Removing noise from pyrosequenced amplicons

Background In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has allowed much larger read numbers from PCR amplicons than ever before. This has revolutionised the study of microbial diversity as it is now possible to sequence a substantial fraction of the 16S rRNA genes in a community. However, there is a growing realisation that because of the large read numbers and the lack of consensus sequences it is vital to distinguish noise from true sequence diversity in this data. Otherwise this leads to inflated estimates of the number of types or operational taxonomic units (OTUs) present. Three sources of error are important: sequencing error, PCR single base substitutions and PCR chimeras. We present AmpliconNoise, a development of the PyroNoise algorithm that is capable of separately removing 454 sequencing errors and PCR single base errors. We also introduce a novel chimera removal program, Perseus, that exploits the sequence abundances associated with pyrosequencing data. We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms

Surgical Application of Human Amniotic Membrane and Amnion-Chorion Membrane in the Oral Cavity and Efficacy Evaluation: Corollary With Ophthalmological and Wound Healing Experiences

Due to its intrinsic properties, there has been growing interest in human amniotic membrane (hAM) in recent years particularly for the treatment of ocular surface disorders and for wound healing. Herein, we investigate the potential use of hAM and amnion-chorion membrane (ACM) in oral surgery. Based on our analysis of the literature, it appears that their applications are very poorly defined. There are two options: implantation or use as a cover material graft. The oral cavity is submitted to various mechanical and biological stimulations that impair membrane stability and maintenance. Thus, some devices have been combined with the graft to secure its positioning and protect it in this location. This current opinion paper addresses in detail suitable procedures for hAM and ACM utilization in soft and hard tissue reconstruction in the oral cavity. We address their implantation and/or use as a covering, storage format, application side, size and number, multilayer use or folding, suture or use of additional protective covers, re-application and resorption/fate. We gathered evidence on pre- and post-surgical care and evaluation tools. Finally, we integrated ophthalmological and wound healing practices into the collected information. This review aims to help practitioners and researchers better understand the application of hAM and ACM in the oral cavity, a place less easily accessible than ocular or cutaneous surfaces. Additionally, it could be a useful reference in the generation of new ideas for the development of innovative protective covering, suturing or handling devices in this specific indication. Finally, this overview could be considered as a position paper to guide investigators to fulfill all the identified criteria in the future

BRCA1 mutations in Algerian breast cancer patients: high frequency in young, sporadic cases

Breast cancer rates and median age of onset differ between Western Europe and North Africa. In Western populations, 5 to 10 % of breast cancer cases can be attributed to major genetic factors such as BRCA1 and BRCA2, while this attribution is not yet well defined among Africans. To help determine the contribution of BRCA1 mutations to breast cancer in a North African population, we analysed genomic DNA from breast cancer cases ascertained in Algiers. Both familial cases (at least three breast cancers in the same familial branch, or two with one bilateral or diagnosed before age 40) and sporadic cases less than 38 years of age were studied. Complete sequencing plus quantitative analysis of the BRCA1 gene was performed. 9.8 % (5/51) of early-onset sporadic and 36.4 % (4/11) of familial cases were found to be associated with BRCA1 mutations. This is in contrast 10.3 % of French HBOC families exhibiting a BRCA1 mutation. One mutation, c.798_799delTT, was observed in two Algerian families and in two families from Tunisia, suggesting a North African founder allele. Algerian non-BRCA1 tumors were of significantly higher grade than French non-BRCA tumors, and the age at diagnosis for Algerian familial cases was much younger than that for French non-BRCA familial cases. In conclusion, we observed a much higher frequency of BRCA1 mutations among young breast cancer patients than observed in Europe, suggesting biological differences and that the inclusion criterea for analysis in Western Europe may not be applicable for the Northern African population.</p

Energy Transfer in Mixed Lanthanides Complexes: Towards High-Performance Pressure Sensors Based on the Luminescence Intensity Ratio

International audienceIn this study, we present a reversible pressure-sensing material with high sensitivity. Mixed βdiketonate complexes of Tb 3+ and Eu 3+ [(Ln)(acac) 3 phen] are synthesized with phenanthroline as an ancillary ligand. The organic ligands provide the antenna effect to make the Ln 3+ complex excitable at 405 nm. Eu 3+ emission results from efficient energy transfer (ET) from Tb 3+. Under 405 nm excitation, the emission intensity of Tb 3+ decreases whereas the emission intensity of Eu 3+ increases with pressure, making this complex a potential pressure sensor based on luminescent-intensity-ratio (LIR) up to 700 MPa. This study then discusses the application of this Tb 3+ /Eu 3+ complex for pressure sensing depending on measurement conditions. The addition of the optically neutral ion Y 3+ to the system can reduce the impact of pressure-induced structural defects on the emission, thus improving the reversibility of the LIR variation as a function of pressure. Therefore, a self-calibrating, reliable, and reversible pressure-sensing material is proposed here, with remarkable pressure sensitivity compared to a peak shift-based pressure sensor

