Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

N-Heterocyclic carbene complexes of silver, rhodium and iron: structures, dynamics and catalysis

The research performed in the framework of this Master Thesis has been directly inspired by the recent work of an organometallic research group led by Professor Maria Cristina Cassani on a topic related to the structures, dynamics and catalytic activity of N-heterocyclic carbene-amide rhodium(I) complexes1. A series of [BocNHCH2CH2ImR]X (R = Me, X = I, 1a’; R = Bz, X = Br, 1b’; R = trityl, X = Cl, 1c’) amide-functionalized imidazolium salts bearing increasingly bulky N-alkyl substituents were synthetized and characterized. Subsequently, these organic precursors were employed in the synthesis of silver(I) complexes as intermediate compounds on a way to rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl, R = Me (3a’), R = Bz (3b’), R = trityl (3c’); X = I, R = Me (4a’)). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. However, while the rotation barriers calculated for the complexes in which R = Me, Bz (3a’,b’ and 4a) matched the experimental values, this was not true in the trityl case 3c’, where the experimental value was very similar to that obtained for compound 3b’ and much smaller with respect to the calculated one. In addition, the energy barrier derived for 3c’ from line shape simulation showed a strong dependence on the temperature, while the barriers measured for 3a’,b’ did not show this effect. In view of these results and in order to establish the reasons for the previously found inconsistency between calculated and experimental thermodynamic data, the first objective of this master thesis was the preparation of a series of rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-benzyl-3-R-imidazolin-2-ylidene; X = Cl, R = Me, Bz, trityl, tBu), containing the benzyl substituent as a chiral probe, followed by full characterization. The second objective of this work was to investigate the catalytic activity of the new rhodium compounds in the hydrosilylation of terminal alkynes for comparison purposes with the reported complexes. Another purpose of this work was to employ the prepared N-heterocyclic ligands in the synthesis of iron(II)-NHC complexes.

Anaerobic oxidation of ethanol over spinel mixed oxides: the first step in the steam-iron process for H2 production

The future hydrogen demand is expected to increase, both in existing industries (including upgrading of fossil fuels or ammonia production) and in new technologies, like fuel cells. Nowadays, hydrogen is obtained predominantly by steam reforming of methane, but it is well known that hydrocarbon based routes result in environmental problems and besides the market is dependent on the availability of this finite resource which is suffering of rapid depletion. Therefore, alternative processes using renewable sources like wind, solar energy and biomass, are now being considered for the production of hydrogen. One of those alternative methods is the so-called “steam-iron process” which consists in the reduction of a metal-oxide by hydrogen-containing feedstock, like ethanol for instance, and then the reduced material is reoxidized with water to produce “clean” hydrogen (water splitting). This kind of thermochemical cycles have been studied before but currently some important facts like the development of more active catalysts, the flexibility of the feedstock (including renewable bio-alcohols) and the fact that the purification of hydrogen could be avoided, have significantly increased the interest for this research topic. With the aim of increasing the understanding of the reactions that govern the steam-iron route to produce hydrogen, it is necessary to go into the molecular level. Spectroscopic methods are an important tool to extract information that could help in the development of more efficient materials and processes. In this research, ethanol was chosen as a reducing fuel and the main goal was to study its interaction with different catalysts having similar structure (spinels), to make a correlation with the composition and the mechanism of the anaerobic oxidation of the ethanol which is the first step of the steam-iron cycle. To accomplish this, diffuse reflectance spectroscopy (DRIFTS) was used to study the surface composition of the catalysts during the adsorption of ethanol and its transformation during the temperature program. Furthermore, mass spectrometry was used to monitor the desorbed products. The set of studied materials include Cu, Co and Ni ferrites which were also characterized by means of X-ray diffraction, surface area measurements, Raman spectroscopy, and temperature programmed reduction.

