Antigenic stimulation is more efficient than LPS in inducing nitric oxide production by human mononuclear cells on the in vitro granuloma reaction in schistosomiasis

Nitric oxide (NO) is an extremely important and versatile messenger in biological systems. It has been identified as a cytotoxic factor in the immune system, presenting anti- or pro-inflammatory properties under different circumstances. In murine monocytes and macrophages, stimuli by cytokines or lipopolysaccharide (LPS) are necessary for inducing the immunologic isoform of the enzyme responsible for the high-output production of NO, nitric oxide synthase (iNOS). With respect to human cells, however, LPS seems not to stimulate NO production in the same way. Addressing this issue, we demonstrate here that peripheral blood mononuclear cells (PBMC) obtained from schistosomiasis-infected patients and cultivated with parasite antigens in the in vitro granuloma (IVG) reaction produced more nitrite in the absence of LPS. Thus, LPS-induced nitrite levels are easily detectable, although lower than those detected only with antigenic stimulation. Concomitant addition of LPS and L-N-arginine methyl ester (L-NAME) restored the ability to produce detectable levels of nitrite, which had been lost with L-NAME treatment. In addition, LPS caused a mild decrease of the IVG reaction and its association with L-NAME was responsible for reversal of the L-NAME-exacerbating effect on the IVG reaction. These results show that LPS alone is not as good an NO inducer in human cells as it is in rodent cells or cell lines. Moreover, they provide evidence for interactions between LPS and NO inhibitors that require further investigation.

A study of the interaction between Helicobacter pylori and components of the human fibrinolytic system

The interaction of plasminogen, tissue plasminogen activator (t-PA) and urokinase with a clinical strain of Helicobacter pylori was studied. Plasminogen bound to the surface of H. pylori cells in a concentration-dependent manner and could be activated to the enzymatic form, plasmin, by t-PA. Affinity chromatography assays revealed a plasminogen-binding protein of 58.9 kDa in water extracts of surface proteins. Surface-associated plasmin activity, detected with the chromogenic substrate CBS 00.65, was observed only when plasminogen and an exogenous activator were added to the cell suspension. The two physiologic plasminogen activators, t-PA and urokinase, were also shown to bind to and remain active on the surface of bacterial cells. epsilon-Aminocaproic acid caused partial inhibition of t-PA binding, suggesting that the kringle 2 structure of this activator is involved in the interaction with surface receptors. The activation of plasminogen by t-PA, but not urokinase, strongly depended on the presence of cells and a 25-fold enhancer effect on the initial velocity of activation by t-PA compared to urokinase was established. Furthermore, a relationship between cell concentration and the initial velocity of activation was demonstrated. These findings support the concept that plasminogen activation by t-PA on the bacterial surface is a surface-dependent reaction which offers catalytic advantages.

Effects of caffeine on the electrophysiological, cognitive and motor responses of the central nervous system

Caffeine is the most consumed psychoactive substance in the world. The effects of caffeine have been studied using cognitive and motor measures, quantitative electroencephalography (qEEG) and event-related potentials. However, these methods are not usually employed in combination, a fact that impairs the interpretation of the results. The objective of the present study was to analyze changes in electrophysiological, cognitive and motor variables with the ingestion of caffeine, and to relate central to peripheral responses. For this purpose we recorded event-related potentials and eyes-closed, resting EEG, applied the Stroop test, and measured reaction time. Fifteen volunteers took caffeine (400 mg) or placebo in a randomized, crossover, double-blind design. A significant reduction of alpha absolute power over the entire scalp and of P300 latency at the Fz electrode were observed after caffeine ingestion. These results are consistent with a stimulatory effect of caffeine, although there was no change in the attention (Stroop) test or in reaction time. The qEEG seems to be the most sensitive index of the changes produced by caffeine in the central nervous system since it proved to be capable of detecting changes that were not evident in the tests of cognitive or motor performance.

