The relevance of bacterial isoprenoid biosynthetic pathways for host-microbe interactions

This thesis was undertaken to investigate the relevance of two bacterial isoprenoid biosynthetic pathways (Mevalonate (MVAL) and 2-C-methyl-D-erythritol 4-phosphate (MEP)) for host-microbe interactions. We determined a significant reduction in microbial diversity in the murine gut microbiota (by next generation sequencing) following oral administration of a common anti-cholesterol drug Rosuvastatin (RSV) that targets mammalian and bacterial HMG-CoA reductase (HMG-R) for inhibition of MVAL formation. In tandem we identified significant hepatic and intestinal off-target alterations to the murine metabolome indicating alterations in inflammation, bile acid profiles and antimicrobial peptide synthesis with implications on community structure of the gastrointestinal microbiota in statin-treated animals. However we found no effect on local Short Chain Fatty Acid biosynthesis (metabolic health marker in our model). We demonstrated direct inhibition of bacterial growth in-vitro by RSV which correlated with reductions in bacterial MVAL formation. However this was only at high doses of RSV. Our observations demonstrate a significant RSV-associated impact on the gut microbiota prompting similar human analysis. Successful deletion of another MVAL pathway enzyme (HMG-CoA synthase (mvaS)) involved in Listeria monocytogenes EGDe isoprenoid biosynthesis determined that the enzyme is non-essential for normal growth and in-vivo pathogenesis of this pathogen. We highlight potential evidence for alternative means of synthesis of the HMG-CoA substrate that could render mvaS activity redundant under our test conditions. Finally, we showed by global gene expression analysis (Massive Analysis of cDNA Ends (MACE RNA-seq) a significant role for the penultimate MEP pathway metabolite (E)-4-hydroxy-3-methyl-2-but-2-enyl pyrophosphate (HMBPP) in significant up regulation of genes of immunity and antigen presentation in THP-1 cells at nanomolar levels. We infected THP-1 cells with wild type or HMBPP under/over-producing L. monoctyogenes EGDe mutants and determined subtle effects of HMBPP upon overall host responses to Listeria infection. Overall our findings provide greater insights regarding bacterial isoprenoid biosynthetic pathways for host-microbe/microbe-host dialogue.

A multilevel algorithm for force-directed graph drawing

We describe a heuristic method for drawing graphs which uses a multilevel technique combined with a force-directed placement algorithm. The multilevel process groups vertices to form clusters, uses the clusters to define a new graph and is repeated until the graph size falls below some threshold. The coarsest graph is then given an initial layout and the layout is successively refined on all the graphs starting with the coarsest and ending with the original. In this way the multilevel algorithm both accelerates and gives a more global quality to the force- directed placement. The algorithm can compute both 2 & 3 dimensional layouts and we demonstrate it on a number of examples ranging from 500 to 225,000 vertices. It is also very fast and can compute a 2D layout of a sparse graph in around 30 seconds for a 10,000 vertex graph to around 10 minutes for the largest graph. This is an order of magnitude faster than recent implementations of force-directed placement algorithms.

Maintenance therapy with cisapride after healing of erosive oesophagitis:a double-blind placebo-controlled trial

There are few data on the role of prokinetic agents as maintenance therapy in moderately severe reflux oesophagitis despite the high relapse rate of this condition after healing.

Detection of sensor decalibration using the asymptotic local approach

A novel method for the detection of linear decalibration of sensors is proposed. The presence of a fault is indicated as a change in the mean of a white noise sequence. A simulation example is described which shows the success of the technique.

An Investigation Into Improving Off-Design Performance in a Turbocharger Turbine Utilizing Non-Radial Blading

Off-design performance now plays a vital role in the design decisions made for automotive turbocharger turbines. Of particular interest is extracting more energy at high pressure ratios and lower rotational speeds. In this region of operation the U/C value will be low and the rotor will experience high values of positive incidence at the inlet. The positive incidence causes flow to separate on the suction surface and produces high blade loading at inlet, which drives tip leakage. A CFD analysis has been carried out on a number of automotive turbines utilizing non-radial fibred blading. To help improve secondary flows yet meet stress requirements a number of designs have been investigated. The inlet blade angle has been modified in a number of ways. Firstly, the blading has been adjusted as to provide a constant back swept angle in the span wise direction. Using the results of the constant back swept blading studies, the back swept blade angle was then varied in the span wise direction. In addition to this, in an attempt to avoid an increase in stress, the effect of varying the leading edge profile of the blade was investigated. It has been seen that off-design performance is improved by implementing back swept blading at the inlet. Varying the inlet angle in the span wise direction provided more freedom for meeting stress requirements and reduces the negative impact on blade performance at the design point. The blade leading edge profile was seen to offer small improvements during off-design operation with minimal effects on stress within the rotor. However, due to the more pointed nature of the leading edge, the rotor was less tolerant to flow misalignment at the design point.

