Metabolomics standards initiative: ontology working group work in progress

In this article we present the activities of the Ontology Working Group (OWG) under the Metabolomics Standards Initiative (MSI) umbrella. Our endeavour aims to synergise the work of several communities, where independent activities are underway to develop terminologies and databases for metabolomics investigations. We have joined forces to rise to the challenges associated with interpreting and integrating experimental process and data across disparate sources (software and databases, private and public). Our focus is to support the activities of the other MSI working groups by developing a common semantic framework to enable metabolomics-user communities to consistently annotate the experimental process and to enable meaningful exchange of datasets. Our work is accessible via a public webpage and a draft ontology has been posted under the Open Biological Ontology umbrella. At the very outset, we have agreed to minimize duplications across omics domains through extensive liaisons with other communities under the OBO Foundry. This is work in progress and we welcome new participants willing to volunteer their time and expertise to this open effort. See the MSI Ontology Working Group website for a complete list of members and contributors. Web URL:     

Proposed reporting requirements for the description of NMR-based metabolomics experiments

The amount of data generated by NMR-based metabolomic experiments is increasing rapidly. Furthermore, diverse techniques increase the need for informative and comprehensive meta-data. These factors present a challenge in the dissemination, interpretation, reviewing and comparison of experimental results using this technology. Thus, there is a strong case for unification and standardisation of the data representation for both academia and industry. Here, a systems analysis of an NMR-based metabolomics experiment is presented in order to reveal the reporting requirements. An in-depth analysis of the NMR component of a metabolomics experiment has been produced, and a first round of data standard development completed. This has focussed on both one- and two-dimensional ¹H NMR experiments, but is also applicable to higher dimensions and other nuclei. We also report the modelling of this schema using Unified Modelling Language (UML), and have extended this to a proof-of-concept implementation of the standard as an XML schema.     

Genetic selection on a behavioural fear trait is associated with changes in heart rate variability in quail

This study investigated whether genetic selection on a divergent behavioural trait of fearfulness (tonic immobility duration) was related to changes in the nervous control of the heart. Quail selected for either long or short tonic immobility (LTI or STI, respectively) duration was compared with an unselected control line (CTI). The autonomic control of the heart was assessed by heart rate variability analysis and pharmacological blockades. Quail were surgically fitted with a telemetric device. Heart rate before injection did not differ between the three lines. The vagal-sympathetic effect (VSE) at rest differed significantly from 1 in CTI and STI quail, suggesting that parasympathetic activity was dominant. In LTI quail, VSE did not differ from 1, suggesting a balance between parasympathetic and sympathetic activities. The intrinsic heart rate reached after the successive injections of propranolol and atropine did not differ between lines and was higher than the heart rate at rest in STI, which was in line with results of VSE at rest. After atropine injection, the sympathetic activity indicated by the low-frequency power was lower in CTI than in the two selected quail. After propranolol injection, the parasympathetic activity indicated by the root of the mean squares of successive differences and the high-frequency power was higher in STI than in CTI and LTI quail. Selection on tonic immobility duration thus appears to be associated with changes in the sympathovagal control of the heart, which may influence behavioural responses to stressful situations.     

Altered processing of sensorimotor feedback in schizophrenia

Schizophrenia is characterized by an altered sense of the reality, associated with hallucinations and delusions. Some theories suggest that schizophrenia is related to a deficiency of the system that generates information about the sensory consequences of the actions realized by the subject. This system monitors the reafferent information resulting from an action and allows its anticipation. In the present study, we examined visual-event-related potentials (ERPs) generated by a sensorimotor task in 15 patients with schizophrenia and 15 normal controls. The visual feedback from hand movements performed by the subjects was experimentally distorted. Behavioral results showed that patients were impaired in recognizing their own movements. The ERP signal in patients also differed from those of control subjects. In patients, the ERP waveform was affected during the early part of the response (200 ms). This early effect in schizophrenic patients reveals a modified processing of the visual consequence of their actions.     

