Type de poste: 
CDD
Date de début: 
January 2018
Durée: 
2 years
Ville: 
Villeneuve d'Ascq (Lille) 59655 FRANCE
Nom du contact: 
GREC Sébastien
Mail du contact: 
sebastien.grec@univ-lille1.fr
Plateforme: 
bilille
Missions: 

The FV_UGSF team is part of the UMR 8576 University of Lille 1 / CNRS, Structural and Functional Glycobiology Unit (UGSF: http://ugsf-umr-glycobiologie.univ-lille1.fr). The team currently consists of 8 assistant-professors/professor and 2 Ph.D. students studying the biological regulations involved in the formation, maturation and degradation of cellulosic fibers in flax and hemp (http://ugsf-umr-glycobiologie.univ-lille1.fr/--181-?lang=fr) ((Haag et al., 2017)., (Day et al., 2013), ((Chantreau et al., 2014).
One of the themes of our team concerns the study by metabarcoding of the biological processes related to the degradation of plant biomass (cell wall) by microorganisms. In this project we are using a metabarcoding approach coupled with the prediction of enzymatic functions (CAZy) and a biochemical approach developed in collaboration with the INRA FARE UMR (Reims). We now wish to complete our analyses by a metatranscriptomic approach targeting the mRNAs actually expressed by microorganisms during flax dew retting (Morvan et al., 2003) and involved in cell wall degradation. The development of this latter approach will be the first task of the proposed Post-Doctoral internship.
The second task will consist in applying metabarcoding to study the biodegradation of other sources of plant polymers (other species, plant fiber-based materials).

Bibliography

  • Akin, D. E. (2013). Linen most useful: Perspectives on structure, chemistry, and enzymes for retting flax. ISRN Biotechnol. 2013, 23. doi:http://dx.doi.org/10.5402/2013/186534.
  • Chantreau, M., Portelette, A., Dauwe, R., Kiyoto, S., Crônier, D., Morreel, K., ... Hawkins, S. (2014). Ectopic lignification in the flax lignified bast fiber1 mutant stem is associated with tissue-specific modifications in gene expression and cell wall composition. The Plant Cell, 26(11), 4462–82. http://doi.org/10.1105/tpc.114.130443
  • Day, A., Fénart, S., Neutelings, G., Hawkins, S., Rolando, C., & Tokarski, C. (2013). Identification of cell wall proteins in the flax ( Linum usitatissimum ) stem. PROTEOMICS, 13(5), 812–825. http://doi.org/10.1002/pmic.201200257
  • Haag, K., Padovani, J., Fita, S., Trouvé, J.-P., Pineau, C., Hawkins, S., ... Beaugrand, J. (2017). Influence of flax fibre variety and year-to-year variability on composite properties. Industrial Crops and Products, 98, 1–9. http://doi.org/10.1016/j.indcrop.2016.12.028
  • Morvan, C., Andème-Onzighi, C., Girault, R., Himmelsbach, D. S., Driouich, A., & Akin, D. E. (2003). Building flax fibres: More than one brick in the walls. Plant Physiology and Biochemistry. http://doi.org/10.1016/j.plaphy.2003.07.001
Connaissances: 

The candidate will be familiar with various bioinformatics tools used for the processing of data from high- throughput sequencing (cleaning, assembly, alignment), database requests (CAZy, InterPro,Greengenes, Silva, KEGG, GO...), programming (Bash, Python, Perl...). Experience in dedicated tools such as mothur, QIIME, SAMSA or IMP would be appreciated. Knowledge of the statistical tools required for data analysis is also required (R). The candidate should also master different practical aspects related to the preparation of biological samples (i.e. a minimum of molecular biology skills are required).

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