Laboratory study of grouted macadams impregnated with mine waste geopolymeric binder

A new type of pavement has been gaining popularity over the last few years in Europe. It comprises a surface course with a semi-flexible material that provides significant advantages in comparison to both concrete and conventional asphalt, having both rut resistance and a degree of flexibility. It also provides good protection against the ingress of water to the foundation, since it has an impermeable surface. The semi-flexible material, generally known as grouted macadam, comprises an open-graded asphalt skeleton with 25% to 35% voids into which a cementitious slurry is grouted. This hybrid mixture provides good rut resistance and a surface highly resistant to fuel and oil spillage. Such properties allow it to be used in industrial areas, airports and harbours, where those situations are frequently associated with heavy and slow traffic. Grouted Macadams constitute a poorly understood branch of pavement technology and have generally been relegated to a role in certain specialist pavements whose performance is predicted on purely empirical evidence. Therefore, the main objectives of this project were related to better understanding the properties of this type of material, in order to predict its performance more realistically and to design pavements incorporating grouted macadam more accurately. Based on a standard mix design, several variables were studied during this project in order to characterise the behaviour of Grouted Macadams in general, and the influence of those variables on the fundamental properties of the final mixture. In this research project, one approach was used to the design of pavements incorporating Grouted Macadams: a traditional design method, based on laboratory determined of the stiffness modulus and the compressive strength.

The release of zinc and lead from mine tailings

Mining and processing of metal ores are important causes of soil and groundwater contamination in many regions worldwide. Metal contaminations are a serious risk for the environment and human health. The assessment of metal contaminations in the soil is therefore an important task. A common approach to assess the environmental risk emanating from inorganic contaminations to soil and groundwater is the use of batch or column leaching tests. In this regard, the suitability of leaching tests is a controversial issue. In the first part of this work the applicability and comparability of common leaching tests in the scope of groundwater risk assessment of inorganic contamination is reviewed and critically discussed. Soil water sampling methods (the suction cup method and centrifugation) are addressed as an alternative to leaching tests. Reasons for limitations of the comparability of leaching test results are exposed and recommendations are given for the expedient application of leaching tests for groundwater risk assessment. Leaching tests are usually carried out in open contact with the atmosphere disregarding possible changes of redox conditions. This can affect the original metal speciation and distribution, particularly when anoxic samples are investigated. The influence of sample storage on leaching test results of sulfide bearing anoxic material from a former flotation dump is investigated in a long-term study. Since the oxidation of the sulfide-bearing samples leads to a significant overestimation of metal release, a feasible modification for the conduction of common leaching tests for anoxic material is proposed, where oxidation is prevented efficiently. A comparison of leaching test results to soil water analyzes have shown that the modified saturation soil extraction (SSE) is found to be the only of the tested leaching procedures, which can be recommended for the assessment of current soil water concentrations at anoxic sites if direct investigation of the soil water is impossible due to technical reasons. The vertical distribution and speciation of Zn and Pb in the flotation residues as well as metal concentrations in soil water and plants were investigated to evaluate the environmental risk arising from this site due to the release of metals. The variations in pH and inorganic C content show an acidification of the topsoil with pH values down to 5.5 in the soil and a soil water pH of 6 in 1 m depth. This is due to the oxidation of sulfides and depletion in carbonates. In the anoxic subsoil pH conditions are still neutral and soil water collected with suction cups is in equilibrium with carbonate minerals. Results from extended x-ray absorption fine-structure (EXAFS) spectroscopy confirm that Zn is mainly bound in sphalerite in the subsoil and weathering reactions lead to a redistribution of Zn in the topsoil. A loss of 35% Zn and S from the topsoil compared to the parent material with 10 g/kg Zn has been observed. 13% of total Zn in the topsoil can be regarded as mobile or easily mobilizable according to sequential chemical extractions (SCE). Zn concentrations of 10 mg/L were found in the soil water, where pH is acidic. Electron supply and the buffer capacity of the soil were identified as main factors controlling Zn mobility and release to the groundwater. Variable Pb concentrations up to 30 µg/L were observed in the soil water. In contrast to Zn, Pb is enriched in the mobile fraction of the oxidized topsoil by a factor of 2 compared to the subsoil with 2 g/kg Pb. 80% of the cation exchange capacity in the topsoil is occupied by Pb. Therefore, plant uptake and bioavailability are of major concern. If the site is not prevented from proceeding acidification in the future, a significant release of Zn, S, and Pb to the groundwater has to be expected. Results from this study show that the assessment of metal release especially from sulfide bearing anoxic material requires an extensive comprehension of leaching mechanisms on the one hand and on weathering processes, which influence the speciation and the mobility of metals, on the other hand. Processes, which may change redox and pH conditions in the future, have to be addressed to enable sound decisions for soil and groundwater protection and remediation.