Quantitative refinement of reaction-based biomodels

In the field of molecular biology, scientists adopted for decades a reductionist perspective in their inquiries, being predominantly concerned with the intricate mechanistic details of subcellular regulatory systems. However, integrative thinking was still applied at a smaller scale in molecular biology to understand the underlying processes of cellular behaviour for at least half a century. It was not until the genomic revolution at the end of the previous century that we required model building to account for systemic properties of cellular activity. Our system-level understanding of cellular function is to this day hindered by drastic limitations in our capability of predicting cellular behaviour to reflect system dynamics and system structures. To this end, systems biology aims for a system-level understanding of functional intraand inter-cellular activity. Modern biology brings about a high volume of data, whose comprehension we cannot even aim for in the absence of computational support. Computational modelling, hence, bridges modern biology to computer science, enabling a number of assets, which prove to be invaluable in the analysis of complex biological systems, such as: a rigorous characterization of the system structure, simulation techniques, perturbations analysis, etc. Computational biomodels augmented in size considerably in the past years, major contributions being made towards the simulation and analysis of large-scale models, starting with signalling pathways and culminating with whole-cell models, tissue-level models, organ models and full-scale patient models. The simulation and analysis of models of such complexity very often requires, in fact, the integration of various sub-models, entwined at different levels of resolution and whose organization spans over several levels of hierarchy. This thesis revolves around the concept of quantitative model refinement in relation to the process of model building in computational systems biology. The thesis proposes a sound computational framework for the stepwise augmentation of a biomodel. One starts with an abstract, high-level representation of a biological phenomenon, which is materialised into an initial model that is validated against a set of existing data. Consequently, the model is refined to include more details regarding its species and/or reactions. The framework is employed in the development of two models, one for the heat shock response in eukaryotes and the second for the ErbB signalling pathway. The thesis spans over several formalisms used in computational systems biology, inherently quantitative: reaction-network models, rule-based models and Petri net models, as well as a recent formalism intrinsically qualitative: reaction systems. The choice of modelling formalism is, however, determined by the nature of the question the modeler aims to answer. Quantitative model refinement turns out to be not only essential in the model development cycle, but also beneficial for the compilation of large-scale models, whose development requires the integration of several sub-models across various levels of resolution and underlying formal representations.

SENSORY ANALYSIS OF A MODEL SYSTEM USING 5'-IMP AND CYSTEINE AT DIFFERENT pH

Sensory analysis was used to get an overall flavour description of a reaction mixtures containing 5'-IMP and Cysteine. Ribose/cysteine systems were used as reference systems. Results from triangle and aroma profiling show a clear correlation between the terms used and the volatile analysis described in literature for these model systems. For instance reactions at pH 3.0 and 4.5 for 5'-IMP/cysteine systems, which were described as "meaty" and "boiled meat" by panellists, presented, in the literature, the higher number of "meaty" compounds in volatile analysis (1, 7, 8, 20) .

Rheological behavior and color stability of anthocyanins from Merlot (Vitis vinifera L.) and Bordô (Vitis labrusca L.) grapes in a jam model system

Anthocyanins are the pigments responsible for the color of most red grapes and are easily degraded following various reaction mechanisms affected by oxygen, enzymes, pH, and temperature among other variables. In this study, a jam model system was developed using Merlot and Bordô grape extracts and polysaccharides (xanthan and locust bean gums) and different temperatures (45, 55 and 65 °C). The stability of the anthocyanin pigments and the rheological behavior of the jam model system were studied. For the determination of the stability, the half-life time and first-order reaction rate constants for the anthocyanin pigments were calculated. The rheological behavior was determined through the Power law model. The jam model system produced using a temperature of 45 °C showed the best results for the anthocyanin half-life time. The first-order reaction rate constants for the 45, 55, and 65 °C treatments were not significantly different among each other (p > 0.05). It was observed that with an increase in the jam model system temperature there was an increase in the index of consistency.

A reaction engineering approach to homogeneously catalyzed glycerol hydrochlorination

