Observational needs for improving ocean and coupled reanalysis, S2S prediction, and decadal prediction

Developments in observing system technologies and ocean data assimilation (DA) are symbiotic. New observation types lead to new DA methods and new DA methods, such as coupled DA, can change the value of existing observations or indicate where new observations can have greater utility for monitoring and prediction. Practitioners of DA are encouraged to make better use of observations that are already available, for example, taking advantage of strongly coupled DA so that ocean observations can be used to improve atmospheric analyses and vice versa. Ocean reanalyses are useful for the analysis of climate as well as the initialization of operational long-range prediction models. There are many remaining challenges for ocean reanalyses due to biases and abrupt changes in the ocean-observing system throughout its history, the presence of biases and drifts in models, and the simplifying assumptions made in DA solution methods. From a governance point of view, more support is needed to bring the ocean-observing and DA communities together. For prediction applications, there is wide agreement that protocols are needed for rapid communication of ocean-observing data on numerical weather prediction (NWP) timescales. There is potential for new observation types to enhance the observing system by supporting prediction on multiple timescales, ranging from the typical timescale of NWP, covering hours to weeks, out to multiple decades. Better communication between DA and observation communities is encouraged in order to allow operational prediction centers the ability to provide guidance for the design of a sustained and adaptive observing network

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

Data from: Song playback increases songbird density near low to moderate use roads

Many songbird species avoid roads. Although acoustic masking, vehicle collision, and edge effects are likely culprits, spatial avoidance also occurs along low use roads and at locations distant from the pavement. Neophobia may be one factor contributing to avoidance in these regions. In this case, playback of bird song, generally a signal of high-quality habitat, may reduce avoidance and increase territory establishment. We investigated whether playback of song from 6 migratory species increased territory establishment along low to moderate use roads in a community of songbird species. We determined whether the intensity and regularity of anthropogenic noise altered the pattern of response, and whether particular life-history traits predicted which species were responsive to playback. Territory density was significantly higher where song playback was present. Species-specific responses were variable, with 11 species increasing territory density by >30% at playback sites and 6 species decreasing in density. Noise level did not significantly impact establishment. Foraging behavior, habitat, and song frequency predicted which species were most responsive to playback. These results are similar to a companion study conducted near forest edges that did not contain roads, and suggests that song playback may be a viable method for increasing songbird use of near road habitats. Although additional work is needed to understand the variable responses of particular species and to address vital issues, such as the reproductive success of lured birds, this study highlights a behavioral management technique that may have significant conservation implications along the vast worldwide network of roads

Raw territory and noise data

Data is provided for average territories/ha for 30 bird species; broken down by the control and experimental (playback) treatment. Raw noise event data is also provided, followed by PCA1 and PCA2

Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane.

Buchnera aphidicola is an intracellular bacterial symbiont of aphids and maintains a small genome of only 600 kbps. Buchnera is thought to maintain only genes relevant to the symbiosis with its aphid host. Curiously, the Buchnera genome contains gene clusters coding for flagellum basal body structural proteins and for flagellum type III export machinery. These structures have been shown to be highly expressed and present in large numbers on Buchnera cells. No recognizable pathogenicity factors or secreted proteins have been identified in the Buchnera genome, and the relevance of this protein complex to the symbiosis is unknown. Here, we show isolation of Buchnera flagellum basal body proteins from the cellular membrane of Buchnera, confirming the enrichment of flagellum basal body proteins relative to other proteins in the Buchnera proteome. This will facilitate studies of the structure and function of the Buchnera flagellum structure, and its role in this model symbiosis

The EU-FP7 ERA-CLIM2 project contribution to advancing science and production of Earth-system climate reanalyses

International audienceERA-CLIM2 is a European Union Seventh Framework Project started in January 2014. It aims to produce coupled reanalyses, which are physically consistent data sets describing the evolution of the global atmosphere, ocean, land-surface, cryosphere and the carbon cycle. ERA-CLIM2 has contributed to advancing the capacity for producing state-of-the-art climate reanalyses that extend back to the early 20th century. It has led to the generation of the first ensemble of coupled ocean, sea-ice, land and atmosphere reanalyses of the 20th century. The project has funded work to rescue and prepare observations, and to advance the data51assimilation systems required to generate operational reanalyses, such as the ones planned by the European Union Copernicus Climate Change Service. This paper summarizes the main goals of the project, discusses some of its main areas of activities, and presents some of its key results