Matrix-assisted diffusion-ordered spectroscopy:application of surfactant solutions to the resolution of isomer spectra

The component spectra of a mixture of isomers with nearly identical diffusion coefficients cannot normally be distinguished in a standard diffusion-ordered spectroscopy (DOSY) experiment but can often be easily resolved using matrix-assisted DOSY, in which diffusion behaviour is manipulated by the addition of a co-solute such as a surfactant. Relatively little is currently known about the conditions required for such a separation, for example, how the choice between normal and reverse micelles affects separation or how the isomer structures themselves affect the resolution. The aim of this study was to explore the application of sodium dodecyl sulfate (SDS) normal micelles in aqueous solution and sodium 1,4-bis(2-ethylhexyl)sulfosuccinate (AOT) aggregates in chloroform, at a range of concentrations, to the diffusion resolution of some simple model sets of isomers such as monomethoxyphenols and short chain alcohols. It is shown that SDS micelles offer better resolution where these isomers differ in the position of a hydroxyl group, whereas AOT aggregates are more effective for isomers differing in the position of a methyl group. For both the normal SDS micelles and the less well-defined AOT aggregates, differences in the resolution of the isomers can in part be rationalised in terms of differing degrees of hydrophobicity, amphiphilicity and steric effects. Copyright © 2012 John Wiley & Sons, Ltd.

Fatty acids, monocytes and ageing

Elevated free fatty acids (FFA) are a feature of ageing and a risk factor for metabolic disorders such as cardiovascular disease (CVD) and type-2 diabetes (T2D). Elevated FFA contribute to insulin resistance, production of inflammatory cytokines and expression of adhesion molecules on immune cells and endothelial cells, risk factors for CVD and T2D. Molecular mechanisms of FFA effects on monocyte function and how FFA phenotype is affected by healthy ageing remain poorly understood. This thesis evaluated the effects of the two major FFA in plasma, oleate and palmitate on monocyte viability, cell surface antigen expression, and inflammatory activation in THP-1 monocytes. Palmitate but not oleate increased cell surface expression of CD11b and CD36 after 24h, independent of mitochondrial superoxide, but dependent on de novo synthesis of ceramides. LPS-mediated cytokine production in THP-1 monocytes was enhanced and decreased following incubation with palmitate and oleate respectively. In a model of monocyte-macrophage differentiation, palmitate induced a pro-inflammatory macrophage phenotype which required de novo ceramide synthesis, whilst oleate reduced cytokine secretion, producing a macrophage with enhanced clearance apoptotic cells. Plasma fatty acid analysis in young and mid-life populations revealed age-related increases in both the SFA and MUFA classes, especially the medium and very long chain C14 and C24 fatty acids, which were accompanied by increases in the estimated activities of desaturase enzymes. Changes were independently correlated with increased PBMC CD11b, plasma TNF-a and insulin resistance. In conclusion, the pro-atherogenic phenotype, enhanced LPS responses in monocytes, and pro-inflammatory macrophage in the presence of palmitate but not oleate is reliant upon de novo ceramide synthesis. Age-related increases in inflammation, cell surface integrin expression are related to increases in both the MUFA and SFA fatty acids, which in part may be explained by altered de novo fatty acid synthesis.

Hierarchical macroporous-mesoporous SBA-15 sulfonic acid catalysts for biodiesel synthesis

Hierarchical macroporous-mesoporous SBA-15 silicas have been synthesised via dual-templating routes employing liquid crystalline surfactants and polystyrene beads. These offer high surface areas and well-defined, interconnecting macro- and mesopore networks with respective narrow size distributions around 300 nm and 3-5 nm for polystyrene:tetraethoxysilane ratios ≥2:1. Subsequent functionalisation with propylsulfonic acid yields the first organized, macro-mesoporous solid acid catalyst. The enhanced mass transport properties of these new bi-modal solid acid architectures confer significant rate enhancements in the transesterification of bulky glyceryl trioctanoate, and esterification of long chain palmitic acid, over pure mesoporous analogues. This paves the way to the wider application of hierarchical catalysts in biofuel synthesis and biomass conversion. © 2010 The Royal Society of Chemistry.

