Time-resolved fluorescence observation of di-tyrosine formation in horseradish peroxidase upon ultrasound treatment leading to enzyme inactivation

The application of ultrasound to a solution can induce cavitional phenomena and generate high localised temperatures and pressures. These are dependent of the frequency used and have enabled ultrasound application in areas such as synthetic, green and food chemistry. High frequency (100 kHz to 1 MHz) in particular is promising in food chemistry as a means to inactivate enzymes, replacing the need to use periods of high temperature. A plant enzyme, horseradish peroxidase, was studied using time-resolved fluorescence techniques as a means to assess the effect of high frequency (378 kHz and 583 kHz) ultrasound treatment at equivalent acoustic powers. This uncovered the fluorescence emission from a newly formed species, attributed to the formation of di-tyrosine within the horseradish peroxidase structure caused by auto-oxidation, and linked to enzyme inactivation.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Wide Field of View Spectroscopy Using Fabry-Perot Interferometers

We present a high resolution spectrometer consisting of dual solid Fabry-Perot Interferometers (FPIs). This work is intended to be an all inclusive documentation of the instrument including discussion of the design of this instrument, the methods used in data reduction, and the analysis of these data. Each FPI is made of a single piece of L-BBH2 glass which has a high index of refraction n~2.07 with a thickness on the order of 100 μm. Each is then coated with partially reflective mirrors to create a resonant cavity and thus achieve a spectral resolution of R~30,000. Running the FPIs in tandem reduces the overlapping orders and allows for a much wider free spectral range and higher contrast. We will also discuss the properties of the FPIs which we have measured. This includes the tuning of the FPIs which is achieved by adjusting the temperature and thus changing the FPI gap and the refractive index of the material. The spectrometer then moves spatially in order to get spectral information at every point in the field of view. We select spectral lines for further analysis and create maps of the line depths across the field. Using this technique we are able to measure the fluorescence of chlorophyll in plants and attempt to observe zodiacal light. In the chlorophyll analysis we are able to detect chlorophyll fluorescence using the line depth in a plant using the sky as a reference solar spectrum. This instrument has possible applications in either a cubesat or aerial observations to measure bulk plant activity over large areas.

Adaptive coatings based on polyaniline for direct 2D observation of diffusion processes in microfluidic systems

[EN] Therefore the understanding and proper evaluation of the flow and mixing behaviour at microscale becomes a very important issue. In this study, the diffusion behaviour of two reacting solutions of HCI and NaOH were directly observed in a glass/polydimethylsiloxane microfluidic device using adaptive coatings based on the conductive polymer polyaniline that are covalently attached to the microchannel walls. The two liquid streams were combined at the junction of a Y-shaped microchannel, and allowed to diffuse into each other and react. The results showed excellent correlation between optical observation of the diffusion process and the numerical results. A numerical model which is based on finite volume method (FVM) discretisation of steady Navier-Stokes (fluid flow) equations and mass transport equations without reactions was used to calculate the flow variables at discrete points in the finite volume mesh element. The high correlation between theory and practical data indicates the potential of such coatings to monitor diffusion processes and mixing behaviour inside microfluidic channels in a dye free environment.

Remoção de metais pesados em efluentes sintéticos utilizando vermiculita como adsorvente

Heavy metals are used in many industrial processestheirs discard can harm fel effects to the environment, becoming a serious problem. Many methods used for wastewater treatment have been reported in the literature, but many of them have high cost and low efficiency. The adsorption process has been used as effective for the metal remoal ions. This paper presents studies to evaluate the adsorption capacity of vermiculite as adsorbent for the heavy metals removal in a synthetic solution. The mineral vermiculite was characterized by differents techniques: specific surface area analysis by BET method, X-ray diffraction, raiosX fluorescence, spectroscopy in the infraredd region of, laser particle size analysis and specific gravity. The physical characteristics of the material presented was appropriate for the study of adsorption. The adsorption experiments weredriveal finite bath metod in synthetic solutions of copper, nickel, cadmium, lead and zinc. The results showed that the vermiculite has a high potential for adsorption, removing about 100% of ions and with removal capacity values about 85 ppm of metal in solution, 8.09 mg / g for cadmium, 8.39 mg/g for copper, 8.40 mg/g for lead, 8.26 mg/g for zinc and 8.38 mg/g of nickel. The experimental data fit in the Langmuir and Freundlich models. The kinetic datas showed a good correlation with the pseudo-second order model. It was conducteas a competition study among the metals using vermiculiti a adsorbent. Results showed that the presence of various metals in solution does not influence their removal at low concentrations, removing approximat wasely 100 % of all metals present in solutions