The production of biodiesel through transesterification has created a surplus of glycerol on the international market. In few years, glycerol has become an inexpensive and abundant raw material, subject to numerous plausible valorisation strategies. Glycerol hydrochlorination stands out as an economically attractive alternative to the production of biobased epichlorohydrin, an important raw material for the manufacturing of epoxy resins and plasticizers. Glycerol hydrochlorination using gaseous hydrogen chloride (HCl) was studied from a reaction engineering viewpoint. Firstly, a more general and rigorous kinetic model was derived based on a consistent reaction mechanism proposed in the literature. The model was validated with experimental data reported in the literature as well as with new data of our own. Semi-batch experiments were conducted in which the influence of the stirring speed, HCl partial pressure, catalyst concentration and temperature were thoroughly analysed and discussed. Acetic acid was used as a homogeneous catalyst for the experiments. For the first time, it was demonstrated that the liquid-phase volume undergoes a significant increase due to the accumulation of HCl in the liquid phase. Novel and relevant features concerning hydrochlorination kinetics, HCl solubility and mass transfer were investigated. An extended reaction mechanism was proposed and a new kinetic model was derived. The model was tested with the experimental data by means of regression analysis, in which kinetic and mass transfer parameters were successfully estimated. A dimensionless number, called Catalyst Modulus, was proposed as a tool for corroborating the kinetic model. Reactive flash distillation experiments were conducted to check the commonly accepted hypothesis that removal of water should enhance the glycerol hydrochlorination kinetics. The performance of the reactive flash distillation experiments were compared to the semi-batch data previously obtained. An unforeseen effect was observed once the water was let to be stripped out from the liquid phase, exposing a strong correlation between the HCl liquid uptake and the presence of water in the system. Water has revealed to play an important role also in the HCl dissociation: as water was removed, the dissociation of HCl was diminished, which had a retarding effect on the reaction kinetics. In order to obtain a further insight on the influence of water on the hydrochlorination reaction, extra semi-batch experiments were conducted in which initial amounts of water and the desired product were added. This study revealed the possibility to use the desired product as an ideal “solvent” for the glycerol hydrochlorination process. A co-current bubble column was used to investigate the glycerol hydrochlorination process under continuous operation. The influence of liquid flow rate, gas flow rate, temperature and catalyst concentration on the glycerol conversion and product distribution was studied. The fluid dynamics of the system showed a remarkable behaviour, which was carefully investigated and described. Highspeed camera images and residence time distribution experiments were conducted to collect relevant information about the flow conditions inside the tube. A model based on the axial dispersion concept was proposed and confronted with the experimental data. The kinetic and solubility parameters estimated from the semi-batch experiments were successfully used in the description of mass transfer and fluid dynamics of the bubble column reactor. In light of the results brought by the present work, the glycerol hydrochlorination reaction mechanism has been finally clarified. It has been demonstrated that the reactive distillation technology may cause drawbacks to the glycerol hydrochlorination reaction rate under certain conditions. Furthermore, continuous reactor technology showed a high selectivity towards monochlorohydrins, whilst semibatch technology was demonstrated to be more efficient towards the production of dichlorohydrins. Based on the novel and revealing discoveries brought by the present work, many insightful suggestions are made towards the improvement of the production of αγ-dichlorohydrin on an industrial scale.

Modifications to the Suzuki reaction and mechanistic insights on the NBS mediated cleavage of benzylidene acetals /

One of the most challenging tasks for a synthetic organic chemist today, is the development of chemo, regio, and stereoselective methodologies toward the total synthesis of macromolecules. r . The objective of my thesis was to develop methodologies towards this end. The first part of my project was to develop highly functionalized chirons from D-glucose, a cheap, chiral starting material, to be utilized in this capacity. The second part of the project dealt with modifying the carbon-carbon bond forming Suzuki reaction, which is utilized quite often as a means of combining molecular sub units in total synthesis applications. As previously stated the first area of the project was to develop high value chirons from D-glucose, but the mechanism of their formation was also investigated. The free radical initiated oxidative fragmentation of benzylidene acetals was investigated through the use of several test-case substrates in order to unravel the possible mechanistic pathways. This was performed by reacting the different acetals with N-bromosuccinimide and benzoyl peroxide in chlorobenzene at 70^C in all cases. Of the three mechanistic pathways discussed in the literature, it was determined, from the various reaction products obtained, that the fragmentation of the initial benzylic radical does not occur spontaneously but rather, oxidation proceeds to give the benzyl bromide, which then fragments via a polar pathway. It was also discovered that the regioselectivity of the fragmentation step could be altered through incorporation of an allylic system into the benzylidene acetal. This allows for the acquisition of a new set of densely functionalized. chiral, valuable synthetic intermediates in only a few steps and in high yields from a-Dglucose. The second part of the project was the utilization of the phosphonium salt room temperature ionic liquid tetradecyltrihexylphosphonium chloride (THPC) as an efficient reusable medium for the palladium catalyzed Suzuki cross-coupling reaction of aryl halides, including aryl chlorides, under mild conditions. The cross-coupling reactions were found to proceed in THPC containing small amounts of water and toluene using potassium phosphate and 1% Pd2(dba)3. Variously substituted iodobenzenes, including electron rich derivatives, reacted efficiently in THPC with a variety of arylboronic acids and afforded complete conversion within 1 hour at 50 ^C. The corresponding aryl bromides also reacted under these conditions with the addition of a catalytic amount of triphenylphosphine that allowed for complete conversion and high isolated yields. The reactions involving aryl chlorides were considerably slower, although the addition of triphenylphosphine and heating at 70 ^C allowed high conversion of electron deficient derivatives. Addition of water and hexane to the reaction products results in a triphasic system in which the top hexane phase contained the biaryl products, the palladium catalyst remained fully dissolved in the central THPC layer, while the inorganic salts were extracted into the lower aqueous phase. The catalyst was then recycled by removing the top and bottom layers and adding the reagents to the ionic liquid which was heated again at 50 ^C; resulting in complete turnover of iodobenzene. Repetition of this procedure gave the biphenyl product in 82-97% yield (repeated five times) for both the initial and recycled reaction sequences.