The role of lipid geometry in designing liposomes for the solubilisation of poorly water soluble drugs

Liposomes are well recognised for their ability to improve the delivery of a range of drugs. More commonly they are applied for the delivery of water-soluble drugs, but given their structural attributes, they can also be employed as solubilising agents for low solubility drugs as well as drug targeting agents. To further explore the potential of liposomes as solubilising agents, we have investigated the role of bilayer packaging in promoting drug solubilisation in liposome bilayers. The effect of alkyl chain length and symmetry was investigated to consider if using 'mis-matched' phospholipids could create 'voids' within the bilayers, and enhance bilayer loading capacity. Lipid packing was investigated using Langmuir studies, which demonstrated that increasing the alkyl chain length enhanced lipid packing, with condensed monolayers forming, whilst asymmetric lipids formed less condensed monolayers. However, this more open packing did not translate into improved drug loading, with the longer chain, condensed bilayers formed from long-chain, saturated lipids offering higher drug loading capacity. These studies demonstrate that liposomes formulated from longer chain, saturated lipids offer enhanced solubilisation capacity. However the molecular size, rather than lipophilicity, of the drug to be incorporated was also a key factor dominating bilayer incorporation efficiency. © 2012 Elsevier B.V. All rights reserved.

Synthesis and screening of potential antimicrobial compounds

Tuberculosis (TB), an infection caused by human pathogen Mycobacterium tuberculosis, continues to kill millions each year and is as prevalent as it was in the pre-antimicrobial era. With the emergence of continuously-evolving multi-drug resistant strains (MDR) and the implications of the HIV epidemic, it is crucial that new drugs with better efficacy and affordable cost are developed to treat TB. With this in mind, the first part of this thesis discusses the synthesis of libraries of derivatives of pyridine carboxamidrazones, along with cyclised (1,2,4-triazole and 1,2,4-oxadiazole) and fluorinated analogues. Microbiological screening against M. tuberculosis was carried out at the TAACF, NIAID and IDRI (USA). This confirmed the earlier findings that 2-pyridyl-substituted carboxamidrazones were more active than the 4-pyridyl-substituted carboxamidrazones. Another important observation was that upon cyclisation of these carboxamidrazones, a small number of the triazoles retained their activity while in most of the remaining compounds the activity was diminished. This might be attributed to the significant increase in logP value caused by cyclisation of these linear carboxamidrazones, resulting in high lipophilicity and decreased permeability. Another reason might be that the rigidity conferred upon the compound due to cyclisation, results in failure of the compound to fit into the active site of the putative target enzyme. In order to investigate the potential change to the compounds’ metabolism in the organism and/or host, the most active compounds were selected and a fluorine atom was introduced in the pyridine ring. The microbiological results shows a drastic improvement in the activity of the fluorinated carboxamidrazone amides as compared to their non fluorinated counterpart. This improvement in the activity could possibly be the result of the increased cell permeability caused by the fluorine. In a subsidiary strand, a selection of long-chain , -unsaturated carboxylic esters, -keto, -hydroxy carboxylic esters and -keto, -hydroxy carboxylic esters, structurally similar to mycolic acids, were synthesised. The microbiological data revealed that one of the open chain compound was active against the Mycobacterium tuberculosis H37Rv strain and some resistant isolates. The possible compound activity could be its potential to disrupt mycobacterial cell wall synthesis by interfering with the FAS-II pathway.

Indirect ties in knowledge networks:a social network analysis with ordered weighted averaging operators

This PhD thesis analyses networks of knowledge flows, focusing on the role of indirect ties in the knowledge transfer, knowledge accumulation and knowledge creation process. It extends and improves existing methods for mapping networks of knowledge flows in two different applications and contributes to two stream of research. To support the underlying idea of this thesis, which is finding an alternative method to rank indirect network ties to shed a new light on the dynamics of knowledge transfer, we apply Ordered Weighted Averaging (OWA) to two different network contexts. Knowledge flows in patent citation networks and a company supply chain network are analysed using Social Network Analysis (SNA) and the OWA operator. The OWA is used here for the first time (i) to rank indirect citations in patent networks, providing new insight into their role in transferring knowledge among network nodes; and to analyse a long chain of patent generations along 13 years; (ii) to rank indirect relations in a company supply chain network, to shed light on the role of indirectly connected individuals involved in the knowledge transfer and creation processes and to contribute to the literature on knowledge management in a supply chain. In doing so, indirect ties are measured and their role as means of knowledge transfer is shown. Thus, this thesis represents a first attempt to bridge the OWA and SNA fields and to show that the two methods can be used together to enrich the understanding of the role of indirectly connected nodes in a network. More specifically, the OWA scores enrich our understanding of knowledge evolution over time within complex networks. Future research can show the usefulness of OWA operator in different complex networks, such as the on-line social networks that consists of thousand of nodes.

