Mechanism of action of cyclic antimicrobial peptides

This PhD thesis is the result of the combination of experimental and computational techniques with the aim of understanding the mechanism of action of de novo cyclic decapeptides with high antimicrobial activity. By experimental techniques the influence of the replacement of the phenylalanine for tryptophan residue in their antimicrobial activity was tested and the stability in human serum was also analyzed, in order to evaluate their potential therapeutic application as antitumor agents. On the other hand, the interaction amongst the peptide BPC194 c(KKLKKFKKLQ), the best candidate from the whole library of cyclic peptides, and a model anionic membrane was simulated. The results showed a structure-function relationship derived from the stable conformation of the peptides involved in the membrane permeabilization. As a result, a rational design was performed being BPC490 the peptide with best antimicrobial activity compared with the best active peptide from the original library.

Study of tyrosine kinases and protein tyrosine phosphorylation

In recent years, our increased understanding of the complex signal transduction mechanisms that regulate cellular function has fueled huge advances in all aspects of biomedical science and cell biology. Platelet and megakaryocyte function is no exception to this. In the last 10 yr our understanding of the receptor biochemistry and the systems that they control has been pivotal in the development of new strategies to inhibit platelet function and thereby prevent thrombosis. Experimental techniques have become more and more elegant, however; the basic toolbox that a researcher requires to study signaling in platelets and megakaryoctes is described in this and several subsequent chapters.

CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment.

Complex spatiotemporal haemodynamic response following sensory stimulation in the awake rat

Detailed understanding of the haemodynamic changes that underlie non-invasive neuroimaging techniques such as blood oxygen level dependent functional magnetic resonance imaging is essential if we are to continue to extend the use of these methods for understanding brain function and dysfunction. The use of animal and in particular rodent research models has been central to these endeavours as they allow in-vivo experimental techniques that provide measurements of the haemodynamic response function at high temporal and spatial resolution. A limitation of most of this research is the use of anaesthetic agents which may disrupt or mask important features of neurovascular coupling or the haemodynamic response function. In this study we therefore measured spatiotemporal cortical haemodynamic responses to somatosensory stimulation in awake rats using optical imaging spectroscopy. Trained, restrained animals received non-noxious stimulation of the whisker pad via chronically implanted stimulating microwires whilst optical recordings were made from the contralateral somatosensory cortex through a thin cranial window. The responses we measure from un-anaesthetised animals are substantially different from those reported in previous studies which have used anaesthetised animals. These differences include biphasic response regions (initial increases in blood volume and oxygenation followed by subsequent decreases) as well as oscillations in the response time series of awake animals. These haemodynamic response features do not reflect concomitant changes in the underlying neuronal activity and therefore reflect neurovascular or cerebrovascular processes. These hitherto unreported hyperemic response dynamics may have important implications for the use of anaesthetised animal models for research into the haemodynamic response function.

Pozzolanic behavior of bamboo leaf ash: Characterization and determination of the kinetic parameters

The paper presents a characterization and study of the pozzolanic behavior between calcium hydroxide (CH) and bamboo leaf ash (BLAsh), which was obtained by calcining bamboo leaves at 600 degrees C for 2 h in a laboratory electric furnace. To evaluate the pozzolanic behavior the conductometric method was used, which is based on the measurement of the electrical conductivity in a BLAsh/CH solution with the reaction time. Later, the kinetic parameters are quantified by applying a kinetic-diffusive model. The kinetic parameters that characterize the process (in particular, the reaction rate constant and free energy of activation) were determined with relative accuracy in the fitting process of the model. The pozzolanic activity is quantitatively evaluated according to the values obtained of the kinetic parameters. Other experimental techniques, such as X-ray diffraction (XRD) and scanning electron microscopy (SEM), were also employed. The results show that this kind of ash is formed by silica with a completely amorphous nature and a high pozzolanic activity. The correlation between the values of free energy of activation (Delta G(#)) and the reaction rate constants (K) are in correspondence with the theoretical studies about the rate processes reported in the literature. (C) 2010 Elsevier Ltd. All rights reserved.

