Synthesis of unusual alpha-amino acids and study of the effect of their incorporation into antimicrobial peptides. Total synthesis of biactive marine natural products and analogues thereof

The principle theme of this thesis was the synthesis of bioactive compounds. To this end, this work was focus on two main projects. The first one, which was carried out in the Department of Chemistry of the University of Girona under the supervision of Dr Montserrat Heras, concerned the synthesis of new unnatural amino acids bearing a pyrimidine ring within their side chain for incorporation into the antimicrobial peptide BP100 following a rational design in order to improve its biological profile. On the other hand, the second chapter of this thesis was developed in collaboration with the Laboratoire de Chimie Organique (ESPCI-ParisTech, Paris, France) under the guidance of Pr Janine Cossy and Dr Arseniyadis. This chapter was centered on the total synthesis of three marine natural products with complex structures and interesting biological activities: acremolide B, (–) bitungolide F and lyngbouilloside.

Understanding mixing efficiency in the oceans. Do the nonlinearities of the equation of state matter?

There exist two central measures of turbulent mixing in turbulent stratified fluids that are both caused by molecular diffusion: 1) the dissipation rate D(APE) of available potential energy APE; 2) the turbulent rate of change Wr, turbulent of background gravitational potential energy GPEr. So far, these two quantities have often been regarded as the same energy conversion, namely the irreversible conversion of APE into GPEr, owing to the well known exact equality D(APE)=Wr, turbulent for a Boussinesq fluid with a linear equation of state. Recently, however, Tailleux (2009) pointed out that the above equality no longer holds for a thermally-stratified compressible, with the ratio ξ=Wr, turbulent/D(APE) being generally lower than unity and sometimes even negative for water or seawater, and argued that D(APE) and Wr, turbulent actually represent two distinct types of energy conversion, respectively the dissipation of APE into one particular subcomponent of internal energy called the "dead" internal energy IE0, and the conversion between GPEr and a different subcomponent of internal energy called "exergy" IEexergy. In this paper, the behaviour of the ratio ξ is examined for different stratifications having all the same buoyancy frequency N vertical profile, but different vertical profiles of the parameter Υ=α P/(ρCp), where α is the thermal expansion coefficient, P the hydrostatic pressure, ρ the density, and Cp the specific heat capacity at constant pressure, the equation of state being that for seawater for different particular constant values of salinity. It is found that ξ and Wr, turbulent depend critically on the sign and magnitude of dΥ/dz, in contrast with D(APE), which appears largely unaffected by the latter. These results have important consequences for how the mixing efficiency should be defined and measured in practice, which are discussed.

Resistivity imaging survey of the Roman barrows at Bartlow, Cambridgeshire, UK

Resistivity imaging was carried out on four large Roman barrows at Bartlow in Cambridgeshire. The geophysical survey formed part of a wider research project designed to record and assess the landscape context of the largest surviving Roman burial mounds in Britain. The barrows today range in height from 6.6 m to 13.2 m and their steep profile loosed particular practical and modelling challenges. Data were obtained using a Campus Geopulse resistance meter with up to 50 electrodes spaced at 1 m intervals and lines up to 76 m long. A total of 24 lines was obtained. Topographic corrections were applied to the pseudosections, whichwere inverted using Res 2 Dinv and Res3 Dinv. Resistivity imaging was particularly successful in identifying evidence for the antiquarian explorations of the site. Central collapse features or in-filled tunnels image as high resistance features in all barrows and in one (Barrow IV) there is also a low resistance feature in the approximate position of a known antiquarian tunnel. Barrow VI had a thick covering of high-resistivity that may relate to nineteenth century landscaping and reconstruction of this monument. Resistivity imaging also revealed possible evidence for ancient revetments in all four large barrows. Copyright (c) 2006 John Wiley & Sons, Ltd.