Cellular impermeability and uptake of biocides and antibiotics in Gram-positive bacteria and mycobacteria

Gram-positive bacteria possess a permeable cell wall that usually does not restrict the penetration of antimicrobials. However, resistance due to restricted penetration can occur, as illustrated by vancomycin-intermediate resistant Staphylococcus aureus strains (VISA) which produce a markedly thickened cell wall. Alterations in these strains include increased amounts of nonamidated glutamine residues in the peptidoglycan and it is suggested that the resistance mechanism involves 'affinity trapping' of vancomycin in the thickened cell wall. VISA strains have reduced doubling times, lower sensitivity to lysostaphin and reduced autolytic activity, which may reflect changes in the D-alanyl ester content of the wall and membrane teichoic acids. Mycobacterial cell walls have a high lipid content, which is assumed to act as a major barrier to the penetration of antimicrobial agents. Relatively hydrophobic antibiotics such as rifampicin and fluoroquinolones may be able to cross the cell wall by diffusion through the hydrophobic bilayer composed of long chain length mycolic acids and glycolipids. Hydrophilic antibiotics and nutrients cannot diffuse across this layer and are thought to use porin channels which have been reported in many species of mycobacteria. The occurrence of porins in a lipid bilayer supports the view that the mycobacterial wall has an outer membrane analogous to that of gram-negative bacteria. However, mycobacterial porins are much less abundant than in the gram-negative outer membrane and allow only low rates of uptake for small hydrophilic nutrients and antibiotics.

Uncertainty propagation in the model web:a case study with e-Habitat

eHabitat is a Web Processing Service (WPS) designed to compute the likelihood of finding ecosystems with equal properties. Inputs to the WPS, typically thematic geospatial "layers", can be discovered using standardised catalogues, and the outputs tailored to specific end user needs. Because these layers can range from geophysical data captured through remote sensing to socio-economical indicators, eHabitat is exposed to a broad range of different types and levels of uncertainties. Potentially chained to other services to perform ecological forecasting, for example, eHabitat would be an additional component further propagating uncertainties from a potentially long chain of model services. This integration of complex resources increases the challenges in dealing with uncertainty. For such a system, as envisaged by initiatives such as the "Model Web" from the Group on Earth Observations, to be used for policy or decision making, users must be provided with information on the quality of the outputs since all system components will be subject to uncertainty. UncertWeb will create the Uncertainty-Enabled Model Web by promoting interoperability between data and models with quantified uncertainty, building on existing open, international standards. It is the objective of this paper to illustrate a few key ideas behind UncertWeb using eHabitat to discuss the main types of uncertainties the WPS has to deal with and to present the benefits of the use of the UncertWeb framework.

Optimisation of chromatographic separation of oxidised phospholipids and detection with targeted approaches provides greater coverage of the oxidised lipidome

Phospholipid oxidation by adventitious damage generates a wide variety of products with potentially novel biological activities that can modulate inflammatory processes associated with various diseases. To understand the biological importance of oxidised phospholipids (OxPL) and their potential role as disease biomarkers requires precise information about the abundance of these compounds in cells and tissues. There are many chemiluminescence and spectrophotometric assays available for detecting oxidised phospholipids, but they all have some limitations. Mass spectrometry coupled with liquid chromatography is a powerful and sensitive approach that can provide detailed information about the oxidative lipidome, but challenges still remain. The aim of this work is to develop improved methods for detection of OxPLs by optimisation of chromatographic separation through testing several reverse phase columns and solvent systems, and using targeted mass spectrometry approaches. Initial experiments were carried out using oxidation products generated in vitro to optimise the chromatography separation parameters and mass spectrometry parameters. We have evaluated the chromatographic separation of oxidised phosphatidylcholines (OxPCs) and oxidised phosphatidylethanolamines (OXPEs) using C8, C18 and C30 reverse phase, polystyrene – divinylbenzene based monolithic and mixed – mode hydrophilic interaction (HILIC) columns, interfaced with mass spectrometry. Our results suggest that the monolithic column was best able to separate short chain OxPCs and OxPEs from long chain oxidised and native PCs and PEs. However, variation in charge of polar head groups and extreme diversity of oxidised species make analysis of several classes of OxPLs within one analytical run impractical. We evaluated and optimised the chromatographic separation of OxPLs by serially coupling two columns: HILIC and monolith column that provided us the larger coverage of OxPL species in a single analytical run.

Water temperature reconstructions based on paired Uk'37 and Tex86 records, and paired surface and subsurface Mg/Ca records

This dataset contains the collection of available published paired Uk'37 and Tex86 records spanning multi-millennial to multi-million year time scales, as well as a collection of Mg/Ca-derived temperatures measured in parallel on surface and subsurface dwelling foraminifera, both used in the analyses of Ho and Laepple, Nature Geoscience 2016. As the signal-to-noise ratios of proxy-derived Holocene temperatures are relatively low, we selected records that contain at least the last deglaciation (oldest sample >18kyr BP).

