Modelling spatial distributions of alpine vegetation : a graph theory approach to delineate ecologically-consistent species assemblages

This work was partly funded by the French Ministry of Ecology, Sustainable Development and Energy in support of the development of the CARHab project (2011-2015) on mapping the terrestrial habitats of France. In addition, this work benefited from a synergy with the Divgrass project (Plant Functional Diversity of Permanent Grasslands) (CESAB/FRB funded, France).Safeguarding biodiversity has been one of the most important issues on the environmental and forest policies agenda since the 1990's. The problem remains in terms of decisions and knowledge on where to set appropriate conservation targets. Hence, we need detailed and reliable information about habitat structure and composition and methods for estimating this information over the whole spatial domain. In answer to this target, in France, the Ministry of Ecology launched an ambitious project to map the terrestrial vegetation at a scale of 1:25 000 known as CarHab. This project initiated in 2011, will be used as a strategic spatial planning tool in answer to key issues in relation to biodiversity, conservation, green infrastructures and to report on the conservation status of habitats and species of community interest. We use species-distribution models (SDMs) to identify areas that are ecologically suitable for the presence of species based on specific habitat characteristics. Available techniques using graph theory enable identification of groups of species (assemblages) based on ecological affinities. Species co-occurrences (present within the same assessment plot), revealing a shared ecological niche, are analysed using algorithms derived from graph theory in order to define different nodes of species affinities. Thus, the resulting assemblages are based on ecological similarities. Hence, these assemblages are used to develop models of the potential distribution of alpine vegetation communities. The BIOMOD platform is used to facilitate the simultaneous implementation of different modelling approaches that can be compared in order to choose the most suitable and accurate for each species assemblage obtained from graph theory. Using the different relevant spatially explicit results provides a more comprehensive vision of the communities' spatial distributions.PostprintPeer reviewe

Targeting of tail-anchored proteins to yeast mitochondria in vivo

AbstractTail-anchored proteins are inserted into intracellular membranes via a C-terminal transmembrane domain. The topology of the protein is such that insertion must occur post-translationally, since the insertion sequence is not available for membrane insertion until after translation of the tail-anchored polypeptide is completed. Here, we show that the targeting information in one such tail-anchored protein, translocase in the outer mitochondrial membrane 22, is contained in a short region flanking the transmembrane domain. An equivalent region is sufficient to specify the localisation of Bcl2 and SNARE proteins to the secretory membranes. We discuss the targeting process for directing members of this protein family to the secretory and mitochondrial membranes in vivo

Control of membrane protein homeostasis by a chaperone-like glial cell adhesion molecule at multiple subcellular locations

The significance of crosstalks among constituents of plasma membrane protein clusters/complexes in cellular proteostasis and protein quality control (PQC) remains incompletely understood. Examining the glial (enriched) cell adhesion molecule (CAM), we demonstrate its chaperone-like role in the biosynthetic processing of the megalencephalic leukoencephalopathy with subcortical cyst 1 (MLC1)-heteromeric regulatory membrane protein complex, as well as the function of the GlialCAM/MLC1 signalling complex. We show that in the absence of GlialCAM, newly synthesized MLC1 molecules remain unfolded and are susceptible to polyubiquitination-dependent proteasomal degradation at the endoplasmic reticulum. At the plasma membrane, GlialCAM regulates the diffusional partitioning and endocytic dynamics of cluster members, including the ClC-2 chloride channel and MLC1. Impaired folding and/or expression of GlialCAM or MLC1 in the presence of diseases causing mutations, as well as plasma membrane tethering compromise the functional expression of the cluster, leading to compromised endo-lysosomal organellar identity. In addition, the enlarged endo-lysosomal compartments display accelerated acidification, ubiquitinated cargo-sorting and impaired endosomal recycling. Jointly, these observations indicate an essential and previously unrecognized role for CAM, where GliaCAM functions as a PQC factor for the MLC1 signalling complex biogenesis and possess a permissive role in the membrane dynamic and cargo sorting functions with implications in modulations of receptor signalling

Ubr1-induced selective endophagy/autophagy protects against the endosomal and Ca2+-induced proteostasis disease stress

