Understanding the factors influencing the ET characteristics of redox proteins confined at an electrochemical interface is of fundamental importance from both pure (fundamental science) and applied (biosensory) perspectives. This thesis reports on progress made in the emerging field of coupled electrochemical characterization and optical imaging in moving the analysis of redox-active films to molecular scales. More specifically the combination of cyclic voltammetry and wide-field Total Internal Reflection (TIRF) microscopy, here named ‘Fluorescent Cyclic Voltammetry’ (FCV), was applied to monitoring the response of surface-confined redox active proteins at submonolayer concentrations. The combined submicrometre spatial resolution and photon capture efficiency of an inverted TIRF configuration enabled the redox reactions of localized populations of proteins to be directly imaged at scales down to a few hundreds of molecules. This represents a 6-9 orders of magnitude enhancement in sensitivity with respect to classical current signals observed in bioelectrochemical analysis. Importantly, measurements of redox potentials at this scale could be achieved from both natural and artificially designed bioelectrochemical fluorescent switches and shed fundamental light on the thermodynamic and kinetic dispersion within a population of surface confined metalloproteins. The first three chapters of this thesis provide an overview of the relevant literature and a theoretical background to both the rapidly expanding fields of electroactive monolayers bioelectrochemistry and TIRF imaging. The initial design and construction of a robust electrochemically and optically addressable fluorescent switch, crucial to the applicability of FCV is reported in chapter 5. The generation of optically transparent, and chemically modifiable electrode surfaces suitable for FCV are also described. Chapter 6 describes the response of the surface confined azurin-based switch. Analysis of the spatially-resolved redox reaction of zeptomole samples in various conditions enables the mapping of thermodynamic dispersion across the sampled areas. In chapter 7 the newly developed FCV detection method was extended to investigate more complex bioelectrochemical systems containing multiple electron transferring redox centres and responding optically at different wavelengths. This approach provides a platform for spectral resolution of different electrochemical processes on the same sample. Finally in chapter 8 an electrochemical procedure is proposed for investigating the kinetic response of redox proteins using a fundamentally new methodology based on interfacial capacitance. In using variations in the surface chemistry to tune the rate of electron transfer, the approach was shown to be a robust and facile means of characterising redox active films in considerably more detail than possible through standard electrochemical methodologies. Ultimately, it can be applied to probe dispersion within protein populations and represents a powerful means of analysing molecular films more generally.

In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.

The Type Three Secretion Systems (T3SSs) of Gram-negative bacteria, including Shigella, Salmonella, and Enteropathogenic/Enterohaemorrhagic Escherichia coli (EPEC/EHEC), pass virulence factors directly into the host to mediate invasion. Prior to secretion down the narrow T3SS channel, effector proteins associate with chaperone proteins. The binding enables the T3SS to keep effectors soluble and partially unfolded for secretion. In the first part of this thesis, the association of one promiscuous chaperone, Spa15 of Shigella flexneri, with three of its cognate effectors has been studied. In addition to the role this plays in secretion, the binding of one particular substrate leads to Spa15 being involved in the regulation of the T3SS. The oligomerisation and impact of substrate binding upon Spa15 has been determined by crystallography and EPR. Once secreted, T3SS effectors subvert the host cytoskeleton for the benefit of the bacteria. Soluble homologues of Spa15 effectors from EHEC and Salmonella have been purified, and their interactions with host GTPases which lead to stress fibre phenotypes observed. The Twin Arginine Translocation (Tat) pathway provides a contrasting view of bacterial secretion. Instead of preventing folding in the cytoplasm, it is a criterion of transport that the protein be folded. One of the reasons for internal folding is the necessity to insert cofactors which could not be incorporated externally. In the second part of this thesis, a protein which exemplifies this necessity is studied. This is PhoD, the model protein for Tat export from Bacillus subtilis. PhoD is an alkaline phosphodiesterase expressed to scavenge phosphate in times of phosphate deficiency. The structure of PhoD has been solved, and the protein is shown to be able to cleave a component of its own cell wall. It uses an unusual catalytic site more reminiscent of the eukaryotic purple acid phosphatases than of other currently known alkaline phosphatases. Furthermore this site appears to require metal binding before export from the bacterial cytoplasm.

