Flora Todesco (UMR IAM) and Beatrice Belfiori (CNR-IBBR Perugia) will give a seminar, Friday May 29th; LEGFroom ; 1.30 pm, entitled :
« Tuber magnatum in France: myth or reality? »
Author Archives: eric
Seminar B. Goodell
Barry Goodell will give a seminar entitled :
“Decomposition of lignocellulose by the chelator-mediated Fenton (CMF) system in brown rot fungi, and the role these fungi play in carbon sequestration and cycling ”
the 27th May at Champenoux at 13h30 in the conference room
Barry Goodell is invited by the Lorraine University (IAM and LERMAB) this scientific stay is also supported by ARBRE.
Abstract: Goodell – Decay Mechanisms -Carbon Cycling- LabEx ARBRE Abstract
Article: Environmental Microbiology
A Rincón, B Santamaría‐Pérez, SG Rabasa, A Coince, B Marçais, …
Environmental Microbiology
Abstract
Fungi are principal actors of forest soils implied in many ecosystem services and the mediation of tree’s responses. Forecasting fungal responses to environmental changes is necessary for maintaining forest productivity, although our partial understanding of how abiotic and biotic factors affect fungal communities is restricting the predictions. We examined fungal communities of P. sylvestris along elevation gradients to check potential responses to climate change associated factors. Fungi of roots and soils were analysed at a regional scale, by using a high-throughput sequencing approach. Overall soil fungal richness increased with pH, while did not vary with climate. However, when representative sub-assemblages, i.e. Ascomycetes/Basidiomycetes, and families were analysed, they differentially answered to climatic and edaphic variables. This response was dependent on where they settled, i.e. soil vs roots, and/or on their life style, i.e. mycorrhizal or not, suggesting different potential functional weights within the community. Our results revealed a highly compartmentalized and contrasted response of fungal communities in forest soils. The different response of fungal sub-assemblages indicated a range of possible selective direct and indirect (i.e. via host) impacts of climatic variations on these communities, of unknown functional consequences, that helps understanding potential fungal responses under future global change scenarios.
Article: Microbial Ecology Resources
C Plomion, JM Aury, J Amselem, T Alaeitabar, V Barbe, C Belser, …
Molecular Ecology Resources
Abstract
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (> 2 kb) corresponding to 1.34 Gb. Fifty percent of the assembly was accounted for by 1,468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
PHC Kolmogorov 2015
Proposition de l’Université d’État de Tioumen (Russie) à participer conjointement au programme PHC (Partenariat Hubert Curien) Kolmogorov 2015.
Kolmogorov est le partenariat Hubert Curien (PHC) franco-russe de coopération pour la science et la technologie.
L’objectif de ce programme est de favoriser de nouvelles coopérations entre chercheurs et de développer les échanges scientifiques et techniques de haute qualité entre les universités et les institutions de recherche des deux pays.
Seuls les domaines suivants sont concernés par cet appel à projets :
- Climat – Environnement terrestre & marins (Océanographie physique, Biologie marine, écosystèmes marins et terrestres, Impact du changement climatique)
- Santé (Maladies infectieuses et maladie neurodégénératives, maladies chroniques non transmissibles)
- Sciences pour l’ingénieur (catalyse, stockage de l’énergie, calcul haute performance)
- Photonique des micro- et nano-systèmes.
Toutes les informations et modalités pratiques de cet appel sont disponibles à cette adresse : http://www.campusfrance.org/kolmogorov
Vous trouverez ici une liste de sujets de recherche proposée par l’Université d’Etat de Tioumen. Si certains sujets vous intéressent, merci le faire savoir à marie-caroline.devigne@univ-lorraine.fr par retour de mail avant le 11 mai 2015.
La date limite de co-dépôt des dossiers de candidature est fixée au 11 juin 2015.
PhD defense: T. Payen
The PhD defense of T. Payen will be held the 4th May at 1pm in the conference room of the INRA Center at Champenoux.
Title: “Contribution à l’étude de l’évolution des génomes de champignons ectomycorhiziens du genre Tuber (Pézizomycètes) par génomique comparative”
Abstract:
Truffles are ectomycorrhizal (ECM) fungi, belonging to Tuber genus in the Pezizomycete Class, that form symbiotic associations with numerous trees and shrubs. The Pezizomycetes constitute an early diverging lineage of Ascomycota composed of saprophytic, mycorrhizal and pathogenic species. Some Pezizomycetes, such as truffles and morels,are widely recognized by scientist and lay-person alike. Despite their importance, the genomic structure and evolution within the Pezizomycetes is largely unknown. The aims of my thesis were to characterize the structure and the evolution of the truffle and other Pezizomycete genomes. A comparative analysis performed using eight Pezizomycete fungi, among them three truffles, showed that the genome of truffles has evolved by a size expansion, mainly due to gypsy retrotransposons, in the common ancestor of Tuberaceae about 150 Mya. Then, a loss of the number of gene models, such as plant cell wall degrading enzymes occurred in the common ancesto! r of Tuber spp about 100 Mya. This study provides new insights into the evolution of the truffles, and ECM symbiosis in general, and highlights cases of divergence and convergence between Basidiomycota and truffle symbiotic species. A comparative analysis in T. melanosporum allowed characterizing a resource of more than 400,000 single nucleotide polymorphisms. This population genomic analysis allowed identifying candidate genomic regions with trace of selection. Finally, a more detailed characterization of T. melanosporum gypsy retrotransposons showed that the major invasive waves are old, but that more recently some elements have moved suggesting that retrotransposons continue to play an important role in the evolution of the truffle genome.
