Peruzzo, F. | bioRxiv Science

bioRxiv2021

An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second- generation single cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

plant biology↗

bioRxiv2019

Spatial patterns emerging from a stochastic process near criticality

There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a minimal model framework for the dynamics of a community of individuals which undergoes local birth-death, immigration and local jumps on a regular lattice. We study its properties when the system is close to its critical point. Even if this model violates detailed balance, within a physically relevant regime dominated by fluctuations, it is possible to calculate analytically the probability density function of the number of individuals living in a given volume, which captures the close-to-critical behavior of the community across spatial scales. We find that the resulting distribution satisfies an equation where spatial effects are encoded in appropriate functions of space, which we calculate explicitly. The validity of the analytical formulae is confirmed by simulations in the expected regimes. We finally discuss how this model in the critical-like regime is in agreement with several biodiversity patterns observed in tropical rain forests.

ecology↗