Effect of 24-epibrassinolide on growth of in vitro shoot tips of different yam (Dioscorea Spp.) species

In this work we compared the effect of the growth regulator content of the culture medium on the growth of in vitro shoot tips of five yam accessions belonging to four yam species (one Dioscorea alata, one D. rotundata, one D. cay-enensis and two D. trifida). Medium S contained 0.6 μM benzyl adenine, 1.07 μM naphthalene acetic acid and 0.23 μM gibberellic acid while medium EBR contained 0.23 μM gibberellic acid and 0.1 μM 24-epibrassinolide. After 2 months of culture, oxidation level was significantly reduced on medium EBR compared to medium S for four of the five acces-sions tested. By contrast, medium EBR did not have any positive effect on shoot length since length of shoots produced after 2 months of culture on medium S and EBR were similar, except with accession 3-45T, for which shoot length was shorter on medium S compared to medium EBR. These results underline the potential of 24-epibrassinolide to reduce oxidation phenomena during in vitro culture and call for its utilization for regeneration of cryopreserved yam shoot tips, which is often impeded by oxidation phenomena

Multi-scale engineering for neuronal cell growth and differentiation

In this paper we investigate the role of micropatterning and molecular coating for cell culture and differentiation of neuronal cells (Neuro2a cell line) on a polydimethylsiloxane substrate. We investigate arrays of micrometric grooves (line and space) capable to guide neurite along their axis. We demonstrate that pattern dimensions play a major role due to the deformation of the cell occasioned by grooves narrower than typical cell dimension. A technological compromise for optimizing cell density, differentiation rate and neurite alignment has been obtained for 20 lm wide grooves which is a dimension comparable with the average cell dimension. This topographical engineered pattern combined with double-wall carbon nanotubes coating enabled us to obtain adherent cell densities in the order of 104 cells/cm2 and a differentiation rate close to 100%

Champs Conditionnels Aléatoires pour l'Annotation d'Arbres

National audienceAvec en vue la transformation de documents semi-structurés de type XML, nous nous intéressons au problème de l'annotation de tels documents par apprentissage statistique, à partir d'exemples de documents déjà annotés. Afin de modéliser la probabilité d'une annotation connaissant un document, nous nous plaçons dans le cadre des champs conditionnels aléatoires. Ce modèle a déjà fait ses preuves pour l'annotation de séquences : nous l'adaptons ici aux arbres ordonnés d'arité non bornée. Nous étudions l'expressivité du nouveau modèle ainsi introduit en le comparant aux automates d'arbres stochastiques (ou grammaires régulières probabilistes d'arbres). Nous présentons aussi en détail l'algorithme de recherche de l'annotation la plus probable et l'algorithme d'inférence pour ce modèle. Ces algorithmes sont implantés dans une librairie Tree CRF écrite en JAVA. Ces travaux sont des préliminaires qui nous permettront par la suite d'étudier les applications du modèle pour la transformation de documents

Conditional Random Fields for XML Applications

XML tree labeling is the problem of classifying elements in XML documents. It is a fundamental task for applications like XML transformation, schema matching, and information extraction. In this paper we propose XCRFs, conditional random fields for XML tree labeling. Dealing with trees often raises complexity problems. We describe optimization methods by means of constraints and combination techniques that allow XCRFs to be used in real tasks and in interactive machine learning programs. We show that domain knowledge in XML applications easily transfers in XCRFs thanks to constraints and combination of XCRFs. We describe an approach based on XCRF to learn tree transformations. The approach allows to solve xml data integration tasks and restructuration tasks. We have developed an open source toolbox for XCRFs. We use it to propose a Web service for the generation of personalized RSS feeds from HTML pages

Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>is the main causative agent of malaria. Of the 5 484 predicted genes of <it>P. falciparum</it>, about 57% do not have sufficient sequence similarity to characterized genes in other species to warrant functional assignments. Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes. Gene expression data have been widely used in the recent years to help functional annotation in an intra-species way via the so-called <it>Guilt By Association </it>(GBA) principle.</p> <p>Results</p> <p>We propose a new method that uses gene expression data to assess inter-species annotation transfers. Our approach starts from a set of likely orthologs between a reference species (here <it>S. cerevisiae </it>and <it>D. melanogaster</it>) and a query species (<it>P. falciparum</it>). It aims at identifying clusters of coexpressed genes in the query species whose coexpression has been conserved in the reference species. These conserved clusters of coexpressed genes are then used to assess annotation transfers between genes with low sequence similarity, enabling reliable transfers of annotations from the reference to the query species. The approach was used with transcriptomic data sets of <it>P. falciparum</it>, <it>S. cerevisiae </it>and <it>D. melanogaster</it>, and enabled us to propose with high confidence new/refined annotations for several dozens hypothetical/putative <it>P. falciparum </it>genes. Notably, we revised the annotation of genes involved in ribosomal proteins and ribosome biogenesis and assembly, thus highlighting several potential drug targets.</p> <p>Conclusions</p> <p>Our approach uses both sequence similarity and gene expression data to help inter-species gene annotation transfers. Experiments show that this strategy improves the accuracy achieved when using solely sequence similarity and outperforms the accuracy of the GBA approach. In addition, our experiments with <it>P. falciparum </it>show that it can infer a function for numerous hypothetical genes.</p

Probiotics for the Control of Parasites: An Overview

Probiotics are defined as live organisms, which confer benefits to the host. Their efficiency was demonstrated for the treatment of gastrointestinal disorders, respiratory infections, and allergic symptoms, but their use is mostly limited to bacterial and viral diseases. During the last decade, probiotics as means for the control of parasite infections were reported covering mainly intestinal diseases but also some nongut infections, that are all of human and veterinary importance. In most cases, evidence for a beneficial effect was obtained by studies using animal models. In a few cases, cellular interactions between probiotics and pathogens or relevant host cells were also investigated using in vitro culture systems. However, molecular mechanisms mediating the beneficial effects are as yet poorly understood. These studies indicate that probiotics might indeed provide a strain-specific protection against parasites, probably through multiple mechanisms. But more unravelling studies are needed to justify probiotic utilisation in therapeutics

Plasmodium falciparum PfA-M1 aminopeptidase is trafficked via the parasitophorous vacuole and marginally delivered to the food vacuole

<p>Abstract</p> <p>Background</p> <p>The <it>Plasmodium falciparum </it>PfA-M1 aminopeptidase, encoded by a single copy gene, displays a neutral optimal activity at pH 7.4. It is thought to be involved in haemoglobin degradation and/or invasion of the host cells. Although a series of inhibitors developed against PfA-M1 suggest that this enzyme is a promising target for therapeutic intervention, the biological function(s) of the three different forms of the enzyme (p120, p96 and p68) are not fully understood. Two recent studies using PfA-M1 transfections have also provided conflicting results on PfA-M1 localization within or outside the food vacuole. Alternative destinations, such as the nucleus, have also been proposed.</p> <p>Methods</p> <p>By using a combination of techniques, such as cellular and biochemical fractionations, biochemical analysis, mass-spectrometry, immunofluorescence assays and live imaging of GFP fusions to various PfA-M1 domains, evidence is provided for differential localization and behaviour of the three different forms of PfA-M1 in the infected red blood cell which had not been established before.</p> <p>Results</p> <p>The high molecular weight p120 form of PfA-M1, the only version of the protein with a hydrophobic transmembrane domain, is detected both inside the parasite and in the parasitophorous vacuole while the processed p68 form is strictly soluble and localized within the parasite. The transient intermediate and soluble p96 form is localized at the border of parasitophorous vacuole and within the parasite in a compartment sensitive to high concentrations of saponin. Upon treatment with brefeldin A, the PfA-M1 maturation is blocked and the enzyme remains in a compartment close to the nucleus.</p> <p>Conclusions</p> <p>The PfA-M1 trafficking/maturation scenario that emerges from this data indicates that PfA-M1, synthesized as the precursor p120 form, is targeted to the parasitophorous vacuole <it>via </it>the parasite endoplasmic reticulum/Golgi, where it is converted into the transient p96 form. This p96 form is eventually redirected into the parasite to be converted into the processed p68 form that is only marginally delivered to the parasite food vacuole. These results provide insights on PfA-M1 topology regarding key compartments of the infected red blood cells that have important implications for the development of inhibitors targeting this plasmodial enzyme.</p