Keywords: Tuber melanosporum, truffles, Pezizomycete, bioinformatic, comparative genomic
Article: Plant Journal
F Baldacci‐Cresp, J Moussawi, JC Leplé, R Van Acker, A Kohler, …
The Plant Journal
Summary
REALLY INTERESTING NEW GENE (RING) proteins play important roles in the regulation of many processes by recognizing target proteins for ubiquitination. Previously, we have shown that the expression of PtaRHE1, encoding a Populus tremula x P. alba RING-H2 protein with E3 ubiquitin ligase activity, is associated with tissues undergoing secondary growth. To further elucidate the role of PtaRHE1 in vascular tissues, we have undertaken a reverse genetic analysis in poplar. Within stem secondary vascular tissues, PtaRHE1 and its corresponding protein are expressed predominantly in the phloem. Down-regulation of PtaRHE1 in poplar by artificial miRNA triggers alterations in phloem fiber patterning characterized by an increased portion of secondary phloem fibers that have a reduced cell wall thickness and a change in lignin composition with lower amounts of syringyl units as compared to wild type plants. Following a RNA-seq analysis, a biological network involving hormone, stress signalling as well as developmental processes could be delineated. Several candidate genes possibly associated with the altered phloem fiber phenotype observed in amiRPtaRHE1 poplar were identified. Altogether, our data suggest a regulatory role for PtaRHE1 in secondary phloem fiber development.
ECOS Sud – Chile 2015
ECOS Sud – Chile 2015
Cet appel à projets concerne la recherche de base dans tous les champs disciplinaires. Il doit s’agir d’une collaboration sur un projet scientifique commun. Les critères de sélection essentiels sont l’excellence du projet et des équipes, la formation de jeunes chercheurs et l’impact socio-économique.
Le programme fournit un appui pour :
- les missions dédiées au développement du projet pour chercheurs confirmés d’une durée comprise entre 14 et 31 jours (ECOS-Sud assure le coût du transport A/R jusqu’au Chili pour les français et paie des per diem pour les chiliens se rendant en France),
- le coût du transport jusqu’au Chili pour les doctorants et post-doctorants français se rendant en stage, ainsi que les frais de séjours pour des stages doctoraux ou post-doctoraux en France des jeunes chiliens n’excédant pas trois mois,
La fiche-projet disponible via en pièce-jointe devra parvenir dûment remplie à la Direction des Relations Internationales et Européennes de l’Université de Lorraine ( drie-cooperation-contact@univ-lorraine.fr ) pour le lundi 25 mai au plus tard.
Redox meeting
Announcement of a redox symposium that will be held in Nancy on 18./19. May (organized by J. Herrmann, JP Jacquot and N. Rouhier)
PhD Contract
Young scientist contract (PhD) offered by INRA within the doctoral school RP2E (Université de Lorraine)
Call for applications – April 2015: here
Inra and the Doctoral School RP2E offer during 2015 one “Contrat Jeune Scientifique” (Young Scientist Contract) for 3 years (duration for completion of a PhD). Research will take place at Nancy (France). Candidates may choose among the five topics offered this year:
Topic 1 : Calcium, magnesium and potassium sources in the soil and their bioavailability in forest ecosystems: identification and quantification of bioavailability processes in ex situ conditions at a very fine scale.
Topic 2 : Upscaling morphological, physiological and molecular determinisms of transpiration from the leaf level to water use at the whole plant level in poplar trees.
Topic 3: How are ectomycorrhizal fungi modulating plant hormonal signaling pathways, in particular jasmonic acid?
Topic 4 : Intra-annual dynamics of wood formation and carbon sequestration in conifer and deciduous temperate forests
Topic 5: Understanding detoxification systems developed by wood-decaying fungi and potential application to evaluate the natural durability of wood
The topics and contact persons for specific information are provided in the documents attached to this announcement.
Applications
Applicants to this contract should send the application files including:
- – A detailed CV with all details about obtained degrees, fulfilled training and results,
- – A motivation letter indicating the selected topic and the plans of the candidate for his/her future career,
- – A recommendation letter provided by a professor or a researcher who supervised the candidate during his/her training.
