Molecular analysis of virulence mechanisms associated with adherent-invasive Escherichia coli (AIEC)

Crohn's Disease (CD) is a chronic inflammatory bowel disease of unknown etiology. Recent work has shown that a new pathotype of Escherichia coli, Adherent Invasive E. coli (AIEC) may be associated with CD. AIEC has been shown to adhere to and invade epithelial cells and to replicate within macrophages (together this is called the AIEC phenotype). In this thesis, the AIEC phenotype of 84 E. coli strains were determined in order to identify the prevalence of this phenotype within the E. coli genus. This study showed that a significant proportion of E. coli strains (approx. 5%) are capable of adhering to and invading epithelial cells and undergoing intramacrophage replication. Moreover, the results presented in this study indicate a correlation between survival in macrophage and resistance to grazing by amoeba supporting the coincidental evolution hypothesis that resistance to amoebae could be a driving force in the evolution of pathogenicity in some bacteria, such as AIEC. In addition, this study has identified an important regulatory role for the CpxA/R two component system (TCS) in the invasive abilities of AIEC HM605, a colonic mucosa-associated CD isolate. A mutation in cpxR was shown to be defective in the invasion of epithelial cells and this defect was shown to be independent of motility or the expression of Type 1 fimbriae, factors that have been shown to be involved in the invasion of another strain of AIEC, isolated from a patient with ileal CD, called LF82. The CpxA/R TCS responds to disturbances in the cell envelope and has been implicated in the virulence of a number of Gram negative pathogens. In this study it is shown that the CpxA/R TCS regulates the expression of a potentially novel invasin called SinH. SinH is found in a number of invasive strains of E. coli and Salmonella. Moreover work presented here shows that a critical mechanism underpinning AIEC persistence in macrophages is the repair of DNA bases damaged by macrophage oxidants. Together these findings provide evidence to suggest that AIEC are a diverse group of E. coli and possess diverse molecular mechanisms and virulence factors that contribute to the AIEC phenotype. In addition, AIEC may have gone through different evolutionary histories acquiring various molecular mechanisms ultimately culminating in the AIEC phenotype. The gastrointestinal (GI) tract harbors a diverse microbiota; most are symbiotic or commensal however some bacteria have the potential to cause disease (pathobiont). The work presented here provides evidence to support the model that AIEC are pathobionts. AIEC strains can be carried as commensals in healthy guts however, when the intestinal homeostasis is disrupted, such as in the compromised gut of CD patients, AIEC may behave as opportunistic pathogens and cause and/or contribute to disease by driving intestinal inflammation.

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.

Neural mechanisms of context effects on face recognition: automatic binding and context shift decrements.

Although people do not normally try to remember associations between faces and physical contexts, these associations are established automatically, as indicated by the difficulty of recognizing familiar faces in different contexts ("butcher-on-the-bus" phenomenon). The present fMRI study investigated the automatic binding of faces and scenes. In the face-face (F-F) condition, faces were presented alone during both encoding and retrieval, whereas in the face/scene-face (FS-F) condition, they were presented overlaid on scenes during encoding but alone during retrieval (context change). Although participants were instructed to focus only on the faces during both encoding and retrieval, recognition performance was worse in the FS-F than in the F-F condition ("context shift decrement" [CSD]), confirming automatic face-scene binding during encoding. This binding was mediated by the hippocampus as indicated by greater subsequent memory effects (remembered > forgotten) in this region for the FS-F than the F-F condition. Scene memory was mediated by right parahippocampal cortex, which was reactivated during successful retrieval when the faces were associated with a scene during encoding (FS-F condition). Analyses using the CSD as a regressor yielded a clear hemispheric asymmetry in medial temporal lobe activity during encoding: Left hippocampal and parahippocampal activity was associated with a smaller CSD, indicating more flexible memory representations immune to context changes, whereas right hippocampal/rhinal activity was associated with a larger CSD, indicating less flexible representations sensitive to context change. Taken together, the results clarify the neural mechanisms of context effects on face recognition.

