Axis 3

Plants are excellent models to study fundamental biological mechanisms and often have allowed breakthrough discoveries such as the existence of a small RNA-based immune system (short-interfering siRNAs). Due to the extensive genetic and genomic resources, the ease of transgenic production with controlled levels of ectopic expression, or the wide use of imaging technologies, plants are useful models for the dissection of basic cellular processes including differentiation of stem cells, transcriptional and post-transcriptional gene regulation and genome dynamics. The capacity of plants to adapt their growth to environmental stimuli through epigenetic modifications that could be transmitted to their progeny strengthens their use for the elucidation of these regulatory mechanisms. Several high throughput techniques such as ChIP-seq enabling the analysis of various epigenetic marks (DNA methylation, histone modifications, chromatin status) at the whole-genome level, and RNA-seq permitting the complete description of the transcriptome (mRNA, non-coding RNA, truncated RNA, small RNAs) are now available to understand epigenetic mechanisms. Research aimed at understanding plant development is occurring from cellular to organism level: cell growth, cell proliferation and cell differentiation (i.e. the cytoskeleton and cell wall, hormone signalling, control of transcription). A major limitation in the analysis of plant development is that it deals with a complex system, composed of many components that interact. An integrated view, incorporating the complex datasets available is no longer possible without adequate mathematical and informatics tools. In addition, to understand how the function of genes is translated into the cellular activities that shape organs, a much more detailed and quantitative description of organ growth is required. Therefore, systems biology, involving more global and multidisciplinary approaches is becoming more and more important. The rapidly evolving field of live-cell imaging will create the opportunity for quantitative live cell biology. Photon microscopy now allows an nm scale spatial resolution, while high sensitivity allows single molecule imaging. Besides FT-IR microspectroscopy already adopted, UV microscopy and MALDI-TOF imaging could be developed to visualize metabolites at subcellular resolution. The production of high throughput data (transcriptome, proteome, metabolome) but also detailed spatio-temporal description of expression patterns using imaging techniques can lead to an unprecedented level of analysis of growth and differentiation processes at organism level.

Important scientific issues in this field are for instance

• Cellular and organelle biology, meiosis, cell cycle and division, intracellular transport
• Signal transduction, hormone metabolism and signalling, posttranslational modification
• Molecular, cellular and genetic determinism of plant organogenesis and growth
• Developmental mechanisms (vegetative growth, reproduction) and their evolution
• Genome structure, dynamic, regulation of gene expression and epigenetics
• Systemic approaches of developmental and physiological mechanisms