ALBERT

Description: Oceanic and atmospheric global numerical models represent explicitly the large-scale dynamics while the smaller-scale processes are not resolved so that their effects in the large-scale dynamics are included through subgrid-scale parameterizations. These parameterizations represent small-scale effects as a function of the resolved variables. In this work, data assimilation principles are used not only to estimate the parameters of subgrid-scale parameterizations but also to uncover the functional dependencies of subgrid-scale processes as a function of large-scale variables. Two data assimilation methods based on the ensemble transform Kalman filter (ETKF) are evaluated in the two-scale Lorenz ’96 system scenario. The first method is an online estimation that uses the ETKF with an augmented space state composed of the model large-scale variables and a set of unknown global parameters from the parameterization. The second method is an offline estimation that uses the ETKF to estimate an augmented space state composed of the large-scale variables and by a space dependent model error term. Then a polynomial regression is used to fit the estimated model error as a function of the large-scale model variables in order to develop a parameterization of small-scale dynamics. The online estimation shows a good performance when the parameter-state relationship is assumed to be quadratic polynomial function. The offline estimation captures better some of the highly nonlinear functional dependencies found in the subgrid-scale processes. The nonlinear and nonlocal dependence found in an experiment with shear-generated small-scale dynamics is also recovered by the offline estimation method. Therefore, the combination of these two methods could be a useful tool for the estimation of the functional form of subgrid-scale parameterizations.

Description: In this study, the microbial community structures of the endosphere of the halophyte Arthrocnemum macrostachyum were evaluated from two locations in Mallorca, Spain, focusing on three plant compartments (roots, green and red stems) compared to the rhizospheric soil where the plants grew. The physicochemical parameters of the rhizospheric soils differed between locations, and the soils were characterized by different microbial community structures. Accordingly, the endophytic community composition, mainly composed of putatively halophilic organisms, was highly influenced by the rhizospheric soil microbiota, as revealed by the co-occurrence of the major endophytic taxa in the endosphere and the rizospheric soils. Moreover, the reduction of diversity from the endorhizosphere towards the red leaves may support the fact that part of colonization of the plant by bacteria could have an origin in the rhizospheric soils through the roots and subsequent migration to the aerial parts of the plant. Finally, there were certain relevant ubiquitous taxa, such as Chromohalobacter canadensis , Rudaea cellulosilytica (never reported before as endophytic), Psychrobacter sp., Bradyrhizobium sp. and Halomonas sp., that, due their moderate halophilic nature, seemed to find an optimal environment inside the plants. Some of these relevant endophytes were not always detectable in their respective soils, and were probably part of the soils’ rare biosphere, which would gain preponderance in a favorable endophytic environment.

Description: Ensembl Genomes ( http://www.ensemblgenomes.org ) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project ( http://www.ensembl.org ). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.

Description: The orbital elements of Comet Halley are known to a very high precision, suggesting that the calculation of its future dynamical evolution is straightforward. In this paper we seek to characterize the chaotic nature of the present day orbit of Comet Halley and to quantify the time-scale over which its motion can be predicted confidently. In addition, we attempt to determine the time-scale over which its present day orbit will remain stable. Numerical simulations of the dynamics of test particles in orbits similar to that of Comet Halley are carried out with the mercury 6.2 code. On the basis of these we construct survival time maps to assess the absolute stability of Halley's orbit, frequency analysis maps to study the variability of the orbit, and we calculate the Lyapunov exponent for the orbit for variations in initial conditions at the level of the present day uncertainties in our knowledge of its orbital parameters. On the basis of our calculations of the Lyapunov exponent for Comet Halley, the chaotic nature of its motion is demonstrated. The e-folding time-scale for the divergence of initially very similar orbits is approximately 70 yr. The sensitivity of the dynamics on initial conditions is also evident in the self-similarity character of the survival time and frequency analysis maps in the vicinity of Halley's orbit, which indicates that, on average, it is unstable on a time-scale of hundreds of thousands of years. The chaotic nature of Halley's present day orbit implies that a precise determination of its motion, at the level of the present-day observational uncertainty, is difficult to predict on a time-scale of approximately 100 yr. Furthermore, we also find that the ejection of Halley from the Solar system or its collision with another body could occur on a time-scale as short as 10 000 yr.

Description: SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr .

Description: X-linked adrenomyeloneuropathy (AMN) is an inherited neurometabolic disorder caused by malfunction of the ABCD1 gene, characterized by slowly progressing spastic paraplegia affecting corticospinal tracts, and adrenal insufficiency. AMN is the most common phenotypic manifestation of adrenoleukodystrophy (X-ALD). In some cases, an inflammatory cerebral demyelination occurs associated to poor prognosis in cerebral AMN (cAMN). Though ABCD1 codes for a peroxisomal transporter of very long-chain fatty acids, the molecular mechanisms that govern disease onset and progression, or its transformation to a cerebral, inflammatory demyelinating form, remain largely unknown. Here we used an integrated -omics approach to identify novel biomarkers and altered network dynamic characteristic of, and possibly driving, the disease. We combined an untargeted metabolome assay of plasma and peripheral blood mononuclear cells (PBMC) of AMN patients, which used liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (LC-Q-TOF), with a functional genomics analysis of spinal cords of Abcd1 – mouse. The results uncovered altered nodes in lipid-driven proinflammatory cascades, such as glycosphingolipid and glycerophospholipid synthesis, governed by the β-1,4-galactosyltransferase (B4GALT6), the phospholipase 2 (PLA2G4C) and the choline/ethanolamine phosphotransferase (CEPT1) enzymes. Confirmatory investigations revealed a non-classic, inflammatory profile, consisting on the one hand of raised plasma levels of several eicosanoids derived from arachidonic acid through PLA2G4C activity, together with also the proinflammatory cytokines IL6, IL8, MCP-1 and tumor necrosis factor-α. In contrast, we detected a more protective, Th2-shifted response in PBMC. Thus, our findings illustrate a previously unreported connection between ABCD1 dysfunction, glyco- and glycerolipid-driven inflammatory signaling and a fine-tuned inflammatory response underlying a disease considered non-inflammatory.

Description: DYT6 dystonia is caused by mutations in THAP1 [Thanatos-associated (THAP) domain-containing apoptosis-associated protein] and is autosomal dominant and partially penetrant. Like other genetic primary dystonias, DYT6 patients have no characteristic neuropathology, and mechanisms by which mutations in THAP1 cause dystonia are unknown. Thap1 is a zinc-finger transcription factor, and most pathogenic THAP1 mutations are missense and are located in the DNA-binding domain. There are also nonsense mutations, which act as the equivalent of a null allele because they result in the generation of small mRNA species that are likely rapidly degraded via nonsense-mediated decay. The function of Thap1 in neurons is unknown, but there is a unique, neuronal 50-kDa Thap1 species, and Thap1 levels are auto-regulated on the mRNA level. Herein, we present the first characterization of two mouse models of DYT6, including a pathogenic knockin mutation, C54Y and a null mutation. Alterations in motor behaviors, transcription and brain structure are demonstrated. The projection neurons of the deep cerebellar nuclei are especially altered. Abnormalities vary according to genotype, sex, age and/or brain region, but importantly, overlap with those of other dystonia mouse models. These data highlight the similarities and differences in age- and cell-specific effects of a Thap1 mutation, indicating that the pathophysiology of THAP1 mutations should be assayed at multiple ages and neuronal types and support the notion of final common pathways in the pathophysiology of dystonia arising from disparate mutations.

Description: Microbial plankton communities do not always respond to inorganic nutrient additions in coastal waters off NW Spain. However, enhanced growth of phytoplankton and heterotrophic bacteria has been observed when exposed to both inorganic (nitrate, ammonium and phosphate) and organic (amino acids and glucose) nutrient amendments, suggesting the existence of a coupling between both microbial compartments. The aim of this paper was to assess the role of the phytoplankton–bacterioplankton coupling in the response of primary producers to nutrient additions. Changes in bacterial production (BP), primary production, and chlorophyll a concentration were measured after different nutrient addition treatments on natural microbial communities where bacterial activity was blocked with antibiotics. The results obtained in this study show that phytoplankton biomass and production respond only to the nutrient inputs when heterotrophic bacteria are active. The response of coastal microbial plankton to nutrient inputs might thus be eventually dependent on the BP of secondary metabolites necessary for phytoplankton growth (e.g. B 12 vitamin).

Description: We present a 3-D model of P and S velocities beneath El Hierro Island, constructed using the traveltime data of more than 13 000 local earthquakes recorded by the Instituto Geográfico Nacional (IGN, Spain) in the period from 2011 July to 2012 September. The velocity models were performed using the LOTOS code for iterative passive source tomography. The results of inversion were thoroughly verified using different resolution and robustness tests. The results reveal that the majority of the onshore area of El Hierro is associated with a high-velocity anomaly observed down to 10–12-km depth. This anomaly is interpreted as the accumulation of solid igneous rocks erupted during the last 1 Myr and intrusive magmatic bodies. Below this high-velocity pattern, we observe a low-velocity anomaly, interpreted as a batch of magma coming from the mantle located beneath El Hierro. The boundary between the low- and high-velocity anomalies is marked by a prominent seismicity cluster, thought to represent anomalous stresses due to the interaction of the batch of magma with crust material. The areas of recent eruptions, Orchilla and La Restinga, are associated with low-velocity anomalies surrounding the main high-velocity block. These eruptions took place around the island where the crust is much weaker than the onshore area and where the melted material cannot penetrate. These results put constraints on the geological model that could explain the origin of the volcanism in oceanic islands, such as in the Canaries, which is not yet clearly understood.