Optical doping and damage formation in AIN by Eu implantation

AlN films grown on sapphire were implanted with 300 keV Eu ions to fluences from 3×1014 to 1.4×1017 atoms/cm2 in two different geometries: “channeled” along the c-axis and “random” with a 10° angle between the ion beam and the surface normal. A detailed study of implantation damage accumulation is presented. Strong ion channeling effects are observed leading to significantly decreased damage levels for the channeled implantation within the entire fluence range. For random implantation, a buried amorphous layer is formed at the highest fluences. Red Eu-related photoluminescence at room temperature is observed in all samples with highest intensities for low damage samples (low fluence and channeled implantation) after annealing. Implantation damage, once formed, is shown to be stable up to very high temperatures.FCT - POCI/FIS/57550/2004FCT - PTDC/FIS/66262/2006FCT - PTDC/CTM/100756/200

Association of Fecal Microbial Diversity and Taxonomy with Selected Enzymatic Functions

Few microbial functions have been compared to a comprehensive survey of the human fecal microbiome. We evaluated determinants of fecal microbial β-glucuronidase and β-glucosidase activities, focusing especially on associations with microbial alpha and beta diversity and taxonomy. We enrolled 51 healthy volunteers (26 female, mean age 39) who provided questionnaire data and multiple aliquots of a stool, from which proteins were extracted to quantify β-glucuronidase and β-glucosidase activities, and DNA was extracted to amplify and pyrosequence 16S rRNA gene sequences to classify and quantify microbiome diversity and taxonomy. Fecal β-glucuronidase was elevated with weight loss of at least 5 lb. (P = 0.03), whereas β-glucosidase was marginally reduced in the four vegetarians (P = 0.06). Both enzymes were correlated directly with microbiome richness and alpha diversity measures, directly with the abundance of four Firmicutes Clostridia genera, and inversely with the abundance of two other genera (Firmicutes Lactobacillales Streptococcus and Bacteroidetes Rikenellaceae Alistipes) (all P = 0.05–0.0001). Beta diversity reflected the taxonomic associations. These observations suggest that these enzymatic functions are performed by particular taxa and that diversity indices may serve as surrogates of bacterial functions. Independent validation and deeper understanding of these associations are needed, particularly to characterize functions and pathways that may be amenable to manipulation

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/human​n. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.National Institutes of Health (U.S.) (U54HG004968

Colonic bacterial metabolites and human health

The influence of the microbial-mammalian metabolic axis is becoming increasingly important for human health. Bacterial fermentation of carbohydrates (CHOs) and proteins produces short-chain fatty acids (SCFA) and a range of other metabolites including those from aromatic amino acid (AAA) fermentation. SCFA influence host health as energy sources and via multiple signalling mechanisms. Bacterial transformation of fibre-related phytochemicals is associated with a reduced incidence of several chronic diseases. The 'gut-liver axis' is an emerging area of study. Microbial deconjugation of xenobiotics and release of aromatic moieties into the colon can have a wide range of physiological consequences. In addition, the role of the gut microbiota in choline deficiency in non-alcoholic fatty liver disease (NAFLD) and insulin resistance is receiving increased attention

Endor study of Cr5+ in the antiferroelectric NH4H2AsO4

We have verified that the proton Slater configurations associated with the Cr5+ centre in antiferroelectric ADA were of the lateral type : such a situation enhances the coupling of the centre With its environment. The results are compared with those obtained previously for the Cr5+ centre in ferroelectric KDA.Nous avons vérifié que les configurations de Slater des protons associées au centre Cr5+ étaient de type latéral dans l'antiferroélectrique ADA : une telle situation favorise le couplage du centre avec son environnement. Les résultats sont comparés à ceux obtenus précédemment pour le centre Cr 5+ dans le ferroélectrique KDA

Mise en évidence par ENDOR des configurations de domaines dans la phase ferroélectrique du cristal de KH2 AsO4 irradié