Terrigenous biomarker proxies analysed in the Amazon River system

Paleoenvironmental studies based on terrigenous biomarker proxies from sediment cores collected close to the mouth of large river systems rely on a proper understanding of the processes controlling origin, transport and deposition of biomarkers. Here, we contribute to the understanding of these processes by analyzing long-chain n-alkanes from the Amazon River system. We use the dD composition of long-chain n-alkanes from river bed sediments from the Amazon River and its major tributaries, as well as marine core-top samples collected off northeastern South America as tracers for different source areas. The d13C composition of the same compounds is used to differentiate between long-chain n-alkanes from modern forest vegetation and petrogenic organic matter. Our d13C results show depleted d13C values (-33 to -36 per mil) in most samples, indicating a modern forest source for most of the samples. Enriched values (-31 to -33 per mil) are only found in a few samples poor in organic carbon indicating minor contributions from a fossil petrogenic source. Long-chain n-alkane dD analyses show more depleted values for the western tributaries, the Madeira and Solimões Rivers (-152 to -168 per mil), while n-alkanes from the lowland tributaries, the Negro, Xingu and Tocantins Rivers (-142 to -154 per mil), yield more enriched values. The n-alkane dD values thus reflect the mean annual isotopic composition of precipitation, which is most deuterium-depleted in the western Amazon Basin and more enriched in the eastern sector of the basin. Samples from the Amazon estuary show a mixed long-chain n-alkane dD signal from both eastern lowland and western tributaries. Marine core-top samples underlying the Amazon freshwater plume yield dD values similar to those from the Amazon estuary, while core-top samples from outside the plume showed more enriched values. Although the variability in the river bed data precludes quantitative assessment of relative contributions, our results indicate that long-chain n-alkanes from the Amazon estuary and plume represent an integrated signal of different regions of the onshore basin. Our results also imply that n-alkanes are not extensively remineralized during transport and that the signal at the Amazon estuary and plume includes refractory compounds derived from the western sector of the Basin. These findings will aid in the interpretation of plant wax-based records of marine sediment cores collected from the adjacent ocean.

(Table 1) TOC, d13C, concentrations of C37 alkenones, crenarchaeol and GDGTs of turbidites

One of the primary prerequisites for the application of organic proxies is that they should not be substantially affected by diagenesis. However, studies have shown that oxic degradation of biomarker lipids can affect their relative distribution. We tested the diagenetic stability of the UK'37 and TEX86 palaeothermometers upon long term oxygen exposure. For this purpose, we studied the distributions of alkenones and glycerol dialkyl glycerol tetraethers (GDGTs) in different sections of turbidites at the Madeira Abyssal Plain (MAP) that experienced different degrees of oxygen exposure. Sediments were deposited anoxically on the shelf and then transported by turbidity currents to the MAP, which has oxic bottom water. This resulted in partial degradation of the turbidite organic matter as a result of long term exposure to oxic bottom water. Concentrations of GDGTs and alkenones were reduced by one to two orders of magnitude in the oxidized parts of the turbidites compared to the unoxidized parts, indicating substantial degradation. High-resolution analysis of the Pleistocene F-turbidite showed that the UK'37 index of long chain alkenones increased only slightly (0.01, corresponding to <0.5 °C) in the oxidized part of the turbidite, suggesting minor preferential degradation of the C37:3 alkenone, in agreement with previous studies. TEX86 values showed a small increase (0.02, corresponding to ~2 °C) in the F-turbidite, like UK'37 , while for other Pliocene/Miocene turbidites it either remained unchanged or decreased substantially (up to 0.06, corresponding to ~6 °C). Previous observations showed that the BIT index, a proxy for the contribution of soil organic matter to total organic carbon, was always substantially higher in the oxidized part in all the turbidites, as a result of preferential degradation of marine-derived GDGTs. This relative increase in soil-derived GDGTs affects TEX86, as the isoprenoid GDGT distribution on the continent can be quite different from that in the marine environment. Our results indicate that the organic proxies are affected by long term oxic degradation to different extents; this should be taken into account when applying these proxies in palaeoceanographic studies of sediments which have been exposed to prolonged oxic degradation.

