The effect of concentration and duration of normobaric oxygen in reducing caspase-3 and -9 expression in a rat-model of focal cerebral ischaemia.

The aim of this study was to determine the effect of different concentrations of normobaric oxygen (NBO) on neurological function and the expression of caspase-3 and -9 in a rat model of acute cerebral ischaemia. Sprague-Dawley rats (n=120) were randomly divided into four groups (n=30 per group), including 3 groups given NBO at concentrations of 33%, 45% or 61% and one control group given air (21% oxygen). After 2 h of ischaemic occlusion, each group was further subdivided into six subgroups (n=5) during reperfusion according to the duration (3, 6, 12, 24, 48 or 72 h) and concentration of NBO (33%, 45% or 61%) or air treatment. The Fluorescence Quantitative polymerase chain reaction (PCR) and immunohistochemistry were used to detect caspase-3 and -9 mRNA and protein relative expression respectively. The Neurologic Impairment Score (NIS) was significantly lower in rats given 61% NBO ≥3 h after reperfusion when compared to the control group (P<0.05, Mann–Whitney U). NBO significantly reduced caspase-3 and -9 mRNA and protein expression when compared to the control group at all NBO concentrations and time points (P<0.05, ANOVA). The expression of caspase-3 and -9 was lower in the group given 61% NBO compared any other group, and this difference was statistically significant when compared to the group given 33% NBO for ≥48 h and the control group (both P<0.05, ANOVA). These findings indicate that NBO may inhibit the apoptotic pathway by reducing caspase-3 and -9 expression, thereby promoting neurological functional recovery after stroke.

Estratégias terapêuticas baseadas na modulação da atividade enzimática das caspases

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

B Cell Activation in Insulin Resistance and Obesity

Our group has demonstrated that inflammatory diseases such as type 2 diabetes (DM), inflammatory bowel disease (IBD), and periodontal disease (PD) are associated with altered B cell function that may contribute to disease pathogenesis. B cells were found to be highly activated with characteristics of inflammatory cells. Obesity is a pre-disease state for cardiovascular disease and type 2 diabetes and is considered a state of chronic inflammation. Therefore, we sought to better characterize B cell function and phenotype in obese patients. We demonstrate that (Toll-like receptor) TLR4 and CD36 expression by B cells is elevated in obese subjects, suggesting increased sensing of lipopolysaccharide (LPS) and other TLR ligands. These ligands may be of microbial, from translocation from a leaky gut, or host origin. To better assess microbial ligand burden and host response in the bloodstream, we measured LPS binding protein (LBP), bacterial/permeability increasing protein (BPI), and high mobility group box 1 (HMGB1). Thus far, our data demonstrate an increase in LBP in DM and obesity indicating increased responses to TLR ligands in the blood. Interestingly, B cells responded to certain types of LPS by phosphorylating extracellular-signal-regulated kinases (ERK) 1/2. A better understanding of the immunological state of obesity and the microbial and endogenous TLR ligands that may be activating B cells will help identify novel therapeutics to reduce the risk of more dangerous conditions, such as cardiovascular disease.

Emergence of Tri-Phasic Muscle Activation from the Non-linear Interactions of Central and Spinal Neural Network Circuits

The origin of the tri-phasic burst pattern, observed in the EMGs of opponent muscles during rapid self-terminated movements, has been controversial. Here we show by computer simulation that the pattern emerges from interactions between a central neural trajectory controller (VITE circuit) and a peripheral neuromuscularforce controller (FLETE circuit). Both neural models have been derived from simple functional constraints that have led to principled explanations of a wide variety of behavioral and neurobiological data, including, as shown here, the generation of tri-phasic bursts.

Tryptophan degradation in irritable bowel syndrome: evidence of indoleamine 2,3-dioxygenase activation in a male cohort

