Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection

The present study aims to investigate small RNA interactions with putative disease response genes in the model grass species Brachypodium distachyon. The fungal pathogen Fusarium culmorum (Fusarium herein) and phytohormone salicylic acid treatment were used to induce the disease response in Brachypodium. Initially, 121 different putative disease response genes were identified using bioinformatic and homology based approaches. Computational prediction was used to identify 33 candidate new miRNA coding sequences, of which 9 were verified by analysis of small RNA sequence libraries. Putative Brachypodium miRNA target sites were identified in the disease response genes, and a subset of which were screened for expression and possible miRNA interactions in 5 different Brachypodium lines infected with Fusarium. An NBS-LRR family gene, 1g34430, was polymorphic among the lines, forming two major genotypes, one of which has its miRNA target sites deleted, resulting in altered gene expression during infection. There were siRNAs putatively involved in regulation of this gene, indicating a role of small RNAs in the B. distachyon disease response.     

Interactions of oxovanadates and selected oxomolybdates with proteins

The interactions of phosphoglucose isomerase with solutions of rapidly interconverting oxovanadates are described. Quantitative speciation analyses of vanadate monomer, dimer, tetramer and pentamer were performed under the conditions of the enzyme assay. 2D EXSY⁵¹V NMR spectroscopy was used to demonstrate that the oligoanions are sufficiently long-lived to be recognized by the enzyme as different species. The observations are consistent with the vanadate tetramer being responsible for the observed inhibition. Selected oxomolybdates ([(CH₃)₂AsMo₄OH]^2– and [(NH₃C₂H₄P)₂Mo₅O₂₁]^2–) were also found to inhibit 6-phosphogluconate dehydrogenase, glucose-6-phosphate dehydrogenase, glycerol-3-phosphate dehydrogenase and fructose-1,6-bisphosphate aldolase. The selectivities and affinities of these proteins for the oxometalates are discussed.     

Defining the stimulus—A memoir

The eminent psychophysicist, S.S. Stevens, once remarked that, “the basic problem of psychology was the definition of the stimulus” (Stevens, 1951, p. 46). By expanding the traditional definition of the stimulus, the study of animal learning has metamorphosed into animal cognition. The main impetus for that change was the recognition that it is often necessary to postulate a representation between the traditional S and R of learning theory. Representations allow a subject to represent a stimulus it learned previously that is currently absent. Thus, in delayed matching-to-sample, one has to assume that a subject responds to a representation of the sample during test if it responds correctly. Other examples, to name but a few, include concept formation, spatial memory, serial memory, learning a numerical rule, imitation and metacognition. Whereas a representation used to be regarded as a mentalistic phenomenon that was unworthy of scientific inquiry, it can now be operationally defined. To accommodate representations, the traditional discriminative stimulus has to be expanded to allow for the role of representations. The resulting composite can account for a significantly larger portion of the variance of performance measures than the exteroceptive stimulus could by itself.     

Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1

In Sphingomonas sp. A1, alginate is degraded by alginate lyases to its constituent monosaccharides, which are nonenzymatically converted to an α-keto acid, namely, 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH). The properties of the DEH-metabolizing enzyme and its gene in strain A1 were characterized. In the presence of alginate, strain A1 cells inducibly produced an NADPH-dependent DEH reductase (A1-R) in their cytoplasm. Molecular cloning of the enzyme gene indicated that A1-R belonged to the short-chain dehydrogenase/reductase superfamily and catalyzed the conversion of DEH to 2-keto-3-deoxy-d-gluconic acid most efficiently at around pH 7.0 and 50 °C. Crystal structures of A1-R and its complex with NADP were determined at around 1.6 Å resolution by X-ray crystallography. The enzyme consists of three layers (α/β/α), with a coenzyme-binding Rossmann fold. NADP is surrounded by positively charged residues, and Gly-38 and Arg-39 are crucial for NADP binding. Site-directed mutagenesis studies suggest that Ser-150, Tyr-164, and Lys-168 located around the Rossmann fold constitute the catalytic triad. To our knowledge, this is the first report on molecular cloning and structure determination of a bacterial DEH reductase responsible for alginate metabolism.     

