Investigations into the effect of nucleoside modifications on the physicochemical properties and biological function of DNA and RNA

This thesis explores the effect of chemical nucleoside modification on the physicochemical and biological properties of nucleic acids. Positional alteration on the Watson-Crick edge of purines and pyrimidines, the “C-H” edge of pyrimidines, as well as both the Hoogsteen and sugar edges of purines were attempted by means of copper catalyzed azide-alkyne cycloaddition. For this purpose, nucleic acid building blocks carrying terminal alkynes were synthesized and introduced into oligonucleotides by solid-phase oligonucleotide chemistry. rnOf particular interest was the effect of nucleoside modification on hydrogen bond formation with complementary nucleosides. The attachment of propargyl functionalities onto the N2 of guanosine and the N4 of 5-methylcytosine, respectively, followed by incorporation of the modified analogs into oligonucleotides, was successfully achieved. Temperature dependent UV-absorption melting measurements with duplexes formed between modified oligonucleotides and a variety of complementary strands resulted in melting temperatures for the respective duplexes. As a result, the effect that both the nature and the site of nucleoside modification have on base pairing properties could thus be assisted. rnTo further explore the enzymatic recognition of chemically modified nucleosides, the oligonucleotide containing the N2-modified guanosine derivative on the 5’-end, which was clicked to a fluorescent dye, was subjected to knockdown analyses of the eGFP reporter gene in the presence of increasing concentrations of siRNA duplexes. From these dose-dependent experiments, a clear effect of 5’-labeling on the knockdown efficiency could be seen. In contrast, 3’-labeling was found to be relatively insignificant.rn

Physicochemical properties and 3D geostatistical simulations of the Herten and the Descalvado aquifer analogs

This data set presents a comprehensive characterisation of the sedimentary structures from important groundwater hosting formations in Germany (Herten aquifer analog) and Brazil (Descalvado aquifer analog). Multiple 2-D outcrop faces are described in terms of hydraulic, thermal and chemical properties and interpolated in 3D using stochastic techniques. For each aquifer analog, multiple 3D realisations of the facies heterogeneity are provided using different stochastic simulations settings. These are unique analogue data sets that can be used by the wider community to implement approaches for characterising aquifer formations.

Sediment physicochemical properties condition pollutant association : a multivariate study of polybrominated diphenyl ethers on the Mendoza River irrigation areas

This work is a multidisciplinary environmental study that provides new insights into the relationships between sediment-organic matter characteristics and polybrominated diphenyl ethers (PBDEs) concentration. The aim of the present multivariate study was to correlate factors influencing PBDEs accumulation in sediment by using principal component analysis (PCA). Organic matter studies by Fourier Transform-Infrared spectroscopy and physicochemical analyses (Total Organic Carbon, pH, electrical conductivity) of sediment samples were considered for PCA. Samples were collected from an artificial irrigation network on the Mendoza River irrigation areas. PCA provided a comprehensive analysis of the studied variables, identifying two components that explained 63% of the data variance. Those factors were mainly associated to organic matter degradation degree, which represent a new insight into the relationships between organic matter in sediments and PBDEs fate. In this sense it was possible to determine that not only the content but also the type of organic matter (chemical structure) could be relevant when evaluating PBDEs accumulation and transport in the environment. Typification of organic matter may be a useful tool to predict more feasible areas where PBDE, may accumulate, as well as sediment transportation capability.

Physicochemical properties and fish occurrence in 35 Icelandic lakes housing Arctic charr (Salvelinus alpinus)

The common occurrence of parallel phenotypic patterns suggests that a strong relationship exists between ecological dynamics and micro-evolution. Comparative studies from a large number of populations under varying sets of ecological drivers could contribute to a better understanding of this relationship. We used data on morphology of arctic charr (Salvelinus alpinus) and ecological factors from 35 Icelandic lakes to test the hypothesis that morphological patterns among monomorphic charr populations from different lakes are related to interlake variation in ecological characteristics. There is extensive phenotypic diversity among populations of Icelandic charr, and populations are easily distinguished based on overall body morphology. The results obtained in the present study showed that the morphological diversity of charr was related to large-scale diversity in lake ecology. Variation in charr morphology was related to water origin (e.g. spring fed versus run-off), bedrock age, and fish community structure. The present study shows how various ecological factors can shape the biological diversity that we observe.

Time Evolution of Physicochemical Properties of Carrots During the Drying Process

This study is aimed to determine the properties of Nantes carrots while drying by hot air at three different temperatures (50, 60 and 70 ºC). The chemical properties evaluated were: moisture, pro- tein, fibre, ash, sugars and water activity, and the physical properties were: texture, color, density and porosity. The results showed that the drying at 70 ºC affected mostly the chemical properties analyzed. Regarding the texture, similar changes were recorded in terms of hardness, gumminess and chewiness at the temperature of 70 ºC that affected these properties the most. Regarding color, in general the vari- ations in a* and b* along drying were not meaningful, although some discoloration was observed (in- crease in L*). The porosity increased due to the decrease in humidity. The final porosity measured for the carrots dried at 70 ºC was; however, lower than those for 50 and 60 ºC.

