The ProDom database of protein domain families: more emphasis on 3D

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics

Photoluminescence properties of GaN grown on compliant silicon-on-insulator substrates

A compliant substrate approach has been employed to release lattice-mismatch caused strain in GaN epilayers through stress absorption in the substrate. GaN layers have been grown on silicon-on-insulator (SOI) substrates by low-pressure metalorganic chemical vapor deposition. Photoluminescence measurements at 4 K show the spectrum of grown GaN being dominated by UV emission around 3.47 eV related to neutral-donor bound excitons. The much weaker yellow luminescence shows a broad spectrum around 2.16 eV. Peak position of the UV emission changes both with measurement temperature and strain. At room temperature, the UV peak is red shifted by 64 meV corresponding well to the band-gap temperature dependence. Strain-induced blue shift of the peak, compared to unstrained GaN, is much less than for growth on sapphire, indicating strain relief in the GaN by growth on SOI. Further reduction of the blue shift is consistent with increased electron mobility. © 1997 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70808/2/APPLAB-71-26-3880-1.pd

Croissance de boîtes quantiques In(Ga)As sur substrats de silicium et de SOI pour la réalisation d'émetteurs de lumière

Cette thèse porte sur l étude de la croissance auto-organisée de boîtes quantiques d In(Ga)As sur substrat de silicium visant à l intégration monolithique d un émetteur de lumière sur silicium à base d un matériau semiconducteur III-V. Le développement d un tel système se heurte à deux verrous majeurs : le premier provient d un très fort désaccord de maille qui rend difficile l élaboration de boîtes quantiques d In(Ga)As sur Si présentant de bonnes qualités structurales et optiques, et le second provient de la nature électronique de l interface entre In(Ga)As et le Si dont il est prédit qu elle est de type II et donc peu efficace pour l émission de lumière. L approche que nous avons proposée consiste à insérer des BQs d In(Ga)As dans un puits quantique de silicium dans SiO2, fabriqué sur un substrat SOI. Les effets attendus de confinement quantique dans le puits de Si favoriseraient une interface In(Ga)As/Si de type I. D un point de vue expérimental, nous avons donc étudié l influence de différents paramètres de croissance (température de croissance, rapport V/III, quantité d In(Ga)As déposé, teneur en indium des boîtes quantiques ) sur le mode de croissance et sur les propriétés structurales et optiques des BQs d In(Ga)As épitaxiées sur substrat de Si(001). Nous avons proposé une interprétation des phénomènes microscopiques qui régissent la formation des boîtes quantiques d In(Ga)As sur Si en fonction de la teneur en indium. Nous avons aussi montré qu il est possible de fabriquer des boîtes quantiques d In0,4Ga0,6As sur Si ne présentant pas de défauts structuraux liés à la relaxation plastique. La luminescence attendue des boîtes quantiques n a pas pu être obtenue, probablement en raison de deux conditions requises mais antagonistes: la fabrication de boîtes quantiques de très haute qualité structurale (possible uniquement pour de l In(Ga)As avec une teneur en In inférieure à 50%) et un alignement de bandes à l interface BQs In(Ga)As/Si de type I (possible théoriquement pour une teneur en In supérieure ou égale à 70%). Ce travail a permis d enrichir la connaissance et le savoir-faire concernant l élaboration de boîtes quantiques d In(Ga)As sur substrat de Si(001) et l encapsulation de ces boîtes quantiques par du silicium dans un réacteur d épitaxie par jets moléculaires III-V.This thesis focuses on the study of the self-organized growth of In(Ga)As quantum dots (QDs) on a silicon substrate. The purpose of this work is to pave the way for a monolithic integration of III-V semiconductor-based light emitter on silicon. One of the big challenges of this project is to overcome the high lattice mismatch between InGaAs and Si which can induce structural defects in the QDs. Another key challenge comes from the expected type II In(Ga)As/Si interface that is detrimental for efficient light emission. In order to solve the interface type issue, we suggested to insert the In(Ga)As QD plane inside a thin silicon layer grown on a SOI substrate. Confinement effects of the Si/SiO2 quantum well are expected to raise the X-valley of the Si conduction band above the -valley, leading to a type I interface in both direct and reciprocal space. The influence of different parameters (such as the amount of deposited In(Ga)As, the growth temperature, the V/III ratio and the gallium content...) on the growth mode and on the structural and optical properties of the In(Ga)As QDs grown on Si(001) are experimentally studied. We propose an interpretation of the microscopic phenomena governing the formation of the QDs as a function of gallium content. We finally show the possibility of making In0,4Ga0,6As QDs on Si(001) substrates, these QDs being free of plastic relaxation -related structural defects. The expected luminescence from the QDs was not obtained probably due to two incompatible conditions: the first, required for growing high structural quality QDs (possible only for In(Ga)As containing less than 50% of In) and the second, essential for maintaining a type I interface band alignment (theoretically possible for an In content greater than 50%). This work is contributing to the understanding of In(Ga)As QDs growth on Si(001) substrates and to the know-how of capping such QDs with silicon inside a III-V molecular beam epitaxy reactor.LYON-Ecole Centrale (690812301) / SudocSudocFranceF

Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants

The species Bifidobacterium longum currently comprises four subspecies: B. longum subsp. longum, B. longum subsp. infantis, B. longum subsp. suis and B. longum subsp. suillum. Recently, several studies on B. longum suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to B. longum subsp. suis DSM 20210T and B. longum subsp. suillum JCM1995T [average nucleotide identity (ANI) of 98.1%) while showed an ANI of 96.5% with both B. longum subsp. infantis and B. longum subsp. longum. The current work describes five novel additional B. longum strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species B. longum with B. longum subsp. suis and B. longum subsp. suillum as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to B. longum subsp. infantis, show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies, B. longum subsp. suis and B. longum subsp. suillum. Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name Bifidobacterium longum subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T =CCOS 2034T ), is proposed

Optical properties of cubic AlGaN

In this work we report optical characterization on several cubic c-AlGaN layers grown by MBE on SiC on Si pseudo-substrates, with different aluminum concentrations ranging from 0 to 70 %. Excitation power evolution of AlGaN photoluminescence (PL) spectra as well as reflectivity spectra allow to attribute PL peak to band gap recombination. PL energy dependence versus aluminum concentration is given. Reflectivity investigations are performed in the energy range between 1.5 eV and 4 eV on the samples. Theoretical calculations of multilayered structure reflectivity are fitted to experimental results, allowing an accurate determination of refractive index evolution versus Al concentration. From this analysis, qualitative information about interface roughness at AlGaN/SiC is also be derived.SFERERegion Rhône-AlpesConsejo Nacional de Ciencia y Tecnologí

Narcisse: a mirror view of conserved syntenies

New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr

Culture of Mouse Embryonic Stem Cells with Serum but without Exogenous Growth Factors Is Sufficient to Generate Functional Hepatocyte-Like Cells

