Optical Bloch equations and enhanced decay of Rabi oscillations in strong driving fields

Optical Bloch equations are widely used for describing dynamics in a system consisting molecules, electromagnetic waves, and a thermal bath. We analyze applicability of these equations to a single molecule imbedded in a solid matrix. Classical Bloch equations and the limits of their applicability are derived from more general master equations. Simple and intuitively appealing picture based on stochastic Bloch equations shows that at low temperatures, contrary to common believes, a strong driving field can not only suppress but can also increase decay rates of Rabi oscillations. A physical system where predicted effects can be observed experimentally is suggested. (c) 2005 Elsevier B.V. All rights reserved.

Assembly of Human Papillomavirus Type-16 Virus-Like Particles: Multifactorial Study of Assembly and Competing Aggregation

Pentameric capsomeres of human papillomavirus capsid protein L1 expressed in Escherichia coli self-assemble into virus-like particles (VLPs) in vitro. A multifactorial experimental design was used to explore a wide range of solution conditions to optimize the assembly process. The degree of assembly was measured using an enzyme-linked immunosorbent assay, and a high-throughput turbidity assay was developed to monitor competing aggregation. The presence of zinc ions in the assembly buffer greatly increased the incidence of aggregation and had to be excluded from the experiment for meaningful analysis. Assembly of VLPs was optimal at a pH of about 6.5, calcium and sodium ions had no measurable effect, and dithiothreitol and glutathione inhibited assembly. Tryptophan fluorescence spectroscopy demonstrated that an increase in urea concentration reduced the rate of VLP formation but had no effect on the final concentration of assembled VLPs. This study demonstrates the use of the hanging-drop vapor-diffusion crystallization method to screen for conditions that promote aggregation and the use of tryptophan fluorescence spectroscopy for real-time monitoring of the assembly process.

Determination of the orientational distribution and orientation factor for transfer between membrane-bound fluorophores using a confocal microscope

Orientational fluorophores have been a useful tool in physical chemistry, biochemistry, and more recently structural biology due to the polarized nature of the light they emit and that fact that energy can be transferred between them. We present a practical scheme in which measurements of the intensity of emitted fluorescence can be used to determine limits on the mean and distribution of orientation of the absorption transition moment of membrane-bound. uorophores. We demonstrate how information about the orientation of. uorophores can be used to calculate the orientation factor k(2) required for use in FRET spectroscopy. We illustrate the method using images of AlexaFluor probes bound to MscL mechanosensitive transmembrane channel proteins in spherical liposomes.

The significance of hand wash compliance on the transfer of dermal lipids in contact lens wear

Aim: The aim of this study was to assess the impact of hand washing regimes on lipid transference to contact lenses. The presence of lipids on contact lenses can affect visual acuity and enhance spoilation. Additionally, they may even mediate and foster microbial transfer and serve as a marker of potential dermal contamination. Methods and materials: A social hand wash and the Royal College of Nursing (RCN) hand wash were investigated. A 'no-wash regime' was used as control. The transfer of lipids from the hand was assessed by Thin Layer Chromatography (TLC). Lipid transference to the contact lenses was studied through fluorescence spectroscopy (FS). Results: Iodine staining, for presence of lipids, on TLC plates indicated the 'no-wash regime' score averaged at 3.4 ± 0.8, the social wash averaged at 2.2 ± 0.9 and the RCN averaged at 1.2 ± 0.3 on a scale of 1-4. The FS of lipids on contact lenses for 'no washing' presented an average of 28.47 ± 10.54 fluorescence units (FU), the social wash presented an average of 13.52 ± 11.12. FU and the RCN wash presented a much lower average 6.47 ± 4.26. FU. Conclusions: This work demonstrates how the method used for washing the hands can affect the concentration of lipids, and the transfer of these lipids onto contact lenses. A regime of hand washing for contact lens users should be standardised to help reduce potentially transferable species present on the hands. © 2011 British Contact Lens Association.