Background: Irritable bowel syndrome (IBS) is a common disorder that affects 10–15% of the population. Although characterised by a lack of reliable biological markers, the disease state is increasingly viewed as a disorder of the brain-gut axis. In particular, accumulating evidence points to the involvement of both the central and peripheral serotonergic systems in disease symptomatology. Furthermore, altered tryptophan metabolism and indoleamine 2,3-dioxygenase (IDO) activity are hallmarks of many stress-related disorders. The kynurenine pathway of tryptophan degradation may serve to link these findings to the low level immune activation recently described in IBS. In this study, we investigated tryptophan degradation in a male IBS cohort (n = 10) and control subjects (n = 26). Methods: Plasma samples were obtained from patients and healthy controls. Tryptophan and its metabolites were measured by high performance liquid chromatography (HPLC) and neopterin, a sensitive marker of immune activation, was measured using a commercially available ELISA assay. Results: Both kynurenine levels and the kynurenine:tryptophan ratio were significantly increased in the IBS cohort compared with healthy controls. Neopterin was also increased in the IBS subjects and the concentration of the neuroprotective metabolite kynurenic acid was decreased, as was the kynurenic acid:kynurenine ratio. Conclusion: These findings suggest that the activity of IDO, the immunoresponsive enzyme which is responsible for the degradation of tryptophan along this pathway, is enhanced in IBS patients relative to controls. This study provides novel evidence for an immune-mediated degradation of tryptophan in a male IBS population and identifies the kynurenine pathway as a potential source of biomarkers in this debilitating condition.

Mammalian cell cultures as a model system for the determination of cytotoxicity induced by cholesterol oxidation products

Oxysterols are products of cholesterol oxidation, which may be produced endogenously or may be absorbed from the diet where they are commonly found in foods of animal origin. Oxysterols are known to be cyctotoxic to cells in culture and mode of toxicity has been identified as apoptosis in certain cell lines. The cytotoxicity of the oxysterols 25-hydroxycholesterol (25-OH) and 7β-hydroxycholesterol (7β-OH) was examined in two human cell lines, HepG2, a hepatoma cell line, and U937, a monocytic cell line. Both 25-OH and 7β-OH were cytotoxic to the HepG2 cell line but apoptotic cells were not detected and it was concluded that cells underwent necrosis. 25-OH was not cytotoxic to the U937 cell line but it was found to have a cytostatic effect. 7β-OH was shown to induce apoptosis in the U937 line. The mechanism of oxysterol-induced apoptosis has not yet been fully elucidated, however the generation of an oxidative stress and the depletion of glutathione have been associated with the initial stages of the apoptotic process. The concentration of cellular antioxidant enzyme, superoxide dismutase (SOD) was increased in association with 7β-OH induced apoptosis in the U937 cell line. There was no change in the glutathione concentration or the SOD activity of HepG2 cells, which underwent necrosis in the presence of 7β-OH. Many apoptotic pathways center on the activation of caspase-3, which is the key executioner protease of apoptosis. Caspase-3 activity was also shown to increase in association with 7β-OH-induced apoptosis in U937 cells but there was no significant increase in caspase-3 activity in HepG2 cells. DNA fragmentation is regarded as the biochemical hallmark of apoptosis, therefore the comet assay as a measure of DNA fragmentation was assessed as a measure of apoptosis. The level of DNA fragmentation induced by 7β-OH, as measured using the comet assay, was similar for both cell lines. Therefore, it was concluded that the comet assay could not be used to distinguish between 7β-OH-induced apoptosis in U937 cells and 7β-OH-induced necrosis in HepG2 cells. The cytotoxicity and apoptotic potency of oxysterols 25-OH, 7β-OH, cholesterol- 5a,6a-epoxide (a-epoxide), cholesterol-5β,6β-epoxide (β-epoxide), 19-hydroxy-cholesterol (19-OH), and 7-ketocholesterol (7-keto) was compared in the U937 cell line. 7 β-OH, β-epoxide and 7-keto were found to induce apoptosis in U937 cells. 7β-OH-induced apoptosis was associated with a decrease in the cellular glutathione concentration and an increase in SOD activity, 7-keto and β-epoxide did not affect the glutathione concentration or the SOD activity of the cells.a-Epoxide, 19-OH and 25-OH were not cytotoxic to the U937 cell line.

The role of metabolism in the pathogenesis of adherent invasive Escherichia coli (AIEC)

