A atividade catalítica de clusters trigonais de acetato de rutênio e porfirinas supramoleculares contendo quatro unidades de clusters periféricos ou complexos de bis(bipiridina)rutênio, na oxidação de substratos orgânicos por iodosil-benzeno ou terc-butil-hidroperóxido, é abordada nesta tese. Foram feitos estudos cinéticos para elucidar o mecanismo de catálise, com especial destaque para duas espécies supramoleculares isoméricas representadas por Mn(3-TRPyP) ou Mn(4-TRPyP), nos quais os complexos de bis(bipiridina)(cloro)rutênio se coordenam à tetrapiridilporfirina através das posições meta ou para da ponte piridínica, respectivamente. Além da maior seletividade proporcionada pelos catalisadores supramoleculares, a substituição do íon cloreto pela água nos complexos periféricos de rutênio, intensificou a atividade catalítica, gerando novos sítios ativos, do tipo Ru(IV)=O. Também foram estudados clusters trinucleares de rutênio, altamente reativos, no estado Ru(III)Ru(IV)Ru(IV)=O. Estes foram gerados eletroquimicamente em solução aquosa, apresentando pronunciada atividade catalítica na oxidação do alcool benzílico. Finalmente, uma espécie dimérica de cluster, ainda inédita, com ponte oxo, foi caracterizada e investigada do ponto de vista catalítico. / The catalytic activity of trinuclear ruthenium clusters and supramolecular tetrapyridylporphyrins containing four peripheral cluster units or bis(bipyridine)ruthenium complexes, in the oxidation of organic substrates by iodosylbenzene or tert-butil-hydroperoxide, is dealt with in this thesis. Kinetic studies were performed in order to elucidate the mechanisms of catalysis involving two isomeric species denoted Mn(3-TRPyP) or Mn(4-TRPyP), in which the bis(bipyridine)(chloro)ruthenium complexes are bound to the tetrapyridylporphyrin center, at the meta or para positions of the pyridine bridge, respectively. In addition to the improved selectivity by such supramolecular catalysts, the substitution of the chloride ion by water in the peripheral ruthenium complexes, greatly enhanced their catalytic activity by generating new Ru(IV)=O reactive sites. Highly reactive trinuclear ruthenium clusters of the type Ru(III)Ru(IV)Ru(IV)=O were also generated electrochemically in aqueous solution, exhibiting pronounced catalytic activity in the oxidation of benzyl alcohol. Finally, a novel dimeric oxo-bridged cluster species was characterized, and its role in catalysis investigated.

<p>Iron oxide nanoparticles were prepared using co-precipitation method in the presence and absence of beta-cyclodextrin (&beta / -CD). Such materials were characterized using transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), attenuated total reflection Fourier transform infrared (ATR-FTIR), X-ray diffraction (XRD), cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA). The TEM shows that the surface morphology has no difference between nanoparticles prepared in the presence and absence of beta-cyclodextrin (&beta / -CD), amorphous particles with high surface area and dimensions of about 100 nm by 500 nm. The amorphous states of nanoparticles are confirmed further by XRD. The ATR-FTIR analysis confirms inclusion complex between &beta / -CD and nanoparticles.</p>

<p>Iron oxide nanoparticles were prepared using co-precipitation method in the presence and absence of beta-cyclodextrin (&beta / -CD). Such materials were characterized using transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), attenuated total reflection Fourier transform infrared (ATR-FTIR), X-ray diffraction (XRD), cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA). The TEM shows that the surface morphology has no difference between nanoparticles prepared in the presence and absence of beta-cyclodextrin (&beta / -CD), amorphous particles with high surface area and dimensions of about 100 nm by 500 nm. The amorphous states of nanoparticles are confirmed further by XRD. The ATR-FTIR analysis confirms inclusion complex between &beta / -CD and nanoparticles.</p>