Mouse embryonic stem cells (mESC) have been used to study lineage specification in vitro, including towards a hepatocyte-like fate, and such investigations guided lineage differentiation protocols for human (h)ESC. We recently described a four-step protocol to induce hepatocyte-like cells from hESC which also induced hepatocyte-like cell differentiation of mouse induced pluripotent stem cells. As ESC also spontaneously generate hepatocyte-like cells, we here tested whether the growth factors and serum used in this protocol are required to commit mESC and hESC to hepatocyte-like cells. Culture of mESC from two different mouse strains in the absence of serum and growth factors did not induce primitive streak/definitive endoderm genes but induced default differentiation to neuroectoderm on day 6. Although Activin-A and Wnt3 induced primitive streak/definitive endoderm transcripts most robustly in mESC, simple addition of serum also induced these transcripts. Expression of hepatoblast genes occurred earlier when growth factors were used for mESC differentiation. However, further maturation towards functional hepatocyte-like cells was similar in mESC progeny from cultures with serum, irrespective of the addition of growth factors, and irrespective of the mouse strain. This is in contrast to hESC, where growth factors are required for specification towards functional hepatocyte-like cells. Culture of mESC with serum but without growth factors did not induce preferential differentiation towards primitive endoderm or neuroectoderm. Thus, although induction of primitive streak/definitive endoderm specific genes and proteins is more robust when mESC are exposed to a combination of serum and exogenous growth factors, ultimate generation of hepatocyte-like cells from mESC occurs equally well in the presence or absence of exogenous growth factors. The latter is in contrast to what we observed for hESC. These results suggest that differences exist between lineage specific differentiation potential of mESC and hESC, requiring optimization of different protocols for ESC from either species

Human Embryonic and Rat Adult Stem Cells with Primitive Endoderm-Like Phenotype Can Be Fated to Definitive Endoderm, and Finally Hepatocyte-Like Cells

Stem cell-derived hepatocytes may be an alternative cell source to treat liver diseases or to be used for pharmacological purposes. We developed a protocol that mimics mammalian liver development, to differentiate cells with pluripotent characteristics to hepatocyte-like cells. The protocol supports the stepwise differentiation of human embryonic stem cells (ESC) to cells with characteristics of primitive streak (PS)/mesendoderm (ME)/definitive endoderm (DE), hepatoblasts, and finally cells with phenotypic and functional characteristics of hepatocytes. Remarkably, the same protocol can also differentiate rat multipotent adult progenitor cells (rMAPCs) to hepatocyte-like cells, even though rMAPC are isolated clonally from cultured rat bone marrow (BM) and have characteristics of primitive endoderm cells. A fraction of rMAPCs can be fated to cells expressing genes consistent with a PS/ME/DE phenotype, preceding the acquisition of phenotypic and functional characteristics of hepatocytes. Although the hepatocyte-like progeny derived from both cell types is mixed, between 10–20% of cells are developmentally consistent with late fetal hepatocytes that have attained synthetic, storage and detoxifying functions near those of adult hepatocytes. This differentiation protocol will be useful for generating hepatocyte-like cells from rodent and human stem cells, and to gain insight into the early stages of liver development

Effect of Lactobacillus rhamnosus CGMCC1.3724 supplementation on weight loss and maintenance in obese men and women

The present study investigated the impact of a Lactobacillus rhamnosus CGMCC1.3724 (LPR) supplementation on weight loss and maintenance in obese men and women over 24 weeks. In a double-blind, placebo-controlled, randomised trial, each subject consumed two capsules per d of either a placebo or a LPR formulation (1·6×108 colony-forming units of LPR/capsule with oligofructose and inulin). Each group was submitted to moderate energy restriction for the first 12 weeks followed by 12 weeks of weight maintenance. Body weight and composition were measured at baseline, at week 12 and at week 24. The intention-to-treat analysis showed that after the first 12 weeks and after 24 weeks, mean weight loss was not significantly different between the LPR and placebo groups when all the subjects were considered. However, a significant treatment×sex interaction was observed. The mean weight loss in women in the LPR group was significantly higher than that in women in the placebo group (P=0·02) after the first 12 weeks, whereas it was similar in men in the two groups (P=0·53). Women in the LPR group continued to lose body weight and fat mass during the weight-maintenance period, whereas opposite changes were observed in the placebo group. Changes in body weight and fat mass during the weight-maintenance period were similar in men in both the groups. LPR-induced weight loss in women was associated not only with significant reductions in fat mass and circulating leptin concentrations but also with the relative abundance of bacteria of the Lachnospiraceae family in faeces. The present study shows that the Lactobacillus rhamnosus CGMCC1.3724 formulation helps obese women to achieve sustainable weight los

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyper-activity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.Peer reviewe