Classification non supervisée d'un graphe de co-expression avec des méta-données pour la détection de micro-ARNs

National audienceNous présentons dans cet article une méthode de classification non supervisée de sommets d'un graphe qui est utilisée dans un contexte biologique particulier. La problématique est de détecter de manière non supervisée des micro-ARNs probables. Pour ce faire, nous utilisons une approche multi-noyaux permettant d'intégrer des informations sur le graphe de co-expression et des informations supplémentaires sur les sommets de ce graphe. Cette approche est rendue robuste par une technique de bagging de classifications. Les résultats obtenus donnent des groupes de miRNAs potentiels dont certains permettent de discriminer avec une bonne confiance les vrais miRNAs des faux positifs

Sous les scories, une nécropole : un petit ensemble funéraire du Haut-Empire (Coulans-sur-Gée, « Les Brochardières », Sarthe)

Localisée en périphérie de la commune de Coulans-sur-Gée, à environ quinze kilomètres à l’ouest du Mans, la parcelle ZS 37 au lieu-dit « Les Brochardières » était jusqu’à récemment vouée au pâturage. La fouille qui s’est déroulée entre le 27 février et le 15 mars 2012 a permis de mettre au jour une nécropole à crémations partiellement conservée, installée le long d’une limite parcellaire d’origine probablement antique (matérialisée par une haie ou un chemin). Quatre dépôts ont été clairement identifiés, datés du courant du iie siècle de notre ère jusqu’au début du iiie siècle par le mobilier céramique. L’organisation interne et le matériel issu des fosses présentent une grande diversité. Les dépôts sont de type mixte et/ou en ossuaire, dans des fosses probablement couvertes, ayant ménagé un espace vide. Les céramiques sont d’origine locale, seule une forme témoigne de l’existence de vaisselle importée. Par la suite, un atelier de réduction directe du minerai de fer a été installé vers le milieu du iiie siècle de notre ère au bord du parcellaire préexistant, comprenant une aire de calcination, un bas fourneau et un amas de scories, le tout arasé. À une date indéterminée, une partie de ces vestiges a servi à exhausser la bande de roulement du chemin proche.About 15 kms from the french city of Le Mans, a partially preserved necropolis with cremations was found in 2012 along a plot of land probably inherited from the Roman period. Four graves have been identified, dated from the IInd to the beginning of the IIIrd century thanks to the pottery. Internal organisation and artefacts from those pits are very diversified. Deposits are of different types : ossuaries, pyre debris being redeposited, and deposits which includes both of the previous types. Pottery-wares used to place the ossuary, as well as the vessels deposited in the structures are from local origin, only one was imported. Afterwards, a steel industry settled in the mid IIIrd century.Im Jahr 2012 wurde rund 15 km westlich der französischen Stadt Le Mans eine teilweise erhaltene römische Nekropole mit Brandbestattungen nachgewiesen. Das betroffene Flurstück ZS 37 in der Flur „Les Brochardières“ war erst jüngst zur Beweidung freigegeben worden. Die Ausgrabung des Gräberfeldes fand vom 27 Februar bis zum 15 März 2012 statt. Sie hat gestattet, ein teilweise erhaltenes Brandgräberfeld freizulegen, das entlang einer durch eine Hecke oder einen Weg markierten Flurstücksgrenze angelegt worden war. Diese reicht vermutlich in die römische Zeit zurück. Vier Grabdeponierungen konnten eindeutig identifiziert werden. Sie können durch die Keramikfunde einem Zeitraum vom 2. bis zum frühen 3. Jh. n. Chr. zugewiesen werden. Die Bestattungssitten sowie das Fundmaterial aus den Grabgruben zeichnen sich durch große Diversität aus. Bei den Grabdeponierungen treten verschiedene Typen auf: Leichenbranddeponierungen sowie Brandschüttungen oder eine Mischung beider Bestattungssitten. Diese wurden in abgedeckten Gruben beigesetzt, bei denen offenbar stets ein Hohlraum erhalten blieb. Die Grabkeramik wurde dazu genutzt, den Leichenbrand zu deponieren. Die Keramikformen verweisen auf lokale Produktion; eine einzige Keramikform belegt auf das Auftreten von Importkeramik. Außerdem wurde ein Werkplatz entdeckt, an dem Roheisen verarbeitet wurde. Er wurde im Laufe des 3. Jahrhunderts n. Chr. am Rande des bereits existierenden Flurstücks angelegt und umfasste einen Röstplatz, einen Rennofen und eine Schlackenhalde, die jedoch alle bereits erodiert waren. Zu einem nicht näher bestimmbaren Zeitpunkt diente ein Teil dieser Hinterlassenschaften offenbar dazu, die Fahrbahn des nahegelegenen Weges zu erhöhen