Magister Scientiae - MSc / Iron oxide nanoparticles were prepared using co-precipitation method in the presence and absence of beta-cyclodextrin β-CD). Such materials were characterized using transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), attenuated total reflection Fourier transform infrared (ATR-FTIR), X-ray diffraction (XRD), cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA). The TEM shows that the surface morphology has no difference between nanoparticles prepared in the presence and absence of beta-cyclodextrin β-CD), amorphous particles with high surface area and dimensions of about 100 nm by 500 nm. The amorphous states of nanoparticles are confirmed further by XRD. The ATR-FTIR analysis confirms inclusion complex between β-CD and nanoparticles. The nanoparticles synthesized were used to develop an electrochemical sensor for phenolic endocrine disruptors by modifying the surface area of glassy carbon electrode (GCE). Electrochemical characterization of the iron oxide β-CD nano-composites, studied in 0.1 M potassium chloride (KCl) using chronoamperometry,showed that the surface concentration of the adsorbed composite material was 8.5 x 10-8 mol/cm2. Sensor analysis of bisphenol A (BPA) was carried out using cyclic voltammetry (CV) and square wave voltammetry (SWV) based on amperometric techniques which gave a linear range of 0.50 × 10-6 M to 50 × 10-6 M; limit of detection of 0.156 x 10-6 M and order of magnitude of linearity of 2.03. Hence, the sensor was further used to study 4-tert-octylphenol (TOP); the results showed that the sensitivity and the limit of detection were 11.31 nA L/mol and 0.249 x 10-6 M, respectively and order of magnitude of linearity of 2.00. / South Africa

No description available.

A plethora of naturally-produced steroid hormones, or artificial homologues of them, are being introduced into the aquatic and terrestrial environments each year. Two examples of these are the natural oestrogen 17-oestradiol (E2) and the oestrogen receptor antagonist, Bisphenol A (BPA), both of which target the ribonucleoprotein telomerase through upregulation of its telomerase reverse transcriptase component, TERT. The main objectives of this study were firstly to isolate and characterize the actual mRNA sequence for the telomerase catalytic subuninit, Tert, in rainbow trout (Oncorhynchus mykiss) (Walbaum, 1792) and European purple sea urchin (Paracentrotus lividus) (Lamarck, 1816), with the aim of developing qPCR assays for the amplification and quantification of Tert. Further objectives were to use these assays in controlled exposure studies to establish whether and to what extent the aforementioned chemicals regulate Tert transcription and by doing so further understand the mechanism of Telomerase gene expression and the extent to which environmental oestrogen can interfere. The initial step of sequence characterization and assay devlopment was successful in the case of rainbow trout where two possible splice variants of Tert mRNA are identified, omTertShort and omTertLong. Two qPCR assays were developed for the relative quantification of both of these splice variants in rainbow trout samples, the latter of these successfully amplifying its target in test samples. In order to demonstrate in vitro and in vivo modulation of telomerase activity and mRNA expression, early life-stages of rainbow trout and purple sea urchin, as well as rainbow trout hepatocytes, were exposed to a range of concentrations of E2 and BPA. Purple sea urchin embryos were exposed to 200, 20 and 2 ng E2/ml for 28 hours until they had reached the stage of pluteus larvaes. Rainbow trout embryos were exposed to 500, 20 and 0.1 ng E2/ml and 600 and 150 ng BPA/ml for 167 days from immediately after fertilization. Rainbow trout hepatocytes were exposed to 20 and 2 ng E2/ml for 48 hours. The results from this study show that telomerase activity as well as TERT mRNA expression can be significantly modulated by exposure to oestrogens and other oestrogenic chemicals. E2 concentrations as low as 20 ng/ml lead to an increase in telomerase activity early-life stages of purple sea urchin and upregulation in the transcription of Tert mRNA in unhatched rainbow trout embryos. BPA induced similar response (600 ng/ml) in hatched rainbow trout alevins larvae. Very high exposures to E2 (500 ng/ml) do however lead to downregulation of Tert mRNA in hatched alevins larvae. Differential regulatory response can be observed between different tissue types of 167 day old fry, with an upregulatory response observed at 0.1 ng E2/ml in liver and muscle tissues, but not in brain. Similarly, brain tissues were observed expressing significantly less mRNA than liver and muscle samples when exposed to BPA (150 ng/ml). It is evident that the previously observed link between environmental oestrogens and telomerase is also present in the two test species examined; purple sea urchin and rainbow trout.

