Preparing thin cross sections of Arabidopsis roots without embedding

ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images

As plant research generates an ever-growing volume of spatial quantitative data, the need for decentralized and user-friendly visualization tools to explore large and complex datasets becomes crucial. Existing resources, such as the Plant eFP (electronic Fluorescent Pictograph) viewer, have played a pivotal role on the communication of gene expression data across many plant species. However, although widely used by the plant research community, the Plant eFP viewer lacks open and user-friendly tools for the creation of customized expression maps independently. Plant biologists with less coding experience can often encounter challenges when attempting to explore ways to communicate their own spatial quantitative data. We present 'ggPlantmap' an open-source R package designed to address this challenge by providing an easy and user-friendly method for the creation of ggplot representative maps from plant images. ggPlantmap is built in R, one of the most used languages in biology, to empower plant scientists to create and customize eFP-like viewers tailored to their experimental data. Here, we provide an overview of the package and tutorials that are accessible even to users with minimal R programming experience. We hope that ggPlantmap can assist the plant science community, fostering innovation, and improving our understanding of plant development and function.

Analysis of Endocytosis and Intracellular Trafficking of Boric Acid/Borate Transport Proteins in Arabidopsis

Plants take up inorganic nutrients from the soil by transport proteins located in the plasma membrane of root cells. Boron (B) is an essential element for plant growth; it taken up and translocated by boric acid channels such as NIP5;1 and borate exporters such as BOR1 in Arabidopsis. NIP5;1 and BOR1 are localized to the plasma membrane of various root cells in polar manners toward soil- and stele-side, respectively, for efficient transport of B. In response to elevated B concentration, BOR1 undergoes vacuolar sorting for degradation to avoid accumulation of B to a toxic level in tissues. The polar localization and vacuolar sorting of the transport proteins are regulated through differential mechanisms of endocytosis and intracellular trafficking. In this chapter, we describe methods for quantitative live-cell imaging of GFP-NIP5;1 and BOR1-GFP as markers for the polar and vacuolar trafficking.

Selection of Agar Reagents for Medium Solidification Is a Critical Factor for Metal(loid) Sensitivity and Ionomic Profiles of Arabidopsis thaliana

For researchers in the plant metal field, the agar reagent used for the solid plate medium is a problematic factor because application of different agar types and even a different lot of the same agar type can mask the plant metal-related phenotypes and impair the reproducibility. In this study, we systematically assessed effects of different agar reagents on metal(loid) sensitivity and element accumulation of the Arabidopsis metal sensitive mutants. Three established mutants (cad1-3, cad1-6, and abcc1/2), and three different types of purified agar reagents (Type A, Type E, and Nacalai) with two independent batches for each reagent were subjected to the analyses. First, we found that element concentrations in the agar reagents largely varied among the agar types. Then the effects of agar reagents on the mutant metal(loid)-sensitivity were examined under As(III), Hg(II), Cd(II), and excess Zn(II) conditions. A significant variation of the mutant metal(loid)-sensitivity was observed among the different agar plates but the variation depended on the combination of metal(loid) stress and agar reagents. Briefly, the type-dependent variation was more evident under As(III) and Hg(II) than Cd(II) or excess Zn(II) conditions. A lot-dependent variation was also observed for Type A and Type E but not for Nacalai: hypersensitive phenotypes of cad1-3, cad1-6, and abcc1/2 under As(III) or Hg(II) treatments were diminished when different batches of the Type A or Type E agar types were used. We also found a significant variation of As and Hg accumulation in the wild-type and cad1-3. Plant As and Hg concentrations were remarkably higher and the difference between the genotypes was more evident when grown with Type A agar plates. We finally analyzed ionomic profiles in the plants exposed to As(III) stress. Agar-type specific ionomic changes in cad1-3 were more observed with the Type A plates than with the Nacalai plates. The presented results overall suggest that suitability of agar reagents for metal(loid)-related phenotyping depends on the experimental design, and an inappropriate selection of agar reagents can mask even very clear phenotypes of the established mutant like cad1-3. We also discuss perspectives on the agar problem in the plant metal study.

Energy costs of salt tolerance in crop plants

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H⁺ -ATPase also is a critical component. One proposed leak, that of Na⁺ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na⁺ and Cl^- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.