On the interaction of bovine serum albumin with ionic surfactants: Temperature induced EPR changes of a maleimide nitroxide reflect local protein dynamics and probe solvent accessibility

The interaction of bovine serum albumin (BSA) with the ionic surfactants sodium dodecylsulfate (SDS, anionic), cetyltrimethylammonium chloride (CTAC, cationic) and N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS, zwitterionic) was studied by electron paramagnetic resonance (EPR) spectroscopy of spin label covalently bound to the single free thiol group of the protein. EPR spectra simulation allows to monitor the protein dynamics at the labeling site and to estimate the changes in standard Gibbs free energy, enthalpy and entropy for transferring the nitroxide side chain from the more motionally restricted to the less restricted component. Whereas SDS and CTAC showed similar increases in the dynamics of the protein backbone for all measured concentrations. HPS presented a smaller effect at concentrations above 1.5 mM. At 10 mM of surfactants and 0.15 mM BSA, the standard Gibbs free energy change was consistent with protein backbone conformations more expanded and exposed to the solvent as compared to the native protein, but with a less pronounced effect for HPS. In the presence of the surfactants, the enthalpy change, related to the energy required to dissociate the nitroxide side chain from the protein, was greater, suggesting a lower water activity. The nitroxide side chain also detected a higher viscosity environment in the vicinity of the paramagnetic probe induced by the addition of the surfactants. The results suggest that the surfactant-BSA interaction, at higher surfactant concentration, is affected by the affinities of the surfactant to its own micelles and micelle-like aggregates. Complementary DLS data suggests that the temperature induced changes monitored by the nitroxide probe reflects local changes in the vicinity of the single thiol group of Cys-34 BSA residue. (C) 2011 Elsevier B.V. All rights reserved.

Using the Higgs to Probe Naturalness

The extreme sensitivity of the mass of the Higgs boson to quantum corrections from high mass states, makes it 'unnaturally' light in the standard model. This 'hierarchy problem' can be solved by symmetries, which predict new particles related, by the symmetry, to standard model fields. The Large Hadron Collider (LHC) can potentially discover these new particles, thereby finding the solution to the hierarchy problem. However, the dynamics of the Higgs boson is also sensitive to this new physics. We show that in many scenarios the Higgs can be a complementary and powerful probe of the hierarchy problem at the LHC and future colliders. If the top quark partners carry the color charge of the strong nuclear force, the production of Higgs pairs is affected. This effect is tightly correlated with single Higgs production, implying that only modest enhancements in di-Higgs production occur when the top partners are heavy. However, if the top partners are light, we show that di-Higgs production is a useful complementary probe to single Higgs production. We verify this result in the context of a simplified supersymmetric model. If the top partners do not carry color charge, their direct production is greatly reduced. Nevertheless, we show that such scenarios can be revealed through Higgs dynamics. We find that many color neutral frameworks leave observable traces in Higgs couplings, which, in some cases, may be the only way to probe these theories at the LHC. Some realizations of the color neutral framework also lead to exotic decays of the Higgs with displaced vertices. We show that these decays are so striking that the projected sensitivity for these searches, at hadron colliders, is comparable to that of searches for colored top partners. Taken together, these three case studies show the efficacy of the Higgs as a probe of naturalness.

Surface enrichment in gold/silver alloys: effects of temperature studied by atom probe tomography

Bimetallic alloys are increasingly used in heterogeneous catalysis. This interest is explained by the emergence of new features that are absent in the parent single metals. Synergistic effects between the two combined elements create a more efficient catalyst. One of the most challenging aspect of multicomponent materials in catalysis is the ability to fine-tune the catalytic properties of an alloy by controlling the nature and composition of the surface [1]. For example, the gold/silver alloy combines a high activity and a large selectivity for a broad range of oxidation reaction.It is well established that the surface composition of alloys may deviate from that of the bulk phase. Surface enrichment has also important consequences in some applications of heterogeneous catalysis. In some cases, the thermal and chemical treatments can lead to opposite trends regarding the nature of the metal prone to surface enrichment. Using atom probe tomography we aim to link the physicochemical conditions the composition of the very first atomic layers of bimetallic catalysts and eventually to fine-tune the catalytic features of the latter.

Scanning probe studies of thin films

The first part of this thesis deals with the phenomenon of thermoelectricity. It involves the improvement of the thermoelectric properties of silicon using innovative nanostructures. My contribution was to help fabricate these thermoelectric devices, and is the focus of this part of the thesis.

The second part and primary focus of this thesis is the analysis of thin films using scanning probe techniques. These surface techniques include atomic force microscopy, electric force microscopy, Kelvin probe force microscopy, and scanning tunneling microscopy. The thin films studied are graphene and molybdenum disulfide, two remarkable materials that display unique two-dimensional qualities. These materials are shown to be useful in studying the properties of adsorbates trapped between them and the substrate on which they rest. Moreover, these adsorbed species are seen to affect the structural and electronic properties of the thin films themselves. Scanning probe analyses are particularly useful in elucidating the properties of these materials, as surface effects play a significant role in determining their characteristics.

The final part of this thesis is concerned with the study of Akt in live cells using protein capture agents previously developed by my colleagues. The activation and degradation of Akt is investigated using various biological assays, including Western blots, in vitro kinase assays, and cell viability assays. Finally, the usefulness of synthetic capture agents in perturbing protein pathways and as delivery agents is assessed and analyzed.

Nitrate in soil solution with use of plant cocktails as green manure in diferent tillage systems in the brazilian semi-arid

Tillage systems strongly affect nutrient transformations and plant availability. The objective of this study was to assess the nitrate dynamic in soil solution in different tillage systems with use of plant cocktail as green manure in fertilized melon (Cucumis melon) in Brazilian semi-arid. The treatments were arranged in four blocks in a split-plot design and included three types of cover crops and two tillage systems, conventional tillage (CT) and no-till (NT). The data showed no strong effect of plant cocktails composition on NO3-N dynamic in the soil. Mean concentration of NO3-N ranged from 19.45 mg L-1 at 15 cm to 60.16 mg L-1 at 50 cm soil depth, indicating high leachability. No significant differences were observed between NT and CT treatments for 15 cm depth. The high soil moisture content at ~ 30 cm depth concentrated high NO3-N in all treatments, mean of 54.27 mg L-1 to NT and 54.62 mg L-1 to CT. The highest NO3-N concentration was observed at 50 cm depth in TC (60.16 mg L-1). High concentration of NO3-N in CT may be attributed to increase in decomposition of soil organic matter and crop residues incorporated into the soil.

Through Wafer 3D Vertical Micro-Coaxial Probe for High Frequency Material Characterization and Millimeter Wave Packaging Systems

This work presents the development of an in-plane vertical micro-coaxial probe using bulk micromachining technique for high frequency material characterization. The coaxial probe was fabricated in a silicon substrate by standard photolithography and a deep reactive ion etching (DRIE) technique. The through-hole structure in the form of a coaxial probe was etched and metalized with a diluted silver paste. A co-planar waveguide configuration was integrated with the design to characterize the probe. The electrical and RF characteristics of the coaxial probe were determined by simulating the probe design in Ansoft’s High Frequency Structure Simulator (HFSS). The reflection coefficient and transducer gain performance of the probe was measured up to 65 GHz using a vector network analyzer (VNA). The probe demonstrated excellent results over a wide frequency band, indicating its ability to integrate with millimeter wave packaging systems as well as characterize unknown materials at high frequencies. The probe was then placed in contact with 3 materials where their unknown permittivities were determined. To accomplish this, the coaxial probe was placed in contact with the material under test and electromagnetic waves were directed to the surface using the VNA, where its reflection coefficient was then determined over a wide frequency band from dc-to -65GHz. Next, the permittivity of each material was deduced from its measured reflection coefficients using a cross ratio invariance coding technique. The permittivity results obtained when measuring the reflection coefficient data were compared to simulated permittivity results and agreed well. These results validate the use of the micro-coaxial probe to characterize the permittivity of unknown materials at high frequencies up to 65GHz.

