Expert-based development of a standard in CO2 sequestration monitoring technology

Bureau of Economic Geolog

Real-scale investigation of the kinematic response of a rockfall protection embankment

This paper addresses the response of rockfall protection embankments when exposed to a rock impact. For this purpose, real-scale impact experiments were conducted with impact energies ranging from 200 to 2200 kJ. The structure was composed of a 4m high cellular wall leaned against a levee. The wall was a double-layer sandwich made from gabion cages filled with either stones or a sand–schreddedtyre mixture. For the first time, sensors were placed in different locations within the structure to measure real-time accelerations and displacements. The test conditions, measurement methods and results are presented in detail. The structure’s response is discussed in a descriptive and phenomenological approach and compared with previous real-scale experiments on other types of embankments

Numerical modeling of CO2 injection into a typical US Gulf Coast anticline structure

AbstractThis paper summarizes recent numerical modeling activities investigating geological CO2 sequestration project at the Cranfield field, Mississippi, USA, performed with the commercial compositional flow simulator CMG-GEM. The oilfield was produced from the 1940’s to the 1960’s but has been the recent recipient of an enhanced oil recovery (EOR) CO2 flood. The subset of actual site operations of interest to the BEG consists of (1) an early phase, object of this paper, in which CO2 is injected into the oil-bearing reservoir (the so-called Phase II) and (2) a second phase (started on December 1, 2009) in which CO2 is injected at a high rate (>100 kt/yr for several years) in the saline aquifer down dip of the reservoir (Phase III). We present the modeling efforts related to the early phase of injection (Phase II, started in July 2008) in which CO2 is injected into the oil-bearing reservoir. The objectives of the modeling effort are to (i) to gain insights on how to approach CO2 injection modeling at the site, (ii) to match recent pressure measurements at several wells including a dedicated observation well, and (iii) to vindicate the necessity of monitoring of reservoir pressure. Its intent is not necessarily to do a full-fledged history match of the historical production period (1940’s–1960’s).We conducted numerous repeat simulation runs to modify boundary conditions, fluid properties, and reservoir properties to match observed fluid responses to production and to injection. A good understanding of subsurface heterogeneities, and composition of the oil and gas components, and boundary conditions of the reservoir is the key to successful history matching. However, allocating the correct distribution of rock properties based on historical geophysical logs remained an area of uncertainty even as additional new data were obtained during characterization because of the complex interplay between depositional environment and strong overprint of diagenetic events. Parameters of utmost importance for a correct description of a flow field, in particular the relationship between porosity and permeability and the nature of permeability spatial variations remain uncertain as well as boundary conditions. The uncertainty was dealt with through sensitivity analyses. Ultimately, the constructed model shows a reasonable match with the data

Convection-diffusion-reaction of CO2-enriched brine in porous media: A pore-scale study

Bureau of Economic Geolog

Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species

Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges

Variability in the durability of CRISPR-Cas immunity

This is the author accepted manuscript. The final version is available from Royal Society via the DOI in this record.The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.Natural Environment Research Council (NERC)Biotechnology & Biological Sciences Research Council (BBSRC)European CommissionEuropean Molecular Biology Organization (EMBO)Leverhulme TrustNatural Sciences and Engineering Research Council of Canad

Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus

Background During the last years the quantification of immune response under immunological challenges, e.g. parasitation, has been a major focus of research. In this context, the expression of immune response genes in teleost fish has been surveyed for scientific and commercial purposes. Despite the fact that it was shown in teleostei and other taxa that the gene for beta-actin is not the most stably expressed housekeeping gene (HKG), depending on the tissue and experimental treatment, the gene has been us Results To establish a reliable method for the measurement of immune gene expression in Gasterosteus aculeatus, sequences from the now available genome database and an EST library of the same species were used to select oligonucleotide primers for HKG, in order to perform quantitative reverse-transcription (RT) PCR. The expression stability of ten candidate reference genes was evaluated in three different tissues, and in five parasite treatment groups, using the three algorithms BestKeeper, geNorm and N Conclusion As they were the most stably expressed genes in all tissues examined, we suggest using the genes for the L13a ribosomal binding protein and ubiquitin as alternative or additional reference genes in expression analysis in Gasterosteus aculeatus.

Evolutionary emergence of infectious diseases in heterogeneous host populations

This is the final version. Available from Public Library of Science via the DOI in this record.The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases.Natural Environment Research Council (NERC)Wellcome TrustBiotechnology & Biological Sciences Research Council (BBSRC)European CommissionMarie Curie ActionsNatural Sciences and Engineering Research Council of CanadaLeverhulme Trus