Exploring the enzymatic landscape: distribution and kinetics of hydrolytic enzymes in soil particle-size fractions

The location of extracellular enzymes within the soil architecture and their association with the various soil components affects their catalytic potential. A soil fractionation study was carried out to investigate: (a) the distribution of a range of hydrolytic enzymes involved in C, N and P transformations, (b) the effect of the location on their respective kinetics, (c) the effect of long-term N fertilizer management on enzyme distribution and kinetic parameters. Soil (silty clay loam) from grassland which had received 0 or 200 kg N ha(-1) yr(-1) was fractionated, and four particle-size fractions (> 200, 200-63, 63-2 and 0. 1-2 mum) were obtained by a combination of wet-sieving and centrifugation, after low-energy ultrasonication. All fractions were assayed for four carbohydrases (beta-cellobiohydrolase, N-acetyl-beta-glucosammidase, beta-glucosidase and beta-xylosidase), acid phosphatase and leucine-aminopeptidase using a microplate fluorimetric assay based on MUB-substrates. Enzyme kinetics (V-max and K-m) were estimated in three particle-size fractions and the unfractionated soil. The results showed that not all particle-size fractions were equally enzymatically active and that the distribution of enzymes between fractions depended on the enzyme. Carbohydrases predominated in the coarser fractions while phosphatase and leucine-aminopeptidase were predominant in the clay-size fraction. The Michaelis constant (K.) varied among fractions, indicating that the association of the same enzyme with different particle-size fractions affected its substrate affinity. The same values of Km were found in the same fractions from the soil under two contrasting fertilizer management regimes, indicating that the Michaelis constant was unaffected by soil changes caused by N fertilizer management. (C) 2004 Elsevier Ltd. All rights reserved.

Uptake kinetics of metals by the earthworm Eisenia fetida exposed to field-contaminated soils

It is well known that earthworms can accumulate metals. However, most accumulation studies focus on Cd-, Cu-, Pb- or Zn-amended soils, additionally few studies consider accumulation kinetics. Here we model the accumulation kinetics of 18 elements by Eisenia fetida, exposed to 8 metal-contaminated and 2 uncontaminated soils. Tissue metal concentration was determined after 3, 7,14, 21, 28 and 42 days. Metal elimination rate was important in determining time to reach steady-state tissue metal concentration. Uptake flux to elimination rate ratios showed less variation and lower values for essential than for non-essential metals. In theory kinetic rate constants are dependent only on species and metal. Therefore it should be possible to predict steady-state tissue metal concentrations on the basis of very few measurements using the rate constants. However, our experiments show that it is difficult to extrapolate the accumulation kinetic constants derived using one soil to another. (C) 2009 Elsevier Ltd. All rights reserved.

Dynamic behavior of Arabidopsis eif4a-iii, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia

Here, we identify the Arabidopsis thaliana ortholog of the mammalian DEAD box helicase, eIF4A-III, the putative anchor protein of exon junction complex (EJC) on mRNA. Arabidopsis eIF4A-III interacts with an ortholog of the core EJC component, ALY/Ref, and colocalizes with other EJC components, such as Mago, Y14, and RNPS1, suggesting a similar function in EJC assembly to animal eIF4A-III. A green fluorescent protein (GFP)-eIF4A-III fusion protein showed localization to several subnuclear domains: to the nucleoplasm during normal growth and to the nucleolus and splicing speckles in response to hypoxia. Treatment with the respiratory inhibitor sodium azide produced an identical response to the hypoxia stress. Treatment with the proteasome inhibitor MG132 led to accumulation of GFP-eIF4A-III mainly in the nucleolus, suggesting that transition of eIF4A-III between subnuclear domains and/or accumulation in nuclear speckles is controlled by proteolysis-labile factors. As revealed by fluorescence recovery after photobleaching analysis, the nucleoplasmic fraction was highly mobile, while the speckles were the least mobile fractions, and the nucleolar fraction had an intermediate mobility. Sequestration of eIF4A-III into nuclear pools with different mobility is likely to reflect the transcriptional and mRNA processing state of the cell.

Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions.

Bilateral high-frequency stimulation of the subthalamic nucleus on attentional performance: transient deleterious effects and enhanced motivation in both intact and parkinsonian rats.

It is now well established that subthalamic nucleus high-frequency stimulation (STN HFS) alleviates motor problems in Parkinson's disease. However, its efficacy for cognitive function remains a matter of debate. The aim of this study was to assess the effects of STN HFS in rats performing a visual attentional task. Bilateral STN HFS was applied in intact and in bilaterally dopamine (DA)-depleted rats. In all animals, STN HFS had a transient debilitating effect on all the variables measured in the task. In DA-depleted rats, STN HFS did not alleviate the deficits induced by the DA lesion such as omissions and latency to make correct responses, but induced perseverative approaches to the food magazine, an indicator of enhanced motivation. In sham-operated controls, STN HFS significantly reduced accuracy and induced perseverative behaviour, mimicking partially the effects of bilateral STN lesions in the same task. These results are in line with the hypothesis that STN HFS only partially mimics inactivation of STN produced by lesioning and confirm the motivational exacerbation induced by STN inactivation.