Humans are unique in their ability to flexibly and rapidly adapt their behaviour and select courses of action that lead to future reward. Several ‘component processes’ must be implemented by the human brain in order to facilitate this behaviour. This thesis examines two such components; (i) the neural substrates supporting action selection during value- guided choice using magnetoencephalography (MEG), and (ii) learning the value of environmental stimuli and other people’s actions using functional magnetic resonance imaging (fMRI). In both situations, it is helpful to formally model the underlying component process, as this generates predictions of trial-to-trial variability in the signal from a brain region involved in its implementation. In the case of value-guided action selection, a biophysically realistic implementation of a drift diffusion model is used. Using this model, it is predicted that there are specific times and frequency bands at which correlates of value are seen. Firstly, there are correlates of the overall value of the two presented options, and secondly the difference in value between the options. Both correlates should be observed in the local field potential, which is closely related to the signal measured using MEG. Importantly, the content of these predictions is quite distinct from the function of the model circuit, which is to transform inputs relating to the value of each option into a categorical decision. In the case of social learning, the same reinforcement learning model is used to track both the value of two stimuli that the subject can choose between, and the advice of a confederate who is playing alongside them. As the confederate advice is actually delivered by a computer, it is possible to keep prediction error and learning rate terms for stimuli and advice orthogonal to one another, and so look for neural correlates of both social and non-social learning in the same fMRI data. Correlates of intentional inference are found in a network of brain regions previously implicated in social cognition, notably the dorsomedial prefrontal cortex, the right temporoparietal junction, and the anterior cingulate gyrus.

Hydrogen bonds are directional, non-covalent interactions between hydrogen and electronegative atoms. Although generally weak, these interactions are critical to the stability of many biological systems including proteins and DNA. This dissertation explores small molecules in which an intramolecular hydrogen bond is the key determinant of conformation. Chapter 1 introduces the protein Grb2 SH3C, details its role in cancer signalling, and delineates the idea of peptidomimetics—small molecules which are functionalized to mimic the structure of a peptide and disrupt protein-protein interactions. Chapter 2 describes a virtual screen for binders to Grb2 SH3C. From a library of 6.3 million compounds, 34 were tested in vitro and two found to bind to the protein in two orthogonal assays. Chapter 3 describes mimics of the polyproline II helix using a benzoylurea scaffold. A small library of these compounds was synthesized and tested for binding to Grb2 SH3C using SPR, a competition assay, and NMR. Chapter 4 describes attempts to mimic a 310 helix using benzamide-based peptidomimetics. The synthesis and in vitro evaluation of these molecules as ligands of Grb2 SH3C is described. Chapter 5 uses quantum chemical calculations to assess the energies of a series of molecular switches. These calculations benchmark a range of modern density functional theory calculations, and attempt to quantify the accuracy of these methods for a large, flexible system. The role of solvation, entropy, geometry, and torsional angles are assessed in accurately calculating the energies of the critical hydrogen bonds.

