Note méthodologique - Évaluer la fonctionnalité de la Trame bleue pour les poissons

Pour que la trame bleue soit fonctionnelle, il est important de diagnostiquer l’effet de la fragmentation des cours d’eau sur les poissons pour restaurer de manière efficace la continuité écologique. Une méthode consiste à utiliser les outils de biotélémétrie pour identifier la capacité des poissons à franchir les ouvrages existants et leurs aménagements et évaluer ainsi l’efficacité de la restauration. Un cas d’étude est présenté concernant le suivi de populations de truite dans des petits cours d’eau de têtes de bassins en Ile-de-France

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism

Erratum: “The eighth data release of the Sloan Digital Sky Survey: first data from SDSS-III” (2011, ApJS, 193, 29)

Section 3.5 of Aihara et al. (2011) described various sources of systematic error in the astrometry of the imaging data of the Sloan Digital Sky Survey (SDSS). In addition to these sources of error, there is an additional and more serious error, which introduces a large systematic shift in the astrometry over a large area around the north celestial pole. The region has irregular boundaries but in places extends as far south as declination δ ≈ 41◦. The sense of the shift is that the positions of all sources in the affected area are offset by roughly 250 mas in a northwest direction. We have updated the SDSS online documentation to reflect these errors, and to provide detailed quality information for each SDSS field

Focus - Modélisation de la continuité écologique des rivières pour les poissons : un outil d’aide à la mise en place des trames bleues

La mise en place de la trame bleue nécessite le développement d’outils de modélisation de la continuité écologique des rivières pour les poissons. Comment fonctionnent ces outils et comment peuvent-ils contribuer à identifier les zones prioritaires à restaurer tout en tenant compte des usages antagonistes du milieu aquatique? Quelques réponses avec l’exemple d’une démarche de modélisation à partir du logiciel Anaqualand

Une approche «paysage aquatique» pour une meilleure connaissance du fonctionnement des ecosystemes fluviaux et l'amelioration de la conservation des peuplements de poissons

[Departement_IRSTEA]MA [TR1_IRSTEA]QSA / HYDRECOEffective management and restoration of habitat for stream fish should consider how the different resource habitats need to be arranged spatially and the location of source populations. As few operational methods are available to study these issues, we propose a riverscape approach based on landscape ecology and stream ecology concepts. It aims at studying the multi-scale relationships between the spatial pattern of fish habitat patches and processes depending on the fish movements. To quantify spatial patterns at nested levels (patch of resource habitat, area of daily activities and area of sub-population), we calculate their composition, configuration, complementation and connectivity with multiple spatial analysis methods: patch metrics, moving window analysis and least cost modelling. Two cyprinid species (Barbus barbus and Chondrostoma nasus) and two reaches of the Seine River (France) were used to test this riverscape approach. Relevance of some metrics and methods of landscape ecology to detect the effects of flow variability and human alterations on fish habitat composition and configuration is demonstrated. Using electrofishing data, we validate the functionality of the resource habitat maps for both species. The longitudinal pattern of their distribution in the natural reach is aggregated in the neighbouring patches of feeding habitat, which seems to match home range of local population of these species. The role of complementation and supplementation of resource habitat in the presence of species is demonstrated. This approach helps evaluating impacts of habitat alteration and isolation and prioritises preservation and restoration policies.Des mesures efficaces de gestion et de restauration des habitats piscicoles devraient considérer l'arrangement spatial des différents habitats ressources et la localisation des populations sources. Comme peu de méthodes opérationnelles sont disponibles pour étudier ces questions, une approche « paysage aquatique » est proposée, couplant les concepts de l'écologie du paysage et de l'écologie des cours d'eau. Elle permet d'étudier l'influence de la structure spatiale et de la connectivité fonctionnelle des habitats aquatiques sur l'organisation des populations de poissons d'eau courante. Pour quantifier la structure spatiale des habitats à différents niveaux d'organisation (tache d'habitat ressource, aire d'activité journalière ou aire de population locale), diverses méthodes d'analyse spatiale ont été utilisées. Elles sont testées pour deux espèces de cyprinidés (Barbus Barbus et Chondrostoma nasus) sur des biefs naturel et aménagé de la Seine. La capacité des méthodes à détecter l'effet de la variabilité hydrologique et du degré d'aménagement sur la composition et la configuration des habitats ressources est étudiée. L'utilisation de données piscicoles issues de pêches électriques a permis de valider la fonctionnalité des cartes d'habitat ressource. La distribution longitudinale dans le bief naturel est agrégée dans des taches voisines d'habitat d'alimentation et semble correspondre aux domaines vitaux de populations locales de ces espèces. Leur présence est aussi expliquée par la complémentation entre les taches d'habitat d'alimentation et de repos. Cette approche peut permettre d'évaluer le degré d'altération et de fragmentation des taches d'habitats piscicoles et hiérarchiser les mesures de préservation et de restauration

