Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling

Human endogenous retroviruses (HERVs) can be divided into distinct families of tens to thousands of paralogous loci. The expression of HERV elements has been detected in all tissues tested to date, particularly germ cells, embryonic tissues and neoplastic tissues. Hence, the study of HERV expression could represent added value in cancer diagnosis. We developed a quantitative assay combining a multiplex degenerate PCR (MD-PCR) amplification, based on the relative conservation of the pol genes, and a colorimetric Oligo Sorbent Array (OLISA(®)). Nine HERV families were selected and amplification primers and capture probes were designed for each family. The features required to achieve efficient amplification of most of the elements of each HERV family and balanced co-amplification of all HERV families were analyzed. We found that MD-PCR reliability, i.e. equivalence of amplification and dose-effect relationship, relied on the adjustment of three critical parameters: the primer degeneracy, the relative concentration of each primer and the total amount of primers in the amplification mixture. The analysis of tumoral versus normal tissues suggests that this assay could prove useful in tumor phenotyping

Arc Deformation and Marginal Basin Opening: Japan Sea as a Case Study

Laurent Jolivet est est Professeur à l'Université d'Orléans depuis le 1er Septembre 2009International audienceWe discuss the opening mechanism of the Japan Sea in Miocene time using (1) tectonic and published paleomagnetic data along the eastern margin from the north of Hokkaido Island to Sado Island, (2) a mechanical model which is tested by small-scale physical modeling, and (3) crustal structure and bathymetric features in the Japan Sea which constrain our kinematic model and preopening reconstructions. Our main conclusions are the following. The eastern margin of the Japan Sea was, as a whole, a dextral shear zone about 100 km wide. This conclusion is supported by the existence of a ductile dextral shear zone in Central Hokkaido (Hidaka Mountains) and associated brittle deformation in western Hokkaido and northeastern Honshu. The stress field during the opening (which ended about 12 Ma ago at the end of the middle Miocene) changes from right-lateral transpression in the north to right-lateral transtension in the south. The western margin, along the Korean peninsula, during the same period, also was an active dextral shear zone. Paleomagnetic results indicate that clockwise rotations occurred in the south during the opening and counterclockwise rotations in the north. We propose a model of right-lateral pull-apart deformation with clockwise rotations of rigid blocks in the southern transtensional domain and counterclockwise rotations in the transpressional one. Small-scale physical models show that the clockwise rotation in transtension is possible provided that the eastern boundary (Pacific side) is free of stress. The opening stopped and compression subsequently began about 12 Ma ago. Finally, we show that the dextral shear, which is distributed over the whole Japan Sea area, is accommodated by N-S trending right-lateral faults and rotation of blocks located between these right-lateral faults

Successful Treatment of Anterior Tracheal Necrosis after Total Thyroidectomy Using Vacuum-Assisted Closure Therapy

Total thyroidectomy involving the adjacent structures of the trachea can cause tracheal damage such as early tracheal necrosis. The authors describe the first case of anterior tracheal necrosis following total thyroidectomy treated using vacuum-assisted closure device. After two weeks of VAC  therapy, there was no evidence of ongoing infection and the trachea was partially closed around a tracheotomy cannula, removed after 3 months. The use of a VAC  therapy to reduce and close the tracheal rent and to create a rapid granulation tissue over tracheal structure appeared as a good opportunity after anterior tracheal necrosis

L’évaluation et l’étude des ensembles funéraires villageois : présentation d’études de cas du diocèse de Tours (Indre-et-Loire)

National audienceSi les occasions d’aborder extensivement les grands ensembles funéraires médiévaux sont rares, en revanche, près d’une quarantaine d'interventions ponctuelles autours des églises ont eu lieu depuis 2010 en Centre-Val-de-Loire. Nous proposons ici un premier bilan de leur intérêt et apports à partir d’une série d’études de cas choisies en Touraine

ATM-Mediated Transcriptional and Developmental Responses to γ-rays in Arabidopsis

ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed

Physical and optical properties of 2010 Eyjafjallajökull volcanic eruption aerosol: ground-based, Lidar and airborne measurements in France

International audienceDuring the Eyjafjallajökull eruption (14 April to 24 May 2010), the volcanic aerosol cloud was observed across Europe by several airborne in situ and ground-based remote-sensing instruments. On 18 and 19 May, layers of depolarizing particles (i.e. non-spherical particles) were detected in the free troposphere above the Puy de Dôme station, (PdD, France) with a Rayleigh-Mie LIDAR emitting at a wavelength of 355 nm, with parallel and crossed polarization channels. These layers in the free troposphere (FT) were also well captured by simulations with the Lagrangian particle dispersion model FLEXPART, which furthermore showed that the ash was eventually entrained into the planetary boundary layer (PBL). Indeed, the ash cloud was then detected and characterized with a comprehensive set of in situ instruments at the Puy de Dôme station (PdD). In agreement with the FLEXPART simulation, up to 65 μg m−3 of particle mass and 2.2 ppb of SO2 were measured at PdD, corresponding to concentrations higher than the 95 percentile of 2 yr of measurements at PdD. Moreover, the number concentration of particles increased to 24 000 cm−3, mainly in the submicronic mode, but a supermicronic mode was also detected with a modal diameter of 2 μm. The resulting optical properties of the ash aerosol were characterized by a low scattering Ångström exponent (0.98), showing the presence of supermicronic particles. For the first time to our knowledge, the combination of in situ optical and physical characterization of the volcanic ash allowed the calculation of the mass-to-extinction ratio (η) with no assumptions on the aerosol density. The mass-to-extinction ratio was found to be significantly different from the background boundary layer aerosol (max: 1.57 g m−2 as opposed to 0.33 ± 0.03 g m−2). Using this ratio, ash mass concentration in the volcanic plume derived from LIDAR measurements was found to be 655 ± 23 μg m−3 when the plume was located in the FT (3000 m above the sea level - a.s.l.). This ratio could also be used to retrieve an aerosol mass concentration of 579 ± 60 μg m−3 on 19 April, when LIDAR observations detected the ash cloud at 3000 m a.s.l. in correspondence with model simulations (FLEXPART). On 22 April, another ash plume entered the BL, and although it was more diluted than during the May episode, the French research aircraft ATR42 that passed over Clermont-Ferrand in the PBL confirmed the presence of particles with a supermicronic mode, again with a modal diameter at 2 μm. This data set combining airborne, ground-based and remote sensing observations with dispersion model simulations shows an overall very good coherence during the volcanic eruption period, which allows a good confidence in the characteristics of the ash particles that can be derived from this unique data set