydrogen peroxide and a complex water-soluble Iron catalyst

Oxidized starch is a key component in the paper industry, where it is used as both surfacing sizer and filler. Large quantities are annually used for this purpose; however, the methods for the oxidation are not environmentally friendly. In our research, we have studied the possibility to replace the harmful oxidation agents, such as hypochlorite or iodates and transition metal catalysts, with a more environmentally friendly oxidant, hydrogen peroxide (H2O2), and a special metal complex catalyst (FePcS), of which only a small amount is needed. The work comprised batch and semi-batch studies by H2O2, ultrasound studies of starch particles, determination of low-molecular by-products and determination of the decomposition kinetics of H2O2 in the presence of starch and the catalyst. This resulted in a waste-free oxidation method, which only produces water and oxygen as side products. The starch oxidation was studied in both semi-batch and batch modes in respective to the oxidant (H2O2) addition. The semi-batch mode proved to yield a sufficient degree of substitution (COOH groups) for industrial purposes. Treatment of starch granules by ultrasound was found to improve the reactivity of starch. The kinetic results were found out to have a rather complex pattern – several oxidation phases were observed, apparently due to the fact that the oxidation reaction in the beginning only took place on the surface, whereas after a prolonged reaction time, partial degradation of the solid starch granules allowed further reaction in the interior parts. Batch-mode experiments enabled a more detailed study of the mechanisms of starch in the presence of H2O2 and the catalyst, but yielded less oxidized starch due to rapid decomposition of H2O2 due to its high concentrations. The effect of the solid-liquid (S/L) ratio in the reaction system was studied in batch experiments. These studies revealed that the presence of the catalyst and the starch enhance the H2O2 decomposition.

Glycolipid and ceramide transfer proteins : important determinants for their function

Lipider är viktiga biomolekyler, eftersom de bygger upp alla cellulära membran. Glykolipider, dvs. lipider som innehåller socker, är dessutom betydelsefulla som signaleringsmolekyler vid olika processer. Det är essentiellt att regleringen av syntesen, nedbrytningen samt transporten av lipider i cellen är noggrant koordinerade, och faktorer som kan påverka lipidmetabolismen är därför viktiga att undersöka. Denna avhandling har undersökt två olika lipidbindande proteiner, glykolipidtransportprotein (GLTP) och ceramidtransportprotein (CERT). GLTPs biologiska funktion är ännu oklar, dock vet man att GLTP har förmåga att binda olika glykolipider samt överföra dessa lipider mellan olika lipidmembraner. CERT har däremot visats kunna transportera ceramid från det endoplastiska retiklet (ER) till Golgi-apparaten, för produktion av sfingomyelin. I detta avhandlingsarbete undersöktes lokaliseringen av GLTP i celler med olika metoder, bl.a. konfokalmikroskopi, samt olika centrifugeringsmetoder. Genom att överuttrycka GLTP i celler och därefter analysera halten nysyntetiserade glykolipider, kunde även sambandet mellan GLTP-uttrycket och dessa lipider undersökas. I avhandlingen identifierades ytterligare en specifik aminosyrasekvens hos GLTP. Denna sekvens visades kunna binda till VAP-A, ett integralt ER protein, med en tidigare fastställd viktig funktion vid regleringen av lipidtransporten. I avhandlingen analyserades även hur ceramidtransporten mellan två olika membraner, medierad av CERT, påverkas av egenskaper i ceramidens omgivning. För att undersöka detta användes artificiella modellmembraner samt fluorimetriska metoder. Sammansättningen och packningen hos lipidmembranerna visades ha en stor betydelse för den CERT-katalyserade ceramidtransporten. Sammanfattningsvis antyder resultaten från avhandlingen att det existerar flera faktorer som kan påverka aktiviteten av GLTP och CERT, vilka i sin tur har förmåga att reglera lipidmetabolismen.