Crohn’s disease (CD) is a chronic, relapsing inflammatory condition affecting the gastrointestinal tract of humans, of which there is currently no cure. The precise etiology of CD is unknown, although it has become widely accepted that it is a multifactorial disease which occurs as a result of an abnormal immune response to commensal enteric bacteria in a genetically susceptible host. Recent studies have shown that a new group of Escherichia coli, called Adherent Invasive Escherichia coli (AIEC) are present in the guts of CD patients at a higher frequency than in healthy subjects, suggesting that they may play a role in the initiation and/or maintenance of the inflammation associated with CD. Two phenotypes define an AIEC and differentiate them from other groups of E. coli. Firstly, AIEC can adhere to and invade epithelial cells; and secondly, they can replicate in macrophages. In this study, we use a strain of AIEC which has been isolated from the colonic mucosa of a CD patient, called HM605, to examine the relationship between AIEC and the macrophage. We show, using a systematic mutational approach, that while the Tricarboxylic acid (TCA) cycle, the glyoxylate pathway, the Entner-Doudoroff (ED) pathway, the Pentose Phosphate (PP) pathway and gluconeogenesis are dispensable for the intramacrophagic growth of HM605, glycolysis is an absolute requirement for the ability of this organism to replicate intracellularly. We also show that HM605 activates the inflammasome, a major driver of inflammation in mammals. Specifically, we show that macrophages infected with HM605 produce significantly higher levels of the pro-inflammatory cytokine IL-1β than macrophages infected with a non-AIEC strain, and we show by immunoblotting that this is due to cleavage of caspase-1. We also show that macrophages infected with HM605 exhibit significantly higher levels of pyroptosis, a form of inflammatory cell death, than macrophages infected with a non-AIEC strain. Therefore, AIEC strains are more pro-inflammatory than non-AIEC strains and this may have important consequences in terms of CD pathology. Moreover, we show that while inflammasome activation by HM605 is independent of intracellular bacterial replication, it is dependent on an active bacterial metabolism. Through the establishment of a genetic screen aimed at identifying mutants which activate the inflammasome to lower levels than the wild-type, we confirm our observation that bacterial metabolism is essential for successful inflammasome activation by HM605 and we also uncover new systems/structures that may be important for inflammasome activation, such as the BasS/BasR two-component system, a type VI secretion system and a K1 capsule. Finally, in this study, we also identify a putative small RNA in AIEC strain LF82, which may be involved in modulating the motility of this strain. Overall this works shows that, in the absence of specialised virulence factors, the ability of AIEC to metabolise within the host cell may be a key determinant of its pathogenesis.

Ab initio calculations of group 4 metallocene reaction mechanisms: atomic layer deposition and bond activation catalysis

Thin film dielectrics based on titanium, zirconium or hafnium oxides are being introduced to increase the permittivity of insulating layers in transistors for micro/nanoelectronics and memory devices. Atomic layer deposition (ALD) is the process of choice for fabricating these films, as it allows for high control of composition and thickness in thin, conformal films which can be deposited on substrates with high aspect-ratio features. The success of this method depends crucially on the chemical properties of the precursor molecules. A successful ALD precursor should be volatile, stable in the gas-phase, but reactive on the substrate and growing surface, leading to inert by-products. In recent years, many different ALD precursors for metal oxides have been developed, but many of them suffer from low thermal stability. Much promise is shown by group 4 metal precursors that contain cyclopentadienyl (Cp = C5H5-xRx) ligands. One of the main advantages of Cp precursors is their thermal stability. In this work ab initio calculations were carried out at the level of density functional theory (DFT) on a range of heteroleptic metallocenes [M(Cp)4-n(L)n], M = Hf/Zr/Ti, L = Me and OMe, in order to find mechanistic reasons for their observed behaviour during ALD. Based on optimized monomer structures, reactivity is analyzed with respect to ligand elimination. The order in which different ligands are eliminated during ALD follows their energetics which was in agreement with experimental measurements. Titanocene-derived precursors, TiCp*(OMe)3, do not yield TiO2 films in atomic layer deposition (ALD) with water, while Ti(OMe)4 does. DFT was used to model the ALD reaction sequence and find the reason for the difference in growth behaviour. Both precursors adsorb initially via hydrogen-bonding. The simulations reveal that the Cp* ligand of TiCp*(OMe)3 lowers the Lewis acidity of the Ti centre and prevents its coordination to surface O (densification) during both of the ALD pulses. Blocking this step hindered further ALD reactions and for that reason no ALD growth is observed from TiCp*(OMe)3 and water. The thermal stability in the gas phase of Ti, Zr and Hf precursors that contain cyclopentadienyl ligands was also considered. The reaction that was found using DFT is an intramolecular α-H transfer that produces an alkylidene complex. The analysis shows that thermal stabilities of complexes of the type MCp2(CH3)2 increase down group 4 (M = Ti, Zr and Hf) due to an increase in the HOMO-LUMO band gap of the reactants, which itself increases with the electrophilicity of the metal. The reverse reaction of α-hydrogen abstraction in ZrCp2Me2 is 1,2-addition reaction of a C-H bond to a Zr=C bond. The same mechanism is investigated to determine if it operates for 1,2 addition of the tBu C-H across Hf=N in a corresponding Hf dimer complex. The aim of this work is to understand orbital interactions, how bonds break and how new bonds form, and in what state hydrogen is transferred during the reaction. Calculations reveal two synchronous and concerted electron transfers within a four-membered cyclic transition state in the plane between the cyclopentadienyl rings, one π(M=X)-to-σ(M-C) involving metal d orbitals and the other σ(C-H)-to-σ(X-H) mediating the transfer of neutral H, where X = C or N. The reaction of the hafnium dimer complex with CO that was studied for the purpose of understanding C-H bond activation has another interesting application, namely the cleavage of an N-N bond and resulting N-C bond formation. Analysis of the orbital plots reveals repulsion between the occupied orbitals on CO and the N-N unit where CO approaches along the N-N axis. The repulsions along the N-N axis are minimized by instead forming an asymmetrical intermediate in which CO first coordinates to one Hf and then to N. This breaks the symmetry of the N-N unit and the resultant mixing of MOs allows σ(NN) to be polarized, localizing electrons on the more distant N. This allowed σ(CO) and π(CO) donation to N and back-donation of π*(Hf2N2) to CO. Improved understanding of the chemistry of metal complexes can be gained from atomic-scale modelling and this provides valuable information for the design of new ALD precursors. The information gained from the model decomposition pathway can be additionally used to understand the chemistry of molecules in the ALD process as well as in catalytic systems.