The cellular defense mechanisms against cumulative endo-lysosomal stress remain incompletely understood. Here, we iden tify Ubr1 as a protein quality control (QC) E3 ubiquitin-ligase that counteracts proteostasis stresses by facilitating endosomal cargo-selective autophagy for lysosomal degradation. Astrocyte regulatory cluster membrane protein MLC1 mutations cause endosomal compartment stress by fusion and enlargement. Partial lysosomal clearance of mutant endosomal MLC1 is accomplished by the endosomal QC ubiquitin ligases, CHIP and Ubr1 via ESCRT-dependent route. As a consequence of the endosomal stress, a supportive QC mechanism, dependent on both Ubr1 and SQSTM1/p62 activities, targets ubiquit inated and arginylated MLC1 mutants for selective endosomal autophagy (endophagy). This QC pathway is also activated for arginylated Ubr1-SQSTM1/p62 autophagy cargoes during cytosolic Ca2+-assault. Conversely, the loss of Ubr1 and/or arginylation elicited endosomal compartment stress. These fndings underscore the critical housekeeping role of Ubr1 and arginylation-dependent endophagy/autophagy during endo-lysosomal proteostasis perturbations and suggest a link of Ubr1 to Ca2+ homeostasis and proteins implicated in various diseases including cancers and brain disorder

Diagnostic strategy and timing of intervention in infected necrotizing pancreatitis: an international expert survey and case vignette study

AbstractBackgroundThe optimal diagnostic strategy and timing of intervention in infected necrotizing pancreatitis is subject to debate. We performed a survey on these topics amongst a group of international expert pancreatologists.MethodsAn online survey including case vignettes was sent to 118 international pancreatologists. We evaluated the use and timing of fine needle aspiration (FNA), antibiotics, catheter drainage and (minimally invasive) necrosectomy.ResultsThe response rate was 74% (N = 87). None of the respondents use FNA routinely, 85% selectively and 15% never. Most respondents (87%) use a step-up approach in patients with infected necrosis. Walled-off necrosis (WON) is considered a prerequisite for endoscopic drainage and percutaneous drainage by 66% and 12%, respectively. After diagnosing infected necrosis, 55% routinely postpone invasive interventions, whereas 45% proceed immediately to intervention. Lack of consensus about timing of intervention was apparent on day 14 with proven infected necrosis (58% intervention vs. 42% non-invasive) as well as on day 20 with only clinically suspected infected necrosis (59% intervention vs. 41% non-invasive).DiscussionThe step-up approach is the preferred treatment strategy in infected necrotizing pancreatitis amongst expert pancreatologists. There is no uniformity regarding the use of FNA and timing of intervention in the first 2–3 weeks of infected necrotizing pancreatitis

La modélisation spatialisée de la végétation : un appui à la cartographie des habitats

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVINInternational audienceDans le cadre du projet CarHAB, la modélisation spatialisée de la distribution de la végétation contribue à la réalisation de la cartographie de la végétation 1/ en ciblant sur les végétations présentes de façon très fragmentaires et difficiles à cartographier par des méthodes de télédétection, 2/ en facilitant la valorisation des jeux de données ponctuelles des CBNs, 3/ en orientant les prospections pour faciliter la réalisation terrain de la carte de végétation par les CBNs 4/ en contribuant à l’alimentation du Fond Blanc par remplissage des polygones issus de la segmentation effectuée dans le cadre du volet télédétection. Dans une première phase l’objectif est de déterminer le potentiel de la modélisation spatialisée pour prédire la distribution d’alliances de végétation. Pour l’instant, les tests ont été réalisés avec la méthode dite du maximum d’entropie (Maxent), qui permet d’estimer la distribution la plus probable d’une espèce ou d’un groupe d’espèces à partir de données de présence géolocalisées et de variables environnementales spatialisées. Cette méthode est basée sur le principe que la meilleure estimation d’une distribution inconnue est celle qui est la moins contraignante (avec le maximum d’entropie) pour l’espèce, où les contraintes sont définies en comparant la distribution des valeurs des variables environnementales aux points d’observation avec leurs valeurs pour des points pris au hasard dans la zone d’étude. Les tests ont été réalisés pour plusieurs alliances de milieux ouverts de la zone test Belledonne CORA, située principalement en Isère : i) pelouses acides d’altitude (trois alliances de la classe 15 du Prodrome, Caricetea curvulae Braun-Blanq. 1948), ii) combes à neige à l‘alpin (Salicion herbaceae Braun-Blanq. in Braun-Blanq. & H. Jenny 1926, iii) prairies de couloirs à l’étage subalpin (Calamagrostion villosae Pawł. in Pawł., Sokolowski & Wallisch 1928), iv) pelouses calcaires (Mesobromion erecti (Braun-Blanq. & Moor 1938) Oberdorfer 1957), v) bas marais acides (Caricion fuscae W.Koch 1926), vi) fourrés arbustifs, l’Alnion viridis A. Schnyd. 1930). La méthode Maxent donne de bons résultats pour la majorité des alliances étudiées. Les résultats ont été vérifiés sur le terrain pendant l’été. Il s’agira pour la suite de déterminer si cette méthode peut être déployée sur d’autres sites ou s’il faut l’adapter ou la compléter par d’autres approches