Fotodegradação de pesticidas: caso do fenarimol

Tese dout. em Química, Unidade de Ciências Exactas e Humanas, Univ. do Algarve, 1997

Transport in the blood of an anti-tumor water-soluble rutheniun cyclopentadienyl complex: a fluorescence study on albumin binding

Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

X-ray fluorescence spectroscopic determination of heavy metals and trace elements in aerial parts of Origanum sipyleum L from Turkey

Purpose: To determine the heavy metal and trace element composition of the powdered aerial parts of Origanum sipyleum L. and its water extract. Methods: The heavy metal and trace elements content of the powdered plant material and 2 % aqueous extract were evaluated by x-ray fluorescence spectroscopy with silicon drift detector SDD at a resolution of 145 eV and 10,000 pulses. The process conditions were 0.1 g sample weight, process time of 300 s at a voltage of 25 kV and 50 kV, and at a current of 0.5 and 1.0 mA under helium atmosphere. Results: The major elements, K, Ca and Na, known as macronutrients, constituted 11990, 10490 and 970 ppm of the powdered drug and 8910, 2991 and 810 ppm of the water extract, respectively. Among other constituents, arsenic, lead and uranium levels were < 1, 2.1 and < 3 ppm, respectively, in the powdered material while in the aqueous extract, the levels were < 1, < 2 and 200 ppm, respectively. Conclusion: O. sipyleum is a potential source of macro- and micronutrients from which useful food additives and health supplements can be derived.

Ultrafast transient absorption spectroscopy: principles and applications

The study of photophysical and photochemical processes crosses the interest of many fields of research in physics, chemistry and biology. In particular, the photophysical and photochemical reactions, after light absorption by a photosynthetic pigment-protein complex, are among the fastest events in biology, taking place on timescales ranging from tens of femtoseconds to a few nanoseconds. Among the experimental approaches developed for this purpose, the advent of ultrafast transient absorption spectroscopy has become a powerful and widely used technique.[1,2] Focusing on the process of photosynthesis, it relies upon the efficient absorption and conversion of the radiant energy from the Sun. Chlorophylls and carotenoids are the main players in the process. Photosynthetic pigments are typically arranged in a highly organized fashion to constitute antennas and reaction centers, supramolecular devices where light harvesting and charge separation take place. The very early steps in the photosynthetic process take place after the absorption of a photon by an antenna system, which harvests light and eventually delivers it to the reaction center. In order to compete with internal conversion, intersystem crossing, and fluorescence, which inevitably lead to energy loss, the energy and electron transfer processes that fix the excited-state energy in photosynthesis must be extremely fast. In order to investigate these events, ultrafast techniques down to a sub-100 fs resolution must be used. In this way, energy migration within the system as well as the formation of new chemical species such as charge-separated states can be tracked in real time. This can be achieved by making use of ultrafast transient absorption spectroscopy. The basic principles of this notable technique, instrumentation, and some recent applications to photosynthetic systems[3] will be described. Acknowledgements M. Moreno Oliva thanks the MINECO for a “Juan de la Cierva-Incorporación” research contract. References [1] U. Megerle, I. Pugliesi, C. Schriever, C.F. Sailer and E. Riedle, Appl. Phys. B, 96, 215 – 231 (2009). [2] R. Berera, R. van Grondelle and J.T.M. Kennis, Photosynth. Res., 101, 105 – 118 (2009). [3] T. Nikkonen, M. Moreno Oliva, A. Kahnt, M. Muuronen, J. Helaja and D.M. Guldi, Chem. Eur. J., 21, 590 – 600 (2015).