Development of IgY antibodies in chickens and IgG in rabbits immunized against proteins of Pythium insidiosum isolated from horses in the state of Rio de Janeiro

Pythiosis is caused by Pythium insidiosum and the occurrence of disease in horses was described in the North and Northwest State of Rio de Janeiro, Brazil. The disease was described in cattle, sheep, humans, and horses in different states and regions across the country. This paper describes the development of IgY and IgG polyclonal antibodies, in chicken and rabbits, respectively against proteins extracted from kunkers and hyphae of P. insidiosum from affected horses. The proteins were recognized by chicken, rabbit and horse antibodies by immunodiffusion and Western blot against majority bands of 27 and 43 KDa, and titrated by ELISA. The antibodies IgY developed by the first time against Brazilian strains of P. insidiosum may represent a valuable tool in the detection of antigens of the pathogen and contribute to further studies aimed at immunotherapy and knowledge about this disease in endemic areas in Rio de Janeiro and in Brazil.

Serum protein concentrations, including acute phase proteins, in calves experimentally infected with Salmonella Dublin

The aim of this study was to evaluate serum protein concentrations in calves experimentally inoculated with Salmonella Dublin. Twelve healthy 10 to 15-day-old Holstein calves were randomly allotted into two groups, control and infected with 10(8) CFU of Salmonella Dublin orally. The calves were subjected to physical evaluation and blood samples were collected shortly before administration of the bacteria and also 24, 48, 72, 96, 120 and 168 hours post-infection. The concentration of serum proteins was determined through sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Thirty serum proteins ranging from molecular weight of 24,000 Da to molecular weight of 236,000 Da were detected. Serum concentrations of ceruloplasmin (125,000 Da), haptoglobin (45,000 Da), acid glycoprotein (40,000 Da) and a 34,000 Da protein were significantly increased in the experimentally infected calves, when compared with their concentrations in the control animals. Therefore, this study showed that S. Dublin infection could lead to the increase of certain serum proteins in calves.

Prediction of 3D structure and ligand-binding properties : ABC transporters and flavodiiron proteins from Synechocystis sp. strain PCC 6803

Cyanobacteria are unicellular, non-nitrogen-fixing prokaryotes, which perform photosynthesis similarly as higher plants. The cyanobacterium Synechocystis sp. strain PCC 6803 is used as a model organism in photosynthesis research. My research described herein aims at understanding the function of the photosynthetic machinery and how it responds to changes in the environment. Detailed knowledge of the regulation of photosynthesis in cyanobacteria can be utilized for biotechnological purposes, for example in the harnessing of solar energy for biofuel production. In photosynthesis, iron participates in electron transfer. Here, we focused on iron transport in Synechocystis sp. strain PCC 6803 and particularly on the environmental regulation of the genes encoding the FutA2BC ferric iron transporter, which belongs to the ABC transporter family. A homology model built for the ATP-binding subunit FutC indicates that it has a functional ATPbinding site as well as conserved interactions with the channel-forming subunit FutB in the transporter complex. Polyamines are important for the cell proliferation, differentiation and apoptosis in prokaryotic and eukaryotic cells. In plants, polyamines have special roles in stress response and in plant survival. The polyamine metabolism in cyanobacteria in response to environmental stress is of interest in research on stress tolerance of higher plants. In this thesis, the potd gene encoding an polyamine transporter subunit from Synechocystis sp. strain PCC 6803 was characterized for the first time. A homology model built for PotD protein indicated that it has capability of binding polyamines, with the preference for spermidine. Furthermore, in order to investigate the structural features of the substrate specificity, polyamines were docked into the binding site. Spermidine was positioned very similarly in Synechocystis PotD as in the template structure and had most favorable interactions of the docked polyamines. Based on the homology model, experimental work was conducted, which confirmed the binding preference. Flavodiiron proteins (Flv) are enzymes, which protect the cell against toxicity of oxygen and/or nitric oxide by reduction. In this thesis, we present a novel type of photoprotection mechanism in cyanobacteria by the heterodimer of Flv2/Flv4. The constructed homology model of Flv2/Flv4 suggests a functional heterodimer capable of rapid electron transfer. The unknown protein sll0218, encoded by the flv2-flv4 operon, is assumed to facilitate the interaction of the Flv2/Flv4 heterodimer and energy transfer between the phycobilisome and PSII. Flv2/Flv4 provides an alternative electron transfer pathway and functions as an electron sink in PSII electron transfer.