Coupled simulations of the Indian monsoon intraseasonal oscillation using a fine-resolution mixed-layer ocean model

The intraseasonal variability (ISV) of the Indian summer monsoon is dominated by a 30–50 day oscillation between “active” and “break” events of enhanced and reduced rainfall over the subcontinent, respectively. These organized convective events form in the equatorial Indian Ocean and propagate north to India. Atmosphere–ocean coupled processes are thought to play a key role the intensity and propagation of these events. A high-resolution, coupled atmosphere–mixed-layer-oceanmodel is assembled: HadKPP. HadKPP comprises the Hadley Centre Atmospheric Model (HadAM3) and the K Profile Parameterization (KPP) mixed-layer ocean model. Following studies that upper-ocean vertical resolution and sub-diurnal coupling frequencies improve the simulation of ISV in SSTs, KPP is run at 1 m vertical resolution near the surface; the atmosphere and ocean are coupled every three hours. HadKPP accurately simulates the 30–50 day ISV in rainfall and SSTs over India and the Bay of Bengal, respectively, but suffers from low ISV on the equator. This is due to the HadAM3 convection scheme producing limited ISV in surface fluxes. HadKPP demonstrates little of the observed northward propagation of intraseasonal events, producing instead a standing oscillation. The lack of equatorial ISV in convection in HadAM3 constrains the ability of KPP to produce equatorial SST anomalies, which further weakens the ISV of convection. It is concluded that while atmosphere–ocean interactions are undoubtedly essential to an accurate simulation of ISV, they are not a panacea for model deficiencies. In regions where the atmospheric forcing is adequate, such as the Bay of Bengal, KPP produces SST anomalies that are comparable to the Tropical Rainfall Measuring Mission Microwave Imager (TMI) SST analyses in both their magnitude and their timing with respect to rainfall anomalies over India. HadKPP also displays a much-improved phase relationship between rainfall and SSTs over a HadAM3 ensemble forced by observed SSTs, when both are compared to observations. Coupling to mixed-layer models such as KPP has the potential to improve operational predictions of ISV, particularly when the persistence time of SST anomalies is shorter than the forecast lead time.

Independent evaluation of the ability of spaceborne radar and lidar to retrieve the microphysical and radiative properties of ice clouds

The combination of radar and lidar in space offers the unique potential to retrieve vertical profiles of ice water content and particle size globally, and two algorithms developed recently claim to have overcome the principal difficulty with this approach-that of correcting the lidar signal for extinction. In this paper "blind tests" of these algorithms are carried out, using realistic 94-GHz radar and 355-nm lidar backscatter profiles simulated from aircraft-measured size spectra, and including the effects of molecular scattering, multiple scattering, and instrument noise. Radiation calculations are performed on the true and retrieved microphysical profiles to estimate the accuracy with which radiative flux profiles could be inferred remotely. It is found that the visible extinction profile can be retrieved independent of assumptions on the nature of the size distribution, the habit of the particles, the mean extinction-to-backscatter ratio, or errors in instrument calibration. Local errors in retrieved extinction can occur in proportion to local fluctuations in the extinction-to-backscatter ratio, but down to 400 m above the height of the lowest lidar return, optical depth is typically retrieved to better than 0.2. Retrieval uncertainties are greater at the far end of the profile, and errors in total optical depth can exceed 1, which changes the shortwave radiative effect of the cloud by around 20%. Longwave fluxes are much less sensitive to errors in total optical depth, and may generally be calculated to better than 2 W m(-2) throughout the profile. It is important for retrieval algorithms to account for the effects of lidar multiple scattering, because if this is neglected, then optical depth is underestimated by approximately 35%, resulting in cloud radiative effects being underestimated by around 30% in the shortwave and 15% in the longwave. Unlike the extinction coefficient, the inferred ice water content and particle size can vary by 30%, depending on the assumed mass-size relationship (a problem common to all remote retrieval algorithms). However, radiative fluxes are almost completely determined by the extinction profile, and if this is correct, then errors in these other parameters have only a small effect in the shortwave (around 6%, compared to that of clear sky) and a negligible effect in the longwave.

Resolution of the uncertainties in the radiative forcing of HFC-134a

HFC-134a (CF3CH2F) is the most rapidly growing hydrofluorocarbon in terms of atmospheric abundance. It is currently used in a large number of household refrigerators and air-conditioning systems and its concentration in the atmosphere is forecast to increase substantially over the next 50–100 years. Previous estimates of its radiative forcing per unit concentration have differed significantly 25%. This paper uses a two-step approach to resolve this discrepancy. In the first step six independent absorption cross section datasets are analysed. We find that, for the integrated cross section in the spectral bands that contribute most to the radiative forcing, the differences between the various datasets are typically smaller than 5% and that the dependence on pressure and temperature is not significant. A “recommended'' HFC-134a infrared absorption spectrum was obtained based on the average band intensities of the strongest bands. In the second step, the “recommended'' HFC-134a spectrum was used in six different radiative transfer models to calculate the HFC-134a radiative forcing efficiency. The clear-sky instantaneous radiative forcing, using a single global and annual mean profile, differed by 8%, between the 6 models, and the latitudinally-resolved adjusted cloudy sky radiative forcing estimates differed by a similar amount.