Competing demands for a complex system : photosystem II repair, photoprotection and quantum yield

Photosynthesis in general is a key biological process on Earth and Photo system II (PSII) is an important component of this process. PSII is the only enzyme capable of oxidizing water and is largely responsible for the primordial build-up and present maintenance of the oxygen in the atmosphere. This thesis endeavoured to understand the link between structure and function in PSII with special focus on primary photochemistry, repair/photodamage and spectral characteristics. The deletion of the PsbU subunit ofPSII in cyanobacteria caused a decoupling of the Phycobilisomes (PBS) from PSII, likely as a result of increased rates of PSII photodamage with the PBS decoupling acting as a measure to protect PSII from further damage. Isolated fractions of spinach thylakoid membranes were utilized to characterize the heterogeneity present in the various compartments of the thylakoid membrane. It was found that the pooled PSIILHCII pigment populations were connected in the grana stack and there was also a progressive decrease in the reaction rates of primary photochemistry and antennae size of PSII as the sample origin moved from grana to stroma. The results were consistent with PSII complexes becoming damaged in the grana and being sent to the stroma for repair. The dramatic quenching of variable fluorescence and overall fluorescent yield of PSII in desiccated lichens was also studied in order to investigate the mechanism by which the quenching operated. It was determined that the source of the quenching was a novel long wavelength emitting external quencher. Point mutations to amino acids acting as ligands to chromophores of interest in PSII were utilized in cyanobacteria to determine the role of specific chromophores in energy transfer and primary photochemistry. These results indicated that the Hl14 ligated chlorophyll acts as the 'trap' chlorophyll in CP47 at low temperature and that the Q130E mutation imparts considerable changes to PSII electron transfer kinetics, essentially protecting the complex via increased non-radiative charge Photosynthesis in general is a key biological process on Earth and Photo system II (PSII) is an important component of this process. PSII is the only enzyme capable of oxidizing water and is largely responsible for the primordial build-up and present maintenance of the oxygen in the atmosphere. This thesis endeavoured to understand the link between structure and function in PSII with special focus on primary photochemistry, repair/photodamage and spectral characteristics. The deletion of the PsbU subunit ofPSII in cyanobacteria caused a decoupling of the Phycobilisomes (PBS) from PSII, likely as a result of increased rates of PSII photodamage with the PBS decoupling acting as a measure to protect PSII from further damage. Isolated fractions of spinach thylakoid membranes were utilized to characterize the heterogeneity present in the various compartments of the thylakoid membrane. It was found that the pooled PSIILHCII pigment populations were connected in the grana stack and there was also a progressive decrease in the reaction rates of primary photochemistry and antennae size of PSII as the sample origin moved from grana to stroma. The results were consistent with PSII complexes becoming damaged in the grana and being sent to the stroma for repair. The dramatic quenching of variable fluorescence and overall fluorescent yield of PSII in desiccated lichens was also studied in order to investigate the mechanism by which the quenching operated. It was determined that the source of the quenching was a novel long wavelength emitting external quencher. Point mutations to amino acids acting as ligands to chromophores of interest in PSII were utilized in cyanobacteria to determine the role of specific chromophores in energy transfer and primary photochemistry. These results indicated that the Hl14 ligated chlorophyll acts as the 'trap' chlorophyll in CP47 at low temperature and that the Q130E mutation imparts considerable changes to PSII electron transfer kinetics, essentially protecting the complex via increased non-radiative charge.