Quels liens entre climatologie, occupation des sols et inondations dans le bassin versant de l'Yzeron (ouest Lyonnais) ? Apport de l'analyse conjointe de données hydroclimatiques et d'images satellitaires très haute résolution

Le bassin versant de l'Yzeron, situé en périphérie immédiate de la ville de Lyon, est un bassin représentatif des bassins versants périurbains français. Il connaît, depuis les années 1970, une augmentation importante de son urbanisation. Ces dernières années, des crues importantes, entraînant des inondations à l'aval du bassin versant ont marqué les esprits, posant la question de l'impact des modifications de l'occupation des sols dans le bassin versant sur le régime des crues. Dans cet article, nous utilisons l'analyse combinée de données hydroclimatiques (pluie, température, évapotranspiration de référence -ET0, débits) et de cartes de l'occupation des sols dérivées d'images satellites SPOT à haute et très haute résolution pour aborder cette question. L'analyse des débits montre l'existence d'une évolution du régime des crues, avec une augmentation significative des crues sub -seuils pour des durées de 1,5h, 3h, 6h, 12h et 36h sur la période 1970-2010. L'analyse de l'échantillon de crues obtenue par cette analyse débit-durée-fréquence montre que les crues les plus importantes sont plutôt liées à des épisodes ayant conduit à un cumul de pluie important (> 80 mm en quelques jours). Une corrélation significative est aussi obtenue entre débit de base et coefficient de ruissellement, ce qui montre que ces crues peuvent être associées à des écoulements sur surfaces saturées. Les évolutions du climat (pluviométrie, température, ET0) ne permettent pas d'expliquer l'augmentation des crues observées. En revanche, l'occupation des sols entre 1990 et 2008 montre une augmentation des sur faces imperméables qui passent de 15,2 % de la surface totale du bassin en 1990 à 18,2 % en 1999 et 22,6 % en 2008. Cette évolution de l'imperméabilisation est mise en regard de l'accroissement de la population du bassin sur cette même période. Enfin, nous illustrons la réponse hydrologique du bassin versant avec deux épisodes pour lesquels le rôle de l'occupation des sols est différent. Le premier, celui du 02/12/2003 est typique d'une réponse par saturation du bassin, avec une contribution majeure des zon es rurales, suite à des cumuls pluviométriques importants. Le second, celui du 09/08/2009 représente un orage d'été, très court mais avec des intensités importantes, conduisant essentiellement à une réponse rapide des zones urbaines et pour lequel l'occupation des sols joue un rôle majeur

Cd2+- or Hg2+-binding proteins can replace the Cu+-chaperone Atx1 in delivering Cu+ to the secretory pathway in yeast

AbstractCopper delivery to Ccc2 – the Golgi Cu+-ATPase – was investigated in vivo, replacing the Cu+-chaperone Atx1 by various structural homologues in an atx1-Δ yeast strain. Various proteins, displaying the same ferredoxin-like fold and (M/L)(T/S)CXXC metal-binding motif as Atx1 and known as Cu+-, Cd2+- or Hg2+-binding proteins were able to replace Atx1. Therefore, regardless of their original function, these proteins could all bind copper and transfer it to Ccc2, suggesting that Ccc2 is opportunistic and can interact with many different proteins to gain Cu+. The possible role of electrostatic potential surfaces in the docking of Ccc2 with these Atx1-homologues is discussed