A dioxaborine cyanine dye as a photoluminescence probe for sensing carbon nanotubes

The unique properties of carbon nanotubes have made them the material of choice for many current and future industrial applications. As a consequence of the increasing development of nanotechnology, carbon nanotubes show potential threat to health and environment. Therefore, development of efficient method for detection of carbon nanotubes is required. In this work, we have studied the interaction of indopentamethinedioxaborine dye (DOB-719) and single-walled carbon nanotubes (SWNTs) using absorption and photoluminescence (PL) spectroscopy. In the mixture of the dye and the SWNTs we have revealed new optical features in the spectral range of the intrinsic excitation of the dye due to resonance energy transfer from DOB-719 to SWNTs. Specifically, we have observed an emergence of new PL peaks at the excitation wavelength of 735 nm and a redshift of the intrinsic PL peaks of SWNT emission (up to 40 nm) in the near-infrared range. The possible mechanism of the interaction between DOB-719 and SWNTs has been proposed. Thus, it can be concluded that DOB-719 dye has promising applications for designing efficient and tailorable optical probes for the detection of SWNTs.

Study of heterostructures of Cu3BiS3–buffer layer measured by Kelvin probe force microscopy measurements (KPFM)

The interface formed between Cu3BiS3 thin films and the buffer layer is a potentially limiting factor to the performance of solar cells based on Al/Cu3BiS3/buffer heterojunctions. The buffer layers of ZnS and In2S3 were grown by coevaporation, and tested as an alternative to the traditional CdS deposited by chemical bath deposition. From the Kelvin probe force microscopy measurements, we found the values of the work function of ZnS, In2S3, and CdS, layers deposited into Cu3BiS3. Additionally, different electronic activity was found for different grain boundaries (GBs), from studies under illumination, we also found the net doping concentration and the density of charged GB states for Cu3BiS3 and Cu3BiS3/CdS.

Monitoring pasture variability: optical OptRx® crop sensor versus Grassmaster II capacitance probe

Estimation of pasture productivity is an important step for the farmer in terms of planning animal stocking, organizing animal lots, and determining supplementary feeding needs throughout the year. The main objective of this work was to evaluate technologies which have potential for monitoring aspects related to spatial and temporal variability of pasture green and dry matter yield (respectively, GM and DM, in kg/ha) and support to decision making for the farmer. Two types of sensors were evaluated: an active optical sensor(OptRx®, which measures the NDVI, Normalized Difference Vegetation Index) and a capacitance probe (GrassMaster II which estimates plant mass). The results showed the potential of NDVI for monitoring the evolution of spatial and temporal patterns of vegetative growth of biodiverse pasture. Higher NDVI values were registered as pasture approached its greatest vegetative vigor, with a significant fall in the measured NDVI at the end of Spring, when the pasture began to dry due to the combination of higher temperatures and lower soil moisture content. This index was also effective for identifying different plant species (grasses/legumes) and variability in pasture yield. Furthermore, it was possible to develop calibration equations between the capacitance and the NDVI (R2 = 0.757; p < 0.01), between capacitance and GM (R2 = 0.799; p<0.01), between capacitance and DM (R2 = 0.630; p<0.01), between NDVI and GM (R2=0.745; p < 0.01), and between capacitance and DM (R2=0.524; p<0.01). Finally, a direct relationship was obtained between NDVI and pasture moisture content (PMC, in %) and between capacitance and PMC (respectively, R2 = 0.615; p<0.01 and R2=0.561; p <0.01) in Alentejo dryland farming systems.

Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location

Nitrobenzoxadiazole (NBD)-labeled lipids are popular fluorescent membrane probes. However, the understanding of important aspects of the photophysics of NBD remains incomplete, including the observed shift in the emission spectrum of NBD-lipids to longer wavelengths following excitation at the red edge of the absorption spectrum (red-edge excitation shift or REES). REES of NBD-lipids in membrane environments has been previously interpreted as reflecting restricted mobility of solvent surrounding the fluorophore. However, this requires a large change in the dipole moment (Dm) of NBD upon excitation. Previous calculations of the value of Dm of NBD in the literature have been carried out using outdated semi-empirical methods, leading to conflicting values. Using up-to-date density functional theory methods, we recalculated the value of Dm and verified that it is rather small (B2 D). Fluorescence measurements confirmed that the value of REES is B16 nm for 1,2-dioleoyl-sn-glycero-3- phospho-L-serine-N-(NBD) (NBD-PS) in dioleoylphosphatidylcholine vesicles. However, the observed shift is independent of both the temperature and the presence of cholesterol and is therefore insensitive to the mobility and hydration of the membrane. Moreover, red-edge excitation leads to an increased contribution of the decay component with a shorter lifetime, whereas time-resolved emission spectra of NBD-PS displayed an atypical blue shift following excitation. This excludes restrictions to solvent relaxation as the cause of the measured REES and TRES of NBD, pointing instead to the heterogeneous transverse location of probes as the origin of these effects. The latter hypothesis was confirmed by molecular dynamics simulations, from which the calculated heterogeneity of the hydration and location of NBD correlated with the measured fluorescence lifetimes/REES. Globally, our combination of theoretical and experiment-based techniques has led to a considerably improved understanding of the photophysics of NBD and a reinterpretation of its REES in particular.

