Toxicity of sulfate and chloride to early life stages of wild rice (Zizania palustris).

Despite the importance of wild rice (Zizania palustris) in the Great Lakes region of North America, its sensitivity to sulfate is not well understood. A 21-d hydroponic experiment was performed to determine the toxicity of sulfate to wild rice seeds and seedlings. Effects of 6 sulfate concentrations ranging from 10 mg/L to 5000 mg/L and of chloride salts at equivalent conductivity were evaluated to determine whether adverse effects were attributable to sulfate or to conductivity-related stress. Sulfate treatment decreased root length, shoot length, and leaf number, and increased phytotoxic effects at concentrations of 5000 mg/L relative to a 50 mg/L control. The time to 30% mesocotyl emergence decreased at 2500 mg/L sulfate, indicating a potential stimulatory effect. Sulfate exposures of ≤ 5000 mg/L had no effect on 5 additional end points. Multiple regression analysis indicated that most observed changes could be attributed to conductivity-related stress rather than sulfate per se, with the exception of shoot length and leaf number. Chloride was more toxic than sulfate, as determined by root length and phytotoxicity. In summary, sulfate concentrations below 5000 mg/L did not adversely affect early-life stage wild rice during a 21-d period, and effects at 5000 mg/L sulfate were attributable to conductivity-related stress rather than sulfate toxicity in 2 of 4 end points.

Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues.

BACKGROUND: BAHD acyltransferases are involved in the synthesis and elaboration of a wide variety of secondary metabolites. Previous research has shown that characterized proteins from this family fall broadly into five major clades and contain two conserved protein motifs. Here, we aimed to expand the understanding of BAHD acyltransferase diversity in plants through genome-wide analysis across five angiosperm taxa. We focus particularly on Populus, a woody perennial known to produce an abundance of secondary metabolites. RESULTS: Phylogenetic analysis of putative BAHD acyltransferase sequences from Arabidopsis, Medicago, Oryza, Populus, and Vitis, along with previously characterized proteins, supported a refined grouping of eight major clades for this family. Taxon-specific clustering of many BAHD family members appears pervasive in angiosperms. We identified two new multi-clade motifs and numerous clade-specific motifs, several of which have been implicated in BAHD function by previous structural and mutagenesis research. Gene duplication and expression data for Populus-dominated subclades revealed that several paralogous BAHD members in this genus might have already undergone functional divergence. CONCLUSIONS: Differential, taxon-specific BAHD family expansion via gene duplication could be an evolutionary process contributing to metabolic diversity across plant taxa. Gene expression divergence among some Populus paralogues highlights possible distinctions between their biochemical and physiological functions. The newly discovered motifs, especially the clade-specific motifs, should facilitate future functional study of substrate and donor specificity among BAHD enzymes.

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.

MOTIVATION: The pre-estimate of the proportion of null hypotheses (π(0)) plays a critical role in controlling false discovery rate (FDR) in multiple hypothesis testing. However, hidden complex dependence structures of many genomics datasets distort the distribution of p-values, rendering existing π(0) estimators less effective. RESULTS: From the basic non-linear model of the q-value method, we developed a simple linear algorithm to probe local dependence blocks. We uncovered a non-static relationship between tests' p-values and their corresponding q-values that is influenced by data structure and π(0). Using an optimization framework, these findings were exploited to devise a Sliding Linear Model (SLIM) to more reliably estimate π(0) under dependence. When tested on a number of simulation datasets with varying data dependence structures and on microarray data, SLIM was found to be robust in estimating π(0) against dependence. The accuracy of its π(0) estimation suggests that SLIM can be used as a stand-alone tool for prediction of significant tests. AVAILABILITY: The R code of the proposed method is available at http://aspendb.uga.edu/downloads for academic use.

Plant secondary metabolism in altered gravity.

Plans by the space program to use plants for food supply and environmental regeneration have led to an examination of how plants grow in microgravity. Because secondary metabolic compounds are so important in determining the nutritional and flavor characteristics of plants-as well as making plants more resistant to biotic and abiotic stresses-their responses to altered gravity are now being studied. These experiments are technically challenging because temperature, humidity, atmospheric composition, light, and water status must be maintained around the plant while simultaneously altering the g-load, either in the free-fall of orbital spacecraft or on a centrifuge rotor. In general, plants have shown increased accumulation of small secondary metabolites in microgravity (<10(-3) g), while these have decreased in hypergravity (>1-g). Gravity-related changes in the plant environment as well as mechanical loading effects account for these responses.