Morphological characteristics of urban water bodies: mechanisms of change and implications for ecosystem function.

The size, shape, and connectivity of water bodies (lakes, ponds, and wetlands) can have important effects on ecological communities and ecosystem processes, but how these characteristics are influenced by land use and land cover change over broad spatial scales is not known. Intensive alteration of water bodies during urban development, including construction, burial, drainage, and reshaping, may select for certain morphometric characteristics and influence the types of water bodies present in cities. We used a database of over one million water bodies in 100 cities across the conterminous United States to compare the size distributions, connectivity (as intersection with surface flow lines), and shape (as measured by shoreline development factor) of water bodies in different land cover classes. Water bodies in all urban land covers were dominated by lakes and ponds, while reservoirs and wetlands comprised only a small fraction of the sample. In urban land covers, as compared to surrounding undeveloped land, water body size distributions converged on moderate sizes, shapes toward less tortuous shorelines, and the number and area of water bodies that intersected surface flow lines (i.e., streams and rivers) decreased. Potential mechanisms responsible for changing the characteristics of urban water bodies include: preferential removal, physical reshaping or addition of water bodies, and selection of locations for development. The relative contributions of each mechanism likely change as cities grow. The larger size and reduced surface connectivity of urban water bodies may affect the role of internal dynamics and sensitivity to catchment processes. More broadly, these results illustrate the complex nature of urban watersheds and highlight the need to develop a conceptual framework for urban water bodies.

Two versions of life: emotionally negative and positive life events have different roles in the organization of life story and identity.

Over 2,000 adults in their sixties completed the Centrality of Event Scale (CES) for the traumatic or negative event that now troubled them the most and for their most positive life event, as well as measures of current PTSD symptoms, depression, well-being, and personality. Consistent with the notion of a positivity bias in old age, the positive events were judged to be markedly more central to life story and identity than were the negative events. The centrality of positive events was unrelated to measures of PTSD symptoms and emotional distress, whereas the centrality of the negative event showed clear positive correlations with these measures. The centrality of the positive events increased with increasing time since the events, whereas the centrality of the negative events decreased. The life distribution of the positive events showed a marked peak in young adulthood whereas the life distribution for the negative events peaked at the participants' present age. The positive events were mostly events from the cultural life script-that is, culturally shared representations of the timing of major transitional events. Overall, our findings show that positive and negative autobiographical events relate markedly differently to life story and identity. Positive events become central to life story and identity primarily through their correspondence with cultural norms. Negative events become central through mechanisms associated with emotional distress.

Identifying the damage mechanisms in paper using the acoustic emission monitoring technique

