Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae

<p>Abstract</p> <p>Background</p> <p>Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (<it>i.e</it>. rice and <it>Sorghum</it>), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in <it>Poaceae</it>.</p> <p>Results</p> <p>We have identified an LTR-retrotransposon, that we named <it>Route66</it>, with more than 95% sequence identity between rice and <it>Sorghum</it>. Using a combination of <it>in silico </it>and molecular approaches, we are able to present a substantial phylogenetic evidence that <it>Route66 </it>has been transferred horizontally between Panicoideae and several species of the genus <it>Oryza</it>. In addition, we show that it has remained active after these transfers.</p> <p>Conclusion</p> <p>This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.</p

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection ar

Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae).

FR2116International audienceIn this paper, we examine how the Spartina system has helped our understanding of the genomic aspects of allopolyploid speciation in the context of biological invasion. More specifically the respective roles of hybridization and genome duplication in the success of newly formed allopolyploid species are explored. Hybridization appears to have triggered genetic and epigenetic changes in the two recently formed European homoploid hybrids S. x towsendii and S. x neyrautii. Deviation from parental structural additivity is observed in both hybrids, with different patterns when considering transposable element insertions or AFLP and methylation alteration. No important changes are observed in the invasive allopolyploid Spartina anglica that inherited the identical genome to S. x townsendii. The repeated rRNA genes are not homogenized in the allopolyploid, and both parental repeats are expressed in the populations examined. Transcriptomic changes suggest possible gene silencing in both hybrids and allopolyploid. In the long-term of evolutionary time, older hexaploid Spartina species (Spartina alterniflora, Spartina maritima and Spartina foliosa) appear to have selectively retained differential homeologous copies of nuclear genes. Waxy gene genealogies suggest a hybrid (allopolyploid) origin of this hexaploid lineage of Spartina. Finally, nuclear and chloroplast DNA data indicate a reticulate origin (alloheptaploid) of the invasive Spartina densiflora. All together these studies stress hybridization as a primary stimulus in the invasive success of polyploid Spartina species

Association between occupational exposure and the clinical characteristics of COPD.

International audienceBACKGROUND: The contribution of occupational exposures to COPD and their interaction with cigarette smoking on clinical pattern of COPD remain underappreciated. The aim of this study was to explore the contribution of occupational exposures on clinical pattern of COPD. METHODS: Cross-sectional data from a multicenter tertiary care cohort of 591 smokers or ex-smokers with COPD (median FEV1 49%) were analyzed. Self-reported exposure to vapor, dust, gas or fumes (VDGF) at any time during the entire career was recorded. RESULTS: VDGF exposure was reported in 209 (35%) subjects aged 31 to 88 years. Several features were significantly associated with VDGF exposure: age (median 68 versus 64 years, p < 0.001), male gender (90% vs 76%; p < 0.0001), reported work-related respiratory disability (86% vs 7%, p < 0.001), current wheezing (71% vs 61%, p = 0.03) and hay fever (15.5% vs 8.5%, p < 0.01). In contrast, current and cumulative smoking was less (p = 0.01) despite similar severity of airflow obstruction. CONCLUSION: In this patient series of COPD patients, subjects exposed to VDGF were older male patients who reported more work-related respiratory disability, more asthma-like symptoms and atopy, suggesting that, even in smokers or ex-smokers with COPD, occupational exposures are associated with distinct patients characteristics

Recent progress in L-H transition studies at JET: Tritium, Helium, Hydrogen and Deuterium

We present an overview of results from a series of L-II transition experiments undertaken at JET since the installation of the ITER-like-wall (JET-ILW), with beryllium wall tiles and a tungsten divertor. Tritium, helium and deuterium plasmas have been investigated. Initial results in tritium show ohmic L-H transitions at low density and the power threshold for the L-H transition (P-LH) is lower in tritium plasmas than in deuterium ones at low densities, while we still lack contrasted data to provide a scaling at high densities. In helium plasmas there is a notable shift of the density at which the power threshold is minimum ((n) over bar (e,min)) to higher values relative to deuterium and hydrogen references. Above (n) over bar (e,min) (He) the L-H power threshold at high densities is similar for D and He plasmas. Transport modelling in slab geometry shows that in helium neoclassical transport competes with interchange-driven transport, unlike in hydrogen isotopes. Measurements of the radial electric field in deuterium plasmas show that E-r shear is not a good indicator of proximity to the L-H transition. Transport analysis of ion heat flux in deuterium plasmas show a non-linearity as density is decreased below (n) over bar (e,min). Lastly, a regression of the JET-ILW deuterium data is compared to the 2008 ITPA scaling law