Adaptation and Evaluation of the Neighborhood Environment Walkability Scale in India (NEWS-India)

Physical inactivity is the fourth leading risk factor for global mortality, with most of these deaths occurring in low and middle-income countries (LMICs) like India. Research from developed countries has consistently demonstrated associations between built environment features and physical activity levels of populations. The development of culturally sensitive and reliable measures of the built environment is a necessary first step for accurate analysis of environmental correlates of physical activity in LMICs. This study systematically adapted the Neighborhood Environment Walkability Scale (NEWS) for India and evaluated aspects of test-retest reliability of the adapted version among Indian adults. Cultural adaptation of the NEWS was conducted by Indian and international experts. Semi-structured interviews were conducted with local residents and key informants in the city of Chennai, India. At baseline, participants (N = 370; female = 47.2%) from Chennai completed the adapted NEWS-India surveys on perceived residential density, land use mix-diversity, land use mix-access, street connectivity, infrastructure and safety for walking and cycling, aesthetics, traffic safety, and safety from crime. NEWS-India was administered for a second time to consenting participants (N = 62; female = 53.2%) with a gap of 2–3 weeks between successive administrations. Qualitative findings demonstrated that built environment barriers and constraints to active commuting and physical activity behaviors intersected with social ecological systems. The adapted NEWS subscales had moderate to high test-retest reliability (ICC range 0.48–0.99). The NEWS-India demonstrated acceptable measurement properties among Indian adults and may be a useful tool for evaluation of built environment attributes in India. Further adaptation and evaluation in rural and suburban settings in India is essential to create a version that could be used throughout India.

Analisador de espectro de baixo custo com frequência de operação entre 2 e 3 GHz

Com o surgimento de novos sistemas de telecomunicações sem fios, que necessitam de maiores potências de emissão e largura de banda disponível, surgem os regulamentos que controlam as emissões rádio. Só assim estas tecnologias podem coexistir em bandas próximas, com o máximo desempenho e com a garantia que os níveis de poluição electromagnética não são ultrapassados. Cada vez mais, regulamentos que limitam a potência da transmissão têm em vista questões de saúde pública e por isso devem ser estritamente respeitados. Para se poder controlar as emissões rádio é necessário um dispositivo que consiga analisar o espectro rádio. Um dos instrumentos fundamentais na metrologia de radiofrequência é o analisador de espectros, que tem como principal função apresentar a potência de porções do espectro em função da frequência. Existem vários tipos de analisadores espectrais, que se baseiam em arquitecturas de recepção distintas. O tipo de analisador define a sua complexidade e o tipo de análises que consegue fazer. Com esta dissertação pretende-se mostrar a implementação de um analisador de espectro portátil, de baixo custo, baseado num receptor heteródino e com uma frequência de operação compreendida entre os 2 e os 3 GHz. Este projecto abrange diversas áreas, desde o hardware de recepção rádio, passando pelo microcontrolador que faz a aquisição de dados e comunicação com o computador, acabando na aplicação que foi desenvolvida em Java para permitir ao utilizador uma interface de utilização simples e funcional. Foi também desenvolvida com sucesso uma antena impressa adequada à banda de frequência referida. Embora tenham existidos problemas simples, um na localização do filtro passa-banda e o outro na resposta do filtro intermédio, os objectivos foram alcançados obtendo-se um analisador de espectro portátil, funcional e de baixo custo, conforme pretendido. O analisador tem um erro máximo na detecção de potência de 2,5 dB e o tempo de varrimento máximo é cerca de 16 segundos com 500 pontos de resolução. Foram realizadas várias medições e uma comparação com um analisador de espectros comercial, para demonstrar o funcionamento e desempenho do analisador desenvolvido, tendo os resultados sido bastante promissores. A funcionalidade deste analisador medir a potência do sinal ao longo do tempo é uma mais-valia face ao analisador comercial utilizado para a comparação.

Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.

L'Écho de Paris

1889/12/01 (Numéro 2023).