Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (3 results)

  • Article
  • Peer Reviewed
The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

GEOCHEM–EZ is a multi-purpose chemical speciation program, designed to replace Geochem-PC, which can only be used in DOS consoles. This program is used in plant nutrition to perform equilibrium speciation computations to estimate the activity of ions in solution and to consider simple complexes and solid phases. It is also important in molecular biological research to modify solution composition for phenotyping and screening transformed organisms (e.g., transgenic Arabidopsis plants), controlling pH, redox conditions, ionic strength (e.g., for protoplast isolations) or for using heterologous systems, such as yeast expressing plant genes.

To enhance the usability and to address several weaknesses of Geochem-PC, we upgraded the program using a Java graphical user interface, improving both the power and function, and allowing it to run on any computer that supports Windows XP, Vista, or Windows 7.

This program includes improvements, such as interactive and illustrated help files, hierarchical organization of options, logical output, and real-time error checking, while maintaining complete backward compatibility to the Geochem-PC format. We added a customizable database of common salts, eliminating the need to parse and calculate the concentration of each metal or ligand. This last feature will make data input more rapid and help eliminate the most common user errors. One can instantly preview input and output files and make necessary corrections (e.g. charge balance the solution), something that formerly involved having to save these files and run the calculations a second time. GEOCHEM-EZ is available as a free download from http://www.plantmineralnutrition.net/Geochem/geochem%20home.htm

    Cover page: Geochem-EZ: a Chemical Speciation Program With Greater Power and Flexibility
    • Article
    • Peer Reviewed
    The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

    The efficient quantification of root traits remains a critical factor in exploiting many genetic resources during the study of root function and development. This is particularly true during the phenotyping of large populations under abiotic stress conditions, including aluminum (Al) toxicity where root growth is quantified in the presence and absence of Al, and phosphorous (P) deficiency, where root architectural responses and differences are often examined. Our present study highlights two root imaging and quantification systems that are being developed and used in our laboratory. We have focused on designing flexible growth, imaging and software tools that enable a multitude of 2D and 3D root system characteristics to be investigated.

      Cover page: Advances to Whole Root System Quantification Tools and Techniques
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2022)
      AbstractDecades of research have revealed relationships between the abundance of coral reef taxa and local conditions, especially at small scales. However, a rigorous test of covariation requires a robust dataset collected across wide environmental or experimental gradients. Here, we surveyed spatial variability in the densities of major coral reef functional groups at 122 sites along a 70 km expanse of the leeward, forereef habitat of Curaçao in the southern Caribbean. These data were used to test the degree to which spatial variability in community composition could be predicted based on assumed functional relationships and site-specific anthropogenic, physical, and ecological conditions. In general, models revealed less power to describe the spatial variability of fish biomass than cover of reef builders (R2 of best-fit models: 0.25 [fish] and 0.64 [reef builders]). The variability in total benthic cover of reef builders was best described by physical (wave exposure and reef relief) and ecological (turf algal height and coral recruit density) predictors. No metric of anthropogenic pressure was related to spatial variation in reef builder cover. In contrast, total fish biomass showed a consistent (albeit weak) association with anthropogenic predictors (fishing and diving pressure). As is typical of most environmental gradients, the spatial patterns of both fish biomass density and reef builder cover were spatially autocorrelated. Residuals from the best-fit model for fish biomass retained a signature of spatial autocorrelation while the best-fit model for reef builder cover removed spatial autocorrelation, thus reinforcing our finding that environmental predictors were better able to describe the spatial variability of reef builders than that of fish biomass. As we seek to understand spatial variability of coral reef communities at the scale of most management units (i.e., at kilometer- to island-scales), distinct and scale-dependent perspectives will be needed when considering different functional groups.
        Top