My interests include evolution of the plant genome with a particular focus on interspecific hybridization and polyploidy, and dynamics of transposable elements (TEs).

TEs account for most nuclear DNA in higher plants and might be a source of genetic variability, because they replicate and reinsert at multiple sites in the genome and may act as mutagenic agents. Moreover, TEs are activated under stress conditions and thus contribute to genome adaptation. Polyploidization which consists in the reuniting of two (or more) genomes in a common nucleus after long periods of divergence can be assimilated to a state of genome stress that could precipitate the activation of TEs. Considering that nearly all angiosperms have experienced at least one episode of polyploidization during their evolution, the question of how TEs can be involved in the formation of a polyploid species is a major task. 

Brassica is an agriculturally important genus that provides a wide range of diploid and allotetraploid species, and is particularly appropriate for studying the evolution of TEs during speciation and polyploidization.
    My main ongoing research project* aims at revealing the impact of a recent polyploidization event on the activation of TEs by analysing the evolution of Brassica -specific TE families (retrotransposons, MITEs, CACTA elements) in newly synthesized Brassica napus lines. The activation of TEs is surveyed at both the structural and functional levels, using a combination of molecular and bioinformatic approaches. This represents part of Véronique Sarilar's PhD project (2008-2011).
    Another part of the project deals with the proteomic and molecular characterization of gene expression and its regulation following a recent allopolyploidy event: comparative proteomics is performed on early (S0-S1) and more advanded (S5) generations of newly synthesized B. napus lines to identify modifications of gene regulation. Our objectives are to determine at which level (during or after transcription) the modifications occur and to evaluate the role that could play TEs, small interfering RNAs and in particular micro RNAs, and/or epigenetic mechanisms (methylation changes) in such modifications. Paulina Martinez-Palacios' PhD work deals with the evolution of snRNA distributions following allopolyploidization in oilseed rape (2010-20xx).

*This research project was partly funded by the 'Agence Nationale de la Recherche' (biodiversity programme):  'Effect of polyploidy on plant genome biodiversity and evolution' / coordinator: Malika Aïnouche (Univ. Rennes I) and collaborators: Anne-Marie Chèvre (IGEPP, INRA Rennes), Eric Jenczewski (INRA, SGAP Versailles), Marie-Angèle Grandbastien (IJPB, INRA Versailles), Boulos Chalhoub (INRA, URGV Evry).

Positions and Education

• 2005-present: Lecturer in the Department of Life Science and Health, at AgroParisTech, Paris; research conducted in the laboratory 'Génétique Evolutive: Adaptation et Redondance' (GEAR), UMR de Génétique Végétale, Gif-sur-Yvette, France

• Transposable elements and evolution of the Brassica genome
• Allopolyploidization and activation of TEs: structural and functional analysis of newly synthesized B.  napus allotetraploids (Véronique Sarilar, PhD student / coll. Philippe Brabant, Johann Joets - UMR GV Le Moulon)
• Role of the Brassica transposable elements in shaping the Brassica genome and gene content (coll. Pat Heslop-Harrison - Univ. Leicester, UK)

• Deciphering the molecular mechanisms responsible for regulation of gene expression in Brassica polyploids by comparative proteomics and transcriptomics (coll. Catherine Damerval, Philippe Brabant - UMR GV Le Moulon; Anne Marmagne - IJPB, INRA Versailles; Anne-Marie Chèvre - IGEPP, INRA Rennes, France)

• Role of micro RNAs and other small non-protein coding RNAs in regulation of gene expression and activation of TEs in Brassica neo-polyploids (Paulina Martinez-Palacios, PhD student /coll: Johann Joets - UMR GV Le Moulon; Martin Crespi and Christine Lelandais - ISV, CNRS Gif-sur-Yvette, France; Claude Thermes, Imagif, CGM Gif-sur-Yvette)
  
  
• 2003-2004: Postdoctoral position, UMR Amélioration des Plantes et Biotechnologies Végétales , INRA-Agrocampus Rennes /France - M. Manzanares-Dauleux
  Molecular and functional characterization of genetic components of resistance to clubroot ( Plasmodiophora brassicae ) in Arabidopsis thaliana and Brassica napus
  Alix K , Lariagon C, Delourme R, Manzanares-Dauleux MJ. 2007. Exploiting natural genetic diversity and mutant resources of Arabidopsis thaliana to study the A. thaliana - Plasmodiophora brassicae interaction. Plant Breeding 126: 218-221 .
  