Os óleos essenciais da Pimenta pseudocaryophyllus (Gomes) Landrum de planta de populações naturais de três ecossistemas, localizados na Ilha de Cananéia, região de restinga, no Morro da Cataia, cidade de Cajati, região de encosta, ambas em área de Mata Atlântica, e na Reserva Natural Morro Grande, cidade de Caldas, região de campos montanos, foram avaliados como promotores de permeação cutânea do diclofenaco de potássio. Os óleos essenciais foram extraídos de partes aéreas das plantas e o rendimento do processo foi entre 0,90% (p/p) e 2,7% (p/p). A análise da composição química mostrou diferenças, indicando tratar-se de três quimiotipos diferentes. A interação dos óleos essenciais e dos componentes majoritários com membrana biológica natural foi avaliada por FT-Raman e ATR- FTIR, indicando a interação com as porções lipídicas do tecido. Foram desenvolvidas seis membranas biológicas artificiais, compostas por ceramidas, ácidos graxos e colesterol em proporções equimolares, que foram caracterizadas por espectroscopia Raman confocal e foram consideradas semelhantes. As membranas foram utilizadas no desenvolvimento do sistema PAMPA (Parallel Artificial Membrane Permeability Assay) para avaliar a segurança e eficácia dos óleos essenciais e componentes majoritário como promotores de permeação do diclofenaco de potássio. Os resultados dos ensaios com o sistema PAMPA foram estatisticamente avaliados. A segurança foi avaliada com o critério de permeação mínima dos óleos através das membranas do sistema PAMPA, verificada pela absorbância mínima do eugenol na solução aceptora. Os óleos essenciais e componentes majoritários foram utilizados no pré-tratamento das membranas, nas concentrações de 0,125%, 0,25%, 0,50% e 2,00% (v/v) em etano!. Ensaios de permeação do diclofenaco de potássio no sistema PAMPA indicaram efeito de promoção da permeação para todos os compostos avaliados. O método de doseamento do fármaco por UV foi validado e utilizado para os ensaios de permeação de formulações de gel em base aquosa contendo o diclofenaco de potássio (1,0% p/p). As amostras de gel foram preparadas com o óleo procedente de Morro Grande, selecionado na etapa de avaliação de segurança, a 0,125% (p/v). Adicionalmente, foram preparadas formulações com citronelol e etanol, na mesma concentração. O óleo essencial da Reserva Natural Morro Grande teve efeito de promoção da permeação superior ao do citronelol e etanol, que foram equivalentes. / The essential oils of the species Pimenta pseudocaryophyllus (Gomes) Landrum collected from natural populations of three existing ecosystems in the Cananéia Island, located at sea level, Cajati city, located in hillside region, both in the Atlantic Forest areas, as well as species collected in the Morro Grande Natural Reserve, region of montane fields, were evaluated as skin permeation enhancers of potassium diclofenac. Essential oils were extracted from the aerial parts of the plants and the process yield was between of 0.90% (w/w) and 2.7% (w/w). The chemical composition analysis showed differences between the plants of three origins, indicating that they are different chemotypes. The interaction of the essential oils and their major components with natural biological membrane was evaluated by FT- Raman and ATR-FTIR, indicating interaction with the Iipid portions of the natural membrane. Six artificial biological membranes have been developed, consisting of ceramides, cholesterol and fatty acids in equimolar proportions, which were characterized by confocal Raman spectroscopy and found to be similar. The membranes were used in developing the PAMPA (Parallel Artificial Membrane Permeability Assay) system to evaluate the safety of the potential permeation enhancers. The test results with PAMPA system were statistically evaluated. Safety was evaluated with the criterion of minimum permeation of the essential oil through the membranes, checked by the minimum absorbance of eugenol in the acceptor solution. The essential oils and the major components were used in the pretreatment of the membranes, at concentrations of 0.125%, 0.25%, 0.50% and 2.00% (v/v) in ethanol. Results indicated permeation enhancement effect for ali compounds evaluated. The analytical method for the quantification of potassium diclofenac was validated and used for the evaluation of the permeation of aqueous based gel formulations containing potassium diclofenac (1.0% w/w). The gel samples were prepared with the oil from Morro Grande Natural Reserve, selected in the safety evaluation step, at 0.125% (w/v). In addition, formulations were prepared with citronellol and ethanol at the same concentration. The essential Gil of Morro Grande Natural Reserve was more efficient as permeation enhancer than citronellol and ethanol under the test conditions.

