Potassium homeostasis in vacuolate plant cells.

Plant cells contain two major pools of K+, one in the vacuole and one in the cytosol. The behavior of K+ concentrations in these pools is fundamental to understanding the way this nutrient affects plant growth. Triple-barreled microelectrodes have been used to obtain the first fully quantitative measurements of the changes in K+ activity (aK) in the vacuole and cytosol of barley (Hordeum vulgare L.) root cells grown in different K+ concentrations. The electrodes incorporate a pH-selective barrel allowing each measurement to be assigned to either the cytosol or vacuole. The measurements revealed that vacuolar aK declined linearly with decreases in tissue K+ concentration, whereas cytosolic aK initially remained constant in both epidermal and cortical cells but then declined at different rates in each cell type. An unexpected finding was that cytoplasmic pH declined in parallel with cytosolic aK, but acidification of the cytosol with butyrate did not reveal any short-term link between these two parameters. These measurements show the very different responses of the vacuolar and cytosolic K+ pools to changes in K+ availability and also show that cytosolic K+ homeostasis differs quantitatively in different cell types. The data have been used in thermodynamic calculations to predict the need for, and likely mechanisms of, active K+ transport into the vacuole and cytosol. The direction of active K+ transport at the vacuolar membrane changes with tissue K+ status.

A mechanism for inducing plant development: the genesis of a specific inhibitor.

Parasitic strategies are widely distributed in the plant kingdom and frequently involve coupling parasite organogenesis with cues from the host. In Striga asiatica, for example, the cues that initiate the development of the host attachment organ, the haustorium, originate in the host and trigger the transition from vegetative to parasitic mode in the root meristem. This system therefore offers a unique opportunity to study the signals and mechanisms that control plant cell morphogenesis. Here we establish that the biological activity of structural analogs of the natural inducer displays a marked dependence on redox potential and suggest the existence of a semiquinone intermediate. Building on chemistry that exploits the energetics of such an intermediate, cyclopropyl-p-benzoquinone (CPBQ) is shown to be a specific inhibitor of haustorial development. These data are consistent with a model where haustorial development is initiated by the completion of a redox circuit.

Distribution of spontaneous plant hybrids.

Natural hybridization is a relatively common feature of vascular plant species and has been demonstrated to have played an important role in their evolution. Nonetheless, it is not clear whether spontaneous hybridization occurs as a general feature of all plant families and genera or whether certain groups are especially prone to spontaneous hybridization. Therefore, we inspected five modern biosystematic floras to survey the frequency and taxonomic distribution of spontaneous hybrids. We found spontaneous hybridization to be nonrandomly distributed among taxa, concentrated in certain families and certain genera, often at a frequency out of proportion to the size of the family or genus. Most of these groups were primarily outcrossing perennials with reproductive modes that stabilized hybridity such as agamospermy, vegetative spread, or permanent odd polyploidy. These data suggest that certain phylogenetic groups are biologically predisposed for the formation and maintenance of hybrids.

Effects of mechanical signaling on plant cell cytosolic calcium.

Mechanical signals are important influences on the development and morphology of higher plants. Using tobacco transformed with the Ca(2+)-sensitive luminescent protein aequorin, we recently reported the effects of mechanical signals of touch and wind on the luminescence and thus intracellular calcium of young seedlings. When mesophyll protoplasts are isolated from these transgenic tobacco plants and mechanically stimulated by swirling them in solution, cytoplasmic Ca2+ increases immediately and transiently up to 10 microM, and these transients are unaffected by an excess of EGTA in the medium. The size of the transient effect is related to the strength of swirling. Epidermal strips isolated from transgenic tobacco leaves and containing only viable guard cells and trichomes also respond to the strength of swirling in solution and can increase their cytoplasmic Ca2+ transiently up to 10 microM. Finally, the moss Physcomitrella patens containing recombinant aequorin exhibits transient increases in cytoplasmic Ca2+ up to 5 microM when swirled in solution. This effect is strongly inhibited by ruthenium red. Our data indicate that the effect of mechanical stimulation can be found in a number of different cell types and in a lower plant as well as tobacco and suggest that mechanoperception and the resulting increase in cytoplasmic Ca2+ may be widespread.

Identification of cDNA clones encoding valosin-containing protein and other plant plasma membrane-associated proteins by a general immunoscreening strategy.

An approach was developed for the isolation and characterization of soybean plasma membrane-associated proteins by immunoscreening of a cDNA expression library. An antiserum was raised against purified plasma membrane vesicles. In a differential screening of approximately 500,000 plaque-forming units with the anti-(plasma membrane) serum and DNA probes derived from highly abundant clones isolated in a preliminary screening, 261 clones were selected from approximately 1,200 antiserum-positive plaques. These clones were classified into 40 groups by hybridization analysis and 5'- and 3'-terminal sequencing. By searching nucleic acid and protein sequence data bases, 11 groups of cDNAs were identified, among which valosin-containing protein (VCP), clathrin heavy chain, phospholipase C, and S-adenosylmethionine:delta 24-sterol-C-methyltransferase have not to date been cloned from plants. The remaining 29 groups did not match any current data base entries and may, therefore, represent additional or yet uncharacterized genes. A full-length cDNA encoding the soybean VCP was sequenced. The high level of amino acid identity with vertebrate VCP and yeast CDC48 protein indicates that the soybean protein is a plant homolog of vertebrate VCP and yeast CDC48 protein.