Habitat modelling: a multi‐models approach to map the potential distribution of alpine vegetation assemblages in France

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVINInternational audienceThis paper presents a method to assess the potential distribution of alpine species assemblages in the crystalline Belledonne-Ecrins Mountains (France), at a relative fine scale. Using ecological variables and vegetation monitoring plots, we computed 8 species distribution models (SDMs) to predict the potential distribution of 6 alpine species assemblages. These vegetation communities were first constructed using graph theory approaches based on species' lists elaborated by the Alpine National Botanical Conservatory (CBNA) from field work on monitoring plots. The goal is to elaborate species assemblages (or modules) that are not constrained by phyto-sociological principles but based on the species co-occurrence at the monitoring plots. Species inside a module are thus linked with each other by their ecological affinities and not by botanical characteristics, sustaining the use of ecological dataset to predict their potential distribution. From expert knowledge, the 6 assemblages were selected for their wide representation on the field, their ecological dissimilarities (contrasted niches) and their botanical consistency. They are essentially distributed in sub-alpine and alpine vegetation levels. Based on the ecological niche theory, species distribution models (SDMs) were used to identify areas that are ecologically suitable for the presence of these 6 assemblages. In all, we used 7 environmental variables, mainly derived from a 25m Digital Elevation Model. Hence, alpine species are greatly influenced by the presence and duration of snow cover and consequently by topography and solar radiation. Moreover, the coarse resolution of climatic data did not match the prerogative of the potential distributions' maps. The BIOMOD platform was used to compute 8 SDMs (ANN, CTA, FDA, GAM, GBM, GLM, RF, and Maxent). Mean models and coefficient of variations were then calculated based on the best model performances (evaluated based upon expert knowledge). This approach, called "ensemble modelling", gives more consistent results and allows a spatial analysis of the level of agreement between models. The use of ensemble modelling, using simple ecological datasets, has shown great potential to provide reliable species ecological niches, having important implications in vegetation mapping and thus on management decisions regarding biodiversity conservation. Actually, the predictions show good correlations with field data, few false overlaps between modules and good correlations between transition communities and modules overlaps, revealing the power of these techniques for vegetation mapping in relative complex and inaccessible areas

The Late Osteoblast/Preosteocyte Cell Line MLO-A5 Displays Mesenchymal Lineage Plasticity In Vitro and In Vivo

The process of osteoblast switching to alternative mesenchymal phenotypes is incompletely understood. In this study, we tested the ability of the osteoblast/preosteocyte osteogenic cell line, MLO-A5, to also differentiate into either adipocytes or chondrocytes. MLO-A5 cells expressed a subset of skeletal stem cell markers, including Sca-1, CD44, CD73, CD146, and CD166. Confluent cultures of cells underwent differentiation within 3 days upon the addition of osteogenic medium. The same cultures were capable of undergoing adipogenic and chondrogenic differentiation under lineage-appropriate culture conditions, evidenced by lineage-specific gene expression analysis by real-time reverse-transcription-PCR, and by Oil Red O and alcian blue (pH 2.5) staining, respectively. Subcutaneous implantation of MLO-A5 cells in a gel foam into NOD SCID mice resulted in a woven bone-like structure containing embedded osteocytes and regions of cartilage-like tissue, which stained positive with both alcian blue (pH 2.5) and safranin O. Together, our findings show that MLO-A5 cells, despite being a strongly osteogenic cell line, exhibit characteristics of skeletal stem cells and display mesenchymal lineage plasticity in vitro and in vivo. These unique characteristics suggest that this cell line is a useful model with which to study aging and disease-related changes to the mesenchymal lineage composition of bone