PAT (Periderm Assessment Toolkit): A Quantitative and Large-Scale Screening Method for Periderm Measurements.

The periderm is a vital protective tissue found in the roots, stems, and woody elements of diverse plant species. It plays an important function in these plants by assuming the role of the epidermis as the outermost layer. Despite its critical role for protecting plants from environmental stresses and pathogens, research on root periderm development has been limited due to its late formation during root development, its presence only in mature root regions, and its impermeability. One of the most straightforward measurements for comparing periderm formation between different genotypes and treatments is periderm (phellem) length. We have developed PAT (Periderm Assessment Toolkit), a high-throughput user-friendly pipeline that integrates an efficient staining protocol, automated imaging, and a deep-learning-based image analysis approach to accurately detect and measure periderm length in the roots of Arabidopsis thaliana. The reliability and reproducibility of our method was evaluated using a diverse set of 20 Arabidopsis natural accessions. Our automated measurements exhibited a strong correlation with human-expert-generated measurements, achieving a 94% efficiency in periderm length quantification. This robust PAT pipeline streamlines large-scale periderm measurements, thereby being able to facilitate comprehensive genetic studies and screens. Although PAT proves highly effective with automated digital microscopes in Arabidopsis roots, its application may pose challenges with nonautomated microscopy. Although the workflow and principles could be adapted for other plant species, additional optimization would be necessary. While we show that periderm length can be used to distinguish a mutant impaired in periderm development from wild type, we also find it is a plastic trait. Therefore, care must be taken to include sufficient repeats and controls, to minimize variation, and to ensure comparability of periderm length measurements between different genotypes and growth conditions.

Flux-based transport enhancement as a plausible unifying mechanism for auxin transport in meristem development.

Plants continuously generate new organs through the activity of populations of stem cells called meristems. The shoot apical meristem initiates leaves, flowers, and lateral meristems in highly ordered, spiralled, or whorled patterns via a process called phyllotaxis. It is commonly accepted that the active transport of the plant hormone auxin plays a major role in this process. Current hypotheses propose that cellular hormone transporters of the PIN family would create local auxin maxima at precise positions, which in turn would lead to organ initiation. To explain how auxin transporters could create hormone fluxes to distinct regions within the plant, different concepts have been proposed. A major hypothesis, canalization, proposes that the auxin transporters act by amplifying and stabilizing existing fluxes, which could be initiated, for example, by local diffusion. This convincingly explains the organised auxin fluxes during vein formation, but for the shoot apical meristem a second hypothesis was proposed, where the hormone would be systematically transported towards the areas with the highest concentrations. This implies the coexistence of two radically different mechanisms for PIN allocation in the membrane, one based on flux sensing and the other on local concentration sensing. Because these patterning processes require the interaction of hundreds of cells, it is impossible to estimate on a purely intuitive basis if a particular scenario is plausible or not. Therefore, computational modelling provides a powerful means to test this type of complex hypothesis. Here, using a dedicated computer simulation tool, we show that a flux-based polarization hypothesis is able to explain auxin transport at the shoot meristem as well, thus providing a unifying concept for the control of auxin distribution in the plant. Further experiments are now required to distinguish between flux-based polarization and other hypotheses.

Dynamic expression of sparc precedes formation of skeletal elements in the Medaka (Oryzias latipes).

Sparc is a secreted calcium-binding glycoprotein that regulates mineralization of bone tissues in mammals. In other vertebrates, its function remains largely unclear. Here, we describe the isolation, genomic organization and expression of the sparc gene in the teleost Medaka (Oryzias latipes), an established vertebrate model for developmental studies. During earliest stages of Medaka embryogenesis, sparc is expressed in the sclerotome compartment of the somites that gives rise to precursor cells of the axial skeleton. Importantly, in this area its expression precedes that of twist-1, which is a crucial regulator of osteoblast formation. Dynamic expression is also found in the floor plate of the neural tube and the notochord. Both structures are passed by migrating skeletal precursors shortly before they differentiate and form the vertebrae. In general, sparc is expressed before the formation and mineralization of bone elements and expression of bone markers like collagen type 1a in the fins and axial skeleton of Medaka embryos. It is also expressed in several non-skeletal tissues of embryos and adult fish, suggesting possible other functions not related to bone mineralization. Taken together, the Medaka sparc gene represents an excellent marker for early sclerotome development. Its restricted and highly dynamic expression suggests a novel function during migration of sclerotome cells and their differentiation into early vertebrae. This marker thus allows the analysis of early skeletal development and formation of extracellular bone matrix in this vertebrate model.