Surgical Application of Human Amniotic Membrane and Amnion-Chorion Membrane in the Oral Cavity and Efficacy Evaluation: Corollary With Ophthalmological and Wound Healing Experiences

International audienceDue to its intrinsic properties, there has been growing interest in human amniotic membrane (hAM) in recent years particularly for the treatment of ocular surface disorders and for wound healing. Herein, we investigate the potential use of hAM and amnion-chorion membrane (ACM) in oral surgery. Based on our analysis of the literature, it appears that their applications are very poorly defined. There are two options: implantation or use as a cover material graft. The oral cavity is submitted to various mechanical and biological stimulations that impair membrane stability and maintenance. Thus, some devices have been combined with the graft to secure its positioning and protect it in this location. This current opinion paper addresses in detail suitable procedures for hAM and ACM utilization in soft and hard tissue reconstruction in the oral cavity. We address their implantation and/or use as a covering, storage format, application side, size and number, multilayer use or folding, suture or use of additional protective covers, re-application and resorption/fate. We gathered evidence on pre- and post-surgical care and evaluation tools. Finally, we integrated ophthalmological and wound healing practices into the collected information. This review aims to help practitioners and researchers better understand the application of hAM and ACM in the oral cavity, a place less easily accessible than ocular or cutaneous surfaces. Additionally, it could be a useful reference in the generation of new ideas for the development of innovative protective covering, suturing or handling devices in this specific indication. Finally, this overview could be considered as a position paper to guide investigators to fulfill all the identified criteria in the future

Les Rencontres de l’humain et du non-humain dans la littérature de voyage et d’exploration anglophone

L’intérêt des voyageurs pour le monde non humain permet-il de considérer le récit de voyage comme un exemple de littérature environnementale ? Les voyageurs, explorateurs et montagnards révèlent-ils dans leurs textes une conscience réelle de la nécessaire interconnexion entre le monde humain et le monde non humain, animal, végétal ou minéral ? Les articles présentés dans ce numéro de Caliban répondront à ces questions et, à travers des œuvres littéraires et des ouvrages géographiques et scientifiques divers, montreront que la conscience réside dans la perception du monde qui nous entoure. Des universitaires et des écrivains participent à ce volume, notamment Kev Reynolds, auteur britannique de plus de quarante guides et récits de voyages dans les montagnes du monde, et Scott Slovic, spécialiste américain de l’écocritique. C’est un numéro interdisciplinaire qui convoque aussi bien la littérature que l’histoire, la pédagogie et l’enseignement de l’écriture du voyage, la géographie, la botanique et les sciences de la nature. Does the interest of travellers in the nonhuman world allow the travel narrative to be regarded as an example of environmental literature? Do travellers, explorers and mountaineers reveal in their texts a real awareness of the vital interconnection between the human world and the nonhuman, animal, plant or mineral worlds? The articles presented in this volume will try to answer these questions and, through literary and various geographical and scientific works, will show that consciousness and mindfulness are at the core of the perception of the world which surrounds us. Among scholars and writers, who summon both literature and history, pedagogy and teaching of travel writing, geography and exploration, botany and physical sciences, Kev Reynolds, British author of more than forty travel guides and travelogues about the mountains of the world, and Scott Slovic, American specialist in Environmental Literature and Ecoriticism, urge us to turn our cultural attention back from the specifically human realm to the wider, other-than-human, living environment

Spécial Tidilem

Sélection d'articles du colloque international Tidilem "TICE et Didactique des Langues Étrangères et Maternelles : la problématique des aides à l'apprentissage" Organisé par le Laboratoire de Recherche sur le Langage les 14 et 15 Septembre 2006 à la Maison des Sciences de l'Homme, Clermont-Ferrand

Effects of acyl-coenzyme A binding protein (ACBP)/diazepam-binding inhibitor (DBI) on body mass index

International audienceIn mice, the plasma concentrations of the appetite-stimulatory and autophagy-inhibitory factor acyl-coenzyme A binding protein (ACBP, also called diazepam-binding inhibitor, DBI) acutely increase in response to starvation, but also do so upon chronic overnutrition leading to obesity. Here, we show that knockout of Acbp/Dbi in adipose tissue is sufficient to prevent high-fat diet-induced weight gain in mice. We investigated ACBP/DBI plasma concentrations in several patient cohorts to discover a similar dual pattern of regulation. In relatively healthy subjects, ACBP/DBI concentrations independently correlated with body mass index (BMI) and age. The association between ACBP/DBI and BMI was lost in subjects that underwent major weight gain in the subsequent 3–9 years, as well as in advanced cancer patients. Voluntary fasting, undernutrition in the context of advanced cancer, as well as chemotherapy were associated with an increase in circulating ACBP/DBI levels. Altogether, these results support the conclusion that ACBP/DBI may play an important role in body mass homeostasis as well as in its failure