Made available in DSpace on 2017-07-24T19:38:10Z (GMT). No. of bitstreams: 1 Adriana Rute Cordeiro.pdf: 1697344 bytes, checksum: c49bee8f561162a88549115390df463d (MD5) Previous issue date: 2013-08-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / This study aimed to develop methods for obtaining extracts for the isolation and chemical analysis of propolis using two samples from the region known as “Campos Gerais do Paraná”. One of the studied propolis samples was produced in the district of Ipiranga and another in the municipality of Ponta Grossa. The utilized general fractionation method allowed obtaining from the same sample the essential oils and then the aqueous extracts and various organic fractions containing chemical components of several polarities. The analyses of the essential oils showed that both samples of propolis contain several components found in Baccharis dracunculifolia, known as vassoura or alecrim do campo, indicating that these are similar to those of green propolis produced in southeastern Brazil. The analyses also demonstrated the presence of phenol compounds such as flavonoids and caffeoylquinic acids, pointing once again that the botanical origin of both propolis includes the alecrim do campo. The analyses of essential oils originating from Ipiranga propolis sample indicated spathulenol and (E)-nerolidol as the main components, while the one acquired in Ponta Grossa showed high proportions of two substances containing aromatic rings in their structures, 2,6-di-t-butyl-p-cresol and benzyl benzoate. The two sesquiterpene alcohols spathulenol and (E)-nerolidol are commonly found in essential oils from B. dracunculifolia and appear in propolis from Ponta Grossa in low percentages, while the two mentioned aromatic compounds are not commonly found in the genus Baccharis. The various analyses of extracts and isolates showed that two aromatic acids may be considered as marker substances for both samples of propolis. The para-hydroxycinnamic acid seemed to be characteristic of propolis from Ipiranga, while the benzoic acid could be considered typical of the sample from Ponta Grossa. Atomic absorption spectrometry analyses that were conducted with both studied propolis did not indicate neither high levels of essential minerals nor the presence of heavy metals, and this fact represents a guarantee that producers have been working in clean environments. / Este estudo buscou desenvolver métodos para a obtenção de extratos destinados ao isolamento e análises químicas de própolis utilizando duas amostras provenientes da Região dos Campos Gerais do Paraná. Uma das amostras de própolis estudadas foi produzida no município de Ipiranga e a outra no município de Ponta Grossa. O método geral de fracionamento utilizado permitiu obter, de uma mesma amostra, os óleos essenciais e em seguida o extrato aquoso e diversos extratos orgânicos contendo substâncias de várias polaridades. As análises dos óleos essenciais demonstraram que ambas as amostras de própolis contém vários componentes também presentes na espécie vegetal Baccharis dracunculifolia, conhecida como vassoura ou alecrim do campo, indicando tratar-se da chamada própolis verde, similares às produzidas na região sudeste do Brasil. As análises também demonstraram a presença de substâncias fenólicas, tanto flavonoides como ácidos cafeoilquínicos, reforçando que a origem botânica das própolis analisadas inclui o alecrim dos campos. As análises de óleos essenciais da amostra de Ipiranga indicaram como componentes principais o espatulenol e o (E)-nerolidol, enquanto que as de Ponta Grossa apresentaram altas proporções de duas substâncias contendo anéis aromáticos em suas estruturas, o 2,6-di-t-butil-p-cresol e o benzilbenzoato. Os dois álcoois sesquiterpênicos espatulenol e (E)-nerolidol são encontrados comumente em óleos essenciais de B. dracunculifolia e aparecem na própolis de Ponta Grossa em baixas porcentagens, enquanto que os dois mencionados compostos aromáticos não são tão comuns em espécies do gênero Baccharis. As diversas análises de extratos e isolamentos demonstraram que dois ácidos aromáticos podem ser considerados como substâncias marcadoras das duas amostras de própolis analisadas. O ácido para-hidroxicinâmico mostrou-se característico da própolis de Ipiranga, enquanto que o ácido benzóico pode ser considerado típico da amostra de Ponta Grossa. As análises por espectrometria de absorção atômica que foram conduzidas com ambas as própolis estudadas não indicaram níveis elevados de metais e nem a presença de metais pesados inconvenientes, sendo mais uma garantia de que os produtores estão trabalhando em ambientes limpos quanto a este aspecto.