The prediction and representation of phase equilibria and physicochemical properties in complex slag systems

The development of new experimental techniques for the determination of phase equilibria in complex slag systems, chemical thermodynamic, and viscosity models is reported. The new experimental data, and new thermodynamic and viscosity models, have been combined in a custom-designed computer software package to produce limiting operability diagrams for slag systems. These diagrams are used to describe phase equilibria and physicochemical properties in complex slag systems. The approach is illustrated with calculations on the system FeO-Fe2O3-CaO-SiO-Al2O3 at metallic iron saturation, slags produced in coal slagging gasifiers, and in the reprocessing of nonferrous smelting slags. This article was presented at the Mills Symposium Molten Metals, Slags and Glasses-Characterisation of Properties and Phenomena held in London in August 2000.

Impact of the counterion on the solubility and physicochemical properties of salts of carboxylic acid drugs

Aim: Salt formation is a widely used approach to improve the physicochemical and solid state properties of an active pharmaceutical ingredient. In order to better understand the relationships between the active drug, the selected counterion and the resultant salt form, crystalline salts were formed using four different carboxylic acid drugs and a closely related series of amine counterions. Thirty-six related crystalline salts were prepared, characterized and the relationship between solubility and dissolution behaviour and other properties of the salt and the counterion studied. Methods: Salts of four model acid drugs, gemfibrozil, flurbiprofen, ibuprofen and etodolac were prepared using the counterions butylamine, hexylamine, octylamine, benzylamine, cyclohexylamine, tert-butylamine, 2-amino-2-methylpropan-1-ol, 2-amino-2-methylpropan-1,3-diol andtris(hydroxymethyl)aminomethane. Salt formation was confirmed, the salts were characterized and their corresponding solubilities determined and rationalized with respect to the counterions' properties. Results and conclusion: The properties of the salt highly dependent on the nature of the counterion and, although there is considerable variation, some general conclusion can be drawn. For the alkyl amines series, increasing chain length leads to a reduction in solubility across all the acidic drugs studied and a reduction in melting point, thus contradicting simplistic relationships between solubility and melting point. Small, compact counterions consistently produce crystalline salts with high melting point accompanied with a modest improvement in solubility and the nature of hydrogen bonding between the ions has a major impact on the solubility. © 2012 Informa Healthcare USA, Inc.

Physicochemical properties of Pt-SO4/Al2O3 alkane oxidation catalysts

A series of sulfated alumina catalysts were synthesised by wet impregnation with sulfate-containing solutions. The degree of surface sulfation and corresponding surface acidity could be readily tuned by varying the molarity of impregnating solution. Strong acid treatments (>0.1 M) induced aluminium-sulfate crystallisation with a concomitant decrease in porosity and surface acidity. Platinum-doped sulfated aluminas showed enhanced activity towards methane, ethane and propane combustion. Activity scaled with the degree of accessible surface sulfate and platinum loading, however C-H bond scission appeared rate-limiting over both pure and presulfated aluminas. The magnitude of sulfate-promoted propane oxidation was greatest under heavily oxidising conditions (C3H6∶O2 > 1:20) but independent of Pt loading, confirming that support-mediated alkane activation is the dominant factor in the promotional mechanism.

Physicochemical properties of WOx/ZrO2 catalysts for palmitic acid esterification

A series of WOx/ZrO2 with various tungsten loadings was prepared via incipient-wetness impregnation of zirconium hydroxide. The resulting thermally processed materials were characterised by XRD, XPS, porosimetry, NH3-TPD and pyridine FTIR spectroscopy to elucidate their composition, morphology and acidity, and subsequently tested in the esterification of palmitic acid with methanol. Catalytic performance was strongly dependent upon calcination temperature and W surface density. Esterification activity increased with increasing surface W density, reaching a maximum at 8.9Wnm-2 corresponding to near monolayer coverage. Subsequent growth of crystalline WO3 lowered activity, consistent with a decrease in the density of active surface sites. Calcination temperatures as high as 800°C increased surface acidity and hence catalytic activity. The formation of polymeric tungstate species on zirconia is necessary to generate the Brönsted acid sites responsible for palmitic acid esterification under mild conditions. © 2014 Elsevier B.V.

Physicochemical properties of hydrogels for use in ophthalmology

This chapter deals with the physicochemical aspects of structure-property relationships in synthetic hydrogels, with particular reference to their application in optometry and ophthalmology. It demonstrates the ways in which the amount of water contained in the hydrogel network can be manipulated by changes in copolymer composition and illustrates the advantages and limitations imposed by use of water as a means of influencing surface, transport and mechanical properties of the gel. The chapter then illustrates how this basic understanding has formed a platform for the development of synthetic interpenetrating networks and macroporous materials, and of hybrids of natural and synthetic hydrogels. The behaviour of these more complex systems is not so centrally dominated by the equilibrium water content as is the case with homogeneous synthetic hydrogels, thus providing advantageous ways of extending the properties and applications of these interesting materials.

Chemical Stabilization and Physicochemical Properties of Soils, HR-97, Special Report, 1966

This project was initiated to gain a better understanding of the phenomena which affect the engineering behavior of soils containing colloidal size particles and to find chemical methods of treatment which could improve the engineering performance of such soils.

Chemical Stabilization and Physicochemical Properties of Soils, HR-97, Final Report, 1966

This project was initiated to gain a better understanding of the phenomena which affect the engineering behavior of soils containing colloidal size particles and to find chemical methods of treatment which could improve the engineering performance of such soils.