Study of the variation of the input impedance of induction machines with frequency

The results of a study of the variation of three-phase induction machines' input impedance with frequency are proposed. A range of motors were analysed, both two-pole and four-pole, and the magnitude and phase of the input impedance were obtained over a wide frequency range of 20 Hz-1 MHz. For test results that would be useful in the prediction of the performance of induction machines during typical use, a test procedure was developed to represent closely typical three-phase stator coil connections when the induction machine is driven by a three-phase inverter. In addition, tests were performed with the motor's cases both grounded and not grounded. The results of the study show that all induction machines of the type considered exhibit a multiresonant impedance profile, where the input impedance reaches at least one maximum as the input frequency is increased. Furthermore, the test results show that the grounding of the motor's case has a significant effect on the impedance profile. Methods to exploit the input impedance profile of an induction machine to optimise machine and inverter systems are also discussed.

Proceedings of the West Africa Built Environment Research (WABER) Conference 2010

FOREWORD Welcome to this West Africa Built Environment Research (WABER) conference taking place here in Ghana. Thank you for coming and welcome to Accra. The main aims of the WABER conference are: to help young researchers and early-career scholars in West Africa to develop their research work and skills through constructive face-to-face interaction with experienced academics; to provide a platform for networking and collaborative work among senior built environment academics in West Africa; and to serve as a vehicle for developing the field of construction management and economics in Africa. Waber 2009 The WABER event in 2009 was held at the British Council in Accra, Ghana on 2-3 June. The event was a resounding success. It attracted participation from 32 researchers, from 12 different institutions, who presented their work to an audience of approximately 100 people. Each presenter received immediate and constructive feedback from an international panel. The event was opened by Professor K.K. Adarkwa, Vice Chancellor of KNUST, Kumasi, Ghana, with several senior academics and researchers from universities, polytechnics, and other institutions in Ghana and Nigeria in attendance. There was also a significant level of attendance by senior construction practitioners in Ghana. Thank you to the School of Construction Management and Engineering, University of Reading, UK for funding the inaugural event in 2009. We are also grateful to all of you who helped to make the event a success and to those of you who have joined us here today to build upon the success and legacy of WABER 2009. Waber 2010 This year, we have 60+ peer-reviewed papers and presentations on topics relating to Building services and maintenance, Construction costs, Construction design and technology, Construction education, Construction finance, Construction procurement, Contract administration, Contract management, Contractor development, Decision support systems, Dispute resolution, Economic development, Energy efficiency, Environment and sustainability, Health and safety, Human resources, Information technology, Marketing, Materials science, Organisation strategy and business performance, Productivity, Project management, Quantity surveying, Real estate and planning, Solar energy systems, Supply chain management and Urban development. We hope that these papers will generate interest among delagates and stimulate discussion here and beyond the conference into the wider community of academia and industry. The delegates at this conference come from 10 different countries. This provides a rich international and multicultural blend and a perfect platform for networking and developing collaborations. This year we are blessed to have three high profile keynote speakers in the persons of Professor George Ofori (National University of Singapore), Dr Roine Leiringer (University of Reading, UK) and Professor Will Hughes (University of Reading, UK). We are also thankful to Dr Chris Harty (University of Reading, UK) who is facilitating the Research Skills Workshop on ‘Writing a scientific article’. Thank you to Dr Sena Agyepong of our conference organising team for her capable management of local organising arrangements. And above all, thank you to all of you for coming to this conference. Enjoy and have a safe journey back home. Dr Samuel Laryea School of Construction Management and Engineering University of Reading, July 2010

