Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics

GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes. DOI: http://dx.doi.org/10.7554/eLife.07597.00

Co-ordinated Changes in the Accumulation of Metal Ions in Maize (Zea mays ssp. mays L.) in Response to Inoculation with the Arbuscular Mycorrhizal Fungus Funneliformis mosseae.

Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of 19 elements was determined in the roots and leaves of a panel of 30 maize varieties, grown under phosphorus-limiting conditions, with or without inoculation with the fungus Funneliformis mosseae. Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a co-ordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants

Arios surveys: hydrographic and chemical data on SW Galician shelf

Este dataset está compuesto por 2 archivos, de los cuales el primero es el conjunto de datos con 1421 análisis de muestras de agua de temperatura, salinidad, oxígeno, nutrientes, pH, alcalinidad, clorofila y materia orgánica, y el otro (Readme.txt) incluye una pequeña descripción de las variables calculadasDurante un año, se estudió la variabilidad a frecuencia mensual (quincenal en la época estival) de los fenómenos de afloramiento y hundimiento en la plataforma gallega frente a la Ría de Vigo y su impacto en las diferentes variables biogeoquímicas y del ciclo del carbono. Se evaluó la importancia relativa de los procesos físicos y biológicos en la variabilidad del sistema del carbonato con especial interés en la acidificación oceánica. Nueve estaciones fueron muestreadas desde el nueve de junio 2017 hasta junio del 2018 desde el borde del talud continental frente Ría de Vigo hasta el interior de la misma en el límite del estuario de San Simón. La salinidad y la temperatura se registraron con una sonda de profundidad de conductividad-temperatura SBE 9/11 conectada al muestreador de roseta con doce botellas de PVC Niskin de 10 L. Las mediciones de la conductividad se convirtieron en valores prácticos de la escala de salinidad con la ecuación de la UNESCO (1986). La precisión de las mediciones de CTD para temperatura y salinidad fueron de 0,004 ºC y 0,005, respectivamente. Las muestras para los análisis de oxígeno disuelto, pH, alcalinidad total, sales de nutrientes, carbono orgánico disuelto fueron recogidas semanalmente con la roseta de 12 botellas Niskin. Para la determinación de nutrientes, las muestras de agua se recogieron en botellas de polietileno de 50 mL y se congelaron (-20ºC) hasta su análisis en el laboratorio utilizando procedimientos estándar de análisis de flujo segmentado. Las precisiones fueron 0,02 micromol/L para nitrito, 0,1 micromol/L para nitrato, 0,05 micromol/L para amonio, 0,02 micromol/L para fosfato y 0,05 micromol/L para silicato. El oxígeno se determinó por titulación potenciométrica de Winkler utilizando un analizador Titrino 720 con una precisión de 0,5 micromol/kg. Las muestras de alcalinidad total (TA) y pH (escala de concentración total de hidrógeno, 25°C) se recogieron en frascos de vidrio de 500 mL y se analizaron en pocas horas en el laboratorio base. El pH del agua de mar se midió espectrofotométricamente siguiendo a Clayton y Byrne (1993) aplicándose una adición de 0,0047 (DelValls & Dickson, 1998). La precisión fue 0,003 unidades de pH. El TA se determinó por titulación a pH 4,4 con HCl, según el método potenciométrico de Pérez y Fraga (1987) con una precisión de 2 micromol/kgCSIC y Plan Nacional de I+D del Gobierno de España1 data csv ‘29MY20170609_hy1.csv’ file and 1 readme.txt filePeer reviewe

Data from: GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes

Iron (Fe) speciation in xylem sap by XANES at a high brilliant synchrotron X-ray source: opportunities and limitations

The development of highly brilliant synchrotron facilities all around the world is opening the way to new research in biological sciences including speciation studies of trace elements in plants. In this paper, for the first time, iron (Fe) speciation in xylem sap has been assessed by X-ray absorption near-edge structure (XANES) spectroscopy at the highly brilliant synchrotron PETRA III, beamline P06. Both standard organic Fe-complexes and xylem sap samples of Fe-deficient tomato plants were analyzed. The high photon flux provided by this X-ray synchrotron source allows on one side to obtain good XANES spectra in a reasonable amount of time (approx. 15 min for 200 eV scan) at low Fe concentrations (sub parts-per-million), while on the other hand may cause radiation damage to the sample, despite the sample being cooled by a stream of liquid nitrogen vapor. Standard Fe-complexes such as Fe(III)-succinate, Fe(III)-α-ketoglutarate, and Fe(III)-nicotianamine are somehow degraded when irradiated with synchrotron X-rays and Fe(III) can undergo photoreduction. Degradation of the organic molecules was assessed by HPLC-UV/Vis analyses on the same samples investigated by X-ray absorption spectroscopy (XAS). Fe speciation in xylem sap samples revealed Fe(III) to be complexed by citrate and acetate. Nevertheless, artifacts created by radiation damage cannot be excluded. The use of highly brilliant synchrotrons as X-ray sources for XAS analyses can dramatically increase the sensitivity of the technique for trace elements thus allowing their speciation in xylem sap. However, great attention must be paid to radiation damage, which can lead to biased results

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