Electrodeposition and characterization of thin selenium films modified with lead ad-atoms

The deposition and characterization of Se films doped with Pb underpotentially deposited (UPD) ad-atoms was studied in this work. The employed experimental techniques were cyclic voltammetry, chronoamperometry, electrochemical impedance spectroscopy, UV-vis spectroscopy and atomic force microscopy. The initial deposition of Se film by chronoamperometry yielded a thin film composed of approximately 700 layers. The Pb UPD on Se was achieved by chronoamperometry in a potential value previously determined in voltammetric experiments. This deposition yielded a deposition charge of approximately 7.5% of the total one. The film resistance altered from 320 Omega cm(2) for Se to 65 Omega cm(2) for the Se/Pb one. Flat band potential values and number of acceptors and donors were also calculated for both films and the values obtained were + 0.95 and -0.51 V for Se and Se/Pb, respectively. The Se coating presented 1.2 x 10(17) cm(3) acceptors while the Se/Pb one presented 3.2 x 10(17) cm(3) donors. The band gap values for both films were 2.4 eV and 1.9 eV, correspondingly. (C) 2008 Elsevier B.V. All rights reserved.

Tratamento de soluções de cromo (III) por flotação a ar dissolvido

O presente trabalho estuda a viabilidade da utilização do processo de flotação a ar dissolvido (FAD) no tratamento de efluentes contendo cromo. Tal processo é analisado comparativamente à sedimentação. Urna revisão dos diferentes tipos de processos de separação ou de recuperação do cromo é, também, aqui apresentada. Soluções contendo 200 mg.l" de cromo tri ou hexavalente foram estudadas quanto às condições ideais de precipitação, às características de sedimentação e de flotação a ar dissalvido em regime descontínuo e contlnuo. Agentes poliméricos foram testados no intuito de melhorar as condições de clarificação. O processo de FAD foi o que apresentou melhores resultados no que se refere a cinética de separação sólido/líquido, e em termos de clarificação das soluções. Estudos de separação sólido/líquido de soluções contendo cromo VI foram feitos por estes dois processos empregando sulfato ferroso e sulfito de sódio como agentes redutores. A FAD mostrou ser eficiente para tratar as soluções quando reduzidas com sulfito de sódio. Porém, no caso da utilização do sulfato ferroso como redutor, o rendimento da FAD diminuiu no tratamento de soluções que continham sólidos suspensos acima de uma concentração crítica. Polímeros também foram empregados neste caso, e confirmaram sua atuação melhorando a cinética de separação sólido/líquido e como agentes que beneficiam a clarificação das soluções. Os resultados dos estudos de flotação por ar dissolvido em uma unidade contínua mostraram que é viavel a FAD sem agentes floculantes ou tensoativos. No entanto, estes aumentam os níveis de clarificação das soluções. Apenas os floculantes a base de amido mostraram-se ineficientes nesta aplicação. Conclui-se que o processo de FAD pode ser utilizado no tratamento de efluentes contendo cromo permitindo obter efluentes finais dentro dos padrões de emissão da legislação brasileira.

Caracterização espectroscópica de peixe do período cretáceo (Bacia do Araripe)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

MIGRATION MEASUREMENTS FROM PLASTIC PACKAGING: A SIMULATION STUDY ON INFLUENCE OF INITIAL CONCENTRATION PROFILE

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Propriedades fisicas do monocristal fe/mgo(100) e estudo da expansao termica da superficie da ag(100)