Using ENDOR spectroscopy, we have reexamined the radical AsO4- 4 created by gamma irradiation in KH2AsO4 crystals. An earlier study by Dalal et al. had shown the existence of two types of domains in the ferro-electric phase. By considering the origin of a small splitting of the ENDOR lines, we show that in fact this technique allows the detection of the four domain types which are expected to exist in KH 2AsO4 as in KH2PO4.Nous avons réexaminé par ENDOR le radical AsO4-4 créé par irradiation gamma dans le cristal de KH2AsO4. L'étude antérieure de Dalal et al. avait mis en évidence l'existence de deux types de domaines en phase ferroélectrique. Par la prise en considération d'un léger dédoublement des raies ENDOR, nous montrons que cette technique permet en fait de déceler les quatre types de domaines qu'il est légitime d'attendre dans KH2AsO 4, à l'image de KH2PO4

Détection par RPE et ENDOR d'un changement de configuration des protons autour d'un radical AsO3h- en phase ferroélectrique du cristal de KH2AsO4 irradié

ESR at variable temperature and ENDOR measurements at 1.5 K show that in the ferroelectric phase of KDA a reversible change takes place in the configuration of the protons of the O—H...O hydrogen bonds linking the lattice and a radical defect (created by gamma irradiation) which is identified as AsO 3H-. The radical configuration L which is stable in the paraelectric phase is derived from Slater configurations of the lateral type. Under the influence which the surroundings lattice exerts in the ferroelectric phase, the radical configuration is transformed partly to the configuration L1 which derives from the high and low Slater configurations.La RPE à température variable et l'ENDOR à 1,5 K nous permettent de montrer qu'en phase ferroélectrique de KDA a lieu un changement réversible de la configuration des protons dans les liaisons hydrogène O—H...O qui relient au réseau un centre radicalaire créé par irradiation aux gammas et que nous identifions à AsO3H-. La configuration radicalaire L stable dans la phase paraélectrique dérive des configurations de Slater du type latéral. Sous l'influence de la contrainte exercée par le milieu en phase ferroélectrique, elle se transforme partiellement en la configuration radicalaire L1 qui dérive des configurations de Slater du type haut et bas

Etude par RPE et ENDOR des conséquences de la transition de phase para-ferroélectrique sur le comportement de radicaux libres dans le cristal de KH2AsO4 irradié

The behaviour at the phase transition and in the ferroelectric phase of the free radicals created by γ irradiation in KDA is now better understood following various EPR and ENDOR studies. The symmetry lowering caused by the appearance of the ferroelectric ordering leads to a splitting of the AsO 2-3 radicals into chemically distinct species, unlike the case of the AsO4-4 radical. Various thermally reversible radical transformations are observed all of which tend to adjust these species to the ferroelectric surroundings.Le comportement à la transition de phase et en phase ferroélectrique des radicaux libres créés par irradiation γ dans KDA est mieux compris, à la suite de diverses études par RPE et ENDOR. L'abaissement de symétrie provoqué par l'apparition de l'ordre ferroélectrique entraîne un dédoublement des radicaux de type AsO2-3 en des espèces chimiquement différentes — ce qui n'est pas le cas pour le radical de type AsO4-4. Diverses transformations radicalaires thermiquement réversibles sont observées et tendent toutes à réaliser une meilleure adaptation de ces espèces à l'environnement ferroélectrique

Étude endor dans le ferroélectrique KH2AsO4 irradié d'un radical libre AsO3H- localisé près d'une impureté

In a previous EPR study we observed transformations of free radicals at the para-ferroelectric phase transition in irradiated potassium arsenate crystals. An ENDOR study of one of the radicals in question has now provided information which consolidates the previous hypotheses. We also show that the existence of these radicals depends on the présence of silicon impurities in the crystal.Lors d'une étude RPE antérieure nous avions mis en évidence des transformations radicalaires à la transition de phase para-ferroélectrique dans le cristal d'arséniate de potassium irradié. L'étude ENDOR de l'un des radicaux libres concernés nous permet maintenant de consolider les hypothèses qui avaient été émises précédemment. Nous montrons aussi que l'existence de ces radicaux est conditionnée par la présence dans le cristal d'une impureté renfermant du silicium