Elephant impact on dragonflies

African elephants and other indigenous megaherbivores have a major impact on local vegetation structure, including aquatic communities, as their big feet and large mass pound the fringes of water bodies. This disturbance is likely to have a profound influence on the structure and composition of insect assemblages in these habitats. We investigated which dragonfly (Odonata) species were tolerant of trampling by elephants and other game. Assemblage composition differed according to extremely high, very high or high disturbance levels. Dragonfly abundance was greatest where impact was high, and decreasing when disturbance became very high or extremely high. Several odonate species are well-adapted to fairly high levels of disturbance, although too much is impoverishing. Medium and low impact sites were geographically separated, and this, combined with much lower disturbance levels, had a considerable influence on promoting regional dragonfly diversity. Several regional specialist species only occurred in the geographically separated, low-impact sites. The full complement of dragonflies is present only when there is a combination of various disturbance levels combined with spatial variation. Elephant impact is similar to that of humans, with too much of either or both, leading to a species-poor, habitat-generalist dragonfly assemblage.     

Unstable, non-mutational expression of resistance to the thymidine analogue, trifluorothymidine in CHO cells.

In Saccharomyces cerevisiae, methyl methanesulphonate and diepoxybutane produced efficiently lethal, as well as mutagenic, damage in nuclear DNA. However, in the same conditions, these agents did not induce cytoplasmic petite mutations and poorly induced point mutations (resistance to erythromycin and chloramphenicol) in mitochondrial DNA. Possible reasons for these differences are discussed.     

Flagellar hook structures of Caulobacter and Salmonella and their relationship to filament structure

Native flagellar hooks from a polarly flagellated bacterium, Caulobacter crescentus, and polyhooks from a peritrichously flagellated bacterium, Salmonella typhimurium. have been studied by densitometry of electron micrographs of negatively stained specimens, followed by computerized Fourier analysis and three-dimensional reconstruction. The two structures are remarkably similar. In both cases, the subunits are arranged along a right-handed basic helix of 2.3 nm pitch with successive subunits separated by an azimuthal angle of 64 to 65 °, and there is a pronounced system of continuous 6-start grooves and ridges on the surface of the structures. The subunit of Salmonella (M_r 42,000, versus 70,000 for Caulobacter) is somewhat thinner and yields a smaller overall hook diameter. The “bent finger” subunit shape and orientation in both cases suggests that the hook could bend readily by a sliding motion in the 11-start direction at inner radii, with the 6-start groove preventing collision at outer radii. The basic helical pitch of the Salmonella hook structure, and the number of subunits per basic helical turn (5.56) makes it highly compatible with the Salmonella flagellar filament (2.6 nm pitch. 5.51 subunits per turn); so also does the elongated shape and tilt angle of the hook and flagellin subunits in the respective structures. The two structures may therefore conjoin directly in the intact flagellum, although participation of a minor protein is not ruled out by the data.     

Degenerate PCR primers for the amplification of fragments from genes encoding response regulators from a range of pathogenic bacteria

Many bacterial responses to environmental stimuli are mediated by response regulators which coordinately regulate genes involved in particular adaptive responses. Degenerate oligonucleotide primers were used to amplify by the polymerase chain reaction (PCR), fragments from genes encoding eleven novel response regulators. Sequence and phylogenetic analysis revealed that phoB, phoP and creB gene fragments had been amplified from Yersinia enterocolitica and Yersinia pseudotuberculosis, and that a creB sequence had been amplified from Campylobacter jejuni. Four amplified fragments from C. jejuni, Listeria monocytogenes, Mycobacterium tuberculosis and Escherichia coli clearly came from response regulator genes, but were not closely related to any of the known genes. Mutagenesis of the newly identified genes should allow us to determine their function and the genes under their control.