In this work we have developed a way to grow Fe/MgO(100) monocrystals by magnetron sputtering DC. We investigated the growing in a temperature range among 100 oC and 300 oC. Structural and magneto-crystalline properties were studied by different experimental techniques. Thickness and surface roughness of the films were investigated by atomic force microscopy, while magneto-crystalline properties were investigated by magneto-optical Kerr effect and ferromagnetic resonance. Our results show that as we increase the deposition temperature, the magneto-crystalline anisotropy of the films also increases, following the equation of Avrami. The best temperature value to make a film is 300 oC. As the main result, we built a base of magnetoresistence devices and as an aplication, we present measurements of Fe/Cr/Fe trilayer coupling. In a second work we investigated the temperature dependence of the first three interlayer spacings of Ag(100) surface using low energy electron diffraction. A linear expansion model of crystal surface was used and the values of Debye temperatures of the first two layers and thermal expansion coefficient were determinated. A relaxation of 1% was found for Ag(100) surface and these results are matched with faces (110) and (111) of the silver. iv

Modelos experimentais de deficiência limbar em coelhos: análise clínica

Objetivo: Comparar em coelhos três modelos experimentais de destruição das células germinativas (CG) do limbo corneano quanto a aspectos clínicos. Métodos: Foram utilizados 54 coelhos, 108 olhos, subdivididos em 3 grupos experimentais: (G1), (G2) e (G3), cada um formado pelos OE de 18 coelhos, submetidos às técnicas experimentais (T1), (T2) e (T3), respectivamente, e um grupo controle, formado pelos 54 olhos contralaterais (OD). Nas três técnicas foi utilizado o n-heptanol. Na T1, o n-heptanol foi aplicado por 5 minutos, para remoção do epitélio límbico. Na T2, além da aplicação do n-heptanol, realizou-se peritomia e remoção da conjuntiva perilímbica até 4 mm do limbo, juntamente com a escarificação do tecido episcleral. Na T3, além dos procedimentos da T2, foi realizada dissecção lamelar do limbo abrangendo aproximadamente 1,5 mm na periferia da córnea e 2 mm na superfície escleral. em todas as córneas dos animais foram estudados seis parâmetros clínicos: neovascularização, perda da transparência, irregularidade da superfície, reparação epitelial, erosão ou defeito epitelial, granuloma e outras lesões corneanas. Resultados: A neovascularização corneana iniciou-se mais precocemente com a T1 e T2; ocorreu em 100% dos casos com as três técnicas, de forma não homogênea, variando de leve a intensa; permaneceu estável a partir do 28º dia até o final do experimento (56º dia), foi maior nos quadrantes superior e inferior e menor nos quadrantes nasal e temporal. A perda da transparência e a irregularidade da superfície corneana foram menores com a T1 que com a T2 e T3, que foram similares entre si. Houve, nas três técnicas experimentais, latência de três dias para o início da reepitelização, que se completou com a T1 no 7º dia e com a T2 e T3 no 14º dia. Erosão epitelial corneana e granuloma corneano foram encontradas de forma similar nas três técnicas experimentais. Conclusões: A T2 e T3 mostraram-se adequadas como possíveis modelos de ampla remoção das CG límbicas, levando a resultados similares nos diversos parâmetros estudados. A T1 se mostrou adequada como modelo de remoção parcial do epitélio límbico. Ocorreu conjuntivalização e neovascularização nas três técnicas experimentais.

