A Molecular Rotor that Measures Dynamic Changes of Lipid Bilayer Viscosity Caused by Oxidative Stress

Oxidation of cellular structures is typically an undesirable process that can be a hallmark of certain diseases. On the other hand, photooxidation is a necessary step of photodynamic therapy (PDT), a cancer treatment causing cell death upon light irradiation. Here, the effect of photooxidation on the microscopic viscosity of model lipid bilayers constructed of 1,2-dioleoyl-sn-glycero-3-phosphocholine has been studied. A molecular rotor has been employed that displays a viscosity-dependent fluorescence lifetime as a quantitative probe of the bilayer's viscosity. Thus, spatially-resolved viscosity maps of lipid photooxidation in giant unilamellar vesicles (GUVs) were obtained, testing the effect of the positioning of the oxidant relative to the rotor in the bilayer. It was found that PDT has a strong impact on viscoelastic properties of lipid bilayers, which ‘travels’ through the bilayer to areas that have not been irradiated directly. A dramatic difference in viscoelastic properties of oxidized GUVs by Type I (electron transfer) and Type II (singlet oxygen-based) photosensitisers was also detected

Molecular rotors as sensors of microscopic viscosity and temperature

Microscale viscosity is a key parameter that defines the physical makeup of a system, controlling viscoelastic properties of microscopic objects. Additionally, microviscosity within a living cell controls the rate of mass transport through a cell and is hence intimately linked to the activity of a cell. Therefore, measuring viscosity on a microscale represents an important challenge within both physical and biological sciences. So far, one of the most informative and convenient ways for doing this is to use fluorescent 'molecular rotors', which are the viscosity-sensitive fluorophores. The characterisation and application of several previously unexplored molecular rotors are the main topics explored in this thesis. First, porphyrin dimers are examined and characterised as dual viscosity sensors capable of measuring viscosity using their two photophysical parameters: the ratio of two peaks in the fluorescence spectrum and the fluorescence lifetime. The dimer was thus characterised as an attractive dual viscosity sensor displaying absorption and emission in the tissue optical window. Then the porphyrin dimers are applied for imaging microviscosity in lipid monolayers and bilayers. Finally, the porphyrin dimer is used for sensing dynamic change of microviscosity in lipid monolayers and living cells undergoing oxidation by singlet oxygen. Secondly, the changes in viscosity of model lipid membranes under oxidation are further examined using the molecular rotor Bdp-C10, which fully embeds in the lipid tail region of the lipid bilayer. Changes in viscosity are measured at several different bilayer positions of the oxidant relative to the rotor: on the surface, inside the tail region and outside the bilayer in the aqueous phase. Additionally, we report striking differences in the dynamic viscosity change during Type I and Type II photosensitisations and uncover the mechanistic details of the oxidation utilising the ability of molecular rotors to provide spatially resolved information. In the last two chapters, we examine if molecular rotors are sensitive to temperature, which is an important topic that has not previously investigated. The molecular rotors demonstrate contrasting types of temperature sensitivity. Lastly, the temperature-dependence of molecular rotors was put to use by employing Kiton Red for measuring temperature in laser-heated aerosol particles and by using one of the porphyrin dimers for performing the first ever to our knowledge dual viscosity and temperature measurement on a microscopic scale.Open Acces

Enhanced lifetime of methane bubble streams within the deep ocean

We have made direct comparisons of the dissolution and rise rates of methane and argon bubbles experimentally released in the ocean at depths from 440 to 830 m. The bubbles were injected from the ROV Ventana into a box open at the top and the bottom, and imaged by HDTV while in free motion. The vehicle was piloted upwards at the rise rate of the bubbles. Methane and argon show closely similar behavior at depths above the methane hydrate stability field. Below that boundary (∼520 m) markedly enhanced methane bubble lifetimes are observed, and are attributed to the formation of a hydrate skin. This effect greatly increases the ease with which methane gas released at depth, either by natural or industrial events, can penetrate the shallow ocean layers

The use of ontologies for effective knowledge modelling and information retrieval

© 2017 The dramatic increase in the use of knowledge discovery applications requires end users to write complex database search requests to retrieve information. Such users are not only expected to grasp the structural complexity of complex databases but also the semantic relationships between data stored in databases. In order to overcome such difficulties, researchers have been focusing on knowledge representation and interactive query generation through ontologies, with particular emphasis on improving the interface between data and search requests in order to bring the result sets closer to users research requirements. This paper discusses ontology-based information retrieval approaches and techniques by taking into consideration the aspects of ontology modelling, processing and the translation of ontological knowledge into database search requests. It also extensively compares the existing ontology-to-database transformation and mapping approaches in terms of loss of data and semantics, structural mapping and domain knowledge applicability. The research outcomes, recommendations and future challenges presented in this paper can bridge the gap between ontology and relational models to generate precise search requests using ontologies. Moreover, the comparison presented between various ontology-based information retrieval, database-to-ontology transformations and ontology-to-database mappings approaches provides a reference for enhancing the searching capabilities of massively loaded information management systems

Synthesis and spectroscopy of benzylamine-substituted BODIPYs for bioimaging

Three new boron dipyrromethene (BODIPY) dyes substituted with a benzylamino group at the 3-position have been synthesized from halogenated BODIPYs by nucleophilic substitution. The spectroscopic and photophysical properties have been explored in different solvents and have been compared with an analogous 8- benzylaminoBODIPY derivative. The position of the benzylamino group has a significant influence on the spectral band positions, fluorescence quantum yields, and fluorescence lifetimes. The 8- benzylaminoBODIPY emits in the blue range, whereas the 3- substituted shows green fluorescence. Additionally, the extension of the conjugation at the 5-position of 3-benzylaminoBODIPY produces a bathochromic shift of the absorption and emission spectra. The solvent effect on their spectroscopic features has been investigated using the generalized Catalán solvent scales. Quantum-chemical calculations have been performed to assess the effect of the position of the substitution on the spectroscopic properties. Finally, the BODIPY dyes have been employed as probes in fluorescence lifetime imaging of living cells, demonstrating their high potential for bioimaging