Physiological and Biochemical Aspects of Iron Nutrition in Grapevine

The objective of this thesis was to study the response mechanisms of grapevine to Fe-deficiency and to potential Fe chlorosis prevention strategies. The results show that the presence of bicarbonate in the nutrient solution shifted the activity of PEPC and TCA cycle enzymes and the accumulation/translocation of organic acids in roots of Fe-deprived plants. The rootstock 140 Ruggeri displayed a typical behavior of calcicole plants under bicarbonate stress. The Fe chlorosis susceptible rootstock 101-14 reacted to a prolonged Fe-deficiency reducing the root activity of PEPC and MDH. Noteworthy, it accumulates high levels of citric acid in roots, indicating a low capacity to utilizing, transporting and/or exudating organic acids into the rhizosfere. In contrast, 110 Richter rootstock is capable to maintain an active metabolism of organic acids in roots, accumulating them to a lesser extent than 101-14. Similarly to 101-14, SO4 genotype displays a strong decrease of mechanisms associated to Fe chlorosis tolerance (PEPC and MDH enzymes). Nevertheless it is able to avoid excessive accumulation of citric acid in roots, similar as 110 Richter rootstock. Intercropping with Festuca rubra increased leaf chlorophyll content and net photosynthesis. In addition, intercropping reduces the activity of PEPC in roots, similary to Fe-chelate supply. Applications of NH4+ with nitrification inhibitor prevents efficiently Fe-deficiency, increases chlorophyll content, and induces similar root biochemical responses as Fe-EDDHA. Without the addition of nitrification inhibitors, the effectiveness of NH4+ supply on Fe chlorosis prevention resulted significantly lower. The aspects intertwined in this investigation highlight the complexity of Fe physiology and the fine metabolic tuning of grapevine genotypes to Fe availability and soil-related environmental factors. The experimental evidences reveal the need to carry out future researches on Fe nutrition maintaining a continous flow of knowledge between theoretical and agronomical perspectives for fully supporting the efforts devoted to convert science into practice.

Oxidative properties of the Iron - Thymine-1-acetic acid - Hydrogen peroxide catalytic system

The oxidation of alcohols and olefins is a pivotal reaction in organic synthesis. However, traditional oxidants are toxic and they often release a considerable amounts of by-products. Here, two IronIII-based systems are shown as oxidative catalyst, working in mild conditions with hydrogen peroxide as primary oxidant. An efficient catalytic system for the selective oxidation of several alcohols to their corresponding aldehydes and ketones was developed and characterized, [Fe(phen)2Cl2]NO3 (phen=1,10-Phenantroline). It was demonstrated that the adoption of a buffered aqueous solution is of crucial importance to ensure both considerable activity and selectivity.The Iron - Thymine-1-acetic acid in-situ complex was studied as catalyst in alcohol oxidations and C-H oxidative functionalization, involving hydrogen peroxide as primary oxidant in mild reaction conditions. The catalytic ability in alcohol oxidations was investigated by Density Functional Theory calculations, however the catalyst still has uncertain structure. The system shows satisfactory activity in alcohol oxidation and aliphatic rings functionalization. The Fe-THA system was studied in cyclohexene oxidation and oxidative halogenations. Halide salts such as NBu4X and NH4X were introduced in the catalytic system as halogens source to obtain cyclohexene derivatives such as halohydrins, important synthetic intermediates.The purpose of this dissertation is to contribute in testing new catalytic systems for alcohol oxidations and C-H functionalization. In particular, most of the efforts in this work focus on studying the Iron - Thymine-1-acetic acid (THA) systems as non-heme oxidative model, which present: •an iron metal centre(s) as a coordinative active site, •hydrogen peroxide as a primary oxidant, •THA as an eco-friendly, biocompatible, low cost coordinating ligand.