Modelos de neovascularização corneana em coelhos: análise morfológica

OBJETIVOS: Comparar em coelhos três modelos experimentais de destruição das células germinativas (CG) do limbo corneano quanto a aspectos morfológicos. MÉTODOS: Foram utilizados 54 coelhos, 108 olhos, subdivididos em 3 grupos experimentais: (G1), (G2) e (G3), formados por 18 coelhos cada, que tiveram o OE submetido às técnicas experimentais (T1), (T2) e (T3), respectivamente, e um grupo controle, formado por 54 olhos contralaterais (OD) dos coelhos do G1, G2 e G3. Quatro parâmetros morfológicos foram estudados: epitélio, resposta inflamatória, vascularização e resposta fibroblástica. RESULTADOS: Com a T1 não houve remoção da totalidade do epitélio límbico, com a T2 houve remoção da quase totalidade do epitélio límbico, com a T3 houve remoção da totalidade do epitélio límbico. A reparação da superfície corneana foi feita por epitélio de fenótipo conjuntival (conjuntivalização) com as três técnicas, havendo aparecimento de células caliciformes a partir do 14º dia, sendo a densidade maior no 28º dia. A resposta inflamatória com a T3 foi mais intensa que com a T1 e T2. A regressão foi mais rápida com a T1 e similar com a T2 e T3. Contribuiu para a turvação corneana principalmente no 14º e 28º dia, concentrando-se, principalmente, na metade estromal anterior, sendo poupada a metade posterior. Foi maior até o 28º dia, decrescendo a partir desse momento. Caracterizou-se, no início, por infiltrado com predomínio de polimorfonucleares e sofreu mudança no 56º dia para infiltrado com predomínio de mononucleares. Os neovasos apareceram a partir do 7º dia, a princípio permearam o estroma do terço médio para cima, progredindo para a superficialização com a regressão do edema estromal. A vascularização com as três técnicas, ao final do experimento, foi superficial no estroma, porém não houve a formação de tecido fibro-escleroso denso ou cicatriz propriamente dita distinta do estroma corneano. CONCLUSÕES: Ocorreu conjuntivalização e neovascularização nas três técnicas experimentais. As T2 e T3 mostraram-se adequadas como possíveis modelos de ampla remoção das CG límbicas, levando a resultados similares nos diversos parâmetros estudados. A T1 se mostrou adequada como modelo de remoção parcial do epitélio límbico.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Aerobic biodegradation of butanol and gasoline blends

This work aimed to assess the aerobic biodegradation of butanol/gasoline, blends (5; 10; 15 and 20% v/v), being the latter compared to the ethanol/gasoline blend (20% v/v). Two experimental techniques were employed, namely the respirometric method and the redox indicator DCPIP test. in the former, experiments simulating the contamination of natural environments (addition of 50 mL of fuel kg(-1) of soil from a non-contaminated site and 20 mL of fuel L(-1) of water from a river) were carried out in biometer flasks (250 mL), used to measure the microbial CO(2) production. The DCPIP test assessed the capability of four inocula to biodegrade the blends of 20%. The addition of butanol at different concentrations enhanced the biodegradation of gasoline in soil. However, no practical gains were observed for concentrations of butanol above 10%. Ethanol showed to have a much faster biodegradation rate than butanol, particularly in water, and the following order of biodegradability was found: ethanol > butanol > gasoline. The addition of the alcohols to the gasoline resulted in positive synergic effects on the biodegradation of the fuels in soil and water matrices. Furthermore, results suggest that, in soil, butanol better enhanced the biodegradation of gasoline than ethanol. (C) 2009 Elsevier Ltd. All rights reserved

Tightly bound gap solitons in a Fermi gas

Within the framework of the mean-field hydrodynamic model of a degenerate Fermi gas ( DFG), we study, by means of numerical methods and variational approximation ( VA), the formation of fundamental gap solitons ( FGSs) in a DFG ( or in a BCS superfluid generated by weak interaction between spin- up and spin- down fermions), which is trapped in a periodic optical- lattice ( OL) potential. An effectively one- dimensional ( 1D) con. guration is considered, assuming strong transverse confinement; in parallel, a proper 1D model of the DFG ( which amounts to the known quintic equation for the Tonks- Girardeau gas in the OL) is considered too. The FGSs found in the first two bandgaps of the OL- induced spectrum ( unless they are very close to edges of the gaps) feature a ( tightly bound) shape, being essentially confined to a single cell of the OL. In the second bandgap, we also find antisymmetric tightly bound subfundamental solitons ( SFSs), with zero at the midpoint. The SFSs are also confined to a single cell of the OL, but, unlike the FGSs, they are unstable. The predicted solitons, consisting of similar to 10(4) - 10(5) atoms, can be created by available experimental techniques in the DFG of Li-6 atoms.