A comparison of the active surveillance of scrapie in the European Union

The abattoir and the fallen stock surveys constitute the active surveillance component aimed at improving the detection of scrapie across the European Union. Previous studies have suggested the occurrence of significant differences in the operation of the surveys across the EU. In the present study we assessed the standardisation of the surveys throughout time across the EU and identified clusters of countries with similar underlying characteristics allowing comparisons between them. In the absence of sufficient covariate information to explain the observed variability across countries, we modelled the unobserved heterogeneity by means of non-parametric distributions on the risk ratios of the fallen stock over the abattoir survey. More specifically, we used the profile likelihood method on 2003, 2004 and 2005 active surveillance data for 18 European countries on classical scrapie, and on 2004 and 2005 data for atypical scrapie separately. We extended our analyses to include the limited covariate information available, more specifically, the proportion of the adult sheep population sampled by the fallen stock survey every year. Our results show that the between-country heterogeneity dropped in 2004 and 2005 relative to that of 2003 for classical scrapie. As a consequence, the number of clusters in the last two years was also reduced indicating the gradual standardisation of the surveillance efforts across the EU. The crude analyses of the atypical data grouped all the countries in one cluster and showed non-significant gain in the detection of this type of scrapie by any of the two sources. The proportion of the population sampled by the fallen stock appeared significantly associated with our risk ratio for both types of scrapie, although in opposite directions: negative for classical and positive for atypical. The initial justification for the fallen stock, targeting a high-risk population to increase the likelihood of case finding, appears compromised for both types of scrapie in some countries.

Urban mammals: what does the future hold? An analysis of the factors affecting patterns of use of residential gardens in Great Britain

1Urban areas are predicted to grow significantly in the foreseeable future because of increasing human population growth. Predicting the impact of urban development and expansion on mammal populations is of considerable interest due to possible effects on biodiversity and human-wildlife conflict. 2The British government has recently announced a substantial housing programme to meet the demands of its growing population and changing socio-economic profile. This is likely to result in the construction of high-density, low-cost housing with small residential gardens. To assess the potential effects of this programme, we analysed the factors affecting the current pattern of use of residential gardens by a range of mammal species using a questionnaire distributed in wildlife and gardening magazines and via The Mammal Society. 3Twenty-two species/species groups were recorded. However, the pattern of garden use by individual species was limited, with only six species/species groups (bats, red fox Vulpes vulpes, grey squirrel Sciurus carolinensis, hedgehog Erinaceus europaeus, mice, voles) recorded as frequent visitors to > 20% of gardens in the survey. 4There was a high degree of association between the variables recorded in the study, such that it was difficult to quantify the effects of individual variables. However, all species/species groups appeared to be negatively affected by the increased fragmentation and reduced proximity of natural and semi-natural habitats, decreasing garden size and garden structure, but to differing degrees. Patterns of garden use were most clearly affected by house location (city, town, village, rural), with garden use declining with increasing urbanization for the majority of species/species groups, except red foxes and grey squirrels. Increasing urbanization is likely to be related to a wide range of interrelated factors, any or all of which may affect a range of mammal species. 5Overall, the probable effects of the planned housing development programme in Britain are not likely to be beneficial to mammal populations, although the pattern of use examined in this study may represent patterns of habitat selection by species rather than differences in distribution or abundance. Consequently, additional data are required on the factors affecting the density of species within urban environments.

Comparison of the global gene expression profiles produced by methylparaben, n-butylparaben and 17 beta-oestradiol in MCF7 human breast cancer cells

Since the alkyl esters of p-hydroxybenzoic acid (parabens) can be measured intact in the human breast and possess oestrogenic properties, it has been suggested that they could contribute to an aberrant burden of oestrogen signalling in the human breast and so play a role in the rising incidence of breast cancer. However, although parabens have been shown to regulate a few single genes (reporter genes, pS2, progesterone receptor) in a manner similar to that of 17 beta-oestradiol, the question remains as to the full extent of the similarity in the overall gene profile induced in response to parabens compared with 17 beta-oestradiol. The GE-Amersham CodeLink 20 K human expression microarray system was used to profile the expression of 19881 genes in MCF7 human breast cancer cells following a 7-day exposure to 5 x 10(-4) m methylparaben, 10(-5) m n-butylparaben and 10(-8) m 17 beta-oestradiol. At these concentrations, the parabens gave growth responses in MCF7 cells of similar magnitude to 17 beta-oestradiol. The study identified genes which are upregulated or downregulated to a similar extent by methylparaben, n-butylparaben and 17 beta-oestradiol. However, the majority of genes were not regulated in the same way by all three treatments. Some genes responded differently to parabens from 17 beta-oestradiol, and furthermore, differences in expression of some genes could be detected even between the two individual parabens. Therefore, although parabens possess oestrogenic properties, their mimicry in terms of global gene expression patterns is not perfect and differences in gene expression profiles could result in consequences to the cells that are not identical to those following exposure to 17 beta-oestradiol. Copyright (c) 2006 John Wiley & Sons, Ltd.

