Stochasticity in cell fate specification and reversal

Plant cells have amazing capacity to regenerate. When isolated, any living mature cell within a plant body is thought to be able to regain totipotency and regenerate into a complete organism. Recently a protocol was developed to enhance totipotency and regeneration in protoplasts isolated from leaf (Chupeau et al., 2013). Transcriptome analysis of the isolated cells revealed that the cells undergo dedifferentiation within 24 hours following the release from the tissue context and acquire stem cell fate within few days, eventually beginning to divide and re-differentiate in a week. While these data are collected from a population of cells, we are interested in cell-to-cell variability, since stochasticity plays important roles in how cells loose and regain identity.

To capture the stochasticity in cell dedifferentiation, stem cell activation, and cell re-differentiation, we will employ the microfluidics lab-on-a-chip technology that allows in situ quantitative observation of single cell behaviours over time. Inspired by cell traps made for other organisms (e.g. Crane et al., 2014), we have developed a bespoke cell trap to hold plant single cells. In each experiment, more than 2,000 cells can be trapped and monitored over several days, using an automated live-imaging platform. The temporal dynamics of fluorescent marker activity in each cell will be characterised and collated to provide new insights into the cell fate reversal and regaining of pluri- or toti-potency. In subsequent experiments, stochasticity will be modulated by induction of stem cell activity or specific cell identify, to test the roles of noise in cell dedifferentiation and re-differentiation. Stochasticity seems to be increased or reduced depending on the architecture of regulatory mechanism, as well as the cell-cell interaction level (Smith and Grima, 2018). Such theories will be incorporated into comparative analysis of differences in stochasticity levels between single-cell and tissue contexts.

This project will experimentally test the roles of stochasticity in cell fate specification and reversal. It will provide a student with first-hand, state-of-the-art trainings in both experimental and computational approaches of systems and integrated biology.


The student will be supervised by the plant cell and developmental biologist Dr Naomi Nakayama, with the secondary supervision by the theoretical physicist Dr Ramon Grima. S/he will be based in the Nakayama group, but will interact with the Grima group on the regular basis. For more information about the both groups, please visit the group websites: www.bfflab.org (the Nakayama Group, also called the Biological Form and Function Lab) and http://grimagroup.bio.ed.ac.uk (the Grima Group).