This paper investigates the use of the acoustic emission (AE) monitoring technique for use in identifying the damage mechanisms present in paper associated with its production process. The microscopic structure of paper consists of a random mesh of paper fibres connected by hydrogen bonds. This implies the existence of two damage mechanisms, the failure of a fibre-fibre bond and the failure of a fibre. This paper describes a hybrid mathematical model which couples the mechanics of the mass-spring model to the acoustic wave propagation model for use in generating the acoustic signal emitted by complex structures of paper fibres under strain. The derivation of the mass-spring model can be found in [1,2], with details of the acoustic wave equation found in [3,4]. The numerical implementation of the vibro-acoustic model is discussed in detail with particular emphasis on the damping present in the numerical model. The hybrid model uses an implicit solver which intrinsically introduces artificial damping to the solution. The artificial damping is shown to affect the frequency response of the mass-spring model, therefore certain restrictions on the simulation time step must be enforced so that the model produces physically accurate results. The hybrid mathematical model is used to simulate small fibre networks to provide information on the acoustic response of each damage mechanism. The simulated AEs are then analysed using a continuous wavelet transform (CWT), described in [5], which provides a two dimensional time-frequency representation of the signal. The AEs from the two damage mechanisms show different characteristics in the CWT so that it is possible to define a fibre-fibre bond failure by the criteria listed below. The dominant frequency components of the AE must be at approximately 250 kHz or 750 kHz. The strongest frequency component may be at either approximately 250 kHz or 750 kHz. The duration of the frequency component at approximately 250 kHz is longer than that of the frequency component at approximately 750 kHz. Similarly, the criteria for identifying a fibre failure are given below. The dominant frequency component of the AE must be greater than 800 kHz. The duration of the dominant frequency component must be less than 5.00E-06 seconds. The dominant frequency component must be present at the front of the AE. Essentially, the failure of a fibre-fibre bond produces a low frequency wave and the failure of a fibre produces a high frequency pulse. Using this theoretical criteria, it is now possible to train an intelligent classifier such as the Self-Organising Map (SOM) [6] using the experimental data. First certain features must be extracted from the CWTs of the AEs for use in training the SOM. For this work, each CWT is divided into 200 windows of 5E-06s in duration covering a 100 kHz frequency range. The power ratio for each windows is then calculated and used as a feature. Having extracted the features from the AEs, the SOM can now be trained, but care is required so that the both damage mechanisms are adequately represented in the training set. This is an issue with paper as the failure of the fibre-fibre bonds is the prevalent damage mechanism. Once a suitable training set is found, the SOM can be trained and its performance analysed. For the SOM described in this work, there is a good chance that it will correctly classify the experimental AEs.

Interactions between multiple large macrofauna species and nematode communities — Mechanisms for indirect impacts of trawling disturbance

Highlights •We exposed meiofauna to 7 different large macrofauna species at high and low densities. •Macrofauna presence altered nematode community structure and reduced their abundance. •Macrofauna species had similar effects by reducing the few dominant nematode species. •Meio–macrofauna resource competition and spatial segregation are the main drivers. •Trawling effects on macrofauna affect nematode communities indirectly. Diverse assemblages of infauna in sediments provide important physical and biogeochemical services, but are under increasing pressure by anthropogenic activities, such as benthic trawling. It is known that trawling disturbance has a substantial effect on the larger benthic fauna, with reductions in density and diversity, and changes in community structure, benthic biomass, production, and bioturbation and biogeochemical processes. Largely unknown, however, are the mechanisms by which the trawling impacts on the large benthic macro- and megafauna may influence the smaller meiofauna. To investigate this, a mesocosm experiment was conducted whereby benthic nematode communities from a non-trawled area were exposed to three different densities (absent, low, normal) of 7 large (> 10 mm) naturally co-occurring, bioturbating species which are potentially vulnerable to trawling disturbance. The results showed that total abundances of nematodes were lower if these large macrofauna species were present, but no clear nematode abundance effects could be assigned to the macrofauna density differences. Nematode community structure changed in response to macrofauna presence and density, mainly as a result of the reduced abundance of a few dominant nematode species. Any detectable effects seemed similar for nearly all macrofauna species treatments, supporting the idea that there may be a general indirect, macrofauna-mediated trawling impact on nematode communities. Explanations for these results may be, firstly, competition for food resources, resulting in spatial segregation of the meio- and macrobenthic components. Secondly, different densities of large macrofauna organisms may affect the nematode community structure through different intensities of bioturbatory disturbance or resource competition. These results suggest that removal or reduced densities of larger macrofauna species as a result of trawling disturbance may lead to increased nematode abundance and hints at the validity of interference competition between large macrofauna organisms and the smaller meiofauna, and the energy equivalence hypothesis, where a trade-off is observed between groups of organisms that are dependent on a common source of energy.