A novel plasma etching and emission monitoring system (PEEMS) to assess protein and lipid spoilation for hydrogel contact lenses

The work presents a new method that combines plasma etching with extrinsic techniques to simultaneously measure matrix and surface protein and lipid deposits. The acronym for this technique is PEEMS - Plasma Etching and Emission Monitoring System. Previous work has identified the presence of proteinaceous and lipoidal deposition on the surface of contact lenses and highlighted the probability that penetration of these spoilants will occur. This technique developed here allows unambiguous identification of the depth of penetration of spoilants to be made for various material types. It is for this reason that the technique has been employed in this thesis. The technique is applied as a 'molecular' scalpel, removing known amounts of material from the target. In this case from both the anterior .and posterior surfaces of a 'soft' contact lens. The residual material is then characterised by other analytical techniques such as UV/visible .and fluorescence spectroscopy. Several studies have be.en carried out for both in vivo and in vitro spoilt materials. The analysis and identification of absorbed protein and lipid of the substrate revealed the importance of many factors in the absorption and adsorption process. The effect of the material structure, protein nature (in terms of size, shape and charge) and environment conditions were examined in order to determine the relative uptake of tear proteins. The studies were extended to real cases in order to study the. patient dependent factors and lipoidal penetration.

The sedimentology and diagenesis of Lower Permian (Rotliegend) sediments: (onshore U.K. and southern North Sea). Available in 2 volumes.

The thesis provides a comparative study of both sedimentology and diagenesis of Lower Permian (Rotliegend) strata, onshore and offshore U.K. (Southern North Sea). Onshore formations studied include the Bridgnorth, Penrith and Hopeman Sandstone, and are dominated by aeolian facies, with lesser amounts of interbedded fluvial sediments. Aeolian and fluvial strata in onshore basins typically grade laterally into alluvial fan breccias at basin margins. Onshore basins represent proximal examples of Rotliegend desert sediments. The Leman Sandstone Formation of the Ravenspurn area in the Southern North Sea displays a variety of facies indicative of a distal sedimentological setting; Aeolian, fluvial, sabkha, and playa lake sediments all being present. "Sheet-like" geometry of stratigraphical units within the Leman Sandstone, and alternation of fluvial and aeolian deposition was climatically controlled. Major first order bounding surfaces are laterally extensive and were produced by lacustrine transgression and regression from the north-west. Diagenesis within Permian strata was studied using standard petrographic microscopy, scanning electron microscopy, cold cathodo-Iuminescence, X-ray diffraction clay analysis, X-ray fluorescence spectroscopy, fluid inclusion microthermometry, and K-Ar dating of illites. The diagenesis of Permian sediments within onshore basins is remarkably similar, and a paragenetic sequence of early haematite, illitic clays, feldspar, kaolinite, quartz and late calcite is observed. In the Leman Sandstone formation, authigenic mineralogy is complex and includes early quartz, sulphates and dolomite, chlorite, kaolinite, late quartz, illite and siderite. Primary lithological variation, facies type, and the interdigitation and location of facies within a basin are important initial controls upon diagenesis. Subsequently, burial history, structure, the timing of gas emplacement, and the nature of sediments within underlying formations may also exersize significant controls upon diagenesis within Rotliegend strata.

Do ‘passive’ medical titanium surfaces deteriorate in service in the absence of wear?

Globally, more than 1000 tonnes of titanium (Ti) is implanted into patients in the form of biomedical devices on an annual basis. Ti is perceived to be ‘biocompatible’ owing to the presence of a robust passive oxide film (approx. 4 nm thick) at the metal surface. However, surface deterioration can lead to the release of Ti ions, and particles can arise as the result of wear and/or corrosion processes. This surface deterioration can result in peri-implant inflammation, leading to the premature loss of the implanted device or the requirement for surgical revision. Soft tissues surrounding commercially pure cranial anchorage devices (bone-anchored hearing aid) were investigated using synchrotron X-ray micro-fluorescence spectroscopy and X-ray absorption near edge structure. Here, we present the first experimental evidence that minimal load-bearing Ti implants, which are not subjected to macroscopic wear processes, can release Ti debris into the surrounding soft tissue. As such debris has been shown to be pro-inflammatory, we propose that such distributions of Ti are likely to effect to the service life of the device.