Background & Aims: Oxidative stress and apoptosis are proposed mechanisms of cellular injury in studies of xenobiotic hepatotoxicity. The aim of this work is to find early signal markers of drug-induced injury of the liver by focusing on select antioxidant/oxidant and apoptotic genes. As well, to address the relationship between conventional liver dysfunction markers and the measured mRNA and protein expressions in the D-galactosamine/lipopolysaccharide and tert-butylhydroperoxide hepatotoxicity models. Furthermore, potential hepatoprotective capabilities of antioxidant polyphenols quercetin and curcumin were evaluated in relation to its modulation of the oxidative stress and apoptotic parameters in the given xenobiotic hepatotoxicity models. Methods: Biochemical markers testing the hepatic function included aminotransferases (ALT, AST) and bilirubin. Measurements of TBARS and conjugated dienes were used to assess lipoperoxidation. Plasma levels of catalase and reduced glutathione were used as indicators of the oxidative status of the cell. Real time PCR was used to analyse the mRNA expressions of the inducible nitric oxide synthase (NOS-2), heme oxygenase-1 (HO-1), superoxide dismutase (SOD-1), glutathione peroxidase (Gpx-1), caspase 3 (Casp3), BH3 interacting domain death agonist (Bid) and Bcl-2...

I started writing this thesis not only to obtain a doctoral degree, but also to compile in a particular way all the work that I have done during this time. The articles published during these years can only give a short overview of my research task. I decided to give my own perspective of the things I have learned and the results I have obtained. Some sections are directly the published articles, but some other are not and contain a significant amount of unpublished data. Even in some cases the published plots have been modified / altered to provide more insight or to maintain consistency. Historical perspectives often provide a deep understanding of the problems and have been briefly discussed in some chapters. This thesis contains theoretical and computer simulation studies to under-stand effects of spatial correlation on dynamics in several complex systems. Based on the different phenomena studied, the thesis has been divided into three major parts: I. Pair hydrophobicity, composition-dependent anomalies and structural trans-formations in aqueous binary mixtures II. Microscopic analysis of hydrophobic force law in a two dimensional (2D) water-like model system III. Diffusion of a tagged particle on a rugged energy landscape with spatial correlations The three parts have been further divided into ten chapters. In the following we provide part-wise and chapter-wise outline of the thesis. Part I consists of six chapters, where we focus on several important aqueous binary mixtures of amphiphilic molecules. To start with, Chapter 1 provides an introduction to non-ideality often encountered in aqueous binary mixtures. Here we briefly discuss the existing ideas of structural transformations associated with solvation of a foreign molecule in water, with particular emphasis on the classic “iceberg” model. Over the last decade, several investigations, especially neutron scattering and diffraction experiments, have questioned the validity of existing theories and have given rise to an alternate molecular picture involving micro aggregation of amphiphilic co-solvents in their aqueous binary mixtures. Such microheterogeneity was also supported by other experiments and simulations. In Chapter 2, we present our calculation of the separation dependence of potential of mean force (PMF) between two methane molecules in water-dimethyl sulfoxide (DMSO) mixture, using constrained molecular dynamics simulation. It helps us to understand the composition-dependence of pair hydrophobicity in this binary solvent. We find that pair hydrophobicity in the medium is surprisingly enhanced at DMSO mole fraction xDMSO ≈ 0.15, which explains several anomalous properties of this binary mixture – including the age-old mystery of DMSO being a protein stabilizer at lower concentration and protein destabilizer at higher concentration. Chapter 3 starts with discussion of non-monotonic composition dependence of several other properties in water-DMSO binary mixture, like diffusion coefficient, local composition fluctuation and fluctuations in total dipole moment of the system. All these properties exhibit weak to strong anomalies at low solute concentration. We attempt to provide