Structures of the bacterial ribosome in classical and hybrid states of tRNA binding

During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of ~3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.     

Rapid screening of wood chemical component variations using transmittance near-infrared spectroscopy

A rapid transmittance near-infrared (NIR) spectroscopy method was developed to predict the variation in chemical composition of solid wood. The effect of sample preparation, sample quantity (single versus stacked multiple wood wafers), and NIR acquisition time on the quantification of alpha-cellulose and lignin content was investigated. Strong correlations were obtained between laboratory wet chemistry values and the NIR-predicted values. In addition to the experimental protocol and method development, improvements in calibration error associated with utilizing stacked multiple wood wafers as opposed to single wood wafers are also discussed.     

Correlations of oil and protein with isoflavone concentration in soybean [Glycine max (L.) Merr.

Twelve isoflavones were detected by high-performance liquid chromatography in seeds of 17 soybean [Glycine max (L.) Merrill] cultivars grown at three locations. 6' '-O-Malonyldaidzin and 6' '-O-malonylgenistin together constituted 71-81% of total isoflavones, which ranged in concentration from 2038 to 9514 microg/g and averaged 5644 microg/g across locations and cultivars. The total as well as several individual isoflavones had a moderate negative correlation with oil across locations and cultivars. Six cultivars had a moderate or strong negative correlation of total isoflavones with oil. Five cultivars had a moderate or strong positive correlation of total isoflavones with protein. These results suggest that judicious selection of germplasm for soybean breeding may facilitate development of soybean lines with desirable isoflavone concentrations.     

Horticultural Use of Copper-Based Fungicides Has Not Increased Copper Concentrations in Sediments in the Mid- and Upper Yarra Valley

The use of Cu-based fungicide can pose a risk to nearby surface water bodies due to the run-off of accumulated Cu from agricultural soils. In 2008, we conducted a reconnaissance survey of the presence and concentration of copper in sediments at 18 sites within the Yarra River Catchment, an important horticultural production system in south-eastern Australia. Observed Cu concentrations in sediment samples from the study sites (mean (95 % confidence interval) 12.0 (10.6–13.6)? mg/kg dry weight) were similar to the concentrations present in the samples from the reference sites (mean (95 % confidence interval) 12.0 (6.7–16.8)? mg/kg dry weight). The data on Cu and other metals in the sediments suggest that that there is unlikely to have been wide spread, diffuse, off-site transport of Cu from the soils of horticultural properties to nearby surface waterways in the Yarra River Catchment and that that observed sediment metal concentrations are unlikely to pose an ecological risk to sediment-dwelling organisms at the study sites.     

Predicting short-term extinction risk for the declining Little Bustard (Tetrax tetrax) in intensive agricultural habitats

Populations of Little Bustard (Tetrax tetrax) have shown pronounced declines in European farmland landscapes over the last 25 years due to the intensification of agricultural practices. In France, the number of breeding males in agricultural habitats has declined by 92% since 1980 as a result of decreases in insect abundance and nest destruction during harvesting. We formulate an age- and sex-structured stochastic model for the remaining Little Bustard population in SW France that has been studied since 1997 and, using actual values of demographic rates, we estimate its extinction risk over a time period of 30 years to be of 0.45. At the level of local populations, the extinction risk ranged between 0.66 and 0.90, largely depending on the initial population size and local fecundity of each population. A comprehensive sensitivity analysis evaluated the influence of uncertain demographic rates and of aspects of the spatial dynamics (sex and age dispersing individuals, sex-biased dispersal and different dispersal rates) on the predicted extinction risks and showed that our model was robust to changes of a wide range of combinations assessed. Given the severity of the current decline, and the spatial issues raised by our analysis, implications of our findings for the conservation of this endangered species are suggested.     

Indirect effects of experimental warming on dissolved organic carbon content in subsurface peat

Purpose

The peatland carbon store is threatened by climate change and is expected to provide positive feedback on air temperature. Most studies indicate that enhanced temperature and microbial activities result in a rise of dissolved organic carbon (DOC) as a consequence of higher peat decomposition. Few of them, however, have investigated the impact of in situ experimental warming on DOC response.