Attenuated total reflectance fourier transform infrared spectroscopy: an analytical technique to understand therapeutic responses at the molecular level

Rapid monitoring of the response to treatment in cancer patients is essential to predict the outcome of the therapeutic regimen early in the course of the treatment. The conventional methods are laborious, time-consuming, subjective and lack the ability to study different biomolecules and their interactions, simultaneously. Since; mechanisms of cancer and its response to therapy is dependent on molecular interactions and not on single biomolecules, an assay capable of studying molecular interactions as a whole, is preferred. Fourier Transform Infrared (FTIR) spectroscopy has become a popular technique in the field of cancer therapy with an ability to elucidate molecular interactions. The aim of this study, was to explore the utility of the FTIR technique along with multivariate analysis to understand whether the method has the resolution to identify the differences in the mechanism of therapeutic response. Towards achieving the aim, we utilized the mouse xenograft model of retinoblastoma and nanoparticle mediated targeted therapy. The results indicate that the mechanism underlying the response differed between the treated and untreated group which can be elucidated by unique spectral signatures generated by each group. The study establishes the efficiency of non-invasive, label-free and rapid FTIR method in assessing the interactions of nanoparticles with cellular macromolecules towards monitoring the response to cancer therapeutics.

Supported silver nanoparticle and near-interface solution dynamics in a deep eutectic solvent

Type III deep eutectic solvents (DES) have attracted significant interest as both environmentally friendly and functional solvents that are, in some ways, advantageous to traditional aqueous systems. While these solvents continue to produce remarkable thin films and nanoparticle assemblies, their interactions with metallic surfaces are complex and difficult to manipulate. In this study, the near-surface region (2-600 nm) of a carbon surface is investigated immediately following silver nanoparticle nucleation and growth. This is accomplished, in situ, using a novel grazing transmission small-angle X-ray scattering approach with simultaneous voltammetry and electrochemical impedance spectroscopy. With this physical and electrochemical approach, the time evolution of three distinct surface interaction phenomena is observed: aggregation and coalescence of Ag nanoparticles, multilayer perturbations induced by nonaggregated Ag nanoparticles, and a stepwise transport of dissolved Ag species from the carbon surface. The multilayer perturbations contain charge-separated regions of positively charged choline-ethylene and negatively charged Ag and Cl species. Both aggregation-coalescence and the stepwise decrease in Ag precursor near the surface are observed to be very slow (∼2 h) processes, as both ion and particle transport are significantly impeded in a DES as compared to aqueous electrolytes. Altogether, this study shows how the unique chemistry of the DES changes near the surface and in the presence of nanoparticles that adsorb the constituent species.

Identifying diffusion sources in large networks: a community structure based approach

The global diffusion of epidemics, rumors and computer viruses causes great damage to our society. It is critical to identify the diffusion sources and promptly quarantine them. However, most methods proposed so far are unsuitable for large networks because of their computational cost and the complex spatiotemporal diffusion processes. In this paper, we develop a community structure based approach to efficiently identify diffusion sources in large networks. We first detect the community structure of a network and assign sensors on community bridge nodes to record diffusion dynamics. From the infection time of bridge sensors, we can determine the very first infected community from which the diffusion started and spread out to other communities. This, therefore, overcomes the scalability issue in source identification problems by narrowing the set of suspects down to the first infected community. Then, to accurately locate the diffusion source from suspects, we utilize an intrinsic feature of diffusion sources that the relative infection time of any node is linear with its effective distance from the diffusion source. Thus, for each suspect, we compute the correlation coefficient to measure the degree of linear dependence between sensors' relative infection times and their effective distances from the suspect, and consider the one with the greatest correlation coefficient as the source. We evaluate our approach in two large networks containing more than 300,000 nodes, which are collected from Twitter. The experiment results show that our method can identify diffusion sources with very high degree of accuracy. Especially when the average community size shrinks, the accuracy of our approach increases dramatically.