T-loop phosphorylation of Arabidopsis CDKA;1 is required for its function and can be partially substituted by an aspartate residue

As in other eukaryotes, progression through the cell cycle in plants is governed by cyclin-dependent kinases. Phosphorylation of a canonical Thr residue in the T-loop of the kinases is required for high enzyme activity in animals and yeast. We show that the Arabidopsis thaliana Cdc21/Cdc28 homolog CDKA; 1 is also phosphorylated in the T-loop and that phosphorylation at the conserved Thr-161 residue is essential for its function. A phospho-mimicry T161D substitution restored the primary defect of cdka; 1 mutants, and although the T161D substitution displayed a dramatically reduced kinase activity with a compromised ability to bind substrates, homozygous mutant plants were recovered. The rescue by the T161D substitution, however, was not complete, and the resulting plants displayed various developmental abnormalities. For instance, even though flowers were formed, these plants were completely sterile as a result of a failure of the meiotic program, indicating that different requirements for CDKA; 1 function are needed during plant development

Control and Dynamic Competition of Bright and Dark Lasing States in Active Nanoplasmonic Metamaterials

Active nanoplasmonic metamaterials support bright and dark modes that compete for gain. Using a Maxwell-Bloch approach incorporating Langevin noise we study the lasing dynamics in an active nano-fishnet structure. We report that lasing of the bright negative-index mode is possible if the higher-Q dark mode is discriminated by gain, spatially or spectrally. The nonlinear competition during the transient phase is followed by steady-state emission where bright and dark modes can coexist. We analyze the influence of pump intensity and polarization and explore methods for mode control.Comment: 5 pages, 4 figure

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed

Neutrino oscillations in structured matter

A layered material structure in a monochromatic neutrino beam produces interference effects that could be used for the measurement of features of the neutrino mass matrix. The phenomenon would be most useful at high energies.Comment: 18 pp of which two figure

Role of the hyporheic heterotrophic biofilm on transformation and toxicity of pesticides

The role of heterotrophic biofilm of water–sediment interface in detoxification processes was tested in abiotic and biotic conditions under laboratory conditions. Three toxicants, a herbicide (Diuron), a fungicide (Dimethomorph) and an insecticide (Chlorpyrifos-ethyl) have been tested in water percolating into columns reproducing hyporheic sediment. The detoxification processes were tested by comparing the water quality after 18 days of percolation with and without heterotrophic biofilm. Tested concentrations were 30 mg.Lx1 of Diuron diluted in 0.1% dimethyl sulfoxide (DMSO), 2 mg.Lx1 of Dimethomorph and 0.1 mg.Lx1 of Chlorpyrifos-ethyl. To characterise the detoxification efficiency of the system, we performed genotoxicity bioassays in amphibian larvae and rotifers and measured the respiration and denitrification of sediments. Although the presence of biofilm increased the production of N-(3,4 dichlorophenyl)-N-(methyl)-urea, a metabolite of diuron, the toxicity did not decrease irrespective of the bioassay. In the presence of biofilm, Dimethomorph concentrations decreased compared with abiotic conditions, from 2 mg.Lx1 to 0.4 mg.Lx1 after 18 days of percolation. For both Dimethomorph and Chlorpyrifos-ethyl additions, assessment of detoxification level by the biofilm depended on the test used: detoxification effect was found with amphibian larvae bioassay and no detoxification was observed with the rotifer test. Heterotrophic biofilm exerts a major influence in the biochemical transformation of contaminants such as pesticides, suggesting that the interface between running water and sediment plays a role in self-purification of stream reaches