Joint interpretation of magnetotelluric, seismic, and well-log data in Hontomín (Spain)

Acknowledgements. This work is dedicated to the memory of Andrés Pérez-Estaún, brilliant scientist, colleague, and friend. The authors sincerely thank Ian Ferguson and an anonymous reviewer for their useful comments on the manuscript. Xènia Ogaya is currently supported in the Dublin Institute for Advanced Studies by a Science Foundation Ireland grant IRECCSEM (SFI grant 12/IP/1313). Juan Alcalde is funded by NERC grant NE/M007251/1, on interpretational uncertainty. Juanjo Ledo, Pilar Queralt and Alex Marcuello thank Ministerio de Economía y Competitividad and EU Feder Funds through grant CGL2014- 54118-C2-1-R. Funding for this Project has been partially provided by the Spanish Ministry of Industry, Tourism and Trade, through the CIUDEN-CSIC-Inst. Jaume Almera agreement (ALM-09-027: Characterization, Development and Validation of Seismic Techniques applied to CO2 Geological Storage Sites), the CIUDEN-Fundació Bosch i Gimpera agreement (ALM-09-009 Development and Adaptation of Electromagnetic techniques: Characterisation of Storage Sites) and the project PIERCO2 (Progress In Electromagnetic Research for CO2 geological reservoirs CGL2009-07604). The CIUDEN project is co-financed by the European Union through the Technological Development Plant of Compostilla OXYCFB300 Project (European Energy Programme for Recovery).

Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

A Finite Element Numerical Algorithm for Modelling and Data Fitting in Complex Systems

Numerical modelling methodologies are important by their application to engineering and scientific problems, because there are processes where analytical mathematical expressions cannot be obtained to model them. When the only available information is a set of experimental values for the variables that determine the state of the system, the modelling problem is equivalent to determining the hyper-surface that best fits the data. This paper presents a methodology based on the Galerkin formulation of the finite elements method to obtain representations of relationships that are defined a priori, between a set of variables: y = z(x1, x2,...., xd). These representations are generated from the values of the variables in the experimental data. The approximation, piecewise, is an element of a Sobolev space and has derivatives defined in a general sense into this space. The using of this approach results in the need of inverting a linear system with a structure that allows a fast solver algorithm. The algorithm can be used in a variety of fields, being a multidisciplinary tool. The validity of the methodology is studied considering two real applications: a problem in hydrodynamics and a problem of engineering related to fluids, heat and transport in an energy generation plant. Also a test of the predictive capacity of the methodology is performed using a cross-validation method.

Effects of plant functional traits on soil stability: intraspecific variability matters

This data set describes different vegetation, soil and plant functional traits (PFTs) of 15 plant species in 30 sampling plots of an agricultural landscape in the Haean-myun catchment in South Korea. We divided the data set into two main tables, the first one includes the PFTs data of the 15 studied plant species, and the second one includes the soil and vegetation characteristics of the 30 sampling plots. For a total of 150 individuals, we measures the maximum plant height (cm) and leaf size (cm**2), which means the leaf surface area for the aboveground compartment of each individual. For the belowground compartment, we measured root horizontal width, which is the maximum horizontal spread of the root, rooting length, which is the maximum rooting depth, root diameter, which is the average root diameter of a the whole root, specific root length (SRL), which is the root length divided by the root dry mass, and root/shoot ratio, which is the root dry mass divided by the shoot dry mass. At each of the 30 studied plots, we estimated three different variables describing the vegetation characteristics: vegetation cover (i.e. the percentage of ground covered by vegetation), species richness (i.e. the number of observed species) and root density (estimated using a 30 cm x 30 cm metallic frame divided into nine 10 cm x 10 cm grids placed on the soil profile), as we calculated the total number of roots that appear in each of the nine grids and then we converted it into percentage based on the root count, following. Moreover, in each plot we estimated six different soil variables: Bulk density (g/cm**3), clay % (i.e. percentage of clay), silt % (i.e. percentage of silt), soil aggregate stability, using mean weight diameter (MWD), penetration resistance (kg/cm**2), using pocket penetrometer and soil shear vane strength (kPa).

Drivers of multi-scale plant community structure in agricultural field margins of South Korea

This data set describes the distribution of a total of 90 plant species growing on field margins of an agricultural landscape in the Haean-myun catchment in South Korea. We conducted our survey between July and August 2011 in 100 sampling plots, covering the whole catchment. In each plot we measured three environmental variables: slope, width of the field margin, and management type (i.e. "managed" for field margins that had signs of management activities from the ongoing season such as cutting or spraying herbicides and "unmanaged" for field margins that had been left untouched in the season). For the botanical survey each plot was sampled using three subplots of one square meter per subplot; subplots were 4 m apart from each other. In each subplot, we estimated three different vegetation characteristics: vegetation cover (i.e. the percentage of ground covered by vegetation), species richness (i.e. the number of observed species) and species abundance (i.e. the number of observed individuals / species). We calculated the percentage of the non-farmed habitats by creating buffer zones of 100, 200, 300, 400 and 500 m radii around each plot using data provided by (Seo et al. 2014). Non-farmed habitats included field margins, fallows, forest, riparian areas, pasture and grassland.

Maize Stress DIESI-MS Data and R Script

Climatic change is an increasing challenge for agriculture that is driving the development of suitable crops in order to ensure supply for both human nutrition and animal feed. In this context, it is increasingly important to understand the biochemical responses of cells to environmental cues at the whole system level, an aim that is being brought closer by advances in high throughput, cost-efficient plant metabolomics. To support molecular breeding activities, we have assessed the economic, technical and statistical feasibility of using direct mass spectrometry methods to evaluate the physiological state of maize (Zea mays L.) plants grown under different stress conditions.