a physical interpretation of such anomalies. Previous analyses often suggested occurrence of a “structural transformation” (or, microheterogeneity) in aqueous binary mixtures of amphiphilic molecules. We show that this structural transformation can be characterized and better understood under the purview of percolation theory. We define the self-aggregates of DMSO as clusters. Analysis of fractal dimension and cluster size distribution with reference to corresponding “universal” scaling exponents, combined with calculation of weight-averaged fraction of largest cluster and cluster size weight average, reveal a percolation transition of the clusters of DMSO in the anomalous concentration range. The percolation threshold appears at xDMSO ≈ 0.15. The molecular picture suggests that DMSO molecules form segregated islands or micro-aggregates at concentrations below the percolation threshold. Close to the critical concentration, DMSO molecules start forming a spanning cluster which gives rise to a bi-continuous phase (of water-rich region and DMSO-rich region) beyond the threshold of xDMSO ≈ 0.15. This percolation transition might be responsible for composition-dependent anomalies of the binary mixture in this low concentration regime. Similar phenomenon is observed for another amphiphilic molecule – ethanol, as discussed in Chapter 4. We again find composition dependent anomalies in several thermophysical properties, such as local composition fluctuation, radial distribution function of ethyl groups and self-diffusion co-efficient of ethanol. Earlier experiments often suggested distinct structural regimes in water-ethanol mixture at different concentrations. Using the statistical mechanical techniques introduced in the previous chapter, we show that ethanol clusters undergo a percolation transition in the anomalous concentration range. Despite the lack of a precise determination of the percolation threshold, estimate lies in the ethanol mole fraction range xEtOH ≈ 0.075 - 0.10. This difficulty is probably due to transient nature of the clusters (as will be discussed in Chapter 6) and finite size of the system. The scaling of ethanol cluster size distribution and the fractal behavior of ethanol clusters, however, conclusively demonstrate their “spanning” nature. To develop a unified understanding, we further study the composition-dependent anomalies and structural transformations in another amphiphilic molecule, tertiary butyl alcohol (TBA) in Chapter 5. Similar to the above-mentioned aqueous binary mixtures of DMSO and ethanol, we demonstrate here that the anomalies occur due to local structural changes involving self-aggregation of TBA molecules and percolation transition of TBA clusters at xTBA ≈ 0.05. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of the largest water cluster. This second transition gives rise to another set of anomalies around. We conclude this part of the thesis with Chapter 6, where we introduce a novel method for understanding the stability of fluctuating clusters of DMSO, ethanol and TBA in their respective aqueous binary mixtures. We find that TBA clusters are the most stable, whereas ethanol clusters are the most transient among the three representative amphiphilic co-solvents. This correlates well with the amplitude of anomalies observed in these three binary mixtures. Part II deals with the topic of hydrophobic force law in water. In the introductory Chapter 7 of this part, we briefly discuss the concept of hydrophobicity which is believed to be of importance in understanding / explaining the initial processes involved in protein folding. We also discuss the experimental observations of Israelachvili (on the force between hydrophobic plates) and the empirical hydrophobic force law. We briefly touch upon the theoretical back-ground, including Lum-Chandler-Weeks theory. We conclude this chapter with a brief account of relevant and important in silico studies so far. In Chapter 8, we present our studies on Mercedes-Benz (MB) model – a two dimensional model system where circular disks interact with an anisotropic potential. This model was introduced by Ben-Naim and was later parametrized by Dill and co-workers to reproduce many of the anomalous properties of water. Using molecular dynamics simulation, we show that hydrophobic force law is indeed observed in MB model, with a correlation length of ξ=3.79. The simplicity of the model enables us to unravel the underlying physics that leads to this long range force