La base de données sur l'écologie des coléoptères saproxyliques (FRISBEE): un outil taxinomique et écologique pour l'évaluation de l'état de conservation des forêts

The FRench Information system on Saproxylic BEetle Ecology (FRISBEE) is aimed at organizing species-specific ecological information for all wood-associated beetle species in France. Four tables are linked in a relational database structure: (i) the reference table, (ii) the taxonomical table, containing information with standardized nomenclature and species patrimonial value, (iii) the ecological table, including 11 wood parameters or ecological traits that categorize the association of a species to different wood attributes, (iv) and the photographic table. The FRISBEE database is meant to serve as a pragmatic tool for assessing the conservation status of forests and for carrying out functional analyses of saproxylic beetle assemblagesLa base de données sur l'écologie des Coléoptères saproxyliques français (FRench Information system on Saproxylic BEetle Ecology, FRISBEE) a pour objectif la compilation organisée de l'information écologique disponible pour toutes les espèces de Coléoptères associées au bois mort ou dépérissant, ou aux micro-habitats connexes. Cette base de données met en relation 4 tables: (i) une table bibliographique, (ii) une table taxinomique, dotée d'une référentiel taxinomique des espèces avec leur valeur patrimoniale, (iii) une table écologique, incluant 11 descripteurs du bois ou traits écologiques caractérisant l'association des insectes aux attributs ligneux, (iv) et une table photographique. La base FRISBEE constitue un outil pragmatique pour l'évaluation de l'état de conservation des forêts ou pour l'analyse fonctionnelle des assemblages d'espèces

Regards méthodologiques sur l’échantillonnage des coléoptères saproxyliques au moyen des pièges-vitres

Saproxylic beetles are species-rich, mostly small and cryptic, and difficult to sample. Different methods are traditionally used to collect saproxylic beetles. These are (i) direct active collection techniques, (ii) rearing techniques and (iii) mass trapping methods. Window-flight trapping is currently the most frequently used technique for catching flying active saproxylic beetles. Thanks to the combination of different trap principles, window-fl ight trap devices may differ by a large number of intrinsic parameters. This paper offers further insight into the infl uence of 3 trap factors on the catches of dead wood associated beetles, by comparing (i) cross-vanes or single-plane WFT (shape effect), (ii) black or transparent CWFT (silhouette effect), (iii) low or high CWFT (height effect). Six ecological data sets from French upland or lowland, deciduous or coniferous forests, with paired freely hanging window traps on each plot, were compiled in this study and analysed with a methodological point of view to compare the efficiency of sampling methods. Trap shape had a signifi cant and strong effect on the abundance and species richness of saproxylic beetles. The single-plane traps caught a higher number of individuals and species. Nevertheless, given time/cost constraints, cross-vanes traps are recommended. Our study shows that black and transparent cross-vanes traps yielded similar saproxylic samples in terms of abundance, richness and overall composition. Our results confirm the vertical differentiation of saproxylic beetle assemblage. They suggest that low cross-vanes window traps yield more species-rich and individual-rich samples than canopy traps. Except Melyrids, no abundant species showed a strong association with top traps. Further optimisation analyses based on larger datasets are required to make sampling methods more reliableLes coléoptères saproxyliques constituent un groupe riche en espèces, souvent petites et cryptiques, et difficiles à échantillonner. Différentes méthodes sont traditionnellement utilisées pour les collecter: les techniques (i) de collecte active, (ii) d'élevage et (iii) de piégeage. Le piège-vitre est actuellement la méthode la plus fréquemment utilisée pour la capture des coléoptères saproxyliques aériens mobiles. Grâce à la combinaison de différents principes, les pièges-vitres comportent de multiples modèles. Cette étude concerne l'influence de 3 facteurs sur les captures de coléoptères saproxyliques, en comparant (i) des pièges plans bidirectionnels ou multidirectionnels en croix (effet de forme), (ii) des pièges transparents ou noirs (effet silhouette), (iii) des pièges suspendus à faible hauteur ou dans la canopée. Six jeux de données écologiques de plaine ou d'altitude, de forêts françaises feuillues ou résineuses, et comportant deux pièges différents appariés parplacette, ont été compilés et analysés pour comparer l'efficacité respective des méthodes. La forme du piège a un fort effet significatif sur l'abondance et la richesse spécifique, à l'avantage des pièges plans. Néanmoins, en raison de contraintes pratiques ou financières, les pièges-croix sont recommandés. Les pièges noirs ou transparents fournissent des échantillons comparables en termes d'abondance, de richesse et de composition. Nos résultats confirment la différenciation verticale des assemblages de coléoptères saproxyliques, les pièges bas capturant davantage d'individus et d'espèces que les pièges de la canopée. A l'exception des Melyridae, aucune espèce n'est associée aux strates hautes. Des analyses complémentaires fondées sur de plus amples jeux de données sont requises pour optimiser les méthodes d'échantillonnage