Raman microscopy of the molybdate minerals koechlinite, iriginite and lindgrenite

A series of molybdate bearing minerals including wulfenite, powellite, lindgrenite and iriginite have been analysed by Raman microscopy. These minerals are closely related and often have related paragenesis. Raman microscopy enables the selection of individual crystals of these minerals for spectroscopic analysis even though several of the minerals can be found in the same matrix because of the paragenetic relationships between the minerals. The molybdenum bearing minerals lindgrenite, iriginite and koechlinite were studied by scanning electron microscopy and compositionally analysed by EDX methods using an electron probe before Raman spectroscopic analyses. The Raman spectra are assigned according to factor group analysis and related to the structure of the minerals. These minerals have characteristically different Raman spectra.

The synthesis and application of novel profluorescent nitroxides as probes for polymer degradation

This PhD project has expanded the knowledge in the area of profluorescent nitroxides with regard to the synthesis and characterisations of novel profluorescent nitroxide probes as well as physical characterisation of the probe molecules in various polymer/physical environments. The synthesis of the first example of an azaphenalene-based fused aromatic nitroxide TMAO, [1,1,3,3-tetramethyl-2,3-dihydro-2-azaphenalen-2-yloxyl, was described. This novel nitroxide possesses some of the structural rigidity of the isoindoline class of nitroxides, as well as some properties akin to TEMPO nitroxides. Additionally, the integral aromatic ring imparts fluorescence that is switched on by radical scavenging reactions of the nitroxide, which makes it a sensitive probe for polymer degradation. In addition to the parent TMAO, 5 other azaphenalene derivatives were successfully synthesised. This new class of nitroxide was expected to have interesting redox properties when the structure was investigated by high-level ab initio molecular orbitals theory. This was expected to have implications with biological relevance as the calculated redox potentials for the azaphenalene ring class would make them potent antioxidant compounds. The redox potentials of 25 cyclic nitroxides from four different structural classes (pyrroline, piperidine, isoindoline and azaphenalene) were determined by cyclic voltammetry in acetonitrile. It was shown that potentials related to the one electron processes of the nitroxide were influenced by the type of ring system, ring substituents or groups surrounding the moiety. Favourable comparisons were found between theoretical and experimental potentials for pyrroline, piperidine and isoindoline ring classes. Substitution of these ring classes, were correctly calculated to have a small yet predictable effect on the potentials. The redox potentials of the azaphenalene ring class were underestimated by the calculations in all cases by at least a factor of two. This is believed to be due to another process influencing the redox potentials of the azaphenalene ring class which is not taken into account by the theoretical model. It was also possible to demonstrate the use of both azaphenalene and isoindoline nitroxides as additives for monitoring radical mediated damage that occurs in polypropylene as well as in more commercially relevant polyester resins. Polymer sample doped with nitroxide were exposed to both thermo-and photo-oxidative conditions with all nitroxides showing a protective effect. It was found that isoindoline nitroxides were able to indicate radical formation in polypropylene aged at elevated temperatures via fluorescence build-up. The azaphenalene nitroxide TMAO showed no such build-up of fluorescence. This was believed to be due to the more labile bond between the nitroxide and macromolecule and the protection may occur through a classical Denisov cycle, as is expected for commercially available HAS units. Finally, A new profluorescent dinitroxide, BTMIOA (9,10-bis(1,1,3,3- tetramethylisoindolin-2-yloxyl-5-yl)anthracene), was synthesised and shown to be a powerful probe for detecting changes during the initial stages of thermo-oxidative degradation of polypropylene. This probe, which contains a 9,10-diphenylanthracene core linked to two nitroxides, possesses strongly suppressed fluorescence due to quenching by the two nitroxide groups. This molecule also showed the greatest protective effect on thermo-oxidativly aged polypropylene. Most importantly, BTMIOA was found to be a valuable tool for imaging and mapping free-radical generation in polypropylene using fluorescence microscopy.