between hydrophobic plates. In accordance with Lum-Chandler-Weeks theory, density fluctuation of MB particles (leading to cavitation) between the hydrophobic rods is clearly distinguishable – but it is not sufficiently long ranged, with density correlation extending only up to ζ=2.45. We find that relative orientation of MB molecules plays an important role in the origin of the hydrophobic force in long range. We define appropriate order parameters to capture the role of orientation, and briefly discuss a plausible approach of an orientation-dependent theory to explain this phenomenon. Part III consists of two chapters and focuses on the diffusion of a Brownian particle on a Gaussian random energy landscape. We articulate the rich history of the problem in the introductory Chapter 9. Despite broad applicability and historical importance of the problem, we have little knowledge about the effect of ruggedness on diffusion at a quantitative level. Every study seems to use the expression of Zwanzig [Proc. Natl. Acad. U.S.A, 85, 2029 (1988)] who derived the effective diffusion coefficient, Deff =D0 exp (-β2ε2 )for a Gaussian random surface with variance ε, but validity of the same has never been tested rigorously. In Chapter 10, we introduce two models of Gaussian random energy surface – a discrete lattice and a continuous field. Using computer simulation and theoretical analyses, we explore many different aspects of the diffusion process. We show that the elegant expression of Zwanzig can be reproduced ex-actly by Rosenfeld diffusion-entropy scaling relationship. Our simulations show that Zwanzig’s expression overestimates diffusion in the uncorrelated Gaussian random lattice – differing even by more than an order of magnitude at moderately high ruggedness (ε>3.0). The disparity originates from the presence of “three-site traps” (TST) on the landscape – which are formed by deep minima flanked by high barriers on either side. Using mean first passage time (MFPT) formalism, we derive an expression for the effective diffusion coefficient, Deff =D0 exp ( -β2ε2)[1 +erf (βε/2)]−1 in the presence of TSTs. This modified expression reproduces the simulation results accurately. Further, in presence of spatial correlation we derive a general expression, which reduces to Zwanzig’s form in the limit of infinite spatial correlation and to the above-mentioned equation in absence of correlation. The Gaussian random field has an inherent spatial correlation. Diffusion coefficient obtained from the Gaussian field – both by simulations and analytical methods – establish the effect of spatial correlation on random walk. We make special note of the fact that presence of TSTs at large ruggedness gives rise to an apparent breakdown of ergodicity of the type often encountered in glassy liquids. We characterize the same using non-Gaussian order parameter, and show that this “breakdown” scales with ruggedness following an asymptotic power law. We have discussed the scope of future work at the end of each chapter when-ever appropriate.

Systematic studies of basal nonsense suppression, orthogonality of tRNAPyl variants, and cross recognition between codons and tRNA anticodons are reported. E. coli displays detectable basal amber and opal suppression but shows a negligible ochre suppression. Although detectable, basal amber suppression is fully inhibited when a pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl_CUA pair is genetically encoded. trnaPyl_CUA is aminoacylated by an E. coli aminoacyl-tRNA synthetase at a low level, however, this misaminoacylation is fully inhibited when both PylRS and its substrate are present. Besides that it is fully orthogonal in E. coli and can be coupled with PylRS to genetically incorporate a NAA at an ochre codon, tRNAPyl_UUA is not able to recognize an UAG codon to induce amber suppression. This observation is in direct conflict with the wobble base pair hypothesis and enables using an evolved M. jannaschii tyrosyl-tRNA synthetase-tRNAPyl_UUA pair and the wild type or evolved PylRS-tRNAPyl_UUA pair to genetically incorporate two different NAAs at amber and ochre codons. tRNAPyl_UCA is charged by E. coli tryptophanyl-tRNA synthetase, thus not orthogonal in E. coli. Mutagenic studies of trnaPyl_UCA led to the discovery of its G73U form which shows a higher orthogonality. Mutating trnaPyl_CUA to trnaPyl_UCCU not only leads to the loss of the relative orthogonality of tRNAPyl in E. coli but also abolishes its aminoacylation by PylRS.