  
• 2002: Temporary position,  UMR Amélioration des Plantes et Biotechnologies Végétales , INRA-Agrocampus Rennes /France - A.-M. Chèvre
  
  • Monitoring introgression of resistance to blackleg in Brassica napus from the B genome of mustards using  genomic in situ hybridisation (GISH)
  • Analysis of the genomic constitution of oilseed rape - wild radish hybrids by GISH in a context of gene flow assessment
    
    
• 2001: Postdoctoral fellow (OECD) in Pat Heslop-Harrison's lab , Department of Biology, University of Leicester, Leicester /United Kingdom - Pat Heslop-Harrison
  The diversity of retrotransposons in Brassica : understanding their phylogeny and evolution
  
  
• 1999-2000: Postdoctoral position, UMR Diversité et Génome des Plantes Cultivées, INRA-Montpellier /France - P. Roumet, J. David
• Implication of peroxidases in clearness of pasta: development of S-SAP markers in durum wheat
• Role of the Ph1 gene in the intergenomic recombination rate in Triticum durum × Aegilops ovata amphiploids
  Benavente E., Alix K. , Dusautoir J.-C., Orellana J. and David J.L. 2001. Early evolution of the chromosomal structure of Triticum turgidum - Aegilops ovata amphiploids carrying and lacking the Ph1 gene. Theoretical and Applied Genetics 103: 1123-1128.
  
  
• 1995-1998: PhD student, Agetrop, CIRAD , Montpellier /France - J.-C. Glaszmann, A. D'Hont
  The repetitive sequences of sugarcane: genome-specificities and phylogeny of the Saccharum complex
  1. Alix K., Paulet F., Glaszmann J.-C. and D’Hont A. 1999. Inter-Alu-like species-specific sequences in the Saccharum complex. Theoretical and Applied Genetics 99: 962-968. 
  2. Alix K., Baurens F.-C., Paulet F., Glaszmann J.-C. and D’Hont A. 1998. Isolation and characterization of a satellite DNA family in the Saccharum complex. Genome 41: 854-864.
  3. D’Hont A., Ison D., Alix K., Roux C. and Glaszmann J.-C. 1998. Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41: 221-225.

Selected Publications

1. Sarilar V., Marmagne A., Brabant P., Joets J., Alix K. 2011. ‘BraSto’, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space. Plant Molecular Biology 77: 59-75. 
2. Marmagne A., Brabant P., Thiellement H. and Alix K. 2010. Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytologist 186: 216-227.
3. Parisod C., Alix K., Just J., Petit M., Sarilar V., Mhiri C., Aïnouche M., Chalhoub B. and Grandbastien M.-A. 2010. Impact of transposable elements on the organization and funtion of allopolyploid genomes. New Phytologist 186: 37-45. 
4. Zerjal T., Joets J., Alix K., Grandbastien M.-A. and Tenaillon M. 2009. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Molecular Biology 71: 99-114.
5. Alix K. , Joets J., Ryder C.D., Moore J., Barker G.C., Bailey J.P., King G.J. and Heslop-Harrison J.S. 2008. The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. The Plant Journal 56: 1030-1044.
6. Pouilly N., Delourme R., Alix K. and Jenczewski E. 2008. Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus . Chromosome Research 16: 683-700.
7. Albertin W., Alix K., Balliau T., Brabant P., Davanture M., Malosse C., Valot B. and Thiellement H. 2007. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8: 56. 
8. Alix K., Ryder C.D., Moore J., King G.J. and Heslop-Harrison J.S. 2005. The genomic organization of retrotransposons in Brassica oleracea. Plant Molecular Biology 59: 839-851. 
9. Alix K. and Heslop-Harrison J.S. 2004. The diversity of retroelements in diploid and allotetraploid Brassica species. Plant Molecular Biology 54: 895-909.  
10. Jenczewski E. and Alix K. 2004. From diploids to allopolyploids: the emergence of efficient pairing control genes in plants. Critical Reviews in Plant Sciences 23: 21-45. 

Teaching at AgroParisTech
UFR Génétique évolutive et amélioration des plantes / Evolutionary genetics and plant breeding

- Population genetics
- Module d’approfondissement – séquence 1, « Biotechnologies et agriculture »/« Biotechnologies and agriculture »
- Module d’approfondissement – séquence 2, « La transformation des plantes par l'homme : de la domestication à la transgénèse »/« Impact of human selection on plants: from domestication to transgenesis »

Second year
- Modules d’approfondissement – séquence 4, (i) « Evolution des génomes » / « Evolution of the genomes », and (ii) « Adaptation des plantes à l'environnement » / « Plants and adaptation to environment »

Third year

• DA Production et Innovation dans les Systèmes Techniques Végétaux (PISTv) / Production and Innovation in Plant Systems:
  - Module « Amélioration des plantes : méthodes, objectifs et acteurs de la filière semences » / « Plant breeding:  methods, aims and breeders »
  - Module « Biotechnologies et génomique végétale » /« Biotechnologies and plant genomics »
  -  Option de spécialisation « Génétique et amélioration des plantes  » /« Genetics and plant breeding  »

• DA Gestion, Innovation et Performances des Entreprises du Vivant (GIPE) / Management, Innovation and Performance of Life Industry:
  - Module de consolidation « Bioingénierie de la valeur santé » / « Biotechnologies and Health »

Conferences and Others

I would be pleased to meet you at the next "International Conference on Polyploidy, Hybridization and Biodiversity" ICPHB 2012 which will take place at Průhonice, near Prague, Czech Republik, May 7-10, 2012.