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Génétique Quantitative et Évolution - Le Moulon

Mélisande BLEIN-NICOLAS

Mélisande BLEIN-NICOLAS

Ingénieure de Recherche, INRAE

  • proteomics,
  • mass spectrometry,
  • integrative biology,
  • systems genetics,
  • quantitative genetics

melisande.blein-nicolas@inrae.fr

01 69 15 68 06

orcid.org/0000-0001-6026-4989

Publications

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • Ferme du Moulon
  • F-91190 Gif-sur-Yvette

Position and education

  • 2015-present: INRA research engineer, PAPPSO, UMR GQE-Le Moulon, Gif-sur-Yvette, France

  • 2010-2015: Post-doctoral fellow, INRA, UMR GQE-Le Moulon, Gif-sur-Yvette, France

    • “Analysis of heterosis for protein abundance under normal and drought conditions in sunflower” (PIA Sunrise)
    • “Genome wide association study for protein expression under normal and water deficit conditions in maize leaves” (PIA Amaizing)
    • “Analysis of heterosis for protein abundance in inter- and intra-specific yeast hybrids grown under grape must fermentation” (ANR HeterosYeast)
  • 2008-2010: Postdoctoral fellow, CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France

    • “Functional validation of the role of CIGR1 in the resistance of rice to blast (Magnaporthe oryzae)
  • 2004-2007: PhD student (MENRT fellowship), IGEPP (formely UMR Amélioration des Plantes et Biotechnologies Végétales), Rennes, France

    • Histological and transcriptomic analyses of the role of the Pch1 gene in the resistance of bread wheat to eyespot Oculimacula yallundae
  • 2004: MsC and Master Degree in Plants Genetics and Breeding, Agrocampus Ouest (formerly École Nationale Supérieure Agronomique de Rennes).

Activities of research and development

I am involved in the management of the PAPPSO proteomic platform (projects management, relationships with users, implementation of a quality policy, support to the scientist in charge of the plateform) and in the design and implementation of developments for the analysis of proteomics data [5,8,9]. I am more particularly in charge of the development of an R package containing functions for the processing and the statistical analysis of protein quantification data (MCQ package). I am also involved in several development projects for metaproteomics (ANR Proteocardis), for the use of natural isotopes in peptide quantification and for the analysis of large experimental designs.

Regarding my research activities, I am interested in understanding how living organisms respond and adapt to environmental changes. I focused on the identification of genes and molecular mechanisms responsible for the variation of adaptative traits, such as plant resistance to pathogenic fungi [2-4], yeasts ability to complete grape juice fermentation [6-7] or drought tolerance in plants. During my PhD and my first post-doctoral fellowship, I addressed this issue by using functional approaches. Since I joined the UMR GQE-Le Moulon, I moved toward more integrated approaches based on the combined analysis of several levels of biological complexity to decipher the genotype/phenotype relationship. Currently, I am developing systems genetics approaches to elucidate the mechanisms underlying drought tolerance in maize. This research takes place within the French investment for the future Amaizing program.

Teaching and training

  • Introduction to mass-spectrometry based proteomics (Licence1 and Master 2 at Université Paris Sud)
  • Proteomics data analysis with the MCQ package (PAPPSO training sessions)