O presente trabalho descreve um programa de computador em linguagem Java que reproduz o modelo compartimental reduzido de célula mitral do bulbo olfativo construído por Davison, Feng e Brown (Brain Res. Bull. 51:393-399,2000), como uma simplificação do modelo detalhado de Bhalla e Bower (J. Neurophysiol., 69:1948-1965, 1993). O modelo reduzido considera a célula mitral como composta por quatro compartimentos, modelados conforme a metodologia de HODGKIN e HUXLEY. Por seu baixo custo computacional, o modelo reduzido permite a construção de modelos de rede de grande porte para o bulbo olfativo. A implementação computacional feita em Java apresenta grande similaridade com a original, indicando uma robustez do modelo com relação a versões em plataformas distintas. / This work describes a computer program written in Java, which reproduces the reduced compartimental model of the mitral cell of the olfactory bulb constructed by Davison, Feng and Brown (Brain Res. Bull. 51:393-399,2000), as a simplified version of the detailed model of Bhalla and Bower (J. Neurophysiol., 69:1948-1965, 1993). The reduced model considers the mitral cell as composed of four compartiments modeled according to the Hodgkin-Huxley formalism. Due to its low computational cost, the reduced model allows the construction of large-scale network models of the olfactory bulb. The computer implementation made in Java shows great similarity with the original, indicating that the model is robust with respect to implementations in different platforms.

As técnicas espectroscópicas utilizam a interação entre luz e matéria como forma de obter informações das características moleculares de um sistema. Os diversos níveis de energia manifestam-se em bandas espectrais que ao serem interpretadas fornecem características sobre estrutura, orientação e interações a nível molecular. O presente trabalho explorou as diversas facetas espectroscópicas, aliadas a técnicas biofísicas/bioquímicas, no intuito de compreender melhor dois tipos de biomoléculas importantes para a maquinaria dos seres vivos: proteínas e peptídeos. O citocromo P450 é uma enzima do tipo monooxigenase e constitui uma das maiores superfamílias de proteínas. Essa hemoproteína foi assim nomeada devido à sua característica absorção na região da Banda de Soret (450 nm), sendo esta uma particularidade natural muito utilizada em estudos por espectroscopia. Além disso, existe interesse de estudar esta família de proteínas em virtude de suas variadas funções metabólicas e biossintéticas, nos mais diversos organismos, como catalisação de esteróides, ácidos graxos, fármacos, carcinógenos químicos e metabólitos de plantas. Em especial, para a P450 de Streptomyces clavuligerus (P450CLA), ainda não se sabe ao certo como e com quais moléculas interage, e como funciona o mecanismo utilizado pela proteína para atuar em vias de síntese como a do ácido clavulânico, importante composto terapêutico. Paralelo ao paradigma de interação de uma proteína e potenciais ligantes, o entendimento dos mecanismos de interação entre peptídeos e membranas lipídicas também são de suma importância para uma melhor compreensão dos sistemas biomoleculares. Peptídeos ativos na membrana desempenham funções fundamentais no sistema de defesa de diversos organismos e decifrar os mecanismos de como essas biomoléculas agem quando inseridas em bicamadas lipídicas pode auxiliar, por exemplo, no desenvolvimento de terapias seguras e eficientes contra doenças degenerativas. Desta forma, aproveitamos as características espectroscópicas naturais de ambas as moléculas para serem empregadas em técnicas de absorção UV/vis, Dicroísmo Circular Eletrônico e Magnético, Ressonância Paramagnética Eletrônica e Ressonância Magnética Nuclear, auxiliados por técnicas termodinâmicas e de fluorescência, de modo a explorar a interação da luz com a matéria, sem interferências de sondas externas, dando enfoque às alterações de estrutura e orientação, nas mais variadas formas de interação entre moléculas de sistemas biológicos. / Spectroscopic techniques use the interaction between light and matter as a way for obtaining information about molecular characteristics of a system. The many energy levels manifest themselves in spectral bands, which when are interpreted, it provides characteristics about structure, orientation and interactions at the molecular level. The present study explored the various spectroscopic facets, allied to biophysical/biochemical techniques, in order to understand better two important biomolecules types for living beings machinery: proteins and peptides. Cytochrome P450 is a monooxygenase-like enzyme and it belongs to one of the largest proteins superfamilies. The hemoprotein received this name due its unique spectral absorption in Soret Band region (450 nm), a natural particularity widely used in spectroscopic studies. In addition, there is interest in studying this protein family by virtue of their several metabolic and biosynthetic functions in the most diverse organisms, such as steroids, fatty acids, drugs, chemical carcinogens and plant metabolites. In particular, regarding P450 from Streptomyces clavuligerus (P450CLA), it is still unclear how and which molecules it interacts with, and how the mechanism used by the protein to act in synthesis pathways such as clavulanic acid, an important therapeutic compound. Parallel to the interaction paradigm between proteins and potential ligands, the interaction mechanisms understanding between peptides and lipid membranes are also of paramount importance for a better understanding of the biomolecular systems. Active membrane peptides play key roles in the defense system of various organisms and to decipher the mechanisms how these biomolecules act when inserted into lipid bilayers, for example in the development of safe and efficient therapies against degenerative diseases. This way, we take advantage of the natural spectroscopic characteristics of both molecules to be used in UV/vis absorption techniques, Electronic and Magnetic Circular Dichroism, Electronic Paramagnetic Resonance and Nuclear Magnetic Resonance, aided by thermodynamic and fluorescence techniques, in order to explore the interaction of light with matter, without interference from external probes, focusing on changes in structure and orientation, in the most varied forms of interaction between biological systems molecules.