Plant taxonomic and phylogenetic turnover increases toward climatic extremes and depends on historical factors in European beech forests

Aims: The effect of biogeographical processes on the spatial turnover component of beta-diversity over large spatial extents remains scarcely understood. Here, we aim at disentangling the roles of environmental and historical factors on plant taxonomic and phylogenetic turnover, while controlling for the effects of species richness and rarity. Location: European beech (Fagus sylvatica) forests in Europe. Methods: We aggregated plant species occurrences from vegetation plots in spatial grid cells of 0.25º × 0.25º to calculate the spatial turnover component of taxonomic (TBD) and phylogenetic (PBD) beta-diversity for each cell. We also calculated the deviation of PBD given TBD (PBD), which measures the importance of phylogenetic turnover after factoring out taxonomic turnover. Beta-diversity was calculated for each grid cell as the mean pairwise dissimilarity between the focal cell and all other cells. We used structural equation modeling (SEM) to examine the relationships between environmental (climate, soil pH, and distance from the geographical distribution limit of beech) and historical (distance from beech glacial refugia) predictors and beta-diversity metrics. Results: We found a geographically consistent variation in taxonomic and phylogenetic turnover. Overall, TBD and PBD increased significantly toward more extreme climatic conditions, on more acidic soils, and toward the margins of beech distribution. The effects of environmental variables and the distance from glacial refugia on beta-diversity metrics were mediated by species richness and rarity. Phylogenetic turnover was low in relation to taxonomic turnover (i.e., high PBD) in areas closer to glacial refugia. Conclusions: Continental-scale patterns of beta-diversity in European beech forests are the result of complementary ecological and evolutionary processes. In general, beech forests are taxonomically and phylogenetically more distinct in climatically marginal areas of their European range. However, the spatial variation of beta-diversity in European beech forest flora is still strongly characterized by the distribution of groups of closely related species that evolved or survived in glacial refugia.The study was supported by the Czech Science Foundation (project no.19-28491X). I.B. and J.A.C. were funded by the Basque Government (IT936-16)

Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe.

Aim:Forest understorey microclimates are often buffered against extreme heat or cold, with important implications for the organisms living in these environments. We quantified seasonal effects of understorey microclimate predictors describing canopy structure, canopy composition and topography (i.e., local factors) and the forest patch size and distance to the coast (i.e., landscape factors). Location:Temperate forests in Europe. Time period:2017-2018. Major taxa studied:Woody plants. Methods:We combined data from a microclimate sensor network with weather-station records to calculate the difference, or offset, between temperatures measured inside and outside forests. We used regression analysis to study the effects of local and landscape factors on the seasonal offset of minimum, mean and maximum temperatures. Results:The maximum temperature during the summer was on average cooler by 2.1 °C inside than outside forests, and the minimum temperatures during the winter and spring were 0.4 and 0.9 °C warmer. The local canopy cover was a strong nonlinear driver of the maximum temperature offset during summer, and we found increased cooling beneath tree species that cast the deepest shade. Seasonal offsets of minimum temperature were mainly regulated by landscape and topographic features, such as the distance to the coast and topographic position. Main conclusions:Forest organisms experience less severe temperature extremes than suggested by currently available macroclimate data; therefore, climate-species relationships and the responses of species to anthropogenic global warming cannot be modelled accurately in forests using macroclimate data alone. Changes in canopy cover and composition will strongly modulate the warming of maximum temperatures in forest understories, with important implications for understanding the responses of forest biodiversity and functioning to the combined threats of land-use change and climate change. Our predictive models are generally applicable across lowland temperate deciduous forests, providing ecologically important microclimate data for forest understories

Soil seed bank responses to edge effects in temperate European forests

Aim The amount of forest edges is increasing globally due to forest fragmentation and land-use changes. However, edge effects on the soil seed bank of temperate forests are still poorly understood. Here, we assessed edge effects at contrasting spatial scales across Europe and quantified the extent to which edges can preserve the seeds of forest specialist plants. Location Temperate European deciduous forests along a 2,300-km latitudinal gradient. Time period 2018-2021. Major taxa studied Vascular plants. Methods Through a greenhouse germination experiment, we studied how edge effects alter the density, diversity, composition and functionality of forest soil seed banks in 90 plots along different latitudes, elevations and forest management types. We also assessed which environmental conditions drive the seed bank responses at the forest edge versus interior and looked at the relationship between the seed bank and the herb layer species richness. Results Overall, 10,108 seedlings of 250 species emerged from the soil seed bank. Seed density and species richness of generalists (species not only associated with forests) were higher at edges compared to interiors, with a negative influence of C : N ratio and litter quality. Conversely, forest specialist species richness did not decline from the interior to the edge. Also, edges were compositionally, but not functionally, different from interiors. The correlation between the seed bank and the herb layer species richness was positive and affected by microclimate. Main conclusions Our results underpin how edge effects shape species diversity and composition of soil seed banks in ancient forests, especially increasing the proportion of generalist species and thus potentially favouring a shift in community composition. However, the presence of many forest specialists suggests that soil seed banks still play a key role in understorey species persistence and could support the resilience of our fragmented forests

Modelling the distribution and compositional variation of plant communities at the continental scale

P. 978-990Aim: To investigate whether (1) environmental predictors allow to delineate the distri- bution of discrete community types at the continental scale and (2) how data complete- ness influences model generalization in relation to the compositional variation of the modelled entities.S

Forest microclimate dynamics drive plant responses to warming

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A>T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Prefrontal Cortex Glutamate Correlates with Mental Perspective-Taking

Background: Dysfunctions in theory of mind and empathic abilities have been suggested as core symptoms in major psychiatric disorders including schizophrenia and autism. Since self monitoring, perspective taking and empathy have been linked to prefrontal (PFC) and anterior cingulate cortex (ACC) function, neurotransmitter variations in these areas may account for normal and pathological variations of these functions. Converging evidence indicates an essential role of glutamatergic neurotransmission in psychiatric diseases with pronounced deficits in empathy. However, the role of the glutamate system for different dimensions of empathy has not been investigated so far. Methodology/Principal Findings: Absolute concentrations of cerebral glutamate in the ACC, left dorsolateral PFC and left hippocampus were determined by 3-tesla proton magnetic resonance spectroscopy (1H-MRS) in 17 healthy individuals. Three dimensions of empathy were estimated by a self-rating questionnaire, the Interpersonal Reactivity Index (IRI). Linear regression analysis showed that dorsolateral PFC glutamate concentration was predicted by IRI factor ‘‘perspective taking’’ (T = 22.710, p = 0.018; adjusted alpha-level of 0.017, Bonferroni) but not by ‘‘empathic concern’ ’ or ‘‘personal distress’’. No significant relationship between IRI subscores and the glutamate levels in the ACC or left hippocampus was detected. Conclusions/Significance: This is the first study to investigate the role of the glutamate system for dimensions of theory of mind and empathy. Results are in line with recent concepts that executive top-down control of behavior is mediated b