A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes

DMTs and Covid-19 severity in MS: a pooled analysis from Italy and France

We evaluated the effect of DMTs on Covid-19 severity in patients with MS, with a pooled-analysis of two large cohorts from Italy and France. The association of baseline characteristics and DMTs with Covid-19 severity was assessed by multivariate ordinal-logistic models and pooled by a fixed-effect meta-analysis. 1066 patients with MS from Italy and 721 from France were included. In the multivariate model, anti-CD20 therapies were significantly associated (OR = 2.05, 95%CI = 1.39–3.02, p < 0.001) with Covid-19 severity, whereas interferon indicated a decreased risk (OR = 0.42, 95%CI = 0.18–0.99, p = 0.047). This pooled-analysis confirms an increased risk of severe Covid-19 in patients on anti-CD20 therapies and supports the protective role of interferon

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Architecting an electro-chemical separation platform : from the business case to the first commercial product

Thesis: S.M. in Engineering and Management, Massachusetts Institute of Technology, System Design and Management Program, 2018.Page 49 blank. Cataloged from PDF version of thesis.Includes bibliographical references (page [48] ).Electrosorption technology is currently gaining significant tractions as a viable separation technique due to its low energy consumption, its intrinsic reversibility and its reagent free nature. As most companies thrive towards a more sustainable approach, electro-chemical based process become more and more attractive. The group of Prof. Hatton of the Chemical Engineering department at MIT has improved further the state of the art of electro-chemical technologies by using functionalized metallocene-based pseudo-capacitors. Their research demonstrates that the technology they developed can selectively remove specific compounds such as carboxylates, sulfonates, phosphonates and potentially heavy metals. The aim of this thesis is to help the technology find a first market fit and build the foundation for a successful scale-up by defining its positioning within the treatment train of the production of the identified markets. Two main markets were identified. The selection of each market was based on the price of the end-product, the size and growth of the market and the numbers of applications and potential customers. The lactic acid and the lithium carbonate markets were selected. Both are growing markets sustaining a real demand over the years to come with very promising and diversified applications. We collected real-life feedbacks and identified the pain points in each respective industry by conducting interviews with professionals in the field. Several unmet needs and possible alignments with the benefits brought by the selective electrosorption technology were identified thanks to this endeavor. New potential production lines were proposed. The new innovative treatment line allows for the simplification of the process train, a reduction of the chemical and reagent needed and a likely decrease in solid waste and wastewater volume.by Adrien A. Moreau.S.M. in Engineering and Managemen

Xylobolus subpileatus , a specialized basidiomycete functionally linked to old canopy gaps

International audienceDocumenting succession in forest canopy gaps provides insights into the ecological processes governing the temporal dynamics of species within communities. We analyzed the fruiting patterns of a rare but widely distributed saproxylic macro- mycete, Xylobolus subpileatus, during the ageing of natural canopy gaps in oak forests. In one of the last remaining Quercus ilex L. old-growth forests (on the island of Corsica, western Mediterranean basin), we systematically recorded and conducted molecular analyses of X. subpileatus basidiomes in 80 dated natural canopy gaps representing a 45-year long sequence of residence time of tree logs on the forest floor. Xylobolus subpileatus fruited exclusively on Q. ilex logs. The probability of fruiting of X. subpileatus significantly increases during the process of wood decomposition to reach its maximum in the oldest gaps, approximately 40 years after treefall. In contrast, the abundance and the richness of saprobic and ectomycorrhizal fruitbodies decrease as canopy gaps age. Our results emphasize the high ecological specialization of X. subpileatus. They also highlight the imperative need to conserve the last patches of old-growth Mediterranean forests to secure the persistence of this endangered and functionally unique macromycete whose presence is highly dependent on old wood in advanced stages of decomposition.L’étude des successions écologiques ayant lieu dans les ouvertures de canopée forestière offre l’opportunité de mieux comprendre les processus écologiques gouvernant la dynamique temporelle des espèces a` l’intérieur des communautés. Nous avons analysé la distribution des fructifications d’une espèce, rare mais largement distribuée, de macromycète saproxilique, Xylobolus subpileatus, au cours du vieillissement de trouées naturelles dans les forêts de chênes. Dans l’une des dernières forêts anciennes de chêne vert (Quercus ilex L.) (île de Corse, ouest du bassin méditerranéen), nous avons échantillonné systématique- ment et analysé moléculairement les basidiomes de X. subpileatus dans 80 trouées datées qui représentent une chronoséquence de 45 ans de temps de résidence au sol des troncs d’arbres. Xylobolus subpileatus ne fructifie que sur les troncs de chêne vert. Sa probabilité de fructification est positivement corrélée a` l’âge des trouées et atteint un maximum dans les plus vieilles trouées (environ 40 ans après la chute de l’arbre). A contrario, l’abondance et la richesse des fructifications de champignons décompo- seurs et ectomycorhiziens décroissent avec le vieillissement de la trouée. Nos résultats soulignent la spécialisation écologique poussée de X. subpileatus et mettent en avant le besoin impératif de préserver les dernières parcelles de forêts anciennes méditerranéennes afin de protéger cette espèce de macromycète fonctionnellement originale dont la présence dépend forte- ment de la complétion du processus naturel de décomposition