Collision mechanisms in one-electron capture by slow H and He- like ions of C, N and O in H and H-2

Translational energy spectroscopy (TES) has been used to study state-selective one-electron capture by H and He-like ions of C, N and O in both H and H-2 within the range 250-900 eV amu(- 1). The main collision mechanisms leading to state-selective electron capture have been identified, their relative importance assessed and compared, where possible, with theoretical predictions and with any previous measurements based on photon emission spectroscopy. For one-electron capture in H-2, the relative importance of contributions from non- dissociative and dissociative capture as well as from two- electron capture into autoionizing states is found to be strikingly different for the cases considered. Our TES measurements in atomic hydrogen provide an important extension of previous measurements to energies below 1000 eV amu(-1) and show that, as the impact energy decreases, electron capture becomes more selective until only a single n product channel is significant. These product main channels are well described by reaction windows calculated using a Landau-Zener approach. However, the same approach applied to the more complex energy- change spectra observed in H-2 is found to be less successful.

Investigation of various growth mechanisms of solid tumour growth within the linear-quadratic model for radiotherapy

The standard linear-quadratic survival model for radiotherapy is used to investigate different schedules of radiation treatment planning to study how these may be affected by different tumour repopulation kinetics between treatments.

Neutral gas depletion mechanisms in dense low-temperature argon plasmas

Neutral gas depletion mechanisms are investigated in a dense low-temperature argon plasma-an inductively coupled magnetic neutral loop (NL) discharge. Gas temperatures are deduced from the Doppler profile of the 772.38 nm line absorbed by argon metastable atoms. Electron density and temperature measurements reveal that at pressures below 0.1 Pa, relatively high degrees of ionization (exceeding 1%) result in electron pressures, p(e) = kT(e)n(e), exceeding the neutral gas pressure. In this regime, neutral dynamics has to be taken into account and depletion through comparatively high ionization rates becomes important. This additional depletion mechanism can be spatially separated due to non-uniform electron temperature and density profiles (non-uniform ionization rate), while the gas temperature is rather uniform within the discharge region. Spatial profiles of the depletion of metastable argon atoms in the NL region are observed by laser induced fluorescence spectroscopy. In this region, the depletion of ground state argon atoms is expected to be even more pronounced since in the investigated high electron density regime the ratio of metastable and ground state argon atom densities is governed by the electron temperature, which peaks in the NL region. This neutral gas depletion is attributed to a high ionization rate in the NL zone and fast ion loss through ambipolar diffusion along the magnetic field lines. This is totally different from what is observed at pressures above 10 Pa where the degree of ionization is relatively low (

Fractal rotation isolates mechanisms for form-dependent motion in human vision

Here, we describe a motion stimulus in which the quality of rotation is fractal. This makes its motion unavailable to the translationbased motion analysis known to underlie much of our motion perception. In contrast, normal rotation can be extracted through the aggregation of the outputs of translational mechanisms. Neural adaptation of these translation-based motion mechanisms is thought to drive the motion after-effect, a phenomenon in which prolonged viewing of motion in one direction leads to a percept of motion in the opposite direction. We measured the motion after-effects induced in static and moving stimuli by fractal rotation. The after-effects found were an order of magnitude smaller than those elicited by normal rotation. Our findings suggest that the analysis of fractal rotation involves different neural processes than those for standard translational motion. Given that the percept of motion elicited by fractal rotation is a clear example of motion derived from form analysis, we propose that the extraction of fractal rotation may reflect the operation of a general mechanism for inferring motion from changes in form.

BRCA1: mechanisms of inactivation and implications for management of patients.

The BRCA1 gene was cloned in 1994 as one of the genes that conferred genetic predisposition to early-onset breast and ovarian cancer. Since then, a genetic test for identification of high-risk individuals has been developed. Despite being implicated in many important cellular pathways, including DNA repair and regulation of transcription, the exact mechanism by which inactivation of BRCA1 might lead to malignant transformation of cells remains unknown. We examine the mechanisms that underlie inactivation of BRCA1 and assess how they affect management of patients, in terms of both primary and secondary cancer prevention strategies. Furthermore, we look at the potential usefulness of BRCA1 as a prognostic tool and as a predictive marker of response to different classes of drugs. Finally, throughout this review, we draw links between the functional consequences of BRCA1 inactivation, in terms of key cellular signalling pathways, and how they might explain specific clinical observations in individuals who carry mutations in the gene.

