The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

Modelling the Limiting Envelopes of Rocks in the Octahedral Plane

The influence of the intermediate principal stress on the behaviour and the mechanical properties of rocks is now widely admitted [1-9]. In this study, we take all the three components of the stress state into account for building and modelling limiting envelopes. Therefore, a particularly convenient method for representing the results is the octahedral plane (also called deviatoric plane or π-plane). In this paper, we first present the automated method we developed for building limiting envelopes from a set of polyaxial (true triaxial) test data. Those developments are then applied for building the failure envelope of the Soignies limestone in various octahedral planes. Three shapes of envelopes are emphasized: triangular, hexagonal and rounded envelopes. The second part of the research deals with the modelling of the failure envelopes. Since the 19th Century, lots of strength criteria have been developed in order to model the materials intrinsic response to loads and to identify the failure behaviour at different stress states. Among theses theories, we focussed on criteria such as Mohr-Coulomb, Drucker-Prager, Griffith-Murrel and Lade [1,10-12], for which the octahedral representation looks like our limiting envelopes. In the future, the modelling job could be extended to other criteria, particularly for taking into account the variability of octahedral shapes

Étude des interactions mécaniques et physico-chimiques entre les argiles et les fluides de forage. Application à l'argile de Boom (Belgique)

Ce travail est motivé par les problèmes posés par la stabilité des puits forés dans des formations argileuses avec des boues de forage à base d'eau. En effet, les roches argileuses ou argilites (shales en anglais) ont la propriété d'absorber de l'eau, entraînant ainsi la déstabilisation des puits, soit par gonflement de certaines espèces minérales, soit par annulation de la pression de soutènement de la paroi par suite de la modification de la pression de pore. La déstabilisation peut être purement mécanique avec une plastification entraînant un cavage du trou, ou dépendre essentiellement des interactions physicochimiques entre le fluide de forage et l'argile. Le but de ce travail est donc de mettre expérimentalement en évidence les mécanismes susceptibles de jouer un rôle dans les phénomènes évoqués, et de tenter de quantifier l'importance de ces mécanismes pour en tenir compte dans les modèles de calcul. Le système expérimental que nous utilisons est basé sur une cellule triaxiale perméable aux rayons X, et donc destinée à un fonctionnement sous scanner (tomographie). Ce système, conçu et construit à l'Institut Français du Pétrole (IFP), est nouveau et nous avons contribué dans le cadre de ce travail à sa mise au point. La démarche consiste à mettre un échantillon d'argile sous confinement au contact avec un fluide de composition déterminée et à voir si les composants de ce fluide migrent dans l'argile ou non. Bien entendu, la tomographie ne permet que d'avoir des densités globales avec des résolutions de loin supérieures à la dimension du pore d'un matériau argileux sous confinement. Il est donc évident que les indications fournies par cette méthode doivent être complétées avec d'autres types de méthodes pour arriver à une étude sélective de la migration des éléments en solution. Pour ce qui concerne le matériau, notre choix s'est porté sur l'argile de Boom en Belgique, d'une part pour sa disponibilité et, d'autre part, pour la grande quantité d'informations disponibles sur ce matériau

Unraveling chalk microtextural properties from indentation tests

© 2016 Elsevier B.V. The petrographical, petrophysical and geomechanical properties of the less commonly studied low permeability or tight chalks are presented in this study. The latter are relevant as potential unconventional reservoirs or intra-reservoir seals. Tight chalks encompass different lithotypes, in which the main factors controlling the petrophysical properties as shown in this study are the non-carbonate content and the degree of cementation. Those parameters strongly modify chalk microtexture and thus its porous network, reducing pore-sizes hence altering poroperm properties. In order to better understand the characteristics of tight chalks, an integrated petrographical, petrophysical and geomechanical study was carried out on a set of 65 chalk samples from Northwestern European outcrops, covering a wide range of lithotypes. The dataset gathered covers a broad spectrum of values for the determined petrophysical (e.g. porosities from 9 to 45%) and geomechanical properties (e.g. strengths from 3 to 60 MPa). In the framework of this study, indentation tests were performed on the chalk samples. This technique proved to be a successful method to quickly estimate rock strength. Indeed, a good linear correlation (R2 = 0.90) has been established between indentation strength and UCS. Furthermore, indentation tests yielded valuable information about the chalk properties, both in terms of petrographical (cementation/clay-content), petrophysical (exponential relationship with porosity) and geomechanical (in relation to the elastic parameter and plasticity index) properties. This cheap and easy-to-operate method is a promising tool to indirectly estimate the mechanical parameters of chalks, when core samples are unavailable for laboratory testing in oil-field wells.status: publishe