Hydroxyl radical generation by cactus-like copper oxide nanoporous carbon catalysts for microcystin-LR environmental remediation

Copper oxide supported on nanoporous activated carbon (CuO-NPAC) is reported for the aqueous phase catalytic degradation of cyanotoxin microcystin-LR (MC-LR). The loading and spatial distribution of CuO throughout the NPAC matrix strongly influence the catalytic efficiency. CuO-NPAC synthesis was optimized with respect to the copper loading and thermal processing, and the physicochemical properties of the resulting materials were characterized by XRD, BET, TEM, SEM, EPR, TGA, XPS and FT-IR spectroscopy. EPR spin trapping and fluorescence spectroscopy showed in situ ˙OH formation via H2O2 over CuO-NPAC as the catalytically relevant oxidant. The impact of reaction conditions, notably CuO-NPAC loading, H2O2 concentration and solution pH, is discussed in relation to the reaction kinetics for MC-LR remediation.

Synthesis and application of novel probes for the detection of cysteine sulphenic acids

Cysteine is a thiol containing amino acid that readily undergoes oxidation by reactive oxygen species (ROS) to form sulphenic (R-SOH) sulphinic (RSO2H) and sulphonic (RSO3H) acids. Thiol modifications of cysteine have been implicated as modulators of cellular processes and represent significant biological modifications that occur during oxidative stress and cell signalling. However, the different oxidation states are difficult to monitor in a physiological setting due to the limited availability of experimental tools. Therefore it is of interest to synthesise and use a chemical probe that selectively recognises the reversible oxidation state of cysteine sulphenic acid to understand more about oxidative signalling. The aim of this thesis was to investigate a synthetic approach for novel fluorescent probe synthesis, for the specific detection of cysteine sulphenic acids by fluorescence spectroscopy and confocal microscopy. N-[2-(Anthracen-2-ylamino)-2-oxoethyl]-3,5-dioxocyclohexanecarboxamide was synthesised in a multistep synthesis and characterised by nuclear magnetic resonance spectroscopy. The optimisation of conditions needed for sulphenic acid formation in a purified protein using human serum albumin (HSA) and the commercially available biotin tagged probe 3-(2,4-dioxocyclohexyl)propyl-5-((3aR,6S,6aS)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl)pentanoate (DCP-Bio1) were identified. This approach was extended to detect sulphenic acids in Jurkat T cells and CD4+ T cells pre- and post-stimulus. Buthionine sulfoximine (BSO) was used to manipulate the endogenous antioxidant glutathione (GSH) in human CD4+ T cells. Then the surface protein thiol levels and sulphenic acid formation was examined. T cells were also activated by the lectin phytohaemagglutinin-L (PHA-L) and formation of sulphenic acid was investigated using SDS-PAGE, western blotting and confocal microscopy. Resting Jurkat cells have two prominent protein bands that have sulphenic acid modifications whereas resting CD4+ T cells have an additional band present. When cells were treated with BSO the number of bands increased whereas activation reduced the number of proteins that were modified. The identities of the protein bands containing sulphenic acids were explored by mass spectrometry. Cysteine oxidation was observed in redox, metabolic and cytoskeletal proteins. In summary, a novel fluorescent probe for detection of cysteine sulphenic acids has been synthesised alongside a model system that introduces cysteine sulphenic acid in primary T cells. This probe has potential application in the subcellular localisation of cysteine oxidation during T cell signalling.