Seasonal acclimatization of non-shivering thermogenesis in common spiny mice (Acomys cahirinus) from different habitats

We compared non-shivering thermogenesis between two adjacent populations of freshly captured common spiny mice (Acomys cahirinus) during both winter and summer. Mice were captured from north- and south-facing slopes (NFS and SFS) of the same valley that represent 'Mediterranean' and 'Desert' habitats, respectively. Oxygen consumption and body temperature responses to an injection of exogenous noradrenaline (NA) were higher during the winter than during the summer. in addition, SFS mice had a lower body temperature response to NA during the summer than the other groups of mice. This suggests that heat dissipation is likely to have been greatest in SFS mice during the summer. Overall this study shows that seasonal acclimatization of NST mechanisms is an important trait for small mammals that inhabit the Mediterranean ecosystem. Differences in physiological capabilities can occur temporally within populations across seasons, and spatially between populations that are only a short distance (200-500 m) apart.

On the need to use steady-state or operando techniques to investigate reaction mechanisms: An in situ DRIFTS and SSITKA-based study example

The nature of the surface species formed at the surface of 2 wt.% Pt/CeO2 catalyst during the forward water-gas-shift (WGS, CO + H2O -> CO2 + H-2) and the reverse reaction (RWGS) were essentially identical. More, the surface concentration of formate, carbonate and carbonyl species was similar in each case. The presence of well-resolved IR bands allowed an unequivocal relative quantitative analysis of each species, avoiding the use of the carboxylate stretching region (1600-1200 cm(-1)). However, the quantitative analysis in the case of an isotopic study was complicated due to the overlapping of the various isotope bands, yet this problem could be overcome by integrating the high-wavenumber part of the bands. The reactivity of the surface species formed under RWGS conditions was followed under two different gaseous streams. Firstly, the reactivity of these intermediates were followed under an inert gas (i.e., At), in which case carbonates were essentially stable and less reactive than formates. Secondly, the reactivity of the same surface species was followed when switching to the corresponding C-13-labelled feed (i.e., (CO2)-C-13 + H-2), in which case carbonates were exchanged significantly faster than formates. While carbonates species have been reported as reaction intermediate under reaction conditions, the increased stability or surface poisoning by these carbonates in the absence of reaction mixture was highlighted. Ultimately, this work re-emphasises the need to use steady-state conditions if the true operando reactivity of the adsorbates and structure of the solid are to be determined. (c) 2005 Elsevier B.V. All rights reserved.

The removal of dyes from textile wastewater: a study of the physical characteristics and adsorption mechanisms of diatomaceous earth

The feasibility of using diatomite for the removal of the problematic reactive dyes as well as basic dyes from textile wastewater was investigated. Methylene blue, Cibacron reactive black and reactive yellow dyes were considered. Physical characteristics of diatomite such as pH(solution), pH(ZPC), surface area, Fourier transform infrared, and scanning electron microscopy were investigated. The surface area of diatomite was found to be 27.80 m(2) g(-1) and the pH(ZPC) occurred around pH of 5.4. The results indicated that the surface charge of diatomite decreased as the pH of the solution increased with the maximum methylene blue removal from aqueous solution occurring at basic pH of around (1011). Adsorption isotherms of diatomite with methylene blue, hydrolysed reactive black and yellow dyes were constructed at different pH values, initial dye concentrations and particle sizes. The experimental results were fitted to the Langmuir, Freundlich, and Henry models. The study indicated that electrostatic interactions play an important role in the adsorption of dyes onto diatomite. A model of the adsorption mechanism of methylene blue onto diatomite is proposed. (C) 2003 Elsevier Ltd. All rights reserved.