Characterization of the structure and iron uptake mechanisms of the Staphylococcus aureus ferric hydroxamate-binding lipoprotein FhuD2

The Reverse Vaccinology (RV) approach allows using genomic information for the delineation of new protein-based vaccines starting from an in silico analysis. The first powerful example of the application of the RV approach is given by the development of a protein-based vaccine against serogroup B Meningococcus. A similar approach was also used to identify new Staphylococcus aureus vaccine candidates, including the ferric hydroxamate-binding lipoprotein FhuD2. S. aureus is a widespread human pathogen, which employs various different strategies for iron uptake, including: (i) siderophore-mediated iron acquisition using the endogenous siderophores staphyloferrin A and B, (ii) siderophore-mediated iron acquisition using xeno-siderophores (the pathway exploited by FhuD2) and (iii) heme-mediated iron acquisition. In this work the high resolution crystal structure of FhuD2 in the iron (III)-siderophore-bound form was determined. FhuD2 belongs to the Periplasmic Binding Protein family (PBP ) class III, and is principally formed by two globular domains, at the N- and C-termini of the protein, that make up a cleft where ferrichrome-iron (III) is bound. The N- and C-terminal domains, connected by a single long α-helix, present Rossmann-like folds, showing a β-stranded core and an α-helical periphery, which do not undergo extensive structural rearrangement when they interact with the ligand, typical of class III PBP members. The structure shows that ferrichrome-bound iron does not come directly into contact with the protein; rather, the metal ion is fully coordinated by six oxygen donors of the hydroxamate groups of three ornithine residues, which, with the three glycine residues, make up the peptide backbone of ferrichrome. Furthermore, it was found that iron-free ferrichrome is able to subtract iron from transferrin. This study shows for the first time the structure of FhuD2, which was found to bind to siderophores ,and that the protein plays an important role in S. aureus colonization and infection phases.

Spin-crossover in metallomesogens of iron(II)

Covalent grafting mesogenic groups to the coordination cores of the parent mononuclear low-spin and spin-crossover compounds afforded metallomesogenic complexes of iron(II). In comparison with the parent complexes the spin-crossover properties of the alkylated derivatives are substantially modified. The type of the modification was found to be dependent on the properties of the parent system and the nature of the used anion, however, the general tendency is the destabilization of the low-spin state at the favor of spin-crossover or high-spin behavior below 400 K. The structural insight revealed the micro-segregated layered organization. The effect of the alkylation of the parent compounds consists first of all in the change of the lattice to a two-dimensional lamellar one retaining significant intermolecular contacts only within the ionic bilayers. The comprehensive analysis of the structural and thermodynamic data in the homologous series pointed at the mechanism of the interplay between the structural modification on melting and the induced anomalous change of the magnetic properties. A family of one-dimensional spin-crossover polymers was synthesized and characterized using a series of spectroscopic methods, X-ray powder diffraction, magnetic susceptibility measurements and differential scanning calorimetry. The copper analogue of was also synthesized and its crystal structure solved. In comparison with the mononuclear systems, the polymeric mesogens of iron(II) are less sensitive to the glass transition, which was attributed to the moderate concomitant variation of the structure. Nevertheless, the observed increase of the magnetic hysteresis with lengthening of the alkyl substituents was ascribed to the interplay of the structural reorganization of the coordination core due to spin-crossover with the structural delay in the spatial reorganization of the mesogenic substituents. The classification of mononuclear and polymeric metallomesogens according to the interactions between the structural- and the spin-transition and analysis of the data on the reported spin-crossover metallomesogens led to the separation of three types, namely: Type i: systems with coupling between the electronic structure of the iron(II) ions and the mesomorphic behavior of the substance; Type ii: systems where both transitions coexist in the same temperature region but are not coupled due to competition with the dehydration or due to negligible structural transformation; Type iii: systems where both transitions occur in different temperature regions and therefore are uncoupled. Fine-tuning, in particular regarding the temperature at which the spin-transition occurs with hysteresis properties responsible for the memory effect, are still a major challenge towards practical implementation of spin-crossover materials. A possible answer to the problem could be materials in which the spin-crossover transition is coupled with another transition easily controllable by external stimuli. In the present thesis we have shown the viability of the approach realized in the mesogenic systems with coupled phase- and spin-transitions.

