Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL

Individual chromosome-based studies of bread wheat are beginning to provide valuable structural and functional information about one of the world's most important crops. As new genome sequences become available, identifying miRNA coding sequences is arguably as important a task as annotating protein coding sequences, but one that is not as well developed. We compared conservation-based identification of conserved miRNAs in 1.5× coverage survey sequences of wheat chromosome 1AL with a predictive method based on pre-miRNA hairpin structure alone. In total, 42 sequences expected to encode conserved miRNAs were identified on chromosome 1AL, including members of several miRNA families that have not previously been reported to be expressed in T. aestivum. In addition, we demonstrate that a number of sequences previously annotated as novel wheat miRNAs are closely related to transposable elements, particularly Miniature Inverted Terminal repeat Elements (MITEs). Some of these TE-miRNAs may well have a functional role, but separating true miRNA coding sequences from TEs in genomic sequences is far from straightforward. We propose a strategy for annotation to minimize the risk of mis-identifying TE sequences as miRNAs.     

Blink test results in patients with central sleep apnea syndrome

Sleep and Biological Rhythms - The aim of the study was to evaluate whether there was a problem in the interneuronal junctions of patients with central sleep apnea using the blink reflex test....     

Histo- and cytochemical demonstration of guanosine triphosphatase activity in the outer segments of rods in the rat retina by means of a newly developed method

Summary Guanosine triphosphatase (GTPase) activity was studied histo- and cytochemically in the rod outer segments of the rat retina by means of a newly developed method. Differences in the distribution pattern of the enzyme activity exist within the outer segment: the activity is more intense at the tip of the rod outer segments near the pigment epithelium than in their proximal portion. Ultracytochemically, the new procedure reveals the reaction product of GTPase activity partly (i) on the extradisk membrane side and (ii) on the disk membranes. This result is in contrast to the cytochemical localization of guanylate cyclase (GCLase), an enzyme also localized at the tip of the rod outer segments: GCLase activity is restricted to the intradisk membrane area of the rod outer segments. The functional role of GTPase activity in the outer segments of rods is discussed.The authors dedicate this paper to Professor K. Ogawa     

Biological rhythm of saliva ghrelin in humans

Background: We previously reported that ghrelin in saliva, orexigenic hormone that induces NPY release, was produced and released by salivary glands in humans. The purpose of this study was to investigate a possible circadian rhythm in saliva ghrelin concentration in human subjects as a function of time and meal. Saliva samples were collected at three-hour intervals throughout a 24-h period in 12 healthy volunteer males and ten healthy volunteer females who were provided with meals on a fixed schedule, and saliva collections were made within 15 minutes after each meal. Saliva ghrelin levels were measured by using a commercial radioimmunoassay (RIA) kit that uses ¹²⁵I-labeled bioactive ghrelin as a tracer and a rabbit polyclonal antibody raised against full-length octanoylated human ghrelin. Immunohistochemical analysis of salivary glands was also performed. The results of this investigation indicated the following. (1) The saliva ghrelin level was slightly higher in female subjects in comparison with male subjects. (2) Saliva ghrelin levels were elevated before each meal and fell to trough levels after eating. (3) Saliva ghrelin levels showed a circadian rhythm that rose throughout the day to a zenith at 0300, then dropped at 0600 - 0900. (4) Saliva ghrelin also weakly correlated with BMI. (5) Immunohistochemical analysis showed that ghrelin was localized in the striated and excretory ducts of salivary glands of human. The present work is the first report of the circadian rhythm of saliva ghrelin level in human subjects as a function of time and meal. Meal plays an important role in lowering saliva ghrelin concentration in humans. However, present data did not exclude whether the circadian changes in saliva ghrelin expression were regulated by the biological clock or by food intake.     

Removal of cadmium(II) ion from aqueous system by dry biomass, immobilized live and heat-inactivated Oscillatoria sp. H1 isolated from freshwater (Mogan Lake)

Oscillatoria sp. H1 (Cyanobacteria, microalgae) isolated from Mogan Lake was used for the removal of cadmium ions from aqueous solutions as its dry biomass, alive and heat-inactivated immobilized form on Ca-alginate. Particularly, the effect of physicochemical parameters like pH, initial concentration and contact time were investigated. The sorption of Cd(II) ions on the sorbent used was examined for the cadmium concentrations within the range of 25-250 mg/L. The biosorption of Cd(II) increased as the initial concentration of Cd(II) ions increased in the medium up to 100 mg/L. Maximum biosorption capacities for plain alginate beads, dry biomass, immobilized live Oscillatoria sp. H1 and immobilized heat-inactivated Oscillatoria sp. H1 were 21.2, 30.1, 32.2 and 27.5 mg/g, respectively. Biosorption equilibrium was established in about 1 h for the biosorption processes. The biosorption was well described by Langmuir and Freundlich adsorption isotherms. Maximum adsorption was observed at pH 6.0. The alginate-algae beads could be regenerated using 50 mL of 0.1 mol/L HCl solution with about 85% recovery.     

In Planta Evidence for the Involvement of a Ubiquitin Conjugating Enzyme (UBC E2 clade) in Negative Regulation of Disease Resistance

One of the three main components of the ubiquitylation system is an ubiquitin-conjugating enzyme (UBC, E2) that attaches ubiquitin (Ub) to a substrate. A strong link has been discovered between ubiquitylation and regulation of plant defense responses against plant pathogens. In this study, the role of UBC in response to pathogen attack is investigated in Arabidopsis thaliana as it has three Ubc gene homologs (Ubc1-1, Ubc2-1, and Ubc3-1). Analysis of single mutants of these three Ubc genes revealed enhanced disease resistance. Moreover, virus-induced gene silencing (VIGS) analysis revealed an enhanced level of resistance of Nicotiana benthamiana following inoculation with avirulent Pto DC3000 and virulent Pto DC3000 hopQ1-1 strains. In addition, RAR1, SGT1, and HSP90 mRNA levels are up-regulated following Ubc2 silencing. This study shows that UBC2 negatively regulates disease resistance via SGT1 level. Sub-cellular localization assay of UBC2 protein indicates its nuclear and cytoplasmic localization in planta.     

Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo‐ and neoduplicated subgenomes

Bread wheat derives from a grass ancestor structured in seven protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing conserved orthologous set (COS) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supra‐dominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat , can be considered as a guide for accelerated dissection of major agronomical traits in wheat.     

Revealing constitutively expressed resistance genes in Agrostis species using PCR-based motif-directed RNA fingerprinting

Agrostis species are mainly used in athletic fields and golf courses. Their integrity is maintained by fungicides, which makes the development of disease-resistance varieties a high priority. However, there is a lack of knowledge about resistance (R) genes and their use for genetic improvement in Agrostis species. The objective of this study was to identify and clone constitutively expressed cDNAs encoding R gene-like (RGL) sequences from three Agrostis species (colonial bentgrass (A. capillaris L.), creeping bentgrass (A. stolonifera L.) and velvet bentgrass (A. canina L.)) by PCR-based motif-directed RNA fingerprinting towards relatively conserved nucleotide binding site (NBS) domains. Sixty-one constitutively expressed cDNA sequences were identified and characterized. Sequence analysis of ESTs and probable translation products revealed that RGLs are highly conserved among these three Agrostis species. Fifteen of them were shown to share conserved motifs found in other plant disease resistance genes such as MLA13, Xa1, YR6, YR23 and RPP5. The molecular evolutionary forces, analysed using the Ka/Ks ratio, reflected purifying selection both on NBS and leucine-rich repeat (LRR) intervening regions of discovered RGL sequences in these species. This study presents, for the first time, isolation and characterization of constitutively expressed RGL sequences from Agrostis species revealing the presence of TNL (TIR-NBS-LRR) type R genes in monocot plants. The characterized RGLs will further enhance knowledge on the molecular evolution of the R gene family in grasses.