Hyperolactone C: determination of its absolute configuration by comparison of experimental and calculated CD spectra

A detailed conformational analysis of hyperolactone C diastereomers and enantiomers ((5R,9R),(5S,9S) and (5S,9R),(5R,9S)) was done with molecular mechanics and density functional theory methods. Time-dependent density functional theory (B3PW91/TZVP) was used to calculate electronic transition energies (UV/vis spectra) and rotational strengths of the respective conformations. The effect of solvation (acetonitrile solution) on excitation energies and electronic circular dichroism was approximated by the polarizable continuum model. By comparison of the simulated CD spectrum with that measured for hyperolactone C isolated from Hypericum lloydii, its absolute configuration can be assigned as (5S,9S).     

Propylphenols are metabolites in the anaerobic biodegradation of propylbenzene under iron-reducing conditions

The metabolism of monoaromatic hydrocarbons by an iron-reducing bacterial enrichment culture originating from diesel-contaminated groundwater was examined using d₇-propylbenzene as a model hydrocarbon. Sequence analysis of the 16S rDNA gene showed that the dominant part (10 of 10 clones) of the enrichment culture consisted of a bacterium closely related to clones found in benzene-contaminated groundwater and to the iron-reducing -proteobacterium, Rhodoferax ferrireducens (similarity values were 99.5% and 98.3%, respectively). In degradation studies conducted over 18 weeks, d₇-propylphenols were detected by gas chromatography–mass spectrometry (GC/MS) as intra-cellular metabolites concomitant with cell growth in the cultures. The amount of propylphenols increased during the exponential growth phase, and by the end of this phase 4 × 10^–14 moles of ferric iron were reduced and 3 × 10^–15 moles propylphenol produced for every cell formed. During the stationary growth phase the cell density was approximately 10⁷ ml^–1, with significantly correlated amounts of propylphenols. Succinate derivates of propylbenzene or phenylpropanol previously shown to be the initial metabolites in the anaerobic degradation of alkylbenzenes could not be identified. This study is the first to report that oxidation of propylbenzene to propylphenols can initiate anaerobic propylbenzene degradation and that iron-reducing bacteria are responsible for this process. In addition, the study shows the importance of taking account of the metabolites adhering to solid phases when determining the extent of biodegradation, so as not to underestimate the extent of the process.     

Regression-based quantitative trait loci mapping: robust, efficient and effective

Regression has always been an important tool for quantitative geneticists. The use of maximum likelihood (ML) has been advocated for the detection of quantitative trait loci (QTL) through linkage with molecular markers, and this approach can be very effective. However, linear regression models have also been proposed which perform similarly to ML, while retaining the many beneficial features of regression and, hence, can be more tractable and versatile than ML in some circumstances. Here, the use of linear regression to detect QTL in structured outbred populations is reviewed and its perceived shortfalls are revisited. It is argued that the approach is valuable now and will remain so in the future.     

Electrostatic contributions to the kinetics and thermodynamics of protein assembly

The role of electrostatic interactions in the assembly of a native protein structure was studied using fragment complementation. Contributions of salt, pH, or surface charges to the kinetics and equilibrium of calbindin D(9k) reconstitution was measured in the presence of Ca(2+) using surface plasmon resonance and isothermal titration calorimetry. Whereas surface charge substitutions primarily affect the dissociation rate constant, the association rates are correlated with subdomain net charge in a way expected for Coulomb interactions. The affinity is reduced in all mutants, with the largest effect (260-fold) observed for the double mutant K25E+K29E. At low net charge, detailed charge distribution is important, and charges remote from the partner EF-hand have less influence than close ones. The effects of salt and pH on the reconstitution are smaller than mutational effects. The interaction between the wild-type EF-hands occurs with high affinity (K(A) = 1.3 x 10(10) M(-1); K(D) = 80 pM). The enthalpy of association is overall favorable and there appears to be a very large favorable entropic contribution from the desolvation of hydrophobic surfaces that become buried in the complex. Electrostatic interactions contribute significantly to the affinity between the subdomains, but other factors, such as hydrophobic interactions, dominate.     

Rotifer community structure in three shallow lakes: seasonal fluctuations and explanatory factors

The present work aimed at studying the rotifer communities of three shallow eutrophic lakes in Portugal (lakes Mira, Vela and Linhos). At the time of the study, Mira and Vela faced large inputs of allochthonous nutrients, while Linhos was facing terrestrialisation, with cycles of dominance-senescence of macrophytes. The three lakes differed in terms of their abiotic features, with Linhos presenting very high nutrient levels and low pH, while Vela and Mira shared most of the characteristics. The rotifer communities of these two lakes were poorly diversified but highly abundant (max. > 2000 ind l⁻¹), with a clear dominance of eurytopic euplanktonic species (mainly Keratella cochlearis). On the other hand, Linhos presented lower abundances (<1000 ind l⁻¹) but higher species richness, mainly due to macrophyte-associated taxa, such as the littoral genera Lepadella, Testudinella and Squatinella. In all lakes, summertime represented a peak in terms of abundance and diversity. Canonical correspondence analysis (CCA) identified two main environmental gradients that shape up the rotifer assemblages: a temporal gradient, mainly related to temperature, and a eutrophy gradient, associated with nitrogenous nutrients. The latter gradient is clearly dependent on between-lake variation, due to the high nutrient levels observed in lake Linhos. Variance partitioning using CCA revealed that the largest portion (27.5%) of the total variation explained (52.1%) was attributed to the interaction between lake and environmental variables.     