Transcriptional profiling of the LPS induced NF-kappaB response in macrophages

BACKGROUND: Exposure of macrophages to bacterial products such as lipopolysaccharide (LPS) results in activation of the NF-kappaB transcription factor, which orchestrates a gene expression programme that underpins the macrophage-dependent immune response. These changes include the induction or repression of a wide range of genes that regulate inflammation, cell proliferation, migration and cell survival. This process is tightly regulated and loss of control is associated with conditions such as septic shock, inflammatory diseases and cancer. To study this response, it is important to have in vitro model systems that reflect the behaviour of cells in vivo. In addition, it is necessary to understand the natural differences that can occur between individuals. In this report, we have investigated and compared the LPS response in macrophage derived cell lines and peripheral blood mononuclear cell (PBMC) derived macrophages. RESULTS: Gene expression profiles were determined following LPS treatment of THP-1 cells for 1 and 4 hours. LPS significantly induced or repressed 72 out of 465 genes selected as being known or putative NF-kappaB target genes, which exhibited 4 temporal patterns of expression. Results for 34 of these genes, including several genes not previously identified as LPS target genes, were validated using real time PCR. A high correlation between microarray and real time PCR data was found. Significantly, the LPS induced expression profile of THP-1 cells, as determined using real time PCR, was found to be very similar to that of human PBMC derived macrophages. Interestingly, some differences were observed in the LPS response between the two donor PBMC macrophage populations. Surprisingly, we found that the LPS response in U937 cells was dramatically different to both THP-1 and PBMC derived macrophages. CONCLUSION: This study revealed a dynamic and diverse transcriptional response to LPS in macrophages, involving both the induction and repression of gene expression in a time dependent manner. Moreover, we demonstrated that the LPS induced transcriptional response in the THP-1 cell line is very similar to primary PBMC derived macrophages. Therefore, THP-1 cells represent a good model system for studying the mechanisms of LPS and NF-kappaB dependent gene expression.

Ingestion of onion soup high in quercetin inhibits platelet aggregation and essential components of the collagen-stimulated platelet activation pathway in man: a pilot study

Epidemiological data suggest that those who consume a diet rich in quercetin-containing foods may have a reduced risk of CVD. Furthermore, in vitro and ex vivo studies have observed the inhibition of collagen-induced platelet activation by quercetin. The aim of the present study was to investigate the possible inhibitory effects of quercetin ingestion from a dietary source on collagen-stimulated platelet aggregation and signalling. A double-blind randomised cross-over pilot study was undertaken. Subjects ingested a soup containing either a high or a low amount of quercetin. Plasma quercetin concentrations and platelet aggregation and signalling were assessed after soup ingestion. The high-quercetin soup contained 69 mg total quercetin compared with the low-quercetin soup containing 5 mg total quercetin. Plasma quercetin concentrations were significantly higher after high-quercetin soup ingestion than after low-quercetin soup ingestion and peaked at 2.59 (SEM 0.42) mu mol/l. Collagen-stimulated (0.5 mu g/ml) platelet aggregation was inhibited after ingestion of the high-quercetin soup in a time-dependent manner. Collagen-stimulated tyrosine phosphorylation of a key component of the collagen-signalling pathway via glycoprotein VI, Syk, was significantly inhibited by ingestion of the high-quercetin soup. The inhibition of Syk tyrosine phosphorylation was correlated with the area under the curve for the high-quercetin plasma profile. In conclusion, the ingestion of quercetin from a dietary source of onion soup could inhibit some aspects of collagen-stimulated platelet aggregation and signalling ex vivo. This further substantiates the epidemiological data suggesting that those who preferentially consume high amounts of quercetin-containing foods have a reduced risk of thrombosis and potential CVD risk.

Expression profiles in the progression of ductal carcinoma in the breast

An understanding of the multi-step nature of cancer as it is in the breast, as a series of pivotal genetic/epigenetic modifications is irrefutably a milestone in diagnostics, prognostics and eventually providing a cure. Here we have utilised a variant of analysis of variance (ANOVA) as a model for the identification and tracking of specific mRNA species whose transcription has been significantly altered at each grade in the progression of ductal carcinoma, making it possible to correlate histological progression with the genetic events underlying breast cancer. We show that in the progression of ductal carcinomas, from grade 1 to 3, there is a reduction in the actual number of mRNA species, which are significantly over or under expressed. We also show that this technique can be employed to generate differential gene expression patterns, whereby the combined expression profile of the tailored spectra of genes in the comparison of each ductal grade is sufficient to render them on clearly separate arms of an array-wise hierarchical cluster dendrogram.