Estudo teórico de intermediários tetraédricos acidez / basicidade e estereosseletividade enzimáticos

The present work aimed first, the theoretical study of tetrahedral intermediate stability formed from carbonyl addition reactions using the second (MP2) and third (MP3) order Møller–Plesset perturbation theory. Linear correlations between electronic energy difference of reactions with Wiberg Indexes and C-O bond lengths were obtained, and was observed that the stability of adducts formed depends directly of electronic density involved between these atoms. The knowing of electronic parameters of these structures has an important hole due to the large use on reactions that in his course forms this tetrahedral intermediate. Employing the ONIOM (B3LYP:AMBER) methodology, was evaluated the stereoselectivity of a enzymatic reaction between CAL B enzyme and a long chain ester. In this study, were obtained the electronic energies of ground state and intermediate state of transesterification rate-determing step from two possible proquirals faces Re and Si. The objective was study the enantioselectivity of CAL B and rationalizes it using quantum theory of atoms in molecules (QTAIM). A theoretical study employing inorganic compounds was performed using ab initio CBS-QB3 method aiming to find a link between thermodynamic and equilibrium involving acids and bases. The results observed showed an excellent relationship between difference in Gibbs free energy, ΔG of acid dissociation reaction and ΔG of hydrolysis reaction of the corresponding conjugate base. It was also observed, a relationship between ΔG of hydrolysis reaction of conjugate acids and their corresponding atomic radius showing that stability plays an important role in hydrolysis reactions. The importance of solvation in acid/base behavior when compared to theoretical and experimental ΔG´s also was evaluated.

Catalisadores bifuncionais à base de silicoaluminofosfato e fosfatos de nióbio para emprego em reações de hidroisomerização e hidrocraqueamento do n-hexadecano

Lubricants and cutting middle distillates typically have large amounts of n-paraffins to increase its freezing point and fluidity. Accordingly, the removal of n-paraffins of long chain lubricants oils and diesel is essential to get a product with good cold flow properties. The development of new catalysts, which exhibit thermal stability and catalytic activity for the hydroisomerization reaction is still a challenge. Thus, silicoaluminophosphates (SAPO) were synthesized by different routes. Have been used also post-synthesis treatment for obtaining hybrid structures and others synthesis have been carried out with mesoporous template (soft and hard-template). Therefore, SAPO have been impregnated with H2PtCl6 solution by the incipient wetness method. Then assessments of catalytic activities in hydroisomerization and hydrocracking reactions of hexadecane have been held. Besides SAPO, niobium phosphate - NbP - were also impregnated with platinum and evaluated in the same reaction. After impregnation, these catalysts have been characterized by X-ray diffraction (XRD), nitrogen adsorption, infrared spectroscopy with adsorbed pyridine (IV-PY), scanning electron microscopy (SEM) and resonance nuclear magnetic 29Si (29Si-NMR). The characterization results by XRD have shown that it has been possible to obtain mesoporous SAPOs. However, for the syntheses with soft template there was collapse of the structure after removal of the organic template. Even so, these catalysts have been actives. It was possible to obtain hybrid materials through the synthesis of SAPO-11 made with hard templates and by means of post-synthesis treatments samples of SAPO-11. Moreover, NbP has shown characteristic XRD of amorphous materials, with high acidity and were active in the conversion of hexadecane.

Catalisadores bifuncionais à base de silicoaluminofosfato e fosfatos de nióbio para emprego em reações de hidroisomerização e hidrocraqueamento do n-hexadecano

Lubricants and cutting middle distillates typically have large amounts of n-paraffins to increase its freezing point and fluidity. Accordingly, the removal of n-paraffins of long chain lubricants oils and diesel is essential to get a product with good cold flow properties. The development of new catalysts, which exhibit thermal stability and catalytic activity for the hydroisomerization reaction is still a challenge. Thus, silicoaluminophosphates (SAPO) were synthesized by different routes. Have been used also post-synthesis treatment for obtaining hybrid structures and others synthesis have been carried out with mesoporous template (soft and hard-template). Therefore, SAPO have been impregnated with H2PtCl6 solution by the incipient wetness method. Then assessments of catalytic activities in hydroisomerization and hydrocracking reactions of hexadecane have been held. Besides SAPO, niobium phosphate - NbP - were also impregnated with platinum and evaluated in the same reaction. After impregnation, these catalysts have been characterized by X-ray diffraction (XRD), nitrogen adsorption, infrared spectroscopy with adsorbed pyridine (IV-PY), scanning electron microscopy (SEM) and resonance nuclear magnetic 29Si (29Si-NMR). The characterization results by XRD have shown that it has been possible to obtain mesoporous SAPOs. However, for the syntheses with soft template there was collapse of the structure after removal of the organic template. Even so, these catalysts have been actives. It was possible to obtain hybrid materials through the synthesis of SAPO-11 made with hard templates and by means of post-synthesis treatments samples of SAPO-11. Moreover, NbP has shown characteristic XRD of amorphous materials, with high acidity and were active in the conversion of hexadecane.