DFT Studies of the Organocatalytic Aldol Reaction and a Frustrated Lewis Pair

The computational study, and in particular the density functional theory (DFT) study of the organocatalytic α-chlorination-aldol reaction and the chiral backbone Frustrated Lewis Pair (FLP) system served as a valuable tool for experimental purposes. This thesis describes methods to consider different transition states of the proline- catalyzed α-chlorination aldol reaction to determine the reasonable transition state in the reaction between the enamine and α-chloro aldehydes. Moreover, the novel intramolecular Frustrated Lewis pair based on a chiral backbone for the asymmetric hydrogenation of imines and enamines was designed and the ability of hydrogen splitting by this new FLP system was examined by computational modeling and calculating the hydrogen activation energy barrier.

Signaling potential gender effect in a spontaneous reporting system : cardiac effects associated with the use of antibiotics

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Studies on nonlinear dynamics of certain reaction systems

The nonlinear dynamics of certain important reaction systems are discussed and analysed in this thesis. The interest in the theoretical and the experimental studies of chemical reactions showing oscillatory dynamics and associated properties is increasing very rapidly. An attempt is made to study some nonlinear phenomena exhibited by the well known chemical oscillator, the BelousovZhabotinskii reaction whose mathematical properties are much in common with the properties of biological oscillators. While extremely complex, this reaction is still much simpler than biological systems at least from the modelling point of view. A suitable model [19] for the system is analysed and the researcher has studied the limit cycle behaviour of the system, for different values of the stoichiometric parameter f, by keeping the value of the reaction rate (k6) fixed at k6 = l. The more complicated three-variable model is stiff in nature.

Prolonged neglect following unilateral disruption of a prefrontal cortical-dorsal striatal system.

We investigated the potential function of the system formed by connections between the medial prefrontal cortex and the dorsomedial striatum in aspects of attentional function in the rat. It has been reported previously that disconnection of the same corticostriatal circuit produced marked deficits in performance of a serial, choice reaction-time task while sparing the acquisition of an appetitive Pavlovian approach behaviour in an autoshaping task (Christakou et al., 2001). Here, we hypothesized that unilateral disruption of the same circuit would lead to hemispatial inattention, contrasting with the global attention deficit following complete disconnection of the system. Combined unilateral lesions of the medial prefrontal cortex (mPFC) and the medial caudate-putamen (mCPu) within the same hemisphere produced a severe and long-lasting contralesional neglect syndrome while sparing the acquisition of autoshaping. These results provide further evidence for the involvement of the medial prefrontal-dorsomedial striatal circuit in aspects of attentional function, as well as insight into the nature of neglect deficits following lesions at different levels within corticostriatal circuitry.

Zinc(II)-pyridylthioazophenol system: synthesis, characterization and crystal structure

Reactivities of pyridylthioazophenols (1) with zinc(II) salts have been studied and the complexes isolated in pure form and characterized. Pyridylthioazophenols react with zinc( II)acetate in MeOH/EtOH at room temperature to give a series of pyridylsulfinylazophenols (2)but no zinc( II) complex. The sulfoxides (2) have been characterized by IR and NMR. One of the pyridylsulfinylazophenols (2a) has been subjected to single-crystal X-ray analysis in order to confirm details of its structure. A series of dimeric zinc( II) complexes of tetradentate NSNO pyridylthioazophenolates has been isolated through reaction of zinc nitrate in MeOH followed by in situ reaction with azide ion, which acts as a mu-(1,1) bridge. All complexes have been characterized spectroscopically. The detailed structure of one of the dinuclear zinc( II) complexes has been established by a single-crystal X-ray structure determination. In complex 3a two octahedrally coordinated zinc( II) ions are bridged by two end-on azide ions. No reactions of pyridylthioazophenols with zinc chloride in refluxing EtOH have been observed.

Towards the total synthesis of colletofragarones: constructing the macrocyclic lactone by high pressure-mediated intramolecular Diels-Alder reaction

We report herein an intramolecular Diels-Alder approach towards the construction of the macrocyclic lactone ring and the perhydrobenzofuran system of the colletofragarones, novel metabolites produced by fungi of the genus Colletotrichum that are responsible for inhibition of germination of the conidia in these species. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.