A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

Cooperation between adsorbates accounts for the activation of atomic layer deposition reactions

Atomic layer deposition (ALD) is a technique for producing conformal layers of nanometre-scale thickness, used commercially in non-planar electronics and increasingly in other high-tech industries. ALD depends on self-limiting surface chemistry but the mechanistic reasons for this are not understood in detail. Here we demonstrate, by first-principle calculations of growth of HfO2 from Hf(N(CH3)2)4–H2O and HfCl4–H2O and growth of Al2O3 from Al(CH3)3–H2O, that, for all these precursors, co-adsorption plays an important role in ALD. By this we mean that previously-inert adsorbed fragments can become reactive once sufficient numbers of molecules adsorb in their neighbourhood during either precursor pulse. Through the calculated activation energies, this ‘cooperative’ mechanism is shown to have a profound influence on proton transfer and ligand desorption, which are crucial steps in the ALD cycle. Depletion of reactive species and increasing coordination cause these reactions to self-limit during one precursor pulse, but to be re-activated via the cooperative effect in the next pulse. This explains the self-limiting nature of ALD.

Investigations into the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy and maternal immune activation

The amygdala is a limbic structure that is involved in many of our emotions and processing of these emotions such as fear, anger and pleasure. Conditions such as anxiety, autism, and also epilepsy, have been linked to abnormal functioning of the amygdala, owing to improper neurodevelopment or damage. This thesis investigated the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy (TLE) and maternal immune activation (MIA). The kainic acid (KA) model of temporal lobe epilepsy (TLE) was used to induce Ammon’s-horn sclerosis (AHS) and to investigate behavioural and cytoarchitectural changes that occur in the amygdala related to Neuropeptide Y1 receptor expression. Results showed that KA-injected animals showed increased anxiety-like behaviours and displayed histopathological hallmarks of AHS including CA1 ablation, granule cell dispersion, volume reduction and astrogliosis. Amygdalar volume and neuronal loss was observed in the ipsilateral nuclei which was accompanied by astrogliosis. In addition, a decrease in Y1 receptor expressing cells in the ipsilateral CA1 and CA3 sectors of the hippocampus, ipsi- and contralateral granule cell layer of the dentate gyrus and ipsilateral central nucleus of the amygdala was found, consistent with a reduction in Y1 receptor protein levels. The results suggest that plastic changes in hippocampal and/or amygdalar Y1 receptor expression may negatively impact anxiety levels. Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the brain and tight regulation and appropriate control of GABA is vital for neurochemical homeostasis. GABA transporter-1 (GAT-1) is abundantly expressed by neurones and astrocytes and plays a key role in GABA reuptake and regulation. Imbalance in GABA homeostasis has been implicated in epilepsy with GAT-1 being an attractive pharmacological target. Electron microscopy was used to examine the distribution, expression and morphology of GAT-1 expressing structures in the amygdala of the TLE model. Results suggest that GAT-1 was preferentially expressed on putative axon terminals over astrocytic processes in this TLE model. Myelin integrity was examined and results suggested that in the TLE model myelinated fibres were damaged in comparison to controls. Synaptic morphology was studied and results suggested that asymmetric (excitatory) synapses occurred more frequently than symmetric (inhibitory) synapses in the TLE model in comparison to controls. This study illustrated that the amygdala undergoes ultrastructural alterations in this TLE model. Maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders such as autism, schizophrenia and also epilepsy. MIA was induced at a critical window of amygdalar development at E12 using bacterial mimetic lipopolysaccharide (LPS). Results showed that MIA activates cytokine, toll-like receptor and chemokine expression in the fetal brain that is prolonged in the postnatal amygdala. Inflammation elicited by MIA may prime the fetal brain for alterations seen in the glial environment and this in turn have deleterious effects on neuronal populations as seen in the amygdala at P14. These findings may suggest that MIA induced during amygdalar development may predispose offspring to amygdalar related disorders such as heightened anxiety, fear impairment and also neurodevelopmental disorders.