Regulation of epidermal tight junctions by calcium ATPases and p38

The epidermis is the upper layer of the skin and keratinocytes are its most abundant cells. Tight junctions are cell junctions located in the granular layer of the epidermis. They maintain the polarity of the cells and regulate the movement of water-soluble molecules. Epidermal tight junctions may lose their integrity when there are defects in intercellular calcium regulation. Hailey-Hailey and Darier´s disease are dominantly inherited, blistering skin diseases. Hailey-Hailey disease is caused by mutations in the ATP2C1 gene encoding a calcium/manganese ATPase SPCA1 of the Golgi apparatus. Darier´s disease is caused by mutations in the ATP2A2 gene encoding a calcium ATPase SERCA2 of the endoplasmic reticulum. p38 regulates the differentiation of keratinocytes. The overall regulation of epidermal tight junctions is not well understood. The present study examined the regulation of tight junctions in the human epidermis with a focus on calcium ATPases and p38. Skin from Hailey-Hailey and Darier´s disease patients was studied by using immunofluorescence labeling which targeted intercellular junction proteins. Transepidermal water loss was also measured. ATP2C1 gene expression was silenced in cultured keratinocytes, by siRNA, which modeled Hailey-Hailey disease. Expression of intercellular junction proteins was studied at the mRNA and protein levels. Squamous cell carcinoma and normal human keratinocytes were used as a model for impaired and normal keratinocyte differentiation, and the role of p38 isoforms alpha and delta in the regulation of intercellular junction proteins was studied. Both p38 isoforms were silenced by adenovirus cell transduction, chemical inhibitors or siRNA and keratinocyte differentiation was assessed. The results of this thesis revealed that: i.) intercellular junction proteins are expressed normally in acantholytic skin areas of patients with Hailey-Hailey or Darier´s disease but the localization of ZO-1 expanded to the stratum spinosum; ii.) tight junction proteins, claudin-1 and -4, are regulated by ATP2C1 in non-differentiating keratinocytes; and iii.) p38 delta regulates the expression of tight junction protein ZO-1 in proliferating keratinocytes and in squamous cell carcinoma derived cells. ZO-1 silencing, however, did not affect the expression of other tight junction proteins, suggesting that they are differently regulated. This thesis introduces new mechanisms involved in the regulation of tight junctions revealing new interactions. It provides novel evidence linking intracellular calcium regulation and tight junctions.

Cytoskeletal proteins in the follicular wall of normal andcystic ovaries of sows

The expression of cytoskeletal proteins was evaluated immunohistochemically in 36 normal ovaries sampled from 18 sows and 44 cystic ovaries sampled from of 22 sows, was evaluated. All sows had history of reproductive problems, such as infertility or subfertility. The immunohistochemically stained area (IHCSA) was quantified through image analysis to evaluate the expression of these proteins in the follicular wall of secondary, tertiary, and cystic follicles. Cytokeratins (CK) immunoreactivity was strong in the granulosa cell layer (GC) and mild in the theca interna (TI) and externa (TE) of the normal follicles. There was severe reduction of the reaction to CK in the GC in the cystic follicles, mainly in the luteinized cysts. The immunoreactivity for vimentin was higher in the GC from normal and cystic follicles in contrast with the other follicular structures. In the luteinized cysts, the IHCSA for vimentin was significantly higher in TI and in both observed cysts, the labeling was more accentuated in TE. Immunohistochemical detection of desmin and α-SMA was restricted to the TE, without differences between the normal and cystic follicles. The results of the current study show that the development of ovarian cysts in sows is associated to changes in the expression of the cytoskeletal proteins CK and vimentin.

Assessing the Potential of the Water Soluble Allelopaths of Marsilea minuta in Rice and Wheat