Synthesis of novel cobalt and iron complexes for sustainable catalytic hydrogenations

Aim of the present work of thesis is to synthesize new non-noble metal based complexes to be employ in redox reactions by a metal-ligand cooperative mechanism. The need of replacing toxic and expensive precious metal complexes with more available and benign metals, has led to the development of new compounds based on cobalt and iron, which are the metals investigated in this study. A carbonyl-tetrahydroborato-bis[(2-diisopropylphosphino)ethyl]amine-cobalt complex bearing a PNP-type ligand is synthesized by a three-step route. Optimization attempt of reaction route were assessed in order to lowering reaction times and solvent waste. New cobalt complex has been tested in esters hydrogenation as well as in acceptorless dehydrogenative coupling of ethanol. Other varieties of substrates were also tested in order to evaluate any possible applications. Concerning iron complex, dicarbonyl-(η4-3,4-bis(4-methoxyphenyl)-2,5-diphenylcyclopenta-2,4-dienone)(1,3-dimethyl-ilidene)iron is synthesized by a three steps route, involving transmetallation of a silver complex, derived from an imidazolium salt, to iron complex. In order to avoid solvent waste, optimization is assessed. Studies were performed to assess activity of triscarbonyl iron precursor toward imidazolium salt and silver complexes.

Nanoparticular iron complex drugs for parenteral administration - physicochemical characterization, biological distribution and pharmacological safety

Iron deficiency is the most common deficiency disease worldwide with many patients who require intravenous iron. Within the last years new kind of parenteral iron complexes as well as generic preparations entered the market. There is a high demand for methods clarifying benefit to risk profiles of old and new iron complexes. It is also necessary to disclose interchangeability between originator and intended copies to avoid severe anaphylactic and anaphylactoid side reaction and assure equivalence of therapeutic effect.rnrnThe investigations presented in this work include physicochemical characterization of nine different parenteral iron containing non-biological complex drugs. rnWe developed an in-vitro assay, which allows the quantification of labile iron in the different complexes and thus it is a useful tool to estimate the pharmaclogical safety regarding iron related adverse drug events. This assay additionally allowed the estimation of complex stability by evaluation of degradation kinetics at the applied conditions.rnrnAn in-ovo study was performed to additionally compare different complexes in respect to body distribution. This in combination with complex stability information allowed the risk estimation of potential local acute and chronic reactions to iron overload.rnrnInformation obtained by the combination of the methods within this work are helpful to estimate the safety and efficacy profile of different iron containing non-biological complex drugs. rnrnPhysicochemical differences between the complexes were demonstrated in respect to size of the inorganic fraction, size and size distribution of the complete particles, structure of the inorganic iron fraction, morphology of the complexes and charge of the complexes. And furthermore significant differences in the biological behavior of different complexes were demonstrated. rnrnThe combination of complex stability and biodistribution as well as the combination of structure, size and stability represent helpful tools for the physicochemical characterization of iron containing non-biological complex drugs and for the estimation of pharmacological safety. This work thus represents an up to date summary of some relevant methods for the characterization of intravenous iron complex drugs in respect to pharmaceutical quality, pharmacological safety and aspects of efficacy. rnrnProspectively, it is worthwhile that the methods within this work will contribute to the development and/or characterization of iron containing nanoparticular formulations with beneficial efficacy and safety profiles.rn

Bioactivity of extracts from extremophile microalgae Coccomyxa sp. on chloride cells in operculum tissue of Fundulus heteroclitus

Microalgae have been studied because of their great potential as a source of new compounds with important value for biotechnology and to understand their strategies of survival in extreme environments. The microalgae Coccomyxa sp., studied in this thesis, is a poly-extremophile witch was isolated from the acid mine drainage of S. Domingos mine. This environment is characterized by low pH (<3) and high concentration of metals, such as copper and iron. The main purpose of the present work was to evaluate the potential bioactivity in an ex-vivo animal model (Fundulus heteroclitus), and expression on selected genes, of cellular extracts obtained from cultures of Coccomyxa sp. at pH 7 without or with exposure to copper (0.6mM Cu²+). The extracts of Coccomyxa sp. cultured at pH 7 exposed to copper show a great potential to be used as epithelial NKCC inhibitors, revealing their potential use as diuretics, but did not show significant effects on gene expression. Coccomyxa sp. could be a good source of cellular extracts with a great potential to be used in pharmaceutical and biotechnology industries.

Diagnosis and treatment of iron-deficiency anaemia during pregnancy and postpartum

Iron-deficiency anaemia during pregnancy and postpartum occurs frequently and may lead to severe maternal and foetal complications. New treatment regimens include intravenous iron administration in particular clinical situations. The aim of the study was to determine optimal diagnostic and therapeutic approaches to iron-deficiency anaemia during pregnancy and postpartum.