Particulate allergens potentiate allergic asthma in mice through sustained IgE-mediated mast cell activation.

Allergic asthma is characterized by airway hyperresponsiveness, inflammation, and a cellular infiltrate dominated by eosinophils. Numerous epidemiological studies have related the exacerbation of allergic asthma with an increase in ambient inhalable particulate matter from air pollutants. This is because inhalable particles efficiently deliver airborne allergens deep into the airways, where they can aggravate allergic asthma symptoms. However, the cellular mechanisms by which inhalable particulate allergens (pAgs) potentiate asthmatic symptoms remain unknown, in part because most in vivo and in vitro studies exploring the pathogenesis of allergic asthma use soluble allergens (sAgs). Using a mouse model of allergic asthma, we found that, compared with their sAg counterparts, pAgs triggered markedly heightened airway hyperresponsiveness and pulmonary eosinophilia in allergen-sensitized mice. Mast cells (MCs) were implicated in this divergent response, as the differences in airway inflammatory responses provoked by the physical nature of the allergens were attenuated in MC-deficient mice. The pAgs were found to mediate MC-dependent responses by enhancing retention of pAg/IgE/FcεRI complexes within lipid raft–enriched, CD63(+) endocytic compartments, which prolonged IgE/FcεRI-initiated signaling and resulted in heightened cytokine responses. These results reveal how the physical attributes of allergens can co-opt MC endocytic circuitry and signaling responses to aggravate pathological responses of allergic asthma in mice.

The cytolytic molecules Fas ligand and TRAIL are required for murine thymic graft-versus-host disease.

Thymic graft-versus-host disease (tGVHD) can contribute to profound T cell deficiency and repertoire restriction after allogeneic BM transplantation (allo-BMT). However, the cellular mechanisms of tGVHD and interactions between donor alloreactive T cells and thymic tissues remain poorly defined. Using clinically relevant murine allo-BMT models, we show here that even minimal numbers of donor alloreactive T cells, which caused mild nonlethal systemic graft-versus-host disease, were sufficient to damage the thymus, delay T lineage reconstitution, and compromise donor peripheral T cell function. Furthermore, to mediate tGVHD, donor alloreactive T cells required trafficking molecules, including CCR9, L selectin, P selectin glycoprotein ligand-1, the integrin subunits alphaE and beta7, CCR2, and CXCR3, and costimulatory/inhibitory molecules, including Ox40 and carcinoembryonic antigen-associated cell adhesion molecule 1. We found that radiation in BMT conditioning regimens upregulated expression of the death receptors Fas and death receptor 5 (DR5) on thymic stromal cells (especially epithelium), while decreasing expression of the antiapoptotic regulator cellular caspase-8-like inhibitory protein. Donor alloreactive T cells used the cognate proteins FasL and TNF-related apoptosis-inducing ligand (TRAIL) (but not TNF or perforin) to mediate tGVHD, thereby damaging thymic stromal cells, cytoarchitecture, and function. Strategies that interfere with Fas/FasL and TRAIL/DR5 interactions may therefore represent a means to attenuate tGVHD and improve T cell reconstitution in allo-BMT recipients.

Stochastic E2F activation and reconciliation of phenomenological cell-cycle models.

The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.