Publications

  • Bassignani A., Plancade S., Berland M., Blein-Nicolas M. , Guillot A., Chevret D., Moritz C., Huet S., Rizkalla S., Clément K., Doré J., Langella O., Juste C.. (2021) Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets. J. Proteome Res.,
  • Plancade S., Berland M., Blein-Nicolas M. , Langella O., Bassignani A., Juste C.. (2021) A combined test for feature selection on sparse metaproteomics data - alternative to missing value imputation. bioRxiv, 2021.06.22.449387
  • Urrutia M., Blein-Nicolas M. , Prigent S., Bernillon S., Deborde C., Balliau T., Maucourt M., Jacob D., Ballias P., Bénard C., Sellier H., Gibon Y., Giauffret C., Zivy M., Moing A.. (2021) Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis. Plant Cell Environ,
  • Blein-Nicolas M. , Negro SS., Balliau T., Welcker C., Cabrera-Bosquet L., Nicolas SD., Charcosset A., Zivy M.. (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res., 11 (30) 1593-1604
  • Belouah I., Nazaret C., Pétriacq P., Prigent S., Bénard C., Mengin V., Blein-Nicolas M. , Denton AK., Balliau T., Augé S., Bouchez O., Mazat JP., Stitt M., Usadel B., Zivy M., Beauvoit B., Gibon Y., Colombié S.. (2019) Modeling Protein Destiny in Developing Fruit. Plant Physiology, 3 (180) 1709-1724
  • Belouah I., Blein-Nicolas M. , Balliau T., Gibon Y., Zivy M., Colombié S.. (2019) Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics, (193) 131-141
  • Henry C., Haller L., Blein-Nicolas M. , Zivy M., Canette A., Verbrugghe M., Mézange C., Boulay M., Gardan R., Samson S., Martin V., André-Leroux G., Monnet V.. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Front. Microbiol., (10) 1329
  • Balliau T., Blein-Nicolas M. , Zivy M.. (2018) Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes, 1 (6) 6
  • Langella O., Valot B., Balliau T., Blein-Nicolas M. , Bonhomme L., Zivy M.. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503
  • Millan-Oropeza A., Henry C., Blein-Nicolas M. , Aubert-Frambourg A., Moussa F., Bleton J., Virolle MJ.. (2017) Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J. Proteome Res., 7 (16) 2597-2613
  • Blein-Nicolas M. , Zivy M.. (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 8 (1864) 883-895
  • Blein-Nicolas M. , Albertin W., da Silva T., Valot B., Balliau T., Masneuf-Pomarède I., Bely M., Marullo P., Sicard D., Dillmann C., de Vienne D., Zivy M.. (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol. Cell Proteomics, 8 (14) 2056-2071
  • Blein-Nicolas M. , Albertin W., Valot B., Marullo P., Sicard D., Giraud C., Huet S., Bourgais A., Dillmann C., de Vienne D., Zivy M.. (2013) Yeast proteome variations reveal different adaptive responses to grape must fermentation. Molecular biology and evolution, 6 (30) 1368-83
  • Blein-Nicolas M. , Xu H., de Vienne D., Giraud C., Huet S., Zivy M.. (2012) Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics. Proteomics, 18 (12) 2797-801
  • Delteil A., Blein M., Faivre-Rampant O., Guellim A., Estevan J., Hirsch J., Bevitori R., Michel C., Morel JB.. (2012) Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence: A mutant resource for disease resistance analysis in rice. Molecular Plant Pathology, 1 (13) 72-82
  • Lorieux M., Blein M., Lozano J., Bouniol M., Droc G., Diévart A., Périn C., Mieulet D., Lanau N., Bès M., Rouvière C., Gay C., Piffanelli P., Larmande P., Michel C., Barnola I., Biderre-Petit C., Sallaud C., Perez P., Bourgis F., Ghesquière A., Gantet P., Tohme J., Morel JB., Guiderdoni E.. (2012) In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches: Characterization of a rice insertion library. Plant Biotechnology Journal, 5 (10) 555-568
  • Blein M., Levrel A., Lemoine J., Gautier V., Chevalier M., Barloy D.. (2009) Oculimacula yallundae lifestyle revisited: relationships between the timing of eyespot symptom appearance, the development of the pathogen and the responses of infected partially resistant wheat plants. Plant Pathology, 1 (58) 1-11
  • Cifuentes M., Blein M., Benavente E.. (2006) A cytomolecular approach to assess the potential of gene transfer from a crop (Triticum turgidum L.) to a wild relative (Aegilops geniculata Roth.). Theor Appl Genet, 4 (112) 657-664