The blood perfusion and NADH/FAD content combined analysis in patients with diabetes foot

Skin blood microcirculation and the metabolism activity of tissue were examined on the patients with type 2 diabetes. Laser Doppler flowmetry (LDF) with 1064 nm laser light source and fluorescence spectroscopy (FS) with excitation light of 365 nm and 450 nm have been used to monitor the blood perfusion and the content of coenzymes NADH and FAD. Concluding, the proposed combined LDF and tissue FS approach allows to identify the significant violations in the blood microcirculation and metabolic activity for type 2 diabetes patients.

Development of photosensitive liposomes for the controlled release of drugs

The facility to controlled triggered release from a “cage” system remains a key requirement for novel drug delivery. Earlier studies have shown that Bis-Azo PC based photosensitive liposomes are beneficial for drug delivery. Thus, the aim of this project was to develop photosensitive liposomes that can be used for the controlled release of drugs through UV irradiation, particularly therapeutic agents for the treatment of psoriasis. Bis-Azo PC was successfully synthesized and incorporated into a range of liposomal formulations, and these liposomes were applied for the controlled release of BSA-FITC. Bis-Azo PC sensitized liposomes were prepared via interdigitation fusion method. IFV containing optimum cholesterol amount in terms of protein loading, stability and photo-trigger release of protein was investigated. Further studies investigated the stability and triggered release of the HMT from IFV. Finally, permeation behavior of HMT and HMT-entrapped IFV through rat skin was examined using Franz cell. Results from protein study indicated that the stable entrapment of the model protein was feasible as shown through fluorescence spectroscopy and maximum of 84% protein release from IFV after 12 min of UV irradiation. Moreover, stability studies indicated that IFV were more stable at 4 0C as compared to 25 0C. Hence, DPPC:Chol:Bis-Azo PC (16:2:1) based IFV was chosen for the controlled release of HMT and these studies exhibited that photo-trigger release and stability data of HMT-entrapped IFV are in line with the protein results. Franz cell work inferred that HMT-entrapped IFV attributed to slower skin permeation as compared to HMT. CLSM also demonstrated that HMT can be used as a fluorescent label for the in vitro skin study. Overall, the work highlighted in this thesis has given useful insight into the potentials of Bis-Azo PC based IFV as a promising carrier for the treatment of psoriasis.

Stream dissolved organic matter bioavailability and composition in watersheds underlain with discontinuous permafrost

We examined the impact of permafrost on dissolved organic matter (DOM) composition in Caribou-Poker Creeks Research Watershed (CPCRW), a watershed underlain with discontinuous permafrost, in interior Alaska. We analyzed long term data from watersheds underlain with varying degrees of permafrost, sampled springs and thermokarsts, used fluorescence spectroscopy, and measured the bioavailabity of dissolved organic carbon (DOC). Permafrost driven patterns in hydrology and vegetation influenced DOM patterns in streams, with the stream draining the high permafrost watershed having higher DOC and dissolved organic nitrogen (DON) concentrations, higher DOC:- DON and greater specific ultraviolet absorbance (SUVA) than the streams draining the low and medium permafrost watersheds. Streams, springs and thermokarsts exhibited a wide range of DOC and DON concentrations (1.5–37.5 mgC/L and 0.14–1.26 mgN/L, respectively), DOC:DON (7.1–42.8) and SUVA (1.5–4.7 L mgC-1 m-1). All sites had a high proportion of humic components, a low proportion of protein components, and a low fluorescence index value (1.3–1.4), generally consistent with terrestrially derivedDOM. Principal component analysis revealed distinct groups in our fluorescence data determined by diagenetic processing and DOM source. The proportion of bioavailable DOC ranged from 2 to 35%, with the proportion of tyrosine- and tryptophan-like fluorophores in the DOM being a major predictor of DOC loss (p\0.05, R2 = 0.99). Our results indicate that the degradation of permafrost in CPCRW will result in a decrease in DOC and DON concentrations, a decline in DOC:DON, and a reduction in SUVA, possibly accompanied by

Molecular characterization of dissolved organic matter in freshwater wetlands of the Florida Everglades