Fast approximate calculation of multiply scattered lidar returns

An efficient method is described for the approximate calculation of the intensity of multiply scattered lidar returns. It divides the outgoing photons into three populations, representing those that have experienced zero, one, and more than one forward-scattering event. Each population is parameterized at each range gate by its total energy, its spatial variance, the variance of photon direction, and the covariance, of photon direction and position. The result is that for an N-point profile the calculation is O(N-2) efficient and implicitly includes up to N-order scattering, making it ideal for use in iterative retrieval algorithms for which speed is crucial. In contrast, models that explicitly consider each scattering order separately are at best O(N-m/m!) efficient for m-order scattering and often cannot be performed to more than the third or fourth order in retrieval algorithms. For typical cloud profiles and a wide range of lidar fields of view, the new algorithm is as accurate as an explicit calculation truncated at the fifth or sixth order but faster by several orders of magnitude. (C) 2006 Optical Society of America.

North Atlantic Oscillation response to transient greenhouse gas forcing and the impact on European winter climate: a CMIP2 multi-model assessment

This study investigates the response of wintertime North Atlantic Oscillation (NAO) to increasing concentrations of atmospheric carbon dioxide (CO2) as simulated by 18 global coupled general circulation models that participated in phase 2 of the Coupled Model Intercomparison Project (CMIP2). NAO has been assessed in control and transient 80-year simulations produced by each model under constant forcing, and 1% per year increasing concentrations of CO2, respectively. Although generally able to simulate the main features of NAO, the majority of models overestimate the observed mean wintertime NAO index of 8 hPa by 5-10 hPa. Furthermore, none of the models, in either the control or perturbed simulations, are able to reproduce decadal trends as strong as that seen in the observed NAO index from 1970-1995. Of the 15 models able to simulate the NAO pressure dipole, 13 predict a positive increase in NAO with increasing CO2 concentrations. The magnitude of the response is generally small and highly model-dependent, which leads to large uncertainty in multi-model estimates such as the median estimate of 0.0061 +/- 0.0036 hPa per %CO2. Although an increase of 0.61 hPa in NAO for a doubling in CO2 represents only a relatively small shift of 0.18 standard deviations in the probability distribution of winter mean NAO, this can cause large relative increases in the probabilities of extreme values of NAO associated with damaging impacts. Despite the large differences in NAO responses, the models robustly predict similar statistically significant changes in winter mean temperature (warmer over most of Europe) and precipitation (an increase over Northern Europe). Although these changes present a pattern similar to that expected due to an increase in the NAO index, linear regression is used to show that the response is much greater than can be attributed to small increases in NAO. NAO trends are not the key contributor to model-predicted climate change in wintertime mean temperature and precipitation over Europe and the Mediterranean region. However, the models' inability to capture the observed decadal variability in NAO might also signify a major deficiency in their ability to simulate the NAO-related responses to climate change.

Fast and frugal framing effects?

Three experiments examine whether simple pair-wise comparison judgments, involving the “recognition heuristic” (Goldstein & Gigerenzer, 2002), are sensitive to implicit cues to the nature of the comparison required. Experiments 1 & 2 show that participants frequently choose the recognized option of a pair if asked to make “larger” judgments but are significantly less likely to choose the unrecognized option when asked to make “smaller” judgments. Experiment 3 demonstrates that, overall, participants consider recognition to be a more reliable guide to judgments of a magnitude criterion than lack of recognition and that this intuition drives the framing effect. These results support the idea that, when making pair-wise comparison judgments, inferring that the recognized item is large is simpler than inferring that the unrecognized item is small.

On the evolution of the solar wind between 1 and 5 AU at the time of the Cassini Jupiter flyby: Multispacecraft observations of interplanetary coronal mass ejections including the formation of a merged interaction region

The Cassini flyby of Jupiter occurred at a time near solar maximum. Consequently, the pre-Jupiter data set reveals clear and numerous transient perturbations to the Parker Spiral solar wind structure. Limited plasma data are available at Cassini for this period due to pointing restrictions imposed on the instrument. This renders the identification of the nature of such structures ambiguous, as determinations based on the magnetic field data alone are unreliable. However, a fortuitous alignment of the planets during this encounter allowed us to trace these structures back to those observed previously by the Wind spacecraft near the Earth. Of the phenomena that we are satisfactorily able to trace back to their manifestation at 1 AU, two are identified as being due to interplanetary coronal mass ejections. One event at Cassini is shown to be a merged interaction region, which is formed from the compression of a magnetic cloud by two anomalously fast solar wind streams. The flux-rope structure associated with this magnetic cloud is not as apparent at Cassini and has most likely been compressed and deformed. Confirmation of the validity of the ballistic projections used here is provided by results obtained from a one-dimensional magnetohydrodynamic projection of solar wind parameters measured upstream near the Earth. It is found that when the Earth and Cassini are within a few tens of degrees in heliospheric longitude, the results of this one-dimensional model predict the actual conditions measured at 5 AU to an impressive degree. Finally, the validity of the use of such one-dimensional projections in obtaining quasi-solar wind parameters at the outer planets is discussed.