To investigate the allelopathic effect of Marsilea minuta against the germination and seedling growths of rice (Oryza sativa) and wheat (Triticum aestivum), germination bioassays were conducted in both Petri dish and soil cultures in laboratory conditions. Rice and wheat seeds were allowed to germinate in a 1, 2, 3, 4, and 5% (w/v) aqueous extract of whole plant and 2, 4, 6, and 8% (w/w) plant residue-incorporated soils of M. minuta. In Petri dish experiments, 5% (w/v) an aqueous extract of M. mimuta showed significantly lower germination percentages (18.8% and 56.3%), root lengths (0.9 and 4.5 cm), shoot lengths (3.3 and 12.4 cm), seedling lengths (4.1 and 25.0 cm), root dry weights (1.4 and 5.6 g), shoot dry weights (1.1 and 9.0 g), seedling biomasses (2.5 and 14.6 g), and seedling vigor indices (77.4 and 957.3) in rice and wheat, respectively. In pot experiments, the M. minuta residue infested soil, with 8% concentration, produced significantly lower germination percentages (25.3 and 37.5%), root lengths (2.7 and 6.1 cm), shoot lengths (6.2 and 16.5 cm), seedling lengths (8.9 and 22.6 cm), root dry weights (2.4 and 5.5 g), shoot dry weights (4.0 and 2.8 g), seedling biomasses (6.4 and 8.3 g), and seedling vigor indices (224.1 and 855.3) in rice and wheat, respectively. The highest phytotoxic action of 5% aqueous whole plant extract of M. minuta against test crops seem to be due to the presence of two potent phenolic compounds, namely p-coumaric acid (2.91 mg L-1) and m-coumaric acid (1.59 mg L-1) as determined by HPLC analysis.

Seeds of species from the ‘caatinga’: proteins, oils and fatty acid contents

The seeds of 14 species from the ‘caatinga’, a dry forest ecosystem of the semiarid region of northeast Brazil, were analysed for total protein and total lipid contents, as well as fatty acid distribution. The seeds of Argemone mexicana L., an introduced and naturalized species in Brazil, commonly found in ‘caatingas’ and other vegetation, were also analysed. The protein contents ranged from 123 g.kg-1 to 551 g.kg-1, higher contents being found in species of Leguminosae, but also in Jatropha mollissima (Pohl) Baill. (Euphorbiaceae, 409 g.kg-1). Oil contents ranged from 10 g.kg-1 to 400 g.kg-1. The contents of protein and oil were found to be inversely proportional in the seeds of most species, the figures for proteins being generally higher than those of oils. Most species presented either oleic or linoleic as predominant fatty acids. Cardiospermum cf. corindum L. presented eicosenoic acid as the predominant fatty acid.

Insecticidal and antifungic proteins of the latex from Manihot glaziovii Muell. Arg.

Analysis of the latex from Manihot glaziovii showed the presence of various enzymatic and inhibitory activities. The latex also presented an inhibitory effect on the development of cowpea weevil (Callosobruchus maculatus) in an artificial seed system and on the development, in an in vitro assay, of phytopathogenic fungi Colletotrichum gloesporioides, Fusarium solani and Macrophomina phaseolina. These results suggest the presence of substances, some of them of protein nature, involved in plant defense mechanisms in this exudation product.

Brazilian soybean Glycine max (L.) Merr. cultivars adapted to low latitude regions: seed composition and content of bioactive proteins

Among the goals of the Brazilian soybean improvement programmes, the breeding strategies for cultivars adapted to low latitudes have been included to extend crop areas and to increase production. Seeds of nine Brazilian soybean cultivars adapted to low latitudes were investigated regarding to their composition, and amino acid and antinutritional/toxic protein contents. Protein (394.5 ± 13.1 to 445.3 ± 8.0 g kg-1 dry matter) and oil (200.6 ± 1.2 to 232.3 ± 4.7 g kg-1 dry matter) contents showed low correlation to each other (r = -0.06). The total carbohydrate (141.7 ± 6.1 to 211.1 ± 15.0 g kg-1 dry matter) and ash contents (48.2 ± 4.2 to 52.2 ± 0.5 g kg-1 dry matter) were similar to data available for other soybean cultivars. All soybean cultivars presented low levels of tryptophan and sulphur amino acids. The lectin (1,152 to 147,456 HU kg-1 flour), trypsin inhibitor (34.45 ± 2.28 to 77.62 ± 2.63 g trypsin inhibited kg-1 flour), toxin (6,210 ± 134 to 34,650 ± 110 LD50 kg-1 flour) and urease (0.74 ± 0.02 to 1.22 ± 0.10 g kg¹ flour) presented variations in their contents amongst the cultivars. Compared to other soybean cultivars, urease was higher, the acute toxicity lower and the lectin and trypsin inhibitor contents similar to data available. In general, soybean cultivars showed similar biochemical composition to those developed in different geographic regions. The relevance of these findings to the agronomic features and to choice of soybean cultivars to be used as food or feed is discussed.