In this study, the molecular composition of dissolved organic matter (DOM), collected from wetlands of the Southern Everglades, was examined using a variety of analytical techniques in order to characterize its sources and transformation in the environment. The methods applied for the characterization of DOM included fluorescence spectroscopy, solid state 13C CPMAS NMR spectroscopy, and pyrolysis-GC/MS. The relative abundance of protein-like components and carbohydrates increased from the canal site to more remote freshwater marsh sites suggesting that significant amounts of non-humic DOM are autochthonously produced within the freshwater marshes, and are not exclusively introduced through canal inputs. Such in situ DOM production is important when considering how DOM from canals is processed and transported to downstream estuaries of Florida Bay.

Selenium Distribution in the Human Retina

Selenium is known to occur in the enzyme, glutathione peroxidase, and plays an important role as an antioxidant. The objective of this investigation was to determine if amounts of selenium are selectively accumulated in different regions of the retina or uniformly distributed with eccentricity. 20 human retinas were analyzed for selenium. 18 of these were sectioned into a disc and two concentric annuli centered on the fovea using trephines having diameters of 3, 11, and 21 mm. The sections had areas of7.1, 93, and 343 mm2, respectively. Corresponding sections of these retinas were combined and analyzed together in sets of n = 5 and n = 11. For two donors, the whole retina of one eye was analyzed for selenium and the other retina was sectioned for analysis as described above. Selenium was determined using atomic fluorescence spectroscopy after digestion of the retinal tissues in nitric acid. The two whole retinas were found to have an average of 0.89 ± 0.49 pmoles/mm2 of selenium as compared to the companion which had 0.84 ± 0.28 pmoles/mm2 as determined from the sum of the selenium amounts measured in the individual sections. The inner, medial, and outer portions of these two sectioned retinas were found to contain an average of5.28 ± 1.1, 1.28 ± 0.44, 0.63 ± 0.22 pmoles/mm2, respectively. The five retinas that were sectioned and pooled for analysis were found to have average amounts of3.64, 1.26, and 0.56 pmoles/mm2 • The 11-sectioned retinas were found to have 1.16, 0.61, and 0.38 pmoles/mm2 respectively in the same three sections. This limited data set indicates that selenium is not uniformly distributed within the human retina but rather concentrated to a greater extent within the macula. If confirmed, these data would support the hypothesis that selenium may be an important antioxidant involved in protection of the macula from radical oxidants.

Photo-Reactivity of Natural Dissolved Organic Matter from Fresh to Marine Waters in the Florida Everglades, USA

Natural dissolved organic matter (DOM) is the major absorber of sunlight in most natural waters and a critical component of carbon cycling in aquatic systems. The combined effect of light absorbance properties and related photo-production of reactive species are essential in determining the reactivity of DOM. Optical properties and in particular excitation–emission matrix fluorescence spectroscopy combined with parallel factor analysis (EEM-PARAFAC) have been used increasingly to track sources and fate of DOM. Here we describe studies conducted in water from two estuarine systems in the Florida Everglades, with a salinity gradient of 2 to 37 and dissolved organic carbon concentrations from 19.3 to 5.74 mg C L−1, aimed at assessing how the quantity and quality of DOM is coupled to the formation rates and steady-state concentrations of reactive species including singlet oxygen, hydroxyl radical, and the triplet excited state of DOM. These species were related to optical properties and PARAFAC components of the DOM. The formation rate and steady-state concentration of the carbonate radical was calculated in all samples. The data suggests that formation rates, particularly for singlet oxygen and hydroxyl radicals, are strongly coupled to the abundance of terrestrial humic-like substances. A decrease in singlet oxygen, hydroxyl radical, and carbonate radical formation rates and steady-state concentration along the estuarine salinity gradient was observed as the relative concentration of terrestrial humic-like DOM decreased due to mixing with microbial humic-like and protein-like DOM components, while the formation rate of triplet excited-state DOM did not change. Fluorescent DOM was also found to be more tightly coupled to reactive species generation than chromophoric DOM.