Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expressionComment: 7 figures, 20 supplementary figures, 6 supplementary tables Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, et al. (2013) Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression. PLoS Genet 9(9): e1003748. doi:10.1371/journal.pgen.100374

Sketching Research in Education through Academic Journals (In French)

This contribution aims at coming up with serious grounds for an evaluation of French research published in scientific journals in the field of Education Science. A reliable method consists in criss-crossing the various databases which play an authoritative part – those of the ISI (Institute for Scientific Information) and others -, in listing the titles of journals they retrieve, and in asking the scientific community what its position is. Hence the scientificity of a journal: a journal is scientific when considered as such by the scientists of its community. In this contribution, a case study is built in Education Science. Some major journals are studied and some conclusions raised.Educational Research, Evaluation, France, Psychology, Sociology, Sociology of Science, Scientific Journals, Scientometrics

An amphioxus orthologue of the estrogen receptor that does not bind estradiol: Insights into estrogen receptor evolution

<p>Abstract</p> <p>Background</p> <p>The origin of nuclear receptors (NRs) and the question whether the ancestral NR was a liganded or an unliganded transcription factor has been recently debated. To obtain insight into the evolution of the ligand binding ability of estrogen receptors (ER), we comparatively characterized the ER from the protochordate amphioxus (<it>Branchiostoma floridae</it>), and the ER from lamprey (<it>Petromyzon marinus</it>), a basal vertebrate.</p> <p>Results</p> <p>Extensive phylogenetic studies as well as signature analysis allowed us to confirm that the amphioxus ER (amphiER) and the lamprey ER (lampER) belong to the ER group. LampER behaves as a "classical" vertebrate ER, as it binds to specific DNA Estrogen Responsive Elements (EREs), and is activated by estradiol (E₂), the classical ER natural ligand. In contrast, we found that although amphiER binds EREs, it is unable to bind E₂and to activate transcription in response to E₂. Among the 7 natural and synthetic ER ligands tested as well as a large repertoire of 14 cholesterol derivatives, only Bisphenol A (an endocrine disruptor with estrogenic activity) bound to amphiER, suggesting that a ligand binding pocket exists within the receptor. Parsimony analysis considering all available ER sequences suggest that the ancestral ER was not able to bind E₂and that this ability evolved specifically in the vertebrate lineage. This result does not support a previous analysis based on ancestral sequence reconstruction that proposed the ancestral steroid receptor to bind estradiol. We show that biased taxonomic sampling can alter the calculation of ancestral sequence and that the previous result might stem from a high proportion of vertebrate ERs in the dataset used to compute the ancestral sequence.</p> <p>Conclusion</p> <p>Taken together, our results highlight the importance of comparative experimental approaches vs ancestral reconstructions for the evolutionary study of endocrine systems: comparative analysis of extant ERs suggests that the ancestral ER did not bind estradiol and that it gained the ability to be regulated by estradiol specifically in the vertebrate lineage, before lamprey split.</p

A hybrid CMV-H1 construct improves efficiency of PEI-delivered shRNA in the mouse brain

RNA-interference-driven loss of function in specific tissues in vivo should permit analysis of gene function in temporally and spatially defined contexts. However, delivery of efficient short hairpin RNA (shRNA) to target tissues in vivo remains problematic. Here, we demonstrate that efficiency of polyethylenimine (PEI)-delivered shRNA depends on the regulatory sequences used, both in vivo and in vitro. When tested in vivo, silencing of a luciferase target gene by shRNA produced from a hybrid construct composed of the CMV enhancer/promoter placed immediately upstream of an H1 promoter (50%) exceeds that obtained with the H1 promoter alone (20%). In contrast, in NIH 3T3 cells, the H1 promoter was more efficient than the hybrid construct (75 versus 60% inhibition of target gene expression, respectively). To test CMV-H1 shRNA efficiency against an endogenous gene in vivo, we used shRNA against thyroid hormone receptor α1 (TRα1). When vectorized in the mouse brain, the hybrid construct strongly derepressed CyclinD1-luciferase reporter gene expression, CyclinD1 being a negatively regulated thyroid hormone target gene. We conclude that promoter choice affects shRNA efficiency distinctly in different in vitro and in vivo situations and that a hybrid CMV-H1 construct is optimal for shRNA delivery in the mouse brain

Ex Situ LIBS Analysis of WEST Divertor Wall Tiles after C3 Campaign

Fuel retention monitoring in tokamak walls requires the development of remote composition analysis methods such as laser-induced breakdown spectroscopy (LIBS). The present study investigates the feasibility of the LIBS method to analyse the composition and fuel retention in three samples from WEST divertor erosion marker tiles after the experimental campaign C3. The investigated samples originated from tile regions outside of strong erosion and deposition regions, where the variation of thin deposit layers is relatively small and facilitates cross-comparison between different analysis methods. The depth profiles of main constituents W, Mo and C were consistent with depth profiles determined by other composition analysis methods, such as glow-discharge optical emission spectroscopy (GDOES) and secondary ion mass spectrometry (SIMS). The average LIBS depth resolution determined from depth profiles was 100 nm/shot. The averaging of the spectra collected from multiple spots of a same sample allowed us to improve the signal-to-noise ratio, investigate the presence of fuel D and trace impurities such as O and B. In the investigated tile regions with negligible erosion and deposition, these impurities were clearly detectable during the first laser shot, while the signal decreased to noise level after a few subsequent laser shots at the same spot. LIBS investigation of samples originating from the deposition regions of tiles may further clarify LIBS’ ability to investigate trace impurities