Material and methods

We studied the response of DOC, dissolved organic nitrogen (DON), phenol oxidase, and fluorescein diacetate activities (FDA) to a 3-year in situ experimental warming using open-top chambers (OTCs) in a Sphagnum-dominated peatland.

Results and discussion

No significant warming of soil was recorded, implying that the simultaneous decrease in DOC and DON and the rise in FDA at the depths of 25 and 40 cm were not caused by the direct effect of OTCs on water temperature, but might instead have been mediated by plant root exudates. The water chemistry suggests that DOC production was compensated by in situ mineralization. We hypothesize that an increased hydrolysis of organic matter (OM) was counterbalanced by the mineralization of dissolved organic matter (DOM) and that microorganisms preferentially used labile compounds originating from increased root exudates.

Conclusions

This trade-off between production of DOC through hydrolysis and consumption in the process of mineralization shows (1) the limitation of using only DOC as an indicator of the sensitivity of peat decomposition to climate warming and (2) the need to improve our understanding of the indirect impact of root exudates.     

The Medi-RIVAGE study (Mediterranean Diet, Cardiovascular Risks and Gene Polymorphisms): rationale, recruitment, design, dietary intervention and baseline characteristics of participants

OBJECTIVE: To report the rationale, recruitment, design, dietary intervention and baseline characteristics of participants in the Medi-RIVAGE study (Mediterranean Diet, Cardiovascular Risks and Gene Polymorphisms). DESIGN: A randomised, parallel trial comparing a new nutritional programme with a conventional programme. SETTING: Centre for Detection and Prevention of Arteriosclerosis, Timone University Hospital, Marseille, France, and collaborating teams. SUBJECTS: Two hundred and twelve male and female volunteers with at least one cardiovascular risk factor. INTERVENTION: A Mediterranean-type diet characterised mainly by the quality of fatty acids, amount of fish, vegetable foodstuffs and fibre was proposed and compared with a usually prescribed, low-fat/cholesterol diet. Body mass index, fasting lipids and lipoproteins, apolipoproteins, glucose, insulin and homocysteine were the main outcome measures. Gene polymorphisms of interest were determined. RESULTS: Characteristics of men in the two arms were comparable with regard to sociodemographic variables, and clinical and biological cardiovascular risk factors. There were few differences between the groups of women (cholesterol-related parameters, P<0.05). There was no difference between arms in allelic distribution of the gene polymorphisms studied. Saturated fat and protein intakes were high while carbohydrate and fibre intakes were low, but with no difference between arms. Overall, the nutritional markers were comparable in both arms with few exceptions. Correlations between nutritional intakes and plasma nutrient levels ranged from 0.19 (beta-carotene) to 0.47 (folate). CONCLUSIONS: The comparability of the two arms is notable and warrants a low risk of biases. Current diet departs from the traditional Mediterranean one. The assessment of nutritional intake is validated by correlations obtained between dietary intake and relevant biomarkers. This will be important to estimate participant compliance and to analyse intervention data.     

A single nucleotide polymorphism (SNP839) in the adh1 reference gene affects the quantitation of genetically modified maize (Zea mays L.)

The real-time PCR methods recommended in the European Union for the quantitation of genetically modified (GM) maize events NK603, GA21, and MON 863 measure the number of copies of the GM event in relation to those of the maize-specific adh1 reference gene. The study reported here revealed that the targeted 70 base pair adh1 region exhibits a single nucleotide polymorphism (SNP839) that hampers the binding of the reverse primer used in the adh1 detection method. Partial fragments of the adh1-A and adh1-F allele were cloned. By allele-specific real-time PCR, it was shown that SNP839 corresponds to a common allelic polymorphism in maize. As a result, the quantitation of the GM maize events mentioned is positively or negatively biased, depending on the adh1 genotype of sample and calibrant. Therefore, it is proposed to revise the quantitative detection methods for NK603, GA21, and MON 863 maize.     