Translating tissue engineering technology platforms into cancer research

Technology platforms originally developed for tissue engineering applications produce valuable models that mimic three-dimensional (3D) tissue organization and function to enhance the understanding of cell/tissue function under normal and pathological situations. These models show that when replicating physiological and pathological conditions as closely as possible investigators are allowed to probe the basic mechanisms of morphogenesis, differentiation and cancer. Significant efforts investigating angiogenetic processes and factors in tumorigenesis are currently undertaken to establish ways of targeting angiogenesis in tumours. Anti-angiogenic agents have been accepted for clinical application as attractive targeted therapeutics for the treatment of cancer. Combining the areas of tumour angiogenesis, combination therapies and drug delivery systems is therefore closely related to the understanding of the basic principles that are applied in tissue engineering models. Studies with 3D model systems have repeatedly identified complex interacting roles of matrix stiffness and composition, integrins, growth factor receptors and signalling in development and cancer. These insights suggest that plasticity, regulation and suppression of these processes can provide strategies and therapeutic targets for future cancer therapies. The historical perspective of the fields of tissue engineering and controlled release of therapeutics, including inhibitors of angiogenesis in tumours is becoming clearly evident as a major future advance in merging these fields. New delivery systems are expected to greatly enhance the ability to deliver drugs locally and in therapeutic concentrations to relevant sites in living organisms. Investigating the phenomena of angiogenesis and anti-angiogenesis in 3D in vivo models such as the Arterio-Venous (AV) loop mode in a separated and isolated chamber within a living organism adds another significant horizon to this perspective and opens new modalities for translational research in this field.

Writing together, learning together : the value and effectiveness of a research writing group for doctoral students

The high level of scholarly writing required for a doctoral thesis is a challenge for many research students. However, formal academic writing training is not a core component of many doctoral programs. Informal writing groups for doctoral students may be one method of contributing to the improvement of scholarly writing. In this paper, we report on a writing group that was initiated by an experienced writer and higher degree research supervisor to support and improve her doctoral students’ writing capabilities. Over time, this group developed a workable model to suit their varying needs and circumstances. The model comprised group sessions, an email group, and individual writing. Here, we use a narrative approach to explore the effectiveness and value of our research writing group model in improving scholarly writing. The data consisted of doctoral students’ reflections to stimulus questions about their writing progress and experiences. The stimulus questions sought to probe individual concerns about their own writing, what they had learned in the research writing group, the benefits of the group, and the disadvantages and challenges to participation. These reflections were analysed using thematic analysis. Following this analysis, the supervisor provided her perspective on the key themes that emerged. Results revealed that, through the writing group, members learned technical elements (e.g., paragraph structure), non-technical elements (e.g., working within limited timeframes), conceptual elements (e.g., constructing a cohesive arguments), collaborative writing processes, and how to edit and respond to feedback. In addition to improved writing quality, other benefits were opportunities for shared writing experiences, peer support, and increased confidence and motivation. The writing group provides a unique social learning environment with opportunities for: professional dialogue about writing, peer learning and review, and developing a supportive peer network. Thus our research writing group has proved an effective avenue for building doctoral students’ capability in scholarly writing. The proposed model for a research writing group could be applicable to any context, regardless of the type and location of the university, university faculty, doctoral program structure, or number of postgraduate students. It could also be used within a group of students with diverse research abilities, needs, topics and methodologies. However, it requires a group facilitator with sufficient expertise in scholarly writing and experience in doctoral supervision who can both engage the group in planned writing activities and also capitalise on fruitful lines of discussion related to students’ concerns as they arise. The research writing group is not intended to replace traditional supervision processes nor existing training. However it has clear benefits for improving scholarly writing in doctoral research programs particularly in an era of rapidly increasing student load.