The EGIM, EMSO generic instrument module, step towards standardization

Peer ReviewedPostprint (published version

The EMSO Generic Instrument Module (EGIM): standardized and interoperable instrumentation for ocean observation

The oceans are a fundamental source for climate balance, sustainability of resources and life on Earth, therefore society has a strong and pressing interest in maintaining and, where possible, restoring the health of the marine ecosystems. Effective, integrated ocean observation is key to suggesting actions to reduce anthropogenic impact from coastal to deep-sea environments and address the main challenges of the 21st century, which are summarized in the UN Sustainable Development Goals and Blue Growth strategies. The European Multidisciplinary Seafloor and water column Observatory (EMSO), is a European Research Infrastructure Consortium (ERIC), with the aim of providing long-term observations via fixed-point ocean observatories in key environmental locations across European seas from the Arctic to the Black Sea. These may be supported by ship-based observations and autonomous systems such as gliders. In this paper, we present the EMSO Generic Instrument Module (EGIM), a deployment ready multi-sensor instrumentation module, designed to measure physical, biogeochemical, biological and ecosystem variables consistently, in a range of marine environments, over long periods of time. Here, we describe the system, features, configuration, operation and data management. We demonstrate, through a series of coastal and oceanic pilot experiments that the EGIM is a valuable standard ocean observation module, which can significantly improve the capacity of existing ocean observatories and provides the basis for new observatories. The diverse examples of use included the monitoring of fish activity response upon oceanographic variability, hydrothermal vent fluids and particle dispersion, passive acoustic monitoring of marine mammals and time series of environmental variation in the water column. With the EGIM available to all the EMSO Regional Facilities, EMSO will be reaching a milestone in standardization and interoperability, marking a key capability advancement in addressing issues of sustainability in resource and habitat management of the oceans.This work was funded by the project EMSODEV (Grant agreement No 676555) supported by DG Research and Innovation of the European Commission under the Research Infrastructures Programme of the H2020. EMSO-link EC project (Grant agreement No 731036) provided additional funding. Other projects which supported the work include Plan Estatal de Investigación Científica y Técnica y de Innovación 2017–2020, project BITER-LANDER PID2020- 114732RB-C32, iFADO (Innovation in the Framework of the Atlantic Deep Ocean, 2017–2021) EAPA_165/2016. The Spanish Government contributed through the “Severo Ochoa Centre Excellence” accreditation to ICM-CSIC (CEX2019-000928-S) and the Research Unit Tecnoterra (ICM-CSIC/UPC). UK colleagues were supported by Climate Linked Atlantic Sector Science (CLASS) project supported by NERC National Capability funding (NE/R015953/1).Peer ReviewedArticle signat per 33 autors/es: Nadine Lantéri; Henry A. Ruh; Andrew Gates; Enoc Martínez; Joaquin del Rio Fernandez; Jacopo Aguzzi; Mathilde Cannat; Eric Delory; Davide Embriaco; Robert Huber; Marjolaine Matabos;George Petihakis; Kieran Reilly; Jean-François Rolin; Mike van der Schaar; Michel André; Jérôme Blandin; Andrés Cianca; Marco Francescangeli; Oscar Garcia; Susan Hartman; Jean-Romain Lagadec; Julien Legrand; Paris Pagonis; Jaume Piera; Xabier Remirez; Daniel M. Toma; Giuditta Marinaro; Bertrand Moreau; Raul Santana; Hannah Wright; Juan José Dañobeitia; Paolo FavaliPostprint (published version

A Whole-Genome Scan for Association With Invasion Success in the Fruit Fly Drosophila Suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BAYPASS. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level

Towards the new Thematic Core Service Tsunami within the EPOS Research Infrastructure

Tsunamis constitute a significant hazard for European coastal populations, and the impact of tsunami events worldwide can extend well beyond the coastal regions directly affected. Understanding the complex mechanisms of tsunami generation, propagation, and inundation, as well as managing the tsunami risk, requires multidisciplinary research and infrastructures that cross national boundaries. Recent decades have seen both great advances in tsunami science and consolidation of the European tsunami research community. A recurring theme has been the need for a sustainable platform for coordinated tsunami community activities and a hub for tsunami services. Following about three years of preparation, in July 2021, the European tsunami community attained the status of Candidate Thematic Core Service (cTCS) within the European Plate Observing System (EPOS) Research Infrastructure. Within a transition period of three years, the Tsunami candidate TCS is anticipated to develop into a fully operational EPOS TCS. We here outline the path taken to reach this point, and the envisaged form of the future EPOS TCS Tsunami. Our cTCS is planned to be organised within four thematic pillars: (1) Support to Tsunami Service Providers, (2) Tsunami Data, (3) Numerical Models, and (4) Hazard and Risk Products. We outline how identified needs in tsunami science and tsunami risk mitigation will be addressed within this structure and how participation within EPOS will become an integration point for community development