Spartina anglica est une espèce exotique hybride qui peuple les zones humides littorales. Elle s’est installée dans le Bassin d’Arcachon au cours des années 1980, envahissant fortement les prés salés et les platiers vaseux préalablement occupés par, respectivement, Spartina maritima et Zostera noltei. Face aux inquiétudes suscitées par cette installation, cette thèse vise à comprendre, par une approche pluridisciplinaire, les mécanismes d’invasion et ses conséquences sur le milieu physique et sur les espèces végétales natives. L’objectif de ce travail est d’étudier l’occupation de niche par S. anglica et ses interactions avec deux espèces intertidales natives : S. maritima et Z. noltei.L’analyse d’images aériennes et satellitales a montré que, 30 ans après l’invasion, dans une zone densément peuplée par la Spartine native, la zone haute des prés salés a peu changé : la Spartine anglaise a occupé des niches vides et n’a pas remplacé la végétation native. Une expérience de transplantation réciproque et de mesures de biomasses confirment ce résultat, en montrant que l’espèce native offre une résistance à la colonisation de l’espèce exotique. L’expansion de la Spartine anglaise vers les replats de marée de l’intérieur du Bassin serait ainsi liée à sa capacité à tolérer les perturbations physiques, à sa forte plasticité de croissance en milieu oxygéné et riche en nutriments et à son comportement auto-facilitateur. Sa forte capacité d’ingénieur d’écosystèmes semble être liée à son système racinaire très développé, qui améliore l’aération des sols fortement anoxiques.Les effets de la colonisation par l’espèce exotique des zones intertidales basses à subtidales sur la Zostère naine sont importants sur le long-terme (dizaines d’années). En tant qu’ingénieur d’écosystèmes, la Spartine exotique favorise l’élévation du sol par sédimentation, entrainant une dessiccation du sédiment, peu favorable à la Zostère. Des mesures physiques au sein de patchs de l’espèce exotique suggèrent que l’élévation du sédiment est toutefois lente, surtout liée à une allocation de biomasse spécifique aux racines ainsi qu’à des rhizomes qui permettent de résister à l’érosion.En termes de gestion et de conservation des prés salés du Bassin d’Arcachon, ces résultats indiquent l’importance de limiter les perturbations physiques et les apports nutritifs qui pourraient rompre la résistance à l’invasion de la Spartine native. Ils supportent aussi l’idée que la Spartine anglaise pourrait être un allié robuste face à l’élévation du niveau de la mer. / Spartina anglica is a hybrid exotic cordgrass that inhabits coastal salt marshes. This species arrived in the Bay of Arcachon in the 1980s and since has importantly colonized the salt marshes and tidal flats formerly only occupied by the native Spartina maritima and Zostera noltei, respectively. This work aims at understanding, with an interdisciplinary perspective, the invasion mechanisms of this exotic cordgrass and the outcoming changes of its introduction in the Bay, both to the physical environment and to the native vegetation. Different approaches were considered in order to assess the niche occupancy by the exotic Spartina and its interactions with the native intertidal species, Spartina maritima and Zostera noltei.The analysis of aerial and satellite images has shown that, in about 30 years after the invasion, within a zone densely populated by the native Spartina, the global high marsh zone did not suffer significant changes with the arrival of the invasive species. Spartina anglica did not replace the existent marsh vegetation, it occupied empty niches along the intertidal area instead. Additionally, experimental works of cross transplantation and biomass measurements have corroborated that the native Spartina maritima offers resistance to the colonization by the exotic Spartina. It was also shown that the invasive occupies the same intertidal niche along the elevation and anoxic gradient than the native. The successful extension of Spartina anglica into the mudflat towards the inner Bay was related to its likely ability to tolerate physical disturbances, its strong growth plasticity in nutrient- and oxygen- rich