Body Wall Force Sensor for Simulated Minimally Invasive Surgery: Application to Fetal Surgery

Surgical interventions are increasingly executed minimal invasively. Surgeons insert instruments through tiny incisions in the body and pivot slender instruments to treat organs or tissue below the surface. While a blessing for patients, surgeons need to pay extra attention to overcome the fulcrum effect, reduced haptic feedback and deal with lost hand-eye coordination. The mental load makes it difficult to pay sufficient attention to the forces that are exerted on the body wall. In delicate procedures such as fetal surgery, this might be problematic as irreparable damage could cause premature delivery. As a first attempt to quantify the interaction forces applied on the patient's body wall, a novel 6 degrees of freedom force sensor was developed for an ex-vivo set up. The performance of the sensor was characterised. User experiments were conducted by 3 clinicians on a set up simulating a fetal surgical intervention. During these simulated interventions, the interaction forces were recorded and analysed when a normal instrument was employed. These results were compared with a session where a flexible instrument under haptic guidance was used. The conducted experiments resulted in interesting insights in the interaction forces and stresses that develop during such difficult surgical intervention. The results also implicated that haptic guidance schemes and the use of flexible instruments rather than rigid ones could have a significant impact on the stresses that occur at the body wall

Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri

The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are under control of external signals and thus quantitative agreement between experimental data and a mathematical model is difficult. Circadian biology has been one notable exception: quantitative models of the internal clock that orchestrates biological processes over the 24-hour diurnal cycle have been constructed for a few organisms, from cyanobacteria to plants and mammals. In most cases, a complex architecture with interlocked feedback loops has been evidenced. Here we present first modeling results for the circadian clock of the green unicellular alga Ostreococcus tauri. Two plant-like clock genes have been shown to play a central role in Ostreococcus clock. We find that their expression time profiles can be accurately reproduced by a minimal model of a two-gene transcriptional feedback loop. Remarkably, best adjustment of data recorded under light/dark alternation is obtained when assuming that the oscillator is not coupled to the diurnal cycle. This suggests that coupling to light is confined to specific time intervals and has no dynamical effect when the oscillator is entrained by the diurnal cycle. This intringuing property may reflect a strategy to minimize the impact of fluctuations in daylight intensity on the core circadian oscillator, a type of perturbation that has been rarely considered when assessing the robustness of circadian clocks

Transcription Profile Analysis Reveals That Zygotic Division Results in Uneven Distribution of Specific Transcripts in Apical/Basal Cells of Tobacco

BACKGROUND: Asymmetric zygotic division in higher plants results in the formation of an apical cell and a basal cell. These two embryonic cells possess distinct morphologies and cell developmental fates. It has been proposed that unevenly distributed cell fate determinants and/or distinct cell transcript profiles may be the underlying reason for their distinct fates. However, neither of these hypotheses has convincing support due to technical limitations. METHODOLOGY/PRINCIPAL FINDINGS: Using laser-controlled microdissection, we isolated apical and basal cells and constructed cell type-specific cDNA libraries. Transcript profile analysis revealed difference in transcript composition. PCR and qPCR analysis confirmed that transcripts of selected embryogenesis-related genes were cell-type preferentially distributed. Some of the transcripts that existed in zygotes were found distinctly existed in apical or basal cells. The cell type specific de novo transcription was also found after zygotic cell division. CONCLUSIONS/SIGNIFICANCE: Thus, we found that the transcript diversity occurs between apical and basal cells. Asymmetric zygotic division results in the uneven distribution of some embryogenesis related transcripts in the two-celled proembryos, suggesting that a differential distribution of some specific transcripts in the apical or basal cells may involve in guiding the two cell types to different developmental destinies

Discovery pipelines for marine resources : an ocean of opportunity for biotechnology?

