Tree species richness induces strong intraspecific variability of beech (Fagus sylvatica) leaf traits and alleviates edaphic stress

Manipulating stand composition is an important management tool that foresters can use to affect the nature of forests and ecosystem processes. In mixed stands, interspecific interactions among trees can cause changes in tree performances. Nevertheless, these interactions are context dependent (cf. stress-gradient hypothesis, SGH). We thus investigated how intraspecific functional changes in leaf trait (19 traits) of European beech (Fagus sylvatica) were influenced by stand composition. We compared pure beech stands with four mixed stands containing from one to three additional tree species along a gradient of edaphic stress (gradient of soil water-holding capacity and rooting depth). First, we demonstrated that stand composition induced strong intraspecific leaf trait variation in beech for LDMC, LMA, phenolic compounds, leaf pH and magnesium concentration, suggesting higher nutrient acquisition by more diverse stands. Nevertheless, these results were modulated by edaphic stress. Mixed stands only conferred an advantage in relatively stressed sites (luvisol and leptosol). Besides, the addition of oak to beech stands had unexpected negative effects in sites with less severe stress (cambisol) as indicated by the null or positive LogRR of LMA, LDMC and phenolics. This study found that stand composition is an important though often-overlooked driver of intraspecific variability in leaf quality, and potentially reflects changes in beech tree physiology and productivity. Our results also suggest that positive interactions prevail in sites with stressful conditions. Such validation of the SGH is rare in natural or managed mature forests. Lastly, we strongly recommend that forest managers consider stand composition and abiotic factors when implementing forest growth models to improve their yield predictions.Peer reviewe

Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

<p>Abstract</p> <p>Background</p> <p>The gene <it>CHEK2 </it>encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though <it>CHEK2 </it>has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether <it>CHEK2 </it>was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in <it>BRCA1</it> or <it>BRCA2</it> had been identified.</p> <p>Methods</p> <p>We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment.</p> <p>Results</p> <p>We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of <it>CHEK2 </it>that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs.</p> <p>Conclusions</p> <p>Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms.</p

L'APPLICATION DU PRINCIPE DE LAÏCITE A LA JUSTICE

Ce rapport sur « l’application de la laïcité à la justice » est le fruit d’un travail collectif mené sur deux années par une équipe d’enseignants-chercheurs (juristes et sociologues) avec le soutien de la mission de recherche « Droit et Justice ».Le sujet est d’autant plus intéressant que la justice n’est sans doute pas un service public comme les autres. Outre une laïcisation plus lente, la justice se distingue également des autres services publics par la diversité des acteurs qui s’y croisent : tous ne sont pas des professionnels (les jurés notamment) et parmi les professionnels, tous ne sont pas des agents publics. Toutes ces personnes ne sont donc pas soumises aux mêmes règles.L’essentiel de la recherche a consisté à voir si le droit positif mettait à la charge de tous les acteurs de la justice une obligation de laïcité et de neutralité religieuse, et le cas échéant selon la même intensité. Parmi ceux-ci, certains acteurs sont par ailleurs amenés à trancher des questions d’ordre religieux susceptibles de les placer sur un terrain qui ne leur est pas familier.Ils ne peuvent pas s’abriter derrière leur neutralité pour ne pas répondre à la question soulevée par ces litiges. La recherche s’est donc portée également sur la manière dont les juges mettenten œuvre leur neutralité dans leur compréhension et leur traitement ou leur qualification du fait religieux.Pour répondre à ces questions, une étude du droit positif complétée par des entretiens auprès des professionnels concernés a été privilégiée

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

BACKGROUND: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS: We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS: The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS: These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.The COGS project is funded through a European Commission's Seventh Framework Programme grant (agreement number 223175 - HEALTH-F2-2009-223175). BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community´s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 16 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defense (W81XWH-10-1- 0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. This study made use of data generated by the Wellcome Trust Case Control consortium. Funding for the project was provided by the Wellcome Trust under award 076113. The results published here are in part based upon data generated by The Cancer Genome Atlas Project established by the National Cancer Institute and National Human Genome Research Institute.This is the author accepted manuscript. The final version is available from BMJ Group at http://dx.doi.org/10.1136/jmedgenet-2015-103529

La transparence en politique

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Variabilité des traits biologiques des feuilles chez le hêtre en fonction de l’environnement compétitif

National audienceDifférentes études ont permis de mettre en évidence les effets bénéfiques des peuplements mélangés feuillus/résineux sur leur rentabilité économique grâce à une meilleure résistance aux perturbations (REF). En revanche les effets bénéfiques sur la productivité et la qualité des bois sont beaucoup plus nuancés. Si certaines études montrent des effets positifs des mélanges sur la productivité en les expliquant par la complémentarité des espèces pour l’utilisation des ressources, d’autres ne montrent rien. L’absence de consensus questionne alors sur la composition des mélanges les plus à même de maximiser cette complémentarité. L’objectif de cette étude était de caractériser la variabilité des traits biologiques des feuilles de hêtre en réponse à l’environnement compétitif de type inter et/ou intraspécifique. Les effets de la composition du peuplement mis en évidence sur le hêtre sont : un stress moindre et une meilleure disponibilité en éléments nutritifs. Ceci peut s’expliquer par trois hypothèses : i) les espèces en mélanges avec le hêtre (dans les peuplements de type F+) sont moins compétitives que ce dernier à l’exception du chêne qui montre une compétitivité équivalente ii) une complémentarité des niches qui augmente la disponibilité des ressources et iii) les espèces présentent dans le peuplement de type F+ ont une litière de meilleure qualité que le hêtre ou les chênes donc une vitesse de recyclage plus rapide, ce qui améliore la qualité du sol. Pour une gestion plus rentable et plus durable des Hêtraies, il conviendrait d’éviter la mise en place de peuplements purs ou des mélanges de type Hêtraie-Chênaie. Cela est particulièrement important sur les rendzines. Des études complémentaires sont nécessaires pour comprendre les mécanismes associés à cet effet composition : e.g. qualité des litières et vitesse de décomposition

Ribosomal Mutations Conferring Macrolide Resistance in Legionella pneumophila

International audienceMonitoring the emergence of antibiotic resistance is a recent issue in the treatment of Legionnaires' disease. Macrolides are recommended as first-line therapy, but resistance mechanisms have not been studied in Legionella species. Our aim was to determine the molecular basis of macrolide resistance in L. pneumophila Twelve independent lineages from a common susceptible L. pneumophila ancestral strain were propagated under conditions of erythromycin or azithromycin pressure to produce high-level macrolide resistance. Whole-genome sequencing was performed on 12 selected clones, and we investigated mutations common to all lineages. We reconstructed the dynamics of mutation for each lineage and demonstrated their involvement in decreased susceptibility to macrolides. The resistant mutants were produced in a limited number of passages to obtain a 4,096-fold increase in erythromycin MICs. Mutations affected highly conserved 5-amino-acid regions of L4 and L22 ribosomal proteins and of domain V of 23S rRNA (G2057, A2058, A2059, and C2611 nucleotides). The early mechanisms mainly affected L4 and L22 proteins and induced a 32-fold increase in the MICs of the selector drug. Additional mutations related to 23S rRNA mostly occurred later and were responsible for a major increase of macrolide MICs, depending on the mutated nucleotide, the substitution, and the number of mutated genes among the three rrl copies. The major mechanisms of the decreased susceptibility to macrolides in L. pneumophila and their dynamics were determined. The results showed that macrolide resistance could be easily selected in L. pneumophila and warrant further investigations in both clinical and environmental settings

Genetic susceptibility factors in familial nasopharyngeal carcinoma

Nasopharyngeal carcinoma is common in Southern China, Hong Kong, Taiwan and Southeast Asian countries. The current study was performed on an exceptionally large multiplex NPC family from Sarawak, Malaysia (denoted as JAQBAB family). We aimed to explore the segregation of deleterious mutation(s) or NPC risk- associated allele within the genomic segment shared identical by descent (IBD) between the affected individuals. Genome-wide SNP-array covering all somatic chromosomes were performed on 11 of the NPC patients and their first-degree family members. The kinship was assessed and pairwise IBD estimation between target individuals were performed. Haplotype phasing was also performed on certain region of interests. Whole-exome sequencing was performed to identify deleterious mutations. The highest IBD score was detected within chromosome 10. Analysis of the exome sequencing data, however, did not find any deleterious mutation within this region that was shared between individuals in the JAQBAB family. Highest IBD score at chromosome 6 was found within the major histocompatibility complex (MHC) region, supporting strong HLA-EBV-NPC association that has been reported in an earlier study. HLA deep sequence-based typing (SBT) and gene sequencing on the 11 NPC patient samples revealed that the segregation of HLA-A*27:07 allele was consistent with the haplotype phasing pattern. Our results suggest that HLA-A*24:07 may harbour the risk allele for NPC among the subjects. However, further analysis is required before any definitive conclusion can be made. Further studies on the HLA-A*24:07 sequence may reveal more specific variation within this gene that can be associated with NPC risk in this family. In addition, further studies on HLA-A and risk of NPC other Southeast-Asian populations may shed more understanding about the association between HLA-A*24:07 and sporadic NPC in this region of the world