patches and its self-facilitator behaviour. This latter trait is related to its strong ecosystem-engineering ability due to its prominent root system and consequent ability to ameliorate the oxygenation of highly anoxic soils.The main effect of the exotic Spartina species on the seagrass is related to its stronger ecosystem-engineering ability, favouring bed accretion up to levels that are not favourable to Z. noltei through enhancement of desiccation stress. However, hydrodynamic and altimetry measurements have shown that the process of bed accretion is slow and, due to the cordgrass’ specific preferential biomass allocation to roots, its efficiency is more linked to its resistance to erosion rather than sediment trapping.The results of this study provide relevant information for the definition of appropriate action and conservation strategies of marsh zones in the Bay of Arcachon, and in particular the importance of limiting physical disturbance and nutrient pollution that could disrupt the biotic resistance of the native cord grass. They also suggest a potentially important role of the exotic species in facing increasing Sea Level Rise.

Field measurements and numerical modelling of the shallow coastal waters offshore in south-western Australia were used to describe changes in the water column's vertical structure and the biological response on temporal scales of the order of hours and days. A cycle of chlorophyll a concentration, primary production, and photosystem II function on a diel timescale, which was related to changes in the solar irradiance and thermal structure, was identified. The diel cycle included (1) vertically well-mixed (or weakly linear) conditions in density and chlorophyll a early in the morning, resulting from vertical mixing through penetrative overnight convection; (2) depleted chlorophyll a concentration in the surface layer during the middle of the day due to photoinhibition; (3) an increased chlorophyll a concentration in the bottom layer by late afternoon due to optimum light conditions; and (4) the formation of a chlorophyll a break point (CBP) at the thermocline, which migrated downwards with the deepening surface mixed layer. On a longer timescale (days), moored acoustic instruments were used to derive echo level (EL), which approximated suspended particulate matter (SPM). Wind events ultimately controlled SPM, a conclusion based on (1) elevated EL during high windgenerated turbulence and bed shear stress, (2) positive time-lagged correlations between wind speed and EL at three field sites with different exposures to wave action, and (3) significant negative correlations between wind speed and depth-differentiated echo level (d(EL)/dz) at all sites. Sea breezes produced a similar response in EL through the water column to a small storm event, and wind-driven SPM resuspension resulted in a reduction in the sub-surface light climate (kd). Near-bed dissolved oxygen concentrations varied in accord with elevated wind speeds, EL and kd, highlighting a possible suppression of photosynthesis. One-dimensional modelling revealed that wind stirring was most often the dominant process in these waters. It was found that for a brief period during thermal stratification there was shear production of turbulent instabilities that migrated from the thermocline to the surface and the seabed. Convective cooling was not able to mix the water column entirely overnight without the addition of wind, and minimum wind speeds were determined for this complete vertical mixing. Bottom-generated turbulence was limited to a small region above the bed, and was deemed insignificant compared with mixing generated at the surface. Minimum wind speeds required for de-stratification and prevention of stratification were determined for summer, autumn and winter. A hypothetical desalination outfall was simulated for all seasons and it was concluded that positioning of the discharge at middepth was preferable compared to at the seabed. The results of this thesis advance the current knowledge of coastal biophysical oceanography and provide new insights into the temporal dynamics of the coastal water column of south-western Australia.