Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Enhancing the ratio of molecular ions to non-covalent compounds in the electrospray interface of LC-MS in quantitative analysis

A common problem encountered during the development of MS methods for the quantitation of small organic molecules by LGMS is the formation of non-covalently bound species or adducts in the electrospray interface. Often the population of the molecular ion is insignificant compared to those of all other forms of the analyte produced in the electrospray, making it difficult to obtain the sensitivity required for accurate quantitation. We have investigated the effects of the following variables: orifice potential, nebulizer gas flow, temperature, solvent composition and the sample pH on the relative distributions of ions of the types MH+, MNa+, MNH+, and 2MNa(+), where M represents a 4 small organic molecule: BAY 11-7082 ((E)-3-[4-methylphenylsulfonyl]-2-propenenitrile). Orifice potential, solvent composition and the sample pH had the greatest influence on the relative distributions of these ions, making these parameters the most useful for optimizing methods for the quantitation of small molecules.

Finding common ground in team-based qualitative research using the convergent interviewing method

Research councils, agencies, and researchers recognize the benefits of team-based health research. However, researchers involved in large-scale team-based research projects face multiple challenges as they seek to identify epistemological and ontological common ground. Typically, these challenges occur between quantitative and qualitative researchers but can occur between qualitative researchers, particularly when the project involves multiple disciplinary perspectives. The authors use the convergent interviewing technique in their multidisciplinary research project to overcome these challenges. This technique assists them in developing common epistemological and ontological ground while enabling swift and detailed data collection and analysis. Although convergent interviewing is a relatively new method described primarily in marketing research, it compares and contrasts well with grounded theory and other techniques. The authors argue that this process provides a rigorous method to structure and refine research projects and requires researchers to identify and be accountable for developing a common epistemological and ontological position.

Quantitative analysis of DNA-protein interactions using double-labeled native gel electrophoresis and fluorescence-based imaging

We have developed a sensitive, non-radioactive method to assess the interaction of transcription factors/DNA-binding proteins with DNA. We have modified the traditional radiolabeled DNA gel mobility shift assay to incorporate a DNA probe end-labeled with a Texas-red fluorophore and a DNA-binding protein tagged with the green fluorescent protein to monitor precisely DNA-protein complexation by native gel electrophoresis. We have applied this method to the DNA-binding proteins telomere release factor-1 and the sex-determining region-Y, demonstrating that the method is sensitive (able to detect 100 fmol of fluorescently labeled DNA), permits direct visualization of both the DNA probe and the DNA-binding protein, and enables quantitative analysis of DNA and protein complexation, and thereby an estimation of the stoichiometry of protein-DNA binding.

Studying phenotypic evolution using multivariate quantitative genetics

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.

Career research in a post-modern era

In recent years, career theory and practice has been challenged to revise and reinvigorate itself in order to remain relevant in the post- modern world. The most fundamental challenge is to produce an identity for career practice that is congruent with the post-modern world. Career research is facing a similar challenge as it has been dominated by methodologies that emanate out of the positivist worldview of the modern era and has been mainly quantitative in nature. In their recent research, the authors have been examining methodologies that accommodate the tenets of the post-modern world – post-modernism, constructivism and career psychology. This article overviews post- modern considerations by exploring the possibilities offered by the Systems Theory Framework of career development and the 'My System of Career Influence' reflection activity as research tools. Examples of recent research are briefly described.

Facilitating soil-and plant-water research through the use of TDR

The development of TDR for measurement of soil water content and electrical conductivity has resulted in a large shift in measurement methods for a breadth of soil and hydrological characterization efforts. TDR has also opened new possibilities for soil and plant research. Five examples show how TDR has enhanced our ability to conduct our soil- and plant-water research. (i) Oxygen is necessary for healthy root growth and plant development but quantitative evaluation of the factors controlling oxygen supply in soil depends on knowledge of the soil water content by TDR. With water content information we have modeled successfully some impact of tillage methods on oxygen supply to roots and their growth response. (ii) For field assessment of soil mechanical properties influencing crop growth, water content capability was added to two portable soil strength measuring devices; (a) A TDT (Time Domain Transmittivity)-equipped soil cone penetrometer was used to evaluate seasonal soil strengthwater content relationships. In conventional tillage systems the relationships are dynamic and achieve the more stable no-tillage relationships only relatively late in each growing season; (b) A small TDR transmission line was added to a modified sheargraph that allowed shear strength and water content to be measured simultaneously on the same sample. In addition, the conventional graphing procedure for data acquisition was converted to datalogging using strain gauges. Data acquisition rate was improved by more than a factor of three with improved data quality. (iii) How do drought tolerant plants maintain leaf water content? Non-destructive measurement of TDR water content using a flat serpentine triple wire transmission line replaces more lengthy procedures of measuring relative water content. Two challenges remain: drought-stressed leaves alter salt content, changing electrical conductivity, and drought induced changes in leaf morphology affect TDR measurements. (iv) Remote radar signals are reflected from within the first 2 cm of soil. Appropriate calibration of radar imaging for soil water content can be achieved by a parallel pair of blades separated by 8 cm, reaching 1.7 cm into soil and forming a 20 cm TDR transmission line. The correlation between apparent relative permittivity from TDR and synthetic aperture radar (SAR) backscatter coefficient was 0.57 from an airborne flyover. These five examples highlight the diversity in the application of TDR in soil and plant research.