Changes of pore morphology, infiltration and earthworm community in a loamy soil under different agricultural managements

Earthworm activity produces changes at different scales of soil porosity, including the mesoporosity (between 1.000 and 30 μm eq. dia.) where both water retention and near-saturated infiltration take place. At this scale, the structural changes are poorly described in temperate agricultural systems, so we do not yet fully understand how these changes occur. The present study was conducted to determine the relationships between the morphology of the mesopores, which is mainly affected by earthworm activity, and the hydrodynamic behaviour (near-saturated infiltration) of topsoil under different agricultural managements inducing a large range of earthworm populations.Investigations were carried out at the soil surface in three fields under different management practices giving rise to three different earthworm populations: a continuous maize field where pig slurry was applied, a rye-grass/maize rotation (3/1 year, respectively) also with pig slurry, and an old pasture sown with white clover and rye-grass.Pore space was quantified using a morphological approach and 2D image analysis. Undisturbed soil samples were impregnated with polyester resin containing fluorescent pigment. The images were taken under UV light, yielding a spatial resolution of 42 μm pixel⁻¹. Pores were classified according to their size (which is a function of their area) and their shape. Hydraulic conductivity K(h) was measured using a disc infiltrometer at four water potentials: −0.05, −0.2, −0.6, and −1.5 kPa. The abundance and ecological categories groups of earthworms were also investigated.Continuous soil tillage causes a decrease in both abundance and functional diversity (cf. maize compared with old pasture) when soil tillage every 4 years causes only a decrease in abundance (cf. rotation compared with old pasture). There were no relationships between total porosity and effective porosity at h=−0.05 kPa. Image analysis was useful in distinguishing the functional difference between the three managements. Fewer roots and anecic earthworms resulted in fewer effective tubular voids under maize. There were fewer packing voids in the old pasture due to cattle trampling. Greater hydraulic conductivity in the pasture phase of rotation may arise from a greater functional diversity than in the maize and absence of cattle trampling compared with the pasture. We point to some significant differences between the three types of agricultural management.A better understanding is required of the influence of agricultural management systems on pore morphology. This study provides a new methodology in which we consider the earthworm activity as well as community in order to assess the effects of agricultural management on soil structure and water movement.     

Cause and duration of mustard incorporation effects on soil-borne plant pathogenic fungi

Two fungal plant pathogens, Rhizoctonia solani AG 2-2 and Fusarium oxysporum f.sp. lini, were studied in relation to general responses of soil fungi and bacteria following incorporation of Brassica juncea. Our aim was to understand to what extent the changes in the biological and physicochemical characteristics of the soil could explain the effects on the studied pathogens and diseases, and to determine the temporal nature of the responses. Short-term effects of mustard incorporation (up to 4 months) were investigated in a microcosm experiment, and compared with a treatment where composted plant material was incorporated. In a field experiment, the responses were followed up to 11 months after removal or incorporation of a mustard crop. In general, responses in the variables measured changed more after incorporation of fresh mustard material than after addition of similar amounts of composted plant material (microcosms) or after removal of the mustard crop (field). The soil inoculum potential of R. solani AG 2-2 decreased directly after incorporation of mustard, but increased later to disease levels above those in the untreated soil. Neither of these effects could be explained by changes in the population density of R. solani AG 2-2. Fusarium spp. were less influenced, although an increase in the suppressiveness to Fusarium wilt was observed after mustard incorporation as compared with the treatment where mustard was removed. The microbial responses to mustard incorporation were more pronounced for bacteria than for fungi. After an initial substantial increase, the bacterial density decreased but remained above the levels in the control treatment throughout the experimental periods. The bacterial community structure was modified up to 8 months after mustard incorporation. We conclude that incorporation of fresh mustard influences soil microbial communities, especially the bacteria, and has a potential to control the pathogenic activity of R. solani 2-2 on a short-term perspective. The time dependency in microbial responses is important and should be taken into consideration for the evaluation of the potential of Brassicas to control plant disease on a field scale.