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant agreement No 645884. CABI is an international intergovernmental organisation, and we gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Department for International Development), China (Chinese Ministry of Agriculture), Australia (Australian Centre for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation),and Switzerland (Swiss Agency for Development and Cooperation). See https://www.cabi.org/about-cabi/who-we-work-with/key-donors/ for full details.Marine microbial diversity offers enormous potential for discovery of compounds of crucial importance in healthcare, food security and bioindustry. However, access to it has been hampered by the difficulty of accessing and growing the organisms for study. The discovery and exploitation of marine bioproducts for research and commercial development requires state-of-the-art technologies and innovative approaches. Technologies and approaches are advancing rapidly and keeping pace is expensive and time consuming. There is a pressing need for clear guidance that will allow researchers to operate in a way that enables the optimal return on their efforts whilst being fully compliant with the current regulatory framework. One major initiative launched to achieve this, has been the advent of European Research Infrastructures. Research Infrastructures (RI) and associated centres of excellence currently build harmonized multidisciplinary workflows that support academic and private sector users. The European Marine Biological Research Infrastructure Cluster (EMBRIC) has brought together six such RIs in a European project to promote the blue bio-economy. The overarching objective is to develop coherent chains of high-quality services for access to biological, analytical and data resources providing improvements in the throughput and efficiency of workflows for discovery of novel marine products. In order to test the efficiency of this prototype pipeline for discovery, 248 rarely-grown organisms were isolated and analysed, some extracts demonstrated interesting biochemical properties and are currently undergoing further analysis. EMBRIC has established an overarching and operational structure to facilitate the integration of the multidisciplinary value chains of services to access such resources whilst enabling critical mass to focus on problem resolution.Publisher PDFPeer reviewe

Arthropod communities in fungal fruitbodies are weakly structured by climate and biogeography across European beech forests

Aim The tinder fungus Fomes fomentarius is a pivotal wood decomposer in European beech Fagus sylvatica forests. The fungus, however, has regionally declined due to centuries of logging. To unravel biogeographical drivers of arthropod communities associated with this fungus, we investigated how space, climate and habitat amount structure alpha and beta diversity of arthropod communities in fruitbodies of F. fomentarius. Location Temperate zone of Europe. Taxon Arthropods. Methods We reared arthropods from fruitbodies sampled from 61 sites throughout the range of European beech and identified 13 orders taxonomically or by metabarcoding. We estimated the total number of species occurring in fruitbodies of F. fomentarius in European beech forests using the Chao2 estimator and determined the relative importance of space, climate and habitat amount by hierarchical partitioning for alpha diversity and generalized dissimilarity models for beta diversity. A subset of fungi samples was sequenced for identification of the fungus’ genetic structure. Results The total number of arthropod species occurring in fruitbodies of F. fomentarius across European beech forests was estimated to be 600. Alpha diversity increased with increasing fruitbody biomass; it decreased with increasing longitude, temperature and latitude. Beta diversity was mainly composed by turnover. Patterns of beta diversity were only weakly linked to space and the overall explanatory power was low. We could distinguish two genotypes of F. fomentarius, which showed no spatial structuring. Main conclusion Fomes fomentarius hosts a large number of arthropods in European beech forests. The low biogeographical and climatic structure of the communities suggests that fruitbodies represent a habitat that offers similar conditions across large gradients of climate and space, but are characterized by high local variability in community composition and colonized by species with high dispersal ability. For European beech forests, retention of trees with F. fomentarius and promoting its recolonization where it had declined seems a promising conservation strategy

Preoperative Brain Tumor Imaging: Models and Software for Segmentation and Standardized Reporting

For patients suffering from brain tumor, prognosis estimation and treatment decisions are made by a multidisciplinary team based on a set of preoperative MR scans. Currently, the lack of standardized and automatic methods for tumor detection and generation of clinical reports, incorporating a wide range of tumor characteristics, represents a major hurdle. In this study, we investigate the most occurring brain tumor types: glioblastomas, lower grade gliomas, meningiomas, and metastases, through four cohorts of up to 4,000 patients. Tumor segmentation models were trained using the AGU-Net architecture with different preprocessing steps and protocols. Segmentation performances were assessed in-depth using a wide-range of voxel and patient-wise metrics covering volume, distance, and probabilistic aspects. Finally, two software solutions have been developed, enabling an easy use of the trained models and standardized generation of clinical reports: Raidionics and Raidionics-Slicer. Segmentation performances were quite homogeneous across the four different brain tumor types, with an average true positive Dice ranging between 80 and 90%, patient-wise recall between 88 and 98%, and patient-wise precision around 95%. In conjunction to Dice, the identified most relevant other metrics were the relative absolute volume difference, the variation of information, and the Hausdorff, Mahalanobis, and object average symmetric surface distances. With our Raidionics software, running on a desktop computer with CPU support, tumor segmentation can be performed in 16–54 s depending on the dimensions of the MRI volume. For the generation of a standardized clinical report, including the tumor segmentation and features computation, 5–15 min are necessary. All trained models have been made open-access together with the source code for both software solutions and validation metrics computation. In the future, a method to convert results from a set of metrics into a final single score would be highly desirable for easier ranking across trained models. In addition, an automatic classification of the brain tumor type would be necessary to replace manual user input. Finally, the inclusion of post-operative segmentation in both software solutions will be key for generating complete post-operative standardized clinical reports.publishedVersio