Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent

This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.International audienceA novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T))

Extending the sub-sea-floor biosphere

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-4209.pdfInternational audienceSub-sea-floor sediments may contain two-thirds of Earth's total prokaryotic biomass. However, this has its basis in data extrapolation from ~500-meter to 4-kilometer depths, whereas the deepest documented prokaryotes are from only 842 meters. Here, we provide evidence for low concentrations of living prokaryotic cells in the deepest (1626 meters below the sea floor), oldest (111 million years old), and potentially hottest (~100 degrees C) marine sediments investigated. These Newfoundland margin sediments also have DNA sequences related to thermophilic and/or hyperthermophilic Archaea. These form two unique clusters within Pyrococcus and Thermococcus genera, suggesting unknown, uncultured groups are present in deep, hot, marine sediments (~54 degrees to 100 degrees C). Sequences of anaerobic methane-oxidizing Archaea were also present, suggesting a deep biosphere partly supported by methane. These findings demonstrate that the sub-sea-floor biosphere extends to at least 1600 meters below the sea floor and probably deeper, given an upper temperature limit for prokaryotic life of at least 113 degrees C and increasing thermogenic energy supply with depth

Projet de Pacte international relatif au droit des êtres humains à l’environnement

Ce projet constitue une proposition de rédaction d'un troisième pacte international relatif au droit des êtres humains à l’environnement. 69 ans après la Déclaration universelle des droits de l’homme et 51 ans après les deux Pactes internationaux relatifs aux droits économique sociaux et culturels et aux droits civils et politiques adoptés par l’Assemblée générale des Nations Unies en 1966, le temps est venu de consacrer le droit de l’homme à l’environnement dans un troisième Pacte international. Projet élaboré par le Centre international de droit comparé de l’environnement (CIDCE) OING à statut consultatif spécial ECOSOC-ONU et un groupe de travail animé par le professeur Michel Prieur et composé de Julien Bétaille, Marie-Anne Cohendet, Hubert Delzangles, Jessica Makowiak et Pascale Steichen (co-auteurs du précis Dalloz de « droit de l’environnement » 7°édition 2016). Grâce au réseau des correspondants du CIDCE (www.cidce.org) le projet de pacte a fait l’objet de commentaires et d’amendements de 40 juristes provenant de 22 pays différents issus d’Amérique du nord et du sud, d’Afrique, d’Asie, d’Europe et du Pacifique. Qu’ils soient tous remerciés ici pour leur collaboration dans des délais très brefs

Projet de Pacte international relatif au droit des êtres humains à l’environnement

Ce projet constitue une proposition de rédaction d'un troisième pacte international relatif au droit des êtres humains à l’environnement. 69 ans après la Déclaration universelle des droits de l’homme et 51 ans après les deux Pactes internationaux relatifs aux droits économique sociaux et culturels et aux droits civils et politiques adoptés par l’Assemblée générale des Nations Unies en 1966, le temps est venu de consacrer le droit de l’homme à l’environnement dans un troisième Pacte international. Projet élaboré par le Centre international de droit comparé de l’environnement (CIDCE) OING à statut consultatif spécial ECOSOC-ONU et un groupe de travail animé par le professeur Michel Prieur et composé de Julien Bétaille, Marie-Anne Cohendet, Hubert Delzangles, Jessica Makowiak et Pascale Steichen (co-auteurs du précis Dalloz de « droit de l’environnement » 7°édition 2016). Grâce au réseau des correspondants du CIDCE (www.cidce.org) le projet de pacte a fait l’objet de commentaires et d’amendements de 40 juristes provenant de 22 pays différents issus d’Amérique du nord et du sud, d’Afrique, d’Asie, d’Europe et du Pacifique. Qu’ils soient tous remerciés ici pour leur collaboration dans des délais très brefs

Filière « Histoire sociale et démographique »

Stéphane Baciocchi et Pascal Cristofoli, ingénieurs d’étudesArnaud Bringé et Bénédicte Garnier, ingénieurs à l’INED Atelier « Analyse des données relationnelles » Pour cette année, les deux composantes de l’atelier (« Introduction à l’analyse des données relationnelles » et « Études de cas ») ont été regroupées de sorte à présenter de manière intégrée et continue l’ensemble des opérations qui règlent la conduite des enquêtes sur les sources et données relationnelles. Nous avons rassemblé, au ..

The ANTENATAL multicentre study to predict postnatal renal outcome in fetuses with posterior urethral valves: objectives and design

Abstract Background Posterior urethral valves (PUV) account for 17% of paediatric end-stage renal disease. A major issue in the management of PUV is prenatal prediction of postnatal renal function. Fetal ultrasound and fetal urine biochemistry are currently employed for this prediction, but clearly lack precision. We previously developed a fetal urine peptide signature that predicted in utero with high precision postnatal renal function in fetuses with PUV. We describe here the objectives and design of the prospective international multicentre ANTENATAL (multicentre validation of a fetal urine peptidome-based classifier to predict postnatal renal function in posterior urethral valves) study, set up to validate this fetal urine peptide signature. Methods Participants will be PUV pregnancies enrolled from 2017 to 2021 and followed up until 2023 in >30 European centres endorsed and supported by European reference networks for rare urological disorders (ERN eUROGEN) and rare kidney diseases (ERN ERKNet). The endpoint will be renal/patient survival at 2 years postnatally. Assuming α = 0.05, 1–β = 0.8 and a mean prevalence of severe renal outcome in PUV individuals of 0.35, 400 patients need to be enrolled to validate the previously reported sensitivity and specificity of the peptide signature. Results In this largest multicentre study of antenatally detected PUV, we anticipate bringing a novel tool to the clinic. Based on urinary peptides and potentially amended in the future with additional omics traits, this tool will be able to precisely quantify postnatal renal survival in PUV pregnancies. The main limitation of the employed approach is the need for specialized equipment. Conclusions Accurate risk assessment in the prenatal period should strongly improve the management of fetuses with PUV

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

Introduction: More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between BRCA1 and BRCA2 mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in BRCA1 and BRCA2 carriers. Methods: We used data from 15,252 BRCA1 and 8,211 BRCA2 carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and triple-negative- (TN) status; morphologic subtypes; histological grade; and nodal involvement. Results: The estimated BC hazard ratios (HRs) for the 74 known BC alleles in BRCA1 carriers exhibited moderate correlations with the corresponding odds ratios from the general population. However, their associations with ER-positive BC in BRCA1 carriers were more consistent with the ER-positive as

Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations.

The prevalence and spectrum of germline mutations in BRCA1 and BRCA2 have been reported in single populations, with the majority of reports focused on White in Europe and North America. The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) has assembled data on 18,435 families with BRCA1 mutations and 11,351 families with BRCA2 mutations ascertained from 69 centers in 49 countries on six continents. This study comprehensively describes the characteristics of the 1,650 unique BRCA1 and 1,731 unique BRCA2 deleterious (disease-associated) mutations identified in the CIMBA database. We observed substantial variation in mutation type and frequency by geographical region and race/ethnicity. In addition to known founder mutations, mutations of relatively high frequency were identified in specific racial/ethnic or geographic groups that may reflect founder mutations and which could be used in targeted (panel) first pass genotyping for specific populations. Knowledge of the population-specific mutational spectrum in BRCA1 and BRCA2 could inform efficient strategies for genetic testing and may justify a more broad-based oncogenetic testing in some populations

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe