Emergence and phylodynamics of Citrus tristeza virus in Sicily, Italy

[EN] Citrus tristeza virus (CTV) outbreaks were detected in Sicily island, Italy for the first time in 2002. To gain insight into the evolutionary forces driving the emergence and phylogeography of these CTV populations, we determined and analyzed the nucleotide sequences of the p20 gene from 108 CTV isolates collected from 2002 to 2009. Bayesian phylogenetic analysis revealed that mild and severe CTV isolates belonging to five different clades (lineages) were introduced in Sicily in 2002. Phylogeographic analysis showed that four lineages co-circulated in the main citrus growing area located in Eastern Sicily. However, only one lineage (composed of mild isolates) spread to distant areas of Sicily and was detected after 2007. No correlation was found between genetic variation and citrus host, indicating that citrus cultivars did not exert differential selective pressures on the virus. The genetic variation of CTV was not structured according to geographical location or sampling time, likely due to the multiple introduction events and a complex migration pattern with intense co- and recirculation of different lineages in the same area. The phylogenetic structure, statistical tests of neutrality and comparison of synonymous and nonsynonymous substitution rates suggest that weak negative selection and genetic drift following a rapid expansion may be the main causes of the CTV variability observed today in Sicily. Nonetheless, three adjacent amino acids at the p20 N-terminal region were found to be under positive selection, likely resulting from adaptation events.A.W. and S.F.E. were supported by grant BFU2012-30805 from the Spanish Secretaria de Estado de Investigacion, Desarrollo e Innovacion and by a grant 22371 from the John Templeton Foundation. 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Spatial distribution of multiple sclerosis lesions in the cervical spinal cord

Background: Spinal cord lesions detected on MRI hold important diagnostic and prognostic value for multiple sclerosis. Previous attempts to correlate lesion burden with clinical status have had limited success however, suggesting that lesion location may be a contributor. Purpose: To explore the spatial distribution of multiple sclerosis lesions in the cervical spinal cord, with respect to clinical status. Material and methods: We included 642 suspected or confirmed multiple sclerosis patients (31 clinically isolated syndrome, and 416 relapsing-remitting, 84 secondary progressive, and 73 primary progressive multiple sclerosis) from 13 clinical sites. Cervical spine lesions were manually delineated on T2- and T2 * -weighted axial and sagittal MRI scans acquired at 3 or 7 Tesla. With an automatic publicly-available analysis pipeline we produced voxelwise lesion frequency maps to identify predilection sites in various patient groups characterised by clinical subtype, Expanded Disability Status Scale score and disease duration. We also measured absolute and normalised lesion volumes in several regions of interest using an atlas-based approach, and evaluated differences within and between groups. Results: The lateral funiculi were more frequently affected by lesions in progressive subtypes than in relapsing in voxelwise analysis (p<0.001), which was further confirmed by absolute and normalised lesion volumes (p<0.01). The central cord area was more often affected by lesions in primary progressive than relapse-remitting patients (p<0.001). Between white and grey matter, the absolute lesion volume in the white matter was greater than in the grey matter in all phenotypes (p<0.001), however when normalising by each region, normalised lesion volumes were comparable between white and grey matter in primary progressive patients. Lesions appearing in the lateral funiculi and central cord area were significantly correlated with Expanded Disability Status Scale score (p<0.001). High lesion frequencies were observed in patients with a more aggressive disease course, rather than a long disease duration. Conclusion: Lesions located in the lateral funiculi and central cord area of the cervical spine may influence clinical status in multiple sclerosis. This work shows the added value of cervical spine lesions, and provides an avenue for evaluating the the distribution of spinal cord lesions in various patient groups

Species diversification – which species should we use?

Large detector systems for particle and astroparticle physics; Particle tracking detectors; Gaseous detectors; Calorimeters; Cherenkov detectors; Particle identification methods; Photon detectors for UV. visible and IR photons; Detector alignment and calibration methods; Detector cooling and thermo-stabilization; Detector design and construction technologies and materials. The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The initial configuration and expected performance of the detector and associated systems. as established by test beam measurements and simulation studies. is described. © 2008 IOP Publishing Ltd and SISSA

Evolution of traditional agroforestry landscapes and development of invasive species: lessons from the Pyrenees (France)

International audienceThe term agroforestry covers practices that are promoted to maintain or even enhance biodiversity. However, the relationship between agroforestry and invasive species is rarely addressed, even though the spread of such species is an important issue, not only ecologically but also economically and socially. Over the past few decades, humans have greatly accelerated the process of biological invasions, to such an extent that they are now recognized as the second cause of rapid decline in biodiversity. In France (as in other parts in Europe) abandonment of agricultural land in remote areas is a major problem having socio-economic, landscape and environmental implications. The objective of the research presented here was to find a method for studying the relationship between traditional agroforestry systems and invasive species, despite a lack of available data. We investigated the evolution of a traditional agroforestry system in the Pyrenean foothills, where invasive species are abundant, by implementing two complementary methods: i/ interviews highlighting the local stakeholders’ perception of landscape evolution, invasive species and the challenges they represent for the local traditional agroforestry landscapes, and ii/ detailed mapping of an area occupied by invasive plants, by means of very high resolution spatial technologies using UAV’s and aerial photography. The results show that invasive species have spread in relation with the abandonment of agricultural land, which has also led to “landscape closure” by the encroachment of natural afforestation. They also underline the difficulty of assessing the spread of invasive species. This situation is of major importance in terms of land-use planning, as the various stakeholders have different perceptions of the problem, and it raises questions about the sustainability of practices and territories