Distribution dynamics of the Tnt1 retrotransposon in tobacco

Retrotransposons contribute significantly to the size, organization and genetic diversity of plant genomes. Although many retrotransposon families have been reported in plants, to this day, the tobacco Tnt1 retrotransposon remains one of the few elements for which active transposition has been shown. Demonstration that Tnt1 activation can be induced by stress has lent support to the hypothesis that, under adverse conditions, transposition can be an important source of genetic variability. Here, we compared the insertion site preference of a collection of newly transposed and pre-existing Tnt1 copies identified in plants regenerated from protoplasts or tissue culture. We find that newly transposed Tnt1 copies are targeted within or close to host gene coding sequences and that the distribution of pre-existing insertions does not vary significantly from this trend. Therefore, in spite of their potential to disrupt neighboring genes, insertions within or near CDS are not preferentially removed with age. Elimination of Tnt1 insertions within or near coding sequences may be relaxed due to the polyploid nature of the tobacco genome. Tnt1 insertions within or near CDS are thus better tolerated and can putatively contribute to the diversification of tobacco gene function. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of the methanolic extract of Chrysanthemum trifurcatum (Desf.) Batt. and Trab. on rat duodenal motility

The effect of the methanolic extract of flowers of Chrysanthemum trifurcatum (Desf.) Batt. and Trab. Var. macrocephalum (viv.) Beg. on the rat duodenum smooth muscle motility was examined in vitro. The extract has shown dose-dependent stimulator effects on the amplitude of the spontaneous contractions. With 0.1 g/ml of extract, maximal stimulation was obtained. With that dose, the variation (%) was significantly 1050 +/- 13 (P<0.001) compared with control and represented 80 +/- 5.83% (P<0.001) of the maximum effect of acetylcholine. Atropine (2 microg/ml) reduced by 81 +/- 4% (P<0.05) the spasmogenic effects of C. trifurcatum and by 92 +/- 3% (P<0.05) the acetylcholine effects, while papaverine (2 microg/ml) completely inhibited the spasmogenic effects of extract. With a fixed dose of acetylcholine added (20 microg/ml), the extract increases its effect, but acetylcholine decreases its action. These results suggested that the methanolic extract of C. trifurcatum could stimulate duodenal smooth muscle contractions through muscarinic receptors. Thy explain the respective traditional use of plant in gastrointestinal problems, especially constipation.     

Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling

Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements. Protection of the genome likely depends on specific DNA motifs that impose limits on the regions that undergo recombination. Although most such motifs remain unidentified, they are theoretically predictable based on their genomic distribution properties. We examined the distribution of the “crossover hotspot instigator,” or Chi, in Escherichia coli, and found that its exceptional distribution is restricted to the core genome common to three strains. We then formulated a set of criteria that were incorporated in a statistical model to search core genomes for motifs potentially involved in genome stability in other species. Our strategy led us to identify and biologically validate two distinct heptamers that possess Chi properties, one in Staphylococcus aureus, and the other in several streptococci. This strategy paves the way for wide-scale discovery of other important functional noncoding motifs that distinguish core genomes from the strain-variable regions.     

Characterization of reemerging chikungunya virus

An unprecedented epidemic of chikungunya virus (CHIKV) infection recently started in countries of the Indian Ocean area, causing an acute and painful syndrome with strong fever, asthenia, skin rash, polyarthritis, and lethal cases of encephalitis. The basis for chikungunya disease and the tropism of CHIKV remain unknown. Here, we describe the replication characteristics of recent clinical CHIKV strains. Human epithelial and endothelial cells, primary fibroblasts and, to a lesser extent, monocyte-derived macrophages, were susceptible to infection and allowed viral production. In contrast, CHIKV did not replicate in lymphoid and monocytoid cell lines, primary lymphocytes and monocytes, or monocyte-derived dendritic cells. CHIKV replication was cytopathic and associated with an induction of apoptosis in infected cells. Chloroquine, bafilomycin-A1, and short hairpin RNAs against dynamin-2 inhibited viral production, indicating that viral entry occurs through pH-dependent endocytosis. CHIKV was highly sensitive to the antiviral activity of type I and II interferons. These results provide a general insight into the interaction between CHIKV and its mammalian host.