Mise au point d'une technique d'amplification commerciale de lots de semis de chêne sous forme de plants bouturés : rapport final

[Departement_IRSTEA]GT [TR1_IRSTEA]33 - CEMAFOR / SYLVAGENStudies on techniques for producing forest plants of Quercus petraea by cuttings were continued in 1999. Two factors were used to assess the results: shoot growth for rooted cuttings and rusticity of the rooting system. Shoot growth obtained during the rooting period using fertilizers in the medium or auxins spray may increase nutrient stocks and, as a result, winter survival. A polyethylene tunnel with confined atmosphere and sub-irrigation was tested for a second year. This more economical and technically simplified technique should give better-rooted and hardier plants. Production costs of the different systems were also studied.La mise au point de la technique de bouturage du chêne sessile s'est poursuivie en 1999 sur deux points particuliers : ramification des boutures enracinées et rusticité du système. Le développement de pousse dans la phase d'enracinement par l'utilisation d'engrais ou d'hormone doit favoriser la constitution de réserves et donc la survie à l'hiver. Un tunnel plastique à atmosphère confinée et subirrigation a été testé pour la seconde année. Cette technique plus simple et économique doit permettre d'obtenir des boutures mieux enracinées et plus robustes. A cette campagne s'est ajoutée une étude des coûts des systèmes employés

Getting from Sea to Nurseries: Considering Tidal Dynamics of Juvenile Habitat Distribution and Connectivity in a Highly Modified Estuarine Riverscape

International audienceProductive and ecologically highly valuable ecosystems, macrotidal estuaries are also characterised by complex habitat and connectivity dynamics driven by tidal and freshwater influence. Organisms living in these constantly changing systems have to match their movement patterns to the shifting habitat mosaic using available windows of connectivity to access habitat patches of interest. This appears particularly important for the juvenile stages of many fish species colonising shallow and intertidal areas of the estuaries as summer nurseries. We apply tools from landscape ecology to investigate the estuarine habitat and connectivity dynamics on the example of juvenile seabass (Dicentrarchus labrax). We test under which conditions spatio-temporal bottlenecks to estuarine nursery colonisation may emerge for this species in a human-modified estuary. Combining a hydrodynamic model of the Seine estuary with remote sensing data allows us to capture structural changes in habitat availability and connectivity at the estuarine scale and at a fine spatio-temporal resolution. With chronological least-cost modelling of successive tidal steps, we assess patterns of nursery accessibility and estimate tidal colonisation fronts for different mobility scenarios. We show that, at certain hydrological conditions, tidal water level variation causes local disruptions of habitat availability and connectivity, creating temporary bottlenecks for seabass juveniles’ movement. Fish mobility appears determinant for their vulnerability to these connectivity disruptions. Our approach allows for quantitative assessment and visualisation of riverscape complexity related to tidal dynamics. It is applicable to other highly dynamic ecosystems, where the mobile nature of connectivity and habitats needs to be integrated into conservation and management planning