Growth of Valley Oak (<Emphasis Type="Italic">Quercus Lobata Nee</Emphasis>) in Four Floodplain Environments in the Central Valley of California

Although there have been numerous studies of California upland oak regeneration and growth there has been no research investigating oak sapling growth in riparian environments. This study looks at the growth response of young valley oak (Quercus lobata Nee), a dominant late successional riparian species in California, across environmental variation on a floodplain. Growth was measured over the course of three years at four different sites. The sites were chosen to represent the range of successional stages and surface age. Growth was significantly higher on younger, unforested sites. There was no difference in growth rate in the two forested sites (early successional cottonwood willow forest and late successional mature oak forest). Herbivory was highest in the cottonwood willow forest, where density of young oaks was also highest. The impact of flooding was measured on the youngest floodplain surface, an open floodplain restoration site where acorns were planted the year our study began. There was a significant negative impact of flooding on sapling growth in all but the first year of growth. Taken together these results suggest that existing forest trees and flooding both inhibit the growth of valley oaks on the floodplain, and that restoration in open sites may be more successful than restoration under an existing canopy.     

The interactive effects of elevated CO<Subscript>2</Subscript>, temperature and initial size on growth and competition between a native C<Subscript>3</Subscript> and an invasive C<Subscript>3</Subscript> grass

A controlled environment experiment was conducted to determine the impact of enhanced carbon dioxide and temperature on competition between the C₃ grasses Austrodanthonia eriantha and Vulpia myuros. Plants were grown in mixtures and monocultures to compare the responses both with and without an interspecific competitor. Temperature and CO₂ were set at current levels (350 ppm CO₂; 20 °C day and 10 °C night temperature), in factorial combination with enhanced levels (700 ppm CO₂; 23 °C day and 13 °C night temperature). To examine the potential impact of initial seedling size on competition under elevated CO₂ and temperature, the two species were combined in mixtures of differing initial sizes. Above-ground growth of all plants was enhanced by increased CO₂ and temperature alone, however the combined temperature and CO₂ treatment showed a sub-additive effect, where growth was less than expected based on the responses to each factor independently. Austrodanthonia in mixture with Vulpia plants of the same initial size experienced a 27 reduction in growth. Austrodanthonia grown in the presence of an initially larger Vulpia plant experienced a 58 reduction in growth. When the Vulpia plant was initially smaller than Austrodanthonia, growth of the Austrodanthonia was reduced by 16%. The growth of Vulpia appeared to be largely unaffected by the presence of Austrodanthonia. Variation in the CO₂ and temperature environment did not affect the pattern of these interspecific interactions, although there was some evidence to suggest that the degree of suppression of Austrodanthonia by Vulpia was less under elevated CO₂. These results do not support the initial advantage hypothesis, as Vulpia was always able to suppress Austrodanthonia, regardless of the initial relative sizes of the competitors. Furthermore, the lack of an effect of changing the CO₂ or temperature environment on the direction of interspecific competition suggests that the competitiveness of the invasive Vulpia will be minimally affected by changes in atmospheric CO₂ concentration or temperature.     

Yersinia pestis kills Caenorhabditis elegans by a biofilm-independent process that involves novel virulence factors

It is known that Yersinia pestis kills Caenorhabditis elegans by a biofilm-dependent mechanism that is similar to the mechanism used by the pathogen to block food intake in the flea vector. Using Y. pestis KIM 5, which lacks the genes that are required for biofilm formation, we show that Y. pestis can kill C. elegans by a biofilm-independent mechanism that correlates with the accumulation of the pathogen in the intestine. We used this novel Y. pestis-C. elegans pathogenesis system to show that previously known and unknown virulence-related genes are required for full virulence in C. elegans. Six Y. pestis mutants with insertions in genes that are not related to virulence before were isolated using C. elegans. One of the six mutants carried an insertion in a novel virulence gene and showed significantly reduced virulence in a mouse model of Y. pestis pathogenesis. Our results indicate that the Y. pestis-C. elegans pathogenesis system that is described here can be